title: G-CSF Rep 4

value: G-CSF


title: Naive Rep 2

status: Public on Feb 03 2014

type: RNA

city: Brisbane

first: Glen

middle: M

last: Boyle

state: Queensland

address: 300 Herston Road Herston

department: Department of Cell and Molecular Biology, Cancer Program

country: Australia

institute: QIMR Berghofer Medical Research Insitute

hyb_protocol: Labelled cRNA was hybridized to MouseRef-8 v2.0 BeadChip Arrays (Illumina Inc, San Diego, CA, USA), and then washed and scanned according to standard Illumina protocols.

data_processing: Data were extracted in GenomeStudio (Illumina) using default analysis settings and no normalization method.  Resulting data were imported into GeneSpring GX v12.5 (Agilent Technologies, Santa Clara, CA, USA).  Expression values were normalized using quantile normalization with default settings.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: CD4+GFP+ nTreg from B6.FoxP3-GFP mice

label_protocol: Biotinylated cRNA was prepared with the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX, USA).

extract_protocol: RNA was extracted using Qiagen RNeasy mini kit as per manufacturer’s instructions, then DNase treated and purified.  RNA concentration was determined using the NanoDrop 2000 (Thermo Scientific, Wilmington, DE, USA).

tag: treatment

value: Saline

tag: strain


title: G-CSF Rep 3

scan_protocol: Labelled cRNA was hybridized to MouseRef-8 v2.0 BeadChip Arrays (Illumina Inc, San Diego, CA, USA), and then washed and scanned according to standard Illumina protocols.


title: INK128+Radiation 2

city: New Haven

first: Thomas

last: Hayman

state: CT

address: 15 York Street

department: Department of Therapeutic Radiology

country: USA

institute: Yale University

description: Polysome-bound RNA

hyb_protocol: See manufacturer's protocols

scan_protocol: See manufacturer's protocols

data_processing: The data were analyzed with Partek Genomics Suite. ANOVA table shows ANOVA analysis from partek for the different comparisons and lists the pvalue and fold change as well as the RMA normalized log2 transformed intensity values.

label: Biotin

organism: Homo sapiens

source_name: PSN1 cells

label_protocol: See manufacturer's protocols

growth_protocol: Cells were grown in RPMI with 10% FBS in an atmosphere of 5% CO2/95% air at 37°C

extract_protocol: Polysome bound mRNA was isolated using sucrose gradient fractionation

treatment_protocol: Cell cultures were irradiated using 320 X-ray source (Precision XRay Inc.) at a dose rate of 2.3 Gy/min.

tag: cell line

tag: cell type

value: pancreatic cancer


title: colorectal carcinoma cells with defunct TP53, biological replicate 1

status: Public on Feb 04 2014

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

department: Diagnostics

country: Germany

institute: Fraunhofer Institute for Cell Therapy and Immunology

description: Expression analysis of custom probes for genomic regions that have been found to be differentially expressed (i) throughout cell cycle progression, (ii) in response to the anti-proliferative and pro-apoptotic p53 pathway, and (iii) the anti-apoptotic and pro-proliferative STAT-3 pathway. In addition, the Agilent custom array (244K) interrogates probes for genomic regions predicted to contain a conserved secondary structure identified by RNAz (Washietl et al. "Fast and reliable prediction of noncoding RNAs." Proc Natl Acad Sci USA. 102:2454-9, 2005.) or Evofold (Pedersen et al. "Identification and classification of conserved RNA secondary structures in the human genome." PLoS Comput Biol. 2:e33, 2006.), as well as known non-coding RNAs from public databases, and the Agilent mRNA probe sets 014850. Colorectal carcinoma cells with defunct TP53.

hyb_protocol: nONCOchip 1.0 arrays were proceed using the Agilent Hybridization Kit, Agilent Hybrization-Chambers and an commercial Hyb-Oven according to the manufacturer's protocol (Agilent One-Color Quick Amp Labeling Kit).

scan_protocol: Arrays were scanned using a GenePix 4200 Scanner and the GenePix Pro 6.1 Software (Molecular Devices) with following settings: laser power: 100%, PMT: 300/400, resolution: 5µm, Focus: 0µm, Lines to Average: 2, Wavelength: 532nm, Filter: Standard Green.

data_processing: The data were analyzed with R (version 2.9.0) and BioConductor (version 2.4). Expression levels were normalized (quantile normalization) and a linear model was fitted using the R package limma in order to identify differentially expressed probes. Reliable variance estimations were obtained by empirical Bayes moderated t-statistics. False discovery rate was controlled by Benjamini-Hochberg adjustment.

label_protocol: 1µg RNA were analyzed on nONCOchip 1.0 array according to the manufacturer's protocol (Agilent One-Color Quick Amp Labeling kit protokoll).

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

value: colorectal carcinoma cells

value: TP53 defunct


title: colorectal carcinoma cells with induced TP53, biological replicate 2

description: Expression analysis of custom probes for genomic regions that have been found to be differentially expressed (i) throughout cell cycle progression, (ii) in response to the anti-proliferative and pro-apoptotic p53 pathway, and (iii) the anti-apoptotic and pro-proliferative STAT-3 pathway. In addition, the Agilent custom array (244K) interrogates probes for genomic regions predicted to contain a conserved secondary structure identified by RNAz (Washietl et al. "Fast and reliable prediction of noncoding RNAs." Proc Natl Acad Sci USA. 102:2454-9, 2005.) or Evofold (Pedersen et al. "Identification and classification of conserved RNA secondary structures in the human genome." PLoS Comput Biol. 2:e33, 2006.), as well as known non-coding RNAs from public databases, and the Agilent mRNA probe sets 014850. Colorectal carcinoma cells with induced TP53.

value: TP53 induced


title: Naive Rep 1


title: INK128+Radiation 1

description: Polysome-bound RNA


title: INK128 3

description: Polysome-bound RNA


title: Radiation 1

description: Polysome-bound RNA


title: INK128 2

description: Polysome-bound RNA


title: INK128 1

description: Polysome-bound RNA


title: Radiation 2

description: Polysome-bound RNA


title: INK128+Radiation 3

description: Polysome-bound RNA


title: G-CSF Rep 1


title: Control 3

description: Polysome-bound RNA


title: Radiation 3

description: Polysome-bound RNA


title: MM_6hVsSym_18dpi_rep3

city: Cuernavaca

first: Sergio

middle: Manuel

last: Encarnación

state: Morelos

address: Av. Universidad S/N

department: Centro de Ciencias Genomicas

country: Mexico

institute: Universidad Nacional Autonoma de México

description: Rhizobium etli CFN42 wild type transcriptional profiling was compared between bacteria cultivated in free-life 6 hours succinate-ammonia and symbiosis 18 days post-inoculation.

hyb_protocol: Both Cy3 and Cy5 labeled cDNAs to be compared were mixed, dried to completion, and then resuspended in 45 ul of hybridization buffer UniHyb (TeleChem International INC). The mixture was hybridized at 42 C for 14 to 16 h. Hybridized arrays were washed with 2X SSC, 0.1% SDS at 42 C for 2 min, and, subsequently, with 0.1X SSC at room temperature for 2 min, and twice with 0.1X SSC at room temperature for 2 min.

scan_protocol: The array was scanned using a pixel size of 10 um with a Scan Array Lite microarray scanner (Perkin-Elmer, Boston, MA).

data_processing: Spot detection, mean signals, mean local background intensities, image segmentation, and signal quantification were determined for the microarray images using the Array-Pro Analyzer 4.0 software (Media Cybernetics, L.P). Row data were normalized for the three the replicates by LOWESS normalization using R2.8.1 and BioConductor (http://www.bioconductor.org) software. Normalized M values (MA = log2 (Intensityexperiment/Intensitycontrol) were transferred into a new worksheet for significance analysis of microarray. Once normalized the M values, these were averaged for each gene along the replicates.  In order to identify those genes that differentially up-regulate during nitrogen fixation, we calculate the z-score over the MA gene distribution and select those genes with z >1.65.

organism: Rhizobium etli CFN 42

source_name: Minimal medium 6 hours, wild type

label_protocol: 10 ug of RNA was labeled with Cy3-dUTP using a CyScribe First-Strand cDNA labeling kit (Amersham Biosciences).

extract_protocol: Total RNA isolated using a RNeasy Mini Kit (QIAGEN, Hilden, Germany)

tag: growth conditions

value: minimal medium succinate-ammonia during 6 hrs

tag: genotype/variation

value: wild type

source_name: Nodules of eighteen days post-inoculation, wild type

label_protocol: 10 ug of RNA was labeled with Cy5-dUTP using a CyScribe First-Strand cDNA labeling kit (Amersham Biosciences).

extract_protocol: Approximately 3 g of nodules were immersed in liquid nitrogen and macerated. Total RNA was isolated by acid hot-phenol extraction as described previously by de Vries et al.

value: Symbiosis with bean 18 days post-inoculation


title: G-CSF Rep 2


title: Control 2

description: Polysome-bound RNA


title: Transiently transfected hEEC from biopsy IV with MIMIC_30d miRNA

city: Valencia

first: Juan

last: Moreno-Moya

address: Catedrático Agustín Escardino

country: Spain

institute: FIVI

description:
MIMIC_30d_IV
each sample was previous tested for total RNA quality using total Nano RNA Labchip in an agilent bioanalyzer and with RIN above 9.0

hyb_protocol: 1.65 ug of cRNA was used to be fragmented in presence of blocking agent and fragmentation buffer for 30' at 60C and cooled. Then sample was mixed with hybridization buffer.

scan_protocol: Microarrays slides were washed and scanned in Genepix Personal 4100A Scanner and scanned in Genepix Pro Software with a spot resolution of 5um in the green channel.

data_processing: Median intensity value of each spot data was log2 transformed and normalized using R software and libraries from bioconductor database. Next, replicated probes were merged by mean using GEPAS.

source_name: primary hEEC_miR-30d mimic

label_protocol: 100ng of total RNA were mixed with spike and mixed with T7 promoter primer for 10' at 65C then cooled at 4C. Next to cDNA synthesis, First strand buffer, DTT, dNTP and RNAse block mix were added and incubated for 2 hours at 40C followed by 15' at 70C. Next for cRNA synthesis, transcription buffer, DTT, NTP, T7 RNA polymerase and Cy3-CTP were added and incubated for 2 hours at 40C and cooled for 5'. Then cRNA was purified according to Qiagen RNEasy kit protocol specifications. Yield and [cRNA] stimated. Then 1.65 ug de cRNA was used to be fragmented in presence of blocking agent and fragmentation buffer for 30' at 60C and cooled. Then sample was mixed with hybridization buffer.

growth_protocol: When hEEC cultures reached 50% confluency cells were transiently transfected with 50nM of either miR-30d mimic or Scramble miRNA using HiPerfect as recommended by the manufacturer (Qiagen, Valencia, CA, USA). After 72 hours post-transfection, cells were subjected to RNA extraction.

extract_protocol: To ensure that miRNA fraction will be recovered we performed RNA extraction using the miRNeasy Kit (Qiagen, Valencia, CA, USA). RNA extracted was quantified using a NanoDrop (Thermo Fisher Scientific Inc, MA, USA) spectrophotometer and the quality of RNA samples was assesed using a Nano LabChip BioAnalyzer 2100 (Agilent Technologies Inc, DE, USA).

value: primary hEEC derived from healthy human endometrial biopsies at LH+0

tag: transfected with

value: miR-30d mimic for 72hr


title: Transiently transfected hEEC from biopsy III with MIMIC_30d miRNA

description:
MIMIC_30d_III
each sample was previous tested for total RNA quality using total Nano RNA Labchip in an agilent bioanalyzer and with RIN above 9.0


title: LLC_E19

city: Carrières sur Seine

first: Damien

last: VALOUR

state: Île-de-France

address: 34, rue Victor HUGO (Bât D)

department: PHASE

country: France

institute: INRA

description: Syntax of the sample names: EmbryoName, EnergyStatus of the mother. Where the energy status is either GH, ELC, LLC. Annotations = Energy balance. Experimental variables: Energy Status = Growing heifers (GH) having a positive energy balance, Early lactating cows (ELC) having a negative energy balance, Late lactating cows (LLC) having a null energy balance. Additional data: Holstein cows. Flushed D18 conceptuses. Animals were managed in accordance with the European Community Directive, 86-609-EC and under the license of French Institute of Agronomical Research (INRA-UCEA).

