title: 15 Days Treatment, Replicate 1

description:
Dye-flip replicate 1 of 2. RNA from 15 days tetracycline-treated L. sigmodontis was compared to age-matched untreated worms.
Day15_rep1

source_name: female adult worms from patent infections in Balb/C IL5 knockout mice, 15 days untreated

tag: gender

value: 15 days

source_name: female adult worms from patent infections in Balb/C IL5 knockout mice, 15 days Tet


title: Colombian 15

status: Public on Apr 08 2010

type: genomic

city: New York

first: Harry

last: Ostrer

state: NY

address: 550 First Avenue, MSB 136

department: Department of Pediatrics

country: USA

institute: NYU Langone Medical Center

description: sample id: D0014057

hyb_protocol: Extraction of DNA from peripheral blood at North Shore - Long Island Jewish, following standard Illumina labeling, hybridization, scanning, and genotype protocol.  See illumina.com

data_processing: Genotyped using Illumina 610-Quad Genotyping BeadChips, which use the SNPs on the 550-v3 Genotyping BeadChip plus an additional 60,000 SNPs for CNV not analyzed in present study.  See illumina.com

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: NYHP

label_protocol: standard Illumina protocol

value: Male

tag: tissue

value: Peripheral blood

tag: disease state

value: Healthy control


title: 36 Days Treatment, Replicate 1

status: Public on Apr 07 2010

type: RNA

city: Bonn

first: Uta

last: Strübing

address: Sigmund-Freud-Str. 25

department: Institute for Medical Microbiology, Immunology and Parasitology

country: Germany

institute: University Hospital Bonn

description:
Dye-flip replicate 1 of 2. RNA from 36 days tetracycline-treated L. sigmodontis was compared to age-matched untreated worms.
Day36_rep1

hyb_protocol: Each sample pair (~24 µl) was resuspended in formamide-based  hybridization buffer (vial 7-Genisphere) (26 µl) and Array 50dT blocker (Genisphere) (2 µl). Two hybridizations were carried out in a sequential manner. The primary hybridization was performed by adding 48 µl of sample to the microarray under a supported glass coverslip (Erie Scientific) at 43°C for 16-20 hours at high humidity in the dark. Prior to the secondary hybridization, slides were gently submerged into 2X SSC, 0.2% SDS (at 43°C) for 11 min., transferred to 2X SSC (at room temperature) for 11 min., transferred to 0.2X SSC (at room temperature) for 11 min., and then spun dry by centrifugation. Secondary hybridization was carried out using the complimentary capture reagents provided in the 3DNA Array 900 kit (Genisphere). For each reaction, the following were added: 3DNA capture reagent with Cy3 (2.5 µl), 3DNA capture reagent with Cy5 (2.5 µl), SDS-based hybridization buffer (vial 6-Genisphere) (26 µl), and nuclease-free water (21 µl). The secondary hybridization solution was incubated in the dark at 80°C for 10 min., then 50°C for 15 min. Hybridization was performed by adding 48 µl secondary hybridization solution to the slide under a supported glass coverslip at 65°C for 4 hours at high humidity in the dark. At hybridization termination, arrays were gently submerged into 2X SSC, 0.2% SDS (at 65°C) for 11 min., transferred to 2X SSC (at room temp.) for 11 min., transferred to 0.2X SSC (at room temperature) for 11 min., and then spun dry by centrifugation.

scan_protocol: Slides were scanned on a Perkin Elmer ScanArray Express HT scanner to detect Cy3 and Cy5 fluorescence. Laser power was kept constant for Cy3/Cy5 scans and PMT was varied for each experiment based on optimal signal intensity with lowest possible background fluorescence. A low PMT setting scan was also performed to recover signal from saturated elements.  Gridding and analysis of images was performed using ScanArray v3.0 (Perkin Elmer).

data_processing: For determining foreground and background intensities of each spot, the adaptive circle spot-finding algorithm was used. Data were normalized using LOWESS. Spots that passed the criteria of an intensity unit > 200 and signal to background ratio > 2 in one of the two channels were marked as “present” and were included in further analyses. Since a cross-species hybridization was performed, only approximately 20% of the cDNA hybridized to the oligos on the array. The log2 transformed values of the normalized and background subtracted ratio of intensities (treated vs. untreated) were used for identification of significant changes in gene expression applying Significance Analysis of Microarrays (SAM, version 3.02, Tusher et al., 2001). The one-class response type was used with a false discovery rate (FDR) ≤ 5% (= q-value ≤ 0.05). The resulting data were filtered for genes having a minimum 2-fold gene expression change.

molecule: total RNA

organism: Litomosoides sigmodontis

source_name: female adult worms from patent infections in Balb/C IL5 knockout mice, 36 days untreated

label_protocol: First strand cDNA was generated by oligo-dT primed reverse transcription (Superscript II, Invitrogen) utilizing the 3DNA Array 900 kit (Genisphere), with Cy3 or Cy5  specific oligo sequences attached to the oligo-dT Primer. One µl of fluorophore specific oligo-dT primer was added to 2 µg of total RNA and the solution was incubated at 80°C for 5 minutes and then cooled on ice for 2 minutes. 0.5 µl RNase inhibitor (Superase-In, Ambion), 2 µl 5x first strand buffer, 0.5 µl dNTP mix (10 mM each dATP, dCTP, dGTP and dTTP), 1 µl 0.1M DTT and 0.5 µl Superscript II RNase H- Reverse Transcriptase were added to each sample. Reverse transcription was carried out at 42°C for 2 hours. The reaction was terminated by adding 1.0 µl of 1.0 M NaOH/100 mM EDTA and incubation at 65°C for 10 minutes following a neutralization with 1.2 µl 2M Tris-HCL, pH 7.5.

growth_protocol: Fully permissive IL-5 KO BALB/c mice (6-8 weeks old) were infected with Litomosoides sigmodontis by mites (Ornithonyssus bacoti) carrying the infective L3 larvae.

extract_protocol: Total RNA was isolated from 5-10 female L. sigmodontis using the Trizol (Invitrogen GmbH, Karlsruhe, Germany) extraction method, following the manufacturer’s protocol with some modifications. Briefly, nematodes in 800 µl Trizol reagent were transferred to 2 ml tubes containing 0.5 mm glass beads and homogenized in a Precellys 24 homogenizer (Peqlab, Erlangen, Germany) 4 x 10 s at 5000 rpm. Instead of chloroform, 80 µl of 1-brom-3-chloro-propane (Sigma-Aldrich, Steinheim, Germany) was used to separate the homogenate into RNA-containing aqueous and DNA containing organic phases. For precipitation of RNA, linear acrylamide (Applied Biosystems, Foster City, USA) was used as co-precipitant with a final concentration of 9 µg/ml and 1 volume isopropanol (Merck, Darmstadt, Germany). RNA was treated with RNAse-free DNAse I (Applied Biosystems) for 1 h at 37°C, followed by clean-up and concentration of the RNA with the RNeasy Minelute kit (Qiagen, Hilden, Germany) as per the manufacturer’s protocol. Total RNA concentration and purity was obtained from an absorbance ratio at 260nm and 280nm. Total RNA quality was then determined by an Agilent 2100 bioanalyzer (Agilent Technologies) according to manufacturer's recommendations.

treatment_protocol: Tetracycline (Tet) treatment of mice started around day 60, when worms were patent and microfilaria are seen in blood of infected mice. Mice were treated daily for 36 days with intraperitoneal injections of 1mg Tet in 200 µl PBS (50mg Tet/kg). At days 6, 15 and 36 after start of Tet treatment, worms from untreated control and Tet-treated mice were recovered from the thoracic cavity. Female worms were snap frozen in liquid nitrogen and stored at -80°C for subsequent RNA isolation.

value: female

tag: developmental stage

value: adult

value: whole body

tag: treatment

value: untreated

tag: timepoint

value: 36 days

source_name: female adult worms from patent infections in Balb/C IL5 knockout mice, 36 days Tet

value: tetracycline treated


title: Colombian 12

description: sample id: D0012392

scan_protocol: Extraction of DNA from peripheral blood at North Shore - Long Island Jewish, following standard Illumina labeling, hybridization, scanning, and genotype protocol.  See illumina.com


title: Colombian 14

description: sample id: D0013175

extract_protocol: Extraction of DNA from peripheral blood at North Shore - Long Island Jewish, following standard Illumina labeling, hybridization, scanning, and genotype protocol.  See illumina.com


title: 15 Days Treatment, Replicate 2 (Dye Flip)

description:
Dye-flip replicate 2 of 2. RNA from 15 days tetracycline-treated L. sigmodontis was compared to age-matched untreated worms.
Day15_rep2


title: Es12, Ectocarpus siliculosus tiling array Chip6

city: Los Altos

first: Manoj

last: Samanta

state: CA

address: 2240 Homestead Court #309

institute: Systemix Institute

description: A High-Resolution Transcriptome Map of the Ectocarpus siliculosus

hyb_protocol: Hybridization was performed by Nimblegen at their Iceland core facility using Nimblegen protocol.

scan_protocol: Features were scanned using Nimblescan software.

data_processing: Custom software tools were used for data processing. Quantile normalization was performed with data on all arrays.

organism: Ectocarpus siliculosus

source_name: genomic DNA from ectocarpus

label_protocol: Standard Nimblegen protocol was used to generate labeled DNA from genomic DNA.

extract_protocol: Genomic DNA was extracted from cells of ectocarpus. The DNA extraction protocol described by Apt et al.^2 was optimised for the Ec 32 strain. About one gram of tissue was ground to a powder under liquid nitrogen in a mortar and pestle using sand. After addition of 2 ml of extraction buffer (100 mM Tris-HCl pH 7.5, 1.5 M NaCl, 2% CTAB, 50 mM EDTA pH 4.5, 50 mM DTT) the tissue was extracted further in a Wheaton glass grinding tube. Extraction buffer was then added to 15 ml final volume, the sample shaken vigorously for 10 min and then incubated at 55°C for 2 hours in the presence of 25 units of proteinase K. After extraction with 1 volume of chloroform:isoamyl alcohol (24:1), polysaccharides were precipitated with 0.3 volumes of 100% ethanol and the chloroform-isoamyl alcohol extraction repeated. RNA was then removed by incubation overnight at 20°C in 4M LiCl and 1% beta-mercaptoethanol and centrifugation at 13,000 rpm for 30 min. The DNA was then precipitated from the supernatant by addition of 0.8 volumes of isopropanol, redissolved in 500 µl of Tris EDTA buffer, extracted with phenol:chloroform:isoamyl alcohol (25:24:1) and then with chloroform:isoamyl alcohol (24:1) and precipitated in 0.3 M sodium acetate and 71% ethanol. The DNA was then purified on a CsCl gradient.

tag: control

value: Genomic DNA from Ectocarpus siliculosus genome


title: Es2, Ectocarpus siliculosus tiling array Chip1


title: Colombian 22

description: sample id: D0018873


title: 6 Days Treatment, Replicate 2 (Dye Flip)

description:
Dye-flip replicate 2 of 2. RNA from 6 days tetracycline-treated L. sigmodontis was compared to age-matched untreated worms.
Day6_rep2

source_name: female adult worms from patent infections in Balb/C IL5 knockout mice, 6 days Tet

value: 6 days

source_name: female adult worms from patent infections in Balb/C IL5 knockout mice, 6 days untreated


title: Es15, Ectocarpus siliculosus tiling array Chip8

source_name: cDNA from ectocarpus

label_protocol: Standard Nimblegen protocol was used to generate labeled cDNA.

extract_protocol: RNA pooled from multiple sources were pooled together and converted into cDNA using standard protocol specificed by Nimblegen.

tag: test

value: Poly-A RNA pooled from mature sporophytes and gametophytes and from immature sporophytes stressed either in high salt medium or by addition of hydrogen peroxide, and converted to cDNA


title: PC-deficient mutant_virulence-induced_rep1

city: Bochum

first: sonja

last: klüsener

address: Universitätsstrasse 150

institute: Ruhr-Universität Bochum

description: This sample is of Agrobacterium tumefaciens str. C58 DpmtA Dpcs mutant in which the PC-biosynthesis genes pmtA (ATU0300) and pcs (ATU1793) are deleted. The cells were grown under virulence-induced conditions. It is the first of three mutant biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by NimbleGen Systems, Inc (Madison, USA) according to the NimbleGenTM Arrays User´s Guide for Gene Expression Analysis (Version 3.0).

