title: Liver_Tob1KO_0hr_rep2

description: Gene expression data from Tob1 null mouse liver at 0hr

source_name: Liver, Tob1 null, 0hr


title: Experiment 2, Blastomere pair D, Cell 2

status: Public on May 15 2010

type: RNA

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

country: USA

institute: GenUs BioSystems, Inc.

description:
Experiment 2, blastomere pair D, cell 2.
Exp2D2

hyb_protocol: Purified cRNA (1 µg) was fragmented to uniform size and applied to Agilent 4x44K Whole Mouse Genome microarrays (Design ID 14868, Agilent Technologies, Santa Clara, CA) in hybridization buffer. All fragmented samples were visualized on the Agilent Bioanalyzer to verify complete fragmentation to ~0.1 kb size before the sample was applied to the array. Arrays were hybridized at 65° C for 17 h on a rotating incubator and washed at 37° C for 1 min.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA). To compare individual expression values across arrays, raw intensity data from each gene probe was normalized to the 75th percentile intensity of probes above background on each array and further scaled assuming maximum correlation for all genes within and across pairs.

molecule: total RNA

organism: Mus musculus

source_name: blastomere cell

label_protocol: Labeled cRNA was prepared from each RNA sample. Briefly, the Poly(A)+ RNA population within total RNA was amplified  by using Arcturus RiboAmp HS reagents (Molecular Devices, Sunnyvale, CA)  as described by others (Somers, Smith et al. 2006; Jones, Cram et al. 2008). After a second round of reverse transcription, second-strand cDNA synthesis, and purification of double-stranded cDNA, in vitro transcription was performed with T7 RNA polymerase.  The resulting cRNA was again assayed by spectrophotometry and on the Agilent Bioanalyzer.

growth_protocol: Embryos were derived from CF-1 females by natural breeding. CF-1 stud males were introduced to the female mice at 17.00 h, and females selected for retrieval of 2-cell stage embryos between 10.00 and 11.00 h the day following observation of the copulatory plug, i.e. ~36 h post coitus, pc.  Oviducts were flushed in CZB-Hepes buffer (Chatot, Ziomek et al. 1989) lacking glucose (mCZB-Hepes) to collect embryos. Micromanipulation of embryos was performed under an inverted microscope (Nikon, DIAPHOT-300) equipped with a standard micromanipulation system (Leitz, Model M).  Two-cell stage embryos were transferred to 2 µl microdrops of Ca+, Mg+ free PBS supplemented with 0.1% polyvinyl alcohol (PBS-PVA), which were covered with mineral oil.  An embryo was secured by using a holding pipette and a slit made in the ZP close to the side of one blastomere by means of a sharp glass needle.  The blunt tip of a glass rod was then used to put pressure on the ZP-enclosed embryo, thereby allowing the blastomere closest to the slit to be squeezed out, generally without apparent damage.  The second blastomere was recovered in a similar manner.

extract_protocol: Total RNA was isolated by using the RNAqueous-Micro® Technology (AM1931; Applied BioSystems), as described by the manufacturer. The procedure employs an initial extraction in guanidinium thiocyanate solution, dilution in ethanol solution, and purification on an RNA-binding glass fiber filter. The concentrated RNA was eluted from the column and assessed for quantity and quality on an Agilent Bioanalyzer with the RNA6000 Pico Lab Chip (Agilent Technologies).

tag: strain

tag: developmental stage

value: 2-cell embryos ~36h post coitus

tag: tissue

value: blastomere cell


title: Experiment 2, Blastomere pair H, Cell 1

description:
Experiment 2, blastomere pair H, cell 1.
Exp2H1


title: Experiment 1, Blastomere pair L, Cell 2

description:
Experiment 1, blastomere pair L, cell 2.
Exp1L2


title: Experiment 2, Blastomere pair D, Cell 1

description:
Experiment 2, blastomere pair D, cell 1.
Exp2D1


title: Liver_Tob1KO_0hr_rep1

city: Boston

first: Hasan

middle: Huseyin

last: Otu

state: MA

address: 4 Blackfan Circle Rm. 238

department: Medicine

institute: Harvard Medical School

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: CEL files were analyzed with dChip using smoothing spline invariant set method with the model based expression algorithm following the perfect match (PM) mismatch (MM) difference model.

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microgram total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Tob1 null mice on a C57BL/6 background were a generous gift from Dr. Indrani Bagchi (University of Ilinois at Urbana-Champaign).  These mice are derived from a line produced and maintained by Dr. Tadashi Yamamoto. Animals were maintained in a pathogenfree facility administered by Harvard Medical School in accordance with the institutional guidelines of Harvard Medical School and Beth Israel Deaconess Medical Center.

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

treatment_protocol: All surgeries were performed according to the National Institutes of Health guidelines for the humane treatment of laboratory animals and with approval of the Harvard Institutional Animal Care and Use Committee. Mice mice were anesthetized with 60mg/kg ketamine (Hospira) and 7mg/kg xylazine (Phoenix Pharmaceuticals), and positioned supine. A transverse incision was made inferior to the xiphoid process, which was excised. The median and left lateral lobes of the liver were eviscerated and ligated. At tissue recovery, mice were anesthetized and weighed. Livers were excised, rinsed, blotted and weighed. Sections were snap frozen in liquid nitrogen, fixed in 10% neutral buffered formalin or preserved in RNAlater (Qiagen). Mortality was less than 5% and not associated with a particular genoptype.

tag: gender

value: male

tag: age

value: 7-10 weeks

value: Liver

tag: genotype/variation

value: Tob1 null


title: N2 vs ok165 (rep2)

city: Salt Lake City

first: Bargavi

last: Thyagarajan

state: UT

address: Huntsman Cancer Institute, 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

hyb_protocol: Agilent Two-color GE Hyb/Wash Protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 um resolution.

data_processing: Images from the microarray scanner were processed in Agilent Feature Extraction software version 8.5.1.1. Lowess normalized log base 10 ratios were produced, and were converted to log base 2.

organism: Caenorhabditis elegans

source_name: L4 larval stage WT whole worms

label_protocol: Agilent Two-Color LRILAK Labeling Protocol

growth_protocol: Standard C. elegans growth protocols on plates were followed. Adult worms were treated with hypochlorite to obtain synchronized progeny. L4 stage larvae were used for RNA extraction and gene expression profiling

extract_protocol: Trizol extraction and phenol/chloroform extraction were performed to obtain total RNA from worm samples. Rneasy kit (Qiagen) was used to clean-up the RNA sample and to perform Dnase treatment.

treatment_protocol: Standard C. elegans growth protocols were used. The worms were grown on plates with OP50 bacteria at 20C

value: N2 (wild type)

value: L4 larval stage

source_name: L4 larval stage ets-4(ok165) mutant whole worms


title: N2 vs uz1 (rep1)

source_name: L4 larval stage ets-4(uz1) mutant whole worms


title: Experiment 1, Blastomere pair I, Cell 2

description:
Experiment 1, blastomere pair I, cell 2.
Exp1I2


title: Experiment 2, Blastomere pair G, Cell 1

description:
Experiment 2, blastomere pair G, cell 1.
Exp2G1


title: Experiment 1, Blastomere pair L, Cell 1

description:
Experiment 1, blastomere pair L, cell 1.
Exp1L1


title: Experiment 1, Blastomere pair I, Cell 1

description:
Experiment 1, blastomere pair I, cell 1.
Exp1I1


title: PBMCs rep 1 activated

status: Public on May 14 2010

city: Hamburg

first: Christoph

last: Ogrodowczyk

address: Falkenried 94

department: Institute for Neural Signal Transduction

country: Germany

institute: ZMNH

hyb_protocol: Standard Affymentrix protocol (IFG Münster, Germany)

data_processing:
RMA processing/normalization.
Using Array Assist 4.0 (Stratagene), filtering genes with change in expression with significance of p<0.05 and a fold change >2 (including Bonferroni correction).

organism: Homo sapiens

source_name: PBMCs healthy donor activated

extract_protocol: Trizol RNA isolation following manufectureres guidlines

treatment_protocol: Buffy coats were separated in Ficoll gradient, supernatant was discarded and layer containing PBMCs carefully collected

tag: protocol

value: PBMC activation


title: PBMCs rep 3 activated

scan_protocol: Standard Affymentrix protocol (IFG Münster, Germany)


title: Experiment 1, Blastomere pair D, Cell 2

description:
Experiment 1, blastomere pair D, cell 2.
Exp1D2


title: PBMCs rep 2 activated

label_protocol: Standard Affymentrix protocol (IFG Münster, Germany)


title: Liver_normal_0hr_rep2

description: Gene expression data from normal mouse liver at 0hr

source_name: Liver, normal, 0hr

value: Wild Type


title: PBMCs rep 3 unactivated

source_name: PBMCs healthy donor unactivated

value: control


title: Liver_normal_0hr_rep1


title: PBMCs rep.1 unactivated


title: PBMCs rep 2 unactivated


title: S. mutans UA159 0.5% sucrose biofilm 30h replicate 1

city: Rochester

first: Marlise

middle: I

last: Klein

state: NY

address: 601 Elmwood Ave.

department: Dentistry - Center for Oral Biology

institute: University of Rochester

hyb_protocol: The slides were hybridized to a mixture containing equal amounts of test and reference cDNA for 16 h at 42°C in a MAUI hybridization chamber (BioMicro Systems). Hybridized slides were washed and scanned using a GenePix scanner (Axon Instruments).

scan_protocol: Hybridized slides were washed and scanned using a GenePix scanner (Axon Instruments, Inc., Union City, CA).

data_processing: Data were analyzed using software available at the J. Craig Venter Institute PFGRC website. Single-channel images of the slides were loaded into Spotfinder and overlaid. A spot grid was created according to PFGRC specifications and manually adjusted to fit all spots. The Microarray Data Analysis System (MIDAS) software was used to normalize the spot intensity data using LOWESS and standard deviation regularization with default setting. MIDAS also utilized In-Slide Replicate Analysis to average the intensities of the spots that were replicated on the microarray slide. Statistical analysis was carried out with BRB array tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) with a cutoff P value of 0.001.

organism: Streptococcus mutans UA159

source_name: S. mutans UA159 biofilm RNA

label_protocol: Once RNA was purified as described above, cDNA was generated from 2ug RNA per sample as described by the protocol available from the Pathogen Functional Genomics Research Center (PFGRC) using Invitrogen Superscript III Reverse Transcriptase (Invitrogen, Gaithersburg, MD) to increase cDNA yields. Purified cDNAs were coupled to Cy3 (experimental samples) or Cy5 (reference cDNA).

growth_protocol: Biofilm preparation. Hydroxyapatite discs (2.93 cm2) were coated with amylase-active sterile clarified human saliva (sHA). Biofilms of S. mutans UA159 were formed on sHA discs placed in a vertical position in batch cultures at 37oC in 5% CO2. The biofilms were grown in buffered tryptone yeast-extract broth, pH 7.0, containing specific concentrations of sucrose and/or starch (soluble starch – 80% amylopectin and 20% amylose; Sigma Chemical Company, St Louis, MO). The concentrations of 0.5% sucrose (suc), 0.5% sucrose + 1% starch (st) and 1% sucrose were used.

