title: WR_52hpf_rep3

description: Wild type retina, 52hpf, pool of ten tissues, biological replicate 3

value: Retina


title: tumor_pat016_T0

status: Public on Jan 03 2014

type: RNA

city: Granada

first: Carlos

last: Cano

address: Periodista Daniel Saucedo Aranda S.N.

country: Spain

institute: University of Granada

description: CRT: Chemoradiation; Cap: Capecitabine; Capox: Capecitabine and Oxaliplatine; cTN: clinical stage; Surg: surgical technique; LAR: Low anterior resection; APR: Abdmino-perineal resection; HART: Hartmann, TRG: Tumor Regression Grade; Downst: Downstaging; Downs: downsizing, Resp: response, CPR: complete pathologic response

hyb_protocol: Hybridization of whole genome human genes included in CodeLink bioarrays (Applied Microarrays, Tempe, AZ, USA) was performed overnight at 37°C in a shaker incubator (Innova 4080, New Brunswick®, NJ, U.S.A.). The hybridization reactions were done in duplicate.

scan_protocol: Microrrays were read with a GenePix 4000B laser scanner (Axon Instruments, CA, USA)

data_processing:
Microrrays were read, quantified and normalized using CodeLink Software 5.0 (Applied Microarrays, Tempe, AZ, USA). Only probes of type ’DISCOVERY’ were taken into account. Negative values for signal intensities were set to 0,0. Probes with missing values for any array were disregarded. Probes were identified by the Codelink Probe IDs (GE-XXXX).
For patients with 2 replicates, average values were computed.

molecule: total RNA

organism: Homo sapiens

source_name: tumor sample from rectal cancer patient

label_protocol: reverse transcription cRNAs were labeled with Cy5 Streptavidine (Amersham Biosciences, Sweden)

extract_protocol: Frozen sample materials were provided by the Tissue and Tumor Bank, Department of Pathology at the Virgen de las Nieves Hospital. RNAs were extracted from macrodissected frozen samples according to standard procedures using Rnesasy minikit (Qiagen Sciences). Quantity and integrity of RNAs were checked by spectrophotometry in a NanoDropTM (ND-1000, DE, USA) and in an ExperionTM automated electrophoresis system (Bio-Rad, Richmond, VI, USA), respectively. Prior to extraction, 8 µm section were stained with hematoxylin and eosin for microscopic examination to check the percentage of tumor cells. The percentage of tumor cells was estimated by an experienced pathologist in each case via visual inspection.

treatment_protocol: The study included a total of 35 consecutive patients with locally advanced rectal cancer treated at Virgen de las Nieves Hospital from 2008 until 2010. Written informed consent was obtained from all the patients, and the study protocol was approved by the local Clinical Research (Ethics) Committee. They were distributed in two subgroups following a histological classification of response to treatment.  Pretherapeutic staging was performed, including complete medical history and physical evaluation, digital rectal examination, endorectal ultrasound, rigid rectoscopy, colonoscopy, PET/TC and chest x-ray. Tumor samples were prospectively obtained during the rectoscopy. All patients subsequently received a total dose of 50.4Gy of radiatio (28 fractions of 1.8Gy) associated with capecitabine or capecitabine  and oxaliplatine. Standardized surgery was performed, including total mesorectal excision, after an interval of 8 weeks after chemoradiotherapy.   Tumor response was assessed in surgical specimen by semi-quantitative pathological examination (regression grade) including UICC stage. Histopathological tumor regression was graded based on the semiquantitative 5 point tumor regression grading (TRG) system: TRG1 or a TRG2 scores were considered Responders, whereas TRG3, TRG4, and TRG5 scores were classified as Non-Responders. In addition, the tumor regression or radiotherapy effects were assessed by positron emission tomography (18F-FDG PET).   Tumor samples of LARC were collected from 35 patients. Nine patients were finally excluded due to the poor quality of the RNA or contradictory results of Mandard´s criteria and histopathological downstaging.

tag: Sex

value: male

tag: age (yrs)

tag: crt

value: Cape

tag: ctn

tag: surg

value: LAR

tag: trg

tag: downst

value: YES

tag: downs

tag: resp

value: NO

tag: cpr


title: JEV_1

city: Aurora

first: Tzu Lip

last: Phang

state: CO

address: 12700 East 19th Avenue

department: Medicine

country: USA

institute: University of Colorado, Denver

description: Adult mice infected with 100 PFU JEV (P3) by ic inoculation.

hyb_protocol: Affymetrix Eukaryotic Target Hybridization protocol (GeneChip¨ Expression Analysis Technical Manual).

scan_protocol: Affymetrix¨ GeneChip¨ Scanner 3000 with GCOS software according to manufacturer's protocol (GeneChip¨ Expression Analysis Technical Manual).

data_processing: Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) using the R/Bioconductor package affy.

label: Biotin

organism: Mus musculus

source_name: whole brain, JEV infection

label_protocol: Affymetrix GeneChip¨ IVT Labeling Kit, according to manufacturer's protocol (GeneChip¨ Expression Analysis Technical Manual).

growth_protocol: None.

extract_protocol: TRIzol (Invitrogen) followed by RNeasy column cleanup (Qiagen) using the manufacturers' protocols.

treatment_protocol: Adult mice were infected with 100 PFU virus by ic inoculation.

tag: strain/background

value: Swiss Webster

tag: tissue

value: whole brain

tag: treatment

value: Japanese encephalitis virus (JEV) infection


title: tumor_pat012_T0

value: female

value: HART


title: J744 SWCNT 2

city: Aarhus

first: Christiane

last: Beer

address: Bartholinsalle 2

department: Department of Public Health

country: Denmark

institute: Aarhus University

description: Gene expression from carbon nanotube treated cells

hyb_protocol: was hybridized overnight to the GeneChip Human Gene 2.0 ST Arrays or GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix).