scan_protocol: Array scanning was performed by NimbleGen Systems, Inc (Madison, USA) according to the NimbleGenTM Arrays User´s Guide for Gene Expression Analysis (Version 3.0).

data_processing:
The raw data (.pair file) was subjected to RMA and quantile normalization (Nimble ScanTM). Data were further analyzed using the GeneSpring gene expression analysis software Version 7.3 (Agilent). The experiment was normalized with the default settings for Affymetrix arrays. First, data was transformed to set measurements of below 0.01 to 0.01 followed by a per-chip normalization to the 50th percentile and a per-gene normalization to median.
For statistical comparisons, the student t-test with a P-value threshold of 0.05 was applied. Comparing cultivation conditions, genes were considered to be differentially expressed at a fold change of >±2.

organism: Agrobacterium fabrum str. C58

label_protocol: cDNA production and cDNA labeling were performed by NimbleGen Systems, Inc (Madison, USA) according to the NimbleGenTM Arrays User´s Guide for Gene Expression Analysis (Version 3.0).

growth_protocol: A. tumefaciens C58 wild type and mutant (DpmtA Dpcs) cells were grown in 50 ml AB minimal medium (Schmidt-Eisenlohr et al. 1999, J. Bacteriol. 181:7485-92) to an OD600 nm of 0.2 at 30°C. To induce virulence gene expression 0.1 mM acetosyringone was added. Control cultures (non-induced) were treated with solvent (DMSO) only. Cells were further incubated for 16 h at 23°C.

extract_protocol: Total RNA was isolated with the hot phenol-extraction procedure described previously (Babst et al. 1996, Mol. Microbiol. 19:827-39). RNA integrity was checked by agarose gel electrophoresis. Precipitated RNA (100 200 µg) was treated with 100 U of recombinant DNase I (Roche, Mannheim, Germany) for 30 min at 37°C in a reaction volume of 110 µl. SUPERase•InTM (100 U; Ambion, Huntingdon, UK) was included in the reaction to inhibit potential RNase activity. RNA samples were cleaned up with RNeasy spin columns (Qiagen, Hilden, Germany) and the eluted RNA was checked again for integrity by agarose gel electrophoresis.

tag: genotype

value: DpmtA Dpcs deletion mutant

tag: phenotype

value: motility defect; altered biofilm formation and stress adaptation


title: Colombian 13

description: sample id: D0012551


title: Colombian 10

description: sample id: D0011065


title: Colombian 11

description: sample id: D0011917


title: Es11, Ectocarpus siliculosus tiling array Chip6


title: Es1, Ectocarpus siliculosus tiling array Chip1


title: PC-deficient mutant_non-induced_rep3

description: This sample is of Agrobacterium tumefaciens str. C58 DpmtA Dpcs mutant in which the PC-biosynthesis genes pmtA (ATU0300) and pcs (ATU1793) are deleted. The cells were grown under non-induced conditions. It is the third of three mutant biological replicates used in this experiment, each from separate cultures.


title: PC-deficient mutant_non-induced_rep1

description: This sample is of Agrobacterium tumefaciens str. C58 DpmtA Dpcs mutant in which the PC-biosynthesis genes pmtA (ATU0300) and pcs (ATU1793) are deleted. The cells were grown under non-induced conditions. It is the first of three mutant biological replicates used in this experiment, each from separate cultures.


title: wild type_virulence-induced_rep3

description: This sample is of wild type Agrobacterium tumefaciens str. C58 grown under virulence-induced conditions. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.

value: wild type

value: normal


title: wild type_virulence-induced_rep2

description: This sample is of wild type Agrobacterium tumefaciens str. C58 grown under virulence-induced conditions. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: Colombian 8

description: sample id: D0009891


title: Colombian 1

description: sample id: D0000983


title: wild type_non-induced_rep2

description: This sample is of wild type Agrobacterium tumefaciens str. C58 grown under non-induced conditions. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: A. tumefaciens_wild type_non-induced


title: Colombian 7

description: sample id: D0009416


title: Colombian 4

description: sample id: D0004362


title: wild type_non-induced_rep1

description: This sample is of wild type Agrobacterium tumefaciens str. C58 grown under non-induced conditions. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: Colombian 25

description: sample id: D0024480


title: Colombian 6

description: sample id: D0004595


title: Colombian 3

description: sample id: D0004356


title: LSF-17 clone, biological rep2

status: Public on Apr 06 2010

city: Richmond

first: Devanand

last: Sarkar

state: VA

address: 1220 E Broad St, Room 7044

department: Department of Human and Molecular Genetics

institute: Virginia Commonwealth University

description: Gene expression data from LSF overexpressing HepG3 clone cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133A 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner GCS 3000.

data_processing: The data were analyzed with the Robust Multiarray Analysis (RMA) method performed on the R environment using functions provided by the BioConductor packages.

source_name: HepG3 cells, LSF overexpressing clone

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

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

value: Hepatocellular carcinoma cells

tag: cell line

value: LSF overexpressing HepG3


title: LSF-17 clone, biological rep3


title: PC-deficient mutant_non-induced_rep2

description: This sample is of Agrobacterium tumefaciens str. C58 DpmtA Dpcs mutant in which the PC-biosynthesis genes pmtA (ATU0300) and pcs (ATU1793) are deleted. The cells were grown under non-induced conditions. It is the second of three mutant biological replicates used in this experiment, each from separate cultures.


title: wild type_virulence-induced_rep1

description: This sample is of wild type Agrobacterium tumefaciens str. C58 grown under virulence-induced conditions. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: wild type_non-induced_rep3

description: This sample is of wild type Agrobacterium tumefaciens str. C58 grown under non-induced conditions. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.


title: Colombian 5

description: sample id: D0004506

value: Male

value: Peripheral blood


title: Control-8 clone, biological rep2

description: Gene expression data from Control HepG3 cells

source_name: HepG3 cells, control


title: LSF-17 clone, biological rep1


title: Colombian 9

description: sample id: D0010678

value: Healthy control


title: Control-8 clone, biological rep3


title: flea biofilm culture rep 6

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_flea biofilm culture rep 6

hyb_protocol: All samples were hybridized for 16 hr at 45C on our custom Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Yp genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Yersinia pestis

source_name: flea biofilm culture

label_protocol: Total RNA (100 ng) was amplified and labeled with Modified biotin-11-CTP (Perkin Elmer; Waltham, MA) and biotin-16-UTP (Roche Molecular Biochemicals, Pleasanton, CA) by using the Message-Amp II-Bacteria amplified antisense RNA (aRNA) kit (Ambion; Austin, TX). Amplified RNA was then fragmented using Ambion’s Fragmentation reagent (Applied Biosystems), hybridized to the RML custom Affymetrix GeneChip.

growth_protocol: The bacterial strain used in this study was Y. pestis KIM6+, which lacks the 70-kb virulence plasmid that is not required for flea infection or blockage. A KIM6+ strain deleted of yitR (y0181) was produced by allelic exchange, using the pCVD442 suicide vector system (11). This mutant was complemented by electroporation with a recombinant pWKS130 plasmid containing the wild-type yitR promoter and orf. The ΔyitR mutant was also transformed with pWKS130 alone to generate an empty vector control strain. For in vitro planktonic samples, bacteria were grown from frozen stocks in brain heart infusion (BHI) medium at 28°C, followed by two successive transfers in Luria Bertani broth supplemented with 100 mM MOPS, pH 7.4 (LB/MOPS) at 21°C. An inoculum of 10^4 cells/ml was added to 50 ml of LB/MOPS and incubated at 21°C with shaking at 250 rpm until exponential (OD600 = 2.5) or stationary phase (OD600 = 4.5).

extract_protocol: Approximately 0.5 ml of the exponential phase culture and 0.25 ml of the stationary phase culture was resuspended in 1ml and 0.5 ml, respectively, of RNAprotect bacterial reagent (Qiagen; Valencia, CA), incubated for 5 min at room temperature, and centrifuged at 21°C for 5 min prior to RNA extraction. RNA was isolated from six independent samples from in vitro and flow cell cultures and two independent samples from pooled blocked fleas (Fig. S1) using the RNeasy Mini Kit (Qiagen). Flea-derived RNA samples were secondarily split into three technical replicates each. RNA integrity was verified on a Bioanalyzer 2100 (Agilent Technologies; Santa Clara, CA).

treatment_protocol: RNA isolation from cultures grown to early stationary growth phase (7 h).

tag: strain


title: Es14, Ectocarpus siliculosus tiling array Chip7


title: Control-8 clone, biological rep1


title: WN19 vs. WN1 T3

city: London

first: Ana

last: Viñuela

state: London

address: St.Thomas' Hospital Campus Westminster Bridge Road

department: Twin Research & Genetic Epidemiology

country: United Kingdom

institute: King's College London

hyb_protocol: Microarrays were hybridized following the Genisphere Array 900 HS protocol with modifications.

scan_protocol: A Perkin & Elmer scanner was used to extract the raw intensities.

data_processing: Preprocessing and normalization was done in the R software [58] using Limma package [59]. Loess method [59] was used for normalization within arrays and normalization between arrays was done using aquantile method [60], both of them included in limma package.

organism: Caenorhabditis elegans

source_name: wn19 214 hours

label_protocol: Labeled cDNA was produced with Array 900 HS kit from Genisphere and Superscript II from Invitrogen. The Nucleospin kit () was used to clean the cDNA samples in order to reduce unspecific binding to the arrays.

growth_protocol: A set of 36 recombinant inbred lines (RILs) generated by crosses between N2 and CB4856 (Li et al., 2006) were used to generate genetical genomics data. The RILs were cultured on standard nematode growth medium (NGM) with E. coli OP50 as food source and a constant temperature of 24ºC. Populations were started with nonmated hermaphrodites and screened regularly to remove any occurring males.

extract_protocol: RNA from nematodes was extracted following the Trizol method, followed by the RNeasy Micro kit (Quiagen, Valencia, CA, USA) to clean up the samples.

treatment_protocol: Reproductive nematodes from 36 RILs were bleached (0.5 M NaOH, 1% hypochlorite) in order to collect age synchronized eggs which were inoculated in 24 dishes (t0). After 40 hours (t1) nematodes from 6 dishes were collected in late L3 stage, frozen in liquid nitrogen and keep them at -80ºC until RNA extraction procedure. The remaining 18 dishes were kept in culture until hour 41 when the nematodes were transferred to fresh NGM dishes (with E. coli OP50) treated with 0.05-0.01 mg/ml of FUDR in order to avoid reproduction. After 30 hours in dishes with FUDR and when reproductive period is about to finish, nematodes were transferred to fresh dishes without FUDR, to prevent starvation. After 23 hours, 96 hours of total culture time (t2), nematodes from 6 dishes were collected and frozen in liquid nitrogen prior to RNA extraction. The remaining 12 dishes were kept at constant temperature until 214 hours of culture (t3), when they were harvest and frozen in liquid nitrogen. All the dishes were visually inspected before the harvest. Any population with contamination, more than one generation (reproduction) or starving nematodes (lacking bacteria) were discarded.

tag: recombinant inbred line

value: Old adults stage (214 hours at 24ºC).

