title: DNA of mouse 440 brain tumor, Female, 119 days

source_name: tumor basal ganglia/midbrain

value: basal ganglia/midbrain tumor


title: time zero dark treated 3

status: Public on Mar 23 2011

type: RNA

city: San Francisco

first: Michael

last: DeSalvo

state: CA

department: Department of Anesthesia

country: USA

institute: UC San Francisco

description:
t0_d3
Fragment from colony 3 taken from experimental aquarium at time zero.

hyb_protocol: Dye-coupled cDNAs were cleaned (MinElute), and Cy3- and Cy5-labeled cDNAs were mixed together in a hybridization buffer containing 0.25% SDS, 25 mM HEPES, and 3x SSC. The hybridization mixtures were boiled for 2 min at 99oC, then allowed to cool at room temperature for 5min. The cooled hybridization mixtures were pipetted under an mSeries Lifterslip (Erie Scientific), and hybridization took place in custom-fabricated hybridization chambers overnight at 63oC. Microarrays were washed twice in 0.6x SSC and 0.01% SDS, followed by a rinse in 0.06x SSC and dried via centrifugation.

scan_protocol: Slides were immediately scanned using an Axon 4000B scanner (Molecular Devices), where care was taken to balance photomultiplier tube (PMT) settings.

data_processing: Gridding was performed using GenePix Pro 6.0. TIGR Express Converter was used to convert GenePix results files into .mev files for input into TIGR MIDAS 2.19 (Saeed et al. 2003). Data for a particular spot were discarded according to the stringent one bad channel policy. Additional data were discarded if spots had been flagged during gridding in GenePix, and if the intensity in either channel was less than 50,000 units. After filtering, background-subtracted median intensity values were LOWESS normalized, and in-slide duplicates were averaged.

molecule: total RNA

organism: Acropora palmata

label_protocol: One μg of total RNA was amplified using the MessageAmp II aRNA kit (Ambion), and 3 μg of aRNA per sample were primed with 10 μg random nonamer for 10 min at 70oC. Reverse transcription (RT) lasted for 2 hr at 50oC using a master mix containing a 4:1 ratio of aminoallyl-dUTP to TTP and SuperScript III reverse transcriptase (Invitrogen). Following RT, single-stranded RNA was hydrolyzed by incubating the RT reactions in 10 μL 0.5M EDTA and 10 μL 1M sodium hydroxide for 15 min at 65oC. After hydrolysis, RT reactions were cleaned using MinElute Reaction Cleanup columns (Qiagen). Cy3 and Cy5 dyes (GE Healthcare) were dissolved in 18 μL dimethyl sulfoxide, and the coupling reactions lasted for 1 hr at room temperature in the dark.

extract_protocol: Total RNA from all frozen coral fragments was isolated using Qiazol lysis reagent (QIAGEN). Live tissue was chiseled off each coral fragment and homogenized using a pre-chilled mortar and pestle. Frozen coral powder was transferred directly to Qiazol. Three chloroform extractions were performed, followed by isopropanol precipitation and three washes in 70% ethanol. RNA pellets were re-dissolved in nuclease-free water and cleaned further with RNeasy Mini columns (QIAGEN). RNA quantity and integrity were assessed with a NanoDrop ND-1000 spectrophotometer and an Agilent 2100 Bioanalyzer, respectively.

treatment_protocol: All aquaria were exposed to shaded ambient light during a four day acclimation period, and these conditions remained for the control aquaria during the entire experiment (roughly 40% of that experienced in the natural reef setting). Temperature in all aquaria during acclimation and experimental periods differed slightly. Following the acclimation period, a fragment from each control and experimental aquaria was sampled (t0-C and t0-D). After time zero sampling, the fiberglass pond containing the experimental tanks was covered with black plastic. The light exposure in the experimental tanks following time zero sampling was 0% of that experienced in the natural reef setting. After 9 days of darkness stress, a fragment of A. palmata was sampled from each control and experimental aquaria (9d-C and 9d-D). All samples were taken at night and frozen in liquid nitrogen.

tag: sample type

value: reference

tag: sample composition

value: pool of RNAs from all samples

source_name: time zero dark treated

tag: treatment

value: darkness

tag: treatment duration

tag: colony


title: time zero dark treated 2

description:
t0_d2
Fragment from colony 2 taken from experimental aquarium at time zero.


title: time zero control 3

description:
t0_c3
Fragment from colony 3 taken from control aquarium at time zero.

source_name: time zero control

value: control


title: time zero dark treated 1

description:
t0_d1
Fragment from colony 1 taken from experimental aquarium at time zero.


title: time zero control 4

description:
t0_c4
Fragment from colony 4 taken from control aquarium at time zero.


title: time zero control 1

description:
t0_c1
Fragment from colony 1 taken from control aquarium at time zero.


title: LE biological rep1

city: Irvine

first: Jacob

last: Biesinger

address: 4058 Donald Bren Hall, University of California Irvine

department: Computer Science

institute: University of California, Irvine

description: Gene Expression from mouse liver

hyb_protocol: The Mouse Gene 1.0 OST (Affymetrix) by hybridizing RNA from Cholesterol and L/E  in triplicate

scan_protocol: See manufacturer's website (Affymetrix)

data_processing: The data were analyzed with the Mouse Gene 1.0 OST using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 25. Differential expression was then assessed using the cyberT analysis program

label: biotin

organism: Mus musculus

source_name: lovastatin/ezetimibe fed

label_protocol: See manufacturer's website (Affymetrix)

growth_protocol: Six-week-old male C57BL/6 mice were obtained from Taconic and maintained on chow diet (2020X, Harlan Teklad Global ) for one week with a 12 hr light 12 hr dark cycle for acclimatization. 6 mice of two groups are subjected as Materials and Methods

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

treatment_protocol: All animal experiments were performed in accordance with accepted standards of animal welfare and with permission of the University of California, Irvine IACUC (protocol 97-1545). One group was maintained on a chow diet and the other two groups were fed either normal chow supplemented with a mixture of lovastatin (100 mg lovastatin [2.5 tablet equivalents]/100 g chow, w/w; Mylan) and ezetimibe (from MERCK/Schering-Plough Pharmaceuticals; 21 mg ezetimibe [2.1 tablet equivalents]/100 g chow, w/w) (LE) or powdered cholesterol (1%, w/w) (Ch).

tag: tissue

value: liver

tag: strain

tag: age

value: 6-week old

tag: gender

value: male


title: LE biological rep3

description: Gene Expression from mouse liver


title: CH biological rep2

description: Gene Expression from mouse liver

source_name: cholesterol fed


title: time zero control 2

description:
t0_c2
Fragment from colony 2 taken from control aquarium at time zero.


title: LE biological rep2

description: Gene Expression from mouse liver


title: Wild type control_6h_Replicate 3

status: Public on Mar 22 2011

type: mixed

city: Norwich

first: Sacha

last: Lucchini

address: Colney Lane

department: Molecular Microbiology

country: United Kingdom

institute: Institute of Food Research

description:
Control_6h: Biological Replicate 3 of 4.
035744B_WT_6.3

hyb_protocol: Slides blocked with DCE according to protocol at PMID 11266573. For hybridisation and washing protocols, see http://www.ifr.ac.uk/safety/Microarrays/protocols.html.

scan_protocol: Axon GenePix4000A, 10um resolution scan, and see http://www.ifr.ac.uk/safety/Microarrays/protocols.html.

data_processing: Data centering was performed by bringing the median ratio (Cy5/Cy3) for each of the 16 blocks to one using the following equation: (Ti) = (Cy5i/Cy3i) - c, where T is the centered ratio, i is the gene index, Cy5 and Cy3 are the red and green intensities and c is the 50th percentile of all Cy5/Cy3 ratios. Flagged features are omitted from the data centering process. Because we used a microarray based on S. Typhimurium strain LT2 to analyse the transcriptional response of a different strain (S. Typhimurium strain SL1344), we removed all the data corresponding to genes present in LT2, but absent from SL1344.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Wild type control, 6h

label_protocol:
Labelling protocol at:
http://www.ifr.ac.uk/safety/Microarrays/protocols.html.

growth_protocol: To prepare cells for RNA extraction, an overnight culture of the relevant strain was grown under antibiotic selection where appropriate, and used to inoculate 1:100 25 ml of fresh antibiotic free LB  in a 250 ml flask incubated with shaking at 250 rpm in a New Brunswick Innova 3100 waterbath at 37C. Samples were removed for RNA extraction at 1 h, 4 h and 6 h after inoculation.

extract_protocol: Total RNA isolation was performed using the Promega SV Total RNA Purification kit (Cat. No.: Z3100). For details, see the protocol at http://www.ifr.ac.uk/safety/Microarrays/protocols.html.

tag: genotype

value: wild type

tag: time

value: 6 hours

molecule: genomic DNA

source_name: Reference genomic DNA

growth_protocol: To prepare genomic DNA, cells were grown in LB under aeration until stationary phase.

extract_protocol: Genomic DNA was isolated using the Qiagen 'Genomic DNA' Kit (Cat. No.: 19060 for the buffer kit; 10243 for the columns).


title: CH biological rep1

description: Gene Expression from mouse liver


title: Wild type control_6h_Replicate 4

description:
Control_6h: Biological Replicate 4 of 4.
035760B_WT_6.4


title: CH biological rep3

description: Gene Expression from mouse liver


title: Wild type control_6h_Replicate 2

description:
Control_6h: Biological Replicate 2 of 4.
035771A_WT_6.2


title: H157-PIA6-6h (vs. PIA7)

city: Bethesda

first: Phillip

middle: A

last: Dennis

state: MD

address: 37 Convent Dr.

department: MOB, CCR

institute: NCI

description:
Analysis used the RNA sample from PIA7-treated H157 cells at 6h as control for comparison to that from PIA6-treated H157 cells at the same time point.
This Sample represents two hybridizations ('dye swap' and 'non-dye swap' experiments).
hv3-5-45.txt: PIA6-Cy5/PIA7-Cy3-6h
hv3-5-46.txt: PIA6-Cy3/PIA7-Cy5-6h

hyb_protocol: The combined Cy3- and Cy5-labeled cDNAs are put in a total volume of 250 ul DEPC H20 and 250 ul of 2X Agilent hybridization buffer. The mixture is then denatured for 2 minutes and applied on the Agillent hybridization chamber/gasket slide in sandwich with the array slide. The hybridization is performed at 65 degree for 16 hours.

scan_protocol: Agilent High-Resolution Microarray Scanner (Cat# G2565CA).

data_processing: IPLab/DeArray image microarray analysis software. The data went through a linear normalization process. No filtering was done on the raw result files. The values in the Sample data table represent the log2 ratio of the cal.ratio column.

organism: Homo sapiens

source_name: H157 cells treated with PIA6 for 6h

label_protocol: 15 microgram of total RNA was reverse transcribed with Anchor Oligo-dT and Aminoallyl dUTP, after NaOH RNA hydrolysis, the labeled Aminoallyl dUTP cDNA is purified with Qiagen, QIAQuick PCR Purification Kit (Cat. # 28104). The Aminoallyl dUTP cDNAs are then coupled with either Cy3 or Cy5 mono NHS Ester Dyes. The Cy Dyes labeled cDNAs are then purified with Qiagen, QIAQuick PCR Purification Kit (Cat. # 28104).

growth_protocol: H157 cells were plated 2x10^6 in T-75 flasks in RPMI medium 1640 containing 10% FBS and incubated for 24h.

extract_protocol: Total RNA was extracted from cells treated in T-75 flasks using TRIzol reagent (Invitrogen) and chloroform, and purified according to the RNeasy midiprep spin kit protocol (Qiagen).

