title: Normal human melanocyte_HEM-LP

status: Public on Dec 01 2010

type: RNA

city: New York

first: Iman

last: Osman

state: NY

address: 522 First Avenue, SML405

department: Urology

country: USA

institute: New York University School of Medicine

description: Gene expression data

hyb_protocol: Standard Affymetrix Hybridization Protocol as recommended by the Affymetrix GeneChip Expression Analysis Technical Manual was used.

scan_protocol: Affymetrix GeneArray Scanner 3000 7G

data_processing: Array data were normalized using the robust multichip average (RMA) and filtered for expression values lower than 16. Data were then log transformed to perform an analysis of variance (ANOVA) and a two-sample unpaired t-test with p-values adjusted for multiple comparisons (Boferroni correction). A single factor, two-level ANOVA design was utilized to examine sources of measured variability and identify differences between the SSM (WM1552c, WM35) and NM cell line (WM39, WM278, LU451, SK-MEL-147) groups. A software package dChip was used to facilitate the analysis.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Melanocyte Cell Line

label_protocol: Affymetrix One-cycle Labeling kit and instructions in the Affymetrix GeneChip Expression Analysis Technical Manual were used.

growth_protocol: Cell lines derived from primary tumors were cultured in Mel 2% medium (Fang et al.Cancer Res, 2005. PMID 16230395), and metastatic cell lines were cultured as previously described (Segura et al. Proc Natl Acad Sci USA, 2009. PMID 19188590 ).

extract_protocol: RNA was isolated from melanoma cell lines using RNAeasy columns (Qiagen, Valencia, CA), and the quality and quantity assessed by UV spectrophotometer.

tag: histological subtype

value: Melanocyte control

tag: cell line

value: Normal human melanocyte, HEM-LP


title: Morphine treated replicate 2 at 48 hpf

type: mixed

city: Minneapolis

first: Xiaoxiao

last: Zhang

address: 312 Church St. SE

institute: University of Minnesota

hyb_protocol: A mixture of labeled RNA and DNA was hybridized to a miRNA microarray (Thomson et al), inside a MAUI mixer in a MAUI hybridization system (BioMicro® System, Inc, Salt Lake City, UT, USA).     Thomson, J.M., Parker, J., Perou, C.M., and S.M. Hammond. 2004. A custom microarray platform for analysis of microRNA gene expression. Nat. Methods 1: 47-53. Epub 2004 Sep 29.

scan_protocol: Slides were scanned with a ScanArray 5000 machine (Perkin Elmer®, Waltham, MA, USA).

data_processing: BlueFuse (BlueGenome, Cambridge, UK) was used to quantify pixel intensities.  GeneSpring GX 7.3.1 (Agilent Technologies) was used for data normalization.

organism: Danio rerio

source_name: Total RNA  from Zebrafish embroys, morphine treated

label_protocol: Total RNA was ligated to a synthetic linker, 5’-pCU-DY547-3’.  Reference DNA oligonucleotides (Invitrogen) complementary to a subset of mammalian miRNAs were combined and labeled with a ULYSIS® Alexa Fluor® 647 kit.

growth_protocol: A natural breeding system has been used to obtain zebrafish embryos. This natural breeding is based on the photoperiod exhibited by the zebrafish in such a way that the egg laying is done during the first light of the day, so it can be controlled with artificial light.

extract_protocol: Trizol® reagent (Invitrogen) was used to extract total RNA from  cells

treatment_protocol: Embryos are collected from the mating cages and kept in an incubator at 28.5º C. Embroys are treated with 10nM Morphine sulphate , and 5hpto sacrifice time.

tag: developmental stage

value: 48 hpf

tag: sample type

value: miRNAs and control RNAs from Zebrafish fish embroys

tag: tissue

value: embryo

label: Alexa Fluor® 647

molecule: other

source_name: Reference DNA

value: synthetic DNA oligos corrresponding to human miRNAs


title: Melanoma cell line_SKMEL29

description: Gene expression data

source_name: Melanoma Cell Line

value: Metastatic melanoma

value: Melanoma cell line, SKMEL29


title: Melanoma cell line_SKMEL94

description: Gene expression data

value: Melanoma cell line, SKMEL94


title: Melanoma cell line_A375

description: Gene expression data

value: Melanoma cell line, A375


title: Melanoma cell line_WM39

description: Gene expression data

value: Primary nodular melanoma

value: Melanoma cell line, WM39


title: Melanoma cell line_SKMEL192

description: Gene expression data

value: Melanoma cell line, SKMEL192


title: Morphine treated replicate 3 at 48 hpf


title: Melanoma cell line_SKMEL197

description: Gene expression data

value: Melanoma cell line, SKMEL197


title: Melanoma cell line_SKMEL187

description: Gene expression data

value: Melanoma cell line, SKMEL187


title: Melanoma cell line_SKMEL103

description: Gene expression data

value: Melanoma cell line, SKMEL103


title: Melanoma cell line_LU451

description: Gene expression data

value: Nodular metastatic melanoma

value: Melanoma cell line, LU451


title: Melanoma cell line_SKMEL100

description: Gene expression data

value: Melanoma cell line, SKMEL100


title: Melanoma cell line_SKMEL147

description: Gene expression data

value: Melanoma cell line, SKMEL147


title: Melanoma cell line_WM278

description: Gene expression data

value: Melanoma cell line, WM278


title: Melanoma cell line_SKMEL85

description: Gene expression data

value: Melanoma cell line, SKMEL85


title: Melanoma cell line_WM1552c

description: Gene expression data

value: Primary superficial spreading melanoma

value: Melanoma cell line, WM1552c


title: Melanoma cell line_WM35

description: Gene expression data

value: Melanoma cell line, WM35


title: Melanoma cell line_SKMEL19

description: Gene expression data

value: Metastatic melanoma

value: Melanoma cell line, SKMEL19


title: Melanoma cell line_501 Mel

description: Gene expression data

value: Melanoma cell line, 501 Mel


title: Melanoma cell line_SKMEL173

description: Gene expression data

value: Melanoma cell line, SKMEL173


title: sciP depletion glu/xyl - rep1

city: Cambridge

first: Michael

last: Laub

state: MA

address: 31 Ames St.

institute: MIT

hyb_protocol: Agilent protocol

scan_protocol: Agilent protocol

data_processing: Arrays were scanned using an Agilent scanner.  Agilent output files were then opened using the command agferead in Matlab 7.9 and the log10 values extracted with no additional processing or filtering.

organism: Caulobacter vibrioides CB15

source_name: sciP depletion - swarmers - glucose

label_protocol: standard Cy3-dCTP incorporation

extract_protocol: Qiagen RNeasy

tag: genotype

value: sciP depletion

tag: condition

value: glucose

tag: cell type

value: G1 cells

source_name: sciP depletion - swarmers - xylose

label_protocol: standard Cy5-dCTP incorporation

value: xylose


title: sciP overexpression - rep1

source_name: wt + empty vector - xylose

tag: strain/condition

value: wild type + empty vector in xylose

source_name: sciP overexpression - xylose

value: wild type + plasmid pJS14-Pxyl-sciP in xylose


title: Normal human melanocyte_HEM-N

description: Gene expression data

value: Melanocyte control

value: Normal human melanocyte, HEM-N


title: Immortalized melanocyte_Hermes2B

description: Gene expression data

value: Immortalized melanocyte, Hermes2B


title: sciP depletion glu/xyl - rep2


title: sciP overexpression - rep2


title: Immortalized melanocyte_Hermes1

description: Gene expression data

value: Immortalized melanocyte, Hermes1


title: Morphine treated replicate 1 at 48 hpf

value: 48 hpf

value: miRNAs and control RNAs from Zebrafish fish embroys

value: embryo

value: synthetic DNA oligos corrresponding to human miRNAs


title: Morphine treated replicate 3 at 24 hpf

value: 24 hpf

label: Alexa Fluor® 657


title: Morphine treated replicate 2 at 16 hpf

value: 16 hpf


title: Morphine treated replicate 3 at 16 hpf


title: Morphine treated replicate 1 at 24 hpf


title: Morphine treated replicate 2 at 24 hpf


title: Control replicate 2 at 16 hpf

source_name: Total RNA  from Zebrafish embroys, control treated


title: Control replicate 2 at 48 hpf


title: Morphine treated replicate 1 at 16 hpf


title: Control replicate 1 at 16 hpf


title: Control replicate 3 at 48 hpf


title: Control replicate 3 at 16 hpf


title: Control replicate 3 at 24 hpf


title: Control replicate 2 at 24 hpf


title: Control replicate 1 at 48 hpf


title: Control replicate 1 at 24 hpf


title: JNK3 null vs. WT hippocampus 2

city: Barcelona

first: Felix

last: Junyent

address: Avda/Diagonal

country: Spain

institute: Universitat de Barcelona

description:
Equal quantities of labeled cDNA were hybridized for 14 h at 42ºC to the 22 thousand oligo mice arrays in UniHyb hybridization solution (TeleChem International, Inc).
Array images were acquired and quantified in a ScanArray 4000 using the accompanying software (Packard BioChips). All images were captured at a 50% scan rate using 65% PMT gain, 70 to 75% laser power, and 10 m resolution. For each spot, the Cy3 and Cy5 mean density value and the Cy3 and Cy5 mean background value were calculated with ArrayPro Analyzer software (Media Cibernetics). In all cases, the fluorescence signal was between seven to ten times more intense than the background signal, and the background was evaluated just beside the labeled spot.
Microarray data analysis were analyzed with the GenArise software, developed by the Computing Unit at the Cellular Physiology Institute of the UNAM. GenArise carries out a number of transformations: background correction, lowest normalization, intensity filter, replicate analysis, and selection of differentially expressed genes. The goal of GenArise is to provide evidence that genes are differentially expressed, and it has been successfully used in other studies. The software identifies differentially expressed genes by calculating an intensity-dependent z-score. It uses a sliding window algorithm to calculate the mean and standard deviation within a window surrounding each data point, and it defines a z-score that measures the number of standard deviations a data point is from the mean: zi = (Ri - mean(R)) / sd(R), where zii is the z-score for each element, Ri is the log-ratio for each element, and sd(R) is the standard deviation of the log-ratio. Applying these criteria, the elements with a z-score > 2 standard deviations correspond  to genes that are likely to be differentially expressed.

organism: Mus musculus

source_name: hippocampus from wild-type mice

label_protocol: For cDNA synthesis, 10 g of total RNA was used as the template, incorporating dUTP-Cy3  with the CyScribe First-Strand cDNA labeling kit (Amersham). Incorporation of the fluorophore was analysed by evaluating the absorbance at 555 nm for Cy3.

extract_protocol: Total RNA was isolated from the hippocampus of each mouse, as described previously. Briefly, tissue was homogenized in the presence of TRizol® reagent (Invitrogen). Chloroform was added and the RNA was precipitated from the aqueous phase with isopropanol at 4ºC. RNA were reconstituted in RNase-free water, and then quantified and checked for RNA integrity with an Agilent 2100 Bioanalyzer.

value: wild type

tag: genetic background

tag: gender

value: male

value: hippocampus

tag: age

value: 50 days old

source_name: hippocampus from Jnk3 null mice

label_protocol: For cDNA synthesis, 10 g of total RNA was used as the template, incorporating dUTP-Cy5 with the CyScribe First-Strand cDNA labeling kit (Amersham). Incorporation of the fluorophore was analysed by evaluating the absorbance at 655 nm for Cy5.

value: Jnk3 null


title: JNK3 null vs. WT hippocampus 1

description:
Equal quantities of labeled cDNA were hybridized for 14 h at 42ºC to the 22 thousand oligo mice arrays in UniHyb hybridization solution (TeleChem International, Inc).
Array images were acquired and quantified in a ScanArray 4000 using the accompanying software (Packard BioChips). All images were captured at a 50% scan rate using 65% PMT gain, 70 to 75% laser power, and 10 m resolution. For each spot, the Cy3 and Cy5 mean density value and the Cy3 and Cy5 mean background value were calculated with ArrayPro Analyzer software (Media Cibernetics). In all cases, the fluorescence signal was between seven to ten times more intense than the background signal, and the background was evaluated just beside the labeled spot.
Microarray data analysis were analyzed with the GenArise software, developed by the Computing Unit at the Cellular Physiology Institute of the UNAM [27]. GenArise carries out a number of transformations: background correction, lowest normalization, intensity filter, replicate analysis, and selection of differentially expressed genes. The goal of GenArise is to provide evidence that genes are differentially expressed, and it has been successfully used in other studies [28,29,30,31]. The software identifies differentially expressed genes by calculating an intensity-dependent z-score. It uses a sliding window algorithm to calculate the mean and standard deviation within a window surrounding each data point, and it defines a z-score that measures the number of standard deviations a data point is from the mean: zi = (Ri - mean(R)) / sd(R), where zii is the z-score for each element, Ri is the log-ratio for each element, and sd(R) is the standard deviation of the log-ratio. Applying these criteria, the elements with a z-score > 2 standard deviations correspond  to genes that are likely to be differentially expressed.