source_name: wn1 214 hours


title: WN11 vs. WN25 T3

source_name: wn11 214 hours

source_name: wn25 214 hours


title: WN24 vs. WN16 T3

source_name: wn24 214 hours

source_name: wn16 214 hours


title: Colombian 2

description: sample id: D0004248

source_name: NYHP


title: flea biofilm culture rep 4

description: Gene expression data from_flea biofilm culture rep 4


title: flea biofilm culture rep 5

description: Gene expression data from_flea biofilm culture rep 5


title: WN33 vs. WN3 T3

source_name: wn33 214 hours

source_name: wn3 214 hours


title: WN28 vs. WN50 T3

source_name: wn28 214 hours

source_name: wn50 214 hours


title: Es5, Ectocarpus siliculosus tiling array Chip3

description: A High-Resolution Transcriptome Map of the Ectocarpus siliculosus


title: flea biofilm culture rep 3

description: Gene expression data from_flea biofilm culture rep 3


title: flea biofilm culture rep 2

description: Gene expression data from_flea biofilm culture rep 2


title: Es4, Ectocarpus siliculosus tiling array Chip2

source_name: genomic DNA from ectocarpus


title: WN76 vs. WN59 T3

source_name: wn76 214 hours

source_name: wn59 214 hours


title: Es6, Ectocarpus siliculosus tiling array Chip3


title: Es3, Ectocarpus siliculosus tiling array Chip2

source_name: cDNA from ectocarpus


title: flowcell biofilm culture rep 6

description: Gene expression data from_flowcell biofilm culture rep 6

source_name: flowcell biofilm culture


title: WN20 vs. WN53 T3

source_name: wn20 214 hours

source_name: wn53 214 hours


title: WN57 vs. WN32 T3

source_name: wn57 214 hours

source_name: wn32 214 hours


title: Es13, Ectocarpus siliculosus tiling array Chip7


title: Es8, Ectocarpus siliculosus tiling array Chip4


title: flowcell biofilm culture rep 4

description: Gene expression data from_flowcell biofilm culture rep 4


title: flea biofilm culture rep 1

description: Gene expression data from_flea biofilm culture rep 1

source_name: flea biofilm culture


title: WN68 vs. WN37 T3

source_name: wn68 214 hours

source_name: wn37 214 hours


title: WN46 vs. WN69 T3

source_name: wn46 214 hours

source_name: wn69 214 hours


title: flowcell biofilm culture rep 3

description: Gene expression data from_flowcell biofilm culture rep 3


title: flowcell biofilm culture rep 5

description: Gene expression data from_flowcell biofilm culture rep 5


title: WN13 vs. WN21 T3

source_name: wn13 214 hours

source_name: wn21 214 hours


title: flowcell biofilm culture rep 2

description: Gene expression data from_flowcell biofilm culture rep 2


title: WN27 vs. WN56 T3

source_name: wn27 214 hours

source_name: wn56 214 hours


title: Colombian 20

description: sample id: D0017586

source_name: NYHP


title: 6 Days Treatment, Replicate 1

description:
Dye-flip replicate 1 of 2. RNA from 6 days tetracycline-treated L. sigmodontis was compared to age-matched untreated worms.
Day6_rep1

source_name: female adult worms from patent infections in Balb/C IL5 knockout mice, 6 days untreated

value: female

value: adult

value: whole body

source_name: female adult worms from patent infections in Balb/C IL5 knockout mice, 6 days Tet


title: WN9 vs. WN62 T3

source_name: wn9 214 hours

source_name: wn62 214 hours


title: WN8 vs. WN41 T3

source_name: wn8 214 hours

source_name: wn41 214 hours


title: WN71 vs. WN79 T3

source_name: wn71 214 hours

source_name: wn79 214 hours


title: stationary phase broth culture rep 6

description: Gene expression data from_stationary phase broth culture rep 6

source_name: stationary phase broth culture


title: Es10, Ectocarpus siliculosus tiling array Chip5

source_name: genomic DNA from ectocarpus


title: flowcell biofilm culture rep 1

description: Gene expression data from_flowcell biofilm culture rep 1

source_name: flowcell biofilm culture


title: WN60 vs. WN77 T3

source_name: wn60 214 hours

source_name: wn77 214 hours


title: stationary phase broth culture rep 5

description: Gene expression data from_stationary phase broth culture rep 5


title: WN19 vs. WN1 T2

source_name: wn19 96  hours

value: Late reproduction stage (96 hours at 24ºC).

source_name: wn1 96 hours


title: WN11 vs. WN25 T2

source_name: wn11 96  hours

source_name: wn25 96 hours


title: WN24 vs. WN16 T2

source_name: wn24 96  hours

source_name: wn16 96 hours


title: WN28 vs. WN50 T2

source_name: wn28 96  hours

source_name: wn50 96 hours


title: stationary phase broth culture rep 4

description: Gene expression data from_stationary phase broth culture rep 4


title: Es9, Ectocarpus siliculosus tiling array Chip5

source_name: cDNA from ectocarpus


title: WN44 vs. WN2 T2

source_name: wn54 96  hours

source_name: wn2 96 hours


title: Es7, Ectocarpus siliculosus tiling array Chip4


title: stationary phase broth culture rep 3

description: Gene expression data from_stationary phase broth culture rep 3


title: WN76 vs. WN59 T2

source_name: wn76 96  hours

source_name: wn59 96 hours


title: WN57 vs. WN32 T2

source_name: wn57 96  hours

source_name: wn32 96 hours


title: stationary phase broth culture rep 1

description: Gene expression data from_stationary phase broth culture rep 1

source_name: stationary phase broth culture


title: WN13 vs. WN21 T2

source_name: wn13 96  hours

source_name: wn21 96 hours


title: WN33 vs. WN3 T2

source_name: wn33 96  hours

source_name: wn3 96 hours


title: stationary phase broth culture rep 2

description: Gene expression data from_stationary phase broth culture rep 2


title: WN46 vs. WN69 T2

source_name: wn46 96  hours

source_name: wn69 96 hours


title: WN71 vs. WN79 T2

source_name: wn71 96  hours

source_name: wn79 96 hours


title: WN44 vs. WN2 T3

source_name: wn54 214 hours

source_name: wn2 214 hours


title: WN9 vs. WN62 T2

source_name: wn9 96  hours

source_name: wn62 96 hours


title: WN27 vs. WN56 T2

source_name: wn27 96  hours

source_name: wn56 96 hours


title: WN8 vs. WN41 T2

source_name: wn8 96  hours

source_name: wn41 96 hours


title: WN20 vs. WN53 T2

source_name: wn20 96  hours

source_name: wn53 96 hours


title: midlog phase broth culture rep 2

description: Gene expression data from_midlog phase broth culture rep 2

source_name: midlog phase broth culture


title: WN60 vs. WN77 T2

source_name: wn60 96  hours

source_name: wn77 96 hours


title: WN11 vs. WN25 T1

source_name: wn11 40 hours

value: Late L3 stage (40 hours at 24ºC).

source_name: wn25 40 hours


title: midlog phase broth culture rep 6

description: Gene expression data from_midlog phase broth culture rep 6


title: WN68 vs. WN37 T2

source_name: wn68 96  hours

source_name: wn37 96 hours


title: WN33 vs. WN3 T1

source_name: wn33 40 hours

source_name: wn3 40 hours


title: midlog phase broth culture rep 5

description: Gene expression data from_midlog phase broth culture rep 5


title: WN24 vs. WN16 T1

source_name: wn24 40 hours

source_name: wn16 40 hours


title: midlog phase broth culture rep 1

description: Gene expression data from_midlog phase broth culture rep 1


title: WN19 vs. WN1 T1

source_name: wn19 40 hours

source_name: wn1 40 hours


title: midlog phase broth culture rep 3

description: Gene expression data from_midlog phase broth culture rep 3


title: midlog phase broth culture rep 4

description: Gene expression data from_midlog phase broth culture rep 4


title: WN28 vs. WN50 T1

source_name: wn28 40 hours

source_name: wn50 40 hours


title: J2-071

city: Summit-Argo

first: Xiangyu

last: Deng

state: IL

address: 6502 S. Archer Rd.

department: National Center for Food Safety and Technology

institute: Illinois Insititute of Technology

description: CGH sample

hyb_protocol: NimbleGen standard protocols for CGH (prepared and hybridized by NimbleGen)

data_processing:
Arrays were processed using Nimblegen's standard protocol for Nimblescan 385K CGH data extraction
binsignal.txt - Binary presence/absence representation of mqlsignal table after intensity cutoffs have been applied.
cutoffs.txt - Cutoff values used for each sample to generate the binsiganl.txt file.
genepf.txt - Positive fraction (PF) values for annotated Listeria monocytogenes genes with probe coverage >90%. Positive fraction is computed as the fraction of probes mapping to that gene that have an intensity exceeding the cutoff.

label: cy3, cy5

organism: Listeria monocytogenes FSL J2-071

source_name: Genomic DNA from Listeria monocytogenes J2-071

growth_protocol: overnight BHI culture

extract_protocol: MasterPureTM Gram Positive DNA Purification kit protocol(http://www.epibio.com/item.asp?id=429)


title: WN20 vs. WN53 T1

source_name: wn20 40 hours

source_name: wn53 40 hours


title: WN76 vs. WN59 T1

source_name: wn76 40 hours

source_name: wn59 40 hours


title: WN44 vs. WN2 T1

source_name: wn54 40 hours

source_name: wn2 40 hours


title: WN68 vs. WN37 T1

source_name: wn68 40 hours

source_name: wn37 40 hours


title: WN71 vs. WN79 T1

source_name: wn71 40 hours

source_name: wn79 40 hours


title: WN60 vs. WN77 T1

source_name: wn60 40 hours

source_name: wn77 40 hours


title: WN27 vs. WN56 T1

source_name: wn27 40 hours

source_name: wn56 40 hours


title: WN46 vs. WN69 T1

source_name: wn46 40 hours

source_name: wn69 40 hours


title: WN57 vs. WN32 T1

source_name: wn57 40 hours

source_name: wn32 40 hours


title: WN9 vs. WN62 T1

source_name: wn9 40 hours

source_name: wn62 40 hours


title: WN8 vs. WN41 T1

source_name: wn8 40 hours

source_name: wn41 40 hours


title: F2-524

description: CGH sample

scan_protocol: NimbleGen standard protocols for CGH (prepared and hybridized by NimbleGen)

organism: Listeria monocytogenes

source_name: Genomic DNA from Listeria monocytogenes F2-524


title: W1-111

description: CGH sample

source_name: Genomic DNA from Listeria monocytogenes W1-111

label_protocol: NimbleGen standard protocols for CGH (prepared and hybridized by NimbleGen)


title: F2-501

description: CGH sample

source_name: Genomic DNA from Listeria monocytogenes F2-501


title: F2-569

description: CGH sample

source_name: Genomic DNA from Listeria monocytogenes F2-569


title: WN13 vs. WN21 T1

source_name: wn13 40 hours

source_name: wn21 40 hours


title: EGD-e8

description: CGH reference

organism: Listeria monocytogenes EGD-e

source_name: Genomic DNA from Listeria monocytogenes EGD-e

value: EGD-e


title: E. coli 8624 qseG deletion mutant

status: Public on Apr 05 2010

city: Baltimore

first: David

middle: A

last: Rasko

state: MD

address: 801 W. Baltimore Street, Room 619

department: Istitute for Genome Sciences/Microbiology and Immunology

institute: University of Maryland School of Medicine

description:
All protocols were done according to manufacturers specifications:
http://www.affymetrix.com/support/technical/manual/expression_manual.affx

data_processing: Data has not been processed other than those protocols within GCOSv1.4

organism: Escherichia coli

growth_protocol: Escherichia coli 8624 qseG deletion mutant grown in DMEM media

extract_protocol: Ambion RiboPure RNA Isolation


title: RNAi NINJA vs Wild Type (Col-0) treated with coronatine Rep 4

city: Madrid

first: Gloria

middle: Garcia

last: Casado

state: Madrid

address: C/Darwin 3

department: Genomica

country: Spain

institute: CNB-CSIC

description: Biological replicate 4 of 4. Gene expression of RNAi NINJA (At4g28910) vs  Wild Type strain (Col-0) treated 6 hours with coronatine 0.5 uM

hyb_protocol: The hybridization experiment was performed according to the manufacture's protocol (Agilent technologies, Agilent 60-mer oligo microarray processing protocol: Two color microarray based gene expression analysis, G4140-90050 ver 5.7)

scan_protocol: Images from Cy3 and Hyper5 channels were equilibrated and captured with a GenePix 4000B (Axon) and spots were converted into numerical data using GenPix software (Axon).

data_processing: Raw intensities were background-substracted by NORMEXP method with a offset of 50. Signals (in log2 scale) were then normalized by LOWESS algorithm (intra-arrays normalization) followed by adjustment of their quantiles (inter-arrays normalization).