hyb_protocol: Prior to hybridization, microarrays were prehybridized for 30 min at 50°C in a filtered solution of 1% BSA, 3.5X SSC, 0.1% SDS and rinsed twice at room temperature in ultrapure water for 5 min with orbital agitation. They were dried using compressed air. Each microarray was co-hybridized with two fluorescently labelled (Cy3 and Cy5) cDNA samples according to the experimental design (reference design). An evaluated amount of 500 ng of each labelled cDNA was fragmented for 30 min at 60°C in 1X fragmentation buffer (Agilent Technologies). KREAblock is a background blocker and was added as 1/4th of the final volume of 200µL (adjusted with ultra-pure water). Hybridisation were performed on the ICE platform (previously, PICT Gem, Jouy en Josas, http://www4.jouy.inra.fr/gabi_eng/Our-resources/ICE-Integrated-Microgenomics-platform). Then, fragmented labelled cDNA samples were diluted in 200µL of Agilent hybridization buffer 2X and hybridized on the 22K bovine oligo-array for 20 h at 60°C in a rotating hybridization oven (Agilent Technologies). After hybridization, microarrays were washed at room temperature with orbital agitation successively twice for 5 min in a 2X SSC-0.1% SDS solution, once for 5 min in a 0.5X SSC-0.1% SDS solution and three times for 5 min in a 0.2X SSC solution. They were finally dried using compressed air.

scan_protocol: Scanner: Agilent G2505B Microarray Scanner System. Raw data set: Feature extraction with GenePix Pro 6.1.0.4 software. GenePix software was used to extract data at the CRB GADIE of Jouy-en-Josas (http://crb-gadie.inra.fr/)

data_processing: Intensity = Signal Median. Normalization = Signal Median were normalized using the Limma functions in R: - NormalizeWithinArrays (log2, loess transformations) - NormalizeBetweenArrays (Aquantile transformation) - Flags = -50

organism: Bos taurus

source_name: Extra-embryonic tissues (EET), Late lactating cows (LLC) having a null energy balance

label_protocol: The amplified RNA were labelled with the ULSTM aRNA Labelling Kit. Briefly, 2µg of amplified RNA were directly labelled with 2µL of Cy(3-5)-ULS. Amplified RNA and Cy-ULS were mixed with 2µL of 10x labelling solution to obtain a 1x labelling solution mixture in a volume of 20µl (adjusted with ultra-pure water). The mixture was incubated at 85°C for 15 min and chilled on ice. Labelled targets were then purified on KREApure columns. Frequencies of dye incorporation (FOI, rate per thousand labelled nucleotides) and cDNA concentrations were estimated for both dyes by measuring the absorbance at 260 nm, 550 nm and 650 nm on a Nanodrop spectrophotometer (Thermo Scientific). The following ratios were calculated: FOI per 1000 bases (Cy3) = 58.5 * Abs550/Abs260, FOI per 1000 bases (Cy5) = 35.1 * Abs650/Abs260.

extract_protocol: Total RNA from extra-embryonic tissues (N=29) were isolated using Trizol (Invitrogen) and linear amplification was performed using MessageAmp aRNA kit (Ambion, Courtaboeuf, France), starting from 1 µg total RNA as in Degrelle et al. (2008).

treatment_protocol: D18 conceptuses were flushed, the embryonic tissues were dissected out and the Extra-embryonic tissues immediately snap-frozen.

tag: breed

value: Holstein

tag: tissue

value: D18 conceptuses

source_name: Pool Placenta - 10 hours amplified RNA from a pool of Placenta.

extract_protocol: Total RNA from Placenta at different stages of pregnancy were isolated using Trizol (Invitrogen), pooled and linear amplification was performed using MessageAmp aRNA kit (Ambion, Courtaboeuf, France), starting from 1 µg total RNA as in Degrelle et al. (2008).

treatment_protocol: Placenta were dissected and tissues were immediately snap-frozen.

value: Pool Placenta Reference


title: MM_6hVsSym_18dpi_rep1


title: Control 1

description: Polysome-bound RNA


title: Transiently transfected hEEC from biopsy II with MIMIC_30d miRNA

description:
MIMIC_30d_II
each sample was previous tested for total RNA quality using total Nano RNA Labchip in an agilent bioanalyzer and with RIN above 9.0


title: Transiently transfected hEEC from biopsy I with MIMIC_30d miRNA

description:
MIMIC_30d_I
each sample was previous tested for total RNA quality using total Nano RNA Labchip in an agilent bioanalyzer and with RIN above 9.0


title: Donor H, time 48 h

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

description: Gene expression data from Donor H, time 48h

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome HG-U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GCOS, GeneChip Operating Software

data_processing: RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization

source_name: primary human monocytes stimulated with CCL2 for 2 h plus LPS for 12 h plus TNF-α for 11 h plus IFN-γ for 7 h; washed and stimulated with IL-10 for 10 h; washed and stimulated with TGF-β for 12 h

label_protocol: Biotinylated cRNA was prepared using GeneChip® 3’ IVT Express kit according to manufacturer's intructions

growth_protocol: Human monocytes were obtained from buffy coats of healthy donors by isolating PBMC on Ficoll-Paque PLUS gradients and subsequent separation with Monocyte Isolation kit II. Monocytes were cultured in RPMI 1640+Glutamax-I Medium (GIBCO, Life Technologies) with 5% human AB serum, and gentamicine.

extract_protocol: Extraction of total RNA was performed using Qiagen miRNeasy kit (Qiagen) according to the manufacturer’s protocol

treatment_protocol: The human primary blood monocytes were exposed in culture to sequential changes of microenvironmental conditions (chemokines and cytokines, temperature, bacterial-derived molecules, etc.) for 48 h.

value: deactivated monocytes

tag: group

value: treated


title: MM_6hVsSym_18dpi_rep2_swap


title: Donor E, time 48 h

description: Gene expression data from Donor E, time 48h


title: Transiently transfected hEEC from biopsy I with Scramble miRNA

description:
SCRAMBLE_I
each sample was previous tested for total RNA quality using total Nano RNA Labchip in an agilent bioanalyzer and with RIN above 9.0

source_name: primary hEEC_scrambled miRNA

value: scramble miRNA for 72hr


title: B cells_d0_rep2

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

description: RMA expression value derived from Expression Console software; core-gene analysis

hyb_protocol: Affymetrix Standard protocol

scan_protocol: Arrays were scanned with a GeneChip3000 7G scanner

data_processing: Scanned images of microarray chips were analysed using the Affymetrix GeneChip Command Console. Gene level analysis of the array data was performed using Affymetrix Expression Console with the default settings of “Core: RMA-Sketch”.

source_name: Primary B cells isolated from peripheral blood and RNA extracted immediately

label_protocol: 100ng of RNA was used to transcribe single stranded cDNA using oligo dT primers. A second strand was then synthesised and the double stranded cDNA purified. This double stranded cDNA was used as a template to generate fluorescently labelled cRNA by in vitro transcription, which was purified and fragmented before being hybridised to the microarray chip.

extract_protocol: RNA was isolated from the B cells using miRVANA RNA extraction kit for total RNA isolation according to the manufacturer's instructions.

tag: ebv status

value: negative

tag: cytokine stimulation


title: INA6 cells with 13 hours of IL-6 withdrawal, biological replicate 3

description: Expression analysis of custom probes for genomic regions that have been found to be differentially expressed (i) throughout cell cycle progression, (ii) in response to the anti-proliferative and pro-apoptotic p53 pathway, and (iii) the anti-apoptotic and pro-proliferative STAT-3 pathway. In addition, the Agilent custom array (244K) interrogates probes for genomic regions predicted to contain a conserved secondary structure identified by RNAz (Washietl et al. "Fast and reliable prediction of noncoding RNAs." Proc Natl Acad Sci USA. 102:2454-9, 2005.) or Evofold (Pedersen et al. "Identification and classification of conserved RNA secondary structures in the human genome." PLoS Comput Biol. 2:e33, 2006.), as well as known non-coding RNAs from public databases, and the Agilent mRNA probe sets 014850. INA6 cells after 13 hours of IL-6 withdrawal.

source_name: Human multiple myeloma cells (INA6) after IL-6 has been withdrawn for 13 hours


title: B cells + EBV_d7_rep2

source_name: Primary B cells isolated from peripheral blood, infected with EBV and cultured for 7 days prior to RNA extraction

value: positive. B cells were infected with EBV at an M.O.I of 50 and then cultured for 7 days in RPMI plus 10% FCS.


title: B cells + EBV_d7_rep3


title: B cells + CD40L/IL4_d7_rep3

source_name: Primary B cells isolated from peripheral blood and cultured for 7 days with CD40L and IL-4

value: CD40L and IL-4. B cells were cultured for 7 days in RPMI plus 10% FCS and 50ng/ml of both soluble CD40L and IL-4.


title: Transiently transfected hEEC from biopsy III with Scramble miRNA

description:
SCRAMBLE_III
each sample was previous tested for total RNA quality using total Nano RNA Labchip in an agilent bioanalyzer and with RIN above 9.0


title: Donor G, time 48 h

description: Gene expression data from Donor G, time 48h


title: B cells + CD40L/IL4_d7_rep2


title: Donor D, time 48 h

description: Gene expression data from Donor D, time 48h


title: P53_ind_chipK_TileShuffle

description: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct P53 on Affymetrix Human Tiling 1.0 array set after induction of P53 expression. Intensities were processed with TileShuffle.

hyb_protocol: Affymetrix Human Tiling 1.0 arrays were proceed using the GCS3000 7G system according to manufacturer's protocol.

scan_protocol: Affymetrix Human Tiling 1.0 array were proceed using the GCS3000 7G system according to manufacturer's protocol.

data_processing: Affymetrix Human Tiling 1.0 probes were mapped to human genome assembly hg18 using the corresponding BPMAP files. Intensities of perfect match (PM) probes were processed with TileShuffle (Otto C, Reiche K, Hackermüller J. "Detection of differentially expressed segments in tiling array data". Bioinformatics. 2012 Jun 1;28(11):1471-9. Epub 2012 Apr 6.) using a window size of 200, the arithmetic mean trimmed by maximal and minimal value as scoring function, four GC content bins, 10000 permutations, and a q-value threshold of 0.05. In order to estimate the significance of a window score we repeatedly permute all probe intensities across the array while interchanging only those that belong to the same sequence-specific affinity bin, recompute the window scores, and compare them with the original ones. By counting the number of permuted windows with higher score, we estimate empirical p-values of windows, and report q-values adjusted according to Benjamini and Hochberg ("Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing". Journal of the Royal Statistical Society. Series B (Methodological), 57:289-300, 1995.).

source_name: Colorectal carcinoma cells (D53wt cells) stably transfected with tetracycline responsive wild type P53

label_protocol: 10µg RNA were analyzed on Affymetrix Human Tiling 1.0 array set according to the manufacturer's protocol.

