title: NPC-TW01 transfected with miR-1 or miR-negative

city: Taipei

first: Chin-Tarng

last: Lin

address: No. 7 Chung-Shan S. Rd

department: Pathology

country: Taiwan

institute: National Taiwan University

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing: Agilent Feature Extraction software

label_protocol: standard Agilent protocol

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

treatment_protocol:
HeLa cells were transfected with miR-1 (Ambion, Pre-miRTM hsa-miR-1 miRNA precursor, Cat# AM17150) and miR-negative (Ambion, Pre-miRTM miRNA precursor negative control #1, Cat# AM17110) separately. After 24 hours, cells were re-transfected once.
NPC-TW01 cells were transfected with miR-1 (Ambion, Pre-miRTM hsa-miR-1 miRNA precursor, Cat# AM17150) and miR-negative (Ambion, Pre-miRTM miRNA precursor negative control #1, Cat# AM17110) separately. After 24 hours, cells were re-transfected once.
For transfection, 1.5 x 10e5 cells were seeded per well of 6 well culture plate in 1 ml normal culture medium.
The microRNA transfection mixture was prepared by diluting 1 micro-liter of 50 micro-M microRNA in 100 micro-liter Opti-MEM I reduced serum medium  and adding 6 micro-liter of HiPerFect transfection reagent to the diluted microRNA and mixed by vortexing.
After incubation for 10 min at room temperature, the mixture was added with normal culture medium to a final volume of 1 ml, and the microRNA transfection mixture was added to the well that contained cells and then mixed gently.

tag: transfection

value: miR-negative

tag: transfection of microrna


title: Array 29

status: Public on Apr 13 2011

type: RNA

city: Austin

first: Lauren

middle: A

last: O'Connell

state: TX

address: 1 University Station-CO930

department: Section of Integrative Biology

country: USA

institute: University of Texas at Austin

description: Dominant male loop

hyb_protocol: Cy3- and Cy5-labeled samples were combined and mixed with yeast tRNA, polydA/dT, SSC, and SDS and heated to 100C for 2 minutes before being applied to microarray slides. Slides were cover slipped and incubated in custom hybridization chambers in a 65C water bath for 16 hours. Slides were then washed in a series of 3 solutions containing decreasing amounts of SSC and SDS before drying via centrifugation.

scan_protocol: Scanned using a GenePix 4000B array scanner and imaged using GenePix Pro 6.0.

data_processing: Scans were gridded and spots with diameter < 60 were removed from analysis. Intensities were normalized within each array using the LIMMA package for R by loess. A linear model was fit to each array using the lmFit function and significant differences between the two groups (vehicle and ER antagonist treated within either Dominant or Subordinate loops) were found using empirical Bayesian statistics via the function eBayes and corrected for multiple hypothesis testing using FDR. Individual arrays were analyzed by building a contrast matrix from the lmFit data and a Benjamini-Hochberg cut-off was applied to control for multiple hypothesis testing. Single-channel intensities were extracted from the normalized M-values using Microsoft Excel and sample M1 as a reference.

molecule: total RNA

organism: Haplochromis burtoni

label_protocol:
Two rounds of amplification using MessageAmpII kit (Ambion)
500 ng of RNA were primed with 1 uL of 5 ug/ul oligodT and random hexamer solution at 70C for 10 minutes. RNA was reverse transcribed using SuperScriptII Reverse Transcriptase, amino allyl-dUTP/dNTP solution and DTT at 42C for 2 hours. Samples were treated with 1N NaOH and 0.5M EDTA at 65C for 15 minutes then neutralized with 1M HEPES. Samples were purified using the Qiagen MinElute kit and eluted with 0.1M Na bicarbonate. Samples were labeled by mixing 10 uL with Amersham CyDye Post-Labeling Reactive Dye dissolved in 1 uL DMSO in the dark for 1 hour then neutralized with 3M NaOAc and cleaned using the Qiagen MinElute Kit.

extract_protocol: RNA extracted using Trizol following manufacturer's instructions

tag: tissue

value: preoptic area of brain

tag: treatment

value: ER antagonist

value: vehicle


title: Array 37

description: Dominant male loop


title: Healthy bone marrow EPCs, IFNa treated, 225

city: Ann Arbor

first: Celine

middle: C

last: Berthier

state: MI

address: 1150 W. Medical Center Dr, MSRB2

institute: University of Michigan

description:
BM_T_225
Gene expression data from healthy bone-marrow EPCs incubated with IFNa.

hyb_protocol: Standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual).

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

data_processing: The data were analyzed using the GenePattern pipeline: the RMA method and Human Entrez Gene custom CDF annotation version 10 was used for the normalization. Healthy EPCs, lupus EPCs and healthy bone marrow EPCs were normalized separately.

label: biotin

organism: Homo sapiens

source_name: Healthy bone-marrow EPCs incubated with IFNa

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

extract_protocol: Total RNA was isolated with Tri-pure (Roche), and further purified and concentrated using an Rneasy kit (Qiagen).

treatment_protocol: Cells were incubated in the presence or absence of IFNa for 6 hours prior to RNA harvesting.

value: bone marrow

tag: cell type

value: CD133+ endothelial progenitor cells (EPCs)

tag: disease state

value: healthy

value: IFNa


title: HeLa transfected with miR-1 or miR-negative

tag: cell line

value: HeLa


title: Array 25

description: Dominant male loop


title: HXF-HXT:Est

city: Vancouver

first: Won Hee

last: Jung

state: British Columbia

address: 2185 East Mall

department: Michael Smith Laboratories

country: Canada

institute: University of British Columbia

description: VALUE ratio in data table below represents Cy5/Cy3

hyb_protocol: Labelled cDNA hybridised using The 3DNA Array 350 kit (Genisphere).

scan_protocol: Arrays scanned using an Perkin Elmer Scan Array Express.

data_processing:
Data were analyzed using R-2.10.1 and nlme: Linear and Nonlinear Mixed Effects Models and qvalue: Q-value estimation for false discovery rate packages (version 1.22.0). R code is attached as a supplementary file on the Series record.
Each channel was background corrected by subtracting the lowest 10% of foreground signal intensities within each subgrid of the array. The two channels of each array were normalized to each other by Huber's variance stabilization algorithm (Huber et al., 2002). A linear mixed effects model was applied to the normalized data in each channel. A fixed effect was included for each array, for the dye by gene interaction and for each treatment/strain combination. Random effects were included for within-array variability (each gene appeared twice on each array), technical variability (replicate culture was hybridized twice) and biological variability (48 replicate cultures were employed). The pairwise changes between treatments within strain and the pairwise changes between strains with treatment were estimated with standard errors and p-values based Student t statistics; q-values were computed to adjust for the false discovery rate.

organism: Cryptococcus neoformans

source_name: low-iron + 5 uM Transferrin

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript II Kit (Invitrogen) as manufacturers instructions.

growth_protocol: Three biological replicates for each strain were grown in 25 ml of YPD overnight at 30C. Cells were washed twice with low-iron medium (LIM) followed by growth in LIM at 30C for an additional 16 hours in order to eliminate any iron carryover from the rich medium. Cultures were then harvested and washed twice with LIM. The cells were counted and transferred to 50 ml LIM + different iron sources. The cells were then grown at 30C for another 12 h and harvested for RNA extractions.

extract_protocol: RNA was purified with the RNeasy kit (Qiagen) and treated with DNAse (Qiagen) following the manufacturer’s recommendations. The quality of RNA was analyzed with an Agilent 2100 Bioanalyzer

treatment_protocol: Low-iron medium (LIM), LIM + 100 uM of FeCl3, LIM + 5 uM of Transferrin or LIM + 10 uM of Hemin.

tag: genotype/variation

value: hapX mutant

tag: treatment group

value: low-iron + 5 uM Transferrin

source_name: low-iron + 100 uM FeCl3

value: low-iron + 100 uM FeCl3


title: C1F-C1H:Est

source_name: low-iron + 10 uM Hemin

value: cir1 mutant

value: low-iron + 10 uM Hemin


title: C1C-WTC:Est

source_name: low-iron

value: WT

value: low-iron


title: placenta normal third trimester rep.20

city: Tromsø

first: Chris

last: Fenton

address: Thor Knutsen vg 6

department: Microarray

country: Norway

institute: UITO

description: normal placenta

hyb_protocol: The labeled DIG-cRNA (10 micrograms per microarray) was   then injected into each microarray hybridization chamber. Following hybridization at 55oC for 16   hours, the unbound material was washed from the microarrays. Features that retained bound DIG-  labeled cRNA were visualized using the Applied Biosystems Chemiluminescenct detection Kit.   Anti-DIG alkaline phophatase (Roche Applied science) was used to hydrolyze a   chemiluminescence substrate to generate light at 458 nm

scan_protocol: Images were quantified using the integrated ABI1700 software

data_processing: The pre-normalized intensity values were extracted per spot from the data files. Probes  with signal to noise ratio <3.0, or signal means under 9.5, or variability less than 0.1 were removed from dataset. Control spots were filtered out. Arrays were quantile normalized (R preprocessCore library). Missing expression levels were inferred by imputed by KNN (R impute library). Rscript available from authour.

label: DIG

source_name: placenta

label_protocol: Chemiluminescent Fluorescence (Digoxigenin); 0.5 mikrograms of total RNA was processed into digoxigenein (DIG)-labeled cRNA using the Applied Biosystems NanoAMP RT-IVT Labeling Kit.

growth_protocol: patient material

extract_protocol: MagNa Pure Compact RNA isolation Kit (Roche Applied Science)

value: placenta

tag: trimester

value: third


title: Healthy bone marrow EPCs, non-IFNa treated, 233

description:
BM_NT_233
Gene expression data from healthy bone-marrow EPCs not incubated with IFNa.

source_name: Healthy bone-marrow EPCs not incubated with IFNa

value: untreated


title: C1C-HXC:Est


title: C1F-C1T:Est

description: VALUE ratio in data table below represents Cy3/Cy5


title: placenta normal third trimester rep.21

description: normal placenta


title: placenta normal third trimester rep.19

description: normal placenta


title: Array 21

description: Dominant male loop

value: preoptic area of brain

value: ER antagonist


title: Array 19

description: Dominant male loop

value: vehicle


title: Array 23

description: Dominant male loop


title: Healthy bone marrow EPCs, non-IFNa treated, 224

description:
BM_NT_224
Gene expression data from healthy bone-marrow EPCs not incubated with IFNa.

value: bone marrow

value: CD133+ endothelial progenitor cells (EPCs)


title: Healthy bone marrow EPCs, non-IFNa treated, 230

description:
BM_NT_230
Gene expression data from healthy bone-marrow EPCs not incubated with IFNa.

value: healthy


title: C1C-C1T:Est


title: Healthy bone marrow EPCs, non-IFNa treated, 119r

description:
BM_NT_119r
Gene expression data from healthy bone-marrow EPCs not incubated with IFNa.


title: placenta normal third trimester rep.15

description: normal placenta


title: placenta normal third trimester rep.16

description: normal placenta


title: Array 17

description: Dominant male loop


title: Healthy bone marrow EPCs, non-IFNa treated, 227

description:
BM_NT_227
Gene expression data from healthy bone-marrow EPCs not incubated with IFNa.


title: C1C-H3C:Est

value: hap3 mutant


title: placenta normal third trimester rep.17

description: normal placenta


title: Lupus EPCs/CACs, IFNa treated, 219

description:
SLE_T_219
Gene expression data from lupus EPCs/CACs incubated with IFNa.

source_name: Lupus EPCs/CACS incubated with IFNa

growth_protocol: PBMCs containing EPCs and CACs were cultured in endothelial cell-specific enrichment medium on fibronectin-coated wells.

value: peripheral blood

value: endothelial progenitor cells (EPCs)/myeloid circulating angiogenic cells (CACs)

value: lupus

value: IFNa


title: C1C-C1H:Est

value: cir1 mutant

value: low-iron + 10 uM Hemin


title: placenta normal third trimester rep.18

description: normal placenta


title: placenta normal third trimester rep.14

description: normal placenta


title: C1C-C1F:Est

value: low-iron + 100 uM FeCl3

value: low-iron


title: Cdx2-Cdx1 D knockout expression array-4

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

description:
mice were treated with tamoxifen for 5 consecutive days (1mg/day) and the jejunal epithelium was harvested 4 days after completion of the timecourse.  RNA was extracted using the Trizol method and prepared for arrays using manufacturer's instructions (Affymetrix).
Affymetrix mouse 4302 microarray

hyb_protocol: according to manufacturer's instructions (Affymetrix)

data_processing: Microarray expression: RMA (bioconductor) with custom CDF (Mouse4302_Mm_REFSEQ) for background elimination and normalization. Limma for detection of differentially expressed genes between controls and Cdx2 KO or Cdx2-Cdx1 D KO.