scan_protocol: according to affymetrix

data_processing: Quality control was performed in the Expression Console software (Affymetrix) where control probe sets along with labeling and hybridization control in data were analyzed. Furthermore, to evaluate the biological similarity of all samples, principal component analysis and hierarchical clustering (using Euclidian distance and centroid linkage) were performed. Data were quantile normalized in the GeneSpring GX 11.5 software (Agilent) using the iterPLIER16 algorithm.

source_name: J774 cell line, standard cultivation

label_protocol: The Ambion WT Expression Kit (Ambion) was used to label 100 ng total RNA according to the manufacturer’s instructions

growth_protocol: Cells were seeded in T-75 cell culture flasks and the next day the cells (80% confluency) were treated with 10 µg SWCNTs /mL media for 24 hours.

extract_protocol: Total RNA was isolated after 24 hours of exposure using Qiagen RNA easy mini kit as described by the manufacturer.

treatment_protocol: Cells were treated with 10 µg SWCNTs /mL media for 24 hours. The same volume ddH2O was added as control.

tag: protocol

value: exposure for 24 hours to 10 µg/ml single-walled carbon nanotubes


title: J744 SWCNT 1


title: YR_52hpf_rep1

city: West Lafayette

first: Yuk Fai

last: Leung

state: IN

address: 915 W. State Street

department: Biological Sciences

institute: Purdue University

description: Young (smarca4) mutant retina, 52hpf, pool of ten tissues, biological replicate 1

hyb_protocol: Hybridization, washing and staining were done according to a standard procedure from Affymetrix.

scan_protocol: Scanning was done according to a standard procedure from Affymetrix.

data_processing: The probe-level data were background adjusted, normalized and summarized by a Robust Multi-array Average (RMA) algorithm implemented in the software package affy of the Bioconductor project release 1.7 (http://www.bioconductor.org), running in the R statistical environment version 2.2.0 (http://www.r-project.org) using default parameters.

organism: Danio rerio

label_protocol: Affymetrix GeneChip Two-Cycle Target Labeling protocol.

growth_protocol: Fish and embryos were maintained according to Westerfield, M. The zebrafish book. A guide for the laboratory use of zebrafish (Danio rerio), 4th edition. University of Oregon Press, Eugene, 2000.

extract_protocol: Total RNA was extracted from the pooled samples according to: Leung YF, Dowling JE. Gene Expression Profiling of Zebrafish Embryonic Retina. Zebrafish 2005:2:269-283.

treatment_protocol:
The tissues were dissected from developing embryos according to: Zhang L, Leung YF. Microdissection of zebrafish embryonic eye tissues. J Vis Exp. 2010;(40). doi:pii: 2028. Then, the tissues were pooled as one biological replicate.
see sample section

tag: strain

value: AB

tag: genotype

value: young (smarca4)

tag: age


title: JEV_2


title: WR_52hpf_rep1

description: Wild type retina, 52hpf, pool of ten tissues, biological replicate 1

value: Wild-type


title: tumor_pat014_T0

tag: Sex

value: Capox

value: APR


title: J744 control 1

description: Gene expression from water control

value: no exposure, water control


title: WR_52hpf_rep2

description: Wild type retina, 52hpf, pool of ten tissues, biological replicate 2

value: Retina


title: tumor_pat011_T0

value: male

tag: age (yrs)

value: Cape


title: YA_52hpf_rep3

description: Young (smarca4) mutant whole embryos, 52hpf, pool of ten embryos, biological replicate 3

source_name: Young (smarca4) mutant whole embryo, 52hpf, pool of ten embryos

treatment_protocol:
Ten embryos were collected according to: Leung YF, Ma P, Link BA, Dowling JE. Factorial microarray analysis of zebrafish retinal development. Proc Natl Acad Sci U S A. 2008 Sep 2;105(35):12909-14. Then, the samples were pooled as one biological replicate. The young (smarca4) mutants were staged by staging their wild-type siblings.
see sample section

value: Whole embryo


title: YA_52hpf_rep1

description: Young (smarca4) mutant whole embryos, 52hpf, pool of ten embryos, biological replicate 1


title: YA_52hpf_rep2

description: Young (smarca4) mutant whole embryos, 52hpf, pool of ten embryos, biological replicate 2


title: tumor_pat013_T0

tag: crt

value: LAR

value: YES


title: tumor_pat008_T0

tag: ctn

value: NO


title: WA_52hpf_rep3

description: Wild type whole embryos, 52hpf, pool of ten embryos, biological replicate 3

source_name: Wild type whole embryo, 52hpf, pool of ten embryos


title: tumor_pat010_T0

tag: surg


title: tumor_pat009_T0

tag: trg


title: tumor_pat006_T0

tag: downst


title: WA_52hpf_rep1

description: Wild type whole embryos, 52hpf, pool of ten embryos, biological replicate 1


title: WNV_B6

description: Adult mice infected with 100 PFU WNV (NY99) by ic inoculation.

source_name: whole brain, WNV infection

value: Swiss Webster

value: whole brain

value: West Nile virus (WNV) infection


title: tumor_pat005_T0

value: female

tag: downs


title: J744 control 2

description: Gene expression from water control


title: YR_52hpf_rep2

description: Young (smarca4) mutant retina, 52hpf, pool of nine tissues, biological replicate 2

value: AB


title: tumor_pat007_T0

tag: resp


title: YR_52hpf_rep3

description: Young (smarca4) mutant retina, 52hpf, pool of ten tissues, biological replicate 3

value: young (smarca4)


title: tumor_pat004_T0

tag: cpr


title: MCF7-RON/MSP-shMBD4_3

status: Public on Jan 02 2014

city: Salt Lake City

first: Stephanie

last: Cunha

state: Utah

address: 2000 Circle of Hope

department: Oncological Science

institute: Huntsman Cancer Institute, University of Utah

description: RON and MSP were stably expressed in MCF7 cells by retroviral infection (Liu et al., 2011). MCF7-RON/MSP cell line was infected with lentiviral constructs that direct the synthesis of shRNA for MBD4. Triplicate biological replicates of hybridization were performed for each cell line.