extract_protocol: The biofilms were removed from HA disc in sufficient volume of RNALater, according to manufacture instructions, and stored at 4oC, overnight. Next day, the biofilm samples were washed with cold 1X PBS and sonicated at 7 watts for 30 sec (2 sonication-washings). The supernatant was discarded and biofilm pellets were homogenized and RNA extracted by repeated acid-phenol: chloroform extractions, and the nucleic acid was precipitated with 1 volume ice-cold isopropanol and one-tenth volume 3M sodium acetate (pH 5) at –20°C overnight. RNA pellets were resuspended in 50 μL nuclease-free H2O, and treated with DNase I to remove contaminant genomic DNA. Two types of commercially available DNase I treatments were used: (i) on-column DNase I (Qiagen RNeasy Mini Kit, Qiagen Sciences, Germantown, MD, USA) and (ii) protein-engineered DNase I in solution (Turbo DNase, Ambion). An aliquot of the extracted RNA was treated first using Qiagen’s RNeasy on-column DNase I (Q, 2.7 U DNase I/10 μg RNA) and then with Ambion’s Turbo DNase I (T, 2 U Turbo DNase I/10 μg RNA), followed by Qiagen RNeasy MinElute (for DNase I removal) according to the manufacturer’s protocols with the exception of Qiagen’s on-column DNase I. The RNeasy on-column DNase I protocol was modified by adding a washing step with 350 μl of RLT buffer containing 36% ethanol prior to column washing with RW1 buffer (RLT and RW1 buffers are proprietary solutions of Qiagen Sciences). RNA concentrations were determined using a Nanodrop ND-1000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA).The quality of the purified RNA was examined by an Agilent 2100 electrophoresis bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) to verify RNA integrity.

tag: biofilm age

value: 30 hours

tag: growth condition

value: 0.5% sucrose

source_name: wild-type mid-log RNA

growth_protocol: Cells were grown in Brain-Heart medium to OD600 of 0.5 in a 5% CO2 incubator at 37°C.

tag: growth phase

value: mid-log


title: S. mutans UA159 1% sucrose biofilm 24h replicate 3

value: 24 hours

value: 1% sucrose


title: S. mutans UA159 0.5% sucrose + 1% starch biofilm 30h replicate 2

value: 0.5% sucrose + 1% starch


title: N2 vs ok165 (rep1)


title: 0009_T_vs_B

city: Nerviano

first: Roberta

last: Bosotti

state: MI

address: viale Pasteur,10

department: Biotechnology

country: Italy

institute: Nerviano Medical Sciences srl

description: Patient 0009

hyb_protocol: Probe synthesis, hybridization and scanning were performed according to standard operation procedures (Reference Protocol: Agilent Technologies “Two-Color Microarray-Based Gene Expression Analysis” Version 5.0.1).

data_processing: Agilent Feature Extraction Software. Extract data using Agilent Feature Extraction Software: import files obtained with feature extraction into Resolver database and software. Data were normalized using Lowess normalization. Data from dye swaps were combined.

source_name: Tumour treated

growth_protocol: Solid tumor biopsies.

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

treatment_protocol: Pt treated with the Cdk inhibitor PHA-793887 at 44 mg/m2.

tag: treatment

source_name: Tumour baseline

treatment_protocol: Pre-treatment.


title: 0015_T_vs_B

description: Patient 0015

scan_protocol: Probe synthesis, hybridization and scanning were performed according to standard operation procedures (Reference Protocol: Agilent Technologies “Two-Color Microarray-Based Gene Expression Analysis” Version 5.0.1).


title: 0006_T_vs_B

description: Patient 0006

label_protocol: Probe synthesis, hybridization and scanning were performed according to standard operation procedures (Reference Protocol: Agilent Technologies “Two-Color Microarray-Based Gene Expression Analysis” Version 5.0.1).

treatment_protocol: Pt treated with the Cdk inhibitor PHA-793887 at 22 mg/m2.


title: 0003_T_vs_B

description: Patient 0003

treatment_protocol: Pt treated with the Cdk inhibitor PHA-793887 at 11 mg/m2.


title: 0016_T_vs_B

description: Patient 0016


title: 0002_T_vs_B

description: Patient 0002


title: Experiment 1, Blastomere pair D, Cell 1

description:
Experiment 1, blastomere pair D, cell 1.
Exp1D1

value: 2-cell embryos ~36h post coitus


title: 0008_T_vs_B

description: Patient 0008


title: obese, with DM-2, person 8

status: Public on May 13 2010

city: Girona

first: Francisco

middle: Jose

last: Ortega

state: Catalunya

address: Av. de Franca, s/n

department: Unitat de Diabetes, Endocrinologia i Nutricio (UDEN)

country: Spain

institute: Institut d'Investigació Biomedica de Girona (IdIBGi)

description: subcutaneous fat cells from obese woman with DM-2, biological replicate 8 of 9

hyb_protocol: Labeled RNA was dried and resuspended with Hybridization  Buffer and Blocking Agent, incubated 10’ at 100ºC and transfered to an ice water bath for 5’. Samples were hybridized in a volume of 45ul to the Human miRNA V2 Oligo Microarray (Agilent) for 20 hours at 55°C and 20rpm. Microarrays were then washed at room temperature for 5min in Gene Expression Wash Buffer 1 and 5min at 37ºC in Gene Expression Wash Buffer 2 (Agilent Technologies; Palo Alto, CA).

scan_protocol: Arrays were scanned on an Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies for miRNA microarrays with 100% PMT and 5μm resolution. Data was extracted using Agilent Feature Extraction Software (Agilent Technologies; Palo Alto, CA).

data_processing: Extracted Log2-transformed intensities were quantile normalized to make all data comparable.

source_name: subcutaneous fat cells

label_protocol: 500ng of total RNA from each sample was dephosphorylated with Calf Intestinal Alkaline Phosphatase (CIP) at 37ºC for 30’ following a denaturalization and then a ligation for 2h at 16ºC using Agilent miRNA Complete Labeling and Hyb Kit (Agilent Technologies; Palo Alto, CA). In this step a molecule of Cyanine3-pCp is incorporated to the 3’ end of RNA molecules.

growth_protocol: adipose tissue biopsies were obtained from subcutaneous fat depots during elective surgical procedures (cholecystectomy, surgery of abdominal hernia and gastric by-pass surgery), washed, fragmented and immediately flash-frozen in liquid nitrogen before be stored at -80ºC. These subcutaneous fat samples were provided from a group of 28 women with a body mass index (BMI) between 20 and 55Kg/m2 who were invited to participate at the Endocrinology Service of the Hospital Universitari de Girona Dr. Josep Trueta (Girona, Spain). All subjects were of Caucasian origin and reported that their body weight had been stable for at least three months before the study. They had no systemic disease other than type 2 diabetes mellitus (DM-2) and obesity and all were free of any infections in the previous month before the study. Liver disease and thyroid dysfunction were specifically excluded by biochemical work-up. Other exclusion criteria for those patients included the following: 1) clinically significant hepatic, neurological, or other major systemic disease, including malignancy; 2) history of drug or alcohol abuse, defined as >60g/day, or serum transaminase activity more than twice the upper limit of normal; 3) an elevated serum creatinine concentration; 4) acute major cardiovascular event in the previous 6 months; 5) acute illnesses and current evidence of high grade chronic inflammatory or infective diseases; and 6) mental illness rendering the subjects unable to understand the nature, scope, and possible consequences of the study. All subjects gave written informed consent after the purpose of the study was explained to them. The institutional review board of each institution approved the protocol.

extract_protocol: Total RNA, including small RNAs and miRNAs, was extracted, purified and prepared from adipose tissue fragments and cells debris using miRNeasy Mini Kit (QIAgen; Gaithersburg, MD).

tag: type

value: obese

tag: disease state

value: with Type 2 Diabetes Mellitus

value: subcutaneous fat cells


title: obese, without DM-2, person 11

description: subcutaneous fat cells from obese woman without DM-2, biological replicate 11 of 13

value: without Type 2 Diabetes Mellitus


title: obese, with DM-2, person 5

description: subcutaneous fat cells from obese woman with DM-2, biological replicate 5 of 9


title: obese, without DM-2, person 13

description: subcutaneous fat cells from obese woman without DM-2, biological replicate 13 of 13


title: genotype: Wild-Type - rep3

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description: Plants were grown in glasshouse conditions and harvested at the two leaf stage

hyb_protocol: Affymetrix (AGRF)

scan_protocol: Affymetrix (AGRF)

data_processing: The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.

organism: Hordeum vulgare

source_name: whole plant (genotype: Wild-Type)

label_protocol: Affymetrix (AGRF)

extract_protocol: Pine tree extraction method (Chang et al 1993)

tag: germplasm name

value: golden promise

tag: organism part

value: po:0000003 whole plant

value: UD:0000051 vegetative

tag: growth media

value: Cereal mix

tag: genotype

value: wild type


title: obese, without DM-2, person 10

description: subcutaneous fat cells from obese woman without DM-2, biological replicate 10 of 13


title: genotype: Over-expression - rep3

source_name: whole plant (genotype: Over-expression)

value: ODDSOC2 overexpressor


title: CBP liver bio rep 3 slide 2

type: genomic

city: Cambridge

first: Kenzie

last: MacIsaac

address: 77 Massachusetts Ave.

institute: MIT

description: profile of CBP binding in liver hepatocytes

hyb_protocol: 5 – 6 μg immunoenriched Cy5 labeled and input Cy3 labeled DNA was combined and hybridized with tumbling to arrays in Agilent hybridization chambers for 40 hours at 40°C.

scan_protocol: Arrays were scanned according to the manufacturer’s instructions

data_processing: enrichment ratios in the processed data files were generated by calculating median normalized intensity ratios for each spot on the array.

molecule: genomic DNA

source_name: CBP ChIP DNA from liver

label_protocol: DNA was labeled and purified using Invitrogen Bioprime random primer labeling kits

extract_protocol: Hepatocytes were harvested by direct perfusion of the liver in anaesthetized animals using PBS, followed by crosslinking with a 1% formaldehyde solution. The liver was then removed and crosslinked for another 10 minutes followed by neutralization with glycine. This cellular material was homogenized, washed and passed through a sucrose gradient to enrich for hepatocytes. These were rinsed with 1X PBS, pelleted, and either used directly in ChIP experiments, or frozen in liquid nitrogen for later use. Mouse cerebella were harvested from male C57BL/6J mice and crosslinked, homogenized, and neutralized in a similar manner.