organism: Mus musculus

source_name: jejunum epithelium

tag: strain

value: C57BL/6-129 mixed

value: Cdx2-Cdx1 D knockout

value: jejunum epithelium


title: INPUT_MOF_FA

city: Umea

first: Jan

last: Larsson

address: Umea University

department: Molecular Biology

country: Sweden

institute: Umea University

hyb_protocol: Samples were prepared and hybridized to GeneChip Drosophila Tiling 1.0R Array according to Affymetrix specifications.

scan_protocol: Affymetrix procedures followed

data_processing:
The signal intensity data was analyzed with the Affymetrix Tiling Analysis Software (v. 1.1.02) using parameters: one side upper, 90 bp bandwidth and perfect match only. For absolute amount (transcript profile) the bandwidth was set to 0.
The resulting CHP files are generated by the Affymetrix Tiling Analysis Software (v. 1.1.02) using parameters: one side upper, 90 bp bandwidth and perfect match only. For absolute amount (transcript profile, i.e., Input_TP_bw0_N6_signal.chp) the bandwidth was set to 0.

label: Biotin

organism: Drosophila melanogaster

growth_protocol: For each sample treatment condition we used 300ml D. melanogaster Schneider’s line 2 cells (ATCC CRL-1963) grown at 25°C in an Erlenmeyer flasks at a density of 1×10^7 cells/ml in Drosophila SFM medium (Invitrogen) supplemented with 100U/ml Penicillin G, 100µg/ml Streptomycin sulfate and 2mM of L-glutamine.

extract_protocol: For immunoprecipitation, 5-10 mg nuclear extracts were incubated with 5 µl anti-MSL2, 5 µl anti-MOF for 45 minutes at 4°C with agitation. The antibody complexes were precipitated by incubation with 75 µl of Dynabeads conjugated to protein-A (Dynal) for 30 minutes at 4°C with agitation. The supernatant was removed and the beads were washed twice with PBS (150 mM NaCl), 0.1% Triton X-100, 32 U/ml RNasin, 0.5 × Protease inhibitor cocktail and twice in PBS (300 mM NaCl), 0.1% Triton X-100, 32 U/ml RNasin, 0.5 × Protease inhibitor cocktail. The crosslinking in sample FA were reversed by adding 200 µl 0.45 M LiCl to the beads and incubate 3-4 hours at 65°C. RNA were isolated using TRI-reagent (Ambion) followed by a purification using RNeasy kit (Qiagen) according to the instruction by the suppliers. The RNA samples were concentrated and reverse transcribed into cDNA using random primers with the ImPromII first strand synthesis kit (Promega) according to the suppliers recommendations. The single stranded cDNA was purified with QIAquick PCR purification Kit (Qiagen). The purified cDNA samples were amplified using WGA2 GenomePlex Complete whole genome amplification kit (Sigma) according to the recommendations by the supplier.

treatment_protocol: The cells were pelleted, washed 2 times in 100 ml 10 mM HEPES pH 7.4, 140 mM NaCl and resuspended in 50 ml of lysis buffer (20 mM HEPES pH 7.4, 3 mM MgCl2, 0.1% Triton X-100, 1 mM dithioreitol, 0.5mM PMSF, 10 U/ml RNasin and 0.5 × Protease inhibitor cocktail (Roche)).The cells were allowed to swell on ice for 10 minutes and then homogenized on ice with 30 strokes of a Dounce homogenizer. The nuclei were pelleted at 2,000 × g for 5 minutes and used either as native (non-crosslinked) or after formaldehyde crosslinking. For the crosslinked sample (FA) the pelleted nuclei were resuspended in 50 ml lysis buffer and cross-linked by adding formaldehyde to a final concentration of 0.5% and incubated for 10 minutes in room temperature. The crosslinking was stopped by adding glycine (final concentration 0.125M), the nuclei were washed once in lysis buffer and resuspended in 2 ml of sonication buffer (20 mM HEPES pH 7.4, 10% glycerol, 0.1M NaCl, 1 mM MgCl2, 0.1% Triton X-100, 1 mM dithioreitol, 0.5mM PMSF, 10 U/ml RNasin and 0.5 × Protease inhibitor cocktail) and sonicated using a Bioruptor (Diagenode) for 4 minutes setting high (30 sec ON, 30 sec OFF). For the native samples (N1, N3, N6) the pelleted nuclei were resuspended in 2 ml sonication buffer and sonicated for 1, 3 or 6 minutes (N1, N3 and N6, respectively). Cellular debris were removed by centrifugation for 25 minutes, 4°C at 14,000 × g and the supernatants were used for immunoprecipitations.

value: S2 cells (ATCC CRL-1963)

tag: antibody


title: Lupus EPCs/CACs, IFNa treated, 249

description:
SLE_T_249
Gene expression data from lupus EPCs/CACs incubated with IFNa.


title: INPUT_MOF_N1

label_protocol: Samples were prepared and hybridized to GeneChip Drosophila Tiling 1.0R Array according to Affymetrix specifications.


title: INPUT_MOF_N3


title: INPUT_MOF_N6


title: Lupus EPCs/CACs, IFNa treated, 210

description:
SLE_T_210
Gene expression data from lupus EPCs/CACs incubated with IFNa.


title: Lupus EPCs/CACs, IFNa treated, 213

description:
SLE_T_213
Gene expression data from lupus EPCs/CACs incubated with IFNa.


title: placenta normal third trimester rep.12

description: normal placenta

value: placenta

value: third


title: MOF_RIP_FA

value: MOF


title: placenta normal third trimester rep.11

description: normal placenta


title: MOF_RIP_N6


title: Cdx2-Cdx1 D knockout expression array-2

scan_protocol: according to manufacturer's instructions (Affymetrix)

extract_protocol: RNA was extracted using the Trizol method and prepared for arrays using manufacturer's instructions (Affymetrix).

treatment_protocol: mice were treated with tamoxifen for 5 consecutive days (1mg/day) and the jejunal epithelium was harvested 4 days after completion of the timecourse.


title: placenta normal third trimester rep.13

description: normal placenta


title: Cdx2-Cdx1 D knockout expression array-3

label_protocol: according to manufacturer's instructions (Affymetrix)


title: Cdx2-Cdx1 D knockout expression array-1


title: placenta normal third trimester rep.10

description: normal placenta


title: Lupus EPCs/CACs, IFNa treated, 204

description:
SLE_T_204
Gene expression data from lupus EPCs/CACs incubated with IFNa.


title: Cdx2 knockout expression array-3

value: Cdx2 knockout


title: MOF_RIP_N3


title: Cdx2 knockout expression array-2


title: Lupus EPCs/CACs, non-IFNa treated, 251

description:
SLE_NT_251
Gene expression data from lupus EPCs/CACs not incubated with IFNa.

source_name: Lupus EPCs/CACS not incubated with IFNa

value: untreated


title: Cdx2 knockout expression array-1


title: Lupus EPCs/CACs, non-IFNa treated, 215

description:
SLE_NT_215
Gene expression data from lupus EPCs/CACs not incubated with IFNa.

value: peripheral blood


title: placenta normal third trimester rep.9

description: normal placenta


title: Lupus EPCs/CACs, non-IFNa treated, 221

description:
SLE_NT_221
Gene expression data from lupus EPCs/CACs not incubated with IFNa.

value: endothelial progenitor cells (EPCs)/myeloid circulating angiogenic cells (CACs)


title: MOF_RIP_N1


title: placenta normal third trimester rep.7

description: normal placenta


title: placenta normal third trimester rep.8

description: normal placenta


title: Control expression array-2

value: littermate controls


title: MSL2_RIP_FA


title: Lupus EPCs/CACs, IFNa treated, 201

description:
SLE_T_201
Gene expression data from lupus EPCs/CACs incubated with IFNa.

value: lupus

value: IFNa


title: placenta normal third trimester rep.6

description: normal placenta


title: MDSC_Tolerant_anti-CD28_3

city: NANTES

first: Nahzli

last: DILEK

address: 30 Bd Jean-Monnet, CHU Hôtel-Dieu

country: France

institute: INSERM UMR643

description:
Tolerant state
antibodies details: Purified anti-MHC class II (OX6) and anti-CD3 (G4.18) were prepared in our laboratory from the corresponding hybridomas obtained from the European Cell Culture Collection (Salisbury, UK). Goat anti-mouse IgG Dynabeads were purchased from Invitrogen/Life Technologies, cat n 110.33. Anti-CD80 (3H5) and anti-CD86 (24F) mouse antibodies were prepared in our laboratory from hybridoma given by Dr. H. Yagita (Juntendo University School of Medicine, Tokyo, Japan). FITC-conjugated anti-mouse was purchased from Jackson ImmunoResearch Laboratories (West Grove, PA, USA), cat n 715-095-150. Anti-FITC Microbeads were from Miltenyi, cat n 130-048-701.

hyb_protocol: Array hybridization was performed for 16 h at 55°C. An additional 3400 control spots were present on the chip to cover various steps in the hybridization process.

scan_protocol: Chemiluminescence detection, image acquisition, and analysis were performed using the Applied Biosystems chemiluminescence detection kit (part no. 436875D), analyzer (part no. 4338036) and version 1.1 analyzer software (part no. 4336391) according to the manufacturer’s protocol.

data_processing: Microarray raw data were analyzed by the R language and environment for statistical computing and graphics. Genes were identified using the Panther Protein Classification System Probe ID database.

label: Digoxigenin-UTP

organism: Rattus norvegicus

source_name: MDSCs

label_protocol: The Applied Biosystems rat genome survey microarray (part no. 4337467) contained 26,857 60-mer oligonucleotide probes representing 27,088 individual rat genes. An additional 3400 control spots were present on the chip to cover various steps in the hybridization process.  Digoxigenin-UTP labeled cRNA was generated and amplified from 0.5 µg of total RNA from each sample using an Applied Biosystems NanoAmp chemiluminescent reverse transcriptase-in vitro transcription (RT-IVT) labeling kit (part no. 4365715).

growth_protocol: Rats were maintained in an SPF-free animal facility according to the institutional guidelines of the “Institut National de la Santé et de la Recherche Médicale” (INSERM).

extract_protocol: Peripheral blood leucocytes were isolated from heparinized blood by removing erythrocytes with hypotonic lysis solution. A depletion of MHC class II + and CD3+ cells was performed with specific mAbs; followed by anti-mouse IgG-coated Dynabeads (Life Technologies). MDSCs were identified by staining 30 min at 4°C with purified anti-rat CD80/86 (3H5/24F) mAbs and FITC-conjugated anti-mouse IgG secondary Ab (Jackson ImmunoResearch Laboratories). MDSCs were isolated using automated magnetic cell sorting (AutoMACS, Miltenyi) of cells based on their expression of CD80/86.  Total RNA from MDSCs was prepared using the TRIzol (Invitrogen Life Technologies) extraction method. Ten micrograms of total RNA was cleaned up using RNeasy columns (Qiagen). RNA quantity and quality were determined using a NanoDrop spectrophotometer and an Agilent 2100 bioanalyzer. A rRNA 28S/18S ratio of 1.0 ± 0.1 was considered as acceptable for RNA amplification.

treatment_protocol: Lewis 1W (LEW.1W, haplotype RT1u) and Lewis 1A (LEW.1A, haplotype RT1a) rats (Centre d’Elevage Janvier, Le Genest-Saint-Isle, France) share the same genetic background but are MHC I and II mismatched. Heterotopic transplantations of 8 to 12 weeks old LEW.1W kidneys on LEW.1A animals were carried out according to the technique described by Ono & Lindsey. For syngeneic transplantations LEW.1A kidneys on LEW.1A recipients were achieved. Live-sustaining allotransplantations were performed aseptically and a binephrectomy was performed 7 days after transplantation as previously described. Blood urea and creatinine and urine protein/creatinine ratios were measured throughout the posttransplant period. Blood urea < 8 mM and blood creatinine < 40 mM were considered as normal. Transplant tolerance induction was obtained by treating rats with anti-CD28 (JJ319) antibody.