source_name: hippocampus wild-type mice

label_protocol: For cDNA synthesis, 10 g of total RNA was used as the template, incorporating dUTP-Cy3 with the CyScribe First-Strand cDNA labeling kit (Amersham). Incorporation of the fluorophore was analysed by evaluating the absorbance at 555 nm for Cy3

source_name: hippocampus Jnk3 null mice

label_protocol: For cDNA synthesis, 10 g of total RNA was used as the template, incorporating dUTP-Cy5 with the CyScribe First-Strand cDNA labeling kit (Amersham). Incorporation of the fluorophore was analysed by evaluating the absorbance at 655 nm for Cy5


title: S1587-17, acid soil, biologial rep2

city: Campinas

first: Marcelo

last: Menossi

state: SP

address: Rua Monteiro Lobato, 255, Instituto de Biologia, Departamento de Genetica, Evolucao e Bioagentes

department: Genetica, Evolucao e Bioagentes

country: Brazil

institute: Marcelo Menossi

description: Gene expression data from root leaves subjected to soil growth

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

scan_protocol: The image was acquired with Affymetrix GeneChip Scanner 3000-7G using the sotware Affymetrix Command Console.

data_processing: The data were normalized by the RMA method using R/Bioconductor.

label: Biotin

organism: Zea mays

source_name: Leaves from maize genotype S1587-17 grown in acid soil for 3 days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

growth_protocol: Seeds from the tropical maize (Zea mays L.) inbreed lines Cat100-6 (Al-tolerant) and S1587-17 (Al-sensitive) were obtained from the germplasm bank from the University of Campinas. Seeds were geminated for 2 days in moist filter paper and then transferred to germination plastic bags (500 mL each) filled with 1 kg of control or acid soil. Only seedlings with similar initial root length were transferred to the soil bags (20 seeds/bag). Plants were grown in a growth chamber at 26°C (light:dark period of 16:8h). The bags with the seed were weighted and then twice a day the weight was completed with distillated water to keep soil humidity at 15% (v/w).

extract_protocol: The RNA was extracted with the RNeasy Plant Mini Kit (Quiagen, USA). The RNA was evaluated on agarose/formaldehyde gel, quantified in spectrophotometer and stocked in biofreezers.

treatment_protocol: The soil used is a Dark Red Latossol from Fazenda Santa Elisa, Campinas, SP, Brazil (location 22°59’09”S 47°05’25”O, approximately 610 meter above sea level). Soil samples were taken at 20-40 cm depth, sieved through a 4mm mesh and kept inside plastic boxes protected from light. Soil analysis indicated that the original sample presented pH 4.1 and Al content of 10 mmolc/dm3. The acid soil treatment consisted of the original soil with a fertilization to avoid nutritional stress. The control soil was incubated with 0.8 g of Ca(OH)2 per Kg of soil for 1 week prior to fertilization with the same amount of nutrient provided to the acid soil. The incubation with Ca(OH)2 made the pH increase to pH 5.5 and the presence of Al was undetectable. The fertilization comprised the following nutrients (mg/Kg of soil): 56 of N; 38.75 of P; 78 of K; 32 of S; 60 of Mg; 0.5 of B; 0.5 of Cu; 0.01 of Mo; 1.0 of Zn.  The acid soil also received the correction of Ca through the addition of a CaCl2 solution. This was because of the differential incubation of the control soil with Ca(OH)2. The soil was mixed several times to reduce the natural variability of the physical and chemical properties of both soils.

value: leaves


title: S1587-17, control soil, biologial rep2

source_name: Leaves from maize genotype S1587-17 grown in control soil for 3 days


title: S1587-17, control soil, biologial rep3


title: S1587-17, acid soil, biologial rep1


title: S1587-17, acid soil, biological rep3


title: S1587-17, control soil, biologial rep1


title: HSF4_Lens_Null_rep2

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

country: France

institute: IARC WHO

hyb_protocol: 2.2 micrograms of amplified/labeled cDNA was hybridized for 17 hr to the Affymetrix array. Genechips® were processed using protocol EukGE_WS2v4 450 for Genechip® fluidics station 450.

scan_protocol: Affymetrix GeneArray scanner 7G

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

source_name: Lens, Hsf4 null

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

growth_protocol: Newborn HSF4 null and wildtype newborn mice were used.

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

treatment_protocol: Lenses were removed from newborn HSF4 null and wildtype mice.

value: newborn

value: lens

tag: strain

value: ICR

tag: genotype/variation

value: HSF4 null


title: Cat100-6, acid soil, biologial rep2

source_name: Leaves from maize genotype Ca100-6 grown in acid soil for 3 days


title: Lens_Wildtype_rep1

source_name: Lens, wildtype


title: HSF4_Lens_Null_rep1


title: Lens_Wildtype_rep2


title: HaCaT_TNF+IFNg+GW9508_2

city: Kyoto

first: Tomoko

last: Fujita

address: Yoshida Konoe-Cho

department: Medicine

country: Japan

institute: Kyoto University

description: HaCaT cells, stimulated with GW9508 + TNF-a + IFN-g for 30 h

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Human Genome U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (GeneChip 3' IVT Kit User Manual, Affymetrix).

extract_protocol: RNeasy (QIAGEN) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: HaCaT cells were cultured in 96 well-plate and serum-starved for 24h. Then, terbutaline or GW9508 were added and incubated for 5min. TNF-alpha + IFN-gamma were then added and culturedfor another 24 h and cell were collected.

value: HaCaT

value: cell line from epidermal keratinocyte


title: HSF4_Lens_Null_rep3


title: Cat100-6,acid soil, biologial rep1


title: Cat100-6, control soil, biologial rep2

source_name: Leaves from maize genotype Ca100-6 grown in control soil for 3 day


title: Cat100-6, acid soil, biologial rep3


title: Lens_Wildtype_rep3


title: Cat100-6, control soil, biologial rep1


title: HaCaT_TNF+IFNg+terbutaline_3

description: HaCaT cells, stimulated with terbutaline + TNF-a + IFN-g for 27 h


title: HaCaT_TNF+IFNg+GW9508_3

source_name: HaCaT cells, stimulated with GW9508 + TNF-a + IFN-g for 30 h


title: Cat100-6, control soil, biologial rep3


title: HaCaT_TNF+IFNg+terbutaline_1

source_name: HaCaT cells, stimulated with terbutaline + TNF-a + IFN-g for 27 h


title: HaCaT_TNF+IFNg_3

description: HaCaT cells, stimulated with TNF-a+IFN-g for 24 h


title: HaCaT_TNF+IFNg+terbutaline_2


title: INCTC_Bone_marrow_normal_CD34+_Myeloid_12h

type: SAGE

anchor: NlaIII

city: Ribeirão Preto

first: Daniel

middle: Guariz

last: Pinheiro

state: São Paulo

address: Rua Tenente Catão Roxo, 2501

department: Departamento de Genética

institute: Faculdade de Medicina de Ribeirão Preto (Universidade de São Paulo)

description: Bone marrow iliac crest aspirates from healthy adult donors. CD34+ cells were isolated to >95% purity by MACS Indirect CD34 Progenitor Cell Isolation Kit (Miltenyi Biotec) following the manufacturer’s instructions. Cells were cultured for 12 hours under myeloid stimulus, following the growth protocol.

source_name: Bone marrow CD34+ Hematopoietic Stem/Progenitor Cells cultured for 12 hours under myeloid differentiation stimulus

growth_protocol: For myeloid differentiation we used StemSpan (SteamCell Technologies, No. 09600) supplemented with 20% FBS, SCF (100ng/ml), Flt-3lig (50 ng/ml), IL-3 (20ng/ml), IL-6 (20 ng/ml) and GM-CSF (20ng/ml).

extract_protocol: TRIzol® Reagent

tag: organ/tissue

value: bone marrow

tag: tissue preparation

value: iliac crest aspiration

value: CD34+ HSPC cultured for 12 hours under myeloid stimulus


title: Ascl1 overexpression vs. control

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized (Cy3/Cy5 ratio median = 1), background subtracted data obtained from log2 of processed Red signal/processed Green signal.

organism: Rattus norvegicus

source_name: control

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: CG4 cells were grown in DMEM/F12 HAM-based medium containing 2% FBS. The cell were maintained at 37 C and 4.5% CO2

extract_protocol: Cells were lysed in RLT buffer (Qiagen).Total RNA was extracted from the cell lysate using an RNeasy kit (Qiagen).

treatment_protocol: Cells were transfected with pCMV vector encoding either Ascl1 gene or Mock control. Cells were cultured for 48 h before harvesting.

tag: transfection

value: mock vector

value: Ascl1-overexpression vector


title: HaCaT_TNF+IFNg+GW9508_1


title: LCL EBV immortalized (06.08.08/5)

status: Public on Oct 30 2010

city: Innsbruck

first: Roland

last: Hutzinger

address: Fritz-Pregl-Str. 3

country: Austria

institute: Biocenter Innsbruck

description: sizefractionated RNA (18-500 nt)

hyb_protocol: 2.5 µg size-fractionated, labeled RNA was hybridized and detected according to febit standard procedures with modification to a temperature-gradient hybridization starting at 70°C and decreasing in 2-3°C increments per hour to a final temperature of 39°C over a period of 16 hours. Upon hybridization, stringent washing with 0.5xSSPE at 45°C was performed, followed by staining of the hybridized biotin-labeled target RNAs using streptavidin-phycoerythrin (SAPE) in 6xSSPE at 25°C and consecutive signal enhancement with biotinylated anti-steptavidin antibodies and a second round of SAPE staining inside the highly automated Geniom machine (febit biomed gmbh, Heidelberg, Germany).

scan_protocol: The detection was done using the appropriate filter set (Cy3) employing the autoexposure function of the Geniom software. Feature extraction was done using the in-built Geniom feature extraction algorithm.

data_processing: Raw data was read into R as a tab delimited text file. The data was then converted into a matrix, with rows corresponding to the features and columns corresponding to the different samples. The array background was calculated as the median signal intensity of all ‘blank-control’ features on the array and subtracted from the intensity values of all other intensities. Subsequently, the nonpositive values were substituted with ‘10’. After applying quantile normalization to the background adjusted data set, intra-array replicates were combined by their mean intensity.normalization to the background adjusted data set, intra-array replicates were combined by their mean intensity (Vorwerk et al., 2008). Expression of ncRNA genes with ≥ 1000 signal intensity in at least 3 of the five biological replica either in non-infected or in infected samples of the chip experiments were selected and considered to be expressed (Supplementary Table 4). The fold change (FC) of probes of infected versus non-infected was calculated (log2).

source_name: EBV-immortalized RNA

label_protocol: Size-fractionated RNA was labeled with the mirVANA miRNA labeling kit (Ambion, Austin, USA) according to the manufacturers protocol.

growth_protocol: BL2 and LCL B95.8 cell lines were cultured in RPMI 1640 supplemented with 10% FCS, L-glutamine (2mM ml-1) and antibiotics (100 U penicillin ml-1 and 100 µg streptomycin ml-1).