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana Col-0

label_protocol: 5 ug of aminoallyl-labeled aRNA were resuspended in 0.1 M Na2CO3 (pH 9.0) and labeled with Hyper5 and Cy3 Mono NHS Ester (CyTMDye Post-labeling Reactive Dye Pack, Amersham). Samples were purified following the manufacturer's instructions for Megaclear TM (Ambion) and Hyper5  and Cy3 incorporation was measured using 1 ul of the probe in the Nanodrop

growth_protocol: Homozygous T3 plants silencing NINJA (RNAi-NINJA) and Col-0 sterile seeds were vernalized for 3 days at 4ºC, and grown in  Petri dishes (120 mm x 120 mm), containing 1x Murashige-Skoog (MS) pH 6.0; 1 sucrose (w/v);0.7% w/v agar medium. Chamber growth conditions were 16 hours light, 8 hours dark, 22ºC, 70% relative humidity, and 250uE fluorescent illumination.

extract_protocol: The frozen plant tissue (~100 mg) was ground in tiny mortars dipped in liquid nitrogen. The frozen powder was carefully transfered into 1.5 ml microcentrifuge tubes using small funnels and rubber spatulas also cooled with liquid nitrogen. Total RNA was extracted using TRIzol reagent (Invitrogen, 15596-026) according to manufacturer's instructions and purified with an RNeasy mini kit (Qiagen, 74104).1 ug of total RNA was amplified via the aRNA MessageAmp II kit (Ambion, 1751)

treatment_protocol: The seedlins were treated and untreated with 0.5uM Coronatine during 6 hours

value: Col-0 (Wild type)

source_name: Arabidopsis thaliana RNAi NINJA (At4g28910)

tag: rnai

value: NINJA (At4g28910)


title: M1-002

description: CGH sample

source_name: Genomic DNA from Listeria monocytogenes M1-002


title: Luciferase shRNA_2 Days knockdown_rep3

city: Singapore

first: Justin

middle: Jeyakani

last: Joseph Gnanakkan

state: Singapore

address: 60, Biopolis street

department: Computational and Systems Biology

country: Singapore

institute: Genome Institute of Singapore

description:
Luci kd 2 day_3
replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using median (MeV) by performing log2 transformation, followed by median centering on samples and median centering of genes across the samples.

source_name: H1 hESCs

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

growth_protocol: H1 hESCs were grown at 37degress for 5 days before the cells were passaged for OCT4 and Luciferase transfection. Samples were harvested after 2 or 3 days after transfection.

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

treatment_protocol: hESCs that were seeded one day before were transfected with 2ug of the OCT4 or Luciferase shRNA using 6ul of Fugene in 100ul optimen. After 20mins, the transfection mix were added to the cells.

tag: sample type

value: Negative control

tag: cell type

value: embryonic stem cell

tag: protocol

value: control

tag: time

value: 2 Days


title: OCT4 shRNA_3 Days knockdown_rep3

description:
Oct4 kd 3 day_3
replicate 3

value: Sample

value: OCT4 knockdown

value: 3 Days


title: Luciferase shRNA_3 Days knockdown_rep3

description:
Luci kd 3 day_3
replicate 3


title: EGD-e9

description: CGH reference


title: W1-110

description: CGH sample

source_name: Genomic DNA from Listeria monocytogenes W1-110


title: OCT4 shRNA_2 Days knockdown_rep3

description:
Oct4 kd 2 day_3
replicate 3


title: J1-208

description: CGH sample

organism: Listeria monocytogenes FSL J1-208

source_name: Genomic DNA from Listeria monocytogenes J1-208


title: F2-208

description: CGH sample

organism: Listeria monocytogenes FSL F2-208

source_name: Genomic DNA from Listeria monocytogenes F2-208


title: RNAi NINJA vs Wild Type (Col-0) treated with coronatine Rep 3

description: Biological replicate 3 of 4. Gene expression of RNAi NINJA (At4g28910) vs  Wild Type strain (Col-0) treated 6 hours with coronatine 0.5 uM


title: E. coli 8624 qseE deletion mutant

hyb_protocol: All protocols were done according to manufacturers specifications: http://www.affymetrix.com/support/technical/manual/expression_manual.affx

growth_protocol: Escherichia coli 8624 qseE deletion mutant grown in DMEM media


title: RNAi NINJA vs Wild Type (Col-0) treated with coronatine Rep 1

description: Biological replicate 1 of 4. Gene expression of RNAi NINJA (At4g28910) vs  Wild Type strain (Col-0) treated 6 hours with coronatine 0.5 uM


title: OCT4 shRNA_2 Days knockdown_rep2

description:
Oct4 kd 2 day_2
replicate 2


title: OCT4 shRNA_3 Days knockdown_rep2

description:
Oct4 kd 3 day_2
replicate 2


title: EGD-e7

description: CGH reference


title: EGD-e5

description: CGH reference


title: RNAi NINJA vs Wild Type (Col-0) treated with coronatine Rep 2

description: Biological replicate 2 of 4. Gene expression of RNAi NINJA (At4g28910) vs  Wild Type strain (Col-0) treated 6 hours with coronatine 0.5 uM


title: Luciferase shRNA_2 Days knockdown_rep1

description:
Luci kd 2 day_1
replicate 1


title: OCT4 shRNA_3 Days knockdown_rep1

description:
Oct4 kd 3 day_1
replicate 1


title: Untreated-Rep3

city: New Orleans

first: guoshon

last: wang

state: LA

address: 533 Bolivar St.

department: Gene Therapy

institute: LSUHSC

description: Cells were grown on millicells inserts of a 24-well tissue dish. Cells were seeded with 10,000 per millicell initially and used at 24,000 to 46,000 cells.

hyb_protocol: After the prehybridization of the GeneChip, 15 ug of fragmented cDNA was pipetted into a GeneChip and hybridized overnight in the Hybridization Oven 640 at 60 rpm, washed, stained with streptavidin-phycoerythrin using a microfluidics station as described by the manufacture.

scan_protocol: Chips were scanned with the High Resolution 3000 Scanner (G7) and signal and background intensities were quantitated by pixel intensity, and expression signals were analyzed using the GeneChip Operating Software (GCOS 1.4). Expresson signals were scaled to a target intensity of 500.

data_processing: The CEL data file from each array was imported into Genespring GX 7.3 (Agilent Technologies) and preprocessed using the robust multichip average (RMA) method and per gene normalization was applied using the median values of the no EtOH control samples. The CHP files were also imported and the detection call metrics from the CHP files were used to filter out transcripts that were found absent in all nine samples. In addition, transcripts that were not within a standard deviation of 1.4 and exhibiting less than 1.5 fold change were also removed from further analysis. To identify up-regulated and down-regulated transcripts, genes were filtered using the volcano plot with the limit set at p<0.01 and 2.0 fold change. The parametric test, with variance not equal, was applied without multiple test correction.

source_name: airway epithelial cells, lot number, ethanol treated or vehicle untreated

label_protocol: 5 ug total RNA was used for first strand synthesis using T7-(dT)24 primer (Affymetrix) and SuperScript cDNA Synthesis Kit (Invitrogen). Synthesis of biotinylated-labeled cRNA was carried out using the RNA Transcript Labeling Kit (ENZO).

extract_protocol: sample was processed using the Trizol method

tag: human airway epithelial cells were obtained from commercial source


title: RNAi NINJA vs Wild Type (Col-0) Rep 4

description: Biological replicate 4 of 4. Gene expression of RNAi NINJA (At4g28910) vs  Wild Type strain (Col-0)


title: RNAi NINJA vs Wild Type (Col-0) Rep 3

description: Biological replicate 3 of 4. Gene expression of RNAi NINJA (At4g28910) vs  Wild Type strain (Col-0)


title: Fibroblasts in a patient with Pachydermoperiostosis (PDP)

city: Yahata-nishi, kitakyushu

first: Junichi

last: Sakabe

state: Fukuoka

address: 1-1 Iseiga-oka

department: Graduate School of Medicine

country: Japan

institute: University of Occupational and Environmental Health

description: Healthy vs. PDP

hyb_protocol: Hybridized for 16 h at 42 °C. Hybridization buffer and washing protocol was followed by the protocol supplied by Hitachi Software Engineering Co., Ltd. (DNA Chip Research Inc. / AceGene website)

scan_protocol: ScanArray HT (PerkinElmer Japan Co., Ltd.) was used for scanning. Array images were analyzed with ImaGene V6.0.1(BioDiscovery, Inc.).

data_processing: Data from each microarray were normalized by LOWESS normalization.

source_name: Fibroblasts from a healthy male

label_protocol: Amino Allyl aRNA was synthesized by Amino Allyl MessageAmp aRNA Amplification Kit (Ambion). CyeDye coupling and fragmentation were performed using the protocol supplied by Hitachi Software Engineering Co., Ltd. (DNA Chip Research Inc. / AceGene website).

growth_protocol: Fibroblasts were cultured in Dulbecco's Modified Eagle's Medium (DMEM) containg 10% fetal bovine serum.

extract_protocol: Total RNA extracted using Rneasy Mini Kit (QIAGEN) following manufacurer's instruction.

treatment_protocol: Samples were collected within 30 minutes from the time of harvest, and immediately extracted RNA.

tag: disease

tag: gender

value: male

source_name: Fibroblasts from PDP patient

tag: age

value: Pachydermoperiostosis


title: Luciferase shRNA_2 Days knockdown_rep2

description:
Luci kd 2 day_2
replicate 2


title: Luciferase shRNA_3 Days knockdown_rep1

description:
Luci kd 3 day_1
replicate 1


title: Untreated-Rep2


title: EGD-e6

description: CGH reference


title: RNAi NINJA vs Wild Type (Col-0) Rep 2

description: Biological replicate 2 of 4. Gene expression of RNAi NINJA (At4g28910) vs  Wild Type strain (Col-0)


title: 50mM Ethanol-Rep3


title: EGD-e2

description: CGH reference


title: 100mM Ethanol-Rep2


title: EGD-e1

description: CGH reference


title: 50mM Ethanol-Rep1


title: RNAi NINJA vs Wild Type (Col-0) Rep 1

description: Biological replicate 1 of 4. Gene expression of RNAi NINJA (At4g28910) vs  Wild Type strain (Col-0)


title: EGD-e4

description: CGH reference


title: OCT4 shRNA_2 Days knockdown_rep1

description:
Oct4 kd 2 day_1
replicate 1


title: EGD-e3

description: CGH reference


title: 100mM Ethanol-Rep3


title: miRNA profile of sample1

status: Public on Apr 03 2010

city: Chongqing

first: jingyi

last: li

address: Gao Tan Yan

department: institute of immunology

country: China

institute: the third millitary medical university

description:
1.CD4+ T cells isolated from  hydrops articuli cells in rheumatoid arthritis patient as sample1 using CD4+ Microbeads(Militenyi Biotec).
2.isolate the total RNA.

hyb_protocol: Labeled RNA samples were hybridized using Exiqon miRCURYTM Array microarray kit, Cat #208000V8.0, Corning Hybridization Chamber II, Cat #40080, and Ambion Bioarray LifterSlip coverslip.

scan_protocol: Scans were performed by using Genepix 4000B and quantified by using Genepix Pro 6.0 (AXON).

data_processing: Images were processed and quantified using Genepix Pro 6.0 software (Axon Instruments, Union City, CA). The data were filtered (or flagged) on the basis of signal levels and spot quality. Each microarray, scanned at three times were merged into one. The original values of data were amended by subtracting the measured background value and then normalized by subtracting the amended value of U6-snRNA on the same microarry.

source_name: CD4+ T cells

label_protocol: RNA samples were sent to KangChen Bio-tech Inc (Shanghai, China) where they were labeled using the Exiqon mercury Array labeling kit, Cat #208032.