value: myeloid-derived suppressor cells (MDSCs)

tag: transplantation

value: Allogeneic

tag: state

value: Tolerant state

tag: day post transplantation


title: MSL2_RIP_N6


title: Control expression array-3

value: C57BL/6-129 mixed


title: placenta normal third trimester rep.5

description: normal placenta


title: placenta normal third trimester rep.4

description: normal placenta


title: MSL2_RIP_N1


title: Lupus EPCs/CACs, non-IFNa treated, 206

description:
SLE_NT_206
Gene expression data from lupus EPCs/CACs not incubated with IFNa.


title: placenta normal third trimester rep.3

description: normal placenta


title: Lupus EPCs/CACs, non-IFNa treated, 203

description:
SLE_NT_203
Gene expression data from lupus EPCs/CACs not incubated with IFNa.


title: Lupus EPCs/CACs, non-IFNa treated, 212

description:
SLE_NT_212
Gene expression data from lupus EPCs/CACs not incubated with IFNa.


title: Healthy EPCs/CACs, IFNa treated, 112

description:
Ctrl_T_112
Gene expression data from healthy EPCs/CACs incubated with IFNa.

source_name: Healthy EPCs/CACS incubated with IFNa

value: healthy


title: Healthy EPCs/CACs, IFNa treated, 111

description:
Ctrl_T_111
Gene expression data from healthy EPCs/CACs incubated with IFNa.


title: placenta normal third trimester rep.2

description: normal placenta


title: shSin3A_2 [Sin3A samples]

city: Copenhagen

first: Kristine

last: Williams

address: Ole Maaløes vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

hyb_protocol: Affymetrix standard procedure

scan_protocol: Affymetrix standard procedure

data_processing: R/Bioconductor. 'affy' package. RMA function. Statistics performed using the 'limma'  package. ANNOTATION: chip library files downloaded from Custom CDF library at bioconductor. vers13 july 6 2010. http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp . Package name mogene10stv1mmentrezg

source_name: embryonic stem cells

label_protocol: samples were processed with the Whole Transcript Assay Kit as recommended by the manufacterer (Affymetrix)

growth_protocol: Low passage (p17) E14TG2a.4 feeder independent ES cells were cultured on 0.1% gelatin-coated plates in Glasgow medium (Sigma) supplemented with glutamine (Gibco), nonessential amino acids (Gibco), sodium pyruvate (Gibco), 50 ìM ßmercaptoethanol, and 15% foetal bovine serum (HyClone) in the presence of LIF. Recombinant lentiviruses encoding Sin3A shRNA were produced by standard methods employing co-transfection of PLKO.1 shRNA and packaging vectors in 293FT cells. shRNA transduced ES cells were selected 36 hours post transduction with 2 ìg per ml of puromycin for 72 hours.

extract_protocol: RNAeasy (Qiagen)

treatment_protocol: Cells were lentiviral transduced with scrambled or Sin3A shRNA

value: embryonic stem cells

tag: shRNA


title: MSL2_RIP_N3

value: S2 cells (ATCC CRL-1963)


title: shSin3A_1 [Sin3A samples]


title: Healthy EPCs/CACs, IFNa treated, 109

description:
Ctrl_T_109
Gene expression data from healthy EPCs/CACs incubated with IFNa.


title: shSin3A_3 [Sin3A samples]


title: shScr_3 [Sin3A samples]

value: Scrambled


title: placenta normal third trimester  rep1

description: normal placenta

value: placenta

value: third


title: Control expression array-1

value: jejunum epithelium


title: shScr_2 [Sin3A samples]


title: Healthy EPCs/CACs, IFNa treated, 108

description:
Ctrl_T_108
Gene expression data from healthy EPCs/CACs incubated with IFNa.


title: Healthy EPCs/CACs, IFNa treated, 107

description:
Ctrl_T_107
Gene expression data from healthy EPCs/CACs incubated with IFNa.


title: placenta normal first trimester rep.15

description: normal placenta

value: first


title: placenta normal first trimester rep.14

description: normal placenta


title: placenta normal first trimester rep.16

description: normal placenta


title: Healthy EPCs/CACs, non-IFNa treated, 106

description:
Ctrl_NT_106
Gene expression data from healthy EPCs/CACs not-incubated with IFNa.

source_name: Healthy EPCs/CACS not incubated with IFNa

value: peripheral blood

value: untreated


title: placenta normal first trimester rep.12

description: normal placenta


title: Healthy EPCs/CACs, non-IFNa treated, 105

description:
Ctrl_NT_105
Gene expression data from healthy EPCs/CACs not-incubated with IFNa.

value: endothelial progenitor cells (EPCs)/myeloid circulating angiogenic cells (CACs)


title: placenta normal first trimester rep.13

description: normal placenta


title: Healthy EPCs/CACs, IFNa treated, 110

description:
Ctrl_T_110
Gene expression data from healthy EPCs/CACs incubated with IFNa.


title: shScr_1 [Sin3A samples]


title: shTet1#5_2

data_processing: R/Bioconductor. 'affy' package. RMA function. Statistics performed using the 'limma' package. ANNOTATION: chip library files downloaded from Custom CDF library at bioconductor. vers13 july 6 2010. http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp. Package name mogene10stv1mmentrezg

growth_protocol: Low passage (p17) E14TG2a.4 feeder independent ES cells were cultured on 0.1% gelatin-coated plates in Glasgow medium (Sigma) supplemented with glutamine (Gibco), nonessential amino acids (Gibco), sodium pyruvate (Gibco), 50 ìM ßmercaptoethanol, and 15% foetal bovine serum (HyClone) in the presence of LIF. Recombinant lentiviruses encoding TET1 shRNA were produced by standard methods employing co-transfection of PLKO.1 shRNA and packaging vectors in 293FT cells. shRNA transduced ES cells were selected 36 hours post transduction with 2 ìg per ml of puromycin for 72 hours.

treatment_protocol: Cells were lentiviral transduced with scrambled or Tet1 shRNA


title: shTet1#5_3


title: shTet1#5_1


title: placenta normal first trimester rep.11

description: normal placenta


title: shTet1#4_3


title: Healthy EPCs/CACs, non-IFNa treated, 102

description:
Ctrl_NT_102
Gene expression data from healthy EPCs/CACs not-incubated with IFNa.


title: Healthy EPCs/CACs, non-IFNa treated, 103

description:
Ctrl_NT_103
Gene expression data from healthy EPCs/CACs not-incubated with IFNa.


title: Healthy EPCs/CACs, non-IFNa treated, 104

description:
Ctrl_NT_104
Gene expression data from healthy EPCs/CACs not-incubated with IFNa.


title: Healthy EPCs/CACs, non-IFNa treated, 101

description:
Ctrl_NT_101
Gene expression data from healthy EPCs/CACs not-incubated with IFNa.


title: placenta normal first trimester rep.8

description: normal placenta


title: shTet1#4_2


title: placenta normal first trimester rep.10

description: normal placenta


title: placenta normal first trimester rep.5

description: normal placenta


title: placenta normal first trimester rep.9

description: normal placenta


title: placenta normal first trimester rep.6

description: normal placenta


title: shScr_2


title: placenta normal first trimester rep.3

description: normal placenta


title: placenta normal first trimester rep.2

description: normal placenta


title: shScr_1


title: 2-RapCA

city: Columbus

first: Maqsood

last: Chotani

state: OH

address: 700 Children's Drive

department: Center for Cardiovascular and Pulmonary Research

institute: Nationwide Childrens Hospital

description: Biological replicate 2 of 4

hyb_protocol: Arrays were hybridized for 17 hours at 65 degrees Celsius.

scan_protocol: Scanned with Agilent G2505C Microarray Scanner using the AgilentHD_GX_2Color protocol

data_processing: The information about each probe on the array was extracted from the image data using Agilent Feature Extraction 10.9 (FE). This data is stored in the FE “.txt” files. The raw intensity values from these files is imported into the mathematical software package “R”, which is used for all data input, diagnostic plots, normalization and quality checking steps of the analysis process using scripts developed in-house by Peter White specifically for this analysis.

source_name: micro-vascular smooth muscle cells derived from Rap1a knockout murine model transduced with empty Shuttle vector

label_protocol: Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Version 6.5, May 2010

growth_protocol: Microvascular smooth muscle (mVSM) cells were were grown in Ham's growth medium that contained a 50:50 DMEM/F-12 solution, 10% FBS, L-glutamine, and antibiotics/antimycotic (10% FBS Ham's medium).

extract_protocol: Cells were washed twice with PBS  and total RNA was extracted using the Ambion mirVANA kit.

treatment_protocol: Cells were transduced with virus overnight in serum-free (SF)-Ham's medium at time of plating. The medium was replaced next day with 0.5% FBS Ham's medium following one wash in this medium, and cells were allowed to recover for 48 hours.

tag: gender

value: Male

source_name: micro-vascular smooth muscle cells derived from Rap1a knockout murine model transduced with RapCA Shuttle vector


title: placenta normal first trimester rep.1

description: normal placenta


title: placenta normal first trimester rep.4

description: normal placenta


title: 3-RapCA

description: Biological replicate 3 of 4


title: placenta normal first trimester rep.7

description: normal placenta


title: B6 teratoma

city: La Jolla

first: Tongbiao

last: Zhao

state: CA

address: 9500 Gilman Dr

department: Biological Sciences

institute: University of California San Diego

description: Gene expression data from B6ES formed terotama

hyb_protocol: Following digestion, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Genome 430A 2.0 Array

scan_protocol: GeneChips were scanned using a GeneArray Scanner.

data_processing: The data were analyzed with the Affymetrix software Command Console and Expression Console using MAS5.0 Analysis Algorithms.

source_name: Teratoma formed by B6ES

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

growth_protocol: Both B6 and EiPS cells were subcutaneously transplanted to male B6 mice.

extract_protocol: Total RNAs were extracted using a Rneasy total RNA isolation kiit (Qiagen) according to the mannual.

treatment_protocol: Tumors were surgically removed six weeks after transplantation.

tag: tumor

value: Teratoma

tag: tumor source

value: B6 ES cells


title: shTet1#4_1


title: shScr_3


title: 1-RapCA

description: Biological replicate 1 of 4.


title: 4-RapCA

description: Biological replicate 4 of 4


title: EiPS teratoma

description: Gene expression data from EiPS formed terotama

source_name: Teratoma formed by 1E12 iPS

value: EiPS cells


title: 82gsul.2sd.br2b

status: Public on Apr 12 2011

city: Amherst

first: Derek

last: Lovley

state: MA

address: University of Massachusetts at Amherst, Dept. of Microbiology, Morrill IV north room 202

department: Microbiology

institute: University of Massachusetts Amherst

description: total RNA was amplified using the Ambion MessageAmp II- Bacteria kit for polyadenylation and subsequent amplification of total RNA. aRNA was ethanol precipitated and resuspended in nuclease-free water to a total concentration of ~1 ug/ul.

hyb_protocol: Combimatrix 100 ul volume cap.

scan_protocol: Slide was scanned using GenePix software and a GenePix 4000b scanner.

data_processing:
The raw total intensities were treated as follows to generate the M Log2 ratios for this work. Background signal was calculated from a set of negative control spots incorporated into the array. As the negative control sequences are not design specific (ie. are found in all of the ESOAs independent of the organism being sampled) some will inevitably demonstrate strong cross hybridization with the sample of interest. To avoid this issue the negative control spots were ranked according to their total intensity. The average of the lowest 30% was calculated. Background signal was calculated as this mean + 2 standard deviations. The background signal was then subtracted from the total intensity for each spot. Probes whose signal was not greater than zero after background subtraction were omitted from further analysis. For the remaining data, the logged ratios [M=log2 (Ex/Ct)] are then calculated and Lowess global normalization is performed. During the data preprocessing, M vs. A plots before and after normalization, and side-by-side box plots for all arrays are used to assess array quality.(3) LIMMA mixed model analysis (R-package LIMMA(2))is applied to the normalized logged ratios to identify differentially expressed genes. Specifically, biological replicates are treated as a randomized block to allow for modeling correlations within them. LIMMA calculates a moderated t statistic for each probe, which is the ratio of the estimated mean logged intensity ratio and the Empirical Bayes estimate of its standard error. The P-value of each oligo is then corrected for multiple comparisons according to Benjamini and Hockberg's procedure(1) to control the false discovery rate. Oligos are ranked according to the adjusted P-values and were called differentially expressed if the adjusted P-values are < 0.001. Note that multiple oligonucleotide probes from the same gene are analyzed separately and a gene is called differentially expressed if at least half of its probes are called differentially expressed.
1. Benjamini, Y., and Y. Hochberg. 1995. Controlling the False Discovery Rate - a Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B-Methodological 57:289-300.
2. Smyth, G. K. 2004. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3:Article3.
3. Smyth, G. K., and T. Speed. 2003. Normalization of cDNA microarray data. Methods 31:265-73.