extract_protocol: Total RNA from EBV-immortalized and non-infected cells was isolated by using the Tri Reagent (Ambion, Austin, USA) method according to the manufacturers protocol. Five biological replica of total RNA isolated from non-infected BL2 and EBV-immortalized LCL B95.8 cells were size-fragmented from 18-500 nt by 8% denaturating PAGE (PAGE; 7M urea, 1X TBE buffer). RNA fragments were eluted from the gel in NaoAc (0.3 M, pH 5.2, 4°C) over night and concentrated to an end volume of approximately 300 µl. Purification of RNA subsequent to elution was performed by phenol/chloroform extraction. RNA was dissolved in dH20, vigorously vortexed after addition of one volume of PCI [Phenol: Chloroform: Isoamylalcohol; (25:24:1)] and centrifuged (4ºC, 18000x g, 4 min). The upper aqueous phase was collected in a fresh Eppendorf tube, and the same procedure was repeated with one volume of chloroform. The water phase was precipitated with 1/10 volume of 3 M NaOAc (pH 5.5) and three volumes of water-free ethanol. Over-night incubation at -20°C supported efficient precipitation of the nucleic acids. Nucleic acids were pelleted by centrifugation (18000x g, 30 min, 4°C). After removal of the supernatant, the pellet was washed once with 1 ml of 70% ethanol, followed by centrifugation (18000x g, 10 min, 4°C). The pellet was dissolved in RNase-free H20 and the concentration was determined by measuring the absorbance at 260 nm using NanoDrop spectrophotometer.

value: LCL

tag: infection

value: EBV strain B95.8


title: LCL EBV immortalized (06.08.08/4)

description: sizefractionated RNA (18-500 nt)

tag: cell line


title: HaCaT_TNF+IFNg_2

source_name: HaCaT cells, stimulated with TNF-a+IFN-g for 24 h


title: HaCaT_unstimulated_3

description: HaCaT cells, unstimulated

source_name: HaCaT cells, unstimulated


title: INCTC_Bone_marrow_normal_CD34+

description: Bone marrow iliac crest aspirates from healthy adult donors. CD34+ cells were isolated to >95% purity by MACS Indirect CD34 Progenitor Cell Isolation Kit (Miltenyi Biotec) following the manufacturer’s instructions.

source_name: Bone marrow CD34+ Hematopoietic Stem/Progenitor Cells

value: CD34+ HSPC


title: INCTC_Bone_marrow_normal_CD34+_Myeloid_40h

description: Bone marrow iliac crest aspirates from healthy adult donors. CD34+ cells were isolated to >95% purity by MACS Indirect CD34 Progenitor Cell Isolation Kit (Miltenyi Biotec) following the manufacturer’s instructions. Cells were cultured for 40 hours under myeloid stimulus, following the growth protocol.

source_name: Bone marrow CD34+ Hematopoietic Stem/Progenitor Cells cultured for 40 hours under myeloid differentiation stimulus

value: CD34+ HSPC cultured for 40 hours under myeloid stimulus


title: HaCaT_TNF+IFNg_1


title: LCL EBV immortalized (06.08.08/3)

description: sizefractionated RNA (18-500 nt)


title: BL2 EBV non-infected (30.01.08/3)

description: sizefractionated RNA (18-500 nt)

source_name: BL2 non-infected RNA


title: BL2 EBV non-infected (30.01.08/1)

description: sizefractionated RNA (18-500 nt)


title: BL2 EBV non-infected (22.04.08)

description: sizefractionated RNA (18-500 nt)


title: LCL EBV immortalized (06.08.08/2)

description: sizefractionated RNA (18-500 nt)


title: HaCaT_unstimulated_1

description: HaCaT cells, unstimulated


title: LCL EBV immortalized (20.08.08)

description: sizefractionated RNA (18-500 nt)


title: BL2 EBV non-infected (04.03.08)

description: sizefractionated RNA (18-500 nt)


title: organotypic epidermis cdk4 Ras U0126 rep 2

status: Public on Oct 15 2010

city: Stanford

first: Todd

middle: W.

last: Ridky

state: CA

address: 269 Campus Drive

department: Dermatology

institute: Stanford University

description: TR_KC Cdk4Ras UO1 C6_(HG-U133A_2).CEL

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized in a GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix Scaner 3000 G7.

data_processing: Genespring was used to RMA normalize all of the samples.  No baseline was set.

source_name: organotypic epidermis expressing cdk4 and Ras tx with U0126

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: Early passage parimary cervical epithelial cells were grown on devtalized human dermis in 3D organotypic culture.  UO126 treated samples had 5uM U0126 added to the growth media.

extract_protocol: Qiagen RNAEasy columns

treatment_protocol: Tissues were minced prior to RNA extraction

value: cdk4 and Hras expression

tag: agent


title: organotypic epidermis cdk4 Ras rep5

description: TR_KC Cdk4Ras C3_(HG-U133A_2).CEL

source_name: organotypic epidermis expressing cdk4 and Ras


title: organotypic epidermis cdk4 Ras rep4

description: TR_KC cdk4Ras B2_(HG-U133A_2).CEL


title: BL2 EBV non-infected(30.01.08/2)

description: sizefractionated RNA (18-500 nt)


title: HaCaT_unstimulated_2

description: HaCaT cells, unstimulated


title: organotypic epidermis LacZ rep6

description: TR_KC lacZ C2_(HG-U133A_2).CEL

source_name: organotypic epidermis expressing lacZ

value: control


title: organotypic epidermis cdk4 Ras rep7

description: TR_KC Cdk4Ras D3_(HG-U133A_2).CEL


title: organotypic epidermis cdk4 Ras rep3

description: TR_KC cdk4Ras B1_(HG-U133A_2).CEL


title: organotypic epidermis cdk4 Ras U0126 rep1

description: TR_KC Cdk4Ras U01 C5 UO1A_(HG-U133A_2).CEL


title: organotypic epidermis LacZ rep7

description: TR_KC LacZ D1_(HG-U133A_2).CEL


title: organotypic epidermis cdk4 Ras rep6

description: TR_KC Cdk4Ras C4_(HG-U133A_2).CEL


title: organotypic epidermis cdk4 Ras rep

description: TR_KC cdk4Ras A2_(HG-U133A_2).CEL


title: organotypic epidermis cdk4 Ras rep1

description: TR_KC cdk4Ras A1_(HG-U133A_2).CEL


title: organotypic epidermis LacZ rep8

description: TR_KC LacZ D2_(HG-U133A_2).CEL


title: organotypic epidermis LacZ rep4

description: TR_KC LacZ B2_(HG-U133A_2).CEL


title: organotypic epidermis LacZ rep1

description: TR_KC LacZ A1_(HG-U133A_2).CEL


title: organotypic epidermis LacZ rep2

description: TR_KC LacZ A2_(HG-U133A_2).CEL


title: organotypic epidermis LacZ rep3

description: TR_KC LacZ B1_(HG-U133A_2).CEL


title: 345643

status: Public on Oct 01 2010

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description:
A549_Neg2 vs A549 34a_2
Date:2008/04/11

hyb_protocol: Agilent : 1500.0 ng at 62 degree_C during 17 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Interslide norm. : quantile, Intraslide norm. : printtiploess, Background norm. : none, Software used : limmagui

label_protocol: Ambion

extract_protocol: Trizol

tag: label

tag: extract

tag: sample

tag: subject

value: Cells

tag: origin

value: lung adenocarcinoma


title: 345644

description:
A549 34a_2 vs A549_Neg2
Date:2008/04/11

tag: tissue


title: 345232

description:
A549_Neg1 vs A549 34a_1
Date:2008/04/17


title: Osteoblasts_Dlk1-pos_rep1

city: Odense C

first: Basem

last: Abdallah

address: J.B. Winslows Vej 25

department: Dept. of Endocrinology

country: Denmark

institute: Odense University Hospital

hyb_protocol: Hybridization was carried out according to the instructions of the manufacturer.

scan_protocol: The arrays were scanned using the GeneArray scanner (Affymetrix).

data_processing: Affymetrix Expression Console 1.1.1 was used according to default analysis parameters.

source_name: Murine calvarial osteoblasts, transgenically overexpressing Dlk1

label_protocol: cRNA was synthesized from cDNA and biotinylated using the BioArray High Yield RNA transcript labeling kit (Enzo® kit, Enzo Diagnostics, Farmingdale, NY), according to the protocol provided by the manufacturer

growth_protocol: Primary osteoprogenitors (OB) were isolated from the calvariae of neonatal (4-5 days old) mice. The calvarias were cleaned with PBS, digested in trypsin (0.5 mg/mL) (InVitrogen) and EDTA (1.5 mg/mL) (Sigma) for 15 minutes and then subjected to sequential digestion for 15 min. in DMEM containing 1 mg/mL collagenase II (Sigma). Cells obtained by fractions 2-3 were passed through a 75 µm filter, combined as a osteoprogenitor cell population and cultured in standard growth medium consisting of DMEM supplemented with 20% FBS (GIBCO), 2 mmol/L GlutaMax (GIBCO).

extract_protocol: Total RNA was isolated from cultured calvarias WT-OB and DLK1+OB cells using RNeasy Mini kit (Qiagen, Copenhagen, Denmark) according to the manufacturer's instructions.

treatment_protocol: Dlk1+OB were sorted by FACS Diva from freshly cultured calvarial-OB obtained from Col1-Dlk1 mice, to enrich for Dlk1-positive cells. Positive cells are gated by region P4 (purple color) while negative sorted cells are gated by region P5 (yellow color).

value: osteoblast


title: Null liver, tumor tissue, biological rep3

status: Public on Oct 10 2010

city: Nashville

first: srividya

last: bhaskara

state: TN

address: PRB room 512

department: Biochemistry

institute: Vanderbilt University

description: gene expression data from livers of Hdac3-null mice of about 10-mon old.

hyb_protocol: The targets in hybridization cocktail were heat denatured at 99C for 5 minutes, cooled to 45C for 5 minutes, centrifuged and then loaded on the Affymetrix cartridge arrays for a hybridization period of 16 hours at 45C, with rotation of 60RPM in Affymetrix Model 645 Hybridization Oven

scan_protocol: GeneChips were scanned using Affymetrix 7G plus scanner.

data_processing: The data were analyzed with GCOS software and by using Affymetrix default analysis settings and RMA as normalization method signal intensity values are calculated

source_name: tumor liver

label_protocol: Affymetrix  WT Sense reactions, using the Affymetrix WT Sense reaction kit (catalog#900652)

growth_protocol: Mice were aged to 10 months and fed with regular food.

extract_protocol: Total RNA was isolated form livers usinf Perfect Pure Tissue Kit ( 5 prime).

treatment_protocol: Livers were dissected according to the standard procedure for RNA isolation.

value: tumor liver


title: 345695

description:
A549 siE2F3_1 vs A549_Neg1
Date:2008/04/17

source_name: A549 siE2F3


title: Control liver, normal tissue, biological rep1

description: gene expression data from livers of control mice of about 10-mon old.