treatment_protocol: The medium was changed to RPMI medium 1640 with 0.1% FBS and the cells were incubated overnight.  The following morning, cells were treated with 10 microM PIA6 dissolved in DMSO for 0h, 2h, 6h or 12h, and an equal volume of DMSO was added to control samples.  For the PIA comparison, 10 microM PIAs (5, 6, 7, 23, 24, 25) or 10 microM LY294002 (LY) were incubated with the cells for 6h.  In the PIA comparison experiment, the same concentration of PIA7 (an inert analog consisting of only the lipid side chain) was used as a control.

tag: cell line

tag: cell type

value: non-small cell lung cancer

value: phosphatidylinositol ether lipid analogue 6 (PIA6)

value: 6 hr

source_name: H157 cells treated with PIA7 for 6h

value: phosphatidylinositol ether lipid analogue 7 (PIA7)


title: Wild type control_6h_Replicate 1

description:
Control_6h: Biological Replicate 1 of 4.
035676B_WT_6.1


title: hupAB_6h_Replicate 1

description:
hupAB_6h: Biological Replicate 1 of 2.
035764B_hupAB6.1

source_name: hupAB, 6h

value: delta-hupA delta-hupB


title: H157-PIA24-6h (vs. PIA7)

description:
Analysis used the RNA sample from PIA7-treated H157 cells at 6h as control for comparison to that from PIA24-treated H157 cells at the same time point.
This Sample represents two hybridizations ('dye swap' and 'non-dye swap' experiments).
hv3-5-49.txt: PIA24-Cy5/PIA7-Cy3-6h
hv3-5-50.txt: PIA24-Cy3/PIA7-Cy5-6h

source_name: H157 cells treated with PIA24 for 6h

value: phosphatidylinositol ether lipid analogue 24 (PIA24)


title: H157-LY-6h (vs. PIA7)

description:
Analysis used the RNA sample from PIA7-treated H157 cells at 6h as control for comparison to that from LY-treated H157 cells at the same time point.
This Sample represents two hybridizations ('dye swap' and 'non-dye swap' experiments).
hv3-5-53.txt: LY-Cy5/PIA7-Cy3-6h
hv3-5-54.txt: LY-Cy3/PIA7-Cy5-6h

source_name: H157 cells treated with LY for 6h


title: hupB_6h_Replicate 1

description:
hupB_6h: Biological Replicate 1 of 2.
035746A_hupB6.1

source_name: hupB, 6h

value: delta-hupB


title: H157-PIA25-6h (vs. PIA7)

description:
Analysis used the RNA sample from PIA7-treated H157 cells at 6h as control for comparison to that from PIA25-treated H157 cells at the same time point.
This Sample represents two hybridizations ('dye swap' and 'non-dye swap' experiments).
hv3-5-51.txt: PIA25-Cy5/PIA7-Cy3-6h
hv3-5-52.txt: PIA25-Cy3/PIA7-Cy5-6h

source_name: H157 cells treated with PIA25 for 6h

value: phosphatidylinositol ether lipid analogue 25 (PIA25)


title: H157-PIA5-6h (vs. PIA7)

description:
Analysis used the RNA sample from PIA7-treated H157 cells at 6h as control for comparison to that from PIA5-treated H157 cells at the same time point.
This Sample represents two hybridizations ('dye swap' and 'non-dye swap' experiments).
hv3-5-43.txt: PIA5-Cy5/PIA7-Cy3-6h
hv3-5-44.txt: PIA5-Cy3/PIA7-Cy5-6h

source_name: H157 cells treated with PIA5 for 6h

value: phosphatidylinositol ether lipid analogue 5 (PIA5)


title: H157-PIA23-6h (vs. PIA7)

description:
Analysis used the RNA sample from PIA7-treated H157 cells at 6h as control for comparison to that from PIA23-treated H157 cells at the same time point.
This Sample represents two hybridizations ('dye swap' and 'non-dye swap' experiments).
hv3-5-47.txt: PIA23-Cy5/PIA7-Cy3-6h
hv3-5-48.txt: PIA23-Cy3/PIA7-Cy5-6h

source_name: H157 cells treated with PIA23 for 6h

value: phosphatidylinositol ether lipid analogue 23 (PIA23)


title: H157-PIA6-12h (vs. DMSO)

description:
Analysis used the RNA sample from DMSO-treated H157 cells at 12h as control for comparison to that from PIA6-treated H157 cells at the same time point.
This Sample represents two hybridizations ('dye swap' and 'non-dye swap' experiments).
hv3-5-68.txt: PIA6-Cy5/DMSO-Cy3-12h
hv3-5-69.txt: PIA6-Cy3/DMSO-Cy5-12h

source_name: H157 cells treated with PIA6 for 12h

value: 12 hr

source_name: H157 cells treated with DMSO for 12h

value: DMSO


title: hupB_6h_Replicate 2

description:
hupB_6h: Biological Replicate 2 of 2.
035746B_hupB6.2


title: H157-PIA6-2h (vs. DMSO)

description:
Analysis used the RNA sample from DMSO-treated H157 cells at 2h as control for comparison to that from PIA6-treated H157 cells at the same time point.
This Sample represents two hybridizations ('dye swap' and 'non-dye swap' experiments).
hv3-5-64.txt: PIA6-Cy5/DMSO-Cy3-2h
hv3-5-65.txt: PIA6-Cy3/DMSO-Cy5-2h

source_name: H157 cells treated with PIA6 for 2h

value: 2 hr

source_name: H157 cells treated with DMSO for 2h


title: H157-PIA6-6h (vs. DMSO)

description:
Analysis used the RNA sample from DMSO-treated H157 cells at 6h as control for comparison to that from PIA6-treated H157 cells at the same time point.
This Sample represents two hybridizations ('dye swap' and 'non-dye swap' experiments).
hv3-5-66.txt: PIA6-Cy5/DMSO-Cy3-6h
hv3-5-67.txt: HPIA6-Cy3/DMSO-Cy5-6h

source_name: H157 cells treated with DMSO for 6h


title: hupA_6h_Replicate 1

description:
hupA_6h: Biological Replicate 1 of 2.
035678A_hupA6.1

source_name: hupA, 6h

value: delta-hupA


title: Wild type control_4h_Replicate 4

description:
Control_4h: Biological Replicate 4 of 4.
035764A_WT_4.4

source_name: Wild type control, 4h

value: 4 hours


title: hupA_6h_Replicate 2

description:
hupA_6h: Biological Replicate 2 of 2.
035678B_hupA6.2

source_name: Reference genomic DNA

value: wild type


title: Wild type control_4h_Replicate 3

description:
Control_4h: Biological Replicate 3 of 4.
035743A_WT_4.3


title: hupB_4h_Replicate 1

description:
hupB_4h: Biological Replicate 1 of 2.
035675B_hupB4.1

source_name: hupB, 4h


title: hupB_4h_Replicate 2

description:
hupB_4h: Biological Replicate 2 of 2.
035675A_hupB4.2


title: hupAB_4h_Replicate 2

description:
hupAB_4h: Biological Replicate 2 of 2.
035763B_hupAB4.2

source_name: hupAB, 4h


title: hupAB_4h_Replicate 1

description:
hupAB_4h: Biological Replicate 1 of 2.
035763A_hupAB4.1


title: H157-PIA6-0h (vs. DMSO)

description:
Analysis used the RNA sample from DMSO-treated H157 cells at 0h as control for comparison to that from PIA6-treated H157 cells at the same time point.
This Sample represents two hybridizations ('dye swap' and 'non-dye swap' experiments).
hv3-5-62.txt: PIA6-Cy5/DMSO-Cy3-0h
hv3-5-63.txt: PIA6-Cy3/DMSO-Cy5-0h

source_name: H157 cells treated with PIA6 for 0h

value: 0 hr

source_name: H157 cells treated with DMSO for 0h


title: hupA_4h_Replicate 2

description:
hupA_4h: Biological Replicate 2 of 2.
035745A_hupA4.2

source_name: hupA, 4h


title: Wild type control_4h_Replicate 2

description:
Control_4h: Biological Replicate 2 of 4.
035739A_WT_4.2


title: Wild type control_1h_Replicate 7

description:
Control_1h: Biological Replicate 6 of 6. Technical Replicate 2 of 2.
035759B_WT_1.6.2

source_name: Wild type control, 1h

value: 1 hour


title: Wild type control_1h_Replicate 6

description:
Control_1h: Biological Replicate 6 of 6. Technical Replicate 1 of 2.
035759A_WT_1.6.1


title: Wild type control_4h_Replicate 1

description:
Control_4h: Biological Replicate 1 of 4.
035745B_WT_4.1


title: DNA of mouse 491 brain tumor cranial nerve, Male, 190 days

type: genomic

city: Memphis

first: Chunxu

last: Qu

state: TN

address: 262 Danny Thomas Pl

department: Pathology

institute: St Jude Children's Research Institute

description: tissue from mouse brain with high grade glioma.

hyb_protocol: Genomic DNA hybridization to Agilent CGH arrays were performed as per manufacturer' protocol (http://www.agilent.com).

scan_protocol: Scanning was performed as per manufacturer's protocol (http://www.agilent.com).

data_processing: LOWESS normalized log2 ratio (test/reference).  R/aCGHNorm package was used.

source_name: tumor cranial nerve

label_protocol: Genomic DNA Labeling Kit (Enzo Life Sciences, Farmingdale, NY) was used as per manufacturer's protocol.

extract_protocol: Pulverized tissue was lysed in 200mM NaCl, 5mM EDTA, 0.2% SDS, 100mM Tris pH8.5, 100ug/ml proteinase K overnight at 55C, then extracted with phenol/chloroform.

value: cranial nerve tumor

value: Pten, p53, Rb1 knockout

value: Male

source_name: normal genomic DNA with opposite sex to ch1


title: Wild type control_1h_Replicate 5

description:
Control_1h: Biological Replicate 5 of 6.
035740B_WT_1.5


title: hupA_4h_Replicate 1

description:
hupA_4h: Biological Replicate 1 of 2.
035679B_hupA4.1


title: Wild type control_1h_Replicate 4

description:
Control_1h: Biological Replicate 4 of 6.
035679A_WT_1.4


title: Yeast transcriptional response to high (20%) glucose.4

city: Valencia

first: Marcel·lí

last: del Olmo

address: Dr. Moliner, 50

country: Spain

institute: Universitat de València

description: No more description is needed

hyb_protocol: First cDNA-labeled is denaturalised.Place array slide in Hybridization chamber. Add 10ul 3X SSC to slide (well away from spotted array). Add probe sample onto array area. Apply coverslip PROMPTLY over array. Seal hybridization chamber. Incubate @ 63°C ~ 16 hrs. by submerging in water bath immediately. Do different washes with SSC and SDS.

scan_protocol: GenePix 4000 scanner

data_processing: Intensity obtained in each channel for each pair of microarrays was normalised by Lowess by the Fred Hutchinson Cancer Research Center (FHCRC) Genomics Resource utilizing a pipeline of applications, including GeneTraffic and GTExport (GeneTraffic Export).

organism: Saccharomyces cerevisiae

source_name: Yeast cells 1 hour in 2% glucose

label_protocol:
Amino-allyl reverse transcription labeling protocol: Total RNA combined with oligo-dT, 5X First Strand Buffer, 0.1M DTT, 50X aa-dUTP/dNTPs, and SuperScript II.
The cDNA is resuspended and Sodium Bicarbonate is added to sample. Vortex samples and spin down. Add the appropriate dye to the reaction. Vortex samples and spin down. Incubate @ RT - 1 hr in the dark. Clean-up.

extract_protocol: Cells were lysed with glass beads in LETS buffer, and total RNA was extracted with phenol and precipitated with 5M LiCl.