tag: strain

value: liver

tag: chip antibody

value: CBP

source_name: Input DNA from liver hepatocytes


title: obese, without DM-2, person 5

description: subcutaneous fat cells from obese woman without DM-2, biological replicate 5 of 13

tag: tissue


title: genotype: Wild-Type - rep2

tag: developmental stage


title: genotype: Wild-Type - rep1


title: genotype: Over-expression - rep2


title: CBP cerebellum bio rep 1 slide 2

description: profile of CBP binding in cerebellum

source_name: CBP ChIP DNA from cerebellum

value: cerebellum

source_name: Input DNA from cerebellum


title: obese, with DM-2, person 7

description: subcutaneous fat cells from obese woman with DM-2, biological replicate 7 of 9


title: obese, with DM-2, person 4

description: subcutaneous fat cells from obese woman with DM-2, biological replicate 4 of 9


title: obese, with DM-2, person 9

description: subcutaneous fat cells from obese woman with DM-2, biological replicate 9 of 9


title: CBP cerebellum bio rep 2 slide 2

description: profile of CBP binding in cerebellum


title: CBP liver bio rep 3 slide 1


title: obese, without DM-2, person 2

description: subcutaneous fat cells from obese woman without DM-2, biological replicate 2 of 13


title: CBP liver bio rep 1 slide 2


title: obese, without DM-2, person 12

description: subcutaneous fat cells from obese woman without DM-2, biological replicate 12 of 13


title: obese, with DM-2, person 2

description: subcutaneous fat cells from obese woman with DM-2, biological replicate 2 of 9


title: CBP cerebellum bio rep 2 slide 1

description: profile of CBP binding in cerebellum


title: CBP cerebellum bio rep 1 slide 1

description: profile of CBP binding in cerebellum


title: genotype: Over-expression - rep1


title: CBP liver bio rep 2 slide 2


title: CBP liver bio rep 1 slide 1


title: CBP liver bio rep 2 slide 1


title: Leaves S. chacoense vs WT S. chacoense (replica 3)

city: Québec

first: Faiza

last: Tebbji

address: 2705 Boulevard Laurier

country: Canada

institute: CHU Québec

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
Leaves (replica 3)

hyb_protocol: The microarray slides were pre-hybridized for1 hours at 42°C with DIGeasy hybridization buffer (Roche) containing 0.5 ug/ul of yeast tRNA (Roche) and 0.5 ug/ul of salmon sperm DNA (Invitrogen) and subsequently washed with 0.1X SSC and air dried. The slides were then hybridized with labeled cDNAs overnight at 42°C in DIGeasy hybridization buffer with yeast tRNA and salmon sperm DNA. The slides were washed twice for 10 min at 42°C with 1× SSC, 0.1% SDS, twice for 10 min at 37°C with 0.1× SSC, 0.1% SDS, and finally, with quick consecutive washes in three 0.1× SSC baths. Slides were air-dried.

scan_protocol: Slides were scanned with a ScanArray 5000 scanner (Perkin Elmer) at 10-µm resolution.

data_processing: Signal intensity was quantified with QuantArray software (Perkin Elmer) and final Lowess normalization and inspection of the data was done with the GeneSpring package GX v.7.3 (Agilent Technologies).

organism: Solanum chacoense

source_name: leaves tisuues from G4 genotype (greenhouse growth with an average photoperiod of 14-16h per day)

label_protocol: 30 µg of total RNA was reverse transcribed using oligo(dT)21 in the presence of cyanine 3-dCTP (1 mM) or cyanine 5-dCTP (1 mM; Perkin Elmer-Cetus/NEN, Boston, MA, catalog # NEL999) and Superscript III reverse transcriptase (Invitrogen). Thereafter, template RNA was degraded by adding 2.5 units of RNase H (USB) and 1 ug of RNase A (Pharmacia) followed by incubation for 30 min at 37°C. The labeled cDNAs were purified using CyScribe GFX Purification Kit (GE Healthcare Bio-Sciences Inc., Baie d'Urfé, QC, Canada) according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted using the TRIzol ® Reagent according to the manufacturer’s protocol (Invitrogen, Burlington, ON, Canada).

treatment_protocol: Solanum chacoense Bitt. was greenhouse grown with an average photoperiod of 14-16h per day. Plants were hand pollinated and ovules were collected between 0 and 22 days after pollination (DAP) and used for RNA extraction and probe preparations. Leaf, style and anther tissues were collected from the same plant genotype G4

value: Leaves

source_name: Unfertilized ovules

value: Unfertilized ovules


title: Leaves S. chacoense vs WT S. chacoense (replica 4)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
Leaves (replica 4)


title: obese, with DM-2, person 6

description: subcutaneous fat cells from obese woman with DM-2, biological replicate 6 of 9


title: obese, without DM-2, person 7

description: subcutaneous fat cells from obese woman without DM-2, biological replicate 7 of 13


title: obese, without DM-2, person 8

description: subcutaneous fat cells from obese woman without DM-2, biological replicate 8 of 13


title: obese, without DM-2, person 9

description: subcutaneous fat cells from obese woman without DM-2, biological replicate 9 of 13


title: Leaves S. chacoense vs WT S. chacoense (replica 2)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
leaves (replica 2)


title: Styles S. chacoense vs WT S. chacoense (replica 4)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
Styles (replica 4)

source_name: Styles tisuues from G4 genotype (greenhouse growth with an average photoperiod of 14-16h per day)

value: Styles


title: Styles S. chacoense vs WT S. chacoense (replica 3)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
Styles (replica 3)


title: Anthers S. chacoense vs WT S. chacoense (replica 1)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
Anthers (replica 1)

source_name: Anthers tisuues from G4 genotype (greenhouse growth with an average photoperiod of 14-16h per day)

value: Anthers


title: Anthers S. chacoense vs WT S. chacoense (replica 4)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
Anthers (replica 4)


title: Styles S. chacoense vs WT S. chacoense (replica 1)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
Styles (replica 1)


title: Styles S. chacoense vs WT S. chacoense (replica 2)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
Styles (replica 2)


title: 22 DAP S. chacoense vs WT S. chacoense (replica 4)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
22 DAP (replica 4)

source_name: 22 days fertilized ovules from G4 genotype (genotype V22 (S11 and S13 self-incompatibility alleles) was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)

value: Ovules at 22 DAP


title: obese, without DM-2, person 6

description: subcutaneous fat cells from obese woman without DM-2, biological replicate 6 of 13

value: obese


title: Anthers S. chacoense vs WT S. chacoense (replica 2)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
Anthers (replica 2)


title: 22 DAP S. chacoense vs WT S. chacoense (replica 3)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
22 DAP (replica 3)


title: obese, with DM-2, person 3

description: subcutaneous fat cells from obese woman with DM-2, biological replicate 3 of 9

value: with Type 2 Diabetes Mellitus

value: subcutaneous fat cells


title: 22 DAP S. chacoense vs WT S. chacoense (replica 2)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
22 DAP (replica 2)


title: obese, without DM-2, person 4

description: subcutaneous fat cells from obese woman without DM-2, biological replicate 4 of 13

value: without Type 2 Diabetes Mellitus


title: 20 DAP S. chacoense vs WT S. chacoense (replica 3)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
20 DAP (replica 3)

source_name: 20 days fertilized ovules from G4 genotype (genotype V22 (S11 and S13 self-incompatibility alleles) was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)

value: Ovules at 20 DAP


title: Anthers S. chacoense vs WT S. chacoense (replica 3)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
Anthers (replica 3)


title: 22 DAP S. chacoense vs WT S. chacoense (replica 1)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
22 DAP (replica 1)


title: 20 DAP S. chacoense vs WT S. chacoense (replica 2)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
20 DAP (replica 2)


title: 20 DAP S. chacoense vs WT S. chacoense (replica 4)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
20 DAP (replica 4)


title: 18 DAP S. chacoense vs WT S. chacoense (replica 4)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
18 DAP (replica 4)

source_name: 18 days fertilized ovules from G4 genotype (genotype V22 (S11 and S13 self-incompatibility alleles) was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)

value: Ovules at 18 DAP


title: obese, with DM-2, person 1

description: subcutaneous fat cells from obese woman with DM-2, biological replicate 1 of 9


title: obese, without DM-2, person 3

description: subcutaneous fat cells from obese woman without DM-2, biological replicate 3 of 13


title: 18 DAP S. chacoense vs WT S. chacoense (replica 3)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
18 DAP (replica 3)


title: 20 DAP S. chacoense vs WT S. chacoense (replica 1)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
20 DAP (replica 1)


title: 18 DAP S. chacoense vs WT S. chacoense (replica 1)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
18 DAP (replica 1)


title: obese, without DM-2, person 1

description: subcutaneous fat cells from obese woman without DM-2, biological replicate 1 of 13


title: 16 DAP S. chacoense vs WT S. chacoense (replica 3)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
16 DAP (replica 3)

source_name: 16 days fertilized ovules from G4 genotype (genotype V22 (S11 and S13 self-incompatibility alleles) was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)

value: Ovules at 16 DAP


title: non-obese, person 6

description: subcutaneous fat cells from non-obese woman, biological replicate 6 of 6

value: non-obese


title: 14 DAP S. chacoense vs WT S. chacoense (replica 4)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
14 DAP (replica 4)

source_name: 14 days fertilized ovules from G4 genotype (genotype V22 (S11 and S13 self-incompatibility alleles) was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)

value: Ovules at 14 DAP


title: non-obese, person 3

description: subcutaneous fat cells from non-obese woman, biological replicate 3 of 6


title: non-obese, person 2

description: subcutaneous fat cells from non-obese woman, biological replicate 2 of 6


title: non-obese, person 4

description: subcutaneous fat cells from non-obese woman, biological replicate 4 of 6


title: 16 DAP S. chacoense vs WT S. chacoense (replica 1)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
16 DAP (replica 1)


title: 14 DAP S. chacoense vs WT S. chacoense (replica 2)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
14 DAP (replica 2)


title: non-obese, person 1

description: subcutaneous fat cells from non-obese woman, biological replicate 1 of 6


title: 12 DAP S. chacoense vs WT S. chacoense (replica 3)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
12 DAP (replica 3)

source_name: 12 days fertilized ovules from G4 genotype (genotype V22 (S11 and S13 self-incompatibility alleles) was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)

value: Ovules at 12 DAP


title: 16 DAP S. chacoense vs WT S. chacoense (replica 2)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
16 DAP (replica 2)


title: 16 DAP S. chacoense vs WT S. chacoense (replica 4)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
16 DAP (replica 4)


title: 14 DAP S. chacoense vs WT S. chacoense (replica 1)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
14 DAP (replica 1)


title: 12 DAP S. chacoense vs WT S. chacoense (replica 4)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
12 DAP (replica 4)


title: 18 DAP S. chacoense vs WT S. chacoense (replica 2)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
18 DAP (replica 2)


title: 14 DAP S. chacoense vs WT S. chacoense (replica 3)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
14 DAP (replica 3)


title: 12 DAP S. chacoense vs WT S. chacoense (replica 2)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
12 DAP (replica 2)


title: ES and iPS cells IP36D-3-rep2

city: Beijing

first: Qi

last: Zhou

address: No.1 Beichen West Road

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

description: Gene expression data from iPS cell line IP36D-3

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on the GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner GCS3000.

data_processing: RMA method provided by BioConductor was used to quantify microarray signals with default analysis parameters and global scaling to target mean=150.

source_name: Mouse induced pluripotent stem (iPS) cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: ES cells and iPS cells were cultured on mitomycin C treated MEF cells with DMEM plus 15% FBS or 20% Knockout serum replacement (KOSR), 1000u/ml LIF, 2 mM glutamine, 1 mM sodium pyruvate, 0.1 mM β-mercaptoethanol and 0.1 mM nonessential amino acid (NEAA).

treatment_protocol: Cells were collected and pelleted before Trizol was added and stored in -80oC before extraction.

tag: cell line

tag: cell type

value: iPS

value: B6 x D2 F1


title: PeriA_Tg_mice_WAT

city: Sapporo

first: Hideaki

last: Miyoshi

state: Hokkaido

address: Kita-15, Nishi-7, Kita-ku

department: Internal Medicine II

country: Japan

institute: Hokkaido University Graduate School of Medicine

description: Gene expression data from perigonadal white adipose tissue in HFD-fed PeriA transgenic mice. The mice are overexpressed human PeriA using the adipocyte specific aP2 promoter/enhancer (Miyoshi, et al. J Lipid Res 2010).