organism: Geobacter sulfurreducens

source_name: pRG-DcuB mutant grown on fumarate

label_protocol: Micromax ASAP direct RNA labeling protocol

growth_protocol: Geobacter sulfurreducens was grown anaerobically to mid-log in batch freshwater media with fumarate as the terminal electron acceptor and acetate as the electron donor.

extract_protocol: Qiagen RNEasy Midi Kit protocol, DNAse Treatment with Ambion DNA-free kit.

value: pRG-DcuB mutant

tag: agent

value: fumarate

source_name: wildtype grown on fumarate

value: wildtype


title: 4_day_old_wildtype_mouse_rep2

city: Trieste

first: Paola

last: Roncaglia

state: TS

address: via Bonomea 265

department: Neurobiology

country: Italy

institute: SISSA/ISAS (International School for Advanced Studies)

hyb_protocol: Labeled cRNA was hybridized on Affymetrix GeneChip Mouse Genome 430A 2.0 Arrays, containing 22,690 probesets corresponding to approximately 14,000 well-characterized mouse genes. Hybridized arrays were stained and washed (GeneChip Fluidics Station 450).

scan_protocol: Hybridized arrays were scanned with the GeneChip Scanner 3000 7G.

data_processing: Cell intensity values and probe detection calls were computed using the Affymetrix GeneChip Operating Software (GCOS). Further data processing was performed in the R computing environment (http://www.r-project.org/) version 2.8.0 with BioConductor packages (http://www.bioconductor.org/). Robust Multi-Array Average (RMA) normalization was applied. Data were then filtered based on Affymetrix detection call and probeset intensity, so that only probesets that had a present call and intensity value >100 in at least one of the arrays were retained. Statistical analysis was performed with limma. P-values were adjusted for multiple testing using Benjamini and Hochberg’s method to control the false discovery rate. Genes with adjusted P values below 0.05 were considered differentially expressed.

source_name: hippocampus

label_protocol: A 10μg-amount of each total RNA sample was labeled according to the standard one-cycle amplification and labeling protocol (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions, treated with DnaseI (Ambion) and purified with the RNeasy Mini kit (Qiagen). RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was quantified with a NanoDrop 1000 spectrophotometer (Thermo Scientific).

value: FVB

tag: developmental stage

value: newborn (4-day-old)

tag: tissue

value: hippocampus

value: Prnp+/+


title: 4_day_old_Prnp_knockout_mouse_rep2


title: 82gsul.2sd.br1b


title: 4_day_old_wildtype_mouse_rep1


title: 82gsul.2sd.br2a


title: 82gsul.2sd.br3a


title: 82gsul.2sd.br3b


title: 81gsul.2sd.br3b

source_name: PCAs CP1 mutant grown on ferric citrate

growth_protocol: Geobacter sulfurreducens was grown anaerobically to mid-log in batch freshwater media with ferric citrate as the terminal electron acceptor and acetate as the electron donor.

value: PCAs CP1 mutant

value: ferric citrate

source_name: wildtype grown on ferric citrate


title: 3_month_old_wildtype_mouse_rep4

value: adult (3-month-old)


title: 3_month_old_wildtype_mouse_rep2


title: 3_month_old_wildtype_mouse_rep3


title: 4_day_old_Prnp_knockout_mouse_rep3


title: 4_day_old_wildtype_mouse_rep3


title: 4_day_old_Prnp_knockout_mouse_rep1


title: 82gsul.2sd.br1a


title: 3_month_old_wildtype_mouse_rep1


title: 3_month_old_Prnp_knockout_mouse_rep4


title: 81gsul.2sd.br2b


title: 81gsul.2sd.br3a


title: 81gsul.2sd.br2a


title: 81gsul.2sd.br1b


title: 81gsul.2sd.br1a


title: Female white Leghorn DNA vs. female Dehong DNA

type: genomic

first: Yanqiang

last: Wang

state: Ohio

address: 12th w street

institute: The Ohio State University

description: Female white Leghorn DNA sample vs. Dehong chicken DNA sample.

hyb_protocol: Array hybridization was performed using the Agilent Oligo aCGH Hybridization Kit (Agilent technologies) for 40 h at 20 rpm in a 65℃ Agilent hybridization oven.

scan_protocol: Arrays were scanned at 3μm resolution using an Agilent Microarray Scanner, and image analysis was performed using Feature Extraction software 10.7  with 90% laser power value and PMT 100%.

data_processing: Agilent Feature Extraction Software 10.7 was used for background subtraction and LOWESS normalization.

molecule: genomic DNA

organism: Gallus gallus

source_name: Female white Leghorn blood

label_protocol: 1.5µg of genomic DNA was digested with restriction enzymes AluI and RsaI and fluorescently labelled using the Agilent Genomic DNA Labeling Kit PLUS (Agilent technologies).Test samples were labelled with cyanine 5-dUTP and the reference sample with cyanine 3-dUTP.

extract_protocol: DNA was extracted using the DNeasy Blood & Tissue kit (QIAGEN No.69504) and Wizard Genomic DNA purification kit (Promega No.A1125) by the standard protocol for each kit separately.

treatment_protocol: Blood samples were taken from adult chicken individuals by syringe and kept in 0.5M EDTA solution in order to avoid cruor. DNA were collected from chicken blood with 0.5 M EDTA and stored at -20°C until DNA isolation.

tag: breed

value: white Leghorn

value: female

value: adult

value: blood

source_name: Dehong chicken

value: Dehong

tag: sample type

value: reference


title: Sum190-E+CG4 (Agilent-021827 miRNA v12.0)

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

description: miRNA expression after treatment with 10nM 17β-Estradiol and 5µM CG-1521 for 48h

hyb_protocol: labeled miRNA was hybridized onto Agilent Human miRNA microarrays v3 (G4771-A) rel 12.0 according to the manufacturer's instructions.

scan_protocol: The arrays were scanned on a Agilent G2565C scanner using the standard settings for 8x15k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.1.1 (Agilent) using default parameters (protocol miRNA-v1_10_Apr08 and Grid: 021827_D_20081121) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: SUM190PT 10nM 17β-Estradiol-with 5µM CG-1521

label_protocol: Cyanine-3 (Cy3) labeled miRNA was prepared from 100ng total RNA using the miRNA Complete Labeling and hyb kit (Agilent) according to the manufacturer's instructions

growth_protocol: SUM190PT cells were grown in Ham's F-12 media supplemented with 5 µg/mL insulin, 1 µg/mL hydrocortisone, 10 mM HEPES, 5mM Ethanolamine, 5µg/mL Transferrin, 10nM Triiodo Thyronine, 50nM Sodium Selenite, 1g/L Bovine Serum Albumin and Antibiotic/Antimycotic at 37° with 5% CO2 and 85% Humidity.

extract_protocol: Total RNA was extracted using the miRNeasy Mini kit (Qiagen Inc., Valencia, CA, USA). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Center for Functional Genomics at State University of New York at Albany (Rensselaer, NY, USA)

treatment_protocol: SUM190PT cells were plated at 1.5 x 10^6 cells per 150 x 25mm dish with 25mL of growth media containing 2%FBS and allowed to adhere for 24h. The media in each plate was then replaced with 25mL fresh media without FBS. After another 24h, each treatment was prepared at 6x concentration, so that 5mL of treatment solution was added to the 25mL growth media.

tag: cell line

tag: er

value: mut (Q317X)


title: 3_month_old_Prnp_knockout_mouse_rep3

tag: genotype/variation


title: Sum190-E+CG2 (Agilent-021827 miRNA v12.0)


title: Sum190-E+CG3 (Agilent-021827 miRNA v12.0)


title: Sum190-CG3 (Agilent-021827 miRNA v12.0)

description: miRNA expression after treatment with 5µM CG-1521 for 48h

source_name: SUM190PT 5µM CG-1521


title: Sum190-E+CG1 (Agilent-021827 miRNA v12.0)


title: Sum190-CG4 (Agilent-021827 miRNA v12.0)


title: BMDCs pre-treated with BI2536 for 1h before stimulation with polyI:C for 4h

city: Cambridge

first: Nicolas

last: Chevrier

state: Massachusetts

address: 415 Main Street

institute: Broad Institute of Harvard and MIT

description: Gene expression data from polyIC-stimulated BMDCs after 1-hour pre-treatment with BI2536

hyb_protocol: Standard Affymetrix protocols for mouse HT arrays

data_processing: RMA

source_name: BI2536 polyIC 4h

growth_protocol: mouse bone marrow-derived CD11c+ dendritic cells

extract_protocol: miRNEASY (QIAGEN) following manufacturer's instructions

treatment_protocol: DMSO or BI 2536 1µM for 1 hour prior stimulation

tag: strain

tag: tissue origin

value: GM-CSF-induced bone marrow

tag: celll type

value: CD11c+ dendritic cells


title: 3_month_old_Prnp_knockout_mouse_rep2


title: 3_month_old_Prnp_knockout_mouse_rep1


title: BMDCs pre-treated with DMSO for 1h before stimulation with polyI:C for 4h

description: Gene expression data from polyIC-stimulated BMDCs after 1-hour pre-treatment with DMSO

scan_protocol: Standard Affymetrix protocols for mouse HT arrays

source_name: DMSO polyIC 4h


title: BMDCs pre-treated with BI2536 for 1h before stimulation with LPS for 4h

description: Gene expression data from LPS-stimulated BMDCs after 1-hour pre-treatment with BI2536

source_name: BI2536 LPS 4h

label_protocol: Standard Affymetrix protocols for mouse HT arrays


title: BMDCs pre-treated with DMSO for 1h before stimulation with LPS for 4h

description: Gene expression data from LPS-stimulated BMDCs after 1-hour pre-treatment with DMSO

source_name: DMSO LPS 4h


title: Sum190-CG1 (Agilent-021827 miRNA v12.0)


title: Sum190-E4 (Agilent-021827 miRNA v12.0)

description: miRNA expression after treatment with 10nM 17β-Estradiol for 48h

source_name: SUM190PT 10nM 17β-Estradiol


title: Male Cobb broiler DNA vs. female Dehong DNA

description: Male Cobb broiler DNA vs. Dehong chicken DNA sample.

source_name: Male Cobb broiler blood

value: Cobb broiler

value: male


title: Sum190-CG2 (Agilent-021827 miRNA v12.0)


title: Male Dou chicken DNA vs. female Dehong DNA

description: Male Dou chicken DNA vs. Dehong chicken DNA sample.

source_name: Male Dou chicken blood

value: Dou


title: Female Dou chicken DNA vs. female Dehong DNA

description: Female Dou chicken DNA vs. Dehong chicken DNA sample.

source_name: Female Dou chicken blood


title: Sum190-E1 (Agilent-021827 miRNA v12.0)


title: Sum190-E3 (Agilent-021827 miRNA v12.0)


title: Sum190-control2 (Agilent-021827 miRNA v12.0)

description: miRNA expression after treatment with vehicle (ethanol and DMSO) for 48h

source_name: SUM190PT Vehicle CTRL


title: Sum190-control4 (Agilent-021827 miRNA v12.0)


title: Sum190-control3 (Agilent-021827 miRNA v12.0)


title: Sum190-E2 (Agilent-021827 miRNA v12.0)


title: Male white Leghorn DNA vs. female Dehong DNA

description: Male white Leghorn DNA sample vs. Dehong chicken DNA sample.

source_name: Male white Leghorn blood


title: Sum190-control1 (Agilent-021827 miRNA v12.0)


title: Sum149-E+CG3 (Agilent-021827 miRNA v12.0)

description: miRNA expression after treatment with 10nM 17β-Estradiol and 7.5µM CG-1521 for 48h

source_name: SUM149PT 10nM 17β-Estradiol-with 7.5µM CG-1521

growth_protocol: SUM149PT cells were grown in Ham's F-12 media with 5% fetal bovine serume supplemented with 5 µg/mL insulin, 1 µg/mL hydrocortisone, 10 mM HEPES and Antimycotic/Antibiotic at 37°C with 5%CO2 and 85% humidity.

treatment_protocol: SUM149PT cells were plated at 1.5 x 10^6 cells per 150 x 25mm dish with 25mL of growth media, and allowed to adhere for 48h prior to treatment. The media in each plate was replaced with 25mL fresh media containing the drug treatment.