tag: Yeast cells 1 hour in 2% glucose

source_name: Yeast cells 1 hour in 20% glucose

label_protocol: Amino-allyl reverse transcription labeling protocol: Total RNA combined with oligo-dT, 5X First Strand Buffer, 0.1M DTT, 50X aa-dUTP/dNTPs, and SuperScript II.The cDNA is resuspended and Sodium Bicarbonate is added to sample. Vortex samples and spin down. Add the appropriate dye to the reaction. Vortex samples and spin down. Incubate @ RT - 1 hr in the dark. Clean-up.

tag: Yeast cells 1 hour in 20% glucose


title: Yeast transcriptional response to high (20%) glucose.5

description: No more description is needed


title: NB4 WEB-2170 24 hours (replicate 1)

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

description: Synthesis of biotinylated cRNA targets, arrays hybridization (Human HG-U133A GeneChip, Affymetrix, Santa Clara,CA), staining and scanning were performed using Affymetrix standard protocols starting from 5μg of total RNA.

hyb_protocol: Affymetrix Human HG-U133A GeneChip arrays hybridization and staining was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA).The fragmented cRNA was then hybridized to an identical lot of Affymetrix Human HG-U133A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.

scan_protocol: GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.

data_processing: Scaling to TGT value=330. The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples.

source_name: NB4 treated with WEB-2170

label_protocol: One-cycle target labeling assays was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). Briefly, biotin-labeled target synthesis was performed, starting from 5 µg of total cellular RNA, according to the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.

extract_protocol: Total RNA was isolated from 1000000 cells using RNeasy Mini kit (Qiagen, Valencia, CA). Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 bioanalyzer.

tag: NB4 cell line

tag: treated with WEB-2170 0.5mM for 24 hours

tag: Human Acute promyelocytic leukemia cell line


title: Yeast transcriptional response to high (20%) glucose.3

description: No more description is needed

hyb_protocol: First cDNA-labeled is denaturalised.Place array slide in Hybridization chamber. Add 10ul  3X SSC to slide (well away from spotted array). Add probe sample onto array area. Apply coverslip PROMPTLY over array. Seal hybridization chamber. Incubate @ 63°C  ~ 16 hrs.  by submerging in water bath immediately. Do different washes with SSC and SDS.

label_protocol:
Amino-allyl reverse transcription labeling protocol:  Total RNA combined with oligo-dT, 5X First Strand Buffer, 0.1M DTT, 50X aa-dUTP/dNTPs, and SuperScript II.
The cDNA is resuspended and Sodium Bicarbonate is added to sample. Vortex samples and spin down. Add the appropriate dye to the reaction. Vortex samples and spin down. Incubate @ RT - 1 hr in the dark. Clean-up.


title: Wild type control_1h_Replicate 3

description:
Control_1h: Biological Replicate 3 of 6.
035770B_WT_1.3


title: NB4 untreated 24 hours (replicate 1)

source_name: NB4 untreated


title: hupB_1h_Replicate 4

description:
hupB_1h: Biological Replicate 2 of 2. Technical Replicate 2 of 2.
035770A_hupB1.4

source_name: hupB, 1h


title: hupB_1h_Replicate 3

description:
hupB_1h: Biological Replicate 1 of 2. Technical Replicate 2 of 2.
035747B_hupB1.3


title: hupAB_1h_Replicate 2

description:
hupAB_1h: Biological Replicate 1 of 2. Technical Replicate 2 of 2.
035742B_hupAB1.2

source_name: hupAB, 1h

value: delta-hupA delta-hupB


title: Wild type control_1h_Replicate 2

description:
Control_1h: Biological Replicate 2 of 6.
035738B_WT_1.2


title: hupAB_1h_Replicate 1

description:
hupAB_1h: Biological Replicate 1 of 2. Technical Replicate 1 of 2.
035742A_hupAB1.1


title: Wild type control_1h_Replicate 1

description:
Control_1h: Biological Replicate 1 of 6.
035738A_WT_1.1


title: Drosophila Salivary Glands, Rad21 DamID

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description: Drosophila Salivary Glands, Rad21 DamID

hyb_protocol: Hybridizations were done using standard protocols (see http://microarrays.nki.nl/download/protocols.html).

scan_protocol: Microarrays were scanned in an Agilent scanner.

data_processing:
Values of all reporters except NimbleGen control reporters were extracted from pair files, represented as log2-ratios and normalized using the the loess() function in R with parameter control=loess.control(trace.hat='approximate'). Values from 2 replicates were median centered and averaged (VALUE). Normalized value for each individual replicate are also provided (REP_1 and REP_2).
For Replicate_1 ('CMF_306483_S01' raw data files), Dam-fusion sample is labelled with Cy3 and Dam-only with Cy5.  For Replicate_2 ('CMF_331686_S01' raw data files), Dam-fusion sample is labelled with Cy5 and Dam-only with Cy3.

organism: Drosophila melanogaster

source_name: DamID on gDNA from salivary glands from transgenic flies, expressing Dam-Rad21

label_protocol: 1 µg DamID DNA was directly labeled by Klenow random priming with Cy5/Cy3 nonamers per manufacturer's protocol (see http://www.nimblegen.com/products/lit/lit.html)

extract_protocol: Salivary Glands from crawling third instar larvae were dissected, gDNA was isolated by phenol-chloroform extraction and DamID samples were prepared as described before (Greil et al. 2006)

tag: genotype/variation

value: w,P{w+, UAST-Dam-myc-Rad21} (X)

value: salivary glands

tag: developmental stage

value: crawling third instar larvae

source_name: DamID on gDNA from salivary glands from transgenic flies, expressing Dam-only


title: NB4 WEB-2170 24 hours (replicate 2)


title: hupB_1h_Replicate 1

description:
hupB_1h: Biological Replicate 1 of 2. Technical Replicate 1 of 2.
035771B_hupB1.1

value: delta-hupB

source_name: Reference genomic DNA


title: hupAB_1h_Replicate 4

description:
hupAB_1h: Biological Replicate 2 of 2. Technical Replicate 2 of 2.
035203B_hupAB1.4


title: Sclera week 8, biological rep4

city: Singapore

first: Wan'e

last: Lim

address: 11 Third Hospital Ave

country: Singapore

institute: Singapore Eye Research Institute

description: Gene expression data from week 8 sclera

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on a Mouse Gene 1.0 ST array(Affymetrix, Inc, Santa Clara, CA). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using Genechip® Hybridzation kit(Affymetrix, Inc, Santa Clara, CA).

scan_protocol: GeneChips were scanned using Genechip® Scanner 3000 7G (Affrymetrix, Inc, Santa Clara, CA).

data_processing: The data were analyzed with Partek Genomics Suite version 6.5 beta and normalized using Genechip robust multiarray averaging (GC-RMA) and batch removal tool.

label: Biotin

source_name: Sclera tissue from week 8 mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA using Genechip® Whole Transcript Sense Target Labeling Assay and (Affymetrix, Inc, Santa Clara, CA).

growth_protocol: Balb/cJ mice (Mus musculus) were obtained from the animal holding unit of the National University of Singapore.

extract_protocol: Total RNA was isolated from single cryogenically ground mouse sclera (n=30, 6 samples each from week 1-, 2-, 3-, 6-and 8-old mice) using MELTTM Total Nucleic Acid Isolation System (Ambion Inc, Austin, TX) according to the manufacturer’s instructions

value: Balb/cJ

value: Week 8


title: Sclera week 8, biological rep6

description: Gene expression data from week 8 sclera


title: hupB_1h_Replicate 2

description:
hupB_1h: Biological Replicate 2 of 2. Technical Replicate 1 of 2.
035747A_hupB1.2


title: hupA_1h_Replicate 2

description:
hupA_1h: Biological Replicate 2 of 2.
035736B_hupA1.2

source_name: hupA, 1h


title: Sclera week 8, biological rep3

description: Gene expression data from week 8 sclera


title: hupA_1h_Replicate 1

description:
hupA_1h: Biological Replicate 1 of 2.
035736A_hupA1.1


title: Sclera week 8, biological rep2

description: Gene expression data from week 8 sclera


title: Sclera week 8, biological rep5

description: Gene expression data from week 8 sclera


title: Sclera week 6, biological rep6

description: Gene expression data from week 6 sclera

source_name: Sclera tissue from week 6 mouse

value: Week 6


title: NB4 untreated 24 hours (replicate 2)


title: Sclera week 6, biological rep5

description: Gene expression data from week 6 sclera


title: Sclera week 6, biological rep3

description: Gene expression data from week 6 sclera


title: Sclera week 6, biological rep2

description: Gene expression data from week 6 sclera


title: Sclera week 6, biological rep4

description: Gene expression data from week 6 sclera


title: Yeast transcriptional response to high (20%) glucose.1

description: No more description is needed


title: Sclera week 6, biological rep1

description: Gene expression data from week 6 sclera


title: Sclera week 3, biological rep6

description: Gene expression data from week 3 sclera

source_name: Sclera tissue from week 3 mouse

value: Week 3


title: Sclera week 3, biological rep4

description: Gene expression data from week 3 sclera


title: Sclera week 8, biological rep1

description: Gene expression data from week 8 sclera


title: hupAB_6h_Replicate 2

description:
hupAB_6h: Biological Replicate 2 of 2.
035760A_hupAB6.2

source_name: hupAB, 6h

value: 6 hours


title: Aedes aegypti salivary gland tags, following infection with dengue virus

type: SAGE

anchor: NlaIII

city: Montpellier

first: David

last: Piquemal

address: 1682, rue de la Valsière

country: France

institute: ACOBIOM

description: The quality of total RNA was checked by capillary electrophoresis analysis using an Agilent BioAnalyser 2100 (Agilent, Palo Alto, CA, USA) and quantities were measured using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, Les Ulis, France).

data_processing: Generation of expression matrices, data annotation, filtering and processing were performed with BIOTAG software (Skuld-Tech, France) (Piquemal et al. Genomics 2002).

organism: Aedes aegypti

extract_protocol: TRIZOL and Dynal Magnetic Beads

treatment_protocol:
Infectious blood meals were offered to 3-day-old, adult, female Ae. aegypti Liverpool mosquitoes using a silicone membrane feeder system (Alto et al., 2005). Human blood was combined with DENV-2
Aedes albopictus C6/36 cells for propagation of the four dengue serotypes (Dengue 1-Hawaii strain, Dengue2-16681 strain, DV3-H87 strain and DV4-814669 strain) were grown in M199 medium (Invitrogen, France) at 28°C. HEK-293T (Human Embryonic Kidney 293) was grown in DMEM at 37°C. All media were supplemented with 10% fetal calf serum (FCS, Lonza, Switzerland) and incubated in a humid atmosphere with 5% CO2.