source_name: normal liver

value: normal liver


title: organotypic epidermis LacZ rep5

description: TR_KC LacZ C1_(HG-U133A_2).CEL


title: 345231

description:
A549_Neg1 vs A549 210_1
Date:2008/04/17


title: Null liver, tumor tissue, biological rep2


title: Osteoblasts_wildtype_rep1

source_name: Murine calvarial osteoblasts, wildtype control

value: wild type


title: 345234

description:
A549_Neg1 vs A549 siCT_1
Date:2008/04/17

source_name: A549 siCT

value: A549 siCT_1


title: 345244

description:
A549 siCT_1 vs A549_Neg1
Date:2008/04/17


title: 345240

description:
A549 210_1 vs A549_Neg1
Date:2008/04/17


title: 345236

description:
A549_Neg1 vs A549 siE2F3_1
Date:2008/04/17


title: 345241

description:
A549 34a_1 vs A549_Neg1
Date:2008/04/17


title: Control liver, normal tissue, biological rep2


title: Null liver, tumor tissue, biological rep1


title: 345229

description:
A549_Neg2 vs A549 siE2F3_2
Date:2008/04/11


title: 314256

description:
TL28 vs TS28
Date:2007/09/25

hyb_protocol: Agilent : 750.0 ng at 62 degree_C during 16 hours

source_name: tumor

value: tumor

value: lung

tag: disease

value: cancer

source_name: non tumoral adjacent tissue

value: non tumoral adjacent tissue


title: 345646

description:
A549_Neg2 vs A549 210_2
Date:2008/04/11


title: 350200

description:
TS584 vs TL584
Date:2008/07/25


title: 345230

description:
A549 siE2F3_2 vs A549_Neg2
Date:2008/04/11


title: 314257

description:
TL55 vs TS55
Date:2007/09/25


title: 345645

description:
A549 210_2 vs A549_Neg2
Date:2008/04/11


title: 350105

description:
TS194 vs TL194
Date:2008/07/23


title: 345647

description:
A549 siCT_2 vs A549_Neg2
Date:2008/04/11

value: A549 siCT_2


title: 345648

description:
A549_Neg2 vs A549 siCT_2
Date:2008/04/11


title: 350103

description:
TS105 vs TL105
Date:2008/07/23


title: 350104

description:
TS148 vs TL148
Date:2008/07/23


title: 350187

description:
TL105 vs TS105
Date:2008/07/23


title: 350190

description:
TS511 vs TL511
Date:2008/07/25


title: 314145

description:
TS25 vs TL25
Date:2007/09/25


title: organotypic epidermis cdk4 Ras rep8

description: TR_KC Cdk4Ras D4_(HG-U133A_2).CEL


title: 350197

description:
TS551 vs TL551
Date:2008/07/25


title: 314064

description:
TS404 vs TL404
Date:2007/09/27


title: 350332

description:
TL511 vs TS511
Date:2008/07/25


title: 314140

description:
TL404 vs TS404
Date:2007/09/27


title: 314258

description:
TL73 vs TS73
Date:2007/09/25


title: 350188

description:
TL148 vs TS148
Date:2008/07/23


title: 350333

description:
TL551 vs TS551
Date:2008/07/25


title: 314148

description:
TS55 vs TL55
Date:2007/09/25


title: 314143

description:
TL541 vs TS541
Date:2007/09/27


title: 350189

description:
TL194 vs TS194
Date:2008/07/23


title: 314147

description:
TS28 vs TL28
Date:2007/09/25


title: 350334

description:
TL584 vs TS584
Date:2008/07/25


title: 314138

description:
TS541 vs TL541
Date:2007/09/27


title: 314253

description:
TL20 vs TS20
Date:2007/09/25


title: 314254

description:
TL25 vs TS25
Date:2007/09/25


title: 314142

description:
TS20 vs TL20
Date:2007/09/25


title: 314252

description:
TS73 vs TL73
Date:2007/09/25


title: 030410

type: other

description:
TS 55 vs TL 55
Date:2007/01/25

hyb_protocol: Agilent : 700.0 ng at 48 degree_C during 16 hours

label_protocol: Ulysis

extract_protocol: MirVana

value: TS 55

value: TL 55


title: 031233

description:
TS 404 vs TL 404
Date:2007/01/19


title: 030407

description:
TS 28 vs TL 28
Date:2007/01/25

value: TS 28

value: TL 28


title: Exponential phase pH 10- 0 min rep 2

city: Omaha

first: Paul

middle: M

last: Dunman

state: NE

address: 986495 Nebraska Medical Center

department: Pathology and Microbiology

institute: University of Nebraska Medical Center

hyb_protocol: 1.5 micrograms (ug) of labeled total RNA was applied to an S. aureus Affymetrix GeneChip hybridized @ 45 degrees Celsius (C) for 16 hr in an Affymetrix hybridization oven.  The sample was then washed 60 times in non-stringent buffer (Wash A; 6X SSPE, 0.01% Tween-20) at 45C followed by 60 washes in stringent buffer (Wash B; 1X MES, 25 mM NaCl, 0.01% Tween-20) at 45 C in an Affymetrix Fluidics station (450).  The sample was then subjected to the following stains/wash steps: 1. 10 min of Stain 1 (1X MES, 1.2 mg BSA, 6 ug Streptavidin) at 25C, 2. 40 washes with Wash A, 3. 10 min of Stain 2 (1X MES, 1.2 mg BSA, 60 ug Goat-IgG, and 3 ug biotinylated antistreptavidin), 4. 10 min of Stain 3 (1X MES, 1.2 mg BSA, 6 ug Streptavidin-Phycoerythrin), 5. 60 washes with Wash A at 25C.

scan_protocol: The GeneChip was scanned in an Affymetrix 7G scanner.

data_processing: The raw signal intensity value and present/absent determinations were calculated based on Affymetrix algorithms (default settings) using GeneChip Operating Software version 1.3

organism: Staphylococcus aureus

source_name: S. aureus strain UAMS-1 exponential phase pH 10- 0 min post-transcriptional arrest

label_protocol: RNA was reverse transcribed, cDNA fragmented, 3’ biotinylated, mixed with exogenous labeled “spike-in” transcripts and hybridized to S. aureus GeneChips following the manufacturer’s recommendations for antisense prokaryotic arrays (Affymetrix, Santa Clara, CA).

growth_protocol: S. aureus colonies from brain heart infusion (BHI) agar plates were used to inoculate a 3-mL culture in BHI medium and were incubated overnight.  The next day, cultures were used to inoculate 200 ml fresh BHI (pH 7.4) to a starting OD600 of 0.05 and incubated with aeration (250 RPM) at 37C. After the bacteria reached an OD600 between 0.3 and 0.4, they were incubated for an additional 30 min (pH adjusted to 10).  At that point, rifampin (200 micrograms per ml) was added to the culture.  Twenty one ml aliquots of cells were removed at 0, 2.5, 5, 15 and 30 min post rifampin treatment.  One milliliters of cell suspension was serial diluted and plated on both BHI medium and BHI medium containing rifampin.  Plates were incubated for 16 hr at 37C and colony forming units per ml were enumerated to measure rifampin resistance.  If any rifampin resistant colonies were detected (10-2 dilution) the experiment was discarded and subsequently repeated.  Total bacterial RNA was extracted from the remaining 20 ml of each aliquot.

extract_protocol: Twenty ml of cells were added to 20 ml ice cold acetone:ethanol (1:1) and stored at -80oC overnight. For RNA isolation, -80oC suspensions were thawed on ice and centrifuged at 5,000 X g at 4oC for 10 min.  The supernatant was removed, the cell pellet was resuspended in 1 ml ice cold TE buffer (10 mM Tris, 1 mM EDTA, pH 8.0), and transferred to a pre-chilled lysing matrix B tube (Q-BIOgene, Irvine, CA).  Cells were lysed by shaking in an FP120 shaker (Q-BIOgene) two times at a setting of 4.5 for 20 s.  Suspensions were then centrifuged at 13,000 X g at 4oC for 10 min and the supernatant was used for RNA isolation with an RNeasy Mini column, following the manufacturer recommendations for on-the-column DNase treatment and RNA purification (Qiagen, Valencia, CA).

treatment_protocol: See Growth Protocol

tag: growth phase

value: exponential phase

tag: treatment group


title: Exponential phase pH 4- 5 min rep 1

source_name: S. aureus strain UAMS-1 exponential phase pH 4- 5 min post-transcriptional arrest

growth_protocol: S. aureus colonies from brain heart infusion (BHI) agar plates were used to inoculate a 3-mL culture in BHI medium and were incubated overnight.  The next day, cultures were used to inoculate 200 ml fresh BHI (pH 7.4) to a starting OD600 of 0.05 and incubated with aeration (250 RPM) at 37C. After the bacteria reached an OD600 between 0.3 and 0.4, they were incubated for an additional 30 min (pH adjusted to 4.0).  At that point, rifampin (200 micrograms per ml) was added to the culture.  Twenty one ml aliquots of cells were removed at 0, 2.5, 5, 15 and 30 min post rifampin treatment.  One milliliters of cell suspension was serial diluted and plated on both BHI medium and BHI medium containing rifampin.  Plates were incubated for 16 hr at 37C and colony forming units per ml were enumerated to measure rifampin resistance.  If any rifampin resistant colonies were detected (10-2 dilution) the experiment was discarded and subsequently repeated.  Total bacterial RNA was extracted from the remaining 20 ml of each aliquot.

tag: strain

value: pH 4- 5 min post-transcriptional arrest


title: Exponential phase pH 4- 30 min rep 2

source_name: S. aureus strain UAMS-1 exponential phase pH 4- 30 min post-transcriptional arrest


title: 030411

description:
TL 55 vs TS 55
Date:2007/01/25


title: Exponential phase pH 10- 15 min rep 1

source_name: S. aureus strain UAMS-1 exponential phase pH 10- 15 min post-transcriptional arrest


title: 030409

description:
TL 28 vs TS 28
Date:2007/01/25


title: Exponential phase pH 10- 30 min rep 2

source_name: S. aureus strain UAMS-1 exponential phase pH 10- 30 min post-transcriptional arrest


title: 030230

description:
TL 20 vs TS 20
Date:2007/01/25

value: TL 20

value: TS 20


title: 030229

description:
TS 20 vs TL 20
Date:2007/01/25


title: Exponential phase pH 10- 5 min rep 1

source_name: S. aureus strain UAMS-1 exponential phase pH 10- 5 min post-transcriptional arrest


title: Exponential phase pH 4- 15 min rep 2

source_name: S. aureus strain UAMS-1 exponential phase pH 4- 15 min post-transcriptional arrest


title: Exponential phase pH 4- 15 min rep 1

value: pH 4- 15 min post-transcriptional arrest


title: Exponential phase pH 10- 30 min rep 1

value: pH 10- 30 min post-transcriptional arrest


title: Exponential phase pH 10- 0 min rep 1

value: pH 10- 0 min post-transcriptional arrest


title: Exponential phase pH 4- 30 min rep 1

value: pH 4- 30 min post-transcriptional arrest


title: Exponential phase pH 10- 15 min rep 2

value: pH 10- 15 min post-transcriptional arrest


title: Exponential phase pH 4- 5 min rep 2


title: 031014

description:
TS 42 vs TL 42
Date:2007/01/29

value: TS 42

value: lung

label_protocol: Stratagene

value: TL 42

value: tumor


title: Exponential phase pH 10- 2.5 min rep 2

source_name: S. aureus strain UAMS-1 exponential phase pH 10- 2.5 min post-transcriptional arrest


title: Exponential phase pH 4- 2.5 min rep 1

source_name: S. aureus strain UAMS-1 exponential phase pH 4- 2.5 min post-transcriptional arrest


title: Exponential phase pH 4 2.5 min rep 2

value: pH 4- 2.5 min post-transcriptional arrest


title: 031235

description:
TL 404 vs TS 404
Date:2007/01/19

value: cancer

value: non tumoral adjacent tissue


title: 030228

description:
TS 450 vs TL 450
Date:2007/02/02


title: 030236

description:
TS 512 vs TL 512
Date:2007/01/30


title: Exponential phase pH 4- 0 min rep 2

source_name: S. aureus strain UAMS-1 exponential phase pH 4- 0 min post-transcriptional arrest

value: pH 4- 0 min post-transcriptional arrest


title: Exponential phase pH 10- 2.5 min rep 1

value: exponential phase

value: pH 10- 2.5 min post-transcriptional arrest


title: Exponential phase pH 4- 0 min rep 1


title: 031081

description:
TS 12 vs TL 12
Date:2007/01/11

value: TS 12

value: TL 12


title: 031083

description:
TL 12 vs TS 12
Date:2007/01/11


title: 031146

description:
TS 25 vs TL 25
Date:2007/01/11

value: TS 25

value: TL 25


title: 031209

description:
TL 25 vs TS 25
Date:2007/01/11


title: Exponential phase pH 7.4 30 min rep 2

source_name: S. aureus strain UAMS-1 exponential phase pH 7.4 30 min post-transcriptional arrest

growth_protocol: S. aureus colonies from brain heart infusion (BHI) agar plates were used to inoculate a 3-mL culture in BHI medium and were incubated overnight.  The next day, cultures were used to inoculate 200 ml fresh BHI (pH 7.4) to a starting OD600 of 0.05 and incubated with aeration (250 RPM) at 37C. After the bacteria reached an OD600 between 0.3 and 0.4, they were incubated for an additional 30 min (pH maintained at 7.4).  At that point, rifampin (200 micrograms per ml) was added to the culture.  Twenty one ml aliquots of cells were removed at 0, 2.5, 5, 15 and 30 min post rifampin treatment.  One milliliters of cell suspension was serial diluted and plated on both BHI medium and BHI medium containing rifampin.  Plates were incubated for 16 hr at 37C and colony forming units per ml were enumerated to measure rifampin resistance.  If any rifampin resistant colonies were detected (10-2 dilution) the experiment was discarded and subsequently repeated.  Total bacterial RNA was extracted from the remaining 20 ml of each aliquot.