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

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

source_name: PeriA transgenic mice, white adipose tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

extract_protocol: Extraction of total RNA was performed by using Ambion Ribopure Kit (Cat.# AM1924), according to the manufacturer's instructions.

tag: genetic background

tag: gender

value: female

tag: age

value: perigonadal white adipose tissue

value: PeriA transgeneic


title: non-obese, person 5

description: subcutaneous fat cells from non-obese woman, biological replicate 5 of 6

source_name: subcutaneous fat cells


title: Control_WT_mice_WAT

description: Gene expression data from perigonadal white adipose tissue in HFD-fed wildtype C57BL/6 mice.

source_name: C57BL/6 mice, white adipose tissue

value: wild type


title: 12 DAP S. chacoense vs WT S. chacoense (replica 1)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
12 DAP (replica 1)

value: Unfertilized ovules


title: ES and iPS cells IP36D-3-rep1


title: ES and iPS cells IP36D-3-rep3


title: obese, 14 days of differentiation, replicate 3

description: mature adipocyte of obese subject, replicate 3 of 3

source_name: Human subcutaneous pre-adipocytes, obese

growth_protocol: Commercially available cryo-preserved human subcutaneous pre-adipocytes from two non-diabetic male subjects with age>40 and Body Mass Index (BMI) <25 or BMI>30Kg/m2 (SP-F-1 or SP-F-3, respectively; Zen-Bio, Inc.) were plated on T-75 cell culture flasks and cultured at 37ºC and 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM)/Nutrient Mix F-12 medium (1:1, v/v) supplemented with Fetal Bovine Serum (FBS) 10%, HEPES 1%, Glutamine 1% and Penicillin/Streptomycin (P/S) at 10U/mL (all from GIBCO, BRL; Grand Island, NY). One week later, human subcutaneous pre-adipocytes were resuspended and cultured (~40.000cells/cm2, 3rd passage) in 6-well plates with Pre-adipocyte Medium (PM; Zen-Bio, Inc.) composed of DMEM/Nutrient Mix F-12 medium (1:1, v/v), FBS 10%, HEPES 1%, Glutamine 1% and P/S 1% in a humidified 37ºC incubator with 5% CO2. Twenty-four hours after plating, cells were checked for complete confluence (day 0). Two weeks after the initiation of differentiation (day 14), cells appeared rounded with large lipid droplets apparent in the cytoplasm. Cells were then considered mature adipocytes (MAs).

treatment_protocol: Differentiation was induced using Differentiation Medium (DM; Zen-Bio, Inc.), composed of PM with human Insulin (Ins), Dexamethasone (DXM), Isobutylmethyl-xanthine (IBMX) and PPARγ agonists (Rosiglitazone, Rs). After 7 days (day 7), DM was replaced with fresh Adipocyte Medium (AM; Zen-Bio Inc.), composed of DMEM/Nutrient Mix F-12 medium (1:1, v/v), FBS, HEPES, Biotin, Panthothenate, human Insulin (Ins), Dexamethasone (DXM), Penicillin, Streptomycin and Amphotericin, according to manufacturers’ guidelines.

value: obsese

tag: day

tag: medium

value: adipocyte

value: human subcutaneous pre-adipocytes


title: 10 DAP S. chacoense vs WT S. chacoense (replica 4)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
10 DAP (replica 4)

source_name: 10 days fertilized ovules from G4 genotype (genotype V22 (S11 and S13 self-incompatibility alleles) was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)

value: Ovules at 10 DAP


title: 8 DAP S. chacoense vs WT S. chacoense (replica 4)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
8 DAP (replica 4)

source_name: 8 days fertilized ovules from G4 genotype (genotype V22 (S11 and S13 self-incompatibility alleles) was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)

value: Ovules at 8 DAP


title: 10 DAP S. chacoense vs WT S. chacoense (replica 3)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
10 DAP (replica 3)


title: 10 DAP S. chacoense vs WT S. chacoense (replica 1)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
10 DAP (replica 1)


title: ES and iPS cells IP20D-3-rep2

description: Gene expression data from iPS cell line IP20D-3


title: ES and iPS cells IP20D-3-rep3


title: 10 DAP S. chacoense vs WT S. chacoense (replica 2)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
10 DAP (replica 2)


title: 8 DAP S. chacoense vs WT S. chacoense (replica 2)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
8 DAP (replica 2)


title: obese, 14 days of differentiation, replicate 2

description: mature adipocyte of obese subject, replicate 2 of 3

tag: type


title: 8 DAP S. chacoense vs WT S. chacoense (replica 3)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
8 DAP (replica 3)


title: obese, 14 days of differentiation, replicate 1

description: mature adipocyte of obese subject, replicate 1 of 3


title: ES and iPS cells IP20D-3-rep1


title: ES and iPS cells IP14D-101-rep2

description: Gene expression data from iPS cell line IP14D-101


title: obese, 7 days of differentiation, replicate 3

description: pre-adipocytes of obese subject after 7 days of differentiation, replicate 3 of 3

value: differentiation


title: ES and iPS cells IP14D-101-rep1


title: obese, 7 days of differentiation, replicate 2

description: pre-adipocytes of obese subject after 7 days of differentiation, replicate 2 of 3


title: 6 DAP S. chacoense vs WT S. chacoense (replica 2)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
6 DAP (replica 2)

source_name: 6 days fertilized ovules from G4 genotype (genotype V22 (S11 and S13 self-incompatibility alleles) was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)

value: Ovules at 6 DAP


title: 6 DAP S. chacoense vs WT S. chacoense (replica 3)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
6 DAP (replica 3)

source_name: Unfertilized ovules


title: obese, 7 days of differentiation, replicate 1

description: pre-adipocytes of obese subject after 7 days of differentiation, replicate 1 of 3


title: 6 DAP S. chacoense vs WT S. chacoense (replica 4)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
6 DAP (replica 4)


title: 6 DAP S. chacoense vs WT S. chacoense (replica 1)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
6 DAP (replica 1)


title: ES and iPS cells IP14D-1-rep3

description: Gene expression data from iPS cell line IP14D-1


title: 8 DAP S. chacoense vs WT S. chacoense (replica 1)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
8 DAP (replica 1)


title: 4 DAP S. chacoense vs WT S. chacoense (replica 4)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
4 DAP (replica 4)

source_name: 4 days fertilized ovules from G4 genotype (genotype V22 (S11 and S13 self-incompatibility alleles) was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)

value: Ovules at 4 DAP


title: obese, 0 days of differentiation, replicate 3

description: undifferentiated pre-adipocytes of obese subject, replicate 3 of 3

value: pre-adipocyte


title: Leaves S. chacoense vs WT S. chacoense (replica 1)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
Leaves (replica 1)

source_name: leaves tisuues from G4 genotype (greenhouse growth with an average photoperiod of 14-16h per day)

value: Leaves


title: ES and iPS cells IP14D-1-rep1

value: iPS


title: ES and iPS cells IP14D-101-rep3


title: ES and iPS cells ESC2-rep3

description: Gene expression data from ES cell line ESC2

source_name: Mouse embryonic stem (ES) cells

value: ES

value: B6 x D2 F1


title: ES and iPS cells IP14D-1-rep2


title: 4 DAP S. chacoense vs WT S. chacoense (replica 1)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
4 DAP (replica 1)


title: control, 14 days of differentiation, replicate 3

description: mature adipocyte of lean subject, replicate 3 of 3

source_name: Human subcutaneous pre-adipocytes, lean

value: lean


title: 2 DAP S. chacoense vs WT S. chacoense (replica 4)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
2 DAP (replica 4)

source_name: 2 days fertilized ovules from G4 genotype (genotype V22 (S11 and S13 self-incompatibility alleles) was used as pollen donor; greenhouse growth with an average photoperiod of 14-16h per day)

value: Ovules at 2 DAP


title: obese, 0 days of differentiation, replicate 2

description: undifferentiated pre-adipocytes of obese subject, replicate 2 of 3


title: control, 14 days of differentiation, replicate 2

description: mature adipocyte of lean subject, replicate 2 of 3


title: obese, 0 days of differentiation, replicate 1

description: undifferentiated pre-adipocytes of obese subject, replicate 1 of 3


title: 4 DAP S. chacoense vs WT S. chacoense (replica 2)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
4 DAP (replica 2)


title: control, 7 days of differentiation, replicate 3

description: pre-adipocytes of lean subject after 7 days of differentiation, replicate 3 of 3


title: ES and iPS cells ESC2-rep2


title: ES and iPS cells R1-rep3

description: Gene expression data from ES cell line R1


title: 4 DAP S. chacoense vs WT S. chacoense (replica 3)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
4 DAP (replica 3)


title: WT S. chacoense vs WT S. chacoense (replica 6)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
WT-unfertilized ovules (replica 6)

source_name: Unfertilized ovules from G4 genotype (greenhouse growth with an average photoperiod of 14-16h per day)


title: 2 DAP S. chacoense vs WT S. chacoense (replica 2)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
2 DAP (replica 2)


title: R98 (Untreated)

city: WP

first: cheng foh

last: le

address: jalan universiti

department: Medical Microbiology

country: Malaysia

institute: University Malaya

description: Gene expression data of a resistant strain

hyb_protocol: Following fragmentation, minimum of 5 ug of cDNA were hybridized for 16 hr at 45C on GeneChip S. pneumoniae Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with Genechip Operating Software (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

organism: Streptococcus pneumoniae

source_name: Resistant strain before exposure

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Prokaryotic Sample and Array Processing Manual, Affymetrix).

growth_protocol: Bacterial strains were primarily grown on 5% horse blood agar and incubated at 37C with 5% CO2 for 12-15 hours. Subsequently, a loop of bacterial culture was inoculated into 10ml of Todd Hewitt broth supplemented with 0.5% yeast extract. These culture flasks was then aerated at 37C with 5% CO2 for 12-15 hours or till it reaches an OD600 of ~0.3 (log phase).

extract_protocol: Hot acid phenol extraction of total RNA was performed as described by Peterson et al (2000) .

treatment_protocol: 1ml of subinhibitory concentration  of penicillin of the strain was added to another batch of the culture which has grown to the log phase. The treated bacterial culture was incubated further for 20 minutes at 37C in the presence of 5% CO2.


title: I81 (Treated)

description: Gene expression data of an intermediate strain after being exposed to penicillin stress

source_name: Intermediate strain after exposure


title: ES and iPS cells R1-rep2


title: ES and iPS cells ESC2-rep1


title: 2 DAP S. chacoense vs WT S. chacoense (replica 1)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
2 DAP (replica 1)


title: R98 (Treated)

description: Gene expression data of a resistant strain after being exposed to penicillin stress

source_name: Resistant strain after exposure


title: WT S. chacoense vs WT S. chacoense (replica 5)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
WT-unfertilized ovules (replica 5)


title: 2 DAP S. chacoense vs WT S. chacoense (replica 3)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
2 DAP (replica 3)


title: S676 (Untreated)

description: Gene expression data of a sensitive strain

source_name: Sensitive strain before exposure


title: I81 (Untreated)

description: Gene expression data of an intermediate strain

source_name: Intermediate strain before exposure


title: control, 7 days of differentiation, replicate 1

description: pre-adipocytes of lean subject after 7 days of differentiation, replicate 1 of 3


title: control, 14 days of differentiation, replicate 1

description: mature adipocyte of lean subject, replicate 1 of 3


title: S676 (Treated)

description: Gene expression data of a sensitive strain after being exposed to penicillin stress

source_name: Sensitive strain after exposure


title: ES and iPS cells R1-rep1


title: Cerebellum, biological rep 3

description: gene expression data from cerebellum

hyb_protocol: Samples were hybridized using standard protocols on Mouse Genome 2.0 arrays, washed and stained in a 450 fluidics device

scan_protocol: GeneChips were scanned using a Genechip scanner 7G

data_processing: Data were analyzed by GCRMA using the R/Bioconductor package

source_name: cerebellum

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

growth_protocol: Tissue samples were harvested from male C57BL/6J. Animals were provided with water and chow without restriction.