value: salivary gland


title: Sclera week 3, biological rep3

description: Gene expression data from week 3 sclera


title: Sclera week 3, biological rep1

description: Gene expression data from week 3 sclera


title: Sclera week 2, biological rep5

description: Gene expression data from week 2 sclera

source_name: Sclera tissue from week 2 mouse

value: Week 2


title: Sclera week 3, biological rep2

description: Gene expression data from week 3 sclera


title: Sclera week 2, biological rep3

description: Gene expression data from week 2 sclera


title: Sclera week 3, biological rep5

description: Gene expression data from week 3 sclera


title: Sclera week 2, biological rep6

description: Gene expression data from week 2 sclera


title: Aedes aegypti salivary gland tags

source_name: Aedes aegypti salivary gland tags

extract_protocol: TRIZOL and Magnetic beads Dynal


title: Sclera week 2, biological rep4

description: Gene expression data from week 2 sclera


title: Sclera week 2, biological rep2

description: Gene expression data from week 2 sclera


title: Liver (SF4)

city: Stanford

first: Jonathan

last: Pollack

address: 269 Campus Drive, CCSR3245A

institute: Stanford University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7702.gif

hyb_protocol: not provided

scan_protocol: Scanner Model = GenePix 4000A

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

source_name: Liver Reference

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: Liver Reference

source_name: Liver (SF4)

tag: disease state

value: normal liver specimen


title: Liver (HK23)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7553.gif

source_name: Liver (HK23)


title: Liver (HK2)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12965.gif

source_name: Liver (HK2)


title: Liver (SF8)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7709.gif

source_name: Liver (SF8)


title: Liver (SF5)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5152.gif

source_name: Liver (SF5)


title: Liver (SF33)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7773.gif

source_name: Liver (SF33)


title: hupAB_1h_Replicate 3

description:
hupAB_1h: Biological Replicate 2 of 2. Technical Replicate 1 of 2.
035203A_hupAB1.3

source_name: hupAB, 1h

value: 1 hour

value: wild type


title: Sclera week 2, biological rep1

description: Gene expression data from week 2 sclera


title: Sclera week 1, biological rep5

description: Gene expression data from week 1 sclera

source_name: Sclera tissue from week 1 mouse

value: Week 1


title: colon met30

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66174.gif

source_name: colon cell line ref

value: colon cell line ref

source_name: colon met30

value: Colon cancer metastatic to liver


title: Yeast transcriptional response to high (20%) glucose.2

description: No more description is needed

source_name: Yeast cells 1 hour in 20% glucose

source_name: Yeast cells 1 hour in 2% glucose


title: Liver (SF16)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7771.gif

source_name: Liver (SF16)


title: Sclera week 1, biological rep6

description: Gene expression data from week 1 sclera


title: Liver (SF9)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7718.gif

source_name: Liver (SF9)


title: Sclera week 1, biological rep3

description: Gene expression data from week 1 sclera


title: Sclera week 1, biological rep4

description: Gene expression data from week 1 sclera


title: Liver (SF19)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5157.gif

source_name: Liver (SF19)


title: Sclera week 1, biological rep1

description: Gene expression data from week 1 sclera


title: colon met24

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66115.gif

source_name: colon met24


title: colon met31

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66175.gif

source_name: colon met31


title: Sclera week 1, biological rep2

description: Gene expression data from week 1 sclera


title: A549_H5N2_5

city: Lyon

first: Julien

last: Textoris

address: Hôpital Edouard herriot - Pavillon P; 5 place d'Arsonval

department: Medical Diagnostic Discovery Department (MD3)

institute: bioMérieux

hyb_protocol: labelled cDNA were hybridized 18h with HuSG9k microarray according to the standard protocol.

scan_protocol: All membranes used in this study belonged to the same batch. After hybridization and exposition on Micro Imager, arrays were scanned in a Fuji BAS 5000 machine and hybridization signals were quantified using the BZ Scan Software

data_processing: Data files were loaded and analyzed with R (v2.9.2) and Bioconductor (v2.4.1) {Gentleman, 2004}, using the NylonArray library developed by the TAGC to support BZScan2 files (library available upon request). Raw data were normalized using quantile normalization. Supervised analysis between groups Infected and Mock samples was conducted using the Significance Analysis of Microarray algorithm {Tusher, 2001}, using siggenes library (v.1.18.0) {Schwender, 2008}. All statistical analysis used corrections for multiple comparisons (Benjamini and Hochberg){Benjamini, 1995}.

source_name: A549 lung epithelial cell infected with H5N2

label_protocol: mRNA were labelled with 33P during the reverse transcription by using the Superscript III RT (Invitrogen),  (α33P)dCTP and an oligodT25.

growth_protocol: The lung epithelial cell line A549 cells were grown as monolayers in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 100 U of penicillin/mL, and 100 ug of streptomycin sulfate/mL at 37°C.

extract_protocol: Total RNA was extracted from cell pellets by using an RNeasy Mini Kit (Qiagen,Valencia,CA) for the BSL2 viruses. For H5N1 infections, total RNA was extracted with Trizol LS (Invitrogen).

treatment_protocol: Inﬂuenza viruses A/New Caledonia/20/99 (H1N1), A/Moscow/10/99 (H3N2), A/Lyon/969/09 (H1N1 SOI-V), A/Turkey/582/2006 (H5N1), A/Finch/England/2051/94 (H5N2), and A/Chicken/Italy/2076/99 (H7N1) were produced in MDCK cells in EMEM supplemented with 2 mM L-glutamine, 100U of penicillin/mL, 100 μg of streptomycin sulfate/mL and 1 μg of trypsin /mL. Viruses were titered by standard plaque assay in MDCK cells.For the microarray analysis, A549 cells were infected with influenza viruses at a multiplicity of infection (moi) of 1 in DMEM supplemented with 2 mM L-glutamine, 100U of penicillin/mL, 100 μg of streptomycin sulfate/mL and 0.5 μg of trypsin /mL. This moi was chosen to ensure that 100% of the cells were infected 24 h postinfection.

tag: infection


title: colon met16

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66105.gif

source_name: colon met16


title: colon met14

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66103.gif

source_name: colon met14


title: colon met6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66095.gif

source_name: colon met6


title: colon met32

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66176.gif

source_name: colon met32


title: colon met15

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66104.gif

source_name: colon met15


title: colon met7

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66096.gif

source_name: colon met7


title: 1aDF macrophage rep2

city: Orlando

first: Seung-Soon

last: Im

state: FL

address: 6400 Sanger Rd.

institute: Sanford-Burnham Medical Research Institute

description: Gene expression data from embryos in slow phase of cellularisation.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on mouse gene 1.0 ST array GeneChips Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with GeneChIP operating software using Affymetrix and GeneSpring software (Agilent technologies). The data were further analyzed by the Cyber-T statistical analysis program (http://cybert.microarray.ics.uci.edu).

source_name: 1aDF macrophages

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

value: SREBP-1a deficinet

tag: macrophages

value: Bone marrow drived macrophage


title: 1aDF macrophage rep1


title: colon met27

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66171.gif

source_name: colon cell line ref

source_name: colon met27


title: A549_H5N2_4


title: WT macrophage rep3

source_name: WT macrophages

value: wildtype


title: 1aDF macrophage rep3


title: WT macrophage rep1

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.


title: colon met9

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66098.gif

source_name: colon met9


title: A549_H5N2_3


title: colon met11

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66100.gif

source_name: colon met11


title: A549_H5N2_2


title: WT macrophage rep2


title: colon met3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66081.gif

source_name: colon met3


title: A549_H5N2_1


title: colon met20

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66110.gif

source_name: colon met20


title: colon met18

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66108.gif

source_name: colon met18


title: colon met26

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66170.gif

source_name: colon met26


title: colon met4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66083.gif

source_name: colon met4


title: colon met19

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66109.gif

source_name: colon met19


title: A549_H3N2_3

source_name: A549 lung epithelial cell infected with H3N2


title: Colon_CA S02-7284

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50508.gif

source_name: common reference RNA

value: common reference RNA

source_name: Colon_CA S02-7284

value: Primary colon cancer


title: A549_H3N2_5


title: A549_H3N2_2


title: A549_H3N2_4


title: colon met34

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66178.gif

source_name: colon met34


title: A549_H3N2_1


title: A549_H5N1_4

source_name: A549 lung epithelial cell infected with H5N1


title: A549_H5N1_5


title: Colon_CA S04-3120(1)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55505.gif


title: colon met35

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66179.gif

source_name: colon met35


title: Colon_CA S03-8169

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50506.gif

source_name: Colon_CA S03-8169


title: A549_H5N1_3


title: colon met13

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66102.gif

source_name: colon cell line ref

source_name: colon met13


title: Colon_CA S04-958

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55506.gif

source_name: Colon_CA S04-958


title: colon met22

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66113.gif

source_name: colon met22


title: A549_H5N1_1


title: colon met21

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66112.gif

source_name: colon met21


title: colon met5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66094.gif

source_name: colon met5


title: CCRF-CEM 700uM prednisolone vs. control 4h treatment Experiment 2

city: Athens

first: George

middle: I

last: Lambrou

state: Attiki

address: Thivon & Levadeias

department: First Department of Pediatrics

country: Greece

institute: National and Kapodistrian University of Athens

description: This experiment has been performed in triplicates: This is the second experiment. In particular, it is the following pair: control (designated as ‘0’) vs. 700uM prednisolone at 4 h (designated as ‘3’) and the experiment is designated as '0vs3_4h_Exp2'

hyb_protocol: Hybridization was performed with the CyScribe Post-Labeling kit (RPN5660, GE Healthcare, former Amersham Inc.) as described by the manufacturer. The fluorescent dyes used were Cy3 and Cy5. cDNAs were purified with PCR product clean-up kit (# 28104, QIAGEN Inc.). Slides were activated at 55C for 30 min in 1% BSA. Samples were applied on the slides, and let to hybridize overnight at 55C. The following day, slides were washed in 200 ml 0.1× SSC and 0,1% SDS for 3× 5 min, in 200 ml 0.1× SSC for 2× 5 min  and in 200 ml ddH2O for 30 sec. Slides were dried by centrifugation at 1500 rpm for 3 min and scanned with a microarray scanner.

scan_protocol: Slides were scanned with a microarray scanner (ScanArray 4000XL) (Perkin Elmer Inc. MA, former GSI Lumonics, USA). Images were generated with ScanArray microarray acquisition software (GSI Lumonics, USA). Image analysis and raw data acquisition were performed with the ImaGene® software from BioDiscovery (California, USA).

data_processing: Foreground values have been background corrected with global background correction. Corrected values have been normalized using division by the 50% percentile, which was performed with the ImaGene software (BioDiscovery Inc.)

source_name: CCRF-CEM cells with no treatment at 4h

growth_protocol: The T-Lymphoblastic Leukemia CCRF-CEM were grown in RPMI-1640 medium supplemented with 2mM L-Glutamine and Streptomycin/Penicillin 100 U/ml (Gibco), 15% FBS (Gibco) at 37C, 5% CO2 and ~100% humidity. Cells were allowed to grow to ~900-1.500×103 cells/ul for CCRF-CEM.

extract_protocol: RNA was isolated with Trizol (Invitrogen Inc.) according to the manufacturer’s instructions. RNA was further processed with RQ1 DNase (Promega Inc. Madison, WI, USA) as described by the manufacturer and then it was cleaned-up with the RNEasy Mini kit (#74104, QIAGEN Inc.). The amount of RNA isolated was measured with a NanoDrop 2000 (Thermo Scientific Inc.) spectrophotometer and RNA integrity was estimated by 2% agarose gel electrophoresis. Samples with a 1.8 to 2.0 A260/A280 ratio were selected. In addition, those that empirically showed a twice as bright 28S band than the 18S band on the gel were utilized. At least 40 μg of RNA from each sample was used.

treatment_protocol: No treatment

value: The CCRF-CEM (ALL) cell line was used as the model. The CCRF-CEM cell line, a CD4+ (Miranda, Wolf et al. 1996) and CD34+ presenting cell line (Naujokat, Sezer et al. 2000)

tag: origin

value: initially obtained from peripheral blood of 2 year old Caucasian female

tag: diagnosis

value: It was diagnosed as lymphosarcoma which progressed later on to acute leukemia (Foley, Lazarus et al. 1965). The child has undergone irradiation therapy and chemotherapy prior to obtaining the cell line. Although remission was achieved at various stages, the disease progressed rapidly (Foley, Lazarus et al. 1965). The cell line has been observed to undergone minor changes after long-term culture, except for the presence of dense granules in the nucleoli (Uzman, Foley et al. 1966). Finally, the CCRF-CEM cell line has been reported to manifest autocrine catalase activity which participates to its mechanisms of growth and progression (Sandstrom and Buttke 1993).