value: mut (M237I)


title: Sum149-E+CG4 (Agilent-021827 miRNA v12.0)


title: Sum149-E+CG2 (Agilent-021827 miRNA v12.0)


title: Sum149-E+CG1 (Agilent-021827 miRNA v12.0)


title: Sum149-CG3 (Agilent-021827 miRNA v12.0)

description: miRNA expression after treatment with 7.5µM CG-1521 for 48h


title: Sum149-CG4 (Agilent-021827 miRNA v12.0)


title: Female Cobb broiler DNA vs. female Dehong DNA

description: Female Cobb broiler DNA vs. Dehong chicken DNA sample.

source_name: Female Cobb broiler blood


title: WT_BHI+bile_30min_repC

city: Chicago

first: Jess

last: Leber

state: IL

address: 920 E. 58th Street CLSC 615

institute: The University of Chicago

description: biological replicate 3 of 3

hyb_protocol: applied to spotted arrays in binding buffer containing HEPES, SSC, tRNA, and SDS at 63 °C for 48 hours (see Leber et al, PloS Pathogens, 2008 for more detail)

scan_protocol: Images were scanned on a Molecular Devices GenePix 4100B scanner, using GenePix Pro software

data_processing: Background subtracted data obtained from log2 of processed Red signal/processed Green signal, using GenePix Pro software

organism: Listeria monocytogenes

source_name: WT 10403S LM grown in BHI + 1% bile

label_protocol: 5 ug amplified RNA was reaction with Cy dye for 60 min, and purified using Zymo clean and concentrate columns (see Leber et al, PloS Pathogens, 2008 for more detail)

growth_protocol: BHI, 37 °C, 250 RPM shaking, midlog

extract_protocol: Trizol with silica beads in MP FastPrep

treatment_protocol: +/- 1% porcine bile (Sigma) for 30 min

source_name: pooled reference total RNA from all samples used in this experiment (6 samples)


title: WT_BHI+bile_30min_repA

description: biological replicate 1 of 3


title: Sum149-CG2 (Agilent-021827 miRNA v12.0)


title: WT_BHI_30min_repC

description: biological replicate 3 of 3

source_name: WT 10403S LM grown in BHI


title: WT_BHI_30min_repB

description: biological replicate 2 of 3


title: WT_BHI+bile_30min_repB

description: biological replicate 2 of 3


title: striatum_D2.12 MouseRef-8

city: Portland

first: Nicole

last: Walter

state: OR

address: 3181 SW Sam Jackson Park Road

department: Behavioral Neuroscience

institute: Oregon Health & Science University

hyb_protocol: An aliquot of aRNA is hybridized to an Illumina BeadChip using proprietary buffers, first at 65⁰C for thirty minutes, then overnight at 58⁰C.

scan_protocol: The arrays are washed and then stained with Cy3-streptavidin, washed again, and then scanned on an Illumina BeadStation bead array scanner.

data_processing: Data from the scanner is consolated using the GenomeStudio software.    Built in quality control measures are monitored in GenomeStudio to look for obvious problems in the hybridization process.  Final output is customized to allow use of a variety of statistical packages, including BioConductor and GeneSifter.

label: biotinylated UTP nucleotide

source_name: striatum, adult, naïve

label_protocol: Total RNA that has passed the QC tests will be amplified using the TotalPrep RNA Amplification Kit (Ambion), which can amplify RNA across a range from 50 to 500 ng. The resultant amplified RNA (aRNA) incorporates a biotinylated UTP nucleotide.

extract_protocol: TRIzol total RNA extraction

value: brain striatum


title: Sum149-CG1 (Agilent-021827 miRNA v12.0)


title: Sum149-E4 (Agilent-021827 miRNA v12.0)

source_name: SUM149PT 10nM 17β-Estradiol


title: Sum149-E3 (Agilent-021827 miRNA v12.0)


title: striatum_D2.10 MouseRef-8


title: striatum_D2.6 MouseRef-8


title: striatum_D2.9 MouseRef-8


title: striatum_D2.5 MouseRef-8


title: striatum_D2.11 MouseRef-8


title: Sum149-E2 (Agilent-021827 miRNA v12.0)


title: striatum_D2.4 MouseRef-8


title: striatum_D2.7 MouseRef-8


title: Sum149-E1 (Agilent-021827 miRNA v12.0)


title: striatum_D2.2 MouseRef-8


title: striatum_D2.8 MouseRef-8


title: striatum_D2.3 MouseRef-8


title: WT_BHI_30min_repA

description: biological replicate 1 of 3


title: HEK293 cells transfected with eEF1Bdelta1 or eEF1BdeltaL

city: Kumamoto

first: Taku

last: Kaitsuka

state: Kumamoto

address: 1-1-1 honjo

department: Department of Molecular Physiology

country: Japan

institute: Graduate School of Life Sciences, Kumamoto University

hyb_protocol: Oligo DNA and hybridization buffer (TOYOBO) were added, and the labeled aRNA hybridyzed oligo DNA microarray contining human 25K transcripts for 16 h at 37°C. (TORAY co. ltd. manufacturer's instructions).

scan_protocol: ScanArray Lite (Perkin Elmer)

data_processing: global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: HEK293 cells, transfected with eEF1Bdelta1

label_protocol: Total RNA (1 microgram) was synthesized into aRNA with the amino allyl aRNA kit (Ambion). The aRNA was labeled with Cy3 monofunctional reactive dye or Cy5 monofunctional reactive dye (GE health care).

growth_protocol: HEK293 cells were maintained in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C with 5% CO2. Cells were seeded at a density of 1x10^6 cells in 100-mm dish.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: HEK293 cells were transfected with expression plasmids encoding flag-tagged-eEF1Bdelta1 protein using lipofectamine LTX reagent (Invitrogen) according to the manufacturer’s instructions. 48h after transfection, cells were harvested.

tag: cell type

value: human embryonic kidney cell

source_name: HEK293 cells, transfected with eEF1BdeltaL

treatment_protocol: HEK293 cells were transfected with expression plasmids encoding flag-tagged-eEF1BdeltaL protein using lipofectamine LTX reagent (Invitrogen) according to the manufacturer’s instructions. 48h after transfection, cells were harvested.


title: Sum149-control4 (Agilent-021827 miRNA v12.0)

source_name: SUM149PT Vehicle CTRL


title: Sum149-control3 (Agilent-021827 miRNA v12.0)


title: striatum_B6.12 MouseRef-8


title: striatum_D2.1 MouseRef-8


title: striatum_D2.78 MOE430 2.0

hyb_protocol: Labeled target is fragmented at 95o C in the presence of high magnesium concentration. The fragmented material is combined with biotinylated hybridization control oligomer and biotinylated control cRNAs for BioB, BioC, BioD and CreX (Affymetrix) in hybridization buffer. Ten g of target is hybridized with the GeneChip (insert array name) array (Affymetrix) overnight, followed by washing, staining with streptavidin-phycoerythrin (Molecular Probes), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs), and a final staining step on the Fluidics Station 450 (Affymetrix). The distribution of fluorescent material on the processed array is determined using the Affymetrix 3000 GeneArray laser scanner with the 7G upgrade.

scan_protocol: Image inspection is performed manually immediately following each scan. All array scanning and data processing on the Affymetrix system is performed with GeneChip Operating System (GCOS) software.

data_processing: The probe-level Cel file is processed with Affymetrix Microarray Suite, version 5.0 (MAS 5.0) software. The GeneChip expression arrays contain control probe sets for both spiked and endogenous RNA transcripts (e.g., BioB, BioC, BioD, CreX and species-specific actin and GAPDH). Following image processing and absolute analysis of the array pattern with MAS, six values are examined to assess overall assay performance: background, noise, average Signal, % Present, ratio of Signal values for probe sets representing the 5’ and 3’ ends of actin and GAPDH transcripts, and total Signal for probe sets for BioB, BioC, BioD and CreX. Assays demonstrating poor or marginal performance are flagged. Using MAS 5.0, array data is globally scaled to a uniform, average target intensity for all assays prior to further analysis.

label: biotin-CTP

label_protocol: Messenger RNA is amplified and labeled from 2 mg of total RNA in two steps. In the first step, mRNA is converted to double-stranded cDNA using Superscript Reverse Transcriptase (Invitrogen) and an oligo-dT primer linked to a T7 RNA polymerase binding site sequence (Affymetrix). In the second step, amplified and labeled cRNA (the target) is produced in an in vitro transcription reaction using T7 RNA polymerase and biotin-CTP (Affymetrix.). Following removal of free nucleotides, target yield is measured by UV260 absorbance.

treatment_protocol: naïve


title: Sum149-control2 (Agilent-021827 miRNA v12.0)


title: striatum_D2.79 MOE430 2.0


title: striatum_B6.10 MouseRef-8


title: striatum_B6.11 MouseRef-8


title: striatum_D2.80 MOE430 2.0


title: striatum_D2.77 MOE430 2.0


title: striatum_D2.76 MOE430 2.0


title: Sum149-control1 (Agilent-021827 miRNA v12.0)


title: striatum_B6.8 MouseRef-8


title: striatum_B6.7 MouseRef-8


title: striatum_D2.74 MOE430 2.0


title: striatum_B6.6 MouseRef-8


title: striatum_D2.73 MOE430 2.0


title: striatum_B6.5 MouseRef-8


title: striatum_B6.9 MouseRef-8


title: striatum_B6.3 MouseRef-8


title: striatum_B6.4 MouseRef-8


title: striatum_D2.71 MOE430 2.0


title: striatum_D2.72 MOE430 2.0


title: striatum_B6.2 MouseRef-8


title: striatum_D2.75 MOE430 2.0


title: Mussel hemolymph_ 48 h post V. splendidus LGP32 injection_48.2 arrayB

city: Padova

first: Laura

last: Varotto

address: via U. Bassi 58/3

department: Biology Department

institute: University of Padova

description: Image processing and signal quantification were performed with ScanArray Express® (PerkinElmer) whose output files report spot data, pixel statistics, quality parameters and the fluorescence intensity values for each probe and channel.

hyb_protocol: Following purification (Gene Elute PCR Clean-up kit, Sigma-Aldrich) and UV-quantification, 500 ng of both reference and test aaRNAs were combined and ethanol-precipitated. Cy3/Cy5-coupled samples were re-suspended in 18 µl of hybridization buffer (5x SSC, 50% formamide, 0.1% SDS), denaturated for 3 min at 70°C and competitively hybridised to the Immunochip for 24 h at 48°C in humidified dual-slide chamber (HybChamber, GeneMachines). Slides were preliminary conditioned for 12 h at 48°C in a solution of 5x SSC, 100 ng/µl salmon sperm ssDNA, 5x Denhardt’s solution and 0.1% SDS); then, reference and test samples were simultaneously hybridised in dye-swap crossed combinations on the two identical arrays of the same slide. The slides were sequentially washed at room temperature with mild shaking in buffer: 1x SSC, 0.2% SDS; 0.1x SSC, 0.2% SDS; 0.2x SSC (4 min each) and 0.1x SSC (3 min), with final drying by air flow.

scan_protocol: Immunochip fluorescence signals were scanned using two lasers (633 nm and 543 nm) at 5 μm resolution with a GSI Lumonics LITE dual confocal laser scanner.

data_processing: Normalisation of the fluorescence signals was performed by using the total and LOWESS (Logfit) algorithm with MIDAS (MIcroarray Data Analysis System, http://www.tigr.org/software). The log2 test/reference ratio of all the normalised fluorescence values was computed.

organism: Mytilus galloprovincialis

source_name: Hemolymph, control

label_protocol: Hemolymph mRNA was linearly amplified from total RNA with the Ambion Message-AmpTM II aRNA Amplification kit. Initially, modified nucleotides 5-(3-aminoallyl)-UTP were incorporated into the aRNA during the in vitro transcription reaction; then, mono-functional NHS-esters of Cy3 or -Cy5 dyes (CyDye Post-Labeling Reactive Dye Pack, Amersham GE Healthcare) were resuspended in DMSO and covalently coupled to the aminoallyl-aRNA probes for 1 h at room temperature in the dark.

extract_protocol: Total RNA was extracted with Trizol reagent (Invitrogen) according to the manufacturer's instructions, and further purified by LiCl precipitation.

tag: biological replica

value: Control pool (N=40)

value: hemolymph

tag: treatment

value: 0.1 ml PBS-NaCl injection into the posterior adductor muscle

tag: time point

value: 48 h post injection

source_name: Hemolymph h 48.2_B

value: 10 to 7 CFU of V. splendidus LGP32 injection into the posterior adductor muscle


title: Mussel hemolymph_ 48 h post V. splendidus LGP32 injection_48.2arrayA

source_name: Hemolymph h 48.2_A


title: striatum_B6.1 MouseRef-8

tag: gender

value: adult


title: striatum_B6.70 MOE430 2.0


title: striatum_B6.66 MOE430 2.0


title: Mussel hemolymph_ 3 h post V. splendidus LGP32 injection_3.2arrayB

value: 3 h post injection

source_name: Hemolymph h 3.2_B


title: striatum_B6.69 MOE430 2.0


title: Mussel hemolymph_ 48 h post V. splendidus LGP32 injection_48.1arrayB

source_name: Hemolymph h 48.1_B


title: Mussel hemolymph_ 48 h post V. splendidus LGP32 injection_48.1arrayA

source_name: Hemolymph h 48.1_A


title: striatum_B6.68 MOE430 2.0


title: striatum_B6.67 MOE430 2.0


title: Expression profile of  mlo3-A ∆cid14 cells

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

hyb_protocol: Equal amounts of Cy5-labeled mutant cDNA and Cy3-labeled wild-type cDNA were mixed and combined with human Cot1DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Data were extracted using Agilent Feature Extraction Software (GE2-v5_95_Feb07 protocol) and subjected to combined rank consistency filtering with LOWES intensity normalization. Background signal was estimated as a median processed signal of 152 oligonucleotides with no homology to S. pombe genome.

organism: Schizosaccharomyces pombe

source_name: log. growing mlo3-A ∆cid14  cells

label_protocol: Ribosomal RNA was depleted with RiboMinus kit (Invitrogen) and total RNA reverse-transcribed and labeled using SuperScript Indirect cDNA labeling kit (Invitrogen).