value: colorectal carcinoma cells (D53wt cells) stably transfected with tetracycline responsive wild type P53


title: Transiently transfected hEEC from biopsy II with Scramble miRNA

description:
SCRAMBLE_II
each sample was previous tested for total RNA quality using total Nano RNA Labchip in an agilent bioanalyzer and with RIN above 9.0


title: B cells_d0_rep3


title: Donor L, time 48 h

description: Gene expression data from Donor L, time 48h


title: Donor C, time 48 h

description: Gene expression data from Donor C, time 48h


title: Transiently transfected hEEC from biopsy IV with Scramble miRNA

description:
SCRAMBLE_IV
each sample was previous tested for total RNA quality using total Nano RNA Labchip in an agilent bioanalyzer and with RIN above 9.0


title: B cells + EBV_d7_rep1


title: Donor A, time 48 h

description: Gene expression data from Donor A, time 48h


title: Donor L, time 24 h

description: Gene expression data from Donor L, time 24h

source_name: primary human monocytes stimulated with CCL2 for 2 h plus LPS for 12 h plus TNF-α for 11 h plus IFN-γ for 7 h; washed and stimulated with IL-10 for 10 h


title: Donor F, time 48 h

description: Gene expression data from Donor F, time 48h


title: B cells_d0_rep1


title: B cells + CD40L/IL4_d7_rep1


title: Donor B, time 48 h

description: Gene expression data from Donor B, time 48h


title: DGM-10963_M0_sm

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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.

source_name: small airway epithelium brushing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: smoking status

value: smoker


title: Donor H, time 24 h

description: Gene expression data from Donor H, time 24h


title: Donor G, time 24 h

description: Gene expression data from Donor G, time 24h


title: DGM-11062_M0_sm


title: DGM-11047_M0_sm

tag: cilia length


title: DGM-11111_M0_sm


title: DGM-11016_M0_sm


title: DGM-11066_M0_sm


title: DGM-11008_M0_sm


title: Donor F, time 24 h

description: Gene expression data from Donor F, time 24h


title: DGM-11038_M0_sm


title: Donor B, time 24 h

description: Gene expression data from Donor B, time 24h


title: DGM-10891_M0_sm


title: DGM-10907_M0_sm


title: DGM-10625_M0_sm


title: DGM-10808_M0_sm


title: DGM-10757_M0_sm


title: Donor D, time 24 h

description: Gene expression data from Donor D, time 24h


title: Donor E, time 24 h

description: Gene expression data from Donor E, time 24h


title: DGM-10880_M0_sm


title: DGM-10919_M0_sm


title: Donor A, time 24 h

description: Gene expression data from Donor A, time 24h


title: Donor L, time 14 h

description: Gene expression data from Donor L, time 14h

source_name: primary human monocytes stimulated with CCL2 for 2 h plus LPS for 12 h plus TNF-α for 11 h plus IFN-γ for 7 h

value: late inflammatory monocytes


title: DGM-10640_M0_sm


title: Donor E, time 14 h

description: Gene expression data from Donor E, time 14h


title: Donor G, time 14 h

description: Gene expression data from Donor G, time 14h


title: DGM-10721_M0_sm


title: DGM-10732_M0_sm


title: Donor H, time 14 h

description: Gene expression data from Donor H, time 14h


title: DGM-10538_M0_sm


title: Donor C, time 24 h

description: Gene expression data from Donor C, time 24h


title: DGM-00221_M0_sm


title: DGM-10774_M0_sm


title: DGM-10672_M0_sm


title: Donor D, time 14 h

description: Gene expression data from Donor D, time 14h


title: Donor F, time 14 h

description: Gene expression data from Donor F, time 14h


title: DGM-10361_M0_sm


title: DGM-10846_M0_sm


title: DGM-10844_M0_sm


title: DGM-10330_M0_sm

value: nonsmoker


title: DGM-10638_M0_sm


title: Donor C, time 14 h

description: Gene expression data from Donor C, time 14h


title: DGM-10698_M0_sm


title: DGM-10707_M0_sm


title: DGM-10522_M0_sm


title: Day 20 set2

city: Delhi

first: Vivek

middle: T

last: Natarajan

state: Delhi

address: Mathura Road

country: India

institute: CSIR-IGIB

description: depigmented

hyb_protocol: hybridization performed as per manufacturer's instructions (illumina)

scan_protocol: scanning performed as per manufacturer's instructions (illumina)

data_processing: Data was processed using bead studio module with average normalization after background subtration

source_name: B16 melanoma cells

label_protocol: labelling was performed as per instructions by manufacturer's using the Illumina total prep RNA labelling kit from Ambion

extract_protocol: Total RNA was isolated from cells using trizol method, isopropanol precipitated RNA was column purified using Qiagen RNA purification kit

treatment_protocol: B16 cells were grown in DMEM supplemented with 10% vol/vol Fetal calf serum, for the set up of the experiment cells were seeded at 100 cells/cm2 and harvested after indicated days (4,8 and 12), on day 12 cells were plated at 10,000 cells /cm2 and harvested on days 16 and 20

tag: growth

value: cells grown in High density 10000 cells per cm2

tag: time

value: Day 20

value: depigmented


title: DGM-10571_M0_sm


title: DGM-10706_M0_sm


title: Donor B, time 14 h

description: Gene expression data from Donor B, time 14h


title: DGM-10569_M0_sm


title: DGM-10519_M0_sm


title: Donor H, time 4 h

description: Gene expression data from Donor H, time 4h

source_name: primary human monocytes stimulated with CCL2 for 2 h plus LPS for 2 h plus TNF-α for 1 h

value: early inflammatory monocytes


title: Donor A, time 14 h

description: Gene expression data from Donor A, time 14h


title: Donor L, time 4 h

description: Gene expression data from Donor L, time 4h


title: RNA from KIT-D816V transgenic zebrafish adult kidney (Cy3) hybridized together with wild-type adult kidney RNA (Cy5)

city: Ottawa

first: Sergey

middle: V

last: Prykhozhij

state: Ontario

address: Room 318/319 | CAREG, 20 Marie-Curie Private

country: Canada

institute: CHEO Research Institute/University of Ottawa

hyb_protocol: Two samples were used per hybridization mixture and were equalized for quantity (2 μg per sample) of labeled aRNA target added. Differences in labeling efficiencies of the two dyes were controlled through the use of dye swaps.  Labeled target mixtures were fragmented for 30 min at 60C using 25X fragmentation buffer – a component of the Agilent Gene Expression Hybridization kit (5188-5242 Agilent Technologies, Santa Clara, CA, USA).  Following fragmentation, samples were made up to 60ul with 2X GExHyb buffer (also a component of Agilent Gene Expression Hybridization kit). Samples were hybridized to Agilent 4x44k zebrafish V3 slides (design ID 026437, part# G2519F) using quad chambers on the TECAN HS4800 Pro instrument (Tecan, Durham, NC, USA).  Hybridization protocol and program were as described for Agilent Two-Colour Microarray-Based Gene Expression Analysis with TECAN HS Pro hybridization:  Briefly, samples were hybridized to slides for 17 hours at 65°C with high agitation frequency.

scan_protocol: Slides were scanned at 5um resolution using a GenePix 4200AL scanner (Molecular Devices, Sunnyvale, CA, USA). Gridding was performed manually using SpotReader (Niles Scientific) and the resulting GPR file was analyzed using Acuity 4 software (Molecular Devices, Sunnyvale, CA, USA). Data was imported and normalized using a whole slide Lowess normalization routine provided by Acuity.

data_processing: Analysis and quality control were assessed with Self-Organizing maps (SOM), Principal Component Analysis (PCA), t-test and volcano plotting of PCA scores vs. log transformation of t-test scores. The top differentially expressed genes were extracted, compiled into lists and then compared between replicates.

organism: Danio rerio

source_name: Tg(actb2:KIT-D816V) transgenic adult kidney

label_protocol: 1ug of each RNA sample to be analyzed was amplified using the Ambion Amino-Allyl MessageAmp II aRNA amplification kit (AM1753 Life Technologies, Carlsbad CA, USA) according to the manufacturer’s instructions.  The quantity of amplified aRNA was assessed using the NanoDrop 2000 spectrophotometer (Nano-Drop, Thermo Scientific, Wilmington, DE, USA) and quality as well as the size distribution was assessed by Experion bioanalyzer (Bio-Rad).  The aRNA samples were then covalently labeled with AlexaFluor 555 or AlexaFluor 647 dyes as per kit instructions (A32756 and A32757, Life Technologies). Target aRNA yield and labeling efficiency were assessed by NanoDrop.

growth_protocol: Zebrafish husbandry was carried out according to standard protocols (Westerfield, 2007). Westerfield, M. (2007)The zebrafish book: a guide for the laboratory use of zebrafish (Danio rerio). 5th ed. The University of Oregon Press.

extract_protocol: RNA was extracted using a combination of the TRIzol (15596-026, Life Technologies, Carlsbad, CA, USA) protocol and the RNeasy Mini Kit (74104, QIAGEN, Toronto, ON, Canada). Briefly, embryos or dissected kidneys were homogenized in TRIzol, and centrifuged after treatment with chloroform to reveal the three-layered product. The supernatant containing RNA was precipitated in an equal volume of 70% ethanol and transferred into the spin columns of the RNeasy kit and purified according to manufacturer’s instructions.

treatment_protocol: No treatments were done.

value: AB

tag: genotype

tag: Stage

value: adults(18-24 months)

source_name: wild-type adult kidney

value: wild-type(AB)


title: RNA from KIT-D816V transgenic zebrafish adult kidney (Cy5) hybridized together with wild-type adult kidney RNA (Cy3)

tag: strain

value: wild-type


title: DGM-10685_M0_sm


title: Donor G, time 4 h

description: Gene expression data from Donor G, time 4h

value: treated


title: RNA from KIT-D816V transgenics (labeled Cy5) hybridized together with wild-type RNA (labeled Cy3) - replicate 2

source_name: wild-type embryos of AB strain

value: 28 hpf

source_name: Tg(actb2:KIT-D816V) transgenic embryos


title: DGM-10568_M0_sm


title: RNA from KIT-D816V transgenics (labeled Cy5) hybridized together with wild-type RNA (labeled Cy3) - replicate 4


title: DGM-10447_M0_sm


title: Donor F, time 4 h

description: Gene expression data from Donor F, time 4h


title: Donor D, time 4 h

description: Gene expression data from Donor D, time 4h


title: WT clenbuterol replicate 3 vs WT control replicate 3

city: Urbana

first: Anna

middle: C

last: Dilger

state: IL

address: Meat Science Lab 1503 S Maryland Drive

department: Animal Science

institute: University of Illinois

description:
D1
Wild-type with clenbuterol treatment (replicate 3) versus wild-type with control treatment (replicate 3).

hyb_protocol: Samples were suspended in SlideHyb#1 (Ambion), applied to slides on a Maui mixer and incubated O/N at 42ûC. After hybridization, the slides were washed sequentially in 1X SSC, 0.2% SDS; 0.1X SSC, 0.2% SDS; and 0.1X SSC for 5 minutes each, and spun dry.

scan_protocol: Scanned on an Axon GenePix 4000B scanner. Images were quantified using Axon GenePix 6.0.

data_processing: Median foreground intensites (no background subtraction) were normalized within arrays by print-tip loess normalization and between arrays using the scale method in limma. Spots with -100 flags were weighted zero before normalizations.

label: Alexa Fluor 647

label_protocol: 1 ug of total RNA was amplified using the amino-allyl MessageAmp II kit from Ambion. Amplified RNA was then labeled with Alexa Fluor 555 or 647 and cleaned in an RNeasy column.

growth_protocol: Wild type (WT) and myostatin null (MN) mice were weaned from dams at 3 weeks of age and individually housed until 7 week of age. They were given free access to a standard chow diet.

extract_protocol: Muscles were disrupted in Trizol with a TissueLyser and isolation of total RNA were carried out according to the manufacturers’ directions (Invitrogen).  Isolated RNA was quantified by spectrophotometry using a spectrophotometer.  Prior to microarray, RNA quality was determined using a 2100 Bioanalyzer (Agilent, Palo Alto, CA).

treatment_protocol: At 5 weeks of age, mice were given free access to either plain tap water (control) or tap water with 20 ppm clenbuterol hydrochloride (clenbuterol). Treatment duration was 2 weeks. Animals were sacrificed and tibialis anterior muscles were dissected from the right hind limbs.

