title: T3_HDF-1, biological rep1

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

description: The mRNA profiles from T3/CMHDF, T3/CMMEF, T3/HDF and T3/MEF were quantitatively determined.

hyb_protocol: Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hr at 45oC on Affymetrix Human Genome U133 plus 2.0 GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips from the hybridization experiments were read by the Affymetrix GeneChip scanner 3000.

data_processing: The data were processed by GeneSpring software version 7.3 GC-RMA preprocessor to use on the CEL files

source_name: hES-T3 cells grown on T3HDF feeder

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms purified cRNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: The differentiated fibroblast-like T3HDF cells (passage 8) were inactivated using mitomycin C (10 ug/ml) and used as autogeneic feeder layer in hES medium to maintain the continuously undifferentiated growth of hES-T3 cells (36 passages on MEF) for additional 14 passages. These hES-T3 cells grown on T3HDF feeder were designated as T3/HDF.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNAs extracted using TRIZOL reagent were quantified spectrophotometrically. The cDNA synthesis was carried out by using SUPERSCRIPTTM one-step RT-PCR kit (Invitrogen). For the reverse transcription step, the whole 5 ul of the resuspended RNAs were incubated for 60 min at 42oC, then 15 min at 72oC in 50 ul of reaction mixture containing 25 ul of 2x Reaction Mix (Invitrogen) and 1 ul of RT/PLANTINUM Taq Mix (Invitrogen). 28.5 ul of the cDNAs present in the 50 ul RT reaction mixture purified by Microarray Target Purification Kit (Roche Applied Science, Indianapolis, ID, USA, http://www.roche-applies-science.com) were used as templates to amplify cDNA by Microarray Target Amplification Kit. The amplified cDNAs were purified by Microarray Target Purification Kit, and complementary RNAs (cRNAs) were synthesized from 200 ng cDNA with Microarray RNA Target Synthesis Kit (Roche Applied Science).

treatment_protocol: No

tag: growth conditions

value: grown on T3HDF feeder


title: T3_MEF-2, biological rep2

status: Public on Jan 12 2011

type: RNA

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: hES-T3 cells grown on MEF feeder

growth_protocol: Human embryonic stem cell line hES-T3, which is one of the five hES cell lines derived in our laboratory, exhibits normal female karyotype (46, XX), and it has been continuously cultured on mitomycin C (10 ug/ml) mitotically inactivated MEF feeder in hES medium under 5% CO2 at 37oC and underwent freezing/thawing processes. The hES culture medium consisted of DMEM/F12 (1:1, GIBCO) supplemented with 20% KSR (Invitrogen), 1% non-essential amino acids, 1 mM L-glutamine, 0.1 mM £]-mercaptoethanol, and 4 ng/ml human basic fibroblast growth factor (bFGF; Life Technologies). Routine passages of hES-T3 cells every 5-7 days were done with collagenase (type IV, 1 mg/ml, Invitrogen) treatment and mechanical scrape. The cryopreserved stock of hES-T3 cells (36 passages) were continuously maintained on MEF feeder for additional 14 passages, and these the hES-T3 cells were designated as T3/MEF.

value: grown on MEF feeder

tag: gender

value: female

tag: cell line


title: liver-CCL4-4weeks-rep1

city: Tokyo

first: Nobuyoshi

last: Kosaka

address: 5-1-1, Tsukiji, Chuo-ku

department: Section for Studies on Metastasis

country: Japan

institute: National Cancer Center Research Institute

description: miRNA expression after 4 weeks in CCL4-administrated mouse liver

hyb_protocol: miRNA microarrays were manufactured by Agilent Technologies, and 100 ng of total RNA was labeled and hybridized using Mouse microRNA Microarray Kit according to manufacture’s protocol (Protocol for use with Agilent microRNA microarrays Version 1.0)

scan_protocol: Scanned on an Agilent G2505B scanner

data_processing: Data were analyzed using GeneSpring GX 7.3.1 software (Agilent Technologies) and normalized as follows: (i) Values below 0.01 were set to 0.01. (ii) Each measurement was divided by the 75th percentile of all measurements to compare one-color expression profiles.

organism: Mus musculus

source_name: Liver, 4 weeks, CCL4, replicate 1

extract_protocol: Total RNA extracted using mirVana miRNA isolation kit following manufacturer's instructions

treatment_protocol: CCL4 or olive oil was administrated intraperitoneally in mouse twice a week for 4 weeks and then administrated once a week for four weeks. Mice were sacrificed on 4, 6, and 8 weeks.

tag: tissue

value: Liver

tag: time

value: 4 weeks

tag: administrated reagent

tag: disease state

value: fibrosis


title: T3_HDF-2, biological rep2


title: T3_MEF-1, biological rep1


title: fully ripe (S4) vs immature (S1) fruit of peach

city: Legnaro

first: claudio

last: Bonghi

state: Padova

address: Viale dell'UNiversità, 16

country: Italy

institute: University of Padova

description: Analysis used to compare transcripts level in fully ripe fruit and immature-green fruit.

hyb_protocol: Pre-hybridisations were carried out by soaking whole glass slides in a solution containing 5X SSC, 0.1% SDS, 5X Denhardt’s solution and 100ng/μL DNA carrier at 48°C for at least 2 h. Then the slides were washed once with a 0.2X SSC solution and dried by centrifuging for 4 min at 1000 rpm. Hybridisations were carried out in 250 µL of hybridisation solution (5X SSC, 0.1% SDS, 25% formamide) containing 100-150 pmol of Cy3- and Cy5-labelled target cDNAs.  The glass slides were placed in a hybridisation chamber (Corning, USA) kept on a water bath at 48°C  at least 36 h. Then the slides were briefly rinsed with 1X SSC 0.1% SDS and washed once the same solution for 5 min. Three additional washes (one with 0.2XSSC 0.1% SDS and two with 0.2X SSC, for 5 min each) at room temperature were performed before drying the glass slides with a brief centrifugation. The probe design and these hybridisation/washing conditions allow the detection of specific genes even within gene families.

scan_protocol: The microarray was scanned with a two channel confocal microarray scanner (ScanArray® Lite, Perkin Elmer, USA) using its dedicated software (ScanArray Express 3.0.0., Perkin Elmer). The laser power and the photomultiplier tube (PMT) were set between 75 and 85 % of maximum. The excitation/emission settings were 543/570 nm for Cy3 and 633/670 nm for Cy5. After laser focusing and balancing of the two channels, scans were conducted at a resolution of 5 μm. For any scan, two separate 16-bit TIFF images were produced.

data_processing:
Software from the TM4 (www.tm4.org) package developed at TIGR (www.tigr.org, Saeed et al., 2003) was used to analyze microarray data.  Images were processed using the Spotfinder 2.2.3. software by means of the Otsu algorithm. Spots were also visually examined to delete the non-uniform ones.  The expression data extracted by Spotfinder were normalized by MIDAS 2.18 using the LOWESS (Locally Weighted Regression Scatter Plot Smoothing, Cleveland, 1979) algorithm with the “block mode”, keeping as reference the Cy3 channel. The “IA” and “IB” values have been used to determine log2(IB/IA) reported in the “VALUE” column.  Normalized split data were loaded in MeV 4.3 and subjected to SAM (Significance Analysis of Microarrays, Tusher et al., 2001) analyses. Since each comparison was repeated at least twice, and a “percentage cutoff filter”, set to 75%, was used to eliminate those gene with less than 3 data points, there were at least 3 values for each gene to be used in the SAM analysis. Lists of clones with significant changes in expression were identified at delta values that gave a false discovery rate (FDR) of about 5%.

Please see 'readme.txt' file on the Series record for the sample labeling scheme for each supplementary file.

organism: Prunus persica

source_name: immature fruit (S1)

label_protocol: Total RNA (20 μg) was converted into target cDNA by reverse transcription using the SuperScriptTM Indirect cDNA Labeling System (Invitrogen, USA) following manufacturer instruction. The amino-modified cDNA was coupled to a monoreactive N-hydroxysuccinimide (NHS)-ester fluorescent dyes: the red-fluorescent cyanine5 (Cy5) and the green-fluorescent cyanine3 (Cy3) (GE Healthcare, USA). A final purification step using Microcon-PCR centrifugal filter devices (Millipore, USA) removed any unincorporated dye. The purity and yield of the labelled cDNA was calculated from the OD values obtained by means of a spectrophotometer using the formulas reported in the SuperScriptTM Indirect cDNA Labeling System instruction manual.

growth_protocol: Fruit from apricot cv ‘Goldrich’ and peach cv 'Fantasia’ was used in the current study. By comparing the position of anchor markers in maps constructed with different Prunus species, it has been demonstrated that the genomes of the diploid Prunus species (including peach and apricot) are essentially collinear thus, at the genome level, the Prunus genus can be treated as a single genetic entity thus the platform developed for massive analysis of peach fruit transcriptome can be extended to apricot.

extract_protocol: Frozen fruit (3 g) was ground in liquid nitrogen to a fine powder and total RNA was extracted as described by Bonghi and co-workers (1998, Planta. 102:346-352). Fifty μg of total RNA were treated with 10 units of RQ1 RNase-Free DNAse (Promega) and 1 unit of RNAguard (RNase INHIBITOR) (Amersham) for 30 min, and then purified by phenol-chlorophorm according to the manufacturer’s instructions. The concentration of RNA was quantified by measuring the absorbance at 260 nm and its integrity was checked electrophoretically on agarose gels.

treatment_protocol: Apricot fruit were harvested 45, 80 and 87 days after full bloom. These harvest days corresponds to immature-green stage (6 weeks before fully-ripe stage), mature-firm-ripe stage (change of peel color, 1 week before fully-ripe stage and onset of climacteric phase) and at fully-ripe stage (full climacteric phase) and designated as S1, S2 and S3 stages,respectively. Samples of 30 fruits were collected from each developmental stage and evaluated for color parameters (L, a*, b* values) using a Minolta colorimeter (model CM2500d), tissue firmness using an Effegi penetrometer, employed with an 8 mm probe and ethylene evolution as described by Tonutti et al., 1997 (J Am Soc Hort Sci 122:642–647). Fruit from each developmental stage were divided into three sub-lots (10 fruit for each) and mesocarp tissue from each sub-lot was removed, immediately frozen in liquid nitrogen and subsequently maintained at -80°C until needed.   Peach fruits (cv Fantasia) were harvested at distinct developmental stages, designated as S1, S2, S3, S4, as described by Trainotti  et al., 2007 (J Exp Bot 58:3299-3308) and stored at -80°C for subsequent molecular analysis.

tag: cultivar

value: Fantasia

tag: developmental stage

value: immature fruit (S1)

source_name: fully ripe fruit (S3)

value: fully ripe fruit (S4)


title: liver-CCL4-6weeks-rep1

description: miRNA expression after 6 weeks in CCL4-administrated mouse liver

source_name: Liver, 6 weeks, CCL4, replicate 1

label_protocol: miRNA microarrays were manufactured by Agilent Technologies, and 100 ng of total RNA was labeled and hybridized using Mouse microRNA Microarray Kit according to manufacture’s protocol (Protocol for use with Agilent microRNA microarrays Version 1.0)

value: 6 weeks


title: CD34+CD200+CD49+Replicate4

city: Baltimore

first: Luis

middle: Andres

last: Garza

state: MD

address: 1550 Orleans St. Suite 204 CRBII Koch

department: Dermatology

country: USA

institute: Johns Hopkins School of Medicine

description: Gene expression data from FACS sorted mouse adult keratinocytes using cell surface markers

hyb_protocol: The cRNA products were fragmented to 200 nucleotides or less, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to U133A Affymetrix microarray for human and 430 v2 for mouse. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.

data_processing:
Affymetrix GeneChip Operating System (GCOS, v. 1.4, Affymetrix, Inc.) was used to quantitate expression signal levels for the arrays; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. These values were exported as .cel files. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Probe pairs were scored positive or negative for detection of the targeted sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau = 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call. The flag values were additionally exported in .chp files.
Affymetrix probe intensities were imported into GeneSpring (v7.2, Agilent Technologies) where probeset signal values were calculated using the GC-RMA algorithm. Upon import of the Affymetrix flag values, the probesets were filtered to retain only those that were flagged P (present) in at least two of the repeat samples. This list was used for condition-based principle components analysis (PCA) to assess global trends in sample similarity. This analysis demonstrated groupings based on sample identity and prompted the use of mixed-model 2-way ANOVA as a means of finding differentially regulated genes between the sites of interest.
GC-RMA signal data was imported into Partek Genomics Solution (PGS, v6.2, Partek, Inc.), where the data were log2 transformed. Probesets not shared between mouse and human chips were removed.  Genes less than p<0.05 in p-values for the identity of sample term of the ANOVA, and less than 2 fold changes between positive and negative populations were also excluded. The resulting enriched gene lists for bulge, secondary hair germ, and CD200highITGA6high cells were then examined for intersection using Partek.

label_protocol: Briefly, 5ug of total RNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.

growth_protocol: Cells were not expanded but isolated enzymatically from mouse skin

extract_protocol: RNAeasy Qiagen protocol

treatment_protocol: Cells were not treated

value: Back Skin

tag: sex

tag: age

value: 50 days

tag: hair stage

value: telogen


title: CD34-CD200-CD49+Replicate1


title: T3_CMMEF-2, biological rep2

source_name: hES-T3 cells grown on feeder-free Matrigel in MEF-conditioned medium

growth_protocol: The MEF cells were cultured in MEF medium overnight, and the mitotically inactivated MEF cells were maintained in hES medium containing 4 ng/ml bFGF. After 24 h, the MEF-conditioned medium was collected and filtered through 0.2 um membrane (PN4612, Pall Life Sciences) . The culture dish was coated with Matrigel diluted with DMEM/F12 (1:30) overnight at 4oC. The cryopreserved stock of hES-T3 cells (36 passages) were continuously maintained on feeder-free Matrigel-coated dish in MEF-conditioned medium (with additional 4 ng/ml bFGF) for 12 passages, and these hES-T3 cells were designated as T3/CMMEF.


title: CD34-CD200+CD49+Replicate1


title: CD34+CD200+CD49+Replicate2


title: fully ripe (S3) vs immature (S1) fruit of apricot

organism: Prunus armeniaca

value: Goldrich

value: fully ripe fruit (S3)


title: CD34+CD200+CD49+Replicate3


title: T3_CMHDF-2, biological rep2

source_name: hES-T3 cells grown on feeder-free Matrigel in T3HDF-conditioned medium

growth_protocol: The T3HDF cells were cultured in DMEM medium overnight, and the mitotically inactivated T3HDF were maintained in hES medium containing 4 ng/ml bFGF. After 24 h, the T3HDF-conditioned medium was collected and filtered through 0.2 um membrane. The culture dish was coated with Matrigel diluted with DMEM/F12 (1:30) overnight at 4oC. The hES-T3 cells (36 passages on MEF feeder) were first grown on T3HDF feeder for 4 passages and then on Matrigel in T3HDF-conditioned medium for additional 4 passages. The hES-T3 cells grown on feeder-free Matrigel-coated dish in T3HDF-conditioned medium (with additional 4 ng/ml bFGF) were designated as T3/CMHDF


title: CD34-CD200+CD49+Replicate2


title: JH39 Xenograft

status: Public on Jan 11 2011

type: genomic

city: San Francisco

first: Alan

middle: Hunter

last: Shain

state: CA

address: 555 MISSION BAY SOUTH BLVD RM 282 # 3118

department: Pathology and Dermatology

institute: University of California San Francisco

hyb_protocol: Hyb was carried out according to all array manufacturers factory protocols.

scan_protocol: Agilent G2505C Microarray Scanner

data_processing: Agilent Feature Extraction Software

molecule: genomic DNA

source_name: JH39 Xenograft

label_protocol: 3 ug of Total Genomic DNA was subject to DpnII digestion and random primer labeled directly incorporating appropriately conjugated cy dyes.

extract_protocol: DNA was extracted using Qiagen Allprep kit

tag: sample type

value: JH39 Xenograft

source_name: Normal Pooled DNA

value: Pooled normal Genomic DNA


title: CD34+CD200+CD49+Replicate1


title: 472 Xenograft

source_name: 472 Xenograft

value: 472 Xenograft


title: apx1 plants-1h vs 0h HL-Rep2

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: Biological replicate 2 of 2. apx1 plants subjected to high light, harvested after 0h and 1h.

hyb_protocol: A mixture of purified and labeled cRNA was hybridised on Agilent arrays followed by (manual) washing, according to the manufacturer’s procedures.

scan_protocol: Arrays were scanned using the Agilent DNA MicroArray Scanner. Images were quantified using Agilent Feature Extraction Software (version 8.1.1.1).

data_processing: Features were extracted with spatial detrending and dye normalization (Linear Lowess) using the Agilent Feature Extraction Software (version 8.1.1.1).

organism: Arabidopsis thaliana

source_name: apx1, 0h HL

label_protocol: Per sample, an amount of 1 µg of total RNA was converted to double-stranded cDNA in a reverse transcription reaction. Subsequently, the sample was converted to antisense cRNA, amplified and labeled with Cyanine 3-CTP (Cy3) or Cyanine 5-CTP (Cy5) in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).

growth_protocol: Arabidopsis thaliana plants were grown on Jiffy-7 soil pellets (Jiffy Products, Norway) in a controlled growth chamber (Weiss technik) at 21-22 °C, 16 h/8 h light regime at 100 μmol.m-2 s-1 photoperiod and 70% relative humidity.

extract_protocol: From two independent experiments, RNA was isolated from middle-aged leaves of 25 wild type (WT), apx1, cat2, and apx1/cat2 plants using TRIzol Reagent (Invitrogen, Carlsbad, CA). Concentration and quality of the RNA was determined with a Nanodrop ND 1000 spectrophotometer and quality was examined using the RNA 6000 Nano Assay (Agilent Technologies 2100 Bioanalyzer).

treatment_protocol: 3- to 4-week-old plants (at the same developmental stage of 1.09-1.10, Boyes et al., 2001) were exposed to a continuous high light irradiation (1000 μmol.m-2.s-1) in a SANYO growth cabinet for 0 or 1 hour.

tag: genotype

tag: treatment

value: 0 hour

tag: plant age

value: 25 days

source_name: apx1, 1h HL

value: high light irradiation

value: 1 hour


title: T3_CMHDF-1, biological rep1

value: grown on feeder-free Matrigel in T3HDF-conditioned medium

value: female


title: T3_CMMEF-1, biological rep1

value: grown on feeder-free Matrigel in MEF-conditioned medium


title: Aspc1 Cell Line

source_name: Aspc1 Cell Line


title: cat2 plants-1h vs 0h HL-Rep2

description: Biological replicate 2 of 2. cat2 plants subjected to high light, harvested after 0h and 1h.

source_name: cat2, 0h HL

value: 27.5 days

source_name: cat2, 1h HL


title: apx1/cat2 plants-1h vs 0h HL-Rep2

description: Biological replicate 2 of 2. apx1/cat2 plants subjected to high light, harvested after 0h and 1h.

source_name: apx1/cat2, 0h HL

value: 32 days

source_name: apx1/cat2, 1h HL


title: JH21 Xenograft

source_name: JH21 Xenograft

value: JH21 Xenograft


title: apx1 plants-1h vs 0h HL-Rep1

description: Biological replicate 1 of 2. apx1 plants subjected to high light, harvested after 0h and 1h.


title: apx1/cat2 plants-1h vs 0h HL-Rep1

description: Biological replicate 1 of 2. apx1/cat2 plants subjected to high light, harvested after 0h and 1h.


title: cat2 plants-1h vs 0h HL-Rep1

description: Biological replicate 1 of 2. cat2 plants subjected to high light, harvested after 0h and 1h.

source_name: cat2,1h HL


title: WT plants-1h vs 0h HL-Rep2

description: Biological replicate 2 of 2. WT plants subjected to high light, harvested after 0h and 1h.

source_name: WT, 0h HL

value: WT

value: 21 days

source_name: WT, 1h HL


title: WT plants-1h vs 0h HL-Rep1

description: Biological replicate 1 of 2. WT plants subjected to high light, harvested after 0h and 1h.


title: Sensitive-Drought-2

city: Lucknow

first: Samir

last: Sawant

state: UP

address: Sikandrabad

department: Plant Molecular Biology Lab

country: India

institute: National Botanical Research Institute

description: Gene expression data from leaf of drought sensitive Gossypium herbaceum after drought treatment.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip CottonGenome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Gene chip scanner 3000.

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.

organism: Gossypium herbaceum

source_name: Leaf sample from one month drought sensitive plant after drought treatment given by alternate watering.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The plants used for leaves collection were grown in a temperature-controlled greenhouse with 16 hour light/8 hour dark photoperiod at 28°C. They were grown in soil mixed with manures in earthen pot.

extract_protocol: Total RNA was isolated from Spectrum plant total RNA Kit (Sigma-Aldrich) according to the manufacturer’s instructions.

treatment_protocol: Drought treatments were imposed by withholding irrigation.

value: leaf tissue

value: One month old plant


title: Tolerant-Water-1

description: Gene expression data from leaf of drought tolerant Gossypium herbaceum in normal watered condition.

source_name: Leaf sample from one month drought tolerant plant in normal watered condition.


title: Sensitive-Water-1

description: Gene expression data from leaf of drought sensitive Gossypium herbaceum in normal watered condition.

source_name: Leaf sample from one month drought sensitive plant in normal watered condition.


title: Tolerant-Water-2


title: Sensitive-Drought-1


title: CD34-CD200-CD49+Replicate3

value: Back Skin

value: 50 days

value: telogen


title: Tolerant-Drought-2

description: Gene expression data from leaf of drought tolerant Gossypium herbaceum after drought treatment.

source_name: Leaf sample from one month drought tolerant plant after drought treatment given by alternate watering.


title: Sensitive-Water-2


title: Tolerant-Drought-1


title: llaf65_0.17_0.1

city: Tallinn

first: Ranno

last: Nahku

address: Akadeemia tee 15b

country: Estonia

institute: TFTAK

description: Investigation of specific growth rate dependent gene expression changes of L. lactis IL1403

hyb_protocol: For hybridization standard Agilent's kits, reagents and equipment were used (See http://www.chem.agilent.com/en-US/products/instruments/dnamicroarrays/Pages/default.aspx )

scan_protocol: Agilent Technologies Microarray Scanner G2565CA was used at 5 mm resolution

data_processing: Image was analized with Genepix 6 pro followed by background substration and global LOWESS normalization in R environment (KTH package). Spots with intensities lower than 100 units in both channels and outliers among technical replicates were removed.

organism: Lactococcus lactis subsp. lactis Il1403

source_name: specific growth rate 0.17 1/h

label_protocol: cDNA was synthesized from 11 μg of total RNA at 46ºC overnight using the following reagents per reaction: 1 μg random primers (Random decamers; Invitrogen, Carlsbad, CA), 6 μL 5 x first strand buffer (Invitrogen), 3 μL 0.1 M DTT (Invitrogen), 0.9 μL dNTPs (final concentrations: dATP 0.5 mM, dCTP 0.5 mM, dGTP 0.5 mM, dTTP 0.3 mM, aminoallyl-dUTP 0.2 mM), 1 μL RNase Inhibitor (Bioron, Ludwigshafen, Germany), 2 μL Superscript III (Invitrogen). RNA strands were hydrolyzed in the samples by adding 4.5 μL 1 M NaOH and incubating at 70ºC for 10 min, after incubation the samples were neutralized with 4.5 μL 1 M HCl. cDNA was purified with MinElute PCR purification kit (QIAGEN) and labeled with Cy3 (CyTM3 Mono Reactive Dye Pack, Amersham, Buckinghamshire, UK) or Cy5 (CyTM5 Mono Reactive Dye Pack, Amersham). Staining was carried out in 10 μL NaHCO3 (pH 9) at room temperature in dark for 1 h and the samples were purified again with MinElute PCR purification kit.

growth_protocol: Lactococcus lactis subsp. lactis IL1403 was cultivated in chemically defined medium containing 70% GIBCO™ F-12 Nutrient Mixture (Invitrogen Corporation, Carlsbad, CA) and 30% modified CDM. Composition of the final medium was as follows (mg/L): limiting substrate D-Glucose – 3500; L-Alanine – 78; L-Arginine – 185; L-Asparagine – 74; L-Aspartic acid – 72; L-Cysteine – 64; L-Glutamic acid – 70; L-Glutamine – 132; Glycine – 58;  L-Histidine – 60; L-Isoleucine – 102; L-Leucine – 207; L-Lysine – 158; L-Methionine – 41; L-Phenylalanine – 86; L-Proline – 92; L-Serine – 163; L-Threonine – 76; L-Trypthophan – 16; L-Tyrosine – 29; L-Valine – 107; Biotin – 0.305; Choline chloride – 9.8; D-Pantothenate – 0.65; Folic Acid – 1.21; Niacinamide – 0.325; Pyridoxine hydrochloride – 0.642; Riboflavin – 0.326; Thiamine hydrochloride – 0.51; Vitamin B12 – 0.98; i-Inisitol – 12.6; CaCl2 – 28; CuSO4 x 5H2O – 0.272; FeSO4 x 7H2O – 0.71; MgCl2 – 58; KCl – 157; NaCl – 5580; Na2PO4 – 99; ZnSO4 x 7H2O – 1; Hypoxanthine-Na – 3; Linoleic Acid – 0.1; Lipoic Acid – 0.1; Phenol Red – 0.8; Putrescine x 2HCl – 0.1; Na-Pyruvate – 77; Thymidine – 0.5.

extract_protocol: Total RNA was extracted with Qiagen's Rneasy Mini Kit

tag: growth rate

value: specific growth rate 0.17 1/h

value: continuous cultivation, A-stat

source_name: specific growth rate 0.1 1/h

value: continuous cultivation, chemostat

value: specific growth rate 0.1 1/h


title: llaf64_0.55_0.1

source_name: specific growth rate 0.55 1/h

value: specific growth rate 0.55 1/h


title: llaf65_0.43_0.1

source_name: specific growth rate 0.43 1/h

value: specific growth rate 0.43 1/h


title: llaf63_0.45_0.1

source_name: specific growth rate 0.45 1/h

value: specific growth rate 0.45 1/h


title: llaf65_0.49_0.1

source_name: specific growth rate 0.49 1/h

value: specific growth rate 0.49 1/h


title: llaf65_0.28_0.1

source_name: specific growth rate 0.28 1/h

value: specific growth rate 0.28 1/h


title: llaf64_0.3_0.1

source_name: specific growth rate 0.3 1/h

value: specific growth rate 0.3 1/h


title: Sensitive-Water-3


title: MIT9313 without iron at t28, biological rep2

city: Cambridge

first: Anne

last: Thompson

state: MA

address: 15 Vassar Street

institute: MIT

description: Gene expression of MIT9313 after resuspension in iron-free media, experimental treatment

hyb_protocol: The cDNA was hybridized to the MD4-9313 custom Affymetrix array in aqueous hybridization solution (100 mM MES, 1 M NaCl, 20 mM EDTA, 0.01% Tween-20, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, 7.8 % DMSO and 3 nM prelabeled Affymetrix hybridization B2 oligo control probe mix) during a 16 h incubation at 45 °C in a GeneChip Hybridization Oven 320 rotating at 60 rpm. Washes and stains were carried out on a GeneChip Fluidics Station 450 (Affymetrix) following the ProkGE_WS2v3 Affymetrix protocol. Briefly, following two stringency washes the array was sequentially incubated with 10 µg/mL streptavidin (Pierce Chemical), 5 µg/mL biotinylated anti-streptavidin goat antibody (Vector Laboratories) and 0.1 mg/mL goat IgG (Sigma) and 10 µg/mL streptavidin-phycoerythrin conjugate (Mol. Probes) each for 10 min at 25 °C and given a final wash.

scan_protocol: The arrays were scanned with the GeneChip Scanner (Affymetrix) at a 2.5 µm resolution with excitation set for 570 nm.

data_processing: Robust multi-chip average (RMA) to normalize background signal between arrays (performed on strain-specific probesets) and lowess normalization at the probe-set level to correct influences of expression-signal intensity on fold change, both implemented in Matlab (The Mathworks, Inc., Natick, MA), and using an Affymetrix library file that was updated in September 2008 to include recently discovered ORFs and non-coding RNAs (MD4-9313a520062.Sep08.cdf). rRNA probesets were disregarded due to amplification bias (Frias-Lopez, pers. comm.).

organism: Prochlorococcus marinus str. MIT 9313

source_name: MIT9313 culture 28 hours after resuspension in iron-free media, experimental treatment

label_protocol: Synthesis of complementary DNA (cDNA), labeling, hybridization, staining and scanning was carried out according to Affymetrix protocols for E.coli with minor changes. Total RNA (2 µg) was denatured at 70 °C and annealed to random hexamer primers (25 ng/µl) at 25 °C for 10 min. The RNA was reverse transcribed to produce cDNA with Superscript II (25 U/µl – Invitrogen Life Technologies) and 0.5 mM dNTPs in the presence of 1 U/µl RNase Out RNase Inhibitor (Invitrogen). The mix was incubated at 25 °C for 10 min followed by 60 min incubations at 37 °C and 42 °C respectively. Superscript II was inactivated with a 10 min incubation at 70 °C. Sodium hydroxide (0.25 N) was used to remove RNA during a 30 min incubation at 65 °C, followed by neutralization with HCl. The cDNA was purified with MinElute PCR purification columns (Qiagen). Fragments of cDNA, 50-200 nt long, were produced from a 10 min incubation at 37 °C with DNase I (0.6 U per µg cDNA), followed by heat inactivation of the DNase I enzyme (10 min at 98 °C). The cDNA fragments were end-labeled with biotin using the BioArray Terminal Labeling Kit (Enzo) during a 60 min incubation at 37 °C. The reaction was stopped by freezing at –20 °C. The quality of biotin end-labeling was verified by gel-shift assays with NeutrAvidin (Pierce Chemicals) on 1% TBE agarose gels.

growth_protocol: MIT9313 was grown at 20µE m-2s-1 (continuous) at 25ºC, in PRO99 media (Moore et al, 2007) modified for trace metal clean work through microwave sterilization of seawater, increase in EDTA to 11.7µM, treatment of major nutrients with Chelex-100 resin (Biorad, Hercules, CA), and treatment of polycarbonate culture vessels sequentially with 0.1% Citranox (Alconox, White Plains, NY), 10% Baker Instra-analyzed HCl (Mallinckrodt Baker, Phillpsburg, NJ), and pH2 HCl for 24 hours each (Keller et al, 1988; Price et al, 1988; Saito et al, 2002).

extract_protocol: RNA was extracted using the mirVana miRNA kit (Ambion, Austin, TX, USA) as in Lindell et al. (2007) with lysozyme added (Tolonen et al, 2006). DNA was removed from RNA using Turbo DNase (Ambion) and SuperaseIN (Ambion) to protect RNA (as in Lindell et al, 2007). Due to low RNA yield for MIT9313, DNase-treated MIT9313 mRNA samples were concentrated using Micron Y-30 columns (Millipore, Billerica, MA) then amplified using the Message Amp TM II-Bacteria Prokaryotic RNA Amplification Kit (Ambion) following the manufacturer’s protocol with a 10-hour linear amplification step.

treatment_protocol: To induce abrupt iron starvation, triplicate cultures were harvested by centrifugation, washed twice with iron-free media, divided and re-suspended in iron-replete (1µM) or iron-free media. RNA (collected as in Lindell et al, 2007) and cell number samples were collected at 0, 16, 28, 53, and 72 hours with iron addition to the iron-deprived cultures at 54 hours to match replete (1µM FeCl3) iron concentrations.

tag: strain

value: minus Fe

value: 28 hours


title: MIT9313 without iron at t28, biological rep1


title: MIT9313 with iron at t53, biological rep1

description: Gene expression of MIT9313 after resuspension in iron-replete media, control treatment

source_name: MIT9313 culture 53 hours after resuspension in iron-replete media, control treatment

value: plus Fe

value: 53 hours


title: MIT9313 without iron at t72 after iron rescue, biological rep2

description: Gene expression of MIT9313 after resuspension in iron-free media, experimental treatment, after iron rescue

source_name: MIT9313 culture 72 hours after resuspension in iron-free media, experimental treatment, after iron rescue at 54 hours

value: 72 hours


title: MIT9313 with iron at t28, biological rep2

source_name: MIT9313 culture 28 hours after resuspension in iron-replete media, control treatment


title: Sensitive-Drought-3

value: leaf tissue

value: One month old plant


title: MIT9313 with iron at t28, biological rep1


title: MIT9313 with iron at t53, biological rep2


title: MIT9313 without iron at t16, biological rep3

source_name: MIT9313 culture 16 hours after resuspension in iron-free media, experimental treatment

value: 16 hours


title: MIT9313 without iron at t53, biological rep1

source_name: MIT9313 culture 53 hours after resuspension in iron-free media, experimental treatment


title: Tolerant-Water-3

source_name: Leaf sample from one month drought tolerant plant in normal watered condition.


title: MIT9313 without iron at t16, biological rep2


title: MIT9313 with iron at t53, biological rep3


title: MIT9313 without iron at t53, biological rep3


title: MIT9313 with iron at t28, biological rep3


title: Tolerant-Drought-3


title: MIT9313 without iron at t53, biological rep2


title: MIT9313 without iron at t72 after iron rescue, biological rep1


title: MIT9313 without iron at t16, biological rep1


title: MIT9313 without iron at t0, biological rep2

source_name: MIT9313 culture just after resuspension in iron-free media, experimental treatment

value: 0 hours


title: MIT9313 without iron at t0, biological rep1


title: MIT9313 with iron at t16, biological rep1

source_name: MIT9313 culture 16 hours after resuspension in iron-replete media, control treatment


title: MIT9313 with iron at t16, biological rep2


title: MIT9313 with iron at t0, biological rep2

source_name: MIT9313 culture just after resuspension in iron-replete media, control treatment


title: MIT9313 with iron at t0, biological rep3


title: MIT9313 with iron at t0, biological rep1


title: Clexane 4a

city: London

first: Yunliang Chen

last: Chen

address: Manresa Road

country: United Kingdom

institute: Thrombosis Research Institute

description: Gene expression after 24hr treatment in FCS free medium

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scans were converted to data files with Agilent's Feature Extraction software (Version 8.5). Expression values were normalized and analyzed on a logarithmic scale. Data were analysed by Gene Spring ANOVA and MetaCore (GeneGo, USA).

source_name: MCF-7 cell

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: MCF-7 cells were maintained in DMEM medium supplemented with 15% foetal bovine serum (PAA,UK), 100 U per ml penicillin, and 100 mg per ml streptomycin, and cultured in a humidified atmosphere of 5% CO2 in air.

extract_protocol: Total RNA was harvested using the TRIzol® isolation method (Invitrogen).

treatment_protocol: MCF-7 cells treated with three type of heparins in serum free medium containing 2 % of Lactalbumin Hydrolysate (LAH, Sigma) for 24 hours.

value: human breast cancer cell


title: Fragmin 3b


title: Fragmin 3a


title: U1 cells stimulated for 6 hours with the TLR8 agonist 3M-002 (Exp. 1/2010)

city: Zurich

first: Roberto

middle: F

last: Speck

state: Zurich

address: Raemistrasse 100

department: Division of Infectious Diseases and Hospital Epidemiology

country: Switzerland

institute: University Hospital of Zurich

description:
u1 cells are cells of human myelo-monocytic origin (folks, t. m., j. justement, a. kinter, c. a. dinarello, and a. s. fauci. 1987. cytokine-induced expression of hiv-1 in a chronically infected promonocyte cell line. science 238: 800-802.)
To assess the effects of TLR8 triggering on the transcriptome in U1 cells, we used the human Toll-like receptor pathway PCR array from SABiosciences (#PAHS-018), according to the instructions of the manufacturer

scan_protocol: fluorescence increase of Sybr green during real-time PCR

data_processing: Delta-Delta CT METHOD   (An approximation method); we used the software module provided by SABiosciences (http://pcrdataanalysis.sabiosciences.com/pcr/arrayanalysis.php)

source_name: U1 cells

label_protocol: Sybr green which is in the master mix for running the real-time PCR

extract_protocol: RNA was extracted from lysates with the RNeasy mini-kit (Qiagen) according to the manufacturer’s instructions. To remove residual DNA, RNA preparations were treated with DNAfree (Ambion, Austin, TX). Reverse transcription was performed with 5 ug of total RNA.

value: stimulated for 6 h with the TLR8 agonist 3M-002 donor


title: UFH 2b


title: Monocyte-derived macrophages - unstimulated donor 74 - 2010

source_name: Monocyte-derived macrophages (MDM) of human origin

growth_protocol: Monocyte-derived macrophages (MDM) have been generated by culturing them in a medium containing human AB serum (5%). MDM were used after 7 days after the initial isolation of monocytes from PBMC of healthy donors.

treatment_protocol: unstimulated MDM

value: monocyte-derived macrophages


title: Monocyte-derived macrophages stimulated for 18 h with the TLR8 agonist 3M-002 donor 74 2010

treatment_protocol: treated for 18 hours with the TLR8 agonist 3M-002


title: U1/DN-MyD88 unstimulated (Exp 1/2010)

description:
u1 cells genetically complemented with a dominant negative mutant of myd88 (dn-myd88) (folks, t. m., j. justement, a. kinter, c. a. dinarello, and a. s. fauci. 1987. cytokine-induced expression of hiv-1 in a chronically infected promonocyte cell line. science 238: 800-802.)
To assess the effects of TLR8 triggering on the transcriptome in U1 cells, we used the human Toll-like receptor pathway PCR array from SABiosciences (#PAHS-018), according to the instructions of the manufacturer

source_name: U1 cells complemented genetically with a dominant negative form of MyD88


title: Clexane 4b


title: U1/DN-MyD88 stimulated with the TLR8 agonist 3M-002 for 6 h (exp. 1/2010)

description:
u1 cells (folks, t. m., j. justement, a. kinter, c. a. dinarello, and a. s. fauci. 1987. cytokine-induced expression of hiv-1 in a chronically infected promonocyte cell line. science 238: 800-802.)
To assess the effects of TLR8 triggering on the transcriptome in U1 cells, we used the human Toll-like receptor pathway PCR array from SABiosciences (#PAHS-018), according to the instructions of the manufacturer


title: UFH 2a


title: Clexane 4c


title: Fragmin 3c


title: MED4 without iron at t70 after iron rescue, biological rep2

description: Gene expression of MED4 after resuspension in iron-free media, experimental treatment, after iron rescue

data_processing: Robust multi-chip average (RMA) to normalize background signal between arrays (performed on strain-specific probesets) and lowess normalization at the probe-set level to correct influences of expression-signal intensity on fold change, both implemented in Matlab (The Mathworks, Inc., Natick, MA), and using an Affymetrix library file that was updated in September 2008 to include recently discovered ORFs and non-coding RNAs (MD4-9313a520062.Sep08.cdf).

organism: Prochlorococcus marinus subsp. pastoris str. CCMP1986

source_name: MED4 culture 70 hours after resuspension in iron-free media, experimental treatment, after iron rescue at 49 hours

growth_protocol: MED4 was grown at 27µEm-2s-1 (continuous) in PRO99 media (Moore et al, 2007) modified for trace metal clean work through microwave sterilization of seawater, increase in EDTA to 11.7µM, treatment of major nutrients with Chelex-100 resin (Biorad, Hercules, CA), and treatment of polycarbonate culture vessels sequentially with 0.1% Citranox (Alconox, White Plains, NY), 10% Baker Instra-analyzed HCl (Mallinckrodt Baker, Phillpsburg, NJ), and pH2 HCl for 24 hours each (Keller et al, 1988; Price et al, 1988; Saito et al, 2002).

extract_protocol: RNA was extracted using the mirVana miRNA kit (Ambion, Austin, TX, USA) as in Lindell et al. (2007). DNA was removed from RNA using Turbo DNase (Ambion) and SuperaseIN (Ambion) to protect RNA (as in Lindell et al, 2007).

treatment_protocol: To induce abrupt iron starvation, triplicate cultures were harvested by centrifugation, washed twice with iron-free media, divided and re-suspended in iron-replete (1µM) or iron-free media. RNA (collected as in Lindell et al, 2007) and cell number samples were collected at 0, 12, 24, 48, and 70 hours with iron addition to the iron-deprived cultures at 49 hours, to match replete (1µM FeCl3) iron concentrations.

value: 70 hours after resuspension


title: Monocyte-derived macrophages (MDM) unstimulated Exp 2010 donor 84

treatment_protocol: unstimulated (control)


title: U1 cells stimulated with the TLR8 agonist 3M-002 for 10 h (exp. 1/2010)

description:
u1 cells are cells of human myeloid-monocytic origin (folks, t. m., j. justement, a. kinter, c. a. dinarello, and a. s. fauci. 1987. cytokine-induced expression of hiv-1 in a chronically infected promonocyte cell line. science 238: 800-802.)
To assess the effects of TLR8 triggering on the transcriptome in U1 cells, we used the human Toll-like receptor pathway PCR array from SABiosciences (#PAHS-018), according to the instructions of the manufacturer

value: stimulated for 10 h with the TLR8 agonist 3M-002 donor


title: UFH 2c


title: Monocyte-derived macrophages stimulated for 18 h with the TLR8 agonist 3M-002 (exp. 2010, donor 84)

treatment_protocol: MDM stimulated for 18 h with the TLR8 agonist 3M-002

value: stimulated for 18 h with the TLR8 agonist 3M-002 donor


title: MED4 without iron at t70 after iron rescue, biological rep1

value: iron-free media, experimental treatment, after iron rescue at 49 hours


title: U1/DN-MyD88 stimulated for 6 h with the TLR8 agonist 3M-002 (1/2007)

description:
u1 cells - cell line of myeloid-monocytic origin - genetically complemented with a dominant negative form of myd88 (dn-myd88) (folks, t. m., j. justement, a. kinter, c. a. dinarello, and a. s. fauci. 1987. cytokine-induced expression of hiv-1 in a chronically infected promonocyte cell line. science 238: 800-802.)
To assess the effects of TLR8 triggering on the transcriptome in U1 cells, we used the human Toll-like receptor pathway PCR array from SABiosciences (#PAHS-018), according to the instructions of the manufacturer


title: U1/DN-MyD88 control 1-2007

treatment_protocol: control - unstimulated, cultured in RPMI (BioWhittaker) supplemented with 5% FCS (PAA Laboratories), 1% glutamine (Invitrogen Life Technologies) and 1% penicillin/streptomycin (Invitrogen Life Technologies).


title: U1 cells treated with the TLR8 agonist 3M-002 for 10 h


title: U1 cells unstimulated (control) - exp 1/2010

description:
u1 cells are cells of myeloid-monocytic origin (folks, t. m., j. justement, a. kinter, c. a. dinarello, and a. s. fauci. 1987. cytokine-induced expression of hiv-1 in a chronically infected promonocyte cell line. science 238: 800-802.)
To assess the effects of TLR8 triggering on the transcriptome in U1 cells, we used the human Toll-like receptor pathway PCR array from SABiosciences (#PAHS-018), according to the instructions of the manufacturer


title: MED4 without iron at t48, biological rep2

description: Gene expression of MED4 after resuspension in iron-free media, experimental treatment

source_name: MED4 culture 48 hours after resuspension in iron-free media, experimental treatment

value: iron-free media, experimental treatment

value: 48 hours after resuspension


title: U1 cells stimulated with the TLR8 agonist 3M-002 for 6 hours

description:
u1 cells; human cells of myleoid-monocytic origin (folks, t. m., j. justement, a. kinter, c. a. dinarello, and a. s. fauci. 1987. cytokine-induced expression of hiv-1 in a chronically infected promonocyte cell line. science 238: 800-802.)
To assess the effects of TLR8 triggering on the transcriptome in U1 cells, we used the human Toll-like receptor pathway PCR array from SABiosciences (#PAHS-018), according to the instructions of the manufacturer


title: U1_control_1/2007

description:
u1 cell line is of myeloid-monocytic orgin, harboring latent hiv (folks, t. m., j. justement, a. kinter, c. a. dinarello, and a. s. fauci. 1987. cytokine-induced expression of hiv-1 in a chronically infected promonocyte cell line. science 238: 800-802.)
To assess the effects of TLR8 triggering on the transcriptome in U1 cells, we used the human Toll-like receptor pathway PCR array from SABiosciences (#PAHS-018), according to the instructions of the manufacturer

source_name: U1 cells (myeloid-monocytic cell line of human origin), unstimulated, control


title: Control 1c


title: Control 1a


title: Control 1b


title: MED4 without iron at t24, biological rep1

source_name: MED4 culture 24 hours after resuspension in iron-free media, experimental treatment

value: 24 hours after resuspension


title: MED4 with iron at t24, biological rep2

description: Gene expression of MED4 after resuspension in iron-replete media, control treatment

source_name: MED4 culture 24 hours after resuspension in iron-replete media, control treatment

value: iron-replete media, control treatment


title: MED4 with iron at t24, biological rep1


title: MED4 without iron at t48, biological rep1


title: MED4 without iron at t24, biological rep2


title: MED4 without iron at t12, biological rep2

source_name: MED4 culture 12 hours after resuspension in iron-free media, experimental treatment

value: 12 hours after resuspension


title: control mismatch shRNA, biol replicate 3

first: Bruno

last: Ferraz-de-Souza

address: 30 Guilford St

department: Clinical & Molecular Genetics Unit

institute: UCL Institute of Child Health

description:
FACSorted viable GFP+ events
gene expression 48h after transfection of shRNA mismatch control

hyb_protocol: Samples were hybridised to GeneChip Human Gene 1.0 ST Arrays (16 hours at 45°C) and stained using the GeneChip Hybridization, Wash and Stain Kit, following manufacturers instructions (all Affymetrix).

scan_protocol: Arrays were scanned on GeneChip Scanner 3000 7G System (Affymetrix)

data_processing: Data were analyzed using the Partek Genomics Suite and R/Bioconductor. Differential gene expression analysis was performed using the limma package in R/Bioconductor. Multiple testing correction was applied according to the Benjamini and Hochberg False Discovery Rate method. A Benjamini-Hochberg-corrected P-value cut-off of 0.05 was used to select significant differentially expressed transcripts in each setting (Over and shRNA). Results were then combined to identify a subset of positively-regulated SF-1 target genes in this system.

source_name: NCI-H295R cells, 48h after transfection with mismatch shRNA

label_protocol: Fragmented biotinylated cRNA were prepared using the GeneChip Whole Transcript Sense Target Labeling Assay kit (Affymetrix) from 200 ng total RNA

growth_protocol: NCI-H295R cells were maintained in 75 cm2 tissue culture flasks with 15 ml of DMEM:F12 supplemented with 2.5% Nu-Serum, 1% ITS+ Premix and 1% P/S. Upon 80-90% confluency (usually every 4 to 6 days), cells were washed with 5 ml PBS and detached from flask through incubation with 3 ml trypsin-EDTA at 37°C for 3 min. Trypsin was inactivated by the addition of 7 ml full medium and resuspended cells were replated at 1:10 dilution. Cells were used for transfection 4 to 5 passages after thawing.

extract_protocol: Total RNA was extracted from transfected cells according to the TRIzol method. Quality control of RNA was assessed with a 2100 Bioanalyzer; all samples had acceptable RIN

treatment_protocol: Cells were transfected with pIRES2 constructs (Over) or shRNA plasmids (shRNA) using Amaxa Nucleofection. Briefly, 10 ug of plasmid DNA were transfected into 5 million cells using nucleofection solution R and program T-020 in a Nucleofector II device. After nucleofection, cells were washed from cuvettes with 500 ul RPMI 1640 and transferred to 6-well plates containing 3 ml of usual growth media per well. Plates were incubated at 37°C for 48h until harvesting for fluorescence-activated cell sorting (FACS). Viable GFP positive events (corresponding to live transfected cells) were pooled in PBS by FACS using a MoFlo XDP cells sorter for RNA extraction.

tag: transfection

value: mismatch shRNA

value: NCI-H295R cells

value: shRNA, control


title: MED4 without iron at t12, biological rep1


title: SF-1 knockdown with shRNA, biol replicate 5

description:
FACSorted viable GFP+ events
gene expression 48h after SF-1 knockdown with shRNA

source_name: NCI-H295R cells, 48h after transfection withSF-1 shRNA

value: SF-1 shRNA

tag: cell line

value: shRNA, intervention


title: A549_Geld_IC20_48h_rep1

city: Boston

first: Lisa

last: Christadore

address: 24 Cummington Street

department: Chemistry

institute: Boston University

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on HG_U133_2.0_Plus cartridge arrays (Affymetrix Hybridization Oven 645). Arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. [program-name = Expression Console, program-version = 1.1.2800.19935]

source_name: A549 cells, 48h growth in presence of Geld, IC20

label_protocol: Affymetrix 3' IVT Express Kit was used to generate and biotin-label cRNA according to manufacturer's protocol.

growth_protocol: A549 cells were maintained in DMEM medium supplemented with 10% FBS, and 10 ug/mL penicillin-streptomycin. Cells were harvested with trypsin prior to use in micrarrray experiments.

extract_protocol: Total RNA was extracted using Rneasy Mini kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: A549 cells were seeded 24 h prior treatment with vehicle (DMSO) or geldanamycin. After the appropriate time point, the medium was collected and confluent cells were trypsinized and frozen in liquid nitrogen until RNA extraction.

tag: tissue

value: lung epithelial

tag: agent

value: geldanamycin, IC20

tag: time point


title: control mismatch shRNA, biol replicate 1


title: A549_Geld_IC20_48h_rep3


title: A549_Geld_IC50_48h_rep3

source_name: A549 cells, 48h growth in presence of Geld, IC50

value: geldanamycin, IC50


title: A549_Geld_IC50_48h_rep2


title: A549_Geld_IC50_24h_rep3

source_name: A549 cells, 24h growth in presence of Geld, IC50


title: control mismatch shRNA, biol replicate 4


title: SF-1 knockdown with shRNA, biol replicate 4


title: A549_dmso_48h_rep1

source_name: A549 cells, 48h growth in presence of vehicle

value: DMSO


title: control mismatch shRNA, biol replicate 2


title: A549_Geld_IC20_48h_rep2


title: A549_Geld_IC50_24h_rep2


title: BT474 genomic DNA

city: Helsinki

first: Henrik

last: Edgren

address: Tukholmankatu 8

country: Finland

institute: Institute for Molecular Medicine, University of Helsinki

hyb_protocol: Labelled tumor and reference samples were combined and hybridized onto the arrays according to manufacturer's (Agilent) instructions. After hybridization, arrays were washed according to manufacturer's instructions.

scan_protocol: Arrays were scanned using a laser scanner from Agilent Technologies. Signal intensities were quantified using the Feature Extraction software from Agilent.

data_processing: Agilent Feature Extraction Software was used for spot quality filtering and normalization.

source_name: pooled genomic DNA from healthy female donors

label_protocol: 3 μg of digested sample or reference DNA (female genomic DNA, Promega) was labeled with Cy5-dUTP and Cy3-dUTP respectively using a Genomic DNA Enzymatic Labeling Kit.

growth_protocol: MCF-7, KPL-4 and BT-474 cells were maintained in DMEM supplemented with 10% FBS, 2 mM (MCF-7, KPL-4) or 4 mM (BT-474) L-glutamine and penicillin/streptomycin. BT-474 cells were further supplemented with 1 mM sodium pyruvate and 0.01 mg/ml bovine insulin. SK-BR-3 cells were maintained in McCoy’s 5A medium with 10% FCS, 1.5 mM L-glutamine and penicillin/streptomycin.

extract_protocol: Genomic DNA was extracted using TRIzol and purified by chloroform extraction and subsequent ethanol precipitation.

tag: gender

value: female

source_name: genomic DNA from breast cancer cell line BT474


title: A549_dmso_48h_rep3


title: A549_dmso_48h_rep2


title: A549_Geld_IC50_48h_rep1


title: MCF7 genomic DNA

value: pooled genomic DNA from healthy female donors

source_name: genomic DNA from breast cancer cell line MCF7


title: MED4 with iron at t12, biological rep1

source_name: MED4 culture 12 hours after resuspension in iron-replete media, control treatment

tag: time


title: KPL4 genomic DNA

source_name: genomic DNA from breast cancer cell line KPL4


title: SF-1 knockdown with shRNA, biol replicate 3


title: MED4 without iron at t0, biological rep2

source_name: MED4 culture just after resuspension in iron-free media, experimental treatment

value: just after resuspension


title: A549_Geld_IC50_24h_rep1


title: A549_dmso_24h_rep2

source_name: A549 cells, 24h growth in presence of vehicle


title: MED4 with iron at t0, biological rep2

source_name: MED4 culture just after resuspension in iron-replete media, control treatment


title: SF-1 knockdown with shRNA, biol replicate 2


title: A549_dmso_24h_rep3


title: MED4 without iron at t0, biological rep1

value: iron-free media, experimental treatment


title: SF-1 knockdown with shRNA, biol replicate 1


title: A549_dmso_24h_rep1


title: overexpression of mutant G35E SF-1, biol replicate 3

description:
FACSorted viable GFP+ events
gene expression 48h after overexpression of functionally-impaired SF-1

source_name: NCI-H295R cells, 48h after transfection with mutant SF-1 cDNA

value: mutant SF-1 cDNA

value: Over, control


title: overexpression of mutant G35E SF-1, biol replicate 2


title: MED4 with iron at t0, biological rep1

value: iron-replete media, control treatment


title: SKBR3 genomic DNA

source_name: genomic DNA from breast cancer cell line SKBR3


title: overexpression of mutant G35E SF-1, biol replicate 1


title: PD-1 low CD8+ CD3+ T cells - rep5

city: Atlanta

first: Jaikumar

last: Duraiswamy

state: GA

address: 1510, Clifton Road, G211, Rollins Research Center

department: Emory Vaccine Center and Department of Microbiology & Immunology

institute: Emory Univesity

hyb_protocol: Labeled targets were hybridized to Affymetrix Human genome U133 Plus 2.0 arrays on the Affymetrix GeneChip Array Station (GCAS) automation platform

scan_protocol: Scanning was performed on an Affymetrix GeneChip HT plate scanner, and Affymetrix software was used to perform image analysis and generate raw intensity data.

data_processing: Gene expression data was summarized with RMA.

label: Biotin

source_name: Peripheral blood cells healthy adults

label_protocol: cDNA was synthesized using the SuperScript Choice cDNA synthesis kit (Invitrogen) and an oligo (dT) primer containing a T7 promoter. The T7 MEGAscript kit (Ambion) was used to amplify cRNA from the cDNA. The cRNA was reverse transcribed with biotinylated nucleotides using the Enzo BioArray High Yield RNA transcript labeling kit in the second round of cRNA synthesis, fragmented for hybridization.

extract_protocol: Total RNA was purified using Trizol® (Invitrogen, Life Technologies Corporation). All RNA samples were checked for purity using a ND-1000 spectrophotometer (NanoDrop Technologies) and for integrity by electrophoresis on a 2100 BioAnalyzer (Agilent Technologies).

tag: cell phenotype

value: PD-1 low CD8+CD3+ Naïve T cells

tag: sorting strategy

value: FACS

tag: source

value: Peripheral blood cells


title: overexpression of wild type SF-1, biol replicate 3

description:
FACSorted viable GFP+ events
gene expression 48h after overexpression of wild type SF-1

source_name: NCI-H295R cells, 48h after transfection with WT SF-1 cDNA

value: WT SF-1 cDNA

value: NCI-H295R cells

value: Over, intervention


title: PD-1 low CD8+ CD3+ T cells - rep2


title: PD-1 low CD8+ CD3+ T cells - rep1


title: PD-1 low CD8+ CD3+ T cells - rep6


title: PD-1 low CD8+ CD3+ T cells - rep3


title: PD-1 low CD8+ CD3+ T cells - rep4


title: overexpression of wild type SF-1, biol replicate 2


title: PD-1 high CD8+ CD3+ T cells - rep4

value: PD-1 high CD8+CD3+ Naïve T cells


title: overexpression of wild type SF-1, biol replicate 1


title: PD-1 high CD8+ CD3+ T cells - rep5


title: PD-1 high CD8+ CD3+ T cells - rep3


title: PD-1 high CD8+ CD3+ T cells - rep1


title: Naive CD8+ CD3+ T cells - rep4

value: CD8+CD3+ Naïve T cells


title: Naive CD8+ CD3+ T cells - rep2


title: PD-1 high CD8+ CD3+ T cells - rep2


title: Naive CD8+ CD3+ T cells - rep3


title: PD-1 high CD8+ CD3+ T cells - rep6


title: Naive CD8+ CD3+ T cells - rep1


title: MED4 with iron at t12, biological rep2

value: 12 hours after resuspension


title: HMECs_Tert_shp53_Ras_Epi

city: MONTPELLIER cedex 5

first: Beatrice

last: ORSETTI

address: 208 rue des apothicaires- CRLC Val d'Aurelle

department: Tumoral Plasticity and Identity

country: France

institute: INSERM-U896 IRCM

hyb_protocol: Labeling products were precipitated with isopropanol and resuspended in 110 μl of NimbleGen Hybridization buffer. Hybridization (48 h at 37°C with mild agitation), washing and drying steps were performed using a TECAN HS4800 hybridization station and arrays were scanned at 5 μm resolution using the GenePix4000B scanner.

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing:
Data were extracted using NimbleScan 2.5 extraction software.
NimbleScan 2.5 processing : Loess for spatial correction, qspline normalization and CGH-segMNT with default parameters exept Min segment lenght =4. Log2 (Test/Control) corrected ratio

source_name: Cell line DNA from Tert/shp53/Ras Epi derivative

label_protocol: 1 μg genomic DNA was labeled using NimbleGen Dual-Color DNA Labeling Kit according to manufacturer's protocol as detailed in user guide (http://www.nimblegen.com/products/cgh/index.html).

extract_protocol: DNA was extracted from 5x10E6 cells using QIAmp DNA miniKit (Qiagen) according to supplier's recommandations. Extracted DNA concentration has been set at 200 ng/μl.

tag: biomaterial type

value: cell line

tag: construction

tag: cell type

value: HMEC cells

tag: phenotype

value: epithelial

source_name: Pool of 20 normal female lymphocyte DNA from heathly donors

value: lymphocytes


title: M. galloprovincialis_1000_control, Zero-time-point_replicate 2

status: Public on Jan 10 2011

city: Pacific Grove

first: Brent

middle: L

last: Lockwood

address: 120 Oceanview Blvd.

department: Biology

institute: Hopkins Marine Station of Stanford University

description:
SC0_ga_2
Biological replicate 2 of 6. M. galloprovincialis control, 1000-mOsm_kg, beginning of experiment.

hyb_protocol: Competitive hybridization (experimental - AlexaFluor 647 versus reference - AlexaFluor 555). We followed the recommended protocols from Agilent Technologies, Inc. for all hybridization and washing steps.

scan_protocol: Microarrays were scanned with an AXON GenePix 4000B scanner (Axon Instruments, Molecular Devices, Sunnyvale, CA, USA).

data_processing: Fluorescent signal intensities for each spot on the microarray were extracted and Lowess normalized within each microarray using Feature Extraction Software (version 9.5.3.1; Agilent Technologies, Inc.). Given the heterologous hybridization design, we performed stringent quality control to eliminate data from probes that had low signal intensities in any one of the 36 samples. We followed the recommendations of Agilent Technologies and considered a probe to have poor hybridization if (1) the signal intensity was less than 150% of the local background and (2) the hybridized spot diameter was less than 30% that of the nominal spot diameter.  Since multiple probes represented each gene on the microarray, data from good probes were summarized by computing the geometric mean of signal intensities for each probe set on a single microarray. We then computed the log2-ratios of the experimental channel divided by the reference channel. In order to minimize the effects of time-of-day on gene expression, we normalized the expression values of the treatment individuals to the median log2-ratio of the time-control samples of the same species. Log2-ratios of the baseline-control samples from the beginning of the experiment were normalized to the median log2-ratio within that group, separately for each species. The normalized log2-ratio data from the treatment samples were compared to those of the baseline-control samples to assess changes in gene expression.

label: Alexa Fluor 647

organism: Mytilus galloprovincialis

label_protocol: Total RNA was reverse-transcribed and amplified with the AminoAllyl MessageAmp II kit (Ambion; Foster City, CA, USA). To reduce problems in transcript binding due to sequence differences between species, we employed a reference design that used separate pools of reference RNA for each species. Reference amplified RNA (aRNA) was created for each species by pooling RNA before and after amplification. The reference pool was made up of RNA from six different samples: two base-line control samples from the beginning of the experiment, two treatment samples from the end of the four-hour hypo-osmotic exposure, and two time-control samples from the end of the four-hour exposure time. aRNAs from reference and experimental samples were separately labeled with Alexa Fluor fluorescent dyes (Invitrogen, Carlsbad, CA, USA), 555 for reference and 647 for control or treatment.

growth_protocol: We collected adult mussels and transported them back to the laboratory of Dr. Lars Tomanek at California Polytechnic State University, San Luis Obispo, as previously described (Lockwood et al. 2010). We chose to conduct our study on adult mussels because the Mytilus transcriptome has only been characterized in adults (Gracey et al. 2008; Lockwood et al. 2010). Mytilus trossulus (Gould 1850) were collected from Newport Harbor, Newport, OR, USA (44°38’25” N, 124°03’10” W), and Mytilus galloprovincialis (Lamarck 1819) were collected from Santa Barbara Harbor, Santa Barbara, CA, USA (34°24’15” N, 119°41’30” W). Specimens were kept in a re-circulating aquarium in which they were common-garden acclimated in seawater (1000 mOs/kg = 35 ‰ salinity) at 13°C for four weeks in order to fully acclimate both species to the same osmotic conditions (Gilles 1972). To ensure that no hybrid individuals were included in our study, we chose both collection sites to be well outside of the California blue mussel hybrid zone (McDonald & Koehn 1988; Braby & Somero 2006b). Molecular species identification was performed on each specimen by published methods (Heath et al. 1995; Rawson et al. 1996).

extract_protocol: Total RNA was extracted from gill tissues with a TissueLyser homogenizer (Qiagen; Valencia, CA, USA) and RNeasy kit (Qiagen).

treatment_protocol: We designed a salinity stress treatment that simulated conditions of increased fresh water input (e.g. rainfall runoff) that mussels might encounter in their natural environment. For example, in bay habitats salinity levels can fall rapidly during heavy runoff, but low salinity conditions are often short-lived due to tidal flux (Braby and Somero 2006b). Therefore, we exposed mussels to an abrupt drop in salinity and sampled after a four-hour exposure to measure acute responses in gene expression. To serve as baseline control groups for each species, six mussels of each species from the common-garden aquarium were sacrificed at the start of the experiment and their gill tissues dissected and frozen on liquid nitrogen. Treatment animals were then transferred from the common-garden aquarium to a tank in which they were exposed to a reduced salinity (hypo-osmotic) shock of 850 mOs/kg (29.75 ‰). To serve as a time-control, 6 mussels of each species were simultaneously transferred to a separate tank that remained at a salinity of 1000 mOs/kg (35 ‰). Osmolality was measured at the beginning of the exposure using an Advanced Instruments, Inc. osmometer (Norwood, MA, USA) and was 858 mOs/kg for the hypo-osmotic exposure and 979 mOsm/kg for both the common-garden aquarium (baseline-control) and the time-control aquarium. We inserted corks between the valves of both the treatment and time-control mussels to prevent the valves from closing during the experiment. While the application of corks was not environmentally realistic, we sought to maximize the hypo-osmotic exposure to the tissues and minimize the inter-individual variation in response to salinity stress that might have resulted from behavioral idiosyncrasies in valve (shell) gaping. After four hours, six treatment and six time-control mussels of each species were sacrificed, and their gill tissues were dissected and frozen on liquid nitrogen. We used gill tissues for this study because (1) stress-induced protein expression has been shown to be responsive to environmental stress in Mytilus gill (Hofmann & Somero 1995; Hofmann & Somero 1996), (2) Mytilus californianus has been shown to have highly similar stress-induced transcriptomes between gill, mantle and adductor muscle (Gracey et al. 2008), indicating that gill can be used as a representative tissue; and (3) the microarray was designed from expressed sequence tag (EST) sequences generated from the gill tissue of the out-group species, M. californianus (Gracey et al. 2008; Lockwood et al. 2010). Tissues were stored at -70°C prior to RNA extraction. During the experiment we concurrently exposed a different set of mussels to a more severe salinity stress of 700 mOs/kg (24.5 ‰). Subsequently, a proteomic comparison of these salinity treatments using 2-dimensional gel electrophoresis revealed that the 700 mOs/kg treatment rendered animals unable to elicit broad changes in protein expression (L. Tomanek, personal communication). This indicated that the 700 mOs/kg treatment was too severe for the animals to respond via the cellular stress response (Kültz 2005). Therefore, we focused our transcriptomic analysis on the more moderate stress of 850 mOs/kg in order to investigate immediate and early responses in gene expression to hypo-osmotic shock.

value: gill

tag: developmental stage

value: adult

tag: treatment

value: 1000 mOsm/kg control

tag: treatment time

value: 0 hours

label: Alexa Fluor 555

source_name: M. galloprovincialis pooled: Time-point zero control, 4 hour control, 850-mOsm_kg_salinity_stress

tag: sample type

value: reference


title: M. galloprovincialis_1000_control, Zero-time-point_replicate 3

description:
SC0_ga_3
Biological replicate 3 of 6. M. galloprovincialis control, 1000-mOsm_kg, beginning of experiment.


title: M. galloprovincialis_1000_control, Zero-time-point_replicate 4

description:
SC0_ga_4
Biological replicate 4 of 6. M. galloprovincialis control, 1000-mOsm_kg, beginning of experiment.


title: Xeno_Tert_shp53_Ras_Mes_B

source_name: Xenograft tumor DNA from shp53_Ras_hTert_HMEC mesenchymal cells from mouse 4

value: xenograft

value: mesenchymal

value: female


title: M. galloprovincialis_1000_control, Zero-time-point_replicate 1

description:
SC0_ga_1
Biological replicate 1 of 6. M. galloprovincialis control, 1000-mOsm_kg, beginning of experiment.


title: M. galloprovincialis_1000_control, 4-hour-time-point_replicate 3

description:
85C_ga_3
Biological replicate 3 of 6. M. galloprovincialis control, 1000-mOsm_kg, 4 hour time point.

value: 4 hours


title: M. galloprovincialis_1000_control, 4-hour-time-point_replicate 1

description:
85C_ga_1
Biological replicate 1 of 6. M. galloprovincialis control, 1000-mOsm_kg, 4 hour time point.


title: M. galloprovincialis_850_salinity_stress_replicate 6

description:
85_ga_6
Biological replicate 6 of 6. M. galloprovincialis salinity stress, 850-mOsm_kg, 4 hours.

value: 850 mOsm/kg salinity stress


title: M. galloprovincialis_1000_control, Zero-time-point_replicate 5

description:
SC0_ga_5
Biological replicate 5 of 6. M. galloprovincialis control, 1000-mOsm_kg, beginning of experiment.


title: M. galloprovincialis_1000_control, 4-hour-time-point_replicate 6

description:
85C_ga_6
Biological replicate 6 of 6. M. galloprovincialis control, 1000-mOsm_kg, 4 hour time point.


title: M. galloprovincialis_1000_control, 4-hour-time-point_replicate 2

description:
85C_ga_2
Biological replicate 2 of 6. M. galloprovincialis control, 1000-mOsm_kg, 4 hour time point.


title: Xeno_Tert_shp53_Ras_Mes_C

source_name: Xenograft tumor DNA from shp53_Ras_hTert_HMEC mesenchymal cells from mouse 5


title: M. galloprovincialis_1000_control, 4-hour-time-point_replicate 5

description:
85C_ga_5
Biological replicate 5 of 6. M. galloprovincialis control, 1000-mOsm_kg, 4 hour time point.


title: M. trossulus_1000_control, Zero-time-point_replicate 6

description:
SC0_tr_6
Biological replicate 6 of 6. M. trossulus control, 1000-mOsm_kg, beginning of experiment.

organism: Mytilus trossulus

source_name: Zero_time_point_control, M. trossulus

source_name: M. trossulus pooled: Time-point zero control, 4 hour control, 850-mOsm_kg_salinity_stress


title: M. galloprovincialis_850_salinity_stress_replicate 5

description:
85_ga_5
Biological replicate 5 of 6. M. galloprovincialis salinity stress, 850-mOsm_kg, 4 hours.


title: M. trossulus_1000_control, Zero-time-point_replicate 4

description:
SC0_tr_4
Biological replicate 4 of 6. M. trossulus control, 1000-mOsm_kg, beginning of experiment.


title: M. galloprovincialis_850_salinity_stress_replicate 2

description:
85_ga_2
Biological replicate 2 of 6. M. galloprovincialis salinity stress, 850-mOsm_kg, 4 hours.


title: M. trossulus_1000_control, Zero-time-point_replicate 2

description:
SC0_tr_2
Biological replicate 2 of 6. M. trossulus control, 1000-mOsm_kg, beginning of experiment.


title: M. trossulus_1000_control, Zero-time-point_replicate 5

description:
SC0_tr_5
Biological replicate 5 of 6. M. trossulus control, 1000-mOsm_kg, beginning of experiment.


title: M. galloprovincialis_850_salinity_stress_replicate 3

description:
85_ga_3
Biological replicate 3 of 6. M. galloprovincialis salinity stress, 850-mOsm_kg, 4 hours.


title: M. galloprovincialis_1000_control, 4-hour-time-point_replicate 4

description:
85C_ga_4
Biological replicate 4 of 6. M. galloprovincialis control, 1000-mOsm_kg, 4 hour time point.


title: Xeno_Tert_shp53_Ras_Mes_ A

source_name: Xenograft tumor DNA from shp53_Ras_hTert_HMEC mesenchymal cells from mouse 1


title: M. galloprovincialis_850_salinity_stress_replicate 4

description:
85_ga_4
Biological replicate 4 of 6. M. galloprovincialis salinity stress, 850-mOsm_kg, 4 hours.


title: M. trossulus_1000_control, Zero-time-point_replicate 1

description:
SC0_tr_1
Biological replicate 1 of 6. M. trossulus control, 1000-mOsm_kg, beginning of experiment.


title: M. trossulus_1000_control, 4-hour-time-point_replicate 5

description:
85C_tr_5
Biological replicate 5 of 6. M. trossulus control, 1000-mOsm_kg, 4 hour time point.

source_name: 4_hour-time_point_control M. trossulus


title: M. trossulus_1000_control, 4-hour-time-point_replicate 6

description:
85C_tr_6
Biological replicate 6 of 6. M. trossulus control, 1000-mOsm_kg, 4 hour time point.


title: M. trossulus_1000_control, Zero-time-point_replicate 3

description:
SC0_tr_3
Biological replicate 3 of 6. M. trossulus control, 1000-mOsm_kg, beginning of experiment.


title: M. galloprovincialis_850_salinity_stress_replicate 1

description:
85_ga_1
Biological replicate 1 of 6. M. galloprovincialis salinity stress, 850-mOsm_kg, 4 hours.


title: M. trossulus_1000_control, 4-hour-time-point_replicate 4

description:
85C_tr_4
Biological replicate 4 of 6. M. trossulus control, 1000-mOsm_kg, 4 hour time point.


title: M. trossulus_850_salinity_stress_replicate 5

description:
85_tr_5
Biological replicate 5 of 6. M. trossulus salinity stress, 850-mOsm_kg, 4 hours.


title: M. trossulus_1000_control, 4-hour-time-point_replicate 2

description:
85C_tr_2
Biological replicate 2 of 6. M. trossulus control, 1000-mOsm_kg, 4 hour time point.


title: M. trossulus_850_salinity_stress_replicate 1

description:
85_tr_1
Biological replicate 1 of 6. M. trossulus salinity stress, 850-mOsm_kg, 4 hours.


title: M. trossulus_1000_control, 4-hour-time-point_replicate 1

description:
85C_tr_1
Biological replicate 1 of 6. M. trossulus control, 1000-mOsm_kg, 4 hour time point.


title: M. trossulus_850_salinity_stress_replicate 2

description:
85_tr_2
Biological replicate 2 of 6. M. trossulus salinity stress, 850-mOsm_kg, 4 hours.


title: M. trossulus_850_salinity_stress_replicate 4

description:
85_tr_4
Biological replicate 4 of 6. M. trossulus salinity stress, 850-mOsm_kg, 4 hours.


title: M. trossulus_1000_control, 4-hour-time-point_replicate 3

description:
85C_tr_3
Biological replicate 3 of 6. M. trossulus control, 1000-mOsm_kg, 4 hour time point.


title: M. galloprovincialis_1000_control, Zero-time-point_replicate 6

description:
SC0_ga_6
Biological replicate 6 of 6. M. galloprovincialis control, 1000-mOsm_kg, beginning of experiment.


title: M. trossulus_850_salinity_stress_replicate 3

description:
85_tr_3
Biological replicate 3 of 6. M. trossulus salinity stress, 850-mOsm_kg, 4 hours.


title: Keratinocytes treated with EFNA1

city: New York

first: Miroslav

last: Blumenberg

state: NY

address: 455 First Ave #874

institute: NYU School of Medicine

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: MAS5 GCOS, RMAExpress summarized using PLM and log2 transformed

source_name: Epidermal keratinocytes treated with EFNA1

label_protocol: Standard Affymetrix protocol

growth_protocol: Standard e.g. as in Banno et al., J Biol Chem 279(31): 32633-32642.

treatment_protocol: ~70% confluent keratinocytes treated with 25 ng/ml EFNA-Fc conjugates (Sigma)

value: EFNA1-Fc conjugate


title: mESC-Dicer_WT-1

first: A

last: Bhutkar

address: 77 Massachusetts Avenue

description: Total RNA from Dicer WT mESCs

hyb_protocol: Performed according to manufacturer's instructions (Affymetrix) for Affymetrix Mouse Exon 1.0 ST arrays.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G; GeneChip® Command Console.

data_processing:
Data were processed using Partek Genomics Suite 6.4 software. RMA was used to summarize and normalize the probe data into probe set expression values. The list of utilized probe sets was defined by custom .ps and .mps files designed to include all core probes and all probes targeting miRNA transcripts. The RMA procedure used included the options adjusted for GC content, probe sequence, RMA background correction, Quantile Normalization and median polish probe set summarization. Expression values for probesets were summarized to a single value per gene based on the same custom .mps file mentioned above using the outlier excluded mean method. This procedure excludes probe set values that are more than 3 standard deviations above the mean or more and 2 standard deviations below the mean. The log fold change (LFC) value for WT/Dcr_null was defined as the difference between the mean expression in Dicer WT mESCs (Dcr_WT) and the mean expression in Dicer null mESCs (Dcr_null).
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.na25.mm9.core+miRNA.SH.11023.mps (Custom .mps file designed to include all core probes and all probes targeting miRNA transcripts ; mouse genome version mm9)

source_name: mESC

extract_protocol: Total RNA was collected using Trizol (Invitrogen) independently from three 10cm dishes of Dicer wild-type and Dicer null mESCs that were plated with 2E6 cells 48hrs prior to collection.

value: mESC

tag: genotype

value: wild type

tag: genetic background

value: mixed 129/B6


title: Keratinocytes treated with EFNA4

source_name: Epidermal keratinocytes treated with EFNA4

extract_protocol: Standard e.g. as in Banno et al., J Biol Chem 279(31): 32633-32642.

tag: agent

value: EFNA4-Fc conjugate


title: Keratinocytes untreated control

source_name: Epidermal keratinocytes untreated control

value: control (untreated)


title: mESC-Dicer_Null-2

description: Total RNA from Dicer Null mESCs

label_protocol: Performed according to manufacturer's instructions (Affymetrix) for Affymetrix Mouse Exon 1.0 ST arrays.

value: Dicer Null


title: mESC-Dicer_Null-3

description: Total RNA from Dicer Null mESCs


title: mESC-Dicer_Null-1

description: Total RNA from Dicer Null mESCs


title: M. trossulus_850_salinity_stress_replicate 6

description:
85_tr_6
Biological replicate 6 of 6. M. trossulus salinity stress, 850-mOsm_kg, 4 hours.

tag: tissue

value: gill


title: Keratinocytes treated with EFNA5

source_name: Epidermal keratinocytes treated with EFNA5

value: EFNA5-Fc conjugate


title: HFF-Pru GRA15KO-3

first: Emily

middle: E

last: Rosowski

address: 77 Massachusetts Ave, 68-258d

hyb_protocol: Following fragmentation, 4 ug of cDNA from uninfected samples or 5 ug of cDNA from infected samples were hybridized on GeneChip Human Genome U133A 2.0 Array in Affymetrix GeneChip Hybridization Oven 640, for 16 hours at 45C, 60rpm.  Arrays were washed and stained in Affymetrix Fluidics Station 450 according to manufacturer's protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 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. The trimmed mean target intensity of each array was arbitrarily set to 500.  Data was then normalized, setting all data to have a minimum value of 50.  Probes called absent or M were also set to have a value of 50.

source_name: HFF + Pru GRA15KO, 18hr

label_protocol: Labeled cDNA were prepared with the NuGEN Applause system from 50-100ng total RNA.

growth_protocol: Human foreskin fibroblasts (HFFs) were grown in T25 flasks (BD Biosciences) at 37C, 5% CO2 to confluency.  Parasite strains were maintained in vitro by serial passage on monolayers of HFFs.

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

treatment_protocol: Parasite strains were syringe lysed, washed at least once with PBS, and added to HFF monolayers for 18-24 hours.  Some samples were also stimulated with human TNF for 6 hours.

value: Human foreskin fibroblast (HFF)

tag: age


title: HFF-Pru GRA15KO-2


title: Keratinocytes treated with EFNA2

source_name: Epidermal keratinocytes treated with EFNA2

value: EFNA2-Fc conjugate


title: HFF-Pru-6

source_name: HFF + Pru, 18hr


title: HFF-Pru GRA15KO-4


title: HFF-Pru GRA15KO-1


title: HFF-Pru GRA15KO-5


title: HFF-Pru-1


title: WTMEF-RH GRA15II-1

hyb_protocol: Following fragmentation, 4 ug of cDNA from uninfected samples or 5 ug of cDNA from infected samples were hybridized on GeneChip Mouse Genome 430A 2.0 Array in Affymetrix GeneChip Hybridization Oven 640, for 16 hours at 45C, 60rpm.  Arrays were washed and stained in Affymetrix Fluidics Station 450 according to manufacturer's protocol.

source_name: WT MEF + RH GRA15II, 24hr

growth_protocol: Mouse embryonic fibroblasts (MEFs) were grown in 12-well plates (BD Biosciences) at 37C, 5% CO2 to confluency.  Parasite strains were maintained in vitro by serial passage on monolayers of Human foreskin fibroblasts (HFFs).

treatment_protocol: Parasite strains were syringe lysed, washed at least once with PBS, and added to MEF monolayers for 18-24 hours.

tag: strain

value: Mouse embryonic fibroblast (MEF)

value: WT


title: p65-/-MEF-RHGRA15II-1

source_name: p65-/- MEF + RH GRA15II, 24hr


title: p65-/-MEF-PruGRA15KO-1

source_name: p65-/- MEF + Pru GRA15KO, 24hr


title: HFF-Pru-3


title: Keratinocytes treated with EFNA3

source_name: Epidermal keratinocytes treated with EFNA3

value: EFNA3-Fc conjugate


title: HFF-Pru-4


title: p65-/-MEF-uninfected-1

source_name: p65-/- MEF, uninfected


title: HFF-Pru-5


title: p65-/-MEF-Pru-1

source_name: p65-/- MEF + Pru, 24hr


title: WTMEF-RH-1

source_name: WT MEF + RH, 24hr


title: WTMEF-PruGRA15KO-1

source_name: WT MEF + Pru GRA15KO, 24hr


title: HFF-cep GRA15II-4

source_name: HFF + cep GRA15II, 24hr


title: WTMEF-Pru-1

source_name: WT MEF + Pru, 24hr


title: HFF-cep GRA15II-3


title: WTMEF-uninfected-1

source_name: WT MEF, uninfected


title: HFF-cep GRA15II-1

description: low MOI


title: HFF-cep GRA15II-2

description: low MOI


title: Normal-ERα-positive breast cancer 74

city: SAINT-CLOUD

first: clairac

last: geraldine

address: 35 rue Daily

department: Oncogenetique

institute: Centre Rene Huguenin

description: Gene expression data from ERα-positive breast tumor without PIK3CA mutation

hyb_protocol: Gene chips were hybridized using standard Affymetrix protocol.

scan_protocol: Gene chips were scanned using standard Affymetrix protocol.

data_processing: BRB Array tools (version 3.6.0 available on http://linus.nci.nih.gov/BRB-ArrayTools.html) were used to import CEL files applying the Robust Method Average (RMA) normalization and to analyze expression genes.

source_name: ERα-positive breast tumors without PIK3CA mutation

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

extract_protocol: Total RNA was extracted from breast tissue samples by using acid-phenol guanidium method.

value: primary unilateral non-metastatic postmenopausal ERα-positive breast tumor

tag: gender

value: woman

value: 60 years


title: HFF-RH-3

source_name: HFF + RH, 18hr


title: HFF-RH GRA15II-1

source_name: HFF + RH GRA15II, 22hr


title: Normal-ERα-positive breast cancer 72

value: 70 years


title: Bcl3-/-_WB_rep4

first: Susan

last: Kandarian

address: 635commonwealth ave, Rm444

department: Health Sciences

description:
9_1591F
Biological replicate 4.

hyb_protocol: 15μg of labeled fragmented cRNA was hybridized on to Affymetrix GeneChip Mouse Genome 430A 2.0 Array (P/N 900499), then washed and stained according to the manufacturer’s protocol.

scan_protocol: The microarray slides were scanned using a GeneChip® Scanner 3000.

data_processing: For data extraction and quality control, Affymetix GeneChip® operation software (GCOS) was used, which created a single intensity value for each probe-set assayed in each sample in a .cel file. Affymetrix .cel files were imported into GenePattern software 3.2.1 (Broad Institute, Cambridge, MA) and a matrix containing an expression value per probe set for each sample was generated by Expression File Creator Module using the Robust Multi-array Average (RMA) algorithm and quantile normalization (Kuehn H, 2008).

source_name: Gastrocnemius and plantaris muscles from a Bcl3-/- mice, weight bearing control

label_protocol: Double-stranded cDNA was synthesized by GeneChip® Two-Cycle cDNA Synthesis Kit (P/N 900432) according to the standard Affymetrix protocol.

growth_protocol: Six-week-old male wild type mice (B6129PF2/J) and age/sex matched Nfkb1-/- mice (B6;129P2-Nfkb1tm1Bal/J) and Bcl3-/- mice (FVB;129P2-Bcl3tm1Ver/J) were purchased from the Jackson Laboratory (Bar harbor, ME).  Animals were provided with chow and water ad labium and housed in the Boston University Animal Care Facility.