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

value: 8-10 weeks

value: cerebellum


title: Cerebellum, biological rep 2

description: gene expression data from cerebellum


title: control, 7 days of differentiation, replicate 2

description: pre-adipocytes of lean subject after 7 days of differentiation, replicate 2 of 3


title: WT S. chacoense vs WT S. chacoense (replica 3)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
WT-unfertilized ovules (replica 3)

value: Unfertilized ovules


title: AAA_macrophage_LIL6

status: Public on May 12 2010

city: Lille

first: David

last: Hot

address: 1 rue du professeur Calmette

department: Center for Infection and Immunity of Lille

country: France

institute: Institut Pasteur de Lille

hyb_protocol: Labeled cDNA obtained from patient RNA and control RNA were mixed together and hybridization buffer was added to a final concentration of 40% formamide, 2.5x Denhardt’s, 0.5% SDS and 4x SSC (sodium saline citrate). Hybridization was performed under a coverslip in a hybridization chamber (CMT, Corning) at 42°C for 16h. Slides were then washed twice in 2x SSC and 0.1% SDS for 5 min at 42°C then once in 0.2x SSC for 1 min at room temperature.

scan_protocol: Arrays were scanned with the Affymetrix® 418 scanner and images were processed with ImaGene 6.0 software (Biodiscovery).

data_processing: The normalization protocol consisted first of a within-array global lowess normalization to correct for dye effect and then of between-array normalization to scale the distribution ratio values between the different slides. Data analysis was performed with the statistical language R (v 2.0.1) more specifically with the LIMMA library (Linear Models for MicroArray data).

source_name: AAA patient macrophage

label_protocol: 5 µg of total RNA was labeled with the Agilent Fluorescent Linear Amplification kit as described by the supplier

extract_protocol: Total RNA extraction using RNA isolation kit Rneasy (Qiagen) following manufacturer's instructions

tag: disease state

value: AAA

value: primary culture of macrophages

value: 12 days

source_name: Mixture of total RNA from heart, colon, placenta and brain (Stratagene)

tag: sample type

value: reference

tag: tissues

value: heart, colon, placenta and brain

tag: manufacturer

value: Stratagene


title: AAA_macrophage_LIL1


title: AAA_macrophage_LIL33

source_name: PAO patient macrophage

value: PAO


title: AAA_macrophage_LIL40


title: AAA_macrophage_LIL18


title: control, 0 days of differentiation, replicate 2

description: undifferentiated pre-adipocytes of lean subject, replicate 2 of 3

value: pre-adipocyte

value: human subcutaneous pre-adipocytes


title: Liver, biological rep 3

description: gene expression data from liver

source_name: liver hepatocytes

value: liver


title: AAA_macrophage_LIL39


title: AAA_macrophage_LIL31


title: WT S. chacoense vs WT S. chacoense (replica 4)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
WT-unfertilized ovules (replica 4)

source_name: Unfertilized ovules


title: control, 0 days of differentiation, replicate 3

description: undifferentiated pre-adipocytes of lean subject, replicate 3 of 3


title: WT S. chacoense vs WT S. chacoense (replica 1)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
WT-unfertilized ovules (replica 1)


title: Cerebellum, biological rep 1

description: gene expression data from cerebellum


title: control, 0 days of differentiation, replicate 1

description: undifferentiated pre-adipocytes of lean subject, replicate 1 of 3


title: WT S. chacoense vs WT S. chacoense (replica 2)

description:
Arrays containing 15,482 data points and are organized in 48 sub-arrays
WT-unfertilized ovules  (replica 2)


title: AAA_macrophage_LIL32


title: Liver, biological rep 2

description: gene expression data from liver


title: MPCu, Rep 2

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

description: Expression array, undifferentiated muscle progenitor cells.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing:
The data were quantile normalised using Illumina BeadStudio software.

The non-normalized data is available in the 'GSE19773_non-normalized.txt' file, which is linked to the Series GSE19773 record as a supplementary file.

source_name: MPC, undifferentiated

label_protocol: Biotinylated cRNA was prepared with the Illumina TotalPrep RNA Amplification Kit.

growth_protocol: The adipose stem cells, bone marrow mesenchymal stem cells and muscle progenitor cells were cultured in DMEM/F12 Glutamax containing 10% FCS and 1% PenStrep.

extract_protocol: RNA was extracted using the RNeasy Mini Kit (Qiagen) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: For adipogenic differentiation, the following protocol was used: 500 ml DMEM F-12 Glutamax, 0.5 mM IBMX, 1 µM dexamethasone, 0.2 mM indomethacin, 10 µg/ ml insulin, 10 % FCS and 1 % PenStrep. For myogenic differentiation, the following protocol was used: 500 ml DMEM F-12 Glutamax, 2 % horse serum and 1 % PenStrep.

value: skeletal muscle

value: mesenchymal stem cells

tag: differentiation

value: undifferentiated


title: Liver, biological rep 1

description: gene expression data from liver

tag: strain


title: MPCmd, Rep 3

description: Expression array, muscle progenitor cells differentiated under myogenic conditions.

source_name: MPC, myogenic differentiated

value: myogenic-differentiated mesenchymal stem cells

value: in vitro differentiated myocytes


title: MPCmd, Rep 1


title: ASCad, Rep 1

description: Expression array, adipose stem cells differentiated under adipogenic conditions.

source_name: ASC, adipogenic differentiated

value: adipogenic-differentiated mesenchymal stem cells

value: in vitro differentiated adipocytes


title: BMMSCu, Rep 1

description: Expression array, undifferentiated bone marrow mesenchymal stem cells.

source_name: BMMSC, undifferentiated

value: bone marrow


title: BMMSCu, Rep 2


title: ASCu, Rep 1

description: Expression array, undifferentiated adipose stem cells.

source_name: ASC, undifferentiated

value: adipose


title: ASCu, Rep 2


title: MPCu, Rep 1


title: MPCmd, Rep 2


title: ASCad, Rep 2


title: Sz patient 0002

type: other

city: Oxford

first: charles

last: lawrie

address: John Radcliffe Hospital

department: NDCLS

country: United Kingdom

institute: University of Oxford

description: Image analysis was carried out with BlueFuse software (BlueGnome, Cambridge, UK)

hyb_protocol: Samples were hybridised using the Array 900microRNA direct kit from Genisphere (Hatfield, PA) as described by the manufacturer on a A-hyb machine (Miltenyi Biotec).

scan_protocol: Slides were scanned on a Perkin-Elmer ArrayExpress scanner

data_processing: Raw image data were global median-normalized within arrays and normalized between arrays using the LIMMA package. The normalized log ratios (average of four replicates per probe) were used for subsequent analysis in Genespring 7.2 (Agilent Technologies, CA, US).

molecule: other

source_name: purified CD4+ from peripheral blood from Sz patient

label_protocol: Enriched microRNA (500ng) samples were labeled with either Cy3 or Cy5 dyes using an Array 900microRNA direct kit from Genisphere (Hatfield, PA)

extract_protocol: MicroRNA was isolated from samples using Trizol (Invitrogen, Paisley, UK) and RNeasy columns as described by the manufacturer (Qiagen, Crawley, UK).

value: female

source_name: tonsil

value: pooled tonsils (n=12)


title: Sz patient 0003


title: Sz patient 0004


title: Sz patient 0001

value: male


title: Sz patient R44

tag: cd4 count


title: Sz patient R45


title: Repl 2. Empty-EGFP transfected hASCs

description: Expression array, Empty-EGFP transfected mesenchymal stem cells

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were quantile normalised using Illumina BeadStudio software Version 3

source_name: MSC, Empty-EGFP transfected, rep2

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

growth_protocol: The mesenchymal stem cells were cultured for seven passages in DMEM/F12 containing 20% FCS and 1 % PenStrep.

treatment_protocol: The mesenchymal stem cells were transfected with H3.3-EGFP or empty-EGFP and sorted by FACS 168 hrs post transfection.

tag: tissue

value: Adipose tissue

value: Mesenchymal stem cells (MSC)

tag: transfection protocol

value: Empty-EGFP


title: Repl 1. Empty-EGFP transfected hASCs

source_name: MSC, Empty-EGFP transfected, rep1


title: Repl 3. Empty-EGFP transfected hASCs

source_name: MSC, Empty-EGFP transfected, rep3


title: Repl 3. H3.3-EGFP transfected hASCs

description: Expression array, H3.3-EGFP transfected mesenchymal stem cells

source_name: MSC, H3.3-EGFP transfected, rep3


title: Repl 2. H3.3-EGFP transfected hASCs

source_name: MSC, H3.3-EGFP transfected, rep2


title: Sz patient R34


title: Sz patient R31


title: Sz patient R38


title: Sz patient R41


title: Sz patient R32


title: Sz patient R35


title: Repl 2. Untransfected hASCs

description: Expression array, untransfected mesenchymal stem cells

source_name: MSC, untransfected, rep2

value: untransfected


title: Repl 1. H3.3-EGFP transfected hASCs

source_name: MSC, H3.3-EGFP transfected, rep1


title: Sz patient R39


title: Sz patient R33


title: Sz patient R42


title: Sz patient R29


title: Repl 1. Untransfected hASCs

source_name: MSC, untransfected, rep1


title: purified_CD4_normal#5

source_name: purified CD4+ cells from healthy patient


title: Sz patient R37


title: Sz patient R30


title: Sz patient R40


title: Sz patient R36


title: purified_CD4_normal#6


title: purified_CD4_normal#1


title: purified CD4+ cells


title: purified_CD4_normal#3


title: Sz patient R46


title: purified_CD4_normal#2


title: U2OS_ERb_Doxy_rep2

city: Emeryville

first: Xiaoyue

last: Zhao

state: CA

address: 5858 Horton St

institute: Bionovo Inc.

description: replicate 2

data_processing: The data were pre-processed using lumi package in R with bgAdjust.affy for background correction, quantile normalization, slide effect removed using linear model, and offset 80 added.

source_name: U2OS cells, ERb vector transfected with Doxycycline added

label_protocol: Biotin-labeled cRNA samples were prepared with 750 ng of total RNA template. Following synthesis and purification, the biotin-labeled samples were evaluated by both 260/280 absorbance spectrophotometry and capillary electrophoresis.