source_name: CCRF-CEM cells treated with 700uM Prednisolone at 4h

treatment_protocol: 700uM Prednisolone at 4h


title: CCRF-CEM 700uM prednisolone vs. control 4h treatment Experiment 3

description: This experiment has been performed in triplicates: This is the third experiment. In particular, it is the following pair: control (designated as ‘0’) vs. 700uM prednisolone at 4 h (designated as ‘3’) and the experiment is designated as '0vs3_4h_Exp3'

label_protocol: Hybridization was performed with the CyScribe Post-Labeling kit (RPN5660, GE Healthcare, former Amersham Inc.) as described by the manufacturer. The fluorescent dyes used were Cy3 and Cy5. cDNAs were purified with PCR product clean-up kit (# 28104, QIAGEN Inc.). Slides were activated at 55C for 30 min in 1% BSA. Samples were applied on the slides, and let to hybridize overnight at 55C. The following day, slides were washed in 200 ml 0.1× SSC and 0,1% SDS for 3× 5 min, in 200 ml 0.1× SSC for 2× 5 min  and in 200 ml ddH2O for 30 sec. Slides were dried by centrifugation at 1500 rpm for 3 min and scanned with a microarray scanner.


title: Colon_CA S03-7586

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48477.gif

source_name: Colon_CA S03-7586


title: Colon_CA S02-3793

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48475.gif

source_name: Colon_CA S02-3793


title: A549_H7N1_5

source_name: A549 lung epithelial cell infected with H7N1


title: colon met8

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66097.gif

source_name: colon met8


title: colon met12

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66101.gif

source_name: colon met12


title: Colon_CA S03-1315

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50507.gif

source_name: common reference RNA


title: A549_H5N1_2

source_name: A549 lung epithelial cell infected with H5N1


title: Colon_CA S03-2999(2)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50343.gif


title: Colon_CA S02-6599

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50338.gif

source_name: Colon_CA S02-6599


title: colon met28

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66172.gif

source_name: colon met28


title: Colon_CA S04-3899(2)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55511.gif


title: colon met23

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66114.gif

source_name: colon cell line ref

source_name: colon met23


title: colon met17

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66107.gif

source_name: colon met17


title: A549_H7N1_4


title: A549_H7N1_3


title: colon met25

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66169.gif

source_name: colon met25


title: Colon_CA S04-2404T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55515.gif

source_name: Colon_CA S04-2404T


title: colon met10

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66099.gif

source_name: colon met10


title: Colon_CA S01-181b

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50345.gif

source_name: Colon_CA 01-181b


title: Colon_CA S01-4400a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50501.gif

source_name: Colon_CA 01-4400a


title: CCRF-CEM 700uM prednisolone vs. control 4h treatment Experiment 1

description: This experiment has been performed in triplicates: This is the first experiment. In particular, it is the following pair: control (designated as ‘0’) vs. 700uM prednisolone at 4 h (designated as ‘3’) and the experiment is designated as '0vs3_4h_Exp1'

source_name: CCRF-CEM cells with no treatment at 4h

source_name: CCRF-CEM cells treated with 700uM Prednisolone at 4h


title: CCRF-CEM 10nM prednisolone vs. 700uM 4h treatment Experiment 2

description: This experiment has been performed in triplicates: This is the second experiment. In particular, it is the following pair: 10nM (designated as ‘1’) vs. 700uM prednisolone at 4 h (designated as ‘3’) and the experiment is designated as '1vs3_4h_Exp2'.

source_name: CCRF-CEM cells with 10nM Prednisolone treatment at 4h

treatment_protocol: 10nM Prednisolone at 4h


title: A549_H7N1_2

source_name: A549 lung epithelial cell infected with H7N1


title: CCRF-CEM 10nM prednisolone vs. 700uM 4h treatment Experiment 1

description: This experiment has been performed in triplicates: This is the first experiment. In particular, it is the following pair: 10nM (designated as ‘1’) vs. 700uM prednisolone at 4 h (designated as ‘3’) and the experiment is designated as '1vs3_4h_Exp1'.


title: Liver (HK41)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9868.gif

source_name: Liver Reference

source_name: Liver (HBV+, HK41)


title: 1305_4H1

city: Cincinnati

last: Barnes

state: OH

address: 3333 Burnet Ave

department: Rheumatology

institute: Cincinnati Childrens Hospital Medical Center

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Data were imported into GeneSpring 7.3 with RMA preprocessing and normalized to median of samples processed immediately.

source_name: PBMC

label_protocol: NuGEN Ovation labeling

extract_protocol: Peripheral blood was drawn and PBMC were isollated over Ficoll.  Samples were stored in Trizol at -80oC until extracted according to manufacturers directions.

tag: subject

value: PBMC

value: 2hr processing delay


title: 1305_2H1

tag: time

value: 0hr processing delay (immediate)


title: 1305_6H1

value: 4hr processing delay


title: CCRF-CEM 10nM prednisolone vs. 700uM 4h treatment Experiment 3

description: This experiment has been performed in triplicates: This is the third experiment. In particular, it is the following pair: 10nM (designated as ‘1’) vs. 700uM prednisolone at 4 h (designated as ‘3’) and the experiment is designated as '1vs3_4h_Exp3'.

tag: cell line


title: A549_H7N1_1


title: 7616_2H1

tag: cell type


title: CCRF-CEM 10nM prednisolone vs. control 4h treatment Experiment 1

description: This experiment has been performed in triplicates: This is the first experiment. In particular, it is the following pair: control (designated as ‘0’) vs. 10 nM prednisolone at 4 h (designated as ‘1’) and the experiment is designated as '0vs1_4h_Exp1'

source_name: CCRF-CEM cells treated with 10nM Prednisolone at 4h

treatment_protocol: 10nM Prednisolone


title: Colon_CA S00-8241c

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50500.gif

source_name: common reference RNA

source_name: Colon_CA 00-8241c


title: A549_H1N1_2

source_name: A549 lung epithelial cell infected with H1N1


title: A549_H1N1_3


title: A549_H1N1_4


title: A549_H1N1_5


title: 7616_4H1


title: CCRF-CEM 10nM prednisolone vs. control 4h treatment Experiment 3

description: This experiment has been performed in triplicates: This is the third experiment. In particular, it is the following pair: control (designated as ‘0’) vs. 10 nM prednisolone at 4 h (designated as ‘1’) and the experiment is designated as '0vs1_4h_Exp3'


title: Colon_CA S04-2988

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55516.gif

source_name: Colon_CA S04-2988


title: CCRF-CEM 10nM prednisolone vs. control 4h treatment Experiment 2

description: This experiment has been performed in triplicates: This is the second experiment. In particular, it is the following pair: control (designated as ‘0’) vs. 10 nM prednisolone at 4 h (designated as ‘1’) and the experiment is designated as '0vs1_4h_Exp2'


title: A549_H1N1_1


title: N.gonorrhoeae-reinfected/anti-TGF-β treatment 2

city: Buffalo

first: Yingru

last: Liu

address: 3435 Main Street

institute: University at Buffalo

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using average normalization, background subtraction with GenomeStudio

source_name: whole vagina

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

extract_protocol: The kit we used to isolate the total RNA is RNeasy Mini Kits from Qiagen Sciences. Catalog number is 74104.

tag: strain

value: BALB/c

value: wild-type

tag: treatment

value: anti-TGF-β treatment


title: colon met29

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66173.gif

source_name: colon cell line ref

value: colon cell line ref

source_name: colon met29


title: 7616_6H2


title: Colon_CA S03-5581B

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50341.gif

source_name: Colon_CA S03-5581B


title: 7638_2H3


title: Colon_CA S03-2999(1)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50339.gif


title: Colon_CA S04-4907(2)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55512.gif


title: Colon_CA S03-1587

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50496.gif


title: A549_Mock_5

source_name: A549 lung epithelial cell mock infected

value: Mock


title: 7638_4H3


title: A549_Mock_4


title: Sham-reinfected 2

value: Sham-reinfected


title: N.gonorrhoeae-reinfected/control IgG treatment 2

value: control IgG treatment


title: N.gonorrhoeae-reinfected/anti-TGF-β treatment 1


title: Colon_CA S01-6169

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50502.gif


title: Sham-reinfected 1


title: A549_Mock_2


title: Colon_CA S03-340

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55509.gif

source_name: Colon_CA S03-340


title: Colon_CA S04-962

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55508.gif

source_name: Colon_CA S04-962


title: 7638_6H3


title: N.gonorrhoeae-infected/anti-TGF-β treatment 2


title: N.gonorrhoeae-reinfected/control IgG treatment 1


title: Colon_CA S02-4594(2)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55513.gif


title: Colon_CA S04-2317

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55507.gif

source_name: Colon_CA S04-2317


title: Epiphyseal cartilage, P8

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

country: Japan

institute: National Center for Child Health and Development

description: Epiphyseal cartilage, P8

hyb_protocol: Biotinylated cRNA was hybridized with a probe array for 16h at 45C, and the hybridized biotinylated cRNA was stained with streptavidin-PE.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner (Palo Alto).

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

source_name: total RNA

label_protocol: cDNA was subjected to in vitro transcription in the presence of biotinylated nucleoside triphosphates using the Enzo BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences), according to the manufacturer's protocol (One-Cycle Target Labeling and Control Reagent package).

extract_protocol: Total cellular RNA was isolated with the RNeasy Mini Kit (Qiagen), according to manufacture's instructions.). Genomic DNA was eliminated by DNase I (TAKARA BIO INC.) treatments.

value: Postnatal epiphyseal cartilage, passage 8 (YubCp8)


title: Epiphyseal cartilage, P7

description: Epiphyseal cartilage, P7

value: Postnatal epiphyseal cartilage, passage 7 (YubCp7)


title: A549_Mock_1


title: A549_Mock_3


title: Epiphyseal cartilage, P6

description: Epiphyseal cartilage, P6

value: Postnatal epiphyseal cartilage, passage 6 (YubCp6)


title: Colon_CA S03-1589 CA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50497.gif

value: common reference RNA

source_name: Colon_CA 503-1589 CA

value: Primary colon cancer


title: Epiphyseal cartilage, P3

description: Epiphyseal cartilage, P3

value: Postnatal epiphyseal cartilage, passage 3 (YubCp3)


title: N.gonorrhoeae-infected/anti-TGF-β treatment 1


title: N.gonorrhoeae-infected/control IgG treatment 2


title: Sham-infected 2

value: Sham-infected


title: Epiphyseal cartilage, P4

description: Epiphyseal cartilage, P4

value: Postnatal epiphyseal cartilage, passage 4 (YubCp4)


title: Epiphyseal cartilage, P2

description: Epiphyseal cartilage, P2

value: Postnatal epiphyseal cartilage, passage 2 (YubCp2)


title: HMC1 17h SerumStarv 4h Imatinib versus HMC1(Serum)

city: Hannover

first: Oliver

last: Dittrich-Breiholz

address: Carl-Neuberg-Str. 1

department: Research Core Unit Genomics

country: Germany

institute: Medical School Hannover

hyb_protocol: cRNA fragmentation, hybridization and washing steps were performed exactly as recommended by the manufacturer “Two-Color Microarray-Based Gene Expression Analysis Protocol V5.5” except that 4 µg of each labeled cRNA were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2505 B at two different PMT settings (100 % and 5 %) to increase the dynamic range of the measurements (extended dynamic range mode).

data_processing: Data extraction and normalization were performed with the “Feature Extraction Software V9.5.3.1” by using the recommended default extraction protocol file: GE2-v5_95_Feb07.xml.

source_name: HMC1 17h SerumStarv 4h Imatinib

label_protocol: 1000ng of total RNA per condition were used to prepare Cy3-, or Cy5-labeled cRNA with the “Low RNA Input Linear Amplification Kit PLUS, Two-Color” (#5188-5340, Agilent Technologies) according to the manufacturer’s recommendations.

growth_protocol: HMC-1(V560G c-Kit) cells were grown in RPMI1640 medium supplemented with 10% FCS.

extract_protocol: RNA was isolated using RNeasy Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. Residual DNA contamination was removed with DNAseI (Invitrogen GmbH, Darmstadt, Germany) according to the manufacturer’s recommendations, and the RNA was again purified with RNeasy Mini kit (Qiagen).