growth_protocol: D4+ T cells from hydrops articuli cells in rheumatoid arthritis patient as sample1

extract_protocol: Isolation of total RNA from CD4+ T cells: 1.Total RNA: High-quality total RNA has been successfully isolated from 3 cells using the RNeasy Mini Kit from QIAGEN P/N 74104; 2.Quantification of RNA: The A260/A280 ratio should be close to 2.0 for pure RNA. For a high-quality total RNA sample,two well-defined band corresponding to the 18S and 28S ribosomal RNAs should be observed using denaturing agarose gel, with ratios approaching 2:1 for the 28S to 18S bands.

value: CD4+ T cells of hydrops articuli cells

value: 39 year old

value: female

tag: disease status

value: rheumatoid arthritis patient


title: miRNA profile of control

description:
1.CD4+ T cells isolated from  healthy person's peripheral blood as control using CD4+ Microbeads(Militenyi Biotec).
2.isolate the total RNA.

source_name: healthy control

growth_protocol: D4+ T cells from healthy person's peripheral blood as control

value: CD4+ T cells

value: 40 years old

value: healthy person


title: Luciferase shRNA_3 Days knockdown_rep2

description:
Luci kd 3 day_2
replicate 2


title: miRNA profile of sample2

source_name: CD4+ T cells of sample2

growth_protocol: D4+ T cells from hydrops articuli cells in rheumatoid arthritis patient as sample2

treatment_protocol: CD4+ T cells isolated from hydrops articuli cells in rheumatoid arthritis patient as sample2 using CD4+ Microbeads(Militenyi Biotec).

value: CD4+ T cells from hydrops articuli cells

value: 41 year old


title: 50mM Ethanol-Rep2


title: Du145 adapted from Knockdown, Second

city: chicago.

first: Wei

last: Du

address: 929 E. 57th Street

institute: University of Chicago

hyb_protocol: HuGene 1.0ST Array was used. Prepare heat blocks at 65oC, 99oC and 45oC, Warm up chips to room temp and label each chip, Heat the 20x eukaryotic Hyb. Ctrls @ 65oC 5 min. Genechip was washed by MicroFluidics Protocol: FS450_0007

scan_protocol: According to Affymetrix protocol, make sure the laser is warmed up prior to 10 minutes. Apply one Tough-Spots to each of the two septa & Press to ensure that the spots remain flat.

data_processing: the RMA normalized data sets from 6 different chips were normalized using the median of housekeeping genes (using the BRB-array tool Vesion 3.2) to adjust for variations between chips.

label_protocol: GeneChip WT terminal Labeling Kit (lot # 4066162), used 100ng Total RNA labeling protocol (version 4)

growth_protocol: Du145 cells grew in high glucose DMEM with 10% FBS+5% CO2, at 37 degree, under hypoxic condition of 1% O2

treatment_protocol: DU145 cells were infected lentivirus to knockdown TSC2 gene expression.

value: Du145, prostate carcinoma cells


title: miR146a-sponge

description: follow the GeneChip®Expression Analysis Technical Manual

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Human 133 plus 2.0 Array.

scan_protocol: The GeneChip arrays were washed and then stained (streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450nm followed by scanning on a GeneChip Scanner 3000.

data_processing: The hybridization data were analyzed using GeneChip Operating software (GCOS 1.4). The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of GCOS 1.4. An invariant set normalization procedure was performed to normalize the different arrays using DNA-chip analyzer [dChip].

label: Biotin

source_name: miR146a-sponge Jurkat T cells

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

growth_protocol: Culture at 37ºC,5%CO2,with RPMI1640 10% FBS for 24 hours

extract_protocol: Isolation of total RNA from  Cells: 1.Total RNA: High-quality total RNA has been successfully isolated from Jurakt-FF3 cells using the RNeasy Mini Kit from QIAGEN P/N 74104. 2.Quantification of RNA: The A260/A280 ratio should be close to 2.0 for pure RNA. For a high-quality total RNA sample,two well-defined band corresponding to the 18S and 28S ribosomal RNAs should be observed using denaturing agarose gel, with ratios approaching 2:1 for the 28S to 18S bands.

treatment_protocol: Jurkat T cells were transformed with FUGW-146a konck down lentivirus vector .

value: Jurkat

value: T cells

tag: treatment group

value: transformed with FUGW-miR146a-sponge knock down lentivirus vector called "microRNA sponge"


title: Du145 TSC2 knockdown, Second


title: 100mM Ethanol-Rep1

source_name: airway epithelial cells-lot number, ethanol treated or vehicle untreated


title: miR146a

source_name: miR146a Jurkat T

treatment_protocol: Jurkat T cells were transformed with FUGW-146a overexpression lentivirus vector .

value: transfected with miR146a overexpression lentivirus vector


title: Untreated-Rep1

data_processing: The CEL data file from each array was imported into Genespring GX 7.3 (Agilent Technologies) and preprocessed using the robust multichip average (RMA) method and per gene normalization was applied using the median values of the no EtOH control samples.  The CHP files were also imported and the detection call metrics from the CHP files were used to filter out transcripts that were found absent in all nine samples.  In addition, transcripts that were not within a standard deviation of 1.4 and exhibiting less than 1.5 fold change were also removed from further analysis.  To identify up-regulated and down-regulated transcripts, genes were filtered using the volcano plot with the limit set at p<0.01 and 2.0 fold change.  The parametric test, with variance not equal, was applied without multiple test correction.

extract_protocol: Sample was processed using the Trizol method.

tag: human airway epithelial cells were obtained from commercial source.


title: Du145 adapted from Knockdown, First


title: Du145 TSC2 knockdown, First


title: FF3

treatment_protocol: Jurkat T cells were transformed with FUGW-FF3 containing eGFP as vector control.

value: transfected with FUGW lentivirus vector as control


title: Du145 control, Second


title: PPMS, N41CASE

status: Public on Apr 02 2010

city: Westmead

middle: Richmond

last: Booth

state: NSW

address: Darcy Rd

department: Immunology

country: Australia

institute: Westmead Millennium Institute

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing:
The data were normalised using cubic spline normalisation with Illumina beadstudio.

Non-normalized data is available in the supplementary file 'GSE17048_non-normalized_data.txt', which is linked to the Series GSE17048 record.

source_name: blood, PPMS

label_protocol: Double-stranded cDNA was then transcribed and amplified in vitro to synthesize biotin-labelled complementary mRNA (cRNA).

extract_protocol: Total RNA was extracted from the whole blood in PAXgene tubes. Total RNA quality was assessed and its concentration was measured using the Agilent RNA 6000 series II Nano kit (Agilent Technologies, CA). 250 ng total RNA from each sample was biotinylated and amplified using Illumina® TotalPrep RNA Amplification Kit (Ambion, TX). Total RNA was reverse transcribed to synthesize the first strand of cDNA, followed by a second strand synthesis.

tag: ms subtype

value: PPMS

tag: tissue

value: whole blood


title: PPMS, P034


title: PPMS, P030


title: PPMS, N33CASE


title: PPMS, P040


title: PPMS, G009P


title: PPMS, N20PR


title: PPMS, N29P


title: PPMS, P027


title: PPMS, N31P


title: Du145 control, First

tag: cell line


title: PPMS, P002


title: PPMS, P001


title: PPMS, G005P


title: PPMS, P039


title: PPMS, P050


title: PPMS, P046


title: PPMS, P049


title: PPMS, G035P


title: PPMS, N21P


title: PPMS, P036


title: PPMS, P008


title: PPMS, P009


title: PPMS, P035


title: PPMS, P012


title: PPMS, P048


title: PPMS, N15P


title: PPMS, G020P


title: PPMS, P028


title: PPMS, P029


title: PPMS, P047


title: PPMS, P045


title: PPMS, P044


title: PPMS, P031


title: PPMS, P043


title: PPMS, P041


title: SPMS, G027S

source_name: blood, SPMS

value: SPMS


title: PPMS, P004


title: SPMS, P037


title: PPMS, P042


title: PPMS, N12P


title: SPMS, N27S


title: PPMS, G017P


title: SPMS, G001S


title: SPMS, P038


title: SPMS, N23S


title: PPMS, P007


title: SPMS, G023S


title: SPMS, N11S


title: PPMS, P052


title: PPMS, N28P


title: SPMS, N22S


title: SPMS, G036S


title: PPMS, P005


title: SPMS, G031S


title: SPMS, G032S


title: SPMS, N25S


title: SPMS, G026S


title: SPMS, N30S


title: SPMS, N24S


title: RRMS, G011R

source_name: blood, RRMS

value: RRMS


title: SPMS, G025S


title: RRMS, G024R


title: RRMS, N08R


title: SPMS, G038S


title: RRMS, N02R


title: RRMS, G030R


title: SPMS, N14S


title: RRMS, G015R


title: RRMS, N09R


title: RRMS, N16R


title: SPMS, G037S


title: RRMS, N10R


title: RRMS, G008R


title: RRMS, N05R


title: RRMS, N26R


title: RRMS, G022R


title: RRMS, G014R


title: RRMS, N40R


title: RRMS, G007R


title: RRMS, G018R


title: RRMS, G016R


title: RRMS, G033R


title: RRMS, G010R


title: RRMS, N03R


title: RRMS, G029R


title: RRMS, N19R


title: RRMS, G019R


title: RRMS, G013R


title: RRMS, G012R


title: RRMS, N06R


title: RRMS, N18R


title: RRMS, G028R


title: RRMS, N07R


title: healthy control, N38C

source_name: blood, HC


title: RRMS, G004R


title: healthy control, C042


title: healthy control, C007


title: RRMS, G021R


title: healthy control, C040


title: RRMS, G034R


title: RRMS, G002R


title: healthy control, C057


title: healthy control, C062


title: healthy control, C046


title: healthy control, C059


title: RRMS, G003R


title: healthy control, C016


title: healthy control, C052


title: healthy control, C018


title: healthy control, C056


title: healthy control, C039


title: healthy control, C051


title: healthy control, N34C


title: healthy control, C038


title: healthy control, C041


title: RRMS, G006R


title: healthy control, C035


title: healthy control, C045


title: healthy control, C049


title: healthy control, N37C


title: healthy control, C033


title: healthy control, C008


title: healthy control, C003


title: healthy control, C048


title: healthy control, N40C


title: healthy control, C036


title: healthy control, C053


title: healthy control, C010


title: healthy control, C054


title: healthy control, C060


title: healthy control, C043


title: healthy control, C047


title: healthy control, C044


title: healthy control, C061


title: healthy control, N36C


title: healthy control, C063


title: healthy control, C050


title: healthy control, C001


title: healthy control, C037


title: healthy control, C055


title: healthy control, C058


title: healthy control, C002


title: Spt5_mES_shControl

city: Cambridge

first: Charles

last: Lin

state: MA

address: 9 Cambridge Center

department: Biology

institute: Massachusetts Institute of Technology

description: AFE_030909_251520410225_S01_1_1_Spt5_mES_shControl

hyb_protocol: Agilent mouse 4x44k custom arrays were hybridized according to the Agilent Mammalian ChIP-on-chip protocol (version 9.1, Nov 2006) was followed.  In brief, mouse Cot1 DNA, Agilent blocking buffer (1X final conc.), Agilent hybridization buffer (1X final conc.), was added to Cy5- and Cy3-labeled DNA.  The mixture was incubated at 95oC for 3 minutes, followed by 37oC for 30 minutes.  Sample was centrifuged for 1 min and sample was hybridized to Agilent DNA microarray.  For experiments testing effects of flavopiridol on NelfA and Spt5 occupancy, and NelfA or Spt5 occupancy following Spt5 or NelfA knockdown, respectively, ChIP samples were hybridized to Agilent arrays MTvB (44,000 features covering the promoter region, from approximately -6kb to +2kb, of approximately 10% of mouse genes – MTvB).  DNA was hybridized to microarray for 40 hours at 65oC.

scan_protocol: Microarray was washed and scanned following the Agilent Mammalian ChIP-on-chip protocol.  The Agilent DNA microarray scanner BA was used.  PMT settings were set manually to normalize bulk signal in the Cy3 and Cy5 channel.