extract_protocol: Total cellular RNA was isolated utilizing the Aurum RNA isolation kit, (Bio-Rad, Hercules, CA), per the manufacturers’ directions. RNA isolates were first quantified by standard spectrophotometry, and then qualitatively evaluated by capillary electrophoresis employing the Bio-Rad Experion system per the manufacturers’ instruction.

tag: cell line


title: U2OS_ERb_DoxyE2_rep2

description: replicate 2

source_name: U2OS cells, ERb vector transfected with Doxycycline added and E2 treatment


title: U2OS_ERb_noDoxy_rep3

description: replicate 3

source_name: U2OS cells, ERb vector transfected without Doxycycline added


title: U2OS_ERb_Doxy_rep3

description: replicate 3


title: U2OS_ERb_noDoxy_rep1

description: replicate 1


title: U2OS_ERb_noDoxy_rep2

description: replicate 2


title: U2OS_ERb_DoxyE2_rep1

description: replicate 1


title: U2OS_ERb_Doxy_rep1

description: replicate 1


title: U2OS_ERa_DoxyE2_rep2

description: replicate 2

source_name: U2OS cells, ERa vector transfected with Doxycycline added and E2 treatment


title: U2OS_ERb_DoxyE2_rep3

description: replicate 3


title: U2OS_ERa_DoxyE2_rep3

description: replicate 3


title: U2OS_ERa_Doxy_rep2

description: replicate 2

source_name: U2OS cells, ERa vector transfected with Doxycycline added


title: U2OS_ERa_DoxyE2_rep1

description: replicate 1


title: U2OS_ERa_Doxy_rep3

description: replicate 3


title: 8M-Aging-BALBCvsC2J-MMAE186-Sample 5

city: Ann Arbor

first: Jun

last: Li

address: 5789A Medical Science II, Box 5618

institute: University of Michigan

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51214.gif
Type of label: reverse

hyb_protocol: not provided

scan_protocol: Axon Instruments (V1.00); Model GenePix 4000A

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

label_protocol: not provided

extract_protocol: not provided

value: 8M months

value: BALBC


title: 4M-Aging-BALBCvsC2J-MMAE185-Sample 4

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51173.gif
Type of label: reverse

value: 4M months


title: 8months C2J/BALBC-MMAE132-Sample 6

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54395.gif
Type of label: normal


title: U2OS_ERa_noDoxy_rep3

description: replicate 3

source_name: U2OS cells, ERa vector transfected without Doxycycline added


title: 4months C2J/BALBC-MMAE148-Sample 4

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54401.gif
Type of label: normal


title: 4M-Aging-BALBCvsC2J-MMAE178-Sample 2

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51027.gif
Type of label: reverse


title: U2OS_ERa_noDoxy_rep1

description: replicate 1


title: U2OS_ERa_noDoxy_rep2

description: replicate 2


title: 4months C2J/BALBC-MMAE140-Sample 1

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54398.gif
Type of label: normal


title: 4months C2J/BALBC-MMAE141-Sample 2

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54399.gif
Type of label: normal


title: P2M-4

city: Hershey

first: Wei

last: Ding

state: PA

address: 500 University Drive

department: Pediatrics

institute: Pennsylvania State University College of Medicine

description: Replicate 4

data_processing: Raw data was extracted from Illumina's Beadstudio v3.0. Normalization was done in Beadstudio v.3 using the Average Normalization method.  The data were then converted to t16 log2 ratios. This was done to generate sufficient number of data points for a one sample t-test (4 replicates for each sample; 4x4).  One sample t-test was performed using Tigr MEV v4.4 with p<0.05. Probe sets with at least a 1.4 fold were considered for the final candidate gene list.

source_name: Passage 2 cells mesenchymal

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

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

value: Pten Loxp/loxp;Alb-Cre

tag: genome/variation

value: Liver-specific Pten deletion

value: liver

tag: cell type

value: liver tumor cells

tag: cell morphology

value: mesenchymal

tag: cell passage


title: P2M-3

description: Replicate 3


title: P2M-2

description: Replicate 2


title: 8months C2J/BALBC-MMAE138-Sample 7

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54396.gif
Type of label: normal

tag: age


title: P2M-1

description: Replicate 1


title: 8months C2J/BALBC-MMAE131-Sample 5

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54382.gif
Type of label: normal


title: 8months C2J/BALBC-MMAE139-Sample 8

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54397.gif
Type of label: normal


title: P2E-4

description: Replicate 4

source_name: Passage 2 cells epithelial

value: epithelial


title: 4M-Aging-BALBCvsC2J-MMAE177-Sample 1

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51028.gif
Type of label: reverse


title: 4M-Aging-BALBCvsC2J-MMAE184-Sample 3

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51035.gif
Type of label: reverse


title: 8M-Aging- BALBCvsC2J-MMAE188-Sample 7

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51268.gif
Type of label: reverse


title: 8M-Aging-BALBCvsC2J-MMAE187-Sample 6

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51215.gif
Type of label: reverse


title: P2E-3

description: Replicate 3


title: P2E-2

description: Replicate 2


title: P2-4

description: Replicate 4

source_name: Passage 2 cells


title: MPCmd, MeDIP, Rep 1

hyb_protocol: Hybridization done by NimbleGen as per normal service protocol. Labeled DNA was hybridized on promoter arrays.

scan_protocol: Scanning done by NimbleGen as per normal service protocol.

data_processing: log2 (MeDIP/Input) with biweight mean of values subtracted.

source_name: MeDIP DNA, myogenic-differentiated MPC

label_protocol: Labeling done by NimbleGen as per normal service protocol.  Input and MeDIP DNA were labeled with Cy3 and Cy5, respectively.

growth_protocol: The muscle progenitors were differentiated with 2% horse serum in DMEM for 6 days.

extract_protocol: Genomic DNA was purified and fragmented by sonication to 300-500 bp fragments. 5-methylcytosine (5-mC)-enriched fragments were immunoprecipitated using anti-5mC antibodies (Diagenode). Precipitated and input DNA was amplified using the WGA2 kit (Sigma-Aldrich) and cleaned up.

treatment_protocol: Genomic DNA was isolated, fragmented and used for MeDIP.

value: myogenic-differentiated muscle progenitor cells

value: in vitro differentiated myocytes

tag: medip antibody

value: 5-methyl cytosine antibody

source_name: Input DNA, myogenic-differentiated MPC

extract_protocol: Genomic DNA was purified and fragmented by sonication to 300-500 bp fragments. Precipitated and input DNA was amplified using the WGA2 kit (Sigma-Aldrich) and cleaned up.

treatment_protocol: Genomic DNA was isolated, fragmented, labeled and hybridized onto arrays.


title: P2-2

description: Replicate 2


title: ASCad, MeDIP, Rep 1

source_name: MeDIP DNA, adipogenic-differentiated MSC

growth_protocol: The mesenchymal stem cells were differentiated with an adipogenic cocktail for 3 weeks.

value: adipogenic-differentiated mesenchymal stem cells

value: in vitro differentiated adipocytes

source_name: Input DNA, adipogenic-differentiated MSC


title: P1-3

description: Replicate 3

source_name: Passage 1 cells


title: 4months C2J/BALBC-MMAE142-Sample 3

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54400.gif
Type of label: normal


title: 8M-Aging-BALBCvsC2J-MMAE199-Sample 8

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51269.gif
Type of label: reverse


title: P2-1

description: Replicate 1


title: P1-2

description: Replicate 2


title: MPCmd, MeDIP, Rep 2


title: ASCad, MeDIP, Rep 2


title: P2-3

description: Replicate 3


title: P1-1

description: Replicate 1


title: P0-4

description: Replicate 4

source_name: Passage 0 cells


title: P0-2

description: Replicate 2


title: U2OS_ERa_Doxy_rep1

description: replicate 1


title: P1-4

description: Replicate 4


title: P2E-1

description: Replicate 1


title: P0-3

description: Replicate 3


title: P0-1

description: Replicate 1


title: MPCu, MeDIP, Rep 2

source_name: MeDIP DNA, undifferentiated skeletal MPC

growth_protocol: The muscle progenitors were cultured in Lonza commercial medium for up to 4-8 passages.

value: skeletal muscle

value: mesenchymal stem cells

value: undifferentiated

source_name: Input DNA, undifferentiated skeletal MPC

growth_protocol: The muscle progenitors were cultured in Lonza commerciall medium for up to 4-8 passages


title: HSCu, MeDIP, Rep 1

source_name: MeDIP DNA, undifferentiated bone marrow HPC

growth_protocol: The CD34+ hematopoietic progenitors were used in an uncultured state.

value: bone marrow

value: hematopoietic progenitor cells

source_name: Input DNA, undifferentiated bone marrow HPC


title: BMMSCu, MeDIP, Rep 2

source_name: MeDIP DNA, undifferentiated bone marrow MSC

growth_protocol: The mesenchymal stem cells were cultured for up to seven passages in DMEM/F12 containing 20% FCS and antibiotics.

source_name: Input DNA, undifferentiated bone marrow MSC


title: MPCu, MeDIP, Rep 1


title: HSCu, MeDIP, Rep 2


title: gapcp1gapcp2 with ABA, biological rep2

status: Public on May 11 2010

city: Burjassot

first: Roc

last: Ros

state: valencia

address: Vicent Andres Estelles

department: Biologia Vegetal

institute: Universitat de Valencia

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

hyb_protocol: Fragmented cRNA (15 μg) was added to 300 μL of hybridization solution, and 200 μL of this mixture was used for hybridization on Arabidopsis ATH1 Genome Arrays for 16 h at 45°C. The standard wash and double-stain protocols (EukGE-WS2v5-450) were applied using an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: The arrays (three replicates of each treatment) were scanned on an Affymetrix GeneChip scanner 3000.

data_processing: Fluorescence images were normalized with the software GCOS from Affymetrix. Data were analyzed and compared using the dChip software  ( http://www.hsph.harvard.edu/~cli/complab/dchip/)

organism: Arabidopsis thaliana

source_name: 15 day old whole seedling

label_protocol: The cRNA was labeled with biotin, and 20 μg of the labeled cRNA was fragmented. The size distribution of the cRNAs and fragmented cRNAs was assessed using an Eppendorf Biophotometer and electrophoresis.

growth_protocol: Seeds were germinated and grown vertically in MS 1/5 with Gamborg vitamins. Light condicitions: 16 hours light, 8 hours dark. Temperature: 22ºC. Light 100 μmol m−2 s−1.

extract_protocol: Total RNA was extracted using the RNeasy plant mini kit (Qiagen).RNA was extracted from three sets of gapcp double mutants and wild type plants grown at the same time. RNA integrity was determined using RNA 6000 Nano Labchips® in an Agilent 2100 Bioanalyzer following the manufactures protocol. The purified RNA (8 μg) was used to generate first-strand cDNA in a reverse transcription reaction (One-Cycle Target Labeling and Control Reagents; Affymetrix). After second-strand synthesis, the double-stranded cDNAs were used to generate cRNA via an in vitro transcriptional reaction.