hyb_protocol: Microarray hybridizations were performed using Agilent SureHyb Hybridization chambers.  Hybridization chambers were loaded onto a rotisserie in an Agilent Hybridization oven and were incubated at 65ºC for 17 hours with a rotational speed of 10 rpm.  Following incubation, the microarray slide was washed for 1 minute each in Gene Expression Wash Buffer 1 (6X SSPE, 0.005% N-lauroylsarcosine; room temperature) and Gene Expression Wash Buffer (0.06X SSPE, 0.005% N-lauroylsarcosine; 31ºC) for 1 minute each.  Microarray slides were briefly dipped in a solution of acetonitrile and dried.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 um resolution.  The scanner performs detection of Cyanine-3 signal on the hybridized slide.

data_processing: TIF files generated from the scanned microarray image are loaded into Agilent Feature Extraction Software version 10.5.  The software automatically positions a grid and finds the centroid positions of each feature on the microarray.  This information is used to perform calculations that include feature intensities, background measurements and statistical analyses.  Data generated by the software is recorded as a tab-delimited text file

label_protocol: The Agilent Quick Amp Labeling Kit is used to generate fluorescently labeled cRNA for one-color microarray hybridizations.  Agilent RNA spike-in controls are combined with input total RNA samples (50 to 1000 ng).  The polyadenylated fraction of the total RNA sample is primed with oligo dT/T7 RNA polymerase promoter oligonucleotide sequences and cDNA synthesis is accomplished through the addition of MMLV-RT.   Following cDNA synthesis, T7 RNA polymerase and dye-labeled nucleotides are combined with the reaction mixture to simultaneously amplify the target material through the generation of cRNA and incorporate cyanine 3-CTP.  Fluorescently labeled, cRNA molecules are purified from the reaction mixture using the Qiagen RNeasy mini kit.  The concentration of the purified samples is determined using a NanoDrop ND-1000 spectrophotometer. Fluorescently labeled cRNA samples (825 ng each) were fragmented and combined with Agilent Hi-RPM Hybridization Buffer.

extract_protocol: Total RNA for gene expression analysis by microarray  was isolated with the RNeasy Kit (Qiagen) and tested for integrity on RNA 6000 NanoChips using an Agilent 2100 Bioanalyzer.

tag: cell line

value: RON and MSP and shMBD4


title: tumor_pat003_T0


title: MCF7-RON/MSP_4

value: RON and MSP


title: WA_52hpf_rep2

description: Wild type whole embryos, 52hpf, pool of ten embryos, biological replicate 2

value: Wild-type

tag: tissue


title: hPTTG1-transfected hPTTG1-/- HCT116 cells, rep1

city: Hualien

first: Yi Chu

last: Liao

address: Rm. D416, No.701, Sec. 3, Zhongyang Rd.

country: Taiwan

institute: Tzu Chi University

hyb_protocol: A total of 10 mg of labeled cRNA from each RT-IVT reaction was hybridized onto Applied Biosystems Human Genome Survey Microarrays following the manufacturer’s recommendations.

scan_protocol: Microarrays were analyzed using the AB1700 Chemiluminescent Microarray Analyzer.

data_processing: Detectable calls for gene expression were based on Applied Biosystems recommendations (signal/noise ratio >3.0 and FLAG values <5000).

label: biotin

source_name: hPTTG1-/- HCT116 human colorectal cancer cell line

label_protocol: One mg of total RNA from each sample was used to synthesize DIG-labeled cRNA as described by the Applied Biosystems Chemiluminescent RT-IVT Labeling protocol (Applied Biosystems, Foster City, CA)

growth_protocol: cells were cultured in McCoy's medium containing 100 µg/ml hygromycin under 37℃ and 5% CO2.

extract_protocol: Total RNA was extracted by Trizol reagent ( Invitrogen, USA).

treatment_protocol: hPTTG1-null was PCR-amplified from the cDNA of 293T cells and then subcloned into a pcDNA3.1 vector (Invitrogen). hPTTG1-null HCT116 cells were transfected with 4 µg  pcDNA3.1-hPTTG1 expression plasmids using Lipofectamine 2000 (Invitrogen) and then selected with hygromycin (100 µg/ml).

tag: sample type

value: HCT116 (CCL-247) with hPTTG1 gene knockout, transfected with pcDNA3.1-hPTTG1

tag: passage

value: within 10

tag: transfection


title: tumor_pat015_T0

value: male

value: Capox

value: HART


title: hPTTG1-/- HCT116 control cells, rep1

treatment_protocol: hPTTG1-null HCT116 cells were transfected with 4 µg pcDNA3.1 plasmids using Lipofectamine 2000 (Invitrogen) and then selected with hygromycin (100 µg/ml).

value: HCT116 (CCL-247) with hPTTG1 gene knockout, transfected with pcDNA3.1

tag: genotype


title: hPTTG1-transfected hPTTG1-/- HCT116 cells, rep2


title: MCF7-RON/MSP-shMBD4_2

tag: treatment


title: MCF7-RON/MSP_3


title: MCF7-RON/MSP-shMBD4_1


title: MCF7_4


title: MCF7_3


title: MCF7-RON/MSP_1


title: MCF7_2


title: tumor_pat002_T0

tag: Sex

value: Cape

value: LAR

value: YES


title: MCF7_1


title: MCF7-RON/MSP_2


title: tumor_pat001_T0

tag: age (yrs)

value: NO


title: normal breast tissue_5437

city: Taipei

first: King-Jen

last: Chang

address: No.1, Changde St., Zhongzheng Dist.