data_processing: Array images were quantified and statistical significance of differential expression for each hybridization was calculated using Agilent’s Feature Extraction Image Analysis software with the default two-color Young lab protocol. Data was processed as described in (Lee et al., 2006a) to calculate enrichment ratios and determine bound regions.

organism: Mus musculus

source_name: input genomic DNA

label_protocol: Purified immunoprecipitated DNA was amplified using two rounds of ligation mediated PCR (LM PCR), as described in (Lee et al., 2006b) and the Agilent Mammalian ChIP-on-chip protocol (version 9.1, Nov 2006).  LM-PCR immunoprecipitated DNA was labeled with Cy5, LM-PCR input DNA was labeled with Cy3 using Invitrogen Bioprime random primer labeling kit.

growth_protocol: V6.5 cells were grown under standard mES cell conditions as described previously (Boyer et al., 2005).  Briefly, cells were grown on 0.2% gelatinized tissue culture plates in ESC media; DMEM-KO supplemented with 15% fetal bovine serum, 1000 U/mL LIF, 100 uM nonessential amino acids, 2 mM L-glutamine, 100 U/mL penicillin, 100 ug/mL streptomycin and 8 nL/mL of 2-mercaptoethanol

extract_protocol: ChIP was done following the Agilent Mammalian ChIP-on-chip protocol (version 9.1, Nov 2006).  In summary, mES cells were grown as described above and cross-linked for 15 minutes at room temperature by the addition of one-tenth of the volume of 11% formaldehyde solution (11% formaldehyde, 50mM Hepes pH7.3, 100mM NaCl, 1mM EDTA pH8.0, 0.5mM EGTA pH8.0) to the growth media followed by two washes with PBS.  Cells were scraped and frozen in liquid nitrogen.  100ul of Dynal magnetic beads (Sigma) were blocked with 0.5% BSA (w/v) in PBS.  Magnetic beads were bound with 10ug of the indicated antibody.  Antibodies used are as follows: Spt5: gift from Yuki Yamaguchi and Hiroshi Handa (Wada et al., 1998); and  NelfA: Santa Cruz (A-20) sc-23599).  Crosslinked cells were lysed with lysis buffer 1 (50mM Hepes pH7.3, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100) and washed with lysis buffer 2 (10mM Tris-HCl pH8.0, 200mM NaCl, 1mM EDTA pH8.0 and 0.5mM EGTA pH8.0).      For Spt5 ChIPs, cells were resuspended and sonicated in lysis buffer 3 (10mM Tris-HCl pH8.0, 100mM NaCl, 1mM EDTA pH8.0, 0.5mM EGTA pH8.0, 0.1% Na-Deoxycholate and 0.5% N-lauroylsarcosine) for 8 cycles at 30 seconds each on ice (18 watts) with 60 seconds on ice between cycles. Triton X-100 was added to a final concentration of 1% to the sonicated lysates. Sonicated lysates were cleared and incubated overnight at 4oC with magnetic beads bound with antibody to enrich for DNA fragments bound by the indicated factor.  Beads were washed four times with RIPA (50mM Hepes pH7.3, 500mM LiCl, 1mM EDTA, 1% NP-40 and 0.7% Na-Deoxycholate) and once with TE + 50mM NaCl.  Bound complexes were eluted in elution buffer (50mM Tris-HCl pH8.0, 10mM EDTA pH8.0, 1% SDS) at 65oC for 15 minutes with occasional vortexing.  Cross-links were reversed overnight at 65oC.  RNA and protein were digested using RNAse A and Proteinase K, respectively and DNA was purified with phenol chloroform extraction and ethanol precipitation.      For NelfA ChIPs,  cells were resuspended and sonicated in sonication buffer (50mM Tris-HCl pH7.5, 140mM NaCl, 1mM EDTA, 1mM EGTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS) for 8 cycles at 30 seconds each on ice (18 watts) with 60 seconds on ice between cycles.  Sonicated lysates were cleared and incubated overnight at 4oC with magnetic beads bound with antibody to enrich for DNA fragments bound by the indicated factor.  Beads were washed three times with sonication buffer, one time with sonication buffer with 500mM NaCl, one time with LiCl wash buffer (20mM Tris pH8.0, 1mM EDTA, 250mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate) and one time with TE.  DNA was eluted in elution buffer.  Cross-links were reversed overnight.  RNA and protein were digested using RNAse A and Proteinase K, respectively and DNA was purified with phenol chloroform extraction and ethanol precipitation.

treatment_protocol:
For location analysis following Spt5 and NelfA knockdown, shRNA plasmids targeting the mouse Spt5 and NelfA mRNAs and an empty plasmid (control) (Open Biosystems, Huntsville, AL RMM4534-NM_013676, RMM4534-NM_011914, and RMM4534_NM_010849, RHS4080) were used.  We purchased and tested each set of shRNA hairpins for ability of each hairpin to knockdown the mRNA of the factor of interest.  We then selected the hairpin that performed the best for use in ChIP-seq analysis.  For Spt5, hairpin TRCN0000092761 was used.  For NelfA, hairpin TRCN0000124874 was used. Viral media was collected 48 hours after co-transfection and the V6.5 mES cells were directly infected with the viral media 24 hours after initial plating of the mES cells. The infection media was 1:2 viral media:mES cell media with 2mM polybrene. The efficiently infected cells were selected for 24 hours post infection with mES cell media containing 2mM puromycin. V6.5 cells were cross-linked 72 hours post selection and frozen for ChIP-Seq experiments and western blotting.
For location analysis on mES cells following treatment with small molecule inhibitors, cells were grown two passages off feeders and prior to formaldehyde crosslinking, the cells were treated by addition of the indicated final concentration of flavopiridol (1μM for 1 hour for ChIP-chip and ChIP-seq experiments), dissolved in DMSO, to the growth medium.  As a control, vehicle alone (DMSO) was added to the growth medium at the same final volume as with drug.  Flavopiridol (Sigma cat #F3055) was purchased from Sigma.

value: V6.5 ES cells

tag: shrna

value: empty

tag: small molecule

value: no

tag: chip antibody

source_name: Spt5 genomic DNA


title: healthy control, C013


title: Spt5_mES_shNelfA

description: AFE_030909_251520410225_S01_1_2_Spt5_mES_shNelfA

value: NelfA


title: Spt5_mES_DMSO

description: AFE_030909_251520410225_S02_1_1_Spt5_mES_DMSO

value: DMSO 1 hour


title: Spt5_mES_Flavopiridol

description: AFE_030909_251520410225_S02_1_2_Spt5_mES_Flavo

value: Flavopiridol 1 hour


title: NelfA_mES_shControl

description: AFE_052108_251520410241_S01_1_3_NelfA_mES_shControl

source_name: NelfA genomic DNA


title: NelfA_mES_shSpt5

description: AFE_052108_251520410241_S01_1_4_NelfA_mES_shSpt5


title: Quadriceps muscle at T1, control patient 4

city: Dublin

first: Kevin

last: Mulhall

address: Belfield

country: Ireland

institute: University College Dublin

description: Gene expression data from quadriceps muscle biopsy of control patient

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hours at 45oC on the Affymetrix U113 Plus 2.0 array. The array was then washed and stained on the GeneChip Fluidics Station 450.

scan_protocol: The array was scanned using the GeneChip Scanner 3000.

data_processing: The raw data from the scanner were analysed using the Rosetta Error Model (Rosetta Resolver 7.0) to generate processed intensity values. The following gene filtering was applied to the data: intensity p-value filter, background filter, fold change filter and signature p-value filter.

source_name: Quadriceps muscle, control patient, T1

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol for 6ug of total RNA (Expression Analysis Technical Manual, 2001, Affymetrix.

extract_protocol: TriReagent extraction of RNA was carried out according to the manufacturer's instructions.

treatment_protocol: Patients in the treatment group received ischaemic preconditioning prior to total knee replacement surgery. Ischaemic preconditioning consisted of three five-minute periods of tourniquet insulflation on the lower operative limb, interrupted by five-minute periods of reperfusion.

tag: tissue type

value: Quadriceps muscle

tag: patient group

value: total knee arthroplasty control patient

tag: time point


title: Quadriceps muscle at T1, control patient 2


title: NelfA_mES_Flavopiridol

description: AFE_030909_251520410225_S02_1_4_NelfA_mES_flavo

tag: cell type


title: panc3.014 combo exon

first: Kim

last: Walter

address: 1550 Orleans St.

institute: Johns Hopkins University

hyb_protocol: Samples were hybridized with the GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the JHMI Microarray Core Facility

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Data were processed using Partek Genomics Suite (Partek Inc., St. Louis MO). Core probesets were imported using RMA defaults with probe GC content correction.  Relative gene expression values were obtained after using the Tukey biweight method to normalize the intensity measurements.

source_name: Panc3.014 cancer cell line, 5-aza-dC and TSA treated

label_protocol: Single stranded cDNA was generated from the amplified cRNA using the WT cDNA Synthesis kit (Affymetrix) and then fragmented and labeled using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Cells were maintained in culture at 37 degrees C in DMEM containing 10% FBS and 2% penicillin-streptomycin.

extract_protocol: RNA was isolated from cell cultures using the Ambion mirVana RNA extraction kit, according to the manufacturer's instructions

treatment_protocol: Cells were treated with 5-aza-dC (Sigma Chemical Co) at 1 umol/L for 4 days and/or 1 umol/L of TSA for 24 hours

value: Male

value: Pancreatic ductal adenocarcinoma

value: Primary pancreatic tumor

value: pancreatic cancer cell line

tag: tumor stage

value: IIB


title: Quadriceps muscle at T1, treatment patient 3

description: Gene expression data from quadriceps muscle biopsy of treatment patient

source_name: Quadriceps muscle, treatment patient, T1

value: total knee arthroplasty treatment patient


title: panc2.5 non exon

source_name: Panc2.5 cancer cell line, untreated

value: Female


title: panc3.014 non exon

source_name: Panc3.014 cancer cell line, untreated


title: Quadriceps muscle at T1, control patient 3


title: Quadriceps muscle at T1, treatment patient 1


title: panc2.8 non exon

source_name: Panc2.8 cancer cell line, untreated


title: panc2.5 combo exon

source_name: Panc2.5 cancer cell line, 5-aza-dC and TSA treated


title: NelfA_mES_DMSO

description: AFE_030909_251520410225_S02_1_3_NelfA_mES_DMSO


title: Quadriceps muscle at T1, treatment patient 2


title: HPDEuntreated-5

source_name: HPDE cells, untreated

value: see Furukawa et al., Am J Pathol, 1996

value: HPDE


title: Quadriceps muscle at T1, control patient 1


title: panc3.014 ca TSA exon

source_name: Panc3.014 cancer cell line, TSA treated


title: Quadriceps muscle at T1, treatment patient 4


title: HPDE combo exon

source_name: HPDE cells, 5-aza-dC and TSA treated


title: panc2.5 ca TSA exon

source_name: Panc2.5 cancer cell line, TSA treated


title: panc2.8 combo exon

source_name: Panc2.8 cancer cell line, 5-aza-dC and TSA treated


title: panc2.8 AZA exon

source_name: Panc2.8 cancer cell line, 5-aza-dC treated


title: Quadriceps muscle at T0, treatment patient 4

source_name: Quadriceps muscle, treatment patient, T0


title: Quadriceps muscle at T0, treatment patient 3


title: panc2.8 ca TSA exon

source_name: Panc2.8 cancer cell line, TSA treated


title: A38-5 cancer combo exon

source_name: A38-5 cancer cell line, 5-aza-dC and TSA treated

value: Liver metastasis

value: IV


title: panc3.014 AZA exon

source_name: Panc3.014 cancer cell line, 5-aza-dC treated


title: HPDE AZA exon

source_name: HPDE cells, 5-aza-dC treated


title: A38-5 cancer exon

source_name: A38-5 cancer cell line, untreated


title: Quadriceps muscle at T0, treatment patient 2


title: Quadriceps muscle at T0, control patient 3

source_name: Quadriceps muscle, control patient, T0


title: Quadriceps muscle at T0, control patient 4


title: Quadriceps muscle at T0, control patient 1


title: Quadriceps muscle at T0, treatment patient 1


title: OvarianCancer_HeyA8_PLKO

city: Chicago

first: Marcus

last: Peter

address: 303 East Superior Street, Lurie 6-123

institute: Northwestern University Feinberg School of Medicine

description: Human ovarian cancer cell line HeyA8, PLKO control

hyb_protocol: Affymetrix hybridization protocol

scan_protocol: Affymetrix scan protocol

data_processing: MAS5.0 transformation algorithm

source_name: Ovarian cancer, HeyA8 cell line, PLKO control

label_protocol: Affymetrix labeling protocol

extract_protocol: Qiagen miRNeasy Mini Kit

tag: genotype/variation

value: PLKO control

value: ovarian cancer


title: Adipose stem cells expanded in fetal bovine serum, biological rep. 4

status: Public on Apr 01 2010

city: Tampere

first: Kaisa-Leena

last: Aho

address: Korkeakoulunkatu 10

department: Department of Signal Processing

country: Finland

institute: Tampere University of Technology

description: Gene expression data from adipose stem cells expanded in fetal bovine serum.