treatment_protocol: Seedlings were treated with  0,75 microM ABA for 8 days

tag: genotype

tag: treatment

value: ABA

value: seedling

tag: ecotype


title: WT+NAM_B

city: Charlottesville

first: Jeffrey

middle: S

last: Smith

email: jss5y@virginia.edu, sb3de@virginia.edu

state: VA

address: 1340 Jefferson Park Avenue

department: Biochemistry and Molecular Genetics

institute: University of Virginia

description: Gene expression data from Wild type cells grown in YPD media with NAM to log phase

hyb_protocol: Following fragmentation, 4 ug of labeled cRNA were hybridized for 16 hr at 45°C on GeneChip Yeast Genome 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed using R/Bioconductor using GCRMA with default settings which include quantile normalization and probe specific background correction.

organism: Saccharomyces cerevisiae

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix one cycle eukaryotic target preparation protocol from 4 µg total RNA (GeneChip® Expression Analysis Technical Manual, 2005, Affymetrix). Approximately 100 µg of labeled cRNA was obtained from each sample.

growth_protocol: Each yeast strain was inoculated into 40 ml YPD media and grown into log phase (OD600 of ~0.5).

extract_protocol: Cells were thawed and total RNA extracted using the hot acid phenol method (Ausuble et al. (editors), 2000 Current Protocols in Molecular Biology. John Wiley & Sons, New York). RNA pellets were resuspended in RNAase-free water.

treatment_protocol: Cells were collected by centrifugation in an Eppendorf 5810R centrifuge at 4°C. The cell pellets were washed with ice cold water, transferred to microfuge tubes and flash frozen in liquid nitrogen.

tag: genotype/variation

value: MATa his3D200 leu2D1 met15D0 trp1D63 ura3-167

tag: growth stage

value: log phase

tag: growth protocol

value: YPD media with NAM


title: FAMA_4h-3

city: Stanford

first: Dominique

last: Bergmann

address: 371 Serra Mall

department: Biological Sciences

institute: Stanford University

description: Gene expression data from 5 day-old Arabidopsis seedlings, 4h EST induction

hyb_protocol: 20 µg of the resulting cRNA was used to hybridize to each ATH1 Arabidopsis GeneChip (Affymetrix) using the manufacturer’s protocols.

scan_protocol: standard Affymetrix protocol

data_processing: The array images were analyzed with the Affymetrix Microarray Suite 5.0 with the target intensity set to 500.

source_name: Whlole seedling, 4h Estrogen induction

label_protocol: Biotinylated complementary RNA (cRNA) was prepared with the bioarray high yield transcript labeling kit (Enzo)

growth_protocol: Sterilized seeds were sowed on MS + Sucrose plates, then keep at 4C for 3 days. Seedlings were grown on vertically oriented plates in a 22 C incubator under 24 hours light for 5 days.

extract_protocol: After 4h or 48h on new plates, samples were collected, frozen in liquid nitrogen and stored at –80 degree until enough material was obtained to do all RNA extractions in the same week.  The Rneasy Plant Mini Kit (QIAGEN) for RNA isolation,

treatment_protocol: Seedlings were transfered with forcepts to plates conatinin MS + Sucrose + 10 μM estrogen  (or new MS + sucrose plates for controls).

value: Columbia

value: Whole seedling

value: 5 day old

tag: time

tag: expression

value: FAMA


title: WT_B (ML8_B)

description: Gene expression data from Wild type cells grown in YPD media to log phase

value: YPD media


title: gapcp1gapcp2 with ABA, biological rep1

tag: tissue


title: WT+NAM_A

source_name: Wild type cells grown in YPD media with NAM to log phase


title: ASCu, MeDIP, Rep 1

source_name: MeDIP DNA, undifferentiated adipose MSC

growth_protocol: The mesenchymal stem cells were cultured for seven passages in DMEM/F12 containing 20% FCS and 1% PenStrep.

value: adipose tissue

tag: differentiation

value: 5-methyl cytosine antibody

source_name: Input DNA, undifferentiated adipose MSC


title: wild type with ABA, biological rep1

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

value: wild type


title: wild type with ABA, biological rep2


title: wild type with ABA, biological rep3


title: ASCu, MeDIP, Rep 2

value: mesenchymal stem cells


title: bna1D_B

description: Gene expression data from bna1∆ strain grown in YPD media to log phase

value: MATa his3D200 leu2D1 met15D0 trp1D63 ura3-167 bna1D::kanMX4


title: BMMSCu, MeDIP, Rep 1

value: bone marrow

value: undifferentiated


title: tna1D_B

description: Gene expression data from tna1∆ strain grown in YPD media to log phase

value: MATa his3D200 leu2D1 met15D0 trp1D63 ura3-167 tna1D::kanMX4


title: tna1D_A

source_name: tna1∆ strain grown in YPD media to log phase


title: gapcp1gapcp2 with ABA, biological rep3

value: ABA

value: seedling


title: pnc1D_B

description: Gene expression data from pnc1∆ strain grown in YPD media to log phase

value: MATa his3D200 leu2D1 met15D0 trp1D63 ura3-167 pnc1D::kanMX4

value: log phase


title: MSC_H3K4me3_rep2

description: ChIP-chip H3.3 EGFP transfected mesenchymal stem cells, Antibody: H3K4me3 (Abcam)

hyb_protocol: Hybridization done by Nimblegen as per normal service protocol

scan_protocol: Scanning done by Nimblegen as per normal service protocol

data_processing: log2 (ChIP/Input) with biweight mean of values subtracted

source_name: H3K4me3 ChIP DNA from mesenchymal stem cells

label_protocol: Labeling done by Nimblegen as per normal service protocol

extract_protocol: Histone ChIPs were done as described (Dahl, Collas, 2007) using 0.5 A260 units chromatin per ChIP. In short, cells were cross-linked in suspension with 1% formaldehyde for 8 min and quenched with glycine. Lysis buffer was added to ~120 µl and samples incubated for 5 min on ice. Cells were sonicated for 14 x 30 sec on ice with 30 sec pauses using a probe sonicator to produce fragments of ~400-500 bp. The lysate was centrifuged, the supernatant collected, chromatin diluted to 0.5 A260 units and 100 µl was incubated with 2.4 μg antibody coupled to Dynabeads Protein A (Invitrogen) for 2 h at 4oC. ChIP material was washed as described [46]. Elution buffer containing 1 % SDS and 50 µg/ ml Proteinase K was added and samples incubated for 2 h at 68oC on a Thermomixer (Eppendorf); after a second extraction both supernatants were pooled. ChIP DNA was purified by phenol-chloroform isoamylalcohol extraction, ethanol-precipitated and dissolved in 50 μl TE buffer. EGFP and H3.3-EGFP were immunoprecipitated from transfected and sorted cells as above, using 50 µl Dynabeads Protein G (Invitrogen) and 5 µl Living Colors® anti-EGFP antibody and 2 A260 units of chromatin per ChIP. For ChIP-on-chip 5 µg (10 µl) RNase A (Roche) was added before ChIP DNA elution. ChIP DNA samples were dissolved in 10 μl MilliQ water.

treatment_protocol: The mesenchymal stem cells were transfected with H3.3-EGFP and sorted by FACS 168 hrs post transfection.

value: Mesenchymal stem cells

value: Adipose tissue

tag: chip antibody

value: H3K4me3 (Abcam)

source_name: Input DNA from H3.3-EGFP transfected mesenchymal stem cells

value: none (input DNA)


title: bna1D_A

source_name: bna1∆ strain grown in YPD media to log phase

value: YPD media


title: WT_A (ML8_A)

source_name: Wild type cells grown in YPD media to log phase

value: MATa his3D200 leu2D1 met15D0 trp1D63 ura3-167


title: pnc1D_A

source_name: pnc1∆ strain grown in YPD media to log phase


title: ASCu Rep 2

description: ASCu Rep 2

source_name: Adipose MSC ChIP DNA

extract_protocol: Genomic DNA was purified and fragmented by sonication to 300-500 bp fragments. 5-methylcytosine (5-mC)-enriched fragments were immunoprecipitated using anti-5mC antibodies. Precipitated and input DNA was amplified using the WGA2 kit (Sigma-Aldrich) and cleaned up. Input and MeDIP DNA were labeled with Cy3 and Cy5 respectively and hybridized on promoter arrays.

value: 5-methyl cytosine antibody, Diagenode

value: none, input DNA


title: npt1D_A

description: Gene expression data from npt1∆ strain grown in YPD media to log phase

value: MATa his3D200 leu2D1 met15D0 trp1D63 ura3-167 npt1D::kanMX4


title: MSC_EGFP-H3.3_rep1

description: ChIP-chip H3.3 EGFP transfected mesenchymal stem cells, Antibody: EGFP (Clontech)

source_name: H3.3-EGFP ChIP DNA from mesenchymal stem cells

value: EGFP (Clontech)


title: MSC_H3K9me3_rep2

description: ChIP-chip H3.3 EGFP transfected mesenchymal stem cells, Antibody: H3K9me3 (Diagenode)

source_name: H3K9me3 ChIP DNA from mesenchymal stem cells

value: H3K9me3 (Diagenode)


title: HeLa 4h IFN-gamma

city: Berlin

first: Elke

last: Krueger

address: Monbijoustr. 2

department: Institute of Biochemistry

institute: Charité Universitaetsmedizin Berlin

description: Gene expression data from monocyte-derived dendritic cells 4 hours after stimulation with IFN-gamma

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133  Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the EukGE-WS_v5_450 protocol

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

data_processing: The data were analyzed with GeneChip Operating Software version 1.4.0.036 (MAS 5.0) using Affymetrix default analysis settings. Normalization was performed by GCRMA.

source_name: HeLa cells stimulated for 4h with IFN-gamma

label_protocol: Total RNA was amplified and labelled using Message AmpII-Biotin enhanced Kit, Ambion

growth_protocol: human HeLa cells were grown under standard conditions in Basal Iscove´s medium containing 10% fetal calf serum (FCS), 2 mM L-glutamine 100 U/ml penicillin and 100µg/ml streptomycin.

extract_protocol: Total RNA was extracted from frozen cell pellets using the High Pure RNA Isolation kit according to the manufacturer’s (Roche) protocol.

treatment_protocol: 1×106 cells/ml were treated with 100 U/ml of human IFN-gamma (recombinant, Roche) for 2, 4, or 6 hours.

value: HeLa

tag: agent

value: IFN-gamma

tag: time point


title: HeLa 2h IFN-gamma

description: Gene expression data from monocyte-derived dendritic cells 2 hours after stimulation with IFN-gamma

source_name: HeLa cells stimulated for 2h with IFN-gamma

tag: cell type


title: WT_B (ML1_B)


title: WT_A (ML1_A)


title: npt1D_B

source_name: npt1∆ strain grown in YPD media to log phase


title: ASCu Rep 1

description: ASCu Rep 1


title: MSC_EGFP-H3.3_rep2


title: MSC_H3K4me3_rep1


title: BCR-ABL1-transformed pre-B cells - STI571 treated in presence of IL-7 rep 3

status: Public on May 10 2010

city: Los Angeles

first: Markus

last: Müschen

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

institute: University of Southern California

description: BCR-ABL1-transformed pre-B cells were incubated with Interleukin-7 (10 ng/ml) and 10 µM STI571 (Imatinib) for 16 hours

hyb_protocol: Standard Affymetrix protocols (see GeneChip Expression Analysis Technical Manual)

data_processing: RMA

source_name: Extracted bone marrow cells from a Slp65-/- mouse

label_protocol: Standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. The complete protocol is available on the manufacturer's web site.