department: Department of Surgery

institute: National Taiwan University Hospital

hyb_protocol: Agilent Oligo Microarray Kit, hybridization protocol version 5.0

scan_protocol: Agilent scanner and Feature Extraction 6.0

data_processing: The log2-ratio gene expression data in the microarray dataset were normalized by quantile normalization.

source_name: Normal human breast tissue

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification Kit, protocol version 2.0

growth_protocol: The breast tumor samples were immediately frozen by liquid nitrogen without any additional growth procedure before RNA extraction.

extract_protocol: Trizol reagent combined with RNAeasy mini kit

treatment_protocol: The breast tumor samples were excised, collected, and snap-frozen in liquid nitrogen immediately before RNA extraction.

tag: gender

value: normal breast tissue

source_name: Stratagene's human common reference RNA

value: Commercially-available reference


title: normal breast tissue_5999

value: female


title: normal breast tissue_5431


title: normal breast tissue_5429


title: normal breast tissue_5427


title: normal breast tissue_5435


title: normal breast tissue_5433


title: normal breast tissue_5425


title: normal breast tissue_5421


title: normal breast tissue_5423


title: normal breast tissue_5415


title: normal breast tissue_5411


title: normal breast tissue_5417


title: normal breast tissue_5419


title: normal breast tissue_5413


title: normal breast tissue_5409


title: normal breast tissue_5293


title: normal breast tissue_5407


title: normal breast tissue_5403


title: normal breast tissue_1593


title: RAG1KO RNA Pol II [proB cells]

type: genomic

first: Eugene

middle: M

last: Oltz

state: MO

address: 660 S Euclid Avenue

department: Pathology and Immunology

institute: Washington Univeristy in St.Louis

description: Chip-chip Rag1KOproB cells RNA Pol IIac

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

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

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

molecule: genomic DNA

source_name: RNA Pol II ChIP DNA from Rag1-/-proB cells

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: 5 million cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for at least 30 min on ice. The crosslinked chromatin was sheared to an average size of 400 bp using a BiorupterTM sonicator (Diagenode). 5 µg of antibody was incubated with Dynabeads ProteinA beads (Invitrogen at 4C for 2-4 hours . The chromatin (from 5 million cells) was diluted 10-fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA 16.7 mM Tris pH8.10, 167 mM NaCl) and added to the anitbody conugated to the Dynabeads overnight at 4C. After incubation, the immune complexes were collected by centrifugation and washed with the following buffers each for 3 min at 4C;low salt (150 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), high-salt buffer (500 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), LiCl buffer (250 mM LiCl, 50 mM Tris pH8.0, 0.5% Na deoxycholate, 1% NP40) and TE (10 mM Tris pH8.0, 1 mM EDTA). The protein-DNA complexes were eluted from the beads in 250 µl elution buffer (1% SDS, 100 mM NaHCO3) at 65C overnight followed by the addition of proteinaseK to 500 µg/ml and incubaton at 56C for 1 hour. Genomic DNA was isolated using QIAquick PCR purification column and subject to whole genome amplication (Sigma).

treatment_protocol: Rag1KO  bone marrow cells of 3-4 week old mice were collected and the CD19+ sorted with magnetic beads

tag: age

value: 3-4 week old

tag: genotype/variation

tag: cell type

value: pro-B cells

tag: chip antibody

value: RNA Pol II

tag: chip antibody vendor

value: abcam

tag: chip antibody cat.#

source_name: Input DNA from Rag1KO proB cells

value: input DNA


title: RAG1KO H3K27ac [proB cells]

description: Chip-chip Rag1KOproB cells -H3K27ac

source_name: H3K27ac ChIP DNA from Rag1-/- proB cells


title: normal breast tissue_1591


title: normal breast tissue_1539


title: normal breast tissue_5405


title: normal breast tissue_1543


title: normal breast tissue_1541


title: Pc7+p53_6hpf_II

city: Tampere

first: Virpi

last: Kivinen

address: Korkeakoulunkatu 10

country: Finland

institute: Tampere University of Technology

description: Gene expression 6h post fertilization with PCSK7 + P53 morpholinos, replicate 2

hyb_protocol: A total of 1.65 µg of sample was hybridized on Agilent 4x44K Zebrafish GE v3 arrays (65ºC, o/n) using Agilent's Gene Expression Hybridization kit. After hybridization, microarrays were washed applying Agilent's Gene Expression Wash Pack with 0.005% Triton X-102 added. Finally Agilent's Stabilization and Drying solution was used.

scan_protocol: Chips were scanned using Agilent Technologies Scanner G2565CA.

data_processing: The scanned images were analyzed with Agilent Feature Extraction software v10.7.1. Only features having corresponding Entrez ID available were retained. Expression value for each probe has been calculated in three phases: 1) If the same Agilent Probe Name appears in the raw data file more than once, the row from the data file that has the highest average expression across all samples is used to represent that Agilent Probe Name. 2) If the same Entrez ID appears in the raw data file more than once, the Agilent Probe Name that has the highest average expression across all samples is used to represent that Entrez ID. Other Agilent Probe Names are discarded. 3) The resulting expression values for each probe are quantile normalized across samples.

source_name: whole fish, 6h, PCSK7+P53 morpholinos, replicate 2

label_protocol: 100ng of total RNA was amplified and Cy3-labeled with Agilent's Low Input Quick Amp Labeling kit.

growth_protocol: Embryos were obtained through natural crosses of wild-type AB strain individuals. The fish were maintained under standard conditions at 28.5°C.