treatment_protocol: HMC-1(V560G c-Kit) cells were serum starved for 17 h, then treated with dimethyl sulfoxide (DMSO) or 5 μM Imatinib for 4 hours prior to stimulation with 100 ng/ml mouse recombinant NGF. After 30 or 120 min the stimulation was stopped in ice-cold PBS. Samples from cells grown in medium supplemented with 10% FCS were analyzed in parallel.


title: Epiphyseal cartilage, P1

description: Epiphyseal cartilage, P1

value: Postnatal epiphyseal cartilage, passage 1 (YubCp1)


title: HMC1 17h SerumStarv 4h Imatinib versus HMC1 17h SerumStarv 4h Imatinib


title: HMC1 17h SerumStarv 4h Imatinib versus HMC1 17h SerumStarv 4h Imatinib 2h NGF

source_name: HMC1 17h SerumStarv 4h Imatinib 2h NGF


title: HMC1 17h SerumStarv 4h Imatinib versus HMC1 17h SerumStarv 4h Imatinib 0.5h NGF


title: Epiphyseal cartilage, P5

description: Epiphyseal cartilage, P5

value: Postnatal epiphyseal cartilage, passage 5 (YubCp5)


title: Colon_CA S03-5280A

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48478.gif

source_name: Colon_CA S03-5280A


title: N.gonorrhoeae-infected/control IgG treatment 1

value: BALB/c

value: wild-type


title: Sham-infected 1


title: Kit+Sca-1+Lin– bone marrow cells of Rb family triple knockout mice Replicate 2

status: Public on Mar 21 2011

first: Christopher

middle: Paul

last: Arnold

address: 269 Campus Drive, CCSR building, Room 3205B

department: Microbiology and Immunology

description: HSPCs with increased mobilization to spleen, enhanced cell cycle entry, and defects in reconstitution potential but capable of in vitro self-renewal.

data_processing: Ct values of miRNA probes were used to indicate corresponding miRNA levels within the cell sample. Non-template control analyses (NTC) were carried out to eliminate probes with high background. Redundant and overlapping probes were also removed. miRNAs with Ct >35 were considered undetectable and transformed to Ct=35.  For comparative analysis, miRNA expression within each sample was normalized by subtracting the median Ct value of detectable miRNAs within the sample from the miRNA Ct value to obtain a ∆Ct value.

label: FAM

extract_protocol: The samples were then lysed, amplified, and quantified using multiplex RT for TaqMan MicroRNA Assays according to manufacturer’s instructions from Applied Biosystems and as described (Chen et al. 2005; Chen et al. 2007)

treatment_protocol: Defined numbers of cells were isolated, stained, and were FACS sorted or aliquoted into each tube.

value: Rb family triple knockout

tag: tissue

value: Hematopoietic/Mutant

value: Mixed 129Sv/J:C57Bl6


title: Kit+Sca-1+Lin– bone marrow cells of Rb family triple knockout mice Replicate 1


title: Kit+Sca-1+Lin– bone marrow cells of AML-ETO9a transgenic mice Replicate 3

description: Enhanced self-renewal and expansion in LT-HSCs due to differentiation blocks.

value: Hematopoietic/Leukemic


title: Colon_CA S01-379(1)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55514.gif

source_name: common reference RNA


title: Kit+Sca-1+Lin– bone marrow cells of AML-ETO9a transgenic mice Replicate 1


title: Kit+Sca-1+Lin– bone marrow cells of AML-ETO9a transgenic mice Replicate 2


title: Kit+Sca-1+Lin– bone marrow cells Replicate 5

description: Enriched for proliferative, non-self-renewing short-term HSCs and committed multipotent progenitors

value: wildtype

value: Hematopoietic


title: Kit+Sca-1+Lin– bone marrow cells Replicate 4


title: Kit+Sca-1+Lin– bone marrow cells Replicate 2


title: Kit+Sca-1+Lin– bone marrow cells Replicate 1


title: Primary neurospheres derived from culture and expansion of NSPC-P0 cells Replicate 3

description: Multipotent NSPCs from P0 neonatal mice

value: Neural


title: Colon_CA S04-3740(2)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55510.gif

value: common reference RNA


title: Colon_CA S02-6986

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48474.gif

source_name: Colon_CA S02-6986

value: Primary colon cancer


title: Liver (SF36)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/12224.gif

source_name: Liver Reference

value: Liver Reference

source_name: Liver (SF36)

value: normal liver specimen


title: Primary isolation of NSPCs from the SVZ and DG regions of postnatal Day 0 mice Replicate 2

description: Multipotent NSPCs from P0 neonatal mice


title: Primary neurospheres derived from culture and expansion of NSPC-P0 cells Replicate 2

description: Multipotent NSPCs from P0 neonatal mice


title: Liver (SF10)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11479.gif

source_name: Liver (SF10)


title: Colon_CA Bluetop t1 (S00-5136)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50499.gif

source_name: Colon_CA Bluetop t1 (S00-5136)


title: Kit+Sca-1+Lin– bone marrow cells Replicate 3


title: Primary isolation of NSPCs from the SVZ and DG regions of postnatal Day 0 mice Replicate 3

description: Multipotent NSPCs from P0 neonatal mice


title: Primary neurospheres derived from culture and expansion of NSPC-P0 cells Replicate 1

description: Multipotent NSPCs from P0 neonatal mice


title: Epiphyseal cartilage, primary

description: Epiphyseal cartilage, primary

value: Postnatal epiphyseal cartilage, primary (YubCp0)


title: MLL-AF10+ Kit+ LSCs from mice transduced with MLL-AF10 oncogene Replicate 2

description: Self-renewing LSCs


title: MLL-AF10+ Kit+ LSCs from mice transduced with MLL-AF10 oncogene Replicate 3

description: Self-renewing LSCs


title: MLL-AF10+ Kit– leukemia cells derived from MLL-LSCs Replicate 1

description: LSC-depleted, non-self-renewing fraction


title: Primary neurospheres derived from cells of the SVZ and DG regions of adult mice Replicate 3

description: Multipotent adult NSPCs


title: MLL-AF10+ Kit+ LSCs from mice transduced with MLL-AF10 oncogene  Replicate 1

description: Self-renewing LSCs


title: MLL-AF10+ Kit– leukemia cells derived from MLL-LSCs Replicate 3


title: Primary neurospheres derived from cells of the SVZ and DG regions of adult mice Replicate 1

description: Multipotent adult NSPCs


title: Primary neurospheres derived from cells of the SVZ and DG regions of adult mice Replicate 2

description: Multipotent adult NSPCs


title: MLL-AF10+ Kit– leukemia cells derived from MLL-LSCs Replicate 2


title: Endoglin+RholowSca-1+Lin– bone marrow cells Replicate 4

description: Quiescent, self-renewing blood stem cells


title: Myoblasts Isolated from forelimb and hindlimb muscle mass Replicate 3

description: Proliferating, committed muscle progenitor cells

value: Muscle


title: Primary isolation of NSPCs from the SVZ and DG regions of postnatal Day 0 mice Replicate 1

description: Multipotent NSPCs from P0 neonatal mice


title: Myoblasts Isolated from forelimb and hindlimb muscle mass Replicate 2


title: Myoblasts Isolated from forelimb and hindlimb muscle mass Replicate 1


title: Myoblasts Isolated from forelimb and hindlimb muscle mass Replicate 4


title: Endoglin+RholowSca-1+Lin– bone marrow cells Replicate 3


title: Endoglin+RholowSca-1+Lin– bone marrow cells Replicate 1


title: Endoglin+RholowSca-1+Lin– bone marrow cells Replicate 2


title: Colon_CA S02-6983

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48476.gif

source_name: Colon_CA S02-6983


title: CD45–CD11b–CD31–Sca1–CD34+integrin-7+ Muscle satellite cells from the tibialis anterior muscles Replicate 1

description: Quiescent, self-renewing muscle stem cells


title: Kit+Sca-1+Lin– cells from spleen from poly:IC treated PTEN control mice Replicate 3

description: Hematopoietic Stem/Progenitor Cells (HSPCs) localized in the spleen


title: CD45–CD11b–CD31–Sca1–CD34+integrin-7+ Muscle satellite cells from the tibialis anterior muscles Replicate 2


title: Kit+Sca-1+Lin– cells from spleen from poly:IC treated PTEN control mice Replicate 2


title: leaf sample 2 (XLe2)

city: Duesseldorf

first: Daniel

last: Schubert

address: Universitaetsstr. 1

department: Institute for Genetics

institute: Heinrich-Heine-University Duesseldorf

description: tissue specific gene expression

hyb_protocol: Array hybridisation was performed by the Imagenes Corp. (Berlin, Germany) as described in the “One-Color Microarray-Based Gene Expression Analysis” Protocol (G4140-90040 Version 5.7, March 2008; http://www.genomics.agilent.com/GenericA.aspx?PageType=Platform&SubPageType=PlatformLiterature&PageID=289).

scan_protocol: Scanning was performed by the Imagenes Corp. (Berlin, Germany) as described in the “One-Color Microarray-Based Gene Expression Analysis” Protocol (G4140-90040 Version 5.7, March 2008; http://www.genomics.agilent.com/GenericA.aspx?PageType=Platform&SubPageType=PlatformLiterature&PageID=289) with an Agilent Technologies Scanner G2505B US45103052.

data_processing: The data is supplied as raw data as received from Imagenes Corp. (Berlin, Germany).  The data was processed by the Imagenes Corp. (Berlin, Germany) as described in the “One-Color Microarray-Based Gene Expression Analysis” Protocol (G4140-90040 Version 5.7, March 2008; http://www.genomics.agilent.com/GenericA.aspx?PageType=Platform&SubPageType=PlatformLiterature&PageID=289).

organism: Arabidopsis thaliana

source_name: young leaves

label_protocol: Probe labelling was performed by the Imagenes Corp. (Berlin, Germany) as described in the “One-Color Microarray-Based Gene Expression Analysis” Protocol (G4140-90040 Version 5.7, March 2008; http://www.genomics.agilent.com/GenericA.aspx?PageType=Platform&SubPageType=PlatformLiterature&PageID=289). A oligo dT / T7 RNA-Polymerase based protocol was used for labelling.

growth_protocol: All plants were grown for 9 weeks under short day conditions (8 h light/16 h darkness) on soil.

extract_protocol: Total RNA was extracted with QIAGEN plant RNeasy kit (Qiagen, Hilden), Superscript II (Invitrogen, Carlsbad) was used for cDNA synthesis.

treatment_protocol: For tissue comparison meristematic tissue (Me) and young leaves (Le) were isolated by manual dissection of whole seedlings.