title: 031013

description:
TL 36 vs TS 36
Date:2007/01/29

value: TL 36

value: TS 36


title: Exponential phase pH 7.4 15 min rep 1

source_name: S. aureus strain UAMS-1 exponential phase pH 7.4 15 min post-transcriptional arrest


title: 342497

description:
TS194 vs TL194
Date:2008/01/10


title: Exponential phase pH 7.4 5 min rep2

source_name: S. aureus strain UAMS-1 exponential phase pH 7.4 5 min post-transcriptional arrest


title: 031012

description:
TS 36 vs TL 36
Date:2007/02/02


title: Exponential phase pH 7.4 15 min rep 2

value: pH 7.4 15 min post-transcriptional arrest


title: 031079

description:
TL 73 vs TS 73
Date:2007/01/29

value: TL 73

value: TS 73


title: 030235

description:
TL 450 vs TS 450
Date:2007/02/02

value: lung


title: Exponential phase pH 7.4 0 min rep 2

source_name: S. aureus strain UAMS-1 exponential phase pH 7.4 0 min post-transcriptional arrest


title: Exponential phase pH 7.4 2.5 min rep 1

source_name: S. aureus strain UAMS-1 exponential phase pH 7.4 2.5 min post-transcriptional arrest


title: 030477

description:
TS 604 vs TL 604
Date:2007/01/31

source_name: tumor

value: tumor


title: 031077

description:
TS 73 vs TL 73
Date:2007/01/29

source_name: non tumoral adjacent tissue


title: 030392

description:
TS 541 vs TL 541
Date:2007/01/30


title: Exponential phase pH 7.4 30 min rep 1

value: pH 7.4 30 min post-transcriptional arrest


title: Exponential phase pH 7.4 5 min rep 1

value: pH 7.4 5 min post-transcriptional arrest


title: Exponential phase pH 7.4 2.5 min rep 2

value: pH 7.4 2.5 min post-transcriptional arrest


title: 030476

description:
TL 541 vs TS 541
Date:2007/01/30

value: cancer

value: non tumoral adjacent tissue


title: 342364

description:
TS584 vs TL584
Date:2008/01/07


title: 030391

description:
TL 512 vs TS 512
Date:2007/01/30


title: 342729

description:
TS208 vs TL208
Date:2008/01/10


title: 342361

description:
TL105 vs TS105
Date:2008/01/07


title: 342368

description:
TL194 vs TS194
Date:2008/01/07


title: 342496

description:
TL584 vs TS584
Date:2008/01/10


title: 030478

description:
TL 604 vs TS 604
Date:2007/01/31


title: Exponential phase pH 7.4 0 min rep 1

value: exponential phase

value: pH 7.4 0 min post-transcriptional arrest


title: 342482

description:
TS551 vs TL551
Date:2008/01/07


title: 342481

description:
TL208 vs TS208
Date:2008/01/07


title: 342728

description:
TL148 vs TS148
Date:2008/01/10


title: 342367

description:
TS105 vs TL105
Date:2008/01/07


title: 031071

description:
TL 42 vs TS 42
Date:2007/01/29

value: TL 42

value: TS 42


title: 342484

description:
TS148 vs TL148
Date:2008/01/07


title: 342734

description:
TS511 vs TL511
Date:2008/01/10


title: 342730

description:
TL551 vs TS551
Date:2008/01/10


title: 342485

description:
TL511 vs TS511
Date:2008/01/10


title: BART-complemented cells, replicate 1

city: Madison

first: Bill

last: Sugden

state: WI

address: 1400 University Avenue

department: Oncology

institute: University of Wisconsin-Madison

description: BART miRNA complemented loss of EBV, replicate 1 of 3

hyb_protocol: Scanned on an Agilent G2565BA scanner.

scan_protocol: Images were recorded and quantified using Agilent’s Scan Control software, version A. 7.0.1 (includes XDR functionality) and Agilent Feature Extraction software (v. 9.5.3).

data_processing: Agilent Feature Extraction software (v. 9.5.3) was used with the manufacturer's default settings.

source_name: S1-1 cells

label_protocol: Labelled cRNA was generated using Agilent's Quick Amp Labeling Kit following the manufacturer's instructions. This procedure uses T7 RNA polymerase, which both amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP.

growth_protocol: Cells were diluted to 3-5x104 cells/mL in culture medium and treated with either 10 ng/mL doxycycline or the vehicle, ethanol. Live cell concentrations were measured every two or four days with a hemocytometer. Cells stained with trypan blue (with a 1:10 dilution of 0.3% trypan blue dissolved in 1x PBS) or exhibiting an aberrant morphology were considered non-viable. After counting, in necessary cells were diluted in fresh medium back to approximately the starting concentration (3-5x104 cells/mL) and doxycycline or ethanol was added.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen), following the manufacturer’s protocols, except RNA precipitation was conducted in the presence of approximately 5 µg/mL linear acrylamide (Ambion) to enhance efficiency of precipitation as previously described (Gaillard and Strauss, 1990). The isolated RNA was then treated with Turbo DNAse (Ambion) following the manufacturer’s instructions and re-purified with TRIzol.

tag: sample type

value: Experimental cells. They were transduced with retrovectors encoding the BART miRNAs, induced for dnEBNA1 expression with doxycycline, and cultured 20 days to evict the virus.

tag: condition

value: EBV evicted with dnEBNA1, BART miRNAs expressed ectopically

value: Control cells. They were transduced with empty retrovectors, mock induced (dnEBNA1 kept off), and cultured 20 days.


title: BART-complemented cells, replicate 2


title: Uncomplemented cells, replicate 1

description: Uncomplemented loss of EBV, replicate 1 of 3

value: Experimental cells. They were transduced with empty retrovectors, induced for dnEBNA1 expression with doxycycline, and cultured 20 days to evict the virus.

value: EBV evicted with dnEBNA1


title: SLE patient 16 peripheral blood cells

city: Ibaraki

first: Norihiro

last: Nishimoto

state: Osaka

address: 7-7-20, Saito-Asagi

institute: Wakayama Medical University

hyb_protocol: The labeled aRNAs (mixture of Cy3 and Cy5) was hybridized onto microarray slide for 16 hours at 42ﾟC. Slides were washed in 2xSSC+0.1% SDS, 2xSSC, 1xSSC, and 0.1xSSC before air pressure drying and scanning.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray Lite (PerkinElmer, Boston, MA) and signal values were calculated using DNASIS Array (Hitachi Software Engineering, Tokyo, Japan).

data_processing: Log2 ratios of Cy3 to Cy5 were calculated and normalized by the method of global ratio median normalization.

source_name: peripheral blood cells from SLE patient 16

label_protocol: Total RNA was amplified. 5-(3-amino allyl)-UTP was incorporated to it using Amino Allyl MessageAmp aRNA Kit (Ambion, Austin, Texas). The amino allyl aRNA was further labeled by coupling reaction with NHS ester fluorescent dye, Cy3/Cy5.

extract_protocol: Peripheral blood was collected directly into PAXGene tubes (Qiagen, Valencia, CA). Total RNA was extracted using PAXGene Blood RNA Kit with the optimal on-column DNase digestion according to the manufacturer`s instructions.

tag: gender

value: female

tag: age

value: systemic lupus erythematosus

source_name: Total RNA from pooled whole blood of 45 healthy individuals

value: peripheral blood


title: SLE patient 22 peripheral blood cells

source_name: peripheral blood cells from SLE patient 22


title: Uncomplemented cells, replicate 2

description: Uncomplemented loss of EBV, replicate 2 of 3


title: SLE patient 20 peripheral blood cells

source_name: peripheral blood cells from SLE patient 20


title: Exponential phase pH 10- 5 min rep 2

source_name: S. aureus strain UAMS-1 exponential phase pH 10- 5 min post-transcriptional arrest


title: BART-complemented cells, replicate 3


title: SLE patient 15 peripheral blood cells

source_name: peripheral blood cells from SLE patient 15


title: SLE patient 21 peripheral blood cells

source_name: peripheral blood cells from SLE patient 21


title: Uncomplemented cells, replicate 3

description: Uncomplemented loss of EBV, replicate 3 of 3


title: SLE patient 17 peripheral blood cells

source_name: peripheral blood cells from SLE patient 17


title: SLE patient 18 peripheral blood cells

source_name: peripheral blood cells from SLE patient 18


title: SLE patient 19 peripheral blood cells

source_name: peripheral blood cells from SLE patient 19


title: SLE patient 13 peripheral blood cells

source_name: peripheral blood cells from SLE patient 13


title: SLE patient 14 peripheral blood cells

source_name: peripheral blood cells from SLE patient 14


title: Kidney Mouse09_Sample02

city: Bar Harbor

first: Peter

middle: Thomas

last: Vedell

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description: We analyzed intensities of 45,905 probes with unique sequences and annotated by Illumina as probes for genomic regions corresponding to protein-coding genes.

hyb_protocol: 1.5µg biotin-labeled cRNA was then hybridized onto Mouse-6 Expression BeadChips (Illumina, San Diego CA) for 16 hours at 55°C.  Post-hybridization staining and washing were performed according to manufacturer’s protocols (Illumina).

scan_protocol: Illumina Sentrix ® Mouse-6 v1.1 BeadChips were scanned using Illumina’s BeadStation 500 scanner.

data_processing:
Images were checked for grid alignment and then quantified using the BeadStudio software.  Control summary graphs generated by BeadStudio were used as quality assurance tools for hybridization, washing stringency, and background.  Integrity of the arrays was investigated using the BeadStudio array images and also using bead level image plots generated using the R/beadarray package.  Mean pixel intensities by bead type, were created using BeadStudio v3.1 and processed within the R/beadarray package (Dunning et al. 2006).
The raw data conains the log base 2 transformed intensities.  A two-step procedure was used for normalization.  Quantile normalization (Bolstad et al. 2003) was applied within each tissue type.  Then, a correction for batch effects was applied separately for each gene performed using an MM-regression estimator described in Yohai (1987) and computed using the R/robustbase software package (Rousseeuw et al. 2009).  The normalized data is also on a log base 2 scale.

source_name: Kidney Mouse09_Sample02

label_protocol: Illumina Sentrix ® Mouse-6 v1.1 BeadChip processing.  For each sample, an in-vitro transcription (IVT) reaction was carried out incorporating biotinylated nucleotides according to the manufacturer’s protocol for Illumina® Totalprep RNA amplification kit (Ambion).

growth_protocol: We obtained twelve C57BL/6J male mice from The Jackson Laboratory. Six pairs of littermates were pair-housed from weaning and put on a 5k52 diet (standard chow containing 6% fat).

extract_protocol: Inguinal fat pad, heart, liver, and both kidneys were extracted, perfused with RNase-free DEPC-treated PBS, cut into pieces not exceeding 0.5 cm in any dimension, and placed in 15 ml conical tubes.  The pieces were divided into 2 aliquots and stored in RNAlater (Ambion, Austin TX).  Each kidney aliquot consisted of one complete kidney.  Tissues were homogenized in TRIzolTM (Invitrogen, Carlsbad, CA).  Total RNA was isolated by standard TRIzolTM  methods according to the manufacturer’s protocols, and quality was assessed using an Agilent 2100 Bioanalyzer instrument and RNA 6000 Nano LabChip assay (Agilent Technologies, Santa Clara, CA).  The RNA was then treated with DNase1 (Qiagen, Valencia, Ca.) according to the manufacturer’s methods.    Total RNA was then reverse transcribed followed by second strand cDNA synthesis.

treatment_protocol: At 10 weeks, body weight was recorded and the mice were euthanized by cervical dislocation. Dissection procedures were started  at 11:00 a.m. after a 4-hour fasting period and were completed within a one-hour time window.