extract_protocol: RNA was extracted from a pool of 18-35 zebrafish embryos / group with an RNeasy Mii Kit (qiagen) according to manufacturer's recommendations.

treatment_protocol: 0.25 - 1.0 pmols of each morpholino was used. All injections were administered into yolk sac of 1-4 cell stage zebrafish embryo. 0.2 M KCl was used as buffer in injection solutions. All injections were carried out using PV830 Pneumatic Pico Pump (PWI).

value: whole fish

tag: hours post fertilization

value: sample


title: RC_6hpf_II

description: Gene expression 6h post fertilization with control morpholino, replicate 2

source_name: whole fish, 6h, control, replicate 2

value: control


title: Pc7+p53_1dpf_III

description: Gene expression 24h post fertilization with PCSK7 + P53 morpholinos, replicate 3

source_name: whole fish, 24h, PCSK7+P53 morpholinos, replicate 3


title: Pc7+p53_6hpf_III

description: Gene expression 6h post fertilization with PCSK7 + P53 morpholinos, replicate 3

source_name: whole fish, 6h, PCSK7+P53 morpholinos, replicate 3


title: RC_6hpf_III

description: Gene expression 6h post fertilization with control morpholino, replicate 3

source_name: whole fish, 6h, control, replicate 3


title: Pc7+p53_1dpf_II

description: Gene expression 24h post fertilization with PCSK7 + P53 morpholinos, replicate 2

source_name: whole fish, 24h, PCSK7+P53 morpholinos, replicate 2


title: Pc7+p53_6hpf_I

description: Gene expression 6h post fertilization with PCSK7 + P53 morpholinos, replicate 1

source_name: whole fish, 6h, PCSK7+P53 morpholinos, replicate 1


title: Pc7+p53_1dpf_I

description: Gene expression 24h post fertilization with PCSK7 + P53 morpholinos, replicate 1

source_name: whole fish, 24h, PCSK7+P53 morpholinos, replicate 1


title: RC_1dpf_III

description: Gene expression 24h post fertilization with control morpholino, replicate 3

source_name: whole fish, 24h, control, replicate 3


title: RC_1dpf_II

description: Gene expression 24h post fertilization with control morpholino, replicate 2

source_name: whole fish, 24h, control, replicate 2


title: RC_1dpf_I

description: Gene expression 24h post fertilization with control morpholino, replicate 1

source_name: whole fish, 24h, control, replicate 1


title: genomic DNA from primary myocytes (donor 2)

city: L'Hospitalet de Llobregat

first: Antonio

last: Gómez

state: Barcelona

address: Av. Gran Vía s/n km. 2,7.

department: Epigenetics and Biology of Cancer Program

institute: IDIBELL

description: primary myocytes (donor 2)

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio software v2010,3

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

growth_protocol: Human adipose-derived stem cells (hASCs) were established from adipose tissue of patients of 30-55 years of age. Lipoaspirates were digested with 0.075% collagenase Type I, prepared in PBS containing 1% BSA for 60 min at 37ºC with constant shaking, followed by filtration through a 100-µm filter. After washing with PBS, cells were treated with erythrocyte lysis buffer. Resultant cells were cultivated at 1,000 cells.cm-2 in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% of fetal bovine serum (FBS). Cultures were washed with buffer 24–48 hours after plating to remove unattached cells, and then re- fed with fresh medium. Only cells that were in passage 5 or 6 were used in these experiments.  The human rhabdomyosarcoma (RD and TE.32.7) and osteosarcoma (MG-63) cell lines were obtained from the American Type Culture Collection (ATCC) (Rockland, MD, USA). Cell lines were maintained in monolayer cultures at 37ºC in an atmosphere containing 5% CO2, with DMEM supplemented with 10% FBS. Primary tissues from bone and muscle were obtained from healthy donors. All the samples were obtained after the donor had given their written informed consent, in accordance with the guidelines of the Ethics Committee of Bio-Health Research Foundation of Eastern Andalusia (Spain). DNA was extracted directly from fresh samples.

extract_protocol: DNA from all the samples was isolated by was applying the QIAamp® DNA Mini Kit (Qiagen Iberia, Spain) following supplier’s instructions.

treatment_protocol: hASCs were differentiated to osteogenic and myogenic lineages by in vitro induction using specific culture medium. Osteogenesis was induced in the presence of DMEM with 10% FBS, dexamethasone (0.1 µM), ß-glycerophosphate (10 mM) and ascorbic acid-2-phosphate (50 µgr.ml-1). After 28 days, the culture medium was removed and cells were washed with PBS and processed. Myogenic induction of hASCs was obtained in the presence of DMEM with 10% FBS, hydrocortisone (50 μM) and horse serum 5% during  42 days.

value: male

value: primary myocytes (donor 2)

tag: individual

value: donor 2


title: genomic DNA from osteosarcoma cell line (ATCC CRL-1427)

description: osteosarcoma cell line (ATCC CRL-1427)

tag: cell line

value: osteosarcoma cell line (ATCC CRL-1427)


title: genomic DNA from primary osteocytes (donor 1)

description: primary osteocytes (donor 1)

value: primary osteocytes (donor 1)

value: donor 1


title: genomic DNA from rhabdomyosarcoma (ATCC CCL-136)

description: rhabdomyosarcoma (ATCC CCL-136)

source_name: RD

value: RD

value: rhabdomyosarcoma (ATCC CCL-136)


title: genomic DNA from rhabdomyosarcoma (ATCC CRL-7731)

description: rhabdomyosarcoma (ATCC CRL-7731)

source_name: TE 32.T

value: TE 32.T

value: rhabdomyosarcoma (ATCC CRL-7731)


title: genomic DNA from primary myocytes (donor 1)

description: primary myocytes (donor 1)

value: primary myocytes (donor 1)


title: mouse 3, Ly6C- F4/80high, biological rep3

city: Debrecen

first: Szilard

last: Poliska

address: Egyetem ter 1.