value: whole young leaves


title: Kit+Sca-1+Lin– cells from spleen from poly:IC treated PTEN control mice Replicate 1


title: WDR5_siG_HOX

first: Kevin

last: Wang

address: 269 Campus Drive CCSR 2142

department: Dermatology

institute: Stanford University School of Medicine

description: WDR5 ChIP in siGFP foreskin fibroblasts

hyb_protocol: Standard Nimblegen hybridization kits and protocols were used, hybridization was performed in Nimblegene MAUI 12 bay machine

scan_protocol: Arrays were scanned with Axon scanner at 5 um resolution according to standard Nimblegen protocols

data_processing:
Arrays were processed using Nimblegens standard protocol for Nimblescan 2.4 ChIP data extraction
log2 ratio of ChIP/INPUT, using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction, log2 ratio created from two raw pair files
For each gff. File: columnA: Chromosome, columnD/E: probe start/stop site, columnF: log2 ratio of ChIP/INPUT

source_name: WDR5 ChIP in siGFP foreskin fibroblasts

label_protocol: Input DNA labeled CY3, and ChIP DNA labeled CY5, Standard Nimblegen ChIP labeling protocol (1 ug of Amplified ChIP DNA, direct incorporation of cy labeled primers with Klenow extension)

growth_protocol: Cells for both ChIP and input Samples were grown in DMEM

extract_protocol: ChIP was performed on 4x10^6 fibroblast cells and Farnham ChIP protocol was used to derive ChIP DNA which was then subjected to one round of amplification with the sigma WGA2 kit. Amplification

tag: chip antibody

value: input

value: siGFP

value: foreskin fibroblasts


title: CD45–CD11b–CD31–Sca1–CD34+integrin-7+ Muscle satellite cells from the tibialis anterior muscles Replicate 4


title: MLL1_siH_HOX

description: MLL1 ChIP in siHOTTIP foreskin fibroblasts

value: siHOTTIP


title: Kit+Sca-1+Lin– cells from the spleens of PTEN–/– mice Replicate 2

description: HSPCs with increased mobilization to spleen and proliferation but decreased self-renewal capacity

value: PTEN–/–


title: Kit+Sca-1+Lin– cells from the spleens of PTEN–/– mice Replicate 3


title: CD45–CD11b–CD31–Sca1–CD34+integrin-7+ Muscle satellite cells from the tibialis anterior muscles Replicate 3


title: H3K27Me3_siG_HOX

description: H3K27me3 ChIP in siGFP foreskin fibroblasts


title: leaf sample 1 (XLe1)

description: tissue specific gene expression


title: leaf sample 1 (Le1)

description: tissue specific histone methylation

hyb_protocol: Array hybridisation was performed by the Imagenes NimbleGen service (Berlin, Germany) as described in the “NimbleGen Array User’s Guide” protocol (http://www.nimblegen.com/products/lit/chip_userguide_v6p1.pdf).

scan_protocol: Scanning was performed by the Imagenes NimbleGen service (Berlin, Germany) as described in the “NimbleGen Array User’s Guide” protocol (http://www.nimblegen.com/products/lit/chip_userguide_v6p1.pdf).

data_processing: For the processed data file gene specific methylation scores ranging from 0 to 100 were calculated as described below:  The array hybridization data was received from Imagenes (Berlin, Germany) as intensity ratios of precipitate and input samples in the GFF-file format. In a first processing step M-Values [M=log2(IP/I) where IP is signal intensity from hybridized immunoprecipitated DNA and I is signal intensity from hybridized input DNA] were determined. The data was analyzed with SignalMap1.9 software (Nimblegen) and the Bioconductor R packages (Gentleman RC. et al., 2004, Genome Biol 5: R80) in an R programming environment. M values were used as input for the Bioconductor package Ringo. The Ringo clustering algorithm has been developed specifically for widely occurring enrichments including those found for histone modifications (Toedling J. et al., 2007, BMC Bioinformatics 8: 221). Prior to cluster detection Ringo applies a running median to smooth the datasets. A window size of 1400 bp was used for running median. The cluster algorithm was executed with a distance cut off of 700 bp and an intensity threshold defined by the 80th percentile. The identified methylation clusters were used to calculate gene specific methylation scores for each annotation [based on TAIR8 genome annotation (www.arabidopsis.org)] and tissue (Me or Le) and scaled so that the maximum equals 100. Further analyses and comparisons of loci-specific methylation scores were calculated with a regular spreadsheet program (Excel, Microsoft). A scale normalisation on the level of methylation scores was performed for the different tissues to account for differences in precipitation efficiency.

label_protocol: Probe labelling was performed by the Imagenes NimbleGen service (Berlin, Germany) as described in the “NimbleGen Array User’s Guide” protocol (http://www.nimblegen.com/products/lit/chip_userguide_v6p1.pdf) based on random priming with Cy3 or Cy5 nonamers.

extract_protocol: For each tissue, 200 mg plant material was harvested on ice, crosslinked with 1% formaldehyde for 15 minutes under vacuum, frozen in liquid nitrogen and stored at -70° until chromatin extraction. A previously described protocol (Schubert D. et al., 2006 [EMBO J 25: 4638-4649]) was used for ChIP. Antibodies specific for H3K27me3 (#07-449) were retrieved from Millipore (Billerica, USA). Chromatin was sheared with a Bioruptor sonicator (10 pulses, 30 seconds each) (Diagenode, Liege, Belgium). Input and precipitated DNA was amplified with a whole genome amplification kit (WGA2, Sigma, St. Louis) as described in “PROT30” of The Epigenome NoE web-page (http://www.epigenome-noe.net/).

tag: genotype


title: H3K27me3_overexpHOTTIP_HOX_lung

description: H3K27me3 ChIP in HOTTIP overexpressing lung fibroblasts

tag: genotype/variation

value: HOTTIP overexpressing

value: lung fibroblasts


title: leaf sample 2 (Le2)

description: tissue specific histone methylation


title: Histone_siH_HOX

description: Histone ChIP in siHOTTIP foreskin fibroblasts

source_name: Pan-histone ChIP in siHOTTIP foreskin fibroblasts

value: Pan-histone


title: H3K4me3_overexpHOTTIP_HOX_lung

description: H3K4me3 ChIP in HOTTIP overexpressing lung fibroblasts


title: Histone_siG_HOX

description: Histone ChIP in siGFP foreskin fibroblasts

source_name: Pan-histone ChIP in siGFP foreskin fibroblasts


title: MLL1_HOX_lung

description: MLL1 ChIP in wildtype lung fibroblasts

source_name: MLL1 ChIP in wildtype lung fibroblasts

value: wildtype


title: WDR5_siH_HOX

description: WDR5 ChIP in siHOTTIP foreskin fibroblasts


title: MLL1_siG_HOX

description: MLL1 ChIP in siGFP foreskin fibroblasts

source_name: MLL1 ChIP in siGFP foreskin fibroblasts


title: meristem sample 1 (Me1)

description: tissue specific histone methylation

source_name: shoot apical meristem

value: meristem enriched tissue sample


title: meristem sample 2 (XMe2)

description: tissue specific gene expression


title: H3K27Me3_siH_HOX

description: H3K27me3 ChIP in siHOTTIP foreskin fibroblasts


title: Kit+Sca-1+Lin– cells from the spleens of PTEN–/– mice Replicate 1

value: Hematopoietic


title: G1ME_WT_rep2

city: Parkville

first: Matthew

middle: Daniel

last: Young

state: Victoria

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: Walter & Eliza Hall Institute of Medical Research

hyb_protocol: Standard Affymetrix hybridisation protocol

scan_protocol: Standard Affymetrix scan protocol

data_processing: Gene expression was assessed in G1ME cells with GeneChip Mouse Genome 430 2.0 microarrays (Affymetrix). For ES & MEF cells, we used expression data from the same microarray platform (GEO GSE8024).  There were 3 technical replicates for ES cells and 2 for G1MEs and MEFs. All microarrays were background corrected and quantile normalized using the gcrma bioconductor R package.

source_name: G1ME Blood Cells

label_protocol: Standard Affymetrix labelling protocol

growth_protocol: Cells were grown in alpha-minimal essential media, supplemented with 20% calf serum 100 ng/mL thrombopoiten, penicillin and streptomycin.

extract_protocol: RNA was extracted QIAGEN RNeasy mini kit including a DNase I treatment,  in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: C58BL/6 Bruce 4 (B4)

value: G1ME cells

value: wild type


title: Salmonella SP Treatment - Rep 2A

status: Public on Mar 20 2011

city: Fayetteville

first: Arunachalam

last: Muthaiyan

state: AR

address: 2435 N Hatch Ave

department: Food Science

institute: University of Arkansas

description: Genes analyzed using these programs were further sorted and grouped based on their function using our in-house software Salmonella Gene Sorter (SAGS).

hyb_protocol: The labeled cDNA was purified (Qiagen PCR purification kit) and hybridized with Salmonella Typhimurium/Typhi version 8 genome microarrays obtained from Pathogen Functional Genomics Resource Center (National Institute of Allergy and Infectious Diseases). Briefly, the slides were prehybridized in a buffer containing 5X SSC, 0.1% SDS and 0.1% BSA, and then washed and blown to dry. The two differentially labelled cDNA samples were dried and the resuspended in hybridization solution [40% deionized formamide, 5X SSC, 0.1% SDS, 0.6 µg/µl sheared Salmon sperm DNA (Ambion)]. The labelled cDNA samples were hybridized with the slides at 42 °C for 18-20 h. After hybridization, the slides were washed in low stringency buffer (2X SSC, 0.1% SDS) for 2 min, then in medium stringency (0.1x SSC, 0.1% SDS) buffer for 5 min and finally high stringency buffer (0.1x SSC) for 10 min.

scan_protocol: Hybridization signals were scanned using an Axon4000B scanner (Molecular Devices, Sunnyvale, CA ) with Acuity 6.0 software and scans were saved as TIFF image.

data_processing: Scans were analyzed using TIGR-Spotfinder (www.tigr.org/software/) software and the local background was subsequently subtracted. The data set was normalized by applying the LOWESS algorithm using TIGR-MIDAS (www.tigr.org/software/) software. The normalized log2 ratio of test/reference signal for each spot was recorded. Genes with less than three data points were considered unreliable, and their data points were discarded. The averaged log2 ratio for each remaining gene on the six replicate slides was ultimately calculated. Significant changes of gene expression were identified with SAM (significance analysis of microarrays; www.tat.stanford.edu/~tibs/SAM/index.html software using one class mode.

source_name: Salmonella Typhimurium

label_protocol: cDNA was generated by using random hexamers (Invitrogen) as primers for reverse transcription. The primers were annealed (70°C for 10 min, followed by snap-freezing in ice for 1 min) to total RNA (2 μg) and were extended with SuperScript II reverse transcriptase (Invitrogen) with 0.1 M dithiothreitol 12.5 mM dNTP/ aa-UTP (Ambion, Austin, TX) mix at 42°C overnight. Residual RNA was removed by alkaline treatment followed by neutralization, and cDNA was purified with a QIAquick PCR purification kit (Qiagen). Purified aminoallyl-modified cDNA was then labeled with Cy3 or Cy5 mono-functional NHS ester cyanogen dyes (Amersham Pharmacia Biotech, Piscataway, NJ) according to the manufacturer’s instruction.

extract_protocol: Total bacterial RNA was extracted from 3 ml of culture which was mixed with 6 ml of bacterial RNA protect solution (Qiagen, Valencia, CA) and the mixture was centrifuged at 3000 rpm for 20 min in swinging-bucket rotor centrifuge to collect the cells. Pellets were resuspended in 1 ml of Trizol (Invitrogen, Grand Island, NY) and the cells were broken using the FastPrep system (Qbiogene, Irvine, CA) at a speed of 6.0 for 40 seconds. From the broken cell lysate RNA was extracted as per the manufacturer’s instructions. Extracted RNA was purified using the RNeasy mini kit (Qiagen). DNase treated and purified mRNA was used for microarray analysis.

treatment_protocol: For control 1 ml of stationary phase S. Typhimurium was exposed to dH2O (pH 4) at 55 C for 1 min.

value: dH2O (pH 4) at 55 C for 1 min

treatment_protocol: In preparation for total RNA extraction, 1 ml of stationary phase S. Typhimurium was exposed to 9ml of the following at 55 C for 1 min: 2.5% solutions of SP (pH 4.0).

value: 2.5% solutions of SP (pH 4.0)


title: G1ME_WT_rep1


title: meristem sample 2 (Me2)

description: tissue specific histone methylation


title: Salmonella SP Treatment - Rep 3A


title: Salmonella SP Treatment - Rep 2B


title: H3K4Me3_siH_HOX

description: H3K4me3 ChIP in siHOTTIP foreskin fibroblasts


title: Salmonella SP Treatment - Rep 1A


title: Salmonella SP Treatment - Rep 1B


title: H3K4me2_siH_HOX

description: H3K4me2 ChIP in siHOTTIP foreskin fibroblasts


title: Salmonella SA Treatment - Rep 2B

treatment_protocol: In preparation for total RNA extraction, 1 ml of stationary phase S. Typhimurium was exposed to 9ml of the following at 55 C for 1 min: 2.5% solutions of SA (pH 4.0).

value: 2.5% solutions of SA (pH 4.0)


title: Salmonella SA Treatment - Rep 1B


title: Salmonella SA Treatment - Rep 3A


title: Salmonella SA Treatment - Rep 3B


title: Salmonella SA Treatment - Rep 1A


title: H3K4Me3_siG_HOX

description: H3K4me3 ChIP in siGFP foreskin fibroblasts

value: input


title: Salmonella SA Treatment - Rep 2A


title: Jejunums from mice fed with control

city: Wuxi

first: Guo-wei

last: Le

address: Lihu Road 1800

country: China

institute: Jiangnan University

description: Gene expression data from jejunums of C57BL/6J mice fed with control diet for 4 weeks.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip mouse genome 430A arrays . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Gene Array TM scanner 3000.

source_name: Jejunums for mice fed with control diet

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

growth_protocol: C57BL/6J male mice (4 week of age, weighing 14.92±0.97 g), were housed under conditions of controlled temperature (23 ± 2 °C) and humidity (60%) with natural light. The mice were allowed to acclimate for two weeks before the commencement of the study.