extract_protocol: Extraction Method: Qiagen_RNeasy_Kit

tag: cell treatment

value: large pre-B cells

tag: genetic background

value: BALB/c

value: bone marrow


title: MSC_H3K9me3_rep1


title: MSC_H3K27me3_rep1

description: ChIP-chip H3.3 EGFP transfected mesenchymal stem cells, Antibody: H3K27me3 (Upstate)

source_name: H3K27me3 ChIP DNA from mesenchymal stem cells

value: H3K27me3 (Upstate)


title: BCR-ABL1-transformed pre-B cells - STI571 treated in presence of IL-7 rep 2

scan_protocol: Standard Affymetrix protocols (see GeneChip Expression Analysis Technical Manual)


title: MSC_H3K27me3_rep2

value: Mesenchymal stem cells


title: sip2gal83 deletion_biological rep1

city: Kgs. Lyngby

first: Jie

last: Zhang

address: Kemitorvet 220

department: CFB

country: Denmark

institute: Technical University of Denmark

description: sip2gal83 deletion_biological rep1

hyb_protocol: Hybridization was done according to the Affymetrix GeneChip Expression Analysis Technical Manual on a GeneChip Fluidics Station FS-400.

scan_protocol: Scanning was done according to the Affymetrix GeneChip Expression Analysis Technical Manual on a GeneChip Scanner 3000.

data_processing: Affymetrix CEL-data files were preprocessed using the statistical language and environment R Language version 2.6. The probe intensities were normalised for background using the robust multiarray average (RMA) method (Irizarry, 2003) using only perfect match (PM) probes. Normalization was performed subsequently using the qspline algorithm (Workman, 2002). Gene expression values were calculated from the PM probes with the medianpolish summary method (Irizarry, 2003). All statistical preprocessing methods were used by invoking them through the affy package (Gautier, 2004).

source_name: sip2gal83 deletion_biological rep1

label_protocol: Labelling was done according to the Affymetrix GeneChip Expression Analysis Technical Manual.

growth_protocol: strains were grown in 1 liter bioreactor at 30°C, pH 5.0 and aerobically, 10 g/L glucose, dilution rate 0.1h-1

extract_protocol: Total RNA was isolated from frozen cell pellets using FastRNA® Pro RED kit (QBiogene, Inc, USA)

treatment_protocol: biomass samples were taken at steadystate, cooled down immediately and centrifuged with cooling. The cell pellets were frozen in liquid nitrogen.

value: sip2Δ gal83Δ


title: sip2gal83 deletion_biological rep2

description: sip2gal83 deletion_biological rep2

source_name: sip2gal83 deletion_biological rep2


title: sip1sip2gal83 deletion_biological rep3

description: sip1sip2gal83 deletion_biological rep3

source_name: sip1sip2gal83 deletion_biological rep3

value: sip1Δ sip2Δ gal83Δ


title: IL-7-dependent pre-B cells - withdrawal of IL-7 rep 1

description: IL-7-dependent large pre-B cells were induced to differentiate by withdrawal of IL-7. Cells were harvested after 16 hours


title: BCR-ABL1-transformed pre-B cells - STI571 treated rep 2

description: BCR-ABL1-transformed pre-B cells were incubated with 10 µM STI571 (Imatinib) for 16 hours


title: BCR-ABL1-transformed pre-B cells - STI571 treated in presence of IL-7 rep 1


title: HeLa 6h IFN-gamma

description: Gene expression data from monocyte-derived dendritic cells 6 hours after stimulation with IFN-gamma

source_name: HeLa cells stimulated for 6h with IFN-gamma


title: sip2gal83 deletion_biological rep3

description: sip2gal83 deletion_biological rep3

source_name: sip2gal83 deletion_biological rep3


title: sip1gal83 deletion_biological rep3

description: sip1gal83 deletion_biological rep3

source_name: sip1gal83 deletion_biological rep3

value: sip1Δ gal83Δ


title: sip1sip2gal83 deletion_biological rep1

description: sip1sip2gal83 deletion_biological rep1

source_name: sip1sip2gal83 deletion_biological rep1


title: sip1sip2gal83 deletion_biological rep2

description: sip1sip2gal83 deletion_biological rep2

source_name: sip1sip2gal83 deletion_biological rep2


title: BCR-ABL1-transformed pre-B cells - STI571 treated rep 3


title: BCR-ABL1-transformed pre-B cells - STI571 treated rep 1


title: IL-7-dependent pre-B cells rep 3

description: IL-7-dependent large pre-B cells were cultured in presence of IL-7 (10 ng/ml).

value: IL-7-dependent pre-B cells


title: HeLa cells unstimulated

description: Gene expression data from unstimulated monocyte-derived dendritic cells

source_name: unstimulated human HeLa cells


title: IL-7-dependent pre-B cells rep 1


title: IL-7-dependent pre-B cells - withdrawal of IL-7 rep 2


title: IL-7-dependent pre-B cells rep 2


title: sip1gal83 deletion_biological rep2

description: sip1gal83 deletion_biological rep2

source_name: sip1gal83 deletion_biological rep2


title: BCR-ABL1-transformed pre-B cells rep 1

description: BCR-ABL1-transformed pre-B cells

value: BCR-ABL1-transformed pre-B cells


title: sip1gal83 deletion_biological rep1

description: sip1gal83 deletion_biological rep1

source_name: sip1gal83 deletion_biological rep1


title: sip1sip2 deletion_biological rep1

description: sip1sip2 deletion_biological rep1

source_name: sip1sip2 deletion_biological rep1

value: sip1Δ sip2Δ


title: sip1sip2 deletion_biological rep2

description: sip1sip2 deletion_biological rep2

source_name: sip1sip2 deletion_biological rep2


title: gal83 deletion_biological rep3

description: gal83 deletion_biological rep3

source_name: gal83 deletion_biological rep3


title: IL-7-dependent pre-B cells - withdrawal of IL-7 rep 3


title: sip1sip2 deletion_biological rep3

description: sip1sip2 deletion_biological rep3

source_name: sip1sip2 deletion_biological rep3


title: BCR-ABL1-transformed pre-B cells rep 3

description: BCR-ABL1-transformed pre-B cells

source_name: Extracted bone marrow cells from a Slp65-/- mouse


title: BCR-ABL1-transformed pre-B cells rep 2

description: BCR-ABL1-transformed pre-B cells


title: gal83 deletion_biological rep1

description: gal83 deletion_biological rep1

source_name: gal83 deletion_biological rep1


title: sip1 deletion_biological rep2

description: sip1 deletion_biological rep2

source_name: sip1 deletion_biological rep2


title: reference strain_biological rep3

description: reference strain_biological rep3

source_name: reference strain_biological rep3

value: wild type


title: sip1 deletion_biological rep1

description: sip1 deletion_biological rep1

source_name: sip1 deletion_biological rep1


title: reference strain_biological rep2

description: reference strain_biological rep2

source_name: reference strain_biological rep2


title: sip2 deletion_biological rep3

description: sip2 deletion_biological rep3

source_name: sip2 deletion_biological rep3


title: reference strain_biological rep1

description: reference strain_biological rep1

source_name: reference strain_biological rep1


title: sip2 deletion_biological rep2

description: sip2 deletion_biological rep2

source_name: sip2 deletion_biological rep2


title: gal83 deletion_biological rep2

description: gal83 deletion_biological rep2

source_name: gal83 deletion_biological rep2


title: sip2 deletion_biological rep1

description: sip2 deletion_biological rep1

source_name: sip2 deletion_biological rep1


title: sip1 deletion_biological rep3

description: sip1 deletion_biological rep3

source_name: sip1 deletion_biological rep3


title: K42A_replicate1

city: Baltimore

first: Edel

middle: Maria

last: Hyland

state: MD

address: 733 North broadway, Rm 320

department: Molecular Biology and Genetics

institute: Johns Hopkins School of MEdicine

description: Hybridization was performed by the Johns Hopkins Medical Institutions Microarray Core Facility.

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual, 2004.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual, 2004.

data_processing: Image analysis using GCOS 1.4, using MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.

source_name: Saccharomyces cerevisiae expressing mutant histone H3 protein

label_protocol: One round amplification protocol for total RNA following Affymetrix’ specifications using T7 promoter oligo dT primer for cDNA synthesis, and ENZO IVT kit (www.affymetrix.com, GeneChip Expression Analysis, Technical Manual, 2003).

growth_protocol: Cells were grown in rich YPD media to log phase and then harvested.

extract_protocol: Hot phenol followed by RNeasy Kit (QIAGEN)

treatment_protocol: Site directed mutagenesis was employed to change amino acid number 42 from lysine to alanine on an plasmid borne (pEMH7) histone H3 protein.

tag: strain

tag: genome/variation

value: expressing plasmid borne histone H3 protein encoding the substitutions K42A


title: wild-type_replicate3

source_name: Saccharomyces cerevisiae expressing wild-type histone protein

treatment_protocol: No treatment.

value: expressing plasmid borne histone H3 protein encoding the wild-type sequence


title: K42L_replicate2

treatment_protocol: Site directed mutagenesis was employed to change amino acid number 42 from lysine to leucine on an plasmid borne (pEMH7) histone H3 protein.

value: expressing plasmid borne histone H3 protein encoding the substitutions K42L


title: wild-type_replicate1

treatment_protocol: No treatment


title: K42Q_replicate1

treatment_protocol: Site directed mutagenesis was employed to change amino acid number 42 from lysine to glutamine on an plasmid borne (pEMH7) histone H3 protein.

value: expressing plasmid borne histone H3 protein encoding the substitutions K42Q


title: wild-type_replicate2


title: K42A_replicate2


title: K42L_replicate1


title: K42Q_replicate2


title: Diff.-FX-ES

city: Ramat Gan

first: Achia

last: Urbach

address: Bar Ilan

department: Faculty of Life Sciences

country: Israel

institute: Bar Ilan University

description: teratoma derived cells line from the FX-ES cells

hyb_protocol: standard Affymetrix protocol

label_protocol: standard Affymetrix protocol

extract_protocol: standard Affymetrix protocol

value: teratoma cell line

tag: sample type


title: Nonspecific siRNA4

status: Public on May 09 2010

city: Nashville

first: Yan

last: Guo

state: TN

address: 639 Preston Research Bld

institute: Vanderbilt Cancer Center

hyb_protocol: Following fragmentation, the RNA was loaded on to the Affymetrix HuGene-1_0-st-v1 GeneChip as directed (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 7G

data_processing: The primary microarray data was normalized using RMA method in Affymetrix Expression Console 1.1 and annotated using latest annotation file based on genome version hg19.  The analysis was done in R using LIMMA package.

source_name: Nonspecific siRNA

label_protocol: The RNA was labeled with GeneChipR One-Cycle Target Labeling and Control Reagents.

growth_protocol: The cell lines were grown in DMEM + 7.5% FBS

extract_protocol: Total RNA was isolated from the cell lines using Qiagen RNeasy Mini kit as directed (Qiagen, Valencia, CA). The quality and quantity of the RNA was determined using the Agilent RNA 6000 NanoLabChip kit and Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: U2OS cells were transfected with siRNA against NT (non-targeting) or CDK9 at 10 nM using Hi-Perfect (Qiagen) and harvested 72 hours after transfection.

tag: cell line

tag: tissue type

value: osteosarcoma


title: Nonspecific siRNA1