department: Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

description: Gene expression data of muscle-derived macrophages

hyb_protocol: Samples were hybridized at 45 degrees Celsius for 16 hours and then standard washing protocol was performed using GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned on GeneChip Scanner 7G (Affymetrix), Affymetrix GeneChip Command Console (AGCC) was used to obtain image files.

data_processing: CHP files were generated using Affymetrix Expression Control. Downstream data analysis was performed in GeneSpring GX 12,  CEL files were imported using RMA algorithm and median normalization was performed.

source_name: mouse 3, Ly6C- F4/80high

label_protocol: Ambion WT Expression Kit (Applied Biosystems) and GeneChip WT Terminal Labeling and Control Kit (Affymetrix) were used for amplifying and labeling 150 ng of RNA samples.

growth_protocol: Muscle injury was caused by cardiotoxin ijection into the tibialis anterior muscle. Macrophages were separated 2 days post-injury from the regenerating muscle.

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

treatment_protocol: CD45+ hematopoietic cells from regenerating muscles were isolated with a magnetic bead selection (Miltenyi). Cells were labeled with PE-conjugated Ly6C and APC-conjugated F4/80 antibodies and then sorted into Ly6C+ F4/80low and Ly6C- F4/80high subsets.

tag: strain

tag: cell surface marker

value: Ly6C- F4/80high

value: muscle-derived tissue macrophage


title: genomic DNA from in vitro induced myocytes (donor 1)

description: in vitro induced myocytes (donor 1)

value: in vitro induced myocytes (donor 1)


title: mouse 3, Ly6C+ F4/80low, biological rep3

source_name: mouse 3, Ly6C+ F4/80low

value: Ly6C+ F4/80low


title: mouse 2, Ly6C+ F4/80low, biological rep2

source_name: mouse 2, Ly6C+ F4/80low


title: genomic DNA from in vitro induced myocytes (donor 2)

description: in vitro induced myocytes (donor 2)

value: in vitro induced myocytes (donor 2)


title: genomic DNA from in vitro induced myocytes (donor 3)

description: in vitro induced myocytes (donor 3)

value: in vitro induced myocytes (donor 3)

value: donor 3


title: mouse 2, Ly6C- F4/80high, biological rep2

source_name: mouse 2, Ly6C- F4/80high


title: RC_6hpf_I

description: Gene expression 6h post fertilization with control morpholino, replicate 1

source_name: whole fish, 6h, control, replicate 1

tag: tissue

value: whole fish

tag: sample type

value: control


title: mouse 1, Ly6C- F4/80high, biological rep1

source_name: mouse 1, Ly6C- F4/80high


title: genomic DNA from in vitro induced osteocytes (donor 3)

description: in vitro induced osteocytes (donor 3)

value: male

value: in vitro induced osteocytes (donor 3)


title: genomic DNA from in vitro induced osteocytes (donor 2)

description: in vitro induced osteocytes (donor 2)

value: in vitro induced osteocytes (donor 2)

value: donor 2


title: genomic DNA from adipose- derived stem cells (donor 2)

description: adipose- derived stem cells (donor 2)

value: adipose- derived stem cells (donor 2)


title: genomic DNA from adipose- derived stem cells (donor 5)

description: adipose- derived stem cells (donor 5)

value: adipose- derived stem cells (donor 5)

value: donor 5


title: SNU216_TEAD4 KD

city: Daejeon

first: Byungho

last: Lim

address: Medical Genomics Research Center, KRIBB, 125 Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology (KRIBB)

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation (Bead Studio version 3).

source_name: SNU216_TEAD4 KD

label_protocol: Labelled cRNA was prepared using Illumina TotalPrep RNA Amplification Kit

extract_protocol: Total RNA was isolated using RNeasy Mini kit

value: gastric cancer cell


title: genomic DNA from in vitro induced osteocytes (donor 1)

description: in vitro induced osteocytes (donor 1)

value: in vitro induced osteocytes (donor 1)

value: donor 1


title: mouse 1, Ly6C+ F4/80low, biological rep1

source_name: mouse 1, Ly6C+ F4/80low

value: muscle-derived tissue macrophage


title: NAC_ABA_2

city: Seoul

first: Do Young

last: Hyeon

state: Select State

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

institute: Seoul National University

description: 12-day-old pTA-ANAC096 transformed transgenic plant seedlings treated with 30 uM Dex only for 0.5 h followed by additional 0.5 h incubation with both 2 uM ABA and 30 uM Dex

hyb_protocol: Standard Agilent hybridization protocols

scan_protocol: Agilent Technologies Scanner G2505C

data_processing: The data were treated using MATLAB 7.13.0 (R2011b)

organism: Arabidopsis thaliana

source_name: Arabidopsis 12-day-old seedlings

label_protocol: Refer to the Agilent Gene Expression System Manual

growth_protocol: pTA empty vector and pTA-ANAC096 transformed transgenic plants were grown in the liquied MS media at 23°C  with 16 h/8 h light/dark cycles for 12 days.

extract_protocol: Total mRNA was extracted using WelPrepTM (JOIN BIO-INNOVATION, Daegu, Korea), and DNA was digested by treatment with DNase I (Ambion, Austin, TX).

treatment_protocol: pTA plants (12-day-old) cultured in liquid medium were treated with 30 uM Dex alone for 1 h (Control) or 30 uM Dex alone for 30 min followed by an additional treatment of 30 min with both 30 uM Dex and 2 uM ABA (ABA). For pTA-ANAC096 plants, 12-day-old seedlings were treated with 30 uM Dex for 1 h (ANAC096) or with 30 uM Dex only for 0.5 h followed by additional 0.5 h incubation with both 2 uM ABA and 30 uM Dex (ANAC096+ABA).