hyb_protocol: Each sample was hybridized to GeneChip® Human Genome U133 Plus 2.0  Array at +45°C overnight (19 h) according to GeneChip® Expression Analysis  Technical Manual (With Specific Protocols for Using the GeneChip®  Hybridization, Wash and Stain Kit). GeneChip® Fluidics Station 450 was used to wash and stain the arrays.

scan_protocol: The arrays were scanned with the GeneChip® Scanner 3000 with AutoLoader.

data_processing: The data were normalized using the RMA algorithm in R/Bioconductor.

label_protocol: Biotinylated cRNA were produced from 2 ug of total RNA according to One-Cycle Target Labeling protocol  from GeneChip® Expression Analysis Technical Manual (With Specific  Protocols for Using the GeneChip® Hybridization, Wash and Stain Kit). Both before and after the amplifications the total RNA / cRNA concentrations  where checked with Nanodrop ND-1000 and totalRNA / cRNA quality was  controlled by BioRad’s Experion electrophoresis station.

growth_protocol: To isolate adipose stem cells, the adipose tissue was manually minced into small fragments and digested with collagenase type I (1.5 mg/mL; Invitrogen, Paisley, UK). The digested tissue was centrifuged and filtered in sequential steps to separate the adipose stem cells from the surrounding tissue.

extract_protocol: Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, Valencia, CA, USA) as per the manufacturer’s instructions.

treatment_protocol: The isolated cells were expanded in media containing DMEM/F-12 1:1 (Invitrogen) supplemented with 1% L-glutamine (GlutaMAX I; Invitrogen), 1% antibiotics/antimycotic (100 U/mL penicillin, 0.1 mg/mL streptomycin, and 0.25 µg/mL amphotericin B; Invitrogen) and 10% FBS (Invitrogen cat# 10108-165). The cells were detached using 1% trypsin (Lonza/Biowhittaker, Verviers, Belgium).

value: adipose stem cell

tag: human donor

value: donor 4


title: 215 cancer exon

source_name: Panc215 cancer cell line, untreated

tag: gender


title: A32-1 cancer AZA exon

source_name: A32-1 cancer cell line, 5-aza-dC treated

tag: disease status

value: Peritoneal metastasis


title: LiverCancer_HepG2_PLKO

description: Human liver cancer cell line HepG2, PLKO control

source_name: Liver cancer, HepG2 cell line, PLKO control

value: liver cancer


title: Adipose stem cells expanded in fetal bovine serum, biological rep. 5

value: donor 5


title: Quadriceps muscle at T0, control patient 2

value: Quadriceps muscle

value: total knee arthroplasty control patient


title: Adipose stem cells expanded in fetal bovine serum, biological rep. 2

value: donor 2


title: Adipose stem cells expanded in allogeneic human serum, biological rep. 1

description: Gene expression data from adipose stem cells expanded in allogeneic human serum.

treatment_protocol: The isolated cells were expanded in media containing DMEM/F-12 1:1 (Invitrogen) supplemented with 1% L-glutamine (GlutaMAX I; Invitrogen), 1% antibiotics/antimycotic (100 U/mL penicillin, 0.1 mg/mL streptomycin, and 0.25 µg/mL amphotericin B; Invitrogen) and 15% heat-inactivated human serum off the clot type AB (alloHS; PAA Laboratories, Pasching, Austria, cat# C15-021, lot# C02106-1878). The cells were detached using TrypLE Select (Invitrogen).

value: donor 1


title: Adipose stem cells expanded in allogeneic human serum, biological rep. 2


title: 215 cancer AZA exon

source_name: Panc215 cancer cell line, 5-aza-dC treated

value: Pancreatic ductal adenocarcinoma

value: Primary pancreatic tumor

value: pancreatic cancer cell line

value: IIB


title: Adipose stem cells expanded in fetal bovine serum, biological rep. 1


title: Adipose stem cells expanded in allogeneic human serum, biological rep. 3

value: donor 3


title: Adipose stem cells expanded in fetal bovine serum, biological rep. 3


title: LiverCancer_HepG2_FAS_shRNA6

description: Human liver cancer cell line HepG2, FAS stable knock-down by shRNA6

source_name: Liver cancer, HepG2 cell line, FAS shRNA6

value: FAS shRNA6 knock-out


title: OvarianCancer_HeyA8_Fas_shRNA4

description: Human ovarian cancer cell line HeyA8, FAS stable knock-down by shRNA4

source_name: Ovarian cancer, HeyA8 cell line, Fas shRNA4

value: Fas shRNA4 knock-out


title: Adipose stem cells expanded in allogeneic human serum, biological rep. 5


title: OvarianCancer_HeyA8_FAS_shRNA6

description: Human ovarian cancer cell line HeyA8, FAS stable knock-down by shRNA6

source_name: Ovarian cancer, HeyA8 cell line, FAS shRNA6

value: ovarian cancer


title: A32-1 cancer exon

source_name: A32-1 cancer cell line, untreated

value: Female

value: IV


title: Arabidopsis php_I

city: East Lansing

first: Sookyung

last: Oh

state: MI

department: Horticulture

institute: Michigan State University

description: Each of two replicates for each genotypes was composed of three independently derived samples.

hyb_protocol: Affymetrix GeneChip Expression Analysis Technical Manual

data_processing:
Data from CEL files were adjusted for background and normalized using Bioconductor GCRMA package (http://www.bioconductor.org).
For supplementary data: Microarray data were analyzed using the statistical algorithms within the Affymetrix Microarray Suite (MAS) 5.0 software.

source_name: php mutant

extract_protocol:
Total RNA was isolated using Qiagen RNAeasy columns (Qiagen, Valencia, CA)
Total RNAs were extracted and used for cDNA synthesis

tag: Arabidopsis php mutants

tag: Expression of >22,600  genes was analyzed in aerial tissues from 14-day-old soil grown wild-type and php mutant plants using the Affymetrix ATH1 GeneChip, and two independent biological replicates.


title: Adipose stem cells expanded in allogeneic human serum, biological rep. 4

value: adipose stem cell

value: donor 4


title: Arabidopsis wild-type_I

source_name: wild-type

label_protocol:
Affymetrix GeneChip Expression Analysis Technical Manual
Total RNA was used for cDNA synthesis.

extract_protocol: Total RNA was isolated using Qiagen RNAeasy columns (Qiagen, Valencia, CA)

tag: Arabidopsis wild-type 14 day old seedling

tag: Expression of >22,600  genes was analyzed in aerial tissues from 14-day-old soil grown wild-type and php mutant plants using the Affymetrix ATH1 GeneChip, and two independnet biological replicates.


title: Arabidopsis wild-type_II

label_protocol:
Affymetrix GeneChip Expression Analysis Technical Manual
Total RNAs were extracted and used for cDNA synthesis.


title: 293T_AuNP_48hr

status: Public on Mar 09 2010

first: Eun-Young

last: Kim

address: 303 E Superior Street

department: Feinberg School of Medicine

institute: Northwestern University

description: Gene expression data from 293T cells treated with AuNP EGFP oligonucleotide complex for 48 hours

hyb_protocol: Following fragmentation, 35 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix Agilent GeneArray Scanner.

data_processing: Normalization for biological and technical replicates and probe—level analysis were performed using FlexArray with the GC—Robust Multichip Average (RMA) option. Probe sets whose absolute expression value did not exceed 5.0 for all arrays were excluded.  Full processed data results (SAM analysis) are available as a supplementary file on the Series record.

source_name: 293T Embryonic Kidney cell

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: PBMCs derived from healthy donors were isolated on Ficoll—Paque gradient, and PBMC and 293T cells were grown in 5% CO2 at 37°C in RPMI1640 medium and DMEM (Invitrogen) with 10% fetal bovine serum supplemented with 100 U/ml penicillin, 100 μg/ml streptomycin, and 200 μM l—glutamine, respectivley.

extract_protocol: Total RNA were extracted from cells by using Qiagen RNeasy kit

treatment_protocol: Cells were seeded at 50% confluent in 24—well plates and treated with 10nM AuNP for 6-, 24, and 48hr and washed twice with PBS

value: Embryonic Kidney cell

tag: cell line

tag: treatment group


title: 293T_AuNP_6hr

description: Gene expression data from 293T cells treated with AuNP EGFP oligonucleotide complex for 6 hours


title: PBMCs_Oligo

description: Gene expression data from PBMCs treated with Oligofectamine without oligonucleotide

source_name: PBMCs

value: PBMCs


title: PBMCs_Oligo_GFP

description: Gene expression data from PBMCs treated with Oligofectamine with EGFP oligonucleotide


title: PBMCs_AuNP_48hr_1

description: Gene expression data from PBMCs treated with AuNP EGFP oligonucleotide complex for 48 hours


title: PBMCs_AuNP_24hr_2

description: Gene expression data from PBMCs treated with AuNP EGFP oligonucleotide complex for 24 hours


title: 293T_AuNP_24hr

description: Gene expression data from 293T cells treated with AuNP EGFP oligonucleotide complex for 24 hours


title: LGMP derived from Hoxa9/Meis1a transduced KLS_sample 2

status: Public on Mar 15 2010

city: Boston

first: Amit

last: Sinha

address: 44 Binney St

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: Purified Lineage- Sca1- CD117+ CD16/32high CD34-/low from mouse sucumbed to AML

hyb_protocol: 3.75 micrograms of biotinylated material was hybridized according to the standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol

data_processing: RMA background correction and quantile normalization done with the GenePattern ExpressionFileCreator module (http://www.broad.mit.edu/cancer/software/genepattern/) which uses the Bioconductor implementation of RMA (http://www.bioconductor.org/). This function computes the Robust Multichip Average expression measure described in Irizarry et al Biostatistics (2003).

source_name: Lin(CD3e; CD4, CD8a, CD19, CD45R, CD127; Gr1, TER119)- Sca1- CD117+ CD34+/low CD16/32high

label_protocol: 10 to 50 nanograms of total RNA was amplified and processed to produce biotinylated cDNA targets using two round of in vitro RNA synthesis

extract_protocol: Trizol extraction following manufacturer's protocol.

tag: genetic background


title: LGMP derived from Hoxa9/Meis1a transduced KLS_sample 3


title: sorted_Lgr5-high_vs_Lgr6-high_colourswitch_1

status: Public on Mar 26 2010

city: Dresden

first: Daniel

middle: E.

last: Stange

address: Fetscherstr. 74

institute: University Clinic Dresden

description: 251486825787_SLOT04_S01_GE2_105_Dec08_1_1.txt

hyb_protocol: according to Agilent guidelines

scan_protocol: according to Agilent guidelines

data_processing: Microarray signal and background information were retrieved using Feature Extraction (V.9.5.3, Agilent Technologies).

source_name: sorted Lgr5 Gfp high cell fraction of dorsal skin

label_protocol: 150 ng of total RNA was labeled using low RNA Input Linear Amp kit (Agilent Technologies, Pato Alto, CA, USA).