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YEA) at 30˚C.

extract_protocol: Total RNA was extracted using Master Pure Yeast RNA purification kit (Epicenter) according manufacturer's instructions.

value: mlo3-A ∆cid14

source_name: log. growing wild-type cells

value: wild-type


title: striatum_B6.65 MOE430 2.0

value: female


title: Mlo3-Flag ChIP in wild-type cells

hyb_protocol: Equal amounts of Cy5-labeled ChIP DNA and Cy3-labeled  whole-cell extract DNA were mixed and combined with human Cot1 DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density  microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.

data_processing: Data were extracted using Agilent Feature Extraction Software (CHIP-v1_95_May07 protocol). Signal was normalized by combined rank consistency filtering with LOWES intensity normalization. Background signal was estimated as a median processed signal of 152 oligonucleotides with no homology to S. pombe genome.

source_name: log. growing Mlo3-Flag cells

label_protocol: ChIP and whole-cell extract DNA was amplified by random-primed PCR and conjugated with Cy5 (ChIP DNA) or Cy3 (whole-cell extract DNA).

extract_protocol: Fixed cells were lysed with glass-beads, DNA sheared by sonication to 500-1000bp fragments and immunoprecipitated by appropriate antibody: Mlo3-Flag (conjugated M2 agarose; Sigma). Immunoprecipitated DNA was  reversed-crosslinked at 65˚C.

treatment_protocol: Exponentially growing cells were fixed in 3% paraformaldehyde at 25˚C and chromatin proteins crosslinked by treatment with 10mM dimethyl adipimidate.

value: immunoprecipitated DNA

value: Whole-cell extract DNA


title: striatum_B6.64 MOE430 2.0


title: Mlo3-Flag ChIP in Clr4  deleted  cells

source_name: log. growing Mlo3-Flag clr4âˆ cells

value: Mlo3-Flag clr4âˆ


title: Mussel hemolymph_ 3 h post V. splendidus LGP32 injection_3.2arrayA

source_name: Hemolymph h 3.2_A


title: SigC regulon, IPTG-induced sigC vs sigC null mutant

city: Bangkok

first: Soraya

last: Chaturongakul

address: 272 Rama 6 Road

country: Thailand

institute: Mahidol University

description: Expression profiles were measured from three independent RNA extractions, resulting in six replicate spots per gene (array contains duplicate spots).

hyb_protocol: Microarray slide blocking was performed prior to hybridization. Slides were incubated for 10 min in a solution containing methyl pyrrilidone, succinic anhydride and sodium borate, and then washed in fresh methyl pyrrilidone for 10 min. Successive 1-min washes in nanopure water (once), 0.1% SDS (3 times), nanopure water (5 times), and 95% EtOH (once). The slides were dried by centrifugation and immersed for 1 h in blocking solution (0.1% BSA, 5X SSC, 0.1% SDS) at 42°C. After blocking, the slides were washed for 1 min each in nanopure water (5 times) and 95% EtOH (2 times) and then dried by centrifugation. For the strains to be compared, labeled cDNAs were combined and dried, then resuspended in 50μl of hybridization buffer (5X SSC, 0.1% SDS, 0.1mM dithiothreitol (DTT), 0.5X formamide, 0.06 μg/μl salmon sperm DNA in DEPC-treated water), denatured at 95°C for 5 min then applied to the slides using mSeries LifterSlips™ (Erie Scientific). Following overnight hybridization at 42°C, the slides were washed in 2X SSC+0.1% SDS (5 min at 42˚C), with subsequent 5-min washes at room temperature in 2X SSC+0.1% SDS, 2X SSC, and 0.2X SSC, followed by final rinse in nanopure water. Slides were dried by centrifugation.

scan_protocol: Images were scanned using a GenePix 4000B scanner (Molecular Devices Corp.). Raw TIFF images were automatically gridded and analyzed using GenePix Pro 6.0 software.

data_processing: Analyses of microarray data were performed in R with Bioconductor using LIMMA software (Smyth, 2005). Background correction was performed using the “normexp” method. For normalization within arrays, the data were weighted for the genomic DNA controls and normalized using print-tip loess method (Smyth & Speed, 2003). The data were then scale normalized between arrays. The correlation between duplicate spots was calculated (Smyth et al., 2005) and a linear model was fitted to the normalized log ratios and empirical Bayes statistics were applied for differential expression analysis.

label: Alexa Fluor 647,Alexa Fluor 555

source_name: Listeria monocytogenes C3-143 (IPTG-iducible sigC expression)

label_protocol: cDNA was synthesized from purified total RNA and labeled with Alexa Fluor dyes using the SuperScript Plus Indirect cDNA Labeling System according to the manufacturer's protocol with following modifications. 10 μg total RNA was combined with 1 μl of random primers included in the kit, incubated at 70°C for 5 min. Following a 5 min on ice, 6 μl 5X First-Strand buffer, 1.5 μl 0.1M dithiothreitol (DTT), 1.5 μl dNTP mix containing aminoallyl-dATP and aminohexyl-dTTP, 1 μl RNaseOUT and 2 μl SuperScript III Reverse Transcriptase were added to the reaction tube. The reverse transcription reaction was carried out at 42ºC overnight. Remaining RNA was hydrolyzed by addition of 15 μl 1N NaOH (70ºC for 10 min) and then neutralized with 15 μl 1N HCl. Each cDNA sample was purified with the QIAquick PCR purification kit (Qiagen) using RNase-free water for the final elution step. cDNA samples were dried in a SpeedVac until reduced to ~3 μl. Each cDNA sample was combined with 2X Coupling Buffer and then added to a vial of DMSO-suspended Alexa Fluor® Reactive Dye and the dye coupling reaction was carried out at room temperature overnight. Labeled cDNA samples were purified with the QIAquick PCR purification kit with an additional 35% Guanidine-HCl wash step and a final elution step in RNase-free water. Purified, labeled cDNA was quantified with UV spectrophotometer readings at wavelengths appropriate to determine the frequency of incorporation (FOI), which is defined as the number of labeled nucleotides incorporated per 1,000 nucleotides of cDNA. cDNA samples with FOIs between 20-50 were used for microarray hybridization.

extract_protocol: RNA was isolated from frozen bacterial pellets with the Qiagen RNeasy Midi kit according to the manufacturer’s protocol for enzymatic and mechanical disruption, except that cells treated with lysozyme followed by sonication on ice for three 30 s bursts at 18–21 W (30 s pauses between bursts). RQ1 DNase treatment of total RNA in the presence of RNasin Plus RNA inhibitor (Promega) was performed according to the manufacturer’s protocol, followed by subsequent phenol:chloroform and chloroform extractions. RNA was ethanol-precipitated overnight, centrifuged and washed with 70% ethanol before resuspension of the final RNA pellet in DEPC-treated water. Total nucleic acid concentration and purity were estimated using absorbance readings (260/280 nm, 260/230 nm) on a NanoDrop ND-1000 spectrophotometer. RNA integrity was checked by agarose gel electrophoresis.

value: wild type

tag: growth condition

value: Listeria monocytogenes C3-143 grown at 37°C until Log phase (OD600 = 0.4) in the presence of 0.5 mM IPTG

source_name: Listeria monocytogenes C3-113 (sigC null mutant)

value: C3-113 (sigC null mutant)

value: Listeria monocytogenes C3-113 grown at 37°C until Log phase (OD600 = 0.4) in the presence of 0.5 mM IPTG


title: striatum_B6.63 MOE430 2.0

source_name: striatum, adult, naïve

value: brain striatum


title: Mussel hemolymph_ 3 h post V. splendidus LGP32 injection_3.1arrayA

value: Control pool (N=40)

value: hemolymph

source_name: Hemolymph h 3.1_A


title: Mussel hemolymph_ 3 h post V. splendidus LGP32 injection_3.1arrayB

value: 0.1 ml PBS-NaCl injection into the posterior adductor muscle

source_name: Hemolymph h 3.1_B


title: SigC regulon, 10403S vs sigC null mutant, Log phase+Heat stress

source_name: Listeria monocytogenes 10403S

value: Listeria monocytogenes 10403S grown at 37°C to Log phase (OD600 = 0.4) then exposed to heat (50°C for 10 min)

value: Listeria monocytogenes C3-113 grown at 37°C to Log phase (OD600 = 0.4) then exposed to heat (50°C for 10 min)


title: ILC_FFPE_alone_rep1

status: Public on Apr 11 2011

city: Bronx

first: olivier

middle: D

last: Loudig

state: New York

address: 1300 Morris Park Avenue

department: Epidemiolkogy and Population Health

institute: Albert Einstein College of Medicine

description: FFPE ILC alone (repeat 1)

hyb_protocol: The labeled PCR amplified miRNA products were hybridized onto beadchip arrays, on the bundles of a sentrix matrix (Illumina) for 16h at 45celsius.

scan_protocol: The bundles holding the arrays were scanned using the beadreader from Illumina.

data_processing: The data obtained from the beadreader was then exported into Genomestudio. Raw data obtained from GenomeStudio was imported into Partek Genomics Suite ( v6.11.0117) and subjected to quantile normalization. Data further analyzed using ANOVA.

source_name: Archived Breast cancer

label_protocol: The labeling procedure was performed during the PCR reaction, using a Cy5 label, supplied in the Illumina microRNA profiling kit and using the V1.0 version.

growth_protocol: Samples were either obtained from patient and frozen at -80c, or formalin-fixed paraffin-embedded and archived for 1 month to 3 years

extract_protocol: Total RNA was extracted from frozen tissue using TRIzol reagent, following manufacturer's instructions. Total RNA from the FFPE specimens was extracted following the procedure described by Loudig et al. 2007.

treatment_protocol: no Treatments were made. These are clinical specimens.