tag: tissue type

value: right kidney

value: male

tag: body weight (g)

tag: age (days)


title: Kidney Mouse12_Sample02

source_name: Kidney Mouse12_Sample02


title: Kidney Mouse11_Sample02

source_name: Kidney Mouse11_Sample02


title: Kidney Mouse10_Sample02

source_name: Kidney Mouse10_Sample02


title: Kidney Mouse12_Sample01

source_name: Kidney Mouse12_Sample01

value: left kidney


title: Kidney Mouse07_Sample02

source_name: Kidney Mouse07_Sample02


title: Kidney Mouse10_Sample01

source_name: Kidney Mouse10_Sample01


title: Kidney Mouse07_Sample01

source_name: Kidney Mouse07_Sample01


title: Kidney Mouse09_Sample01

source_name: Kidney Mouse09_Sample01


title: Kidney Mouse08_Sample02

source_name: Kidney Mouse08_Sample02


title: Kidney Mouse06_Sample02

source_name: Kidney Mouse06_Sample02


title: Kidney Mouse05_Sample02

source_name: Kidney Mouse05_Sample02


title: Kidney Mouse11_Sample01

source_name: Kidney Mouse11_Sample01


title: Kidney Mouse08_Sample01

source_name: Kidney Mouse08_Sample01


title: Kidney Mouse05_Sample01

source_name: Kidney Mouse05_Sample01


title: Kidney Mouse04_Sample01

source_name: Kidney Mouse04_Sample01


title: Kidney Mouse02_Sample02

source_name: Kidney Mouse02_Sample02


title: Kidney Mouse04_Sample02

source_name: Kidney Mouse04_Sample02


title: Heart Mouse12_Sample02

source_name: Heart Mouse12_Sample02

value: Heart


title: Kidney Mouse01_Sample01

source_name: Kidney Mouse01_Sample01


title: Kidney Mouse06_Sample01

source_name: Kidney Mouse06_Sample01


title: Heart Mouse10_Sample02

source_name: Heart Mouse10_Sample02


title: Kidney Mouse02_Sample01

source_name: Kidney Mouse02_Sample01


title: Kidney Mouse01_Sample02

source_name: Kidney Mouse01_Sample02


title: Kidney Mouse03_Sample01

source_name: Kidney Mouse03_Sample01


title: Heart Mouse05_Sample02

source_name: Heart Mouse05_Sample02


title: Kidney Mouse03_Sample02

source_name: Kidney Mouse03_Sample02


title: Heart Mouse11_Sample01

source_name: Heart Mouse11_Sample01


title: Heart Mouse08_Sample01

source_name: Heart Mouse08_Sample01


title: Heart Mouse02_Sample02

source_name: Heart Mouse02_Sample02


title: Heart Mouse11_Sample02

source_name: Heart Mouse11_Sample02


title: Heart Mouse12_Sample01

source_name: Heart Mouse12_Sample01


title: Heart Mouse09_Sample01

source_name: Heart Mouse09_Sample01


title: Heart Mouse06_Sample02

source_name: Heart Mouse06_Sample02


title: Heart Mouse07_Sample01

source_name: Heart Mouse07_Sample01


title: Heart Mouse09_Sample02

source_name: Heart Mouse09_Sample02


title: Heart Mouse08_Sample02

source_name: Heart Mouse08_Sample02


title: Heart Mouse07_Sample02

source_name: Heart Mouse07_Sample02


title: Heart Mouse03_Sample02

source_name: Heart Mouse03_Sample02


title: Heart Mouse02_Sample01

source_name: Heart Mouse02_Sample01


title: Heart Mouse04_Sample02

source_name: Heart Mouse04_Sample02


title: Heart Mouse10_Sample01

source_name: Heart Mouse10_Sample01


title: Heart Mouse06_Sample01

source_name: Heart Mouse06_Sample01


title: Heart Mouse05_Sample01

source_name: Heart Mouse05_Sample01


title: Heart Mouse01_Sample01

source_name: Heart Mouse01_Sample01


title: Heart Mouse01_Sample02

source_name: Heart Mouse01_Sample02


title: Heart Mouse04_Sample01

source_name: Heart Mouse04_Sample01


title: Heart Mouse03_Sample01

source_name: Heart Mouse03_Sample01


title: Adipose Mouse09_Sample02

source_name: Adipose Mouse09_Sample02

value: Adipose


title: Adipose Mouse11_Sample02

source_name: Adipose Mouse11_Sample02


title: Adipose Mouse07_Sample02

source_name: Adipose Mouse07_Sample02


title: Adipose Mouse10_Sample01

source_name: Adipose Mouse10_Sample01


title: Adipose Mouse12_Sample02

source_name: Adipose Mouse12_Sample02


title: Adipose Mouse12_Sample01

source_name: Adipose Mouse12_Sample01


title: Adipose Mouse04_Sample02

source_name: Adipose Mouse04_Sample02


title: Adipose Mouse10_Sample02

source_name: Adipose Mouse10_Sample02


title: Adipose Mouse07_Sample01

source_name: Adipose Mouse07_Sample01


title: Adipose Mouse11_Sample01

source_name: Adipose Mouse11_Sample01


title: Adipose Mouse08_Sample02

source_name: Adipose Mouse08_Sample02


title: Adipose Mouse09_Sample01

source_name: Adipose Mouse09_Sample01


title: Adipose Mouse03_Sample02

source_name: Adipose Mouse03_Sample02


title: Adipose Mouse06_Sample02

source_name: Adipose Mouse06_Sample02


title: Adipose Mouse05_Sample02

source_name: Adipose Mouse05_Sample02


title: Adipose Mouse02_Sample02

source_name: Adipose Mouse02_Sample02


title: Adipose Mouse08_Sample01

source_name: Adipose Mouse08_Sample01


title: Adipose Mouse05_Sample01

source_name: Adipose Mouse05_Sample01


title: Adipose Mouse02_Sample01

source_name: Adipose Mouse02_Sample01


title: Adipose Mouse06_Sample01

source_name: Adipose Mouse06_Sample01


title: Adipose Mouse01_Sample02

source_name: Adipose Mouse01_Sample02


title: RDM4_shaking_culture_30_degrees

city: Beppu

first: Takeshi

last: Hayashi

address: Kitaishigaki 82

department: Faculty of Food and Nutrition

institute: Beppu university

description:
This sample is of the RDM-4 strain of Zymomonas mobilis ZM6. Several RDM strains were isolated from the antibiotics-resistant mutants. The RDM-4 strain showed the most deficient respiration ability, grew well at 39ºC and produced ethanol well both in non-aerobic and aerobic conditions even at 39ºC. The gene expressions under a shaking culture at 30ºC were analyzed.

RDM4_shak
37471502
SOM047NV

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

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

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

organism: Zymomonas mobilis subsp. mobilis ATCC 29191

source_name: Zymomonas mobilis ZM6 RDM-4 strain cultivated under aerobic conditions

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

growth_protocol: Non-aerobic cultivations were performed without shaking with 3 ml working volume in test tube (16.5 φ mm × 165 mm) at 30ºC and 39ºC (high temperature). Aerobic cultivations were carried out in the same manner, but these were shaken at 220 rpm.

extract_protocol: Cells grown until the late logarithmic phase were immediately treated with the RNAprotect bacterial reagent (QIAGEN, CA, USA) for the stabilization of RNA. Total RNAs were extracted with an RNeasy midi kit (QIAGEN), and then concentrated with an RNeasy mini kit (QIAGEN) according to the manufacturer’s instructions.

tag: genotype

value: RDM-4 mutant

tag: respiration phenotype

value: respiration-deficient mutant

tag: culture condition

value: aerobic

tag: temperature


title: RDM4_static_culture_38_degrees

description:
This sample is of the RDM-4 strain of Zymomonas mobilis ZM6. Several RDM strains were isolated from the antibiotics-resistant mutants. The RDM-4 strain showed the most deficient respiration ability, grew well at 39ºC and produced ethanol well both in non-aerobic and aerobic conditions even at 39ºC. Because of the low yield of total RNA extracted at 39ºC, the condition of high-temperature was adopted at 38ºC. The gene expressions under a static culture at 38ºC were analyzed.

RDM4_therm
38353502
SOM047NT

source_name: Zymomonas mobilis ZM6 RDM-4 strain cultivated under non-aerobic conditions at 38 degrees

value: non-aerobic


title: wt_static_culture_30_degrees

description:
This sample is of the wild-type strain of Zymomonas mobilis ZM6. The gene expressions under a static culture at 30ºC were analyzed.

wt-stat
37471202
SOM047NR

source_name: Zymomonas mobilis ZM6 wild-type cultivated under non-aerobic conditions

value: wild-type

value: normal


title: wt_shaking_culture_30_degrees

description:
This sample is of the wild-type strain of Zymomonas mobilis ZM6. The gene expressions under a shaking culture at 30ºC were analyzed.

wt-shak
37471402
SOM047NS

source_name: Zymomonas mobilis ZM6 wild-type cultivated under aerobic conditions


title: Adipose Mouse01_Sample01

source_name: Adipose Mouse01_Sample01


title: Adipose Mouse04_Sample01

source_name: Adipose Mouse04_Sample01


title: Adipose Mouse03_Sample01

source_name: Adipose Mouse03_Sample01


title: 5393 JamA+

city: Milano

first: gabriele

last: bucci

state: MI

address: via olgettina 58

department: CTGB

country: Italy

institute: IRCCS Ospedale San Raffaele

description: Mammary tumor  at early stages of tumor development

hyb_protocol: affymetrix

scan_protocol: gene chip scanner 3000 7G

data_processing: The data were analyzed with Expression Console 1.1 using RMA processing

source_name: mammary tumor

label_protocol: WT terminal labelling kit (www.affymetrix.com)

growth_protocol: MMTV-PyMT mice and MMTV-PyMT JAM-A KO mice

extract_protocol: Trizol (Invitrogen, Carlsbad, CA, USA) solution was used to according to the manufacturer's protocol followed by an additional purification step using the RNA easy kit (Qiagen, Germantown, MD, USA).

treatment_protocol: Mammary tumor were resected at early stages of tumor development

value: MMTV-PyMT

value: mammary tumor


title: 5370 JamA+


title: CMM_1S

status: Public on Sep 30 2010

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

description: Human osteoblast cells treated with melphalen-treated bone marrow stromal cell conditioned media versus human osteoblast cells treated with diluent control treated bone marrow stromal cell conditioned media, biological replicate 1, standard labeling

hyb_protocol: 825ng of Cy3- and Cy5-labeled cRNA are combined and hybridized onto Agilent human whole genome 4x44 microarrys at 65C for 17 hours, then washed according to manufacturers instructions

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: Agilent Feature Extraction Software (v 9.5) was used for background subtraction and LOWESS normalization. Log2 ratios of melphalen-treated samples to controls were computed. Spots for which both channels were not well above background, or for which either channel was a non-uniform outlier according to Feature Extraction had log values replaced by "NA". Spots for which more than 50% of replicates were NA were removed from further analysis. Resulting data is available on Series record (GSE17842_filtered_LogRatio.txt).

source_name: Human Osteoblast Cell Line

label_protocol: Agilent QuckAmp labeling kit using 250 ng of total RNA and Cy3-CTP and Cy5-CTP from Perkin Elmer according to modifed protocol by Syed et al. (2006)

growth_protocol: Grown in complete HOB media without serum

extract_protocol: Qiagen RNAEasy kit, according to manufacturers instructions

treatment_protocol: Bone-marrow stromal cells were treated with 50 ug/ml melphalen, rinsed, fresh serum-free media was added, allowed to condition for 24 hours. This media was collected and used to treat human osteoblast cells for 6 hours

tag: agent

treatment_protocol: Bone-marrow stromal cells were treated with diluent control, rinsed, fresh serum-free media was added, allowed to condition for 24 hours. This media was collected and used to treat human osteoblast cells for 6 hours

value: diluent control


title: 5347 JamA-

value: MMTV-PyMT JAM-A KO

tag: tissue


title: TGF_2F

description: TGF-beta treated human osteoblast vs control human osteoblast, biological replicate 2, flip labeling

data_processing: Agilent Feature Extraction Software (v 9.5) was used for background subtraction and LOWESS normalization. Log2 ratios of TGF-beta samples to controls were computed. Spots for which both channels were not well above background, or for which either channel was a non-uniform outlier according to Feature Extraction had log values replaced by "NA". Spots for which more than 50% of replicates were NA were removed from further analysis. Resulting data is available on Series record (GSE17843_filtered_LogRatio.txt).