value: seedling

tag: cultivar

tag: treatment


title: genomic DNA from adipose- derived stem cells (donor 3)

description: adipose- derived stem cells (donor 3)

value: adipose- derived stem cells (donor 3)


title: 7d Hypoxia cultured hESC line HS360

city: Turku

first: Elisa

last: Närvä

address: Tykistökatu 6

department: Turku Centre for Biotechnology

institute: University of Turku

hyb_protocol: GeneChip Whole Transcript (WT) Sence Target labelling assay Manual, Affymetrix P/N 701880

scan_protocol: Gene Chip Scanner 3000

data_processing:
RMA signal estimates from Chipster Software version 1.4.2 (http://chipster.csc.fi)
probe group file HuEx10stv2_Hs_ENTREZG.cdf
meta-probeset file HuEx10stv2_Hs_ENTREZG.cdf

source_name: 7d Hypoxia cultured hESC line HS360

growth_protocol: Feeder free Matrigel (BD) coated plates, mTeSR1 (StemCell Technologies) media

extract_protocol: RNA was isolated using RNeasy Kit (Qiagen)

treatment_protocol: no treatment

value: hypoxia 4 % O2

tag: time


title: 24h Hypoxia cultured hESC line H9

source_name: 24h Hypoxia cultured hESC line H9

label_protocol: GeneChip Whole Transcript (WT) Sence Target labelling assay Manual, Affymetrix P/N 701880


title: NAC_2

description: 12-day-old pTA-ANAC096 transformed transgenic plant seedlings treated with 30 uM Dex alone for 1h

value: pTA-ANAC096 transformed transgenic plants

value: 30 uM Dex alone for 1h


title: 2h Hypoxia cultured hESC line H9

source_name: 2h Hypoxia cultured hESC line H9


title: SNU216_control

description: replicate 1


title: 2h Normoxia cultured hESC line H9

source_name: 2h Normoxia cultured hESC line H9

value: normoxia 21 % O2


title: ABA_1

description: 12-day-old pTA empty vector transformed transgenic plant seedlings treated with 30 uM Dex alone for 30 min followed by an additional treatment of 30 min with both 30 uM Dex and 2 uM ABA

value: pTA empty vector transformed transgenic plants


title: 7d Normoxia cultured hESC line HS360

source_name: 7d Normoxia cultured hESC line HS360


title: genomic DNA from adipose- derived stem cells (donor 1)

description: adipose- derived stem cells (donor 1)

tag: gender

value: male

value: adipose- derived stem cells (donor 1)


title: 24h Normoxia cultured hESC line HS360

source_name: 24h Normoxia cultured hESC line HS360


title: ABA_2

tag: age

value: 30 uM Dex alone for 30 min followed by an additional treatment of 30 min with both 30 uM Dex and 2 uM ABA


title: NAC_ABA_1

tag: genotype/variation


title: NAC_1


title: 2h Normoxia cultured hESC line HS360

source_name: 2h Normoxia cultured hESC line HS360


title: 2h Hypoxia cultured hESC line HS360

source_name: 2h Hypoxia cultured hESC line HS360


title: Control_2

description: 12-day-old pTA empty vector transformed transgenic plant seedlings treated with 30 uM Dex alone for 1h


title: 24h Hypoxia cultured hESC line HS360

source_name: 24h Hypoxia cultured hESC line HS360


title: Control_1


title: 7d Normoxia cultured hESC line HS401

source_name: 7d Normoxia cultured hESC line HS401


title: C07

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

description: Control participant

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: BeadChips were imaged using HiScan with standard recommended Illumina scanner setting

data_processing: Raw intensities extracted using GenomeStudio v2010.1. Background normalization was conducted by subtracting averaged negative probe intensity from signal A and B. Then quantile normalization was done to control for chip to chip variation. Finally, average beta is recalculated from normalized intensities: methylated intensity / (methylated + unmethylated intensities). Data points with bad detection P values are removed and then imputed. One CpG site, cg22903370, was removed due to >50% of data points missing.

label: Cy3 and Cy5

source_name: buccal swab genomic DNA

extract_protocol: DNA was extracted from buccal swabs using the Isohelix DNA isolation kit following manufacturer's instructions.

tag: Sex

value: F

tag: down synrome status

value: Control

tag: brief praxis score


title: C08

description: Control participant

value: M


title: 7d Hypoxia cultured hESC line HS401

source_name: 7d Hypoxia cultured hESC line HS401


title: Blood-control-03-01

city: Madrid

first: Pablo

last: Lapunzina

state: Madrid

address: Pª de la Castellana, 261

department: Endocrinology

institute: INGEMM

description: Gene expression comparison between normal controls with gene mutated patients

hyb_protocol: One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling. Version 6.5, May 2010.

scan_protocol: Agilent Feature Extraction Software

data_processing: Data analysis were performed by GeneSpring Software, version 12.6 following the user´s guide

source_name: Peripheral Blood, replicate 1

extract_protocol: TRI Reagent® Solution. RNA / DNA / Protein Isolation Reagent. Part Number AM9738 100 mL.

treatment_protocol: Lymphoblast cells were extracted from peripheral blood for both patients and controls with chemagen according manufacturer´s procedures

value: Control 4

tag: genetic defect

value: control

value: Male


title: Blood-control-02-02

description: Gene expression comparison between normal controls and gene mutated patients

label_protocol: One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling. Version 6.5, May 2010.