tag: disease state

value: breast cancer

value: ILC alone

tag: tissue state

value: FFPE


title: ILC_FFPE_alone_rep2

description: FFPE ILC alone (repeat 2)

value: female

tag: tissue


title: ILC_FFPE_synchronous with LCIS_rep2

description: FFPE synchronous ILC (repeat 1)

value: synchronous ILC


title: ILC_FFPE_synchronous with LCIS_rep1

description: FFPE synchronous ILC (repeat 1)


title: SigC regulon, 10403S vs sigC null mutant, stationary phase

value: Listeria monocytogenes 10403S grown at 37°C to stationary phase (OD600 = 1.0 +3 additional hours)

value: Listeria monocytogenes C3-113 grown at 37°C to stationary phase (OD600 = 1.0 +3 additional hours)


title: striatum_B6.62 MOE430 2.0

tag: developmental stage

value: adult


title: Expression profile of  mlo3-A cells

source_name: log. growing mlo3-A cells

value: wild-type


title: LCIS_FFPE_synchronous with ILC_rep2

description: FFPE LCIS synchronous with ILC (repeat 2)

value: LCIS synchronous with ILC


title: normal_FFPE_breast epithelium_rep1

description: FFPE normal lobular epithelium (repeat 1)

value: control

value: normal breast


title: LCIS_FFPE_synchronous with ILC_rep1

description: FFPE LCIS synchronous with ILC (repeat 1)


title: Expression profile of  ∆mlo3 cells

source_name: log. growing ∆mlo3 cells

source_name: log. growing wild type cells


title: striatum_B6.61 MOE430 2.0

value: brain striatum


title: LCIS_FFPE_alone_rep1

description: FFPE LCIS alone (repeat 1)

value: LCIS alone


title: normal_FFPE_breast epithelium_rep2

description: FFPE normal lobular epithelium (repeat 2)


title: normal_Frozen_breast epithelium_rep1

description: Frozen normal lobular epithelium (repeat 1)

source_name: Frozen breast

value: frozen


title: SigH regulon, 10403S vs sigH null mutant, stationary phase

value: wild type

source_name: Listeria monocytogenes C3-126 (sigH null mutant)

value: C3-126 (sigH null mutant)

value: Listeria monocytogenes C3-126 grown at 37°C to stationary phase (OD600 = 1.0 +3 additional hours)


title: normal_Frozen_breast epithelium_rep2

description: Frozen normal lobular epithelium (repeat 2)


title: Expression profile of  mlo3-A ∆h2a.z cells

source_name: log. growing  mlo3-A ∆h2a.z cells

value: mlo3-A ∆h2a.z


title: SigL regulon, 10403S vs sigL null mutant, stationary phase

source_name: Listeria monocytogenes B2-124 (sigL null mutant)

value: B2-124 (sigL null mutant)

value: Listeria monocytogenes B2-124 grown at 37°C to stationary phase (OD600 = 1.0 +3 additional hours)


title: LCIS_FFPE_alone_rep2

description: FFPE LCIS alone (repeat 2)

value: female

value: breast cancer

value: FFPE


title: invasive breast tumor, Rep. 4

city: Berlin

first: Celine

last: Schäfer

address: Augustenburger Platz 1

department: Med. Kl. m.S. Hepatologie und Gastroenterologie

country: Germany

institute: Charité

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Human Genome U133 Plus 2.0 Array.

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

data_processing: GeneSpring GX 10.0 (Agilent) was used for data analysis.

source_name: invasive breast tumor of WAP-TNP8 mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 50 ng total RNA (GeneChip® Two-Cycle Target Labelling Kit (Affymetrix)).

growth_protocol: WAP-TNP8  animals, which selectively synthesize the T/t-antigen under the control of the WAP promoter in mammary gland epithelial cells, were used for this study (Schulze-Garg et al. 2000)

extract_protocol: Rneasy Kit (Qiagen) was used according to the manufacturer's instructions.

treatment_protocol: Breast tissue was snap frozen directly after preparation and stores at -80°C until RNA isolation.

value: breast tumor


title: invasive breast tumor, Rep. 5


title: breast tissue, 4M, Rep. 2

source_name: breast tissue of mice 4 month after activation of the SV40 oncogene (4M)

value: breast


title: Placenta Control Replicate 5

city: Toronto

first: Rosanna

last: Weksberg

state: Ontario

address: 555 University Ave.

department: Genetics and Genome Biology

institute: The Hospital for Sick Children

hyb_protocol: Purification of labelled products, array hybridization and scanning were performed at the Microarray facility, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada according to the Agilent Microarray Analysis of Methylated DNA Immunoprecipitation Manual (Version 1.0, May 2008)

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified by Agilent Feature Extraction software (v9.0) (Santa Clara, CA), using the Human Agilent CpG version 20070820 grid file and CGH V4-91 protocol

data_processing: The background subtracted output raw data was imported to Partek® software, version 6.3 Copyright © 2008, Partek Inc., St. Louis, MO. The imported red and green signals raw data was normalized to baseline, by dividing the red signal (MeDIP fraction) by the green signal (total genomic DNA fraction), log2 transformed and quantile normalized between all the arrays.

source_name: Placenta Control

label_protocol: Total DNA extracted using Qiagen DNeasy Blood and Tissue kit following manufacturer’s instructions; 10mg in a 100 ng/ml concentration was sonicated to sizes 200-1000 bp fragments; a 4mg fraction was immunoprecipitated (IP) using a Methylcytosine antiboidy, following a modified Weber et al., (2005) protocol. 21 ml of immunoprecipitated DNA and 250 ng of sonicated genomic DNA of corresponding sample was labeled using BioPrime® Array CGH Genomic Labeling (Cy3 and Cy5 respectively).

growth_protocol: Samples were randomly collected from the villous portion of human placentae, washed with PBS and transferred and stored in RNAlater; later from each 3 mm fragment distal villi were macrodissected and stored at -80ºC.

tag: sex

value: Male

tag: gestational age

value: 37 wk

value: Placenta

tag: birth weight percentile

tag: delivery

value: C-section

tag: pathology

value: Normal

tag: sample type

value: Methyl immunoprecipitated genomic DNA

tag: antibody

value: anti-methylcytosine

tag: antibody vendor

value: Eurogentec, San Diego, CA

tag: antibody catalog #

value: total input genomic DNA


title: breast tissue, 4M, Rep. 5

tag: strain


title: invasive breast tumor, Rep. 3


title: breast tissue, 5M, Rep. 2

source_name: breast tissue of mice 5 month after activation of the SV40 oncogene (5M)


title: breast tissue, 5M, Rep. 3


title: breast tissue, 5M, Rep. 4


title: invasive breast tumor, Rep. 1


title: invasive breast tumor, Rep. 2


title: breast tissue, 5M, Rep. 1


title: Placenta Control Replicate 7

extract_protocol: Total DNA extracted using Qiagen DNeasy Blood and Tissue kit following manufacturer’s instructions

value: Female

value: 28 wk

value: Vaginal delivery


title: Placenta Control Replicate 6

value: 34 wk


title: breast tissue, 4M, Rep. 4


title: breast tissue, 4M, Rep. 3


title: breast tissue, 5M, Rep. 5


title: Placenta IUGR Replicate 4

source_name: Placenta Case

value: Sm plac, Maternal Vascular Underperfusion


title: Placenta IUGR Replicate 8

value: 30 wk


title: Placenta Control Replicate 4

value: 29 wk


title: Placenta IUGR Replicate 2

value: 33 wk


title: Placenta IUGR Replicate 6

value: Male

value: 31 wk

value: Sm plac, Maternal Vascular Underperfusion, Fetal thrombotic vasculopathy


title: Placenta IUGR Replicate 5

value: Placenta

value: C-section


title: breast tissue, 4M, Rep. 1

value: breast


title: Placenta IUGR Replicate 1

value: Methyl immunoprecipitated genomic DNA

value: anti-methylcytosine


title: Placenta Control Replicate 2

value: 39 wk

value: Normal

value: Eurogentec, San Diego, CA

value: total input genomic DNA


title: Placenta IUGR Replicate 7

value: 36 wk


title: Placenta Control Replicate 3

value: Female

value: Inter-villous thrombosis


title: Placenta Control Replicate 8

value: 26 wk


title: Placenta IUGR Replicate 3

value: 34 wk

value: Sm plac, Maternal Vascular Underperfusion


title: breast tissue, 3M, Rep. 3

source_name: breast tissue of mice 3 month after activation of the SV40 oncogene (3M)


title: breast tissue, 3M, Rep. 4


title: Root_inoculated_-N2_7d_rep1

city: Villeurbanne Cedex

last: ALLOISIO

address: 43 bd du 11 Novembre 1917

institute: CNRS / Univ Lyon 1

description: Gene expression in inoculated roots cultivated without nitrogen and sampled 7 days after inoculation with the bacteria Frankia.

hyb_protocol: The Agilent Hybridization Kit (catalog no. 5188-5242) was used . 600 ng of the labeled sample RNA was used for hybridization according to the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol. The hybridization was performed for 17 h at 65°C. Slides were them washed for 1 min at room temperature in Wash Solution 1 (catalog no. 5188-5325) and 1 min at room temperature in Wash Solution 2, prewarmed to 37°C (catalog no. 5188-5326).

scan_protocol: Scanning  was performed with the Agilent scanner (G2505B) using default parameters for 8 x 15 K formats and the one-color protocol. (scan area 61 X 21.6 mm; scan resolution 5µm; single pass; dye channel is set to green and green PMT is set to 100%).

data_processing: Data were extracted with Feature Extraction 9.1 software (Agilent Technologies) according to the 1-color Agilent protocol (GE1-v5_95_Feb protocol). This software reads and processes microarray image files to prepare them for analysis. Feature Extraction automatically assigns a grid template and a protocol, based on the barcode of the slide. It determines feature intensities, rejects outliers and calculates statistical confidence intervals. Genespring sofware was then used for data processing. Normalization was done as follows: data transformation (Set measurements less than 5.0 to 5.0), per chip : normalized to 50th percentile (probes with presence flags only), per gene : normalized to median. Data were then filtered using flag parameter (Flags (Absent, Marginal, Present) : All control -> Absent, Saturated spot -> Marginal, Spot not uniform -> Marginal, Spot not positive and not significant -> Absent, Spot not above background -> Absent, Population outlier -> Marginal) and each probe must be present for 2/3 of the tested conditions.

organism: Alnus glutinosa

source_name: Root, inoculated, no N2, 7d post inoculation

label_protocol: Five hundred nanograms of RNA and Agilent One-Color RNA Spike-In RNA were labeled with the Agilent Low RNA Input Linear Amplification Kit PLUS, One-Color according to the manufacturer's instructions as follows: 1.2 µl of T7 Promoter Primer was added to 500 ng of RNA and 5 µl of spike-in control (in a 11.5-µl volume) and denatured at 65°C. First-Strand Buffer (to 1x), DTT (to 10 mM), dNTP (to 0.5 mM), Moloney murine leukemia virus (MMLV) reverse transcriptase (1 µl of stock provided in the kit in a 20-µl reaction), and RNaseOut (0.5 µl of stock provided in the kit in a 20-µl reaction) were added. The cDNA was synthesized during the following incubation step (2 h at 40°C). After 10-min denaturation at 65°C and the addition of Cy3-labeled CTP (to 0.3 mM), Transcription Buffer (to 1x), DTT (to 10 mM), NTP (8 µl of stock provided in the kit in a 80-µl reaction), RNaseOUT (0.5 µl of stock provided in the kit in a 80-µl reaction), inorganic phosphatase (0.6 µl of stock provided in the kit in a 80-µl reaction), and T7 RNA polymerase (0.8 µl of stock provided in the kit in a 80-µl reaction), the synthesis of the fluorescent labeled cRNA was performed during the second incubation step (2 h at 40°C). The labeled cRNA was purified with the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol.

growth_protocol: Seeds were grown for one month in a soil/vermiculite substrate (1:1, vol/vol) in a greenhouse. Plantlets were transferred to a Broughton and Dilworth's modified medium with nitrogen in plastic pots and grown for 3 weeks under these hydroponic conditions. Then they were grown for one week without nitrogen. After this starvation step which is necessary for optimal induction of symbiosis,  plants were sub-divided according to the different sampling times and conditions.

extract_protocol: Total RNA was purified from roots and nodules using a RNeasy plant mini kit (Qiagen, Courtaboeuf, France). Residual DNA was removed from RNA samples using the Turbo DNA free kit (Ambion, USA), quantified using a NanoDrop spectrophotometer (Thermo Fisher Scientific, Courtaboeuf, France) and qualitatively assessed using a Bioanalyser 2100 (Agilent p/n G2938A) according to the manufacturer’s instructions (Agilent, Santa Clara, CA, USA).

treatment_protocol: The starting point of the experiment was the day of inoculation of plant with the bacteria (0d). At 0d, a set of plants was inoculated  with the bacteria in the medium without nitrogen and two sets of plants were non-inoculated, one in the medium without nitrogen and one in the medium with nitrogen. Sampling was as follows : at 0d, sampling of one control (non-inoculated roots); at 7 days after inoculation, sampling of 2 controls ( non-inoculated roots cultivated with noitrogen, non-inoculated roots cultivated without nitrogen) and of one symbiosis condition (inoculated roots); at 21 days after inoculation, sampling of nodules (specific organs that develop in symbiosis). All samples were frozen in liquid nitrogen and conserved at -80°C before RNA extraction.