treatment_protocol: Media alone

value: media alone

treatment_protocol: 10 ng/ml treatment with TGF-beta, treated and collected after 6 hours

value: 10 ng/ml TGF-beta


title: 5333 JamA-

value: mammary tumor without JAM-A


title: TGF_4F

description: TGF-beta treated human osteoblast vs control human osteoblast, biological replicate 4, flip labeling


title: 5369 JamA+


title: TGF_6F

description: TGF-beta treated human osteoblast vs control human osteoblast, biological replicate 6, flip labeling


title: CMM_5S

description: Human osteoblast cells treated with melphalen-treated bone marrow stromal cell conditioned media versus human osteoblast cells treated with diluent control treated bone marrow stromal cell conditioned media, biological replicate 5, standard labeling


title: TGF_1S

description: TGF-beta treated human osteoblast vs control human osteoblast, biological replicate 1, standard labeling


title: CMM_3S

description: Human osteoblast cells treated with melphalen-treated bone marrow stromal cell conditioned media versus human osteoblast cells treated with diluent control treated bone marrow stromal cell conditioned media, biological replicate 3, standard labeling


title: TGF_3S

description: TGF-beta treated human osteoblast vs control human osteoblast, biological replicate 3, standard labeling


title: 5346 JamA-


title: CMM_4F

description: Human osteoblast cells treated with melphalen-treated bone marrow stromal cell conditioned media versus human osteoblast cells treated with diluent control treated bone marrow stromal cell conditioned media, biological replicate 4, flip labeling


title: CMM_2F

description: Human osteoblast cells treated with melphalen-treated bone marrow stromal cell conditioned media versus human osteoblast cells treated with diluent control treated bone marrow stromal cell conditioned media, biological replicate 2, flip labeling


title: CMM_6F

description: Human osteoblast cells treated with melphalen-treated bone marrow stromal cell conditioned media versus human osteoblast cells treated with diluent control treated bone marrow stromal cell conditioned media, biological replicate 6, flip labeling


title: melph2

description: Human osteoblast cells treated with melphalen at 50ug/ml hybridized against universal reference RNA (Stratagene), biological replicate 2

data_processing: Agilent Feature Extraction Software (v 9.5) was used for background subtraction and LOWESS normalization. Log2 ratios of melphalen-treated samples to controls were computed. Spots for which both channels were not well above background, or for which either channel was a non-uniform outlier according to Feature Extraction had log values replaced by "NA". Spots for which more than 50% of replicates were NA were removed from further analysis. Resulting data is available on Series record (GSE17839_filtered_LogRatio.txt).

treatment_protocol: 50ug/ml Melphalen treatment for 6 hours

value: 50ug/ml Melphalen

source_name: Stratagene Universal Reference Human RNA

tag: reference


title: melph3

description: Human osteoblast cells treated with melphalen at 50ug/ml hybridized against universal reference RNA (Stratagene), biological replicate 3

value: Stratagene Universal Reference Human RNA


title: melph4

description: Human osteoblast cells treated with melphalen at 50ug/ml hybridized against universal reference RNA (Stratagene), biological replicate 4


title: melph1

description: Human osteoblast cells treated with melphalen at 50ug/ml hybridized against universal reference RNA (Stratagene), biological replicate 1


title: ctrl3

description: Human osteoblast cells treated with dilulant hybridized against universal reference RNA (Stratagene), used as control, biological replicate 3

treatment_protocol: Treatment for 6hr with dilulant (matched to Melphalan) as control


title: ctrl4

description: Human osteoblast cells treated with dilulant hybridized against universal reference RNA (Stratagene), used as control, biological replicate 4

value: dilulant (matched to Melphalan) as control


title: CD34+HPIP-YFP

city: Muenchen

first: Pawandeep

last: Kaur

state: Bavaria

address: Marchioninstrasse 25

department: Hematology

country: Germany

institute: Helmholtz-Muenchen

hyb_protocol: Following fragmentation, 2 ug of cRNA were hybridized for 16 hr at 45C on HG-U133 Plus 2.0 arrays (Affymetrix). GeneChips were washed and stained with standard protocols in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scanner G3000

data_processing: Data were preprocessed using the robust multi-array average (RMA) expression measure (Bioconductor package affy 1.18.1 ). Data analysis and statistical computing were performed with R (2.7.0).

source_name: Cord Blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3ug total RNA

growth_protocol: Cells at 2x10e5/mL were prestimulated for 48 hours in Iscove´s IMDM( GIBCO-Invitrogen, Karlsruhe, Germany) containing a serum substitute (BITTM, Stem Cell Technologies), 10-4M β mercaptoethanol (Sigma-Aldrich, Taufkirchen, Germany), supplemented with the following recombinant human cytokines: 100 ng/mL Flt-3 Ligand, 100 ng/mL SF, 20 ng/mL IL-3, 20 ng/mL G-CSF, and 20 ng/mL IL-6 (Immunotools, Friesoythe, Germany).

extract_protocol: Total RNA was isolated using the RNeasy Micro Kit (Sigma) according to the manufacturer’s instructions and quantified using the Nanodrop ND-1000 UV-vis spectrophotometer (Nanodrop Technologies, USA). The quality of the RNA was controlled using the BioAnalyzer (Agilent Technologies, USA) and exclusively high quality RNA was used for further analysis.

tag: transduction

value: HPIP-wt

tag: cell type


title: CD34+NRPID-YFP

value: mutant NRPID


title: CD34+YFP

value: control


title: ctrl2

description: Human osteoblast cells treated with dilulant hybridized against universal reference RNA (Stratagene), used as control, biological replicate 2


title: ctrl1

description: Human osteoblast cells treated with dilulant hybridized against universal reference RNA (Stratagene), used as control, biological replicate 1


title: SKI-606 treated 4

status: Public on Sep 15 2010

city: La Jolla

first: Roy

last: Williams

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

hyb_protocol: As recommended by illumina

scan_protocol: As suggested by illumina using the illumina scanner

data_processing: Raw data filtered on P value for <0.05 with the remaining data normalised using the affy tools R bioconductor normalize.quantiles routine

label: streptavidin Cy3

source_name: mammary tissue from transgenic mouse line

label_protocol: As suggested by illumina

growth_protocol: Tumors were detected in female mice by manual palpation and measured with the use of calipers.

extract_protocol: Total RNA was isolated by using the mirVana miRNA Isolation Kit (Ambion/Invitrogen) according to the manufacturer’s instructions.  8 ng of total RNA from each mouse was reverse transcribed into cDNA by using iSCRIPT cDNA Synthesis kit (Bio-Rad Laboratories) on a Peltier Thermal Cycler (MJ Research).

treatment_protocol: SKI-606 was formulated in 0.5% methocellulose and 0.4% Tween 80 and administered by oral gavage at 100 mg/kg.

value: mammary

tag: transgenic mouse model

value: MMTV-PyVmT

tag: strain


title: Vehicle-treated


title: SKI-606 treated 2

source_name: T6PNE cells were isolated from human fetal islets; E47 was induced by tamoxifen treatment


title: SKI-606 treated 1


title: Vehicle-treated 2


title: SKI-606 treated 3


title: Vehicle-treated 1


title: organotypic CVX rep2

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

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

source_name: organotypic cervical tissue lac Z control

value: organotypic cervical


title: Vehicle-treated 4


title: organotypic CVX expresing cdk4 and Ras treated with U0126 rep2

source_name: organotypic cervical tissue cdk4 Ras treated with U0126


title: organotypic CVX expresing cdk4 and Ras treated with U0126 rep1


title: organotypic CVX rep1


title: Gm_16_28C_40C4

city: Pacific Grove

first: Cheryl

middle: A

last: Logan

address: 120 Ocean View Blvd

hyb_protocol: Hybridizations were conducted overnight at 65°C in Genetix (Boston, MA, USA) humid hybridization chambers. After hybridization, slides were washed by repeated vigorous immersion in 0.5x SSC and 0.01% SDS for 2 min to remove unbound dye. Slides were then washed in 0.6x SSC on a shaker for 15 min and dried by centrifugation.

scan_protocol: The slides were scanned on an AXON GenePix 4000B microarray scanner in GenePix 4.0 (Axon Instruments, Molecular Devices, Sunnyvale, CA, USA).

data_processing: Raw data for each gene (median pixel intensity of each spot with background correction) were imported from GenePix 4.0 into GeneSpring version 7.3 (Silicon Genetics, Redwood, CA, USA) for subsequent analysis. We normalized the data using intensity-dependent locally weighted linear regression (lowess) transformation to correct for spatial variation in the array due to inconsistencies in printing pins, slide surface variability, and differences in local hybridization conditions across a slide. We normalized and filtered our data in Genespring 7.3. To obtain a set of reliable genes from the normalized data, we discarded all probes that were flagged as irregular by Genepix 4.0 software or by hand (irregularities are generally due to specks of dust or scratches on slides) and genes that showed standard deviations of >1.4. All subsequent analyses were performed on this filtered list comprising 7,488 probes.

organism: Gillichthys mirabilis

source_name: Gillichthys mirabilis, gill tissues, 28C acclim, sampled at 40C

label_protocol: Single stranded cDNA was labeled with either Cy3 (reference samples) or Cy5 (heat shock samples) cyanine monoreactive dye (Amersham, Piscataway, NJ, USA), prepared in 80 µl of dimethylsulfoxide.

growth_protocol: Fish were acclimated to 9C, 19C or 28C for one month

extract_protocol: Total RNA was extracted from gill tissue using the Qiagen Tissuelyser for homogenization and the RNeasy Mini Kit (Qiagen, Valencia, CA, USA).  Total RNA was determined by A260 absorbance using a Nanodrop ND-1000 spectrophotometer (Nanodrop, Wilmington, DE, USA).  Samples were run on 1% agarose gels to confirm RNA integrity. 15 µg of total RNA from each sample were reverse transcribed with 3 µl of AffinityScript enzyme (Agilent Technologies, Santa Clara, CA, USA), 0.75 µl oligo(dT15) and 0.75 µl pdN9 random hexamer primers, and amino-allyl modified dNTPs. RNA templates were removed from the RT reactions by incubation at 65°C for 30 min in 0.2 mol l-1 NaOH and 0.1 mol l-1 EDTA. cDNA was precipitated at -80°C for 20 min in 4.5 µl 3M sodium acetate and 2.5 volumes on 100% ethanol. Samples were centrifuged at 10,000 rpm for 20 min at 4°C and resuspended in 8 µl of nuclease free water and 2 µl of fresh 0.5 M sodium bicarbonate.

treatment_protocol: Fish underwent an acute heat stress ramp (4C/hr) starting at their acclimation temperature. 2-3 fish were sampled at every hour during the heat ramp (or every 4C) until they reach their critical thermal maxima

tag: condition

value: 28C acclim, sampled at 40C

value: Gill tissue

source_name: Gillichthys mirabilis, gill tissue, flow-through seawater tank (~13C), pooled total RNA for reference

value: pooled total RNA


title: Gm_14_28C_40C2


title: Gm_69_9C_control9

source_name: Gillichthys mirabilis, gill tissues, 9C acclim, control

value: 9C acclim, control


title: Gm_61_9C_control7


title: Gm_49_9C_control5


title: Gm_57_9C_control6


title: organotypic CVX expresing cdk4 and Ras rep2

source_name: organotypic cervical tissue cdk4 Ras


title: Gm_47_9C_17C2

source_name: Gillichthys mirabilis, gill tissues, 9C acclim, sampled at 17C

value: 9C acclim, sampled at 17C


title: Gm_46_9C_17C1


title: Gm_65_9C_control8


title: Gm_53_9C_control4


title: Gm_44_9C_control3


title: Gm_43_9C_control2


title: Gm_42_9C_control1


title: Gm_13_28C_40C1


title: Gm_11_28C_36C3

source_name: Gillichthys mirabilis, gill tissues, 28C acclim, sampled at 36C

value: 28C acclim, sampled at 36C


title: Gm_15_28C_40C3


title: Gm_10_28C_36C2


title: Gm_17_28C_control7

source_name: Gillichthys mirabilis, gill tissues, 28C acclim, control

value: 28C acclim, control


title: Gm_9_28C_36C1


title: Gm_7_28C_32C3

source_name: Gillichthys mirabilis, gill tissues, 28C acclim, sampled at 32C

value: 28C acclim, sampled at 32C


title: organotypic CVX expresing cdk4 and Ras rep1


title: Gm_8_28C_control5


title: Gm_5_28C_32C1


title: Gm_6_28C_32C2


title: Gm_3_28C_control3


title: Gm_4_28C_control4


title: Gm_12_28C_control6


title: Gm_31_19C_31C2

source_name: Gillichthys mirabilis, gill tissues, 19C acclim, sampled at 31C

value: 19C acclim, sampled at 31C


title: Gm_35_19C_35C2

source_name: Gillichthys mirabilis, gill tissues, 19C acclim, sampled at 35C

value: 19C acclim, sampled at 35C


title: Gm_34_19C_35C1


title: Gm_30_19C_31C1


title: Gm_38_19C_39C1

source_name: Gillichthys mirabilis, gill tissues, 19C acclim, sampled at 39C

value: 19C acclim, sampled at 39C


title: Gm_39_19C_39C2


title: Gm_1_28C_control1


title: Gm_26_19C_27C1

source_name: Gillichthys mirabilis, gill tissues, 19C acclim, sampled at 27C

value: 19C acclim, sampled at 27C


title: Gm_23_19C_23C2

source_name: Gillichthys mirabilis, gill tissues, 19C acclim, sampled at 23C

value: 19C acclim, sampled at 23C


title: Gm_2_28C_control2


title: Gm_27_19C_27C2


title: Gm_24_19C_23C3


title: Gm_32_19C_31C3


title: Gm_22_19C_23C1


title: TGF_5S

description: TGF-beta treated human osteoblast vs control human osteoblast, biological replicate 5, standard labeling