value: Control 2


title: Blood-control-01-02

source_name: Peripheral Blood, replicate 2

value: Control 1


title: C04

description: Control participant

data_processing:
Raw intensities extracted using GenomeStudio v2010.1. Background normalization was conducted by subtracting averaged negative probe intensity from signal A and B. Then quantile normalization was done to control for chip to chip variation. Finally, average beta is recalculated from normalized intensities: methylated intensity / (methylated + unmethylated intensities). Data points with bad detection P values are removed and then imputed. One CpG site, cg22903370, was removed due to >50% of data points missing.
supplementary matrix contains unmethylated and methylated signal intensities


title: C05

description: Control participant


title: C06

description: Control participant


title: C10

description: Control participant


title: C09

description: Control participant


title: 24h Normoxia cultured hESC line HS401

source_name: 24h Normoxia cultured hESC line HS401


title: Day 8 Mst1/Mst2 knockout embryonic bodies

city: Hong Kong

first: Ping

last: Yuan

address: Prince Wales Hospital

department: Chemical Pathology

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Day 4 embryoid bodies

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using Expression Console software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.

source_name: embryoid bodies

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: ES cells were trypsinized into single cells and then replaced at 1x106 cells in a 10 cm non-adherent dish in ES cell medium devoid of 2i (CHIR99021 and PD0325901) and LIF.Floating EBs were harvested at 4 days or 8 days for RNA extraction

extract_protocol: Total RNA was extract by Trizol and then purified with QIAGEN Rneasy purification kit.

treatment_protocol: Not applicable

tag: genotype

value: Mst1/Mst2 knockout

tag: cell type

value: day 8 embryoid bodies


title: Blood-patient-03-02

tag: individual

value: Patient 1

value: macrocephaly, overgrowth and maturative delay


title: Day 8 wild type embryonic bodies

description: Day 8 embryoid bodies

value: wild type


title: DS10

description: DS participant

value: DS


title: C03

description: Control participant


title: Blood-control-01-01


title: 2h Hypoxia cultured hESC line HS401

source_name: 2h Hypoxia cultured hESC line HS401

value: hypoxia 4 % O2

tag: cell line


title: DS09

description: DS participant


title: 2h Normoxia cultured hESC line HS401

source_name: 2h Normoxia cultured hESC line HS401

value: normoxia 21 % O2


title: Blood-patient-03-01


title: 24h Hypoxia cultured hESC line HS401

source_name: 24h Hypoxia cultured hESC line HS401


title: Blood-patient-01-02

value: Patient 2


title: C02

description: Control participant


title: Blood-patient-02-01

value: Patient 5


title: C01

description: Control participant

value: F

value: Control


title: 7d Hypoxia cultured hESC line H9

source_name: 7d Hypoxia cultured hESC line H9


title: 7d Normoxia cultured hESC line H9

source_name: 7d Normoxia cultured hESC line H9


title: DS08

description: DS participant


title: Blood-patient-02-02


title: Day 4 Mst1/Mst2 knockout embryonic bodies

description: Day 4 embryoid bodies

value: day 4 embryoid bodies


title: Day 4 wild type embryonic bodies

description: Day 4 embryoid bodies


title: DS07

description: DS participant

value: M


title: DS06

description: DS participant


title: siEWS 3 (gene)

status: Public on Jan 01 2014

city: Rome

first: Maria Paola

last: Paronetto

address: Piazza Lauro de Bosis, 6

department: Department of Health Sciences

country: Italy

institute: University of Rome "Foro Italico"

description: HeLa cells transfected with siEWS oligonuclleotides

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

data_processing:
Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: HJAY_r2.pgf
meta-probeset file: HJAY_r2.full.mps

source_name: EWS -/-

growth_protocol: HeLa cells were grown in complete medium (DMEM, 10% FBS, Penicillin/Strptomycin). Before transfection, cells were plated 24 hours before transfection at 40000 per well in 35mm plates in DMEM 10&FBS without antibiotics

extract_protocol: Total RNA was extracted using Rneasy mini kit (Qiagen, cat. N.

treatment_protocol: HeLa cells were plated 24 hours before transfection in 35mm plates in DMEM 10%FBS without antibiotics and transfected with 150pmol of a scrambled or EWS siRNA oligonucleotides using lipofectamine RNAiMAX (Cat. N. 13778-150, Invitrogen) in Optimem Medium (Invitrogen). Five hours after transfection, the medium was removed and replaced with fresh DMEM /10% FBS/Penicillin/Strptomycin). The transfection was repeated for three days in a row, and the fourth days cells were harvested for RNA extraction.

value: Female cervix adenocarcinoma

value: HeLa

tag: transfection

value: siEWS oligonucleotides


title: Scrambled 3 (gene)

description: HeLa cells transfected with scrambled oligonuclleotides

source_name: scrambled

value: scrambled oligonucleotides


title: Blood-patient-01-01

value: Male


title: Root_C

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

institute: GreenGene Biotech Inc.

description: water control treated pepper root

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Capsicum annuum

source_name: root

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Pepper (Capsicum annuum L. cv. Bukwang) seeds were sterilized with 6% sodium hypochlorite and incubated at 25-28C on MS medium until germination. After germination, pepper plants were transplanted to natural pepper field. soil and were grown at 25-28C with a 12h light/dark period.

extract_protocol: Total RNA was extracted as followed by TRI reagent and treated with 1 U of RNase-free Dnase (Promega, Madison, WI, USA) for 10 min at 37 C. RNA quality and concentration was determined by analysis with an Nanodrop, ND-1000 V3.8.1 bioanalyzer at KRIBB (Daejeon, South Korea).

treatment_protocol: Two-week-old pepper seedlings were drenched with 10 mM BTH or water as a control. Under the same condition, whifefly and whitefly + BTH were treated. Each plant was incubated in a transparent plastic cylinder with a diameter of 15 cm and a height of 50 cm.

value: Bukwang

tag: tissue

value: root

value: water


title: Scrambled 2 (gene)

tag: sample type


title