extract_protocol: RNA was isolated using Trizol (Invitrogen)

treatment_protocol: For the Lgr5 and Lgr6 stem cell signature we used cells from Lgr5- or Lgr6-EGFP-ires-CreERT2 knock-in mice, expressing GFP under the control of the Lgr5 or Lgr6 promoter, respectively. 3 mice were combined for each sort. RNA was isolated from FACS sorted cell populations expressing GFP at high levels.

tag: genome/variation

value: Lgr5-EGFP-ires-CreERT2 knock-in mice

value: dorsal skin cells

tag: cell fraction

value: Lgr5 Gfp high

source_name: sorted Lgr6 Gfp high cell fraction of dorsal skin

value: Lgr6-EGFP-ires-CreERT2 knock-in mice

value: Lgr6 Gfp high


title: LGMP derived from Hoxa9/Meis1a transduced KLS_sample 1


title: PBMCs_HIV

description: Gene expression data from PBMCs infected with HIV

value: infected with HIV


title: sorted_Lgr5-high_vs_Lgr6-high_colourswitch_2

description: 251486825787_SLOT04_S01_GE2_105_Dec08_1_2.txt


title: P383_3 pheochromocytoma

status: Public on Feb 14 2010

city: San Antonio

first: Patricia

middle: L.

last: Dahia

state: TX

address: 7703 Floyd Curl Dr MC7880

department: Medicine/Cel&Struct Biology

institute: UTHSCSA

description: sample: P383_3

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0 and dChip.

source_name: flash-frozen tumor specimen

label_protocol: Approximately 10 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Trizol as described in Monti S et al. Blood. 2005 Mar 1;105(5):1851-61.

tag: tumor type

value: pheochromocytoma

tag: genetic class

value: VHL

tag: tumor location

value: adrenal


title: 293T_Control

description: Gene expression data from control 293T cells

tag: cell type

value: control


title: PBMCs_Control_2

description: Gene expression data from control PBMCs


title: PBMCs_AuNP_48hr_2

value: treated with AuNP EGFP oligonucleotide complex for 48 hours


title: PBMCs_AuNP_24hr_1

value: treated with AuNP EGFP oligonucleotide complex for 24 hours


title: 4080752_Tumor_55

status: Public on Mar 02 2010

city: Philadelphia

first: Jay

last: Johnson

state: PA

address: 422 Curie Blvd

department: Pathology and Laboratory Medicine

institute: University of Pennsylvania

hyb_protocol: Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0 Wash A1 Temperature (C)=30 Number of Wash A1 Cycles=10 Mixes per Wash A1 Cycle=2 Wash B Recovery Mixes=0 Wash B Temperature (C)=50 Number of Wash B Cycles=6 Mixes per Wash B Cycle=15 Stain Temperature (C)=35 First Stain Time (seconds)=300 Wash A2 Recovery Mixes=0 Wash A2 Temperature (C)=30 Number of Wash A2 Cycles=10 Mixes per Wash A2 Cycle=4 Second Stain Time (seconds)=300 Third Stain Time (seconds)=300 Wash A3 Recovery Mixes=0 Wash A3 Temperature (C)=35 Number of Wash A3 Cycles=15 Mixes per Wash A3 Cycle=4< Holding Temperature (C)=25

scan_protocol: The probe array was scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Standard Affymetrix protocol

source_name: Liposarcoma

label_protocol: The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).

extract_protocol: Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.

tag: tumor

value: Liposarcoma

tag: subtype

value: dedifferentiated


title: P367 pheochromocytoma

description: sample: P367 [biological replicate of P367_2]

value: SPOR


title: P377 pheochromocytoma

description: sample: P377


title: P369 pheochromocytoma

description: sample: P369

value: extraadrenal


title: healthy control, N32C

first: David

source_name: blood, HC

tag: tissue

value: whole blood


title: P366 pheochromocytoma

description: sample: P366


title: P245 pheochromocytoma

description: sample: P245


title: P216_2 pheochromocytoma

description: sample: P216_2 [biological replicate of P216]


title: P252 pheochromocytoma

description: sample: P252


title: P244 pheochromocytoma

description: sample: P244


title: P412 pheochromocytoma

description: sample: P414


title: PBMCs_Control_1

description: Gene expression data from control PBMCs

value: PBMCs


title: P234 pheochromocytoma

description: sample: P234


title: P381 pheochromocytoma

description: sample: P381


title: P387 pheochromocytoma

description: sample: P387


title: P382 pheochromocytoma

description: sample: P382


title: P370 pheochromocytoma

description: sample: P370


title: P368 pheochromocytoma

description: sample: P368


title: P388 pheochromocytoma

description: sample: P388


title: Adipose tissue 170 SFA Baseline

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described n the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated using RMA

source_name: Subcutaneous adipose tissue, saturated fatty acid rich diet, baseline, individual 170

label_protocol: The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.

growth_protocol: Twenty moderately overweight subjects, both males and females aged between 45-60 years, participated in this study. All subjects gave written informed consent to participate in the study and the study protocol was approved by the Medical Ethical Committee of Wageningen University, the Netherlands.

extract_protocol: Adipose tissue was rinsed with ice-cold phosphate-buffered saline to remove blood and immediately frozen in liquid nitrogen. Total RNA was isolated from adipose tissue using Trizol reagent (Invitrogen, Breda, NL) and purified using the Qiagen RNeasy Micro kit (Qiagen, Venlo, NL). RNA  integrity was checked on an Agilent 2100 bioanalyzer (Agilent Technologies, Amsterdam, NL).

treatment_protocol: Subjects consumed a diet containing high SFA or high MUFA for 8 weeks. Subcutaneous adipose tissue samples were obtained by needle biopsy from the periumbilical area under local anesthesia both before and after the diet intervention, before and after the intervention.

tag: individual

value: Adipose

tag: gender

value: Female

tag: age

value: between 40-65 yrs


title: Adipose tissue 114 SFA Baseline

source_name: Subcutaneous adipose tissue, saturated fatty acid rich diet, baseline, individual 114

value: Male


title: Adipose tissue 122 SFA Baseline

source_name: Subcutaneous adipose tissue, saturated fatty acid rich diet, baseline, individual 122


title: Adipose tissue 169 SFA Baseline

source_name: Subcutaneous adipose tissue, saturated fatty acid rich diet, baseline, individual 169


title: P367_2 pheochromocytoma

description: sample: P367_2 [biological replicate of P367]


title: P359 pheochromocytoma

description: sample: P359


title: Adipose tissue 119 SFA Baseline

source_name: Subcutaneous adipose tissue, saturated fatty acid rich diet, baseline, individual 119


title: Adipose tissue 129 SFA Baseline

source_name: Subcutaneous adipose tissue, saturated fatty acid rich diet, baseline, individual 129


title: Adipose tissue 113 SFA Baseline

source_name: Subcutaneous adipose tissue, saturated fatty acid rich diet, baseline, individual 113


title: P346 pheochromocytoma

description: sample: P346


title: P347 pheochromocytoma

description: sample: P347


title: P345 pheochromocytoma

description: sample: P345


title: Adipose tissue 144 MUFA Final

source_name: Subcutaneous adipose tissue, monounsaturated fatty acid rich diet, after 8 wks intervention, individual 144


title: P336 pheochromocytoma

description: sample: P336


title: Adipose tissue 180 MUFA Final

source_name: Subcutaneous adipose tissue, monounsaturated fatty acid rich diet, after 8 wks intervention, individual 180


title: Adipose tissue 136 MUFA Final

source_name: Subcutaneous adipose tissue, monounsaturated fatty acid rich diet, after 8 wks intervention, individual 136


title: Adipose tissue 146 MUFA Final

source_name: Subcutaneous adipose tissue, monounsaturated fatty acid rich diet, after 8 wks intervention, individual 146


title: P325 pheochromocytoma

description: sample: P325


title: Adipose tissue 109 MUFA Final

source_name: Subcutaneous adipose tissue, monounsaturated fatty acid rich diet, after 8 wks intervention, individual 109


title: P313 pheochromocytoma

description: sample: P313


title: P322 pheochromocytoma

description: sample: P322


title: P329 pheochromocytoma

description: sample: P329


title: P310 pheochromocytoma

description: sample: P310


title: Adipose tissue 110 MUFA Final

source_name: Subcutaneous adipose tissue, monounsaturated fatty acid rich diet, after 8 wks intervention, individual 110


title: Adipose tissue 106 MUFA Final

source_name: Subcutaneous adipose tissue, monounsaturated fatty acid rich diet, after 8 wks intervention, individual 106


title: Adipose tissue 103 MUFA Final

source_name: Subcutaneous adipose tissue, monounsaturated fatty acid rich diet, after 8 wks intervention, individual 103


title: 215 cancer combo exon

city: Baltimore

source_name: Panc215 cancer cell line, 5-aza-dC and TSA treated

tag: disease status

value: Pancreatic ductal adenocarcinoma

value: Primary pancreatic tumor

value: pancreatic cancer cell line

tag: tumor stage

value: IIB


title: P309 pheochromocytoma

description: sample: P309

source_name: flash-frozen tumor specimen

value: pheochromocytoma

value: adrenal


title: Adipose tissue 108 MUFA Final

source_name: Subcutaneous adipose tissue, monounsaturated fatty acid rich diet, after 8 wks intervention, individual 108


title: A32-1 cancer combo exon

source_name: A32-1 cancer cell line, 5-aza-dC and TSA treated

value: Peritoneal metastasis

tag: cell line

value: IV


title: P304 pheochromocytoma

description: sample: P304


title: P297 pheochromocytoma

description: sample: P297


title: Adipose tissue 180 MUFA Baseline

source_name: Subcutaneous adipose tissue, monounsaturated fatty acid rich diet, baseline, individual 180


title: Adipose tissue 144 MUFA Baseline

source_name: Subcutaneous adipose tissue, monounsaturated fatty acid rich diet, baseline, individual 144


title: P306 pheochromocytoma

description: sample: P306


title: Adipose tissue 146 MUFA Baseline

source_name: Subcutaneous adipose tissue, monounsaturated fatty acid rich diet, baseline, individual 146


title: Adipose tissue 136 MUFA Baseline

source_name: Subcutaneous adipose tissue, monounsaturated fatty acid rich diet, baseline, individual 136


title: Adipose tissue 101 MUFA Final

source_name: Subcutaneous adipose tissue, monounsaturated fatty acid rich diet, after 8 wks intervention, individual 101


title: Adipose tissue 109 MUFA Baseline

source_name: Subcutaneous adipose tissue, monounsaturated fatty acid rich diet, baseline, individual 109


title: P389 pheochromocytoma

description: sample: P389


title: P282 pheochromocytoma

description: sample: P282


title: Adipose tissue 110 MUFA Baseline

source_name: Subcutaneous adipose tissue, monounsaturated fatty acid rich diet, baseline, individual 110


title: P288 pheochromocytoma

description: sample: P288


title: P300 pheochromocytoma

description: sample: P300


title: Adipose tissue 108 MUFA Baseline

source_name: Subcutaneous adipose tissue, monounsaturated fatty acid rich diet, baseline, individual 108


title: P276 pheochromocytoma

description: sample: P276


title: P269 pheochromocytoma

description: sample: P269


title: P277 pheochromocytoma

description: sample: P277


title: Adipose tissue 106 MUFA Baseline

source_name: Subcutaneous adipose tissue, monounsaturated fatty acid rich diet, baseline, individual 106


title: P268 pheochromocytoma

description: sample: P268


title: Arabidopsis php_II

scan_protocol: Affymetrix GeneChip Expression Analysis Technical Manual

source_name: php mutant

extract_protocol:
Total RNA was isolated using Qiagen RNAeasy columns (Qiagen, Valencia, CA)
Total RNAs were extracted and used for cDNA synthesis.

tag: Arabidopsis php mutants

tag: Expression of >22,600  genes was analyzed in aerial tissues from 14-day-old soil grown wild-type and php mutant plants using the Affymetrix ATH1 GeneChip, and two independent biological replicates.


title: P281 pheochromocytoma

description: sample: P281