value: Root

tag: culture condition

value: Cultivated without nitrogen

tag: treatment

value: Inoculated with symbiotic Frankia bacteria

value: 7 days regarding inoculation time


title: Root_non-inoculated_-N2_7d_rep3

description: Gene expression in non-inoculated roots cultivated without nitrogen and sampled 7 days post inoculation (control)

source_name: Root, non-inoculated, no N2, 7d post inoculation

value: No inoculation


title: Placenta Control Replicate 1

value: Male

value: Placenta

value: C-section

value: Methyl immunoprecipitated genomic DNA


title: breast tissue, 2M, Rep. 5

source_name: breast tissue of mice 2 month after activation of the SV40 oncogene (2M)

value: breast


title: Root_non-inoculated_-N2_7d_rep2


title: breast tissue, 3M, Rep. 2


title: breast tissue, 2M, Rep. 4


title: breast tissue, 3M, Rep. 1


title: Root_non-inoculated_+N2_7d_rep3

description: Gene expression in non-inoculated roots cultivated with nitrogen and sampled 7 days post inoculation (control)

source_name: Root, non-inoculated, N2, 7d post inoculation

value: Cultivated with nitrogen


title: breast tissue, 2M, Rep. 3


title: IDC 5, biological rep. 5

source_name: tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 µg total RNA (GeneChip® One-Cycle Target Labelling Kit (Affymetrix)).

growth_protocol: Fresh frozen samples were optaint from the Robert-Rössle-Biobank at the ECRC (Experimental and Clinical Research Center).

extract_protocol: Rneasy lipip tissue Kit (Qiagen) was used according to the manufacturer's instructions.

value: tumor

value: IDC


title: Root_inoculated_-N2_7d_rep3


title: IDC 4, biological rep. 4


title: Root_non-inoculated_-N2_7d_rep1

source_name: Root, non-inoculated no N2, 7d post inoculation


title: breast tissue, 3M, Rep. 5


title: breast tissue, 2M, Rep. 2


title: Root_non-inoculated_+N2_7d_rep2


title: IDC 2, biological rep. 2


title: Root_inoculated_-N2_7d_rep2


title: Nodule_-N2_21d_rep3

description: Gene expression in nodules sampled 21 days  after inoculation with the bacteria Frankia on plants cultivated without nitrogen

source_name: Nodule, inoculated, no N2, 21d post inoculation

value: Nodule

value: 21 days regarding inoculation time


title: IDC 3, biological rep. 3


title: Root_non-inoculated_+N2_7d_rep1

description: Gene expression in non-inoculated roots cultivated with nitrogen and sampled 7 days  post inoculation (control)


title: Nodule_-N2_21d_rep2


title: IDC 1, biological rep. 1


title: breast tissue, 1M, Rep. 5

source_name: breast tissue of mice 1 month after activation of the SV40 oncogene (1M)


title: Nodule_-N2_21d_rep1


title: healthy breast 5, biological rep. 5

source_name: healthy

value: healthy


title: breast tissue, 2M, Rep. 1


title: breast tissue, 1M, Rep. 4


title: Root_non-inoculated_-N2_0d_rep2

description: Gene expression in non-inoculated roots cultivated without nitrogen and sampled the day of inoculation (control)

source_name: Root, non-inoculated, no N2, 0d post inoculation (reference time)

value: 0 day regarding inoculation time


title: Root_non-inoculated_-N2_0d_rep3

value: Root


title: healthy breast 4, biological rep. 4


title: breast tissue, 1M, Rep. 3


title: Root_non-inoculated_-N2_0d_rep1

value: Cultivated without nitrogen


title: healthy breast 2, biological rep. 2


title: BPN, 6 weeks old, 5

city: Sydney

middle: J

last: Morris

state: NSW

address: Anderson Stuart Building, room N452, University of Sydney

department: Physiology

country: Australia

institute: University of Sydney

description:
BPN11Y
Gene expression from young normotensive BPN/3J mouse.

hyb_protocol: After fragmentation, ssDNA was hybridized for 17 hr at 45°C to GeneChip Mouse Gene 1.0 ST Arrays. Chips were washed and stained in the Affymetrix GeneChip® Fluidics Stations 450. For all of these steps, the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix) was used according to the manufacturer’s recommendations (GeneChip® Whole Transcript (WT) Sense Target Labelling Assay Manual, version 4, Affymetrix).

scan_protocol: The chips were scanned using the GeneChip® Scanner 3000 7G 4C (Affymetrix) according to the manufacturer’s recommendations (GeneChip® Whole Transcript (WT) Sense Target Labelling Assay Manual, version 4, Affymetrix).

data_processing: The samples were individually normalized using robust-multi-array analysis (RMA) via the package 'Affy' in the R application (version 2.11.1). Differentially expressed genes for each age were identified using the moderated two-sample t-test in the Limma package.

source_name: Male BPN/3J hypothalamus,  6 weeks old

label_protocol: 100ng of total RNA was prepared for hybridisation according to the standard Affymetrix protocol (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual, version 4, Affymetrix).

growth_protocol: Hypothalamus was removed from BPH/2J and BPN/3J strains of mice at peak blood pressure. Tissues were frozen and then RNA was extracted.

extract_protocol: The RNeasy kit (Qiagen) was used for extraction of total RNA according to the manufacturer's instructions.

treatment_protocol: Standard animal house treatment.

tag: gender

value: male

tag: age

value: 6 weeks

value: hypothalamus

tag: blood pressure

value: normotensive


title: healthy breast 3, biological rep. 3

tag: tissue

tag: disease state


title: BPN, 6 weeks old, 4

description:
BPN10Y
Gene expression from young normotensive BPN/3J mouse.


title: breast tissue, 1M, Rep. 1


title: breast tissue, Neg Contr., Rep. 3

source_name: breast tissue of WAP-TNP8 mice bevor activation of the SV40 oncogene


title: breast tissue, Neg Contr., Rep. 5


title: breast tissue, Neg Contr., Rep. 2


title: BPN, 6 weeks old, 2

description:
BPN8Y
Gene expression from young normotensive BPN/3J mouse.


title: DCIS 9, biological rep. 9

source_name: DCIS

value: DCIS


title: BPN, 6 weeks old, 1

description:
BPN6Y
Gene expression from young normotensive BPN/3J mouse.


title: healthy breast 1, biological rep. 1


title: DCIS 8, biological rep. 8


title: breast tissue, Neg Contr., Rep. 4


title: DCIS 6, biological rep. 6


title: BPN, 6 weeks old, 6

description:
BPN12Y
Gene expression from young normotensive BPN/3J mouse.


title: breast tissue, 1M, Rep. 2


title: BPN, 26 weeks old, 5

description:
BPN10
Gene expression from adult normotensive BPN/3J mouse.

source_name: Male BPN/3J hypothalamus,  26 weeks old

value: 26 weeks


title: BPH, 6 weeks old, 4

description:
BPH9Y
Gene expression from young hypertensive BPH/2J mouse.

source_name: Male BPH/2J hypothalamus, 6 weeks old

value: hypertensive


title: BPH, 6 weeks old, 6

description:
BPH12Y
Gene expression from young hypertensive BPH/2J mouse.


title: DCIS 7, biological rep. 7


title: BPH, 6 weeks old, 3

description:
BPH8Y
Gene expression from young hypertensive BPH/2J mouse.


title: BPH, 6 weeks old, 2

description:
BPH2Y
Gene expression from young hypertensive BPH/2J mouse.


title: BPN, 6 weeks old, 3

description:
BPN9Y
Gene expression from young normotensive BPN/3J mouse.


title: BPN, 26 weeks old, 6

description:
BPN11
Gene expression from adult normotensive BPN/3J mouse.


title: breast tissue, Neg Contr., Rep. 1

value: breast


title: breast tissue, BalbC, Rep. 5

source_name: breast tissue of wild type mice (BalbC)

value: BalbC


title: DCIS 4, biological rep. 4

value: tumor


title: BPH, 6 weeks old, 5

description:
BPH11Y
Gene expression from young hypertensive BPH/2J mouse.


title: DCIS 5, biological rep. 5


title: BPN, 26 weeks old, 2

description:
BPN6
Gene expression from adult normotensive BPN/3J mouse.


title: breast tissue, BalbC, Rep. 3


title: BPH, 6 weeks old, 1

description:
BPH1Y
Gene expression from young hypertensive BPH/2J mouse.


title: BPN, 26 weeks old, 1

description:
BPN5
Gene expression from adult normotensive BPN/3J mouse.


title: BPN, 26 weeks old, 3

description:
BPN7
Gene expression from adult normotensive BPN/3J mouse.


title: DCIS 2, biological rep. 2


title: BPH, 26 weeks old, 5

description:
BPH8
Gene expression from adult hypertensive BPH/2J mouse.

source_name: Male BPH/2J hypothalamus, 26 weeks old


title: BPH, 26 weeks old, 3

description:
BPH6
Gene expression from adult hypertensive BPH/2J mouse.


title: DCIS 1, biological rep. 1


title: BPN, 26 weeks old, 4

description:
BPN8
Gene expression from adult normotensive BPN/3J mouse.


title: DCIS 3, biological rep. 3


title: breast tissue, BalbC, Rep. 2


title: BPH, 26 weeks old, 6

description:
BPH9
Gene expression from adult hypertensive BPH/2J mouse.


title: breast tissue, BalbC, Rep. 4


title: breast tissue, BalbC, Rep. 1


title: Strain n9155 replicate 2

status: Public on Apr 09 2011

city: Wuerzburg

first: Biju Joseph

last: Ampattu

address: Josef-Schneider Str 2

department: Department of Microbiology

institute: University of Wuerzburg

description:
n9155-2 .gpr
replicate 2 of 3

hyb_protocol: The labelled DNA were mixed together with two volumes of hybridization buffer (Eurogentec, Belgium) and hybridized onto prehybridized microarray slides using a Tecan Hybridization station.

scan_protocol: The slides were scanned using a Genepix Pro scanner with settings to avoid more than 10% of the spots being saturated.

data_processing: Raw data generated after flagging for obvious cases of stray background and spots with a signal to noise ratio of less than 3 were further analyses using the R package limma.

organism: Neisseria meningitidis

source_name: DNA from Strain_n9155

label_protocol: 4 µg of chromosomal DNA and 4  µg of the pooled common reference were labelled with Cy3 dCTP and Cy5 dCTP using Klenow enzyme and random nonamers and the labelled DNA was precipitated and purified.

growth_protocol: The strains were cultivated on blood agar plates at 37°C

extract_protocol: Chromosomal DNA from the meningococcal strains were isolated using Genomic Tip 20/G (Qiagen, Germany).

source_name: Common Reference

value: Pool of DNA from all strains in this dataset


title: Strain N9155 replicate 1

description:
n9155-1 .gpr
replicate 1 of 3

source_name: DNA from Strain_N9155


title: Strain n8638 replicate 2

description:
n8638-2 .gpr
replicate 2 of 3

source_name: DNA from Strain_n8638


title: BPH, 26 weeks old, 1

description:
BPH4
Gene expression from adult hypertensive BPH/2J mouse.


title: Strain n8638 replicate 3

description:
n8638-3 .gpr
replicate 3 of 3


title: Strain N8638 replicate 1

description:
n8638-1 .gpr
replicate 1 of 3

source_name: DNA from Strain_N8638


title: Strain n9155 replicate 3

description:
n9155-3 .gpr
replicate 3 of 3


title: Strain n7901 replicate 3

description:
n7901-3 .gpr
replicate 3 of 3

source_name: DNA from Strain_n7901


title: BPH, 26 weeks old, 4

description:
BPH7
Gene expression from adult hypertensive BPH/2J mouse.


title: BPH, 26 weeks old, 2

description:
BPH5
Gene expression from adult hypertensive BPH/2J mouse.


title: Strain N7901 replicate 1

description:
n7901-1 .gpr
replicate 1 of 3

source_name: DNA from Strain_N7901


title: Strain n7865 replicate 3

description:
n7865-3 .gpr
replicate 3 of 3

source_name: DNA from Strain_n7865


title: Strain n7901 replicate 2

description:
n7901-2 .gpr
replicate 2 of 3


title: Strain n7865 replicate 1

description:
n7865-1 .gpr
replicate 1 of 3


title: Strain n7127 replicate 3

description:
n7127-3 .gpr
replicate 3 of 3

source_name: DNA from Strain_n7127


title: Strain n7017 replicate 2

description:
n7017-2 .gpr
replicate 2 of 3

source_name: DNA from Strain_n7017