source_name: Human Osteoblast Cell Line

value: 10 ng/ml TGF-beta

value: media alone


title: Gm_37_19C_control7

source_name: Gillichthys mirabilis, gill tissues, 19C acclim, control

value: 19C acclim, control


title: Gm_25_19C_control5


title: Gm_21_19C_control4


title: Gm_19_19C_control2


title: Gm_18_19C_control1


title: Gm_33_19C_control6


title: Gm_20_19C_control3


title: Gm_71_9C_36C2

source_name: Gillichthys mirabilis, gill tissues, 9C acclim, sampled at 36C

value: 9C acclim, sampled at 36C


title: Gm_59_9C_29C2

source_name: Gillichthys mirabilis, gill tissues, 9C acclim, sampled at 29C

value: 9C acclim, sampled at 29C


title: Gm_62_9C_33C1

source_name: Gillichthys mirabilis, gill tissues, 9C acclim, sampled at 33C

value: 9C acclim, sampled at 33C

value: Gill tissue


title: Gm_52_9C_21C3

source_name: Gillichthys mirabilis, gill tissues, 9C acclim, sampled at 21C

value: 9C acclim, sampled at 21C

source_name: Gillichthys mirabilis, gill tissue, flow-through seawater tank (~13C), pooled total RNA for reference

value: pooled total RNA


title: Gm_70_9C_36C1


title: Gm_64_9C_33C3


title: Gm_60_9C_29C3


title: Gm_56_9C_25C3

source_name: Gillichthys mirabilis, gill tissues, 9C acclim, sampled at 25C

value: 9C acclim, sampled at 25C


title: Gm_54_9C_25C1


title: Gm_58_9C_29C1


title: Gm_55_9C_25C2


title: Gm_50_9C_21C1


status: Public on Sep 10 2010

city: Hangzhou

first: Yuejin

last: Hua

state: Zhejiang

address: 268 KaiXuan Road

department: Institute of Nuclear-Agricultural Sciences

country: China

institute: Zhejiang University

description:
raw data file 62.gpr is labeled as follows: DR1790-deletion strains vs. wildtype strains
2 biological replicates with dye swap
raw data file 62.gpr is labeled as follows: DR1790-deletion strains vs. wildtype strains (Cy5/Cy3)
raw data file 83.gpr is labeled as follows: wildtype strains vs. DR1790-deletion strains(Cy5/Cy3)

hyb_protocol: Samples were applied to microarrays enclosed in hybridization chambers. After hybridization, slides were washed sequential. Dye-swap is carried out.

scan_protocol: Scanned on an Genepix 4000B scanner. Images were quantified using GenePix Pro 5.1

data_processing: Normalization and statistical analysis were carried out in the R 2.2.0 computing environment using the linear models for microarray data package (Limma). Within Limma, global LOESS normalization was carried out for each microarray. The 3-replicate spots per gene in each array were used to maximize the robustness of differential expression measurement of each gene via the lmFit function within Limma.

organism: Deinococcus radiodurans

source_name: Total RNA from DR1790-deletion strain

label_protocol: 16 µg of total RNA were primed with 9 µg of Hexadeoxyribonucleotide mixture at 70°C for 10 min, then reversed transcribed at 42°C for 3 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3/5-label

growth_protocol: Cells were grown in an normal condition.

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

tag: genotype/variation

tag: phenotype

value: low growth rate

source_name: Total RNA from wildtype strain

value: Wildtype

value: normal growth rate


title: Gm_51_9C_21C2


title: 2257 - ABCB1neg_2

status: Public on Sep 01 2010

city: St. Louis

first: Olga

last: Agapova

state: MO

address: 660 S Euclid Ave

department: Ophthalmology and Visial Sciences

institute: Washington University School of Medicine

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was normalized by Illumina's average method

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

growth_protocol: OCM1A cell line was grown in RPMI-1640 media supplemented with 10% FBS and L-glutamine/antibiotics

extract_protocol: RNA was extracted with Trizol reagent and  purified by ammonium acetate precipitation. Quality control was performed with Agilent Bioanalyser 2100.

treatment_protocol: MDR1 shift assay (Millipore) was used for detection ABCB1 positive cells. ABCB1 positive and negative cells was sorted using  MoFlo flow cytometer (Cytomation) and collected in TrIzol for RNA isolation

tag: origin

value: uveal melanoma

tag: cell line


title: Gm_63_9C_33C2


title: B6-WT2 melanocytes

status: Public on Sep 05 2010

city: Dusseldorf

first: Charlotte

last: Esser

address: Auf´m Hennekamp 50

department: Molecular Immunology

institute: IUF

description: no additional information

hyb_protocol: RNA was hybridized to MOE430A 2.0 gene chips (Affymetrix).   Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: MAS5 calculated signal intensity

source_name: ex vivo cultivated melanocytes

label_protocol: RNA was biotinylated (Enzo Bio Array™HighYield™ RNA transcript labeling kit (Affymetrix, High Wycombe, UK)) and purified.

growth_protocol: Epidermal cell (eC) suspensions were prepared from tail skin of C57BL/6 and AhR-/- mice as described previously. EC were seeded 1.5x106 cells/ml in 6-well plates in serum free Melanocyte Growth Medium (Promocell, Heidelberg, Germany). Normal mouse melanocytes (NMM) were grown for 6-8 weeks, and passaged when confluent. All cells contained visible amounts of melanin at the end of the culture.

extract_protocol: Total RNA was isolated with Trizol™ (Invitrogen) according to the manufacturers’ instructions. For microarray analysis mRNA was amplified prior to chip-hybridization using the MessageAmp™ Kit of Ambion (Woodward St. Austin, USA).

value: wildtype

tag: gender

value: female

value: skin melanocytes


title: 2263 - ABCB1pos_3

description: replicate 3


title: Control siRNA, 1

first: Michael

last: Rosenfeld

address: 9500 Gilman Drive

department: School of Medicine

institute: HHMI/UCSD

hyb_protocol: hybridization for 18hrs at 58 degree and stained with Streptavidin-Cy3

scan_protocol: Slides were scanned using the illumina BeadArray Reader scanner

data_processing: Raw data was extracted with the Illumina Beadstudio software. The data was processed according to Illumina protocols and normalized using the multi-loess method mloess.

source_name: HeLa cells

label_protocol: RNA was labeled with biotin using the Ambion Illumina TotalPrep RNA Amplification Kit

extract_protocol: Rneasy Mini Kit (QIAGEN)

value: HeLa cells

tag: transfection

value: Control siRNA


title: AhR-KO1 melanocytes

description: no additional information

value: AhR knockout


title: 2256 - ABCB1neg_1

description: replicate 1


title: 2253 - ABCB1pos_2

description: replicate 2


title: LM8/control

city: Ariake, Koto-ward

first: Youya

last: Nakazawa

state: Tokyo

department: Cancer Chemotherapy Center

institute: Japanese Foundation for Cancer Research

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 h at 45°C on Mouse Genome 430 2.0 Array or Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G

data_processing: RMA normalized signal

source_name: control LM8 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8.1 to 15 ug total RNA using GeneChip IVT Labeling Kit.

growth_protocol: LM8 and A375M cells were cultured in MEM and DMEM respectively, containing 10% FBS under 5% CO2, 37°C condition.

extract_protocol: Total RNA was extracted with RNeasy Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Stably knock-downed cell lines were established by infecting with pSIREN-RetroQ-control, pSIREN-RetroQ-mouse Merm1/Wbscr22 or pSIREN-RetroQ-human Merm1/Wbscr22.

value: LM8 murine osteosarcoma

tag: treatment

value: control


title: B6-WT1 melanocytes

description: no additional information


title: LM8/shRNA Merm1/Wbscr22 knock-down

source_name: Merm1/Wbscr22 knock-downed LM8 cells

value: LM8 murine osteoosarcoma

value: Merm1/Wbscr22 knock-down


title: 2258 - ABCB1neg_3

description: replicate 3


title: Control siRNA, 2


title: PHF8siRNA, 2


title: 2252 - ABCB1pos_1

description: replicate 1


title: A375M/control

source_name: control A375M cells

value: A375M human melanoma


title: HEP_HPFH_III-4

status: Public on Aug 31 2010

city: Rotterdam

first: Sjaak

last: Philipsen

address: Dr. Molewaterplein 50

department: Cell Biology

country: Netherlands

institute: Erasmus MC

description: Gene expression data from KLF1 p.K288X/wt HEPs

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station Fluidics 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray scanner 3000

data_processing: The data was normalized by Robust Multi-Array average (RMA) algorithm. We used RMAExpress version 1.0 beta 9. Intensities of probe sets lower than 30 were reset to 30. The intensity values of individual probe sets in each sample were then displayed as the log 2 of the deviations to the calculated geometric means for that probe sets.

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

growth_protocol: Human erythroid progenitor cells (HEPs) were cultured as described (Leberbauer, C. et al. Different steroids co-regulate long-term expansion versus terminal differentiation in primary human erythroid progenitors. Blood 105, 85-94 (2005).) in the presence of recombinant human Epo (1 unit/ml, kind gift of Ortho-Biotech, Tilburg, The Netherlands), recombinant human SCF (50 ng/ml, kind gift of Amgen, Breda, The Netherlands) and dexamethasone (5 × 10−7 M; Sigma, St. Louis, MO, USA).  Cells were counted with an electronic cell counter (CASY-1, Schärfe System, Reutlingen, Germany).

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

tag: tissue type

value: Cultured erythroid progenitors

tag: hpfh

value: HPFH

tag: klf1k288x mutation

value: KLF1 p.K288X/wt

tag: hbf level (%)


title: HEP_wt_II-6

description: Gene expression data from wt/wt HEPs

value: No

value: wt/wt


title: A375M/shRNA Merm1/Wbscr22 knock-down

source_name: Merm1/Wbscr22 knock-downed A375M cells


title: CRI-G1-RS 06

city: San Francisco

first: Natasha

last: Chandiramani

address: 513 Parnassus Av

department: Pathology

institute: University of California San Francisco

description: Rotenone sensitive CRI-G1 cell line; biological sample #6

hyb_protocol: Affymetrix Rat 230 2.0 Array; GeneChip Expression Analysis Technical Manual 701021 Rev. 3

data_processing: GCOS 1.4

label: BIOTIN

source_name: CRI-G1-RS 06

label_protocol: Biotinylated cRNA was prepared using Ambion MessageAmp II-Biotin Enhanced Kit according to the manufacturers's instructions, starting from 1 ug of tRNA/sample.

growth_protocol: Cells were grown in high glucose DMEM with Glutamax, supplemented with 10% FBS and antibotics; six different passages were collected in a paired fashion (one sample for each cell type) ~ 24 h after plating, pelleted and frozen at -80 C until tRNA extraction.

extract_protocol: tRNA was extracted using Quiagen RNeasy kit with on column DNAse digerstion according to the manufacturer's instructions.

treatment_protocol: No treatment.

value: Rotenone sensitive CRI-G1


title: HEP_wt_III-5

description: Gene expression data from wt/wt HEPs