tag: strain/background

value: wild type

tag: age

value: 7 weeks

tag: gender

value: male

value: skeletal muscle (tibialis anterior)

tag: treatment

value: clenbuterol

label: Alexa Fluor 555

value: control


title: DGM-10537_M0_sm

value: smoker


title: RNA from KIT-D816V transgenics (labeled Cy5) hybridized together with wild-type RNA (labeled Cy3) - replicate 1


title: Day 0 set1

description: depigmented

growth_protocol: B16 cells were grown in DMEM supplemented with 10% vol/vol Fetal calf serum,

value: cells grown in High density 10000 cells per cm2

tag: cell line

value: Day 0


title: Donor E, time 4 h

description: Gene expression data from Donor E, time 4h

tag: cell type


title: DGM-10378_M0_sm

value: nonsmoker


title: S/MAR DNA from 3 biological replicates.

type: genomic

city: Raleigh

first: Pete

middle: E

last: Pascuzzi

state: NC

address: 851 Main Campus Drive

institute: North Carolina State University

description: Average S/MARDNA / gDNA (log2) from 3 biological replicates each with 2 technical replicates (6 microarrays).

hyb_protocol: The Cy dye-labeled target and reference samples were co-hybridized on a high-resolution custom-designed NimbleGen tiling array for Arabidopis Chr4. After the overnight hybridization, DyeSaver2 was used to minimize oxidation of Cy dyes.

scan_protocol: Hybridized arrays were scanned 5-μm resolution using a PerkinElmer ScanArray Express scanner and quantified using GenePix Pro software (version 6.01).

data_processing: Microarray signals were quantified with NimbleScan software and exported to limma. All control spots (NG controls, positive and negative controls, and mismatch probes) were removed as were all probes mapping to the heterochromatic knob and pericentromeric DNA. Data was loess and quantile normalized using default settings. Duplicate spots were then averaged. Coefficients were first estimated for each biological replicate from the replicate arrays. Correlation coefficients for probe ratios were >= 0.78 so we estimated a single coefficient from the 6 microarrays.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: S/MAR DNA from nuclei

label_protocol: Amplified target and reference DNA samples (1.5 μg) were labeled with  Cy5 and Cy3 respectively (TriLink Biotechnologies),and incubated with 100 units (exo-) Klenow fragment (New England Biolabs) and dNTP mix (10 mM each in Milli-Q water pH 5.0, New England Biolabs) for 3 hr at 37°C. Reactions (final volume 100 μl) were terminated by addition of 10 μl of 0.5 M EDTA pH 8.0, precipitated with 11.5 μl of 5 M NaCl and equal volume of isopropanol and resuspended in water. Then, 13 μg of the Cy5-labeled target and 13 μg of the Cy3-labeled reference were obtained from three labeling reactions, which were mixed, evaporated, and resuspended in 40 μl of NimbleGen Hybridization Buffer (Roche).

growth_protocol: At (Col-0) cells were grown in Gamborg's B5 basal medium with minor salt, maintained on a rotary shaker at 160 rpm under constant light at 23C, and subcultured weekly. A 7 day culture is split 1:1 into fresh media and grown for 16 hours before nuclei are isolated.

extract_protocol: Protoplasts were prepared from cultured cells followed by nuclei isolation. Approximately 4 million nuclei were treated with 10 mM LIS for histone removal. The resulting nuclear halos were treated with 500 units of EcoRI and 500 units of HindIII to digest the nuclear halo DNA that was not attached to the nuclear matrix. The S/MAR DNA that remained bound to the nuclear matrix was isolated by centrifugation followed by digestion of nuclear matrices with SDS and Proteinase K, which was then followed by phenol/chloroform/IAA extraction. S/MAR DNA was then precipitated by ethanol, and resuspended in RT-grade water.

tag: ecotype

value: light-grown suspension cells

tag: sample type

value: S/MAR DNA

source_name: gDNA from nuclei

value: genomic DNA


title: DGM-10412_M0_sm


title: WT control replicate 4 vs WT clenbuterol replicate 4

description:
D2
Wild-type with control treatment (replicate 4) versus wild-type with clenbuterol treatment (replicate 4).

tag: tissue


title: DGM-10595_M0_sm


title: Donor C, time 4 h

description: Gene expression data from Donor C, time 4h

value: early inflammatory monocytes

tag: group


title: RNA from KIT-D816V transgenics (labeled Cy3) hybridized together with wild-type RNA (labeled Cy5) - replicate 3

value: AB

value: wild-type


title: WT clenbuterol replicate 2 vs MN clenbuterol replicate 4

description:
C2
Wild-type with clenbuterol treatment (replicate 2) versus myostatin null with clenbuterol treatment (replicate 4).

value: myostatin null


title: MN clebuterol replicate 3 vs WT clebuterol replicate 1

description:
C1
Myostatin null with clenbuterol treatment (replicate 3) versus wild-type with clenbuterol treatment (replicate 1).

value: wild type


title: RNA from KIT-D816V transgenics (labeled Cy3) hybridized together with wild-type RNA (labeled Cy5) - replicate 4

value: 28 hpf


title: Donor B, time 4 h

description: Gene expression data from Donor B, time 4h

value: treated


title: DGM-10632_M0_sm

tag: smoking status


title: Donor A, time 4 h

description: Gene expression data from Donor A, time 4h


title: Donor N, time 3.5 h

description: Gene expression data from Donor N, time 3.5h

source_name: primary human monocytes stimulated with CCL2 for 2 h plus LPS for 1.5 h plus TNF-α for 0.5 h


title: MN clenbuterol replicate 2 vs MN control replicate 4

description:
B2
Myostatin null with clenbuterol treatment (replicate 2) versus myostatin null with control treatment (replicate 4).

value: 7 weeks

value: male

value: skeletal muscle (tibialis anterior)


title: Donor O, time 3.5 h

description: Gene expression data from Donor O, time 3.5h


title: MN control replicate 3 vs. MN clenbuterol replicate 1

description:
B1
Myostatin null with control treatment (replicate 3) versus myostatin null with clenbuterol treatment (replicate 1).

value: control

value: clenbuterol


title: Donor M, time 3.5 h

description: Gene expression data from Donor M, time 3.5h


title: RNA from KIT-D816V transgenics (labeled Cy3) hybridized together with wild-type RNA (labeled Cy5) - replicate 1


title: DGM-10518_M0_sm

value: smoker

tag: cilia length


title: MN control replicate 2 vs WT contol replicate 2

description:
A2
Myostatin null with control treatment (replicate 2) versus wild-type with control treatment (replicate 2).


title: Day 3 EBs at 24hr after ER71/Etv2, GATA2 and Scl induction C

city: St. Louis

first: Fang

last: Liu

state: MO

address: 660S Euclid Ave.

department: Pathology & Immunology

institute: Washington University in St. Louis

description: Day 3 EBs at 24hr after ER71/Etv2, GATA2 induction

hyb_protocol: Following fragmentation with NuGen Encore Biotin Module, 2.5 ug of cDNA were hybridized on Exon 1.0 ST Array in the GeneChip Hybridization Oven 640 for 18 hr at 45C. GeneChip were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
Data were processed using Affymetrix Expression Console software. Gene level expression were summarized from the intensities and then normalized using the Robust Multiarray Analysis (RMA) algorithm.
probe_group_file:  MoGene-1_1-st-v1.r4.pgf
meta-probeset file:  MoGene-1_1-st-v1.r4.mps

source_name: Doxycycline treated iB1, ES cell

label_protocol: Biotinylated cDNA were prepared according to the standard NuGen WT-Ovation Pico RNA Amplification system from 500pg-50 ng total RNA.

growth_protocol: Mouse ES cells were maintained on PMEF cells in DMEM with 15% pre-selected fetal calf serum (FCS), 2% LIF, 1% L-glutamine, 1% NEAA and 4.5x 10–4 M MTG. ES cells were differentiated  in IMDM containing 15% differentiation-screened FCS, 1% L-glutamine, 50  g/ml ascorbic acidand 4.5x 10–4 M MTG.

extract_protocol: Total RNA were extracted and purified by RNeasy Mini Kit (Qiagen.)  cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

treatment_protocol: Doxycycline (1µg/ml) was added in iEGS+DOX group from day 2 to 3.

value: embryonic stem cell

value: ER71/Etv2, GATA2 and Scl co-expression

tag: timepoint

value: +DOX

tag: replicate


title: DGM-10423_M0_sm


title: DGM-10368_M0_sm


title: RNA from KIT-D816V transgenics (labeled Cy3) hybridized together with wild-type RNA (labeled Cy5) - replicate 2

tag: genotype


title: DGM-10395_M0_sm


title: Donor N, time 3 h

description: Gene expression data from Donor N, time 3h

source_name: primary human monocytes stimulated with CCL2 for 2 h plus LPS for 1 h


title: DGM-10257_M0_sm


title: Donor M, time 3 h

description: Gene expression data from Donor M, time 3h


title: Donor O, time 3 h

description: Gene expression data from Donor O, time 3h


title: WT control replicate 1 vs. MN control replicate 1

description:
A1
Wild-type with control treatment (replicate 1) versus myostatin null with control treatment (replicate 1).


title: Control EBs on day 3 C

description: Control EBs on day 3

source_name: No doxycycline treated iB1, ES cell

value: -DOX


title: Donor O, time 2 h

description: Gene expression data from Donor O, time 2h

source_name: primary human monocytes stimulated with CCL2 for 2 h

value: monocytes stimulated with CCL2


title: DGM-10322_M0_sm

value: nonsmoker


title: Day 3 EBs at 24hr after ER71/Etv2, GATA2 and Scl induction B

source_name: Doxycycline treated iEGS, ES cell


title: Day 2.5 EBs at 12hr after ER71/Etv2, GATA2 and Scl induction C

description: Day 2.5 EBs at 12hr after ER71/Etv2, GATA2 induction


title: Donor M, time 2 h

description: Gene expression data from Donor M, time 2h


title: Day 2.5 EBs at 12hr after ER71/Etv2, GATA2 and Scl induction B


title: Donor O, time 2.5 h

description: Gene expression data from Donor O, time 2.5h

source_name: primary human monocytes stimulated with CCL2 for 2 h plus LPS for 0.5 hr

value: early inflammatory monocytes


title: DGM-10374_M0_sm

source_name: small airway epithelium brushing


title: DGM-10358_M0_sm


title: DGM-10201_M0_sm


title: Control EBs on day 2.5 B

description: Control EBs on day 2.5

source_name: No doxycycline treated iEGS, ES cell

value: wild-type


title: Control EBs on day 3 B

description: Control EBs on day 3


title: DGM-10351_M0_sm


title: RNA from KIT-D816V transgenics (labeled Cy5) hybridized together with wild-type RNA (labeled Cy3) - replicate 3

tag: Stage

value: AB


title: DGM-10418_M0_sm


title: Day 3 EBs at 24hr after ER71/Etv2, GATA2 and Scl induction A


title: Donor N, time 2.5 h

description: Gene expression data from Donor N, time 2.5h

source_name: primary human monocytes stimulated with CCL2 for 2 h plus LPS for 0.5 h


title: Control EBs on day 2.5 C

description: Control EBs on day 2.5


title: Day 2.5 EBs at 12hr after ER71/Etv2, GATA2 and Scl induction A


title: Control EBs on day 3 A

description: Control EBs on day 3


title: DGM-10369_M0_sm


title: DGM-10383_M0_sm


title: Donor N, time 2 h

description: Gene expression data from Donor N, time 2h


title: DGM-10284_M0_sm


title: Donor M, time 2.5 h

description: Gene expression data from Donor M, time 2.5h


title: Donor O, time 0

description: Gene expression data from Donor O, time 0

source_name: primary human monocytes, fresh monocytes

value: control cells

value: untreated


title: Donor N, time 0

description: Gene expression data from Donor N, time 0


title: Donor M, time 0

description: Gene expression data from Donor M, time 0


title: Donor F, time 0

description: Gene expression data from Donor F, time 0


title: Donor E, time 0

description: Gene expression data from Donor E, time 0


title: DGM-10316_M0_sm


title: DGM-10282_M0_sm


title: 252665513004-4

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

hyb_protocol: Agilent : 1650.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction data processing. Between-array normalization using the quantile normalization  in R, using the limma package

source_name: cutaneous Squamous Cell carcinoma

label_protocol: Agilent - Low RNA input QuickAmp

extract_protocol: Chomzynski

value: cutaneous Squamous Cell carcinoma

tag: transfection

tag: amount in (µg)

tag: strain

value: FVB/N

tag: rin number


title: Donor H, time 0

description: Gene expression data from Donor H, time 0


title: Donor L, time 0

description: Gene expression data from Donor L, time 0


title: Control EBs on day 2.5 A

description: Control EBs on day 2.5

tag: treatment


title: Control differentiated ES cells(EBs) on day 2.25 A


title: DGM-10226_M0_sm


title: Day 2.25 EBs at 6hr after ER71/Etv2, GATA2 and Scl induction A

description: Day 2.25 EBs at 6hr after ER71/Etv2, GATA2 induction


title: DGM-10225_M0_sm


title: 252665513004-2

tag: cell line


title: ST3 #99

description:
ST3 #99
@52055800697862121408403718160338

hyb_protocol: Affy-169 : 300.0 ng at 45 degree_C during 17 hours

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Affyemtrix expression console data processing

extract_protocol: Trizol

value: stage 3 invasive lymphoma tumor

tag: rna amount (ug)

value: T cell specific PTEN KO

tag: disease state

value: T cell lymphoma

tag: genetic background

value: mixed with FVB and C57BL6


title: 252665513004-3

tag: tissue


title: DGM-10261_M0_sm


title: DGM-10163_M0_sm

value: smoker


title: wt #106

description:
wt #106
@52055800697862121408403718160396

tag: cell type

value: thymocyte

value: wt


title: 252665513004-1


title: Donor G, time 0

description: Gene expression data from Donor G, time 0

tag: group


title: ST3 #84

description:
ST3 #84
@52055800672957082808403512663240


title: ST3 #116

description:
ST3 #116
@52055800672957082808403512663134


title: wt #103

description:
wt #103
@52055800672957082808403512663131


title: 252665510703-4


title: Donor D, time 0

description: Gene expression data from Donor D, time 0


title: 252665510704-3

description: mir-NC


title: DGM-10217_M0_sm

tag: smoking status

tag: cilia length


title: 252665510705-2


title: DGM-10180_M0_sm


title: 252665510703-1

description: mir-NC


title: wt #92

description:
wt #92
@52055800697862121408403718160372


title: Donor A, time 0

description: Gene expression data from Donor A, time 0


title: Donor B, time 0

description: Gene expression data from Donor B, time 0


title: OSCC from Sri Lankan patients, KC25

status: Public on Feb 02 2014

city: edinburgh

first: anas

middle: amjad

last: saeed

address: Lauriston building

department: oral surgery

institute: edinburgh dental institute

description: Oral Squamous Cell Carcinoma:  This study aims is to compare specific transcriptomic signatures between UK and Sri Lankan population that are associated with Oral Squamous Cell Carcinoma.

hyb_protocol: 16 hours hybridization / Streptavidin- phycoerythrin Biotinylated anti- Streptavidin antibody, 1.5 hour washing/ staining

scan_protocol: GeneChip Scanner 3000

data_processing: Simpleaffy package from bioconductor in R for data reading. RMA package from bioconductor in R for data normalisation. Siggenes package from bioconductor in R was used to get gene expression values from the normalised data.

source_name: Oral tissue/ Oral cavity

label_protocol: 1mg of amplified RNA labelled and processed through to hybridisation on the Affymetrix arrays. IVT labelling kit for biotin labelling of anti-sense cRNA , 4 hours overnight (Biotinylated Ribonucleotide Analog), 30 minutes Clean-up of Biotinylated cRNA followed by 1 hour fragmentation

extract_protocol: RNA was extracted using the RNeasy ® (Qiagen) method and was labelled and hybridised to Affymetrix GeneChips using the manufacturer’s instructions, 30 minutes clean-up of double stranded cDNA

tag: gender

value: M

tag: age


title: OSCC from Sri Lankan patients, KC26

value: F


title: OSCC from Sri Lankan patients, KC51


title: OSCC from Sri Lankan patients, KC39


title: OSCC from Sri Lankan patients, KC29


title: OSCC from Sri Lankan patients, KC32


title: OSCC from Sri Lankan patients, KC45


title: OSCC from Sri Lankan patients, KC31


title: OSCC from Sri Lankan patients, KC017


title: OSCC from Sri Lankan patients, KC46


title: OSCC from Sri Lankan patients, KC47


title: OSCC from Sri Lankan patients, KC44


title: ST3 #130

description:
ST3 #130
@52055800697862121408403718160412

tag: genotype


title: OSCC from Sri Lankan patients, KC013


title: OSCC from Sri Lankan patients, KC04


title: OSCC from Sri Lankan patients, KC21


title: OSCC from Sri Lankan patients, KC41


title: OSCC from Sri Lankan patients, KC24


title: OSCC from Sri Lankan patients, KC09


title: OSCC from Sri Lankan patients, KC53


title: OSCC from Sri Lankan patients, KC38


title: OSCC from Sri Lankan patients, KC07


title: Donor C, time 0

description: Gene expression data from Donor C, time 0


title: OSCC from Sri Lankan patients, KC015


title: OSCC from Sri Lankan patients, KC016


title: OSCC from Sri Lankan patients, KC20


title: OSCC from Sri Lankan patients, KC02


title: immunoscreening K. pneumoniae 1

type: protein

city: Potsdam

first: Sebastian

last: Hoppe

address: Am Mühlenberg 13

department: Bioanalytics and Biosensorics

description:
slide1023
HaloTag-fusion proteins derived from Klebsiella pneumoniae cDNA and expressed in Acella E.coli overexpression strains.

hyb_protocol: Fusion proteins were spotted and coupled to the microarray surface for one hour at room temperature with 70% humidity. Slides were washed three times with PBSI (PBS + 0.01% Igepal). Incubation with primary antibody (rabbit polyclonal to K. pneumoniae) and secondary antibody (goat polyclonal to rabbit, Chromeo-546 conjugated) were performed for 1.5 h each, with washing (three times) with PBSI after each incubation step. Slides were dried with nitrogen and scanned afterwards.

scan_protocol: Fluorescent array images were collected for Cy3 with a Genepix 4200A fluorescent scanner. Image intensity data were extracted and analyzed using Origin Pro 8G.

data_processing: From the raw data the corrected median fluorescent intensities (F532 median - B532) were used. Then, relative fluorescence intensities were calculated by subtraction the fluorescent intensities of the top compartment by the ones from the bottom compartment. This acknowledges the presence of unspecific interaction of the secondary antibody to the samples. If these values were negative, they were set to zero prior to contrast calculation, otherwise the contrast formula will not work properly. Next, the contrast method was applied by calculating the contrast for each spot of the top compartment. C = [rfi(sample) - median rfi(negative reference)]/[rfi(sample) + median rfi(negative reference)].

molecule: protein

organism: Klebsiella pneumoniae

source_name: crude lysate Acella E.coli + recombinantly expressed proteins

extract_protocol: Fusion proteins were extracted from cultures using EasyLyse Bacterial protein extraction kit (Epicentre)

tag: molecule type

value: recombinant protein (cDNA library)


title: immunoscreening K. pneumoniae 2 rep 2

description:
slide415810
HaloTag-fusion proteins derived from Klebsiella pneumoniae cDNA and expressed in Acella E.coli overexpression strains.


title: immunoscreening K. pneumoniae 2 rep 3

description:
slide415811
HaloTag-fusion proteins derived from Klebsiella pneumoniae cDNA and expressed in Acella E.coli overexpression strains.


title: immunoscreening K. pneumoniae 2

description:
slide1276
HaloTag-fusion proteins derived from Klebsiella pneumoniae cDNA and expressed in Acella E.coli overexpression strains.


title: OSCC from UK patients, OCS 029


title: immunoscreening K. pneumoniae 1 rep 2

description:
slide1306
HaloTag-fusion proteins derived from Klebsiella pneumoniae cDNA and expressed in Acella E.coli overexpression strains.


title: OSCC from UK patients, OCS 015


title: OSCC from UK patients, OCS 031


title: OSCC from UK patients, OCS 026


title: OSCC from UK patients, OCS 032


title: OSCC from UK patients, OCS 024


title: OSCC from UK patients, OCS 027


title: OSCC from UK patients, OCS 011


title: OSCC from UK patients, OCS 025


title: OSCC from Sri Lankan patients, KC01


title: OSCC from UK patients, OCS 014


title: OSCC from UK patients, OCS 012


title: OSCC from UK patients, OCS 022


title: OSCC from UK patients, OCS 013


title: OSCC from UK patients, OCS 020


title: OSCC from UK patients, OCS 016


title: OSCC from UK patients, OCS 007


title: KPEpitopset2_spec2_rep4 [S2_8_2]

description:
raw data file: S2_8.txt
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from K. pneumoniae MGH 78595

hyb_protocol: Slides were blocked using SuperBlock (Pierce) for 2 h at room temperature with mild shaking. Incubation with primary antibody (rabbit polyclonal to C.jejuni, E.coli or S.enterica) was performed overnight at 4°C with mild shaking in a humidity chamber. Secondary antibody (goat polyclonal to rabbit, Chromeo-546 conjugated) was incubated for 1.5 h with mild shaking at room temperature in the dark. After each incubation step, the slides were washed three times with PBSI (PBS + 0.05% IGEPAL). Slides were dried with nitrogen and scanned afterwards.

scan_protocol: Fluorescent array images were collected for Cy3 with a Genepix 4200A fluorescent scanner and a PMT gain of 400. Image intensity data were extracted and analyzed using Origin Pro 8G.

data_processing: From the raw data the corrected median fluorescent intensities (F532 median - B532) were used. Then, relative fluorescence intensities were calculated by subtracting the fluorescent intensities of the chamber incubated with secondary antibody from the other chambers. This was done for all the samples except the positive control Rabbit IgG, as the secondary antibody (Goat antibody to Rabbit IgG) is supposed to bind at this site.  This acknowledges the presence of unspecific interaction of the secondary antibody to the samples.

source_name: proteins


title: OSCC from UK patients, OCS 008


title: KPEpitopset2_spec2_rep3 [S2_8_1]

description:
raw data file: S2_8.txt
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from K. pneumoniae MGH 78597


title: 31.KitWsh.OVA.None

city: Stanford

first: Alex

last: Morgan

state: CA

address: 251 Campus Drive, MSOB X-215

department: Biomedical Informatics

institute: Stanford Medical School

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol; Scanner: 3000 7G System with AutoLoader including external handheld barcode reader; Software: GCOS v1.4

data_processing: Array data was processed using GCRMA in Bioconductor.

label_protocol: Affymetrix protocol

growth_protocol: C57BL/6 wild type (WT), IFN-γ-/- and IFN-γR1-/- mice were purchased from Jackson Laboratory. C57BL/6-KitW-sh/W-sh mice were generously provided by Peter Besmer (Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA); these mice were then backcrossed to C57BL/6J for more than 10 generations. FcεRIγ-/- mice on the C57BL/6 background (B6.129P2-Fcεr1gtm1Rav N12) were purchased from Taconic. Age-matched female mice were used for all experiments.

extract_protocol: TRIzol Reagent (Invitrogen)

treatment_protocol: Mice were immunized by 3 i.p. injections of 50 μg OVA (Sigma-Aldrich) in 0.1 ml PBS on days 1, 4 and 7.  Starting on day 12, mice were challenged i.n. with 20 μg OVA in 30 μl PBS weekly for 9 weeks; control mice received i.p. injections and i.n. challenges with PBS on the same schedule.

tag: genotype/variation

value: KitWsh

tag: exposure

value: OVA

tag: engraftment

value: lung

value: female


title: 30.KitWsh.OVA.None

tag: strain


title: 33.KitWsh.OVA.None


title: 34.KitWsh.PBS.None

value: PBS


title: 36.KitWsh.PBS.None


title: OSCC from UK patients, OCS 006


title: 28.KitWsh.PBS.MCigeR

value: KitWsh/FcεRIγ-/-

value: MCigeR


title: OSCC from UK patients, OCS 004


title: OSCC from UK patients, OCS 003


title: KPEpitopset2_spec2_rep2 [S2_7_2]

description:
raw data file: S2_7.txt
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from K. pneumoniae MGH 78596


title: KPEpitopset2_spec2_rep1 [S2_7_1]

description:
raw data file: S2_7.txt
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from K. pneumoniae MGH 78595


title: 22.KitWsh.PBS.MCifngR

value: MCifngR


title: 26.KitWsh.OVA.MCigeR


title: 25.KitWsh.OVA.MCigeR


title: 24.KitWsh.OVA.MCigeR


title: 23.KitWsh.OVA.MCigeR


title: 29.KitWsh.PBS.MCigeR


title: 27.KitWsh.PBS.MCigeR


title: OSCC from Sri Lankan patients, KC019


title: 32.KitWsh.OVA.None


title: 35.KitWsh.PBS.None


title: OSCC from UK patients, OCS 001


title: KPEpitopset2_spec1_rep4 [S2_2_2]

description:
raw data file: S2_2.txt
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from K. pneumoniae MGH 78594


title: KPEpitopset2_spec1_rep2 [S2_1_2]

description:
raw data file: S2_1.txt
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from K. pneumoniae MGH 78592


title: KPEpitopset2_spec1_rep3 [S2_2_1]

description:
raw data file: S2_2.txt
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from K. pneumoniae MGH 78593


title: 19.KitWsh.OVA.MCifngR


title: K. pneumoniae full-length 15

description:
raw data file: 1983.txt
1983 Ch 3
HaloTag-fusion proteins derived from Klebsiella pneumoniae cDNA and expressed in Acella E.coli overexpression strains.

hyb_protocol: Fusion proteins were spotted and coupled to the microarray surface for one hour at room temperature with 70% humidity. Slides were washed three times with PBSI (PBS + 0.01% Igepal). Incubation with primary antibody (rabbit polyclonal to K.pneumoniae) and secondary antibody (goat polyclonal to rabbit, Chromeo-546 conjugated) were performed for 1.5 h each, with washing (three times) with PBSI after each incubation step. Slides were dried with nitrogen and scanned afterwards.

data_processing: From the raw data the corrected median fluorescent intensities (F532 median - B532) were used. Then, relative fluorescence intensities were calculated by subtracting each corresponding compartment by the compartment incubated only with secondary antibody. This acknowledges the presence of unspecific interaction of the secondary antibody to the samples. Next, normalized value was calculated by dividing the rfi of each sample with the median signal of all sample spots within a compartment. Following, a median value was calculated for each set of sample replicates and these median values were used to calculate a Q-value = [median normalized rfi (sample)]/[median normalized rfi(positive control)]for each positive reference used. Additionally, the error was calculate by error propagation according to Gauss. If the Q-value of the positive reference (taking the error into account) was below that of any negative control, the test was discarded.


title: K. pneumoniae full-length 16

description:
raw data file: 1983.txt
1983 Ch 4
HaloTag-fusion proteins derived from Klebsiella pneumoniae cDNA and expressed in Acella E.coli overexpression strains.


title: KPEpitopset2_spec1_rep1 [S2_1_1]

description:
raw data file: S2_1.txt
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from K. pneumoniae MGH 78591


title: KPEpitopset2_rep4 [S2_6_2]

description:
raw data file: S2_6.txt
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from K. pneumoniae MGH 78589


title: K. pneumoniae full-length 14

description:
raw data file: 1983.txt
1983 Ch 2
HaloTag-fusion proteins derived from Klebsiella pneumoniae cDNA and expressed in Acella E.coli overexpression strains.


title: Gene Expression Profile of Moraxella catarrhalis Grown in Pooled Human Sputum (Rep_3A)

city: Dallas

first: Todd

middle: C.

last: Hoopman

state: TX

address: 5323 Harry Hines Blvd.

department: Microbiology

institute: University of Texas Southwestern Medical Center

hyb_protocol: Equivalent amounts of the Cy5- and Cy3-labeled cDNA samples were mixed, lyophilized, and then dissolved in 21 microliters of H2O. After denaturation for 3 minutes at 94 degrees Celsius these samples were kept on ice until they were used for DNA hybridization. The hybridization mixture containing 15 microliters of 4X hybridization buffer (GE Healthcare), 24 microliters of formamide (40% volume/volume), and 21 microliters of the Cy5- and Cy3-labeled cDNA. The mixture was added to a DNA microarray slide and incubated at 50 degrees Celsius overnight (~ 16 hours). After hybridization the slides were washed twice in 6X SSPE containing 0.01% Tween 20 at 50 degrees Celsius for 5 min, twice in 0.8X SSPE containing 0.001% Tween 20 at 50 degrees Celsius for 5 min, and twice in 0.8X SSPE at room temperature.

scan_protocol: The slides were dried by centrifugation at 900 x g in loosely capped 50-ml conical tubes for 3 minutes. Microarray slides were scanned with a GenePix 4100A microarray reader (Molecular Devices, Sunnyvale, CA) and analyzed with GenePix 4.0 software (Molecular Devices).

data_processing: The Acuity 4.0 software package (Molecular Devices) was utilized to analyze the microarray data. Raw data were first normalized using a ratio-based normalization method to equalize the means and medians of the features to 1 and exclude ratios that were less than 0.1 or greater than 10. Features that were flagged by the software as bad, absent, or not found were also excluded from further analysis. Secondly, a Lowess-based normalization was applied to the microarray data prior to final analysis. The RNA isolated from the bacterial cells grown in chemically defined medium was utilized as the baseline gene expression template. To identify those genes that exhibited an altered expression profile upon exposure to pooled human sputum, a threshold of twofold-increased or decreased expression over the baseline was utilized.

organism: Moraxella catarrhalis ATCC 43617

source_name: Moraxella catarrhalis, grown in 20% pooled human sputum

label_protocol: Five micrograms of total RNA from the bacterial cells exposed to 20% pooled human sputum were mixed with 3.0 micrograms of M. catarrhalis genome directed primers and dried in the Speed-Vac. Once lyophilized the sample was reconstituted with 11 microliters of H2O and heated at 70 degrees Celsius for 5 minutes. The mixture was then cooled to room temperature for 10 minutes. cDNA synthesis was then performed with the Ambion Amino Allyl cDNA synthesis kit per the manufacturer's instructions RNA hydrolysis was accomplished with the addition of 15 microliters of sodium hydroxide (0.1M) and the sample was maintained at 70 degrees Celsius for 15 minutes. 15 microliters of hydrochloric acid (0.1M) was then added and the amino allyl-labeled cDNA was purified with a QIAGEN QIAquick gel extraction kit. After purification, Cy5 dye (GE Heathcare) was added and labelling occured per the manufacturers instructions. The CyDye-labeled cDNA sample was purified by using Microcon YM30 columns. A NanoDrop spectrophotometer was used to measure the concentration of the CyDye-labeled cDNA sample.

growth_protocol: Bacterial cells were grown in 20% pooled human sputum in chemically-defined medium.  The cells were grown at 37 degrees Celsius from and OD600 of 0.05 to a final OD600 of 0.9 and then harvested by centrifugation.

extract_protocol: The entire bacterial culture underwent total RNA extraction by utilization of the Ambion Ribopure Bacteria kit as per manufacturer's instructions and then were treated with DNase I from a MessageClean kit as per manufacturer's instructions.

treatment_protocol: Bacterial cells were exposed to 20% pooled human sputum in chemically-defined medium.

tag: growth protocol

source_name: Moraxella catarrhalis, grown in chemically defined medium

label_protocol: Five micrograms of total RNA from the bacterial cells exposed to chemically defined medium were mixed with 3.0 micrograms of M. catarrhalis genome directed primers and dried in the Speed-Vac. Once lyophilized the sample was reconstituted with 11 microliters of H2O and heated at 70 degrees Celsius for 5 minutes. The mixture was then cooled to room temperature for 10 minutes. cDNA synthesis was then performed with the Ambion Amino Allyl cDNA synthesis kit per the manufacturer's instructions RNA hydrolysis was accomplished with the addition of 15 microliters of sodium hydroxide (0.1M) and the sample was maintained at 70 degrees Celsius for 15 minutes. 15 microliters of hydrochloric acid (0.1M) was then added and the amino allyl-labeled cDNA was purified with a QIAGEN QIAquick gel extraction kit. After purification, Cy5 dye (GE Heathcare) was added and labelling occured per the manufacturers instructions. The CyDye-labeled cDNA sample was purified by using Microcon YM30 columns. A NanoDrop spectrophotometer was used to measure the concentration of the CyDye-labeled cDNA sample.

growth_protocol: Bacterial cells were grown in chemically-defined medium.  The cells were grown at 37 degrees Celsius from and OD600 of 0.05 to a final OD600 of 0.9 and then harvested by centrifugation.

treatment_protocol: Bacterial cells were exposed to chemically-defined medium.

value: grown in chemically-defined medium.


title: 20.KitWsh.PBS.MCifngR


title: Gene Expression Profile of Moraxella catarrhalis Grown in Pooled Human Sputum (Rep_1A)

value: grown in 20% pooled human sputum in chemically-defined medium.


title: KPEpitopset2_rep3 [S2_6_1]

description:
raw data file: S2_6.txt
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from K. pneumoniae MGH 78588


title: 17.KitWsh.OVA.MCifngR


title: 21.KitWsh.PBS.MCifngR


title: Gene Expression Profile of Moraxella catarrhalis Grown in Pooled Human Sputum (Rep_2A)


title: H9 ESC passage 61

city: Bethesda

first: Nasir

last: Malik

state: MD

address: 50 South Drive/Room 1146

department: NIAMS

institute: NIH

description: pluripotent stem cells biological replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with the Gene Expression package of Illumina's Genome Studio software

source_name: cultured ES cell line

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

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

value: embryonic stem cell

tag: cell line

tag: passage

value: passage 61


title: 18.KitWsh.OVA.MCifngR


title: H9 neural stem cells passage 8

description: neural stem cells biological replicate 2

source_name: cultured neural stem cell line

value: neural stem cell

value: passage 8


title: Gene Expression Profile of Moraxella catarrhalis Grown in Pooled Human Sputum (Rep_1B)

growth_protocol: Bacterial cells were grown in chemically-defined medium. The cells were grown at 37 degrees Celsius from and OD600 of 0.05 to a final OD600 of 0.9 and then harvested by centrifugation.

growth_protocol: Bacterial cells were grown in 20% pooled human sputum in chemically-defined medium. The cells were grown at 37 degrees Celsius from and OD600 of 0.05 to a final OD600 of 0.9 and then harvested by centrifugation.


title: Sciencell fetal astrocytes passage 2

description: early passage fetal astrocytes biological replicate 2

source_name: cultured fetal astrocyte

value: Fetal astrocyte

value: passage 2


title: K. pneumoniae full-length 13

institute: Fraunhofer Institute for Cell Therapy and Immunology

description:
raw data file: 1983.txt
1983 Ch 1
HaloTag-fusion proteins derived from Klebsiella pneumoniae cDNA and expressed in Acella E.coli overexpression strains.

value: recombinant protein (cDNA library)


title: NCRM5 iPSC passage 21

source_name: cultured iPSC line

value: induced pluripotent stem cell

value: passae 21


title: Gene Expression Profile of Moraxella catarrhalis Grown in Pooled Human Sputum (Rep_2B)


title: Gene Expression Profile of Moraxella catarrhalis Grown in Pooled Human Sputum (Rep_3B)


title: KPEpitopset2_rep2 [S2_5_2]

description:
raw data file: S2_5.txt
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from K. pneumoniae MGH 78587


title: KPEpitopset2_rep1 [S2_5_1]

description:
raw data file: S2_5.txt
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from K. pneumoniae MGH 78586


title: KPEpitopset1_spec_rep4 [5_2]

description:
raw data file: 5.txt
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from K. pneumoniae MGH 78585


title: K. pneumoniae full-length 12

description:
raw data file: 1977.txt
1977 Ch 4
HaloTag-fusion proteins derived from Klebsiella pneumoniae cDNA and expressed in Acella E.coli overexpression strains.


title: KPEpitopset1_spec_rep3 [5_1]

description:
raw data file: 5.txt
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from K. pneumoniae MGH 78584


title: K. pneumoniae full-length 10

description:
raw data file: 1977.txt
1977 Ch 2
HaloTag-fusion proteins derived from Klebsiella pneumoniae cDNA and expressed in Acella E.coli overexpression strains.


title: K. pneumoniae full-length 11

description:
raw data file: 1977.txt
1977 Ch 3
HaloTag-fusion proteins derived from Klebsiella pneumoniae cDNA and expressed in Acella E.coli overexpression strains.


title: immunoscreening K. pneumoniae 4 rep 3

description:
slide415820
HaloTag-fusion proteins derived from Klebsiella pneumoniae cDNA and expressed in Acella E.coli overexpression strains.


title: KPEpitopset1_spec_rep2 [4_2]

description:
raw data file: 4.txt
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from K. pneumoniae MGH 78583


title: K. pneumoniae full-length 9

description:
raw data file: 1977.txt
1977 Ch 1
HaloTag-fusion proteins derived from Klebsiella pneumoniae cDNA and expressed in Acella E.coli overexpression strains.


title: KPEpitopset1_spec_rep1 [4_1]

description:
raw data file: 4.txt
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from K. pneumoniae MGH 78582


title: immunoscreening K. pneumoniae 4 rep 2

description:
slide415819
HaloTag-fusion proteins derived from Klebsiella pneumoniae cDNA and expressed in Acella E.coli overexpression strains.


title: NCRM5 neural stem cells passage 14

description: neural stem cells biological replicate 1

value: passage 14


title: immunoscreening K. pneumoniae 4

description:
slide415816
HaloTag-fusion proteins derived from Klebsiella pneumoniae cDNA and expressed in Acella E.coli overexpression strains.


title: KPEpitopset1_rep4 [3_2]

description:
raw data file: 3.txt
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from K. pneumoniae MGH 78581


title: 14.KitWsh.PBS.MC

value: KitWsh

value: MC

value: lung

value: female


title: 13.KitWsh.PBS.MC

value: PBS


title: K. pneumoniae full-length 8

description:
raw data file: 416325.txt
416325 Ch 4
HaloTag-fusion proteins derived from Klebsiella pneumoniae cDNA and expressed in Acella E.coli overexpression strains.


title: K. pneumoniae full-length 7

description:
raw data file: 416325.txt
416325 Ch 3
HaloTag-fusion proteins derived from Klebsiella pneumoniae cDNA and expressed in Acella E.coli overexpression strains.


title: 12.KitWsh.OVA.MC

value: OVA


title: KPEpitopset1_rep3 [3_1]

description:
raw data file: 3.txt
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from K. pneumoniae MGH 78580


title: K. pneumoniae full-length 6

description:
raw data file: 416325.txt
416325 Ch 2
HaloTag-fusion proteins derived from Klebsiella pneumoniae cDNA and expressed in Acella E.coli overexpression strains.


title: 16.KitWsh.OVA.MCifngR

value: MCifngR


title: 15.KitWsh.PBS.MC


title: KPEpitopset1_rep2 [2_2]

description:
raw data file: 2.txt
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from K. pneumoniae MGH 78579


title: 11.KitWsh.OVA.MC


title: 9.KitWsh.OVA.MC


title: K. pneumoniae full-length 5

description:
raw data file: 416325.txt
416325 Ch 1
HaloTag-fusion proteins derived from Klebsiella pneumoniae cDNA and expressed in Acella E.coli overexpression strains.


title: K. pneumoniae full-length 4

description:
raw data file: 416379.txt
416379 Ch 4
HaloTag-fusion proteins derived from Klebsiella pneumoniae cDNA and expressed in Acella E.coli overexpression strains.


title: KPEpitopset1_rep1 [2_1]

description:
raw data file: 2.txt
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from K. pneumoniae MGH 78578


title: 7.B6.PBS.None

value: wildtype


title: 8.B6.PBS.None


title: 6.B6.PBS.None


title: Normal OSC tissue from Sri Lankan samples, KN3

description: Oral Squamous Cell Carcinoma:  This study aims is to compare specific transcriptomic signatures between UK and Sri Lankan population that are associated with Oral Squamous Cell Carcinoma.

value: M


title: immunoscreening K. pneumoniae 3 rep 3

description:
slide415822
HaloTag-fusion proteins derived from Klebsiella pneumoniae cDNA and expressed in Acella E.coli overexpression strains.


title: K. pneumoniae full-length 2

description:
raw data file: 416379.txt
416379 Ch 2
HaloTag-fusion proteins derived from Klebsiella pneumoniae cDNA and expressed in Acella E.coli overexpression strains.


title: Normal OSC tissue from Sri Lankan samples, KN5


title: Sciencell fetal astrocyte passage 9

description: late passage fetal astrocytes

value: passage 9


title: immunoscreening K. pneumoniae 3

description:
slide415814
HaloTag-fusion proteins derived from Klebsiella pneumoniae cDNA and expressed in Acella E.coli overexpression strains.


title: immunoscreening K. pneumoniae 3 rep 2

description:
slide415821
HaloTag-fusion proteins derived from Klebsiella pneumoniae cDNA and expressed in Acella E.coli overexpression strains.


title: K. pneumoniae full-length 1

description:
raw data file: 416379.txt
416379 Ch 1
HaloTag-fusion proteins derived from Klebsiella pneumoniae cDNA and expressed in Acella E.coli overexpression strains.


title: Normal OSC tissue from UK samples, V5


title: Normal OSC tissue from Sri Lankan samples, KN2

value: F


title: 5.B6.PBS.None


title: 10.KitWsh.OVA.MC


title: 4.B6.OVA.None


title: K. pneumoniae full-length 3

description:
raw data file: 416379.txt
416379 Ch 3
HaloTag-fusion proteins derived from Klebsiella pneumoniae cDNA and expressed in Acella E.coli overexpression strains.


title: 3.B6.OVA.None


title: Normal OSC tissue from UK samples, M4


title: Normal OSC tissue from UK samples, M3


title: Streptomycete_SF_S-1g_16.5d_rep1

status: Public on Feb 01 2014

city: Beijing

first: Huang

last: Bing

state: Chaoyang district

address: NO.1 Beichen West Road

department: State Key Laboratory of Microbial Resources

country: China

institute: Institute of Microbiology, Chinese Academy of Sciences

description: Gene expression at 16.5d in colony cells exposed simulated 1g during spaceflight

hyb_protocol: Cy3-labelled cRNA was fragmented at 60℃ for 30 minutes in a reaction volume of 250 ml following the manufacturers instructions. Hybridization was performed using the Gene Expression Hybridization Kit (Agilent). After fragmentation, cRNA was hybridized at 65℃ for 17 h with a rotation at 10 rpm. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Arrays were scanned using an Agilent Microarray Scanner System (G2565CA) using one color scan setting for 8*15k array slides with a resolution of 5 μm, 100% and 10% PTM respectively and the two data sets were combined automatically.

data_processing: The signal intensities were normalized using the Feature Extraction Software (Agilent). Data was analyzed using Genespring Software 5.0. Genes with all signals present (flag =P) were selected for analysis. Differentially expressed genes were selected with FC≥2.0 by T-test methods.

organism: Streptomyces coelicolor A3(2)

source_name: Streptomycete colonies,spaceflight,simulated gravity,16.5d,replicate 1

label_protocol: 2 μg RNA was reverse-transcribed into cDNA and then transcribed into cRNA. After RNAeasy column purification, 1.65 μg cRNA was labeled with Cy3 NHS ester and purified according to the manufacturer's instructions.

growth_protocol: The spores of Streptomyces coelicolor A3(2) wild type strain were incubated at 23±0.5℃ for 16.5-day in JCM42 agar medium inside the BIOBOX for spaceflight experiments during Shenzhou-8 space mission.

extract_protocol: Total RNA was extracted from colonies of Streptomyces coelicolor A3(2) wild type strain cultured in JCM42 agar medium for 16.5d using liquid nitrogen and Trizol (Invitrogen) according to the manufacturer’s recommendations. The whole process included the pestling, lysis and purification. At last the total RNA was purified using the Qiagen RNeasy Mini Kit (Qiagen).

treatment_protocol: The spores of Streptomyces coelicolor A3(2) incubated in JCM42 agar medium were cultured and exposed to microgravity (μg) and simulated gravity (S-1g) environment during spaceflight with the corresponding static gravity control (1g) on ground.

value: wild type

tag: strain form

value: colonies

tag: culture position

value: spaceflight (simulated 1g-position)

tag: culture temperature

tag: culture time


title: passage 30_H9 HESC_16Pb_acuteexposure

city: Detroit

first: Douglas

last: Ruden

state: Michigan

address: 275 E. Hancock Ave., Room  291.1

department: Department of Obstetrics and Gynecology

institute: Wayne State University

description:
Undifferentiated. Acute exposure to 16 µg/dl of Pb for 24 hours before DNA extraction.
Bisulphite treatment

hyb_protocol: Provided by Illumina™

scan_protocol: Background correction for array and raw beta value calculation done in Illumina Genome Studio™.

data_processing:
The background corrected raw data from Genome Studio™ was extracted in the form of a .txt file which contained complete annotation information, detection p-value, Average beta for all sample. The acute exposure and chronic exposure experiments were normalised seperately. Normalisation for Inf1/Inf2 probe was carried out using quantile normalization and peak based correction (PBC) poposed by Dedeurwaerder et al. 2011 in R (> 2.13.2) using R package Illumina methylation analyser. The normalised data was filtered using the detection p-value cut off of 0.05. All methylation sites located on sex chromosomes and localizing with SNP sites was removed (dbSNP v132). CpG sites/ probes was assigned to cluster based of correlation of beta values and base pair distance from each other using A-clustering (Sofer et al, 2012). Effect of exposure to increase concentrations of lead was carried out using generalised estimating equation model.
SIGNAL A (intensities of unmethylated probe as intergers), SIGNAL B (Intensities of methylated probe as integers)
Average Beta normalized for probe bias using quantile normalization and peak based correction using Illumina methylation analyser in R (>2.13.2)

label: Cy5 and Cy3

source_name: H9 Human embryonic stem cells, passage 30

label_protocol: Provided by Illumina™

growth_protocol: In these experiments, we used the WA09 hESC line (passages 26-34; WiCell Research Institute, Madison, WI, USA) (Thomson et al. 1998) that is NIH-approved and included in the National Stem Cell Registry.  Human ESCs were maintained on a feeder layer of irradiated mouse embryonic fibroblasts (GlobalStem, Rockville, MD, USA) in hESC medium. . Neural induction of hESCs was performed according to previously published protocols (Chang et al. 2010; Zhang et al. 2001). Briefly, hESC colonies were mechanically dissociated, transferred in 100 mm bacterial plates and maintained as aggregates (embryoid bodies, EBs) for 4 days in a medium composed of 50% hESC medium and 50% N2 medium. N2 medium was made of 1% N2 supplement (Life Technologies Corporation, Carlsbad, CA) and 1% penicillin/streptomycin in DMEM/F12.  On culture day 4, EBs were transferred to a new bacterial plate and cultured for an additional four days in N2 medium supplemented with 3 M retinoic acid (Sigma-Aldrich, St Louis, MO).  On day 8, and over the next 3 days, EBs were cultured in N2 medium, containing 20 ng/ml FGF-2 (N2/FGF-2; Peprotech, Rocky Hill, NJ).  EBs were subsequently transferred to 6-well plates coated with 20g/ml fibronectin (Life Technologies Corporation, Carlsbad, CA) and maintained in N2/FGF-2 medium for an additional 8 days.  Cells differentiating as neuroectodermal cells organized into neural-tube-like rosettes, which were then dissociated and plated in N2/FGF-2 medium on 10 g/ml polyornithine/5 g/ml laminin-coated dishes.  For neuronal differentiation, NPCs were passaged at a 5.105 cells/cm2 density in polyornithine/laminin-coated 12-well dishes and cultured in N2 medium supplemented with 10 ng/ml brain-derived neurotrophic factor (BDNF), 10 ng/ml glial cell-derived neurotrophic factor (GDNF), 10 ng/ml insulin-like growth factor (IGF) (all factors from Peprotech, Rocky Hill, NJ), 200 ng/ml ascorbic acid (Sigma-Aldrich, St Louis, MO) and 100 ng/ml cAMP (Sigma-Aldrich, St Louis, MO), according to a previously published protocol (Hu and Zhang 2010).

extract_protocol: DNA was isolated from control, Pb-exposed hESCs, and hESC-derived NPCs with Qiagen DNA kit. The Quantifiler Human DNA Quantification Kit® (Applied Biosystems) was used to determine the amount of amplifiable DNA.

treatment_protocol: The dose-response effects of Pb acetate on the generation of hESC-derived NPCs were determined in three different experimental paradigms. Paradigm A: hESCs were acutely exposed to the different concentrations of Pb or vehicle, 24 hours prior to DNA extraction.  Paradigm B: hESC colonies were mechanically dissociated into 150-200 pieces of homogeneous size that were randomly distributed into six-well plates.  The 24 hour acute exposure started at day 5 of the differentiation process, a day after initiation of neural induction with retinoic acid (day 5).  Cells then underwent the neural differentiation protocol until day 19.  Paradigm C: hESCs were chronically exposed to Pb during the whole neural differentiation procedure up to day 19 (days 0-19).

tag: differentiation state

value: Undifferentiated


title: passage 30_H9 HESC_noPb_acuteexposure

description:
Undifferentiated. Not exposed to Pb.
Bisulphite treatment


title: passage 30_H9 HESC_32Pb_acuteexposure

description:
Undifferentiated. Acute exposure to 32 µg/dl of Pb for 24 hours  before DNA extraction.
Bisulphite treatment


title: passage 30_H9 HESC_8Pb_acuteexposure

description:
Undifferentiated. Acute exposure to 8 µg/dl of Pb for 24 hours  before DNA extraction.
Bisulphite treatment


title: passage 30_H9 HESC_40Pb_acuteexposure

description:
Undifferentiated. Acute exposure to 40 µg/dl of Pb for 24 hours  before DNA extraction.
Bisulphite treatment


title: passage 30_H9 HESC_24Pb_acuteexposure

description:
Undifferentiated. Acute exposure to 24 µg/dl of Pb for 24 hours  before DNA extraction.
Bisulphite treatment


title: Streptomycete_SM vs.1G_144h_rep1

description: Gene expression at 144h in colony cells in the case of SMG vs.1G

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

scan_protocol: Arrays were scanned using an Agilent Microarray Scanner System (G2565BA)

source_name: Streptomycete colonies,simulated microgravity,144h,replicate 1

label_protocol: 2 μg RNA was reverse-transcribed into cDNA and then transcribed into cRNA respectively. After RNAeasy column purification, 4 μg cRNA from samples of the test group was labeled with Cy3, 4 μg cRNA from samples of the control group was labeled with Cy5 and purified according to the manufacturer's instructions.

growth_protocol: The spores of Streptomyces coelicolor A3(2) wild type strain were incubated at 28℃ for 144h in JCM42 agar medium.

extract_protocol: Total RNA was extracted from colonies of Streptomyces coelicolor A3(2) wild type strain cultured in JCM42 agar medium for 144h using liquid nitrogen and Trizol (Invitrogen) according to the manufacturer’s recommendations. The whole process included the pestling, lysis and purification. At last the total RNA was purified using the Qiagen RNeasy Mini Kit (Qiagen).

treatment_protocol: The spores of Streptomyces coelicolor A3(2) incubated in JCM42 agar medium were cultured and exposed to simulated microgravity condition by a rotating clinostat in the test group's samples; The same spores incubated in JCM42 agar medium were cultured and exposed to gravity condition on ground in the control group's samples.

value: under simulated microgravity (by a rotating clinostat)

source_name: Streptomycete colonies,gravity control,144h,replicate 1

value: under gravity control on ground


title: passage 28_H9 HESC_24Pb_acuteexposure

source_name: H9 Human embryonic stem cells, passage 28


title: passage 28_H9 HESC_noPb_acuteexposure


title: passage 28_H9 HESC_16Pb_acuteexposure

description:
Undifferentiated. Acute exposure to 16 µg/dl of Pb for 24 hours  before DNA extraction.
Bisulphite treatment


title: passage 28_H9 HESC_8Pb_acuteexposure

description:
Undifferentiated Acute exposure to 8 µg/dl of Pb for 24 hours  before DNA extraction.
Bisulphite treatment


title: Streptomycete_SM_96h_rep2

description: Gene expression at 96h in colony cells under simulated microgravity

data_processing: The signal intensities were normalized using the Feature Extraction Software (Agilent). Data was analyzed using Genespring Software 5.0. Genes with all signals present (flag =P) were selected for analysis. Differentially expressed genes were selected with P＜0.05, FC≥2.0 by T-test methods.

source_name: Streptomycete colonies,simulated microgravity,96h,replicate 2

label_protocol: 2 μg RNA was reverse-transcribed into cDNA and then transcribed into cRNA. After RNAeasy column purification, 4 μg cRNA was labeled with Cy3 NHS ester and purified according to the manufacturer's instructions.

growth_protocol: The spores of Streptomyces coelicolor A3(2) wild type strain were incubated at 28℃ for 96h in JCM42 agar medium.

extract_protocol: Total RNA was extracted from colonies of Streptomyces coelicolor A3(2) wild type strain cultured in JCM42 agar medium for 96h using liquid nitrogen and Trizol (Invitrogen) according to the manufacturer’s recommendations. The whole process included the pestling, lysis and purification. At last the total RNA was purified using the Qiagen RNeasy Mini Kit (Qiagen).

value: under simulated microgravity (by clinorotation)


title: Streptomycete_SF_μg_16.5d_rep1

description: Gene expression at 16.5d in colony cells exposed μg during spaceflight

value: spaceflight (μg-position)


title: Streptomycete_SM_96h_rep1

source_name: Streptomycete colonies,simulated microgravity,96h,replicate 1


title: Streptomycete_3G_96h_rep3

description: Gene expression at 96h in colony cells under gravity control

source_name: Streptomycete colonies,gravity control,96h,replicate 3


title: passage 34_H9 HESC_40Pb_acuteexposure

description:
Commited to neural lineage. Acute exposure to 40 µg/dl of Pb for 24 hours of day5 of differentiation before DNA extraction.
Bisulphite treatment

source_name: H9 Human embryonic stem cells, passage 34

value: Commited to neural lineage


title: passage 34_H9 HESC_32Pb_acuteexposure

description:
Commited to neural lineage. Acute exposure to 32 µg/dl of Pb for 24 hours of day5 of differentiation before DNA extraction.
Bisulphite treatment


title: Normal OSC tissue from UK samples, M1

description: Oral Squamous Cell Carcinoma:  This study aims is to compare specific transcriptomic signatures between UK and Sri Lankan population that are associated with Oral Squamous Cell Carcinoma.

source_name: Oral tissue/ Oral cavity


title: passage 28_H9 HESC_32Pb_acuteexposure

description:
Undifferentiated. Acute exposure to 32 µg/dl of Pb for 24 hours before DNA extraction.
Bisulphite treatment


title: Normal OSC tissue from UK samples, M2


title: passage 34_H9 HESC_24Pb_acuteexposure

description:
Commited to neural lineage. Acute exposure to 24 µg/dl of Pb for 24 hours of day5 of differentiation before DNA extraction.
Bisulphite treatment


title: passage 34_H9 HESC_16Pb_acuteexposure

description:
Commited to neural lineage. Acute exposure to 16 µg/dl of Pb for 24 hours of day5 of differentiation before DNA extraction.
Bisulphite treatment


title: Streptomycete_SM_96h_rep3

source_name: Streptomycete colonies,simulated microgravity,96h,replicate 3


title: Streptomycete_2G_96h_rep2

source_name: Streptomycete colonies,gravity control,96h,replicate 2


title: 2.B6.OVA.None

tag: tissue

value: lung

value: female


title: passage 34_H9 HESC_noPb_acuteexposure

description:
Commited to neural lineage. Not exposed to Pb.
Bisulphite treatment


title: passage 34_H9 HESC_8Pb_acuteexposure

description:
Commited to neural lineage. Acute exposure to 8 µg/dl of Pb for 24 hours of day5 of differentiation before DNA extraction.
Bisulphite treatment


title: NPCs_passage27_replicate1(biological)_40Pb_chronicexposure

description:
Neural precursor cells (NPCs) obtained from passage 26 H9 stem cells grown in medium containing 40µg/dl of Pb.
Bisulphite treatment

source_name: H9 Human embryonic stem cells, passage 27

value: Neural precursor cells (NPCs)


title: passage 33_H9 HESC_40Pb_acuteexposure

source_name: H9 Human embryonic stem cells, passage 33


title: NPCs_passage27_replicate1(biological)_32Pb_chronicexposure

description:
Neural precursor cells (NPCs) obtained from passage 26 H9 stem cells grown in medium containing 32µg/dl of Pb.
Bisulphite treatment


title: passage 33_H9 HESC_noPb_acuteexposure


title: passage 33_H9 HESC_8Pb_acuteexposure


title: passage 33_H9 HESC_16Pb_acuteexposure


title: passage 33_H9 HESC_24Pb_acuteexposure


title: NPCs_passage27_replicate1(biological)_24Pb_chronicexposure

description:
Neural precursor cells (NPCs) obtained from passage 26 H9 stem cells grown in medium containing 24µg/dl of Pb.
Bisulphite treatment


title: NPCs_passage27_replicate1(biological)_16Pb_chronicexposure

description:
Neural precursor cells (NPCs) obtained from passage 26 H9 stem cells grown in medium containing 16µg/dl of Pb.
Bisulphite treatment


title: NPCs_passage27_replicate1(biological)_8Pb_chronicexposure

description:
Neural precursor cells (NPCs) obtained from passage 26 H9 stem cells grown in medium containing 8µg/dl of Pb.
Bisulphite treatment


title: NPCs_passage27_replicate1(biological)_noPb_chronicexposure

description:
Neural precursor cells (NPCs) obtained from passage 26 H9 stem cells grown in normal medium (without Pb)
Bisulphite treatment


title: Lonza fetal astrocyte passage 1

description: early passage fetal astrocytes biological replicate 1

tag: cell type

value: Fetal astrocyte

value: passage 1


title: NPCs_passage27_replicate2(biological)_16Pb_chronicexposure


title: NPCs_passage27_replicate2(biological)_8Pb_chronicexposure


title: NPCs_passage27_replicate2(biological)_40Pb_chronicexposure


title: NPCs_passage27_replicate2(biological)_32Pb_chronicexposure


title: NPCs_passage27_replicate2(biological)_noPb_chronicexposure


title: NPCs_passage26_32Pb_chronicexposure

source_name: H9 Human embryonic stem cells, passage 26


title: NPCs_passage27_replicate2(biological)_24Pb_chronicexposure


title: passage 33_H9 HESC_32Pb_acuteexposure


title: NPCs_passage26_40Pb_chronicexposure


title: NPCs_passage26_16Pb_chronicexposure


title: NPCs_passage26_8Pb_chronicexposure


title: NPCs_passage26_noPb_chronicexposure


title: 1.B6.OVA.None

value: wildtype

value: OVA

tag: gender