extract_protocol: Six days after hind limb unloading, mice were anesthetized by Ketamine/Xylazine (100mg/kg, 13mg/kg).  Gastrocnemius and plantaris muscles were harvested from weight bearing and hind limb unloaded wild type mice, Nfkb1-/- mice, and Bcl3-/- mice and processed immediately for RNA isolation or ChIP assay. Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions. Extracted total RNA was treated with RNase-Free DNase I (Qiagen, Valencia, CA) to remove any DNA contamination and purified using a RNeasy Mini kit (Qiagen, Valencia, CA) as previously described (Koncarevic, 2007). Total RNA was quantified by absorption spectrophotometry at 260 and 280nm and quality of total RNA was monitored on a 1% denaturing agarose gel and analysis by a Bioanalyzer 2100 (Agilent, Palo Alto, CA).

treatment_protocol: After 3 days of acclimation, mice were randomly assigned to weight-bearing (WB) or hind limb unloaded (HU) groups.  Mice in the HU group were hind limb unloaded for 6 days using methods described previously (Hunter RB, 2002)  The use of animals in this study was approved by the Institutional Animal Care and Use Committee of Boston University.

value: male

value: gastrocnemius and plantaris muscles

tag: internvention

value: weight bearing


title: Mutated-ERα-positive breast cancer 69

description: Gene expression data from ERα-positive breast tumor with PIK3CA mutation

source_name: ERα-positive breast tumors with PIK3CA mutation

value: 72 years


title: Bcl3-/-_WB_rep3

description:
12_1591A
Biological replicate 3.


title: HFF-RH-4


title: HFF-RH GRA15II-2

source_name: HFF + RH GRA15II, 18hr


title: HFF-RH-2

source_name: HFF + RH, 22hr


title: Normal-ERα-positive breast cancer 68

value: 74 years


title: Mutated-ERα-positive breast cancer 71

value: 73 years


title: Bcl3-/-_6daysHU_rep2

description:
14_1591C
Biological replicate 2.

source_name: Gastrocnemius and plantaris muscles from a Bcl3-/- mice with 6 days of hind limb unloading

value: 6 days of hind limb unloading


title: c-MybTG/c-MybTG mice compare to wild type

city: Sendai

first: Hozumi

last: Motohashi

state: Miyagi

address: 2-1 Seiryo-machi, Aoba-ku

department: Center for Radioisotope Science

institute: Tohoku University Graduate School of Medicine

hyb_protocol: For each two-color comparison, 750 ng of each Cy3- and Cy5-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 17 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model G2505 at 100% PMT in both channels, with a scan resolution of 10um. A scan window of 61 x 21.6 mm was used, then images were cropped to size and saved in a modified two-color TIFF format. Images were examined visually for evidence of foreign debris or major failures.

data_processing: Data was obtained using the Agilent Feature Extraction software (v7.1.1), using default for all parameters.

source_name: Mouse megakaryocyte/erythrocyte lineage-restricted progenitors (MEPs) isolated from wild type bone marrow

label_protocol: 130ng of total RNA was amplified and labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's protocol.

growth_protocol: Bone marrow cells were stained with biotinylated antibodies specific for the following lineage markers: CD3 (KT31.1), CD4 (GK1.5), CD8 (53-6.7), B220 (6B2), Gr-1 (8C5), TER119, CD19 (1D3), IgM (R6-60.2, Pharmingen) and IL-7R chain (A7R34). Lin+ cells were partially removed with sheep anti-rat IgG-conjugated magnetic beads (Dynabeads M-450, Dynal A.S.), and the remaining cells were stained with avidin-Cy5-PE (Tricolor, Caltag). Cells were stained with PE-conjugated anti-FcRII/III (2.4G2), FITC-conjugated CD34 (RAM34) (Pharmingen), Texas red-conjugated anti-Sca-1 (E13-161-7) and APC-conjugated anti-c-Kit (2B8) monoclonal antibodies. All cell populations were sorted or analysed using a highly modified triple laser (488-nm argon laser, 599-nm dye laser and ultraviolet laser) FACS Vantage (Becton Dickinson Immunocytometry Systems). The IL-7R-Lin-Sca-1–c-Kit+ fraction was subdivided into FcR loCD34+, FcRloCD34-, and FcRhiCD34+ populations.  Among them, FcRloCD34- fraction was use as MEPs.

extract_protocol: Total RNA was extracted from MEPs using Isogen (Nippon Gene). RNA was further purified using an RNeasy Mini Kit (Qiagen).

value: wild type

value: MEPs

value: bone marrow

source_name: Mouse megakaryocyte/erythrocyte lineage-restricted progenitors (MEPs) isolated from MEPs of c-MybTG/c-MybTG bone marrow

value: MybTG/c-MybTG


title: HFF-cep-1

source_name: HFF + cep, 24hr

value: Human foreskin fibroblast (HFF)


title: Bcl3-/-_6daysHU_rep1

description:
13_1591B
Biological replicate 1.


title: HFF-cep-2


title: Mutated-ERα-positive breast cancer 73

value: 65 years


title: Normal-ERα-positive breast cancer 64

value: primary unilateral non-metastatic postmenopausal ERα-positive breast tumor

value: 53 years


title: Normal-ERα-positive breast cancer 66

value: woman

value: 62 years


title: Wildtype_WB_rep4

description:
WT-WB4-1545H
Biological replicate 4.

source_name: Gastrocnemius and plantaris muscles from a wild type mice, weight bearing control

value: male


title: Bcl3-/-_6daysHU_rep3

description:
15_1591D
Biological replicate 3.

value: gastrocnemius and plantaris muscles


title: Bcl3-/-_6daysHU_rep4

description:
16_1591E
Biological replicate 4.


title: Bcl3-/-_WB_rep2

description:
11_1591H
Biological replicate 2.

value: weight bearing


title: HFF-nostim,noinfection-3

source_name: HFF, uninfected, unstimulated


title: HFF-nostim,noinfection-1


title: Bcl3-/-_WB_rep1

description:
10_1591G
Biological replicate 1.


title: HFF-RH-1


title: Mutated-ERα-positive breast cancer 57

value: 46 years


title: Normal-ERα-positive breast cancer 62

value: 70 years


title: Normal-ERα-positive breast cancer 49


title: Normal-ERα-positive breast cancer 51

value: 71 years


title: Wildtype_WB_rep3

description:
WT-WB3-1545G
Biological replicate 3.


title: Normal-ERα-positive breast cancer 59

value: 73 years


title: Normal-ERα-positive breast cancer 47


title: Normal-ERα-positive breast cancer 50


title: mESC-Dicer_WT-3

description: Total RNA from Dicer WT mESCs

source_name: mESC

value: mESC

value: wild type

value: mixed 129/B6


title: Wildtype_WB_rep1

description:
WT-WB1-1545E
Biological replicate 1.


title: Wildtype_6daysHU_rep4

description:
WT-HU8-1545D
Biological replicate 4.

source_name: Gastrocnemius and plantaris muscles from a wild type mice with 6 days of hind limb unloading

value: 6 days of hind limb unloading


title: Mutated-ERα-positive breast cancer 46


title: Mutated-ERα-positive breast cancer 52

value: 75 years


title: Wildtype_WB_rep2

description:
WT-WB2-1545F
Biological replicate 2.


title: Normal-ERα-positive breast cancer 45

value: 61 years


title: mESC-Dicer_WT-2

description: Total RNA from Dicer WT mESCs


title: Wildtype_6daysHU_rep3

description:
WT-HU7-1545C
Biological replicate 3.


title: siERK1E224h_3491

city: Urbana

first: Zeynep

last: Madak Erdogan

state: IL

address: 1201 S Goodwin Ave

department: FSHN

institute: UIUC

description:
3491_E_34_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siERK1 treatment 60h, 10 nM E2 for 24h

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix [HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner GCS 3000.

data_processing: The data were analyzed with  GCOS2.1 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: MCF-7 cells were maintained in MEM media with 5% Calf serum

treatment_protocol: MCF-7 human breast cancer cells were transfected with 20 nM of siGENOME ctrl (siGL3),ERK1 or ERK2 (Thermo Scientific) using Dharmafect1 following the manufacturer’s instructions. After 60 h of transfection, cells were treated with 0.1% control ethanol vehicle or 10 nM E2 for 4h or 24h

tag: disease state

value: Breast adenocarcinoma

tag: cell line

tag: sirna

tag: time


title: Normal-ERα-positive breast cancer 37

value: primary unilateral non-metastatic postmenopausal ERα-positive breast tumor


title: p65-/-MEF-RH-1

value: Mouse embryonic fibroblast (MEF)


title: Normal-ERα-positive breast cancer 34

value: woman

value: 74 years


title: Normal-ERα-positive breast cancer 33

value: 64 years


title: siERK1E224h_3498

description:
3498_E_35_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siERK1 treatment 60h, 10 nM E2 for 24h


title: siERK1Veh24h_3492

description:
3492_E_32_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siERK1 treatment 60h, 0.1%EtOH for 24h

value: EtOH


title: Normal-ERα-positive breast cancer 36

value: 53 years


title: Nfkb1-/- _WB_rep2

description:
p105KO-WB10-1545M
Biological replicate 2.

source_name: Gastrocnemius and plantaris muscles from a Nfkb1-/- mice, weight bearing control

value: male

value: gastrocnemius and plantaris muscles

value: weight bearing


title: siERK2E224h_3496

description:
3496_E_30_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siERK2 treatment 60h, 10 nM E2 for 24h


title: Wildtype_6daysHU_rep1

description:
WT-HU5-1545A
Biological replicate 1.


title: Nfkb1-/- _WB_rep4

description:
p105KO-WB12-1545O
Biological replicate 4.


title: Normal-ERα-positive breast cancer 41

value: 78 years


title: Normal-ERα-positive breast cancer 26

value: 68 years


title: Mutated-ERα-positive breast cancer 28

value: 70 years


title: siERK2E224h_3493

description:
3493_E_29_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siERK2 treatment 60h, 10 nM E2 for 24h


title: Nfkb1-/- _WB_rep3

description:
p105KO-WB11-1545N
Biological replicate 3.


title: Normal-ERα-positive breast cancer 29

value: 62 years


title: Normal-ERα-positive breast cancer 31


title: Wildtype_6daysHU_rep2

description:
WT-HU6-1545B
Biological replicate 2.

value: wild type

value: 6 days of hind limb unloading


title: siERK2Veh24h_3495

description:
3495_E_25_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siERK2 treatment 60h, 0.1%EtOH for 24h

value: Breast adenocarcinoma


title: Normal-ERα-positive breast cancer 27

value: primary unilateral non-metastatic postmenopausal ERα-positive breast tumor

value: 69 years


title: siERK1Veh24h_3499

description:
3499_E_31_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siERK1 treatment 60h, 0.1%EtOH for 24h


title: Mutated-ERα-positive breast cancer 42

value: woman

value: 79 years


title: Normal-ERα-positive breast cancer 30


title: siCtrlE224h_3494

description:
3494_E_24_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siCtrl treatment 60h, 10 nM E2 for 24h

value: siCtrl


title: HFF-Pru-2

source_name: HFF + Pru, 18hr

value: Human foreskin fibroblast (HFF)


title: Nfkb1-/- _WB_rep1

description:
p105KO-WB9-1545P
Biological replicate 1.


title: Normal-ERα-positive breast cancer 25

source_name: ERα-positive breast tumors without PIK3CA mutation

value: 52 years


title: Normal-ERα-positive breast cancer 24

value: 55 years


title: Mutated-ERα-positive breast cancer 17

value: 76 years


title: siCtrlE224h_3497

description:
3497_E_23_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siCtrl treatment 60h, 10 nM E2 for 24h


title: Nfkb1-/- _6daysHU_rep4

description:
p105KO-HU13-1545I
Biological replicate 4.

source_name: Gastrocnemius and plantaris muscles from a Nfkb1-/- mice with 6 days of hind limb unloading

value: male

value: gastrocnemius and plantaris muscles


title: siCtrlVeh24h_3490

description:
3490_E_20_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siCtrl treatment 60h, 0.1%EtOH for 24h

value: EtOH


title: siCtrlVeh24h_3501

description:
3501_E_21_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siCtrl treatment 60h, 0.1%EtOH for 24h