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

treatment_protocol: Mice were allocated randomly to two groups and fed either HGD (20% glucose) or regular chow (AIN76). Four weeks later, the experiment was done.

tag: diet

value: regular chow (AIN76)

value: Jejunum

tag: age

value: Ten weeks

tag: gender

value: male


title: Salmonella SP Treatment - Rep 3B


title: Jejunums from mice fed with high-glucose diet

description: Gene expression data from jejunums of C57BL/6J mice fed with HGD for 4 weeks.

source_name: Jejunums for mice fed withHGD

value: HGD (20% glucose)


title: meristem sample 1 (XMe1)

description: tissue specific gene expression


title: SY96-1

status: Public on Mar 19 2011

city: Guangzhou

first: Tong

last: Wu

state: Guangdong

address: Zhongshaner Road

institute: Sun Yat-sen University

description: gene expression data from oral keratinocyte during adaptive immune response

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.    scan protocol GeneChips were scanned

scan_protocol: using the GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: oral keratinocyte from 96h groups

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

growth_protocol: tongue mucosa keratinocyte from 6-8 weeks old C57 mouse

treatment_protocol: BALB/c mice were sacrificed and the tongues, inner part of the cheeks and plates were obtained. After trimming submucosal tissue attached to the oral mucosa, the tongues, plates and cheeks were immersed in dispase II (1.2 units/mL from Roche, Lewes,UK) to be digested at 4 °C overnight. Subsequently, the epithelial layer was enzymatically and mechanically separated from the underlying connective tissue and was further incubated in 0.25% Trypsin/0.02% EDTA (Gibco, Grand Island, NY, USA) for 3-5 min with vigorous pipetting to achieve cell dispersion. After trypsin was inactivated by 10% fetal bovine and washing, the cell suspension was re-suspended in PBS to the concentration of 1×107 cells/ml. After being intraperitoneally anesthesized with chloral hydrate, C57BL/6J mice were given a subcutaneous injection with 50 μl cell suspension obtained from BALB/c mice into the foreneck. Seven days later, 25μl cell suspension was injected to the same C57BL/6J mouse into tongue submucosa under anesthesia. Groups of six C57BL/6J mice at 48h and 96h after tongue submucosal injection and control without any manipulation were sacrificed. Tongues were excised and subcutaneous tissue and blood were trimmed. The epithelia were obtained after being digested in dispase II (1.2 U/mL from Roche, Lewes,UK) at 4 °C overnight. Subsequently, the epithelial layer was enzymatically and mechanically separated from the underlying connective tissue. The epithelial layer was further incubated in 0.25% Trypsin/0.02% EDTA (Gibco, Grand Island, NY, USA) at 37 °C for 3-5min with vigorous pipetting to achieve cell dispersion. After trypsin neutralization by fetal calf serum (FCS) and washing, the keratinocytes were collected for the following experiments.

value: oral keratinocyte

tag: time point

value: tongue

value: BALB/c


title: SY96-2


title: SY96-3


title: Mouse_eye

city: Bethesda

first: Lai

last: Wei

address: 10 Center Dr. Room 2B47

institute: NIH/NEI/NCCAM

description: Pool of 4 eyes from 4 mice.

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: RMA normalization was used to summarize the signal using Partek Genome Suite 6.5.

source_name: eye

label_protocol: According to the MessageAmp™ II-Biotin Enhanced Kit protocol (Ambion).

extract_protocol: Total RNA was extracted from four eyes from four 8-week-old C57B/6 mice using the mirVana RNA isolation kit (Ambion) and pooled together.

value: 8 weeks

value: whole eyes


title: DZ-4

source_name: oral keratinocyte from control groups

value: control


title: SY-3

source_name: oral keratinocyte from 48h groups


title: SY-1


title: 293+avb3 lifted, p66+ vs. p66- infected, 3h

status: Public on Mar 18 2011

city: Milwaukee

first: Jenifer

last: Coburn

state: WI

address: 8701 Watertown Plank Rd.

department: ID/CBID

institute: Medical College of Wisconsin

description:
293+avb3 p66+/ p66- 3hr
293+avb3 lifted

hyb_protocol: The two differently labeled cDNAs were mixed and hybridized using Pronto Microarray Hybridization Kit in a hybridization chamber (Corning, Corning, NY), with the same array slide for 38 to 42 hr according to manufacturer’s instruction.   After a series of washes using the buffers provided in the kit, slides were spun dry.

scan_protocol: The slides were scanned under two laser channels in a Scanarray 4000 scanner (Packard Bioscience, Meriden, CT).

data_processing: Data from at least 3 biological replicate experiments were normalized using Lowess normalization and by the median of the raw intensities for all spots in each sample for each array. Attached sheets contain normalized data and significant differences between conditions.

source_name: p66+ B. burgdorferi 3 hr

label_protocol: 5 to 20 mg of total RNA from uninfected control and infected samples was used to generate cDNA labeled with aminoallyl (aa)-dUTP through a reverse transcription reaction using anchored oligo(dT) primers.  The purified aa-dUTP-labeled cDNAs were coupled in 10 µl 0.1 M NaHCO3 with either Cy3 or Cy5 NHS-ester dye. Cy-dye labeled cDNA was purified using a Cyscribe GFX column (Amersham Biosciences, Piscataway, NJ).

extract_protocol: Cells were washed with phosphate buffered saline (PBS) and harvested for RNA isolation.  The RNA was purified using RNeasy kit (Qiagen, Valencia, CA) with DNase digestion according to manufacturer’s manual. The quality of RNA was checked using a Bioanalyzer (Agilent, Santa Clara, CA).

tag: infection

value: p66+ B. burgdorferi

value: 3 hr

value: transfected HEK-293 derivative expressing integrin avb3

source_name: p66- B. burgdorferi 3 hr

value: p66- B. burgdorferi


title: 293+avb3 lifted, uninfected vs. p66+ infected, 1h

description:
293+avb3 p66+/uninfected 1hr
293+avb3 lifted

source_name: p66+ B. burgdorferi 1 hr

value: 1 hr

source_name: uninfected 1 hr

value: uninfected


title: Liver Pregnant 3

city: Torino

first: Paolo

last: Provero

address: Via Nizza 52

department: Molecular Biotechnology and Health Sciences

institute: University of Turin

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Normalization and background subtraction with RMA as implemented in the 'affy' package of Bioconductor

source_name: Liver of 16-day pregnant mice, pool 3 of two mice

label_protocol: Affymetrix protocol

growth_protocol: Female NOD/SCID mice were obtained from in house breeding at the ISREC mouse facility. Female mice were between 8 and 10 weeks old at the beginning of experiments. Pregnancy was timed by checking for vaginal plugs early mornings for 4 days after setting up breeding couples.

extract_protocol: RNA extraction was done using Qiagen RNAeasy Kit according to the manufacturer’s recommendations

treatment_protocol: Lungs and livers of pregnant and virgin mice were ground in liquid nitrogen and the powder homogenated by resuspending in RLT lysis buffer

tag: pregnancy

value: pregnant

value: liver


title: SY-2


title: Lung Pregnant 3

source_name: Lung of 16-day pregnant mice, pool 3 of two mice

value: lung


title: Liver Virgin 2

source_name: Liver of virgin mice, pool 2 of two mice

value: virgin


title: Liver Virgin 3

source_name: Liver of virgin mice, pool 3 of two mice


title: Liver Virgin 1

source_name: Liver of virgin mice, pool 1 of two mice


title: Liver Pregnant 1

source_name: Liver of 16-day pregnant mice, pool 1 of two mice


title: Liver Pregnant 2

source_name: Liver of 16-day pregnant mice, pool 2 of two mice


title: 293+avb3 lifted, p66+ vs. p66- infected, 1h

description:
293+avb3 p66+/ p66- 1hr
293+avb3 lifted

source_name: p66- B. burgdorferi 1 hr


title: 293+avb3 lifted, uninfected vs. p66- infected, 3h

description:
293+avb3 p66-/uninfected 3hr
293+avb3 lifted

source_name: uninfected 3 hr


title: DZ-6


title: Lung Virgin 3

source_name: Lung of virgin mice, pool 3 of two mice


title: Lung Pregnant 1

source_name: Lung of 16-day pregnant mice, pool 1 of two mice


title: 293+avb3 lifted, uninfected vs. p66- infected, 1h

description:
293+avb3 p66-/uninfected 1hr
293+avb3 lifted


title: DZ-5

source_name: oral keratinocyte from control groups


title: 293 lifted, uninfected vs. p66+ infected, 3h

description:
293 p66+/uninfected 3hr
293 lifted


title: Lung Virgin 1

source_name: Lung of virgin mice, pool 1 of two mice


title: Lung Virgin 2

source_name: Lung of virgin mice, pool 2 of two mice


title: 293+avb3 lifted, uninfected vs. p66+ infected, 3h

description:
293+avb3 p66+/uninfected 3hr
293+avb3 lifted

source_name: p66+ B. burgdorferi 3 hr


title: 293 lifted, uninfected vs. p66+ infected, 1h

description:
293 p66+/uninfected 1hr
293 lifted

source_name: p66+ B. burgdorferi 1 hr


title: Lung Pregnant 2

source_name: Lung of 16-day pregnant mice, pool 2 of two mice


title: 293 lifted, uninfected vs. p66- infected, 3h

description:
293 p66-/uninfected 3hr
293 lifted

source_name: p66- B. burgdorferi 3 hr


title: 293 lifted, uninfected vs. p66- infected, 1h

description:
293 p66-/uninfected 1hr
293 lifted

source_name: uninfected 1 hr


title: Eahy lifted, uninfected vs. p66+ infected, 3hr

description:
Eahy p66+/uninfected 3hr
Eahy lifted


title: Eahy lifted, uninfected vs. p66+ infected, 1hr

description:
Eahy p66+/uninfected 1 hr
Eahy lifted


title: Eahy lifted, p66+ vs. p66- infected, 3hr

description:
Eahy p66+/ p66- 3 hr
Eahy lifted


title: Eahy lifted, p66+ vs. p66- infected, 1hr

description:
Eahy p66+/ p66- 1 hr
Eahy lifted


title: Eahy lifted, uninfected vs. p66- infected, 3hr

description:
Eahy p66-/uninfected 3hr
Eahy lifted


title: Eahy lifted, uninfected vs. p66- infected, 1hr

description:
Eahy p66-/uninfected 1 hr
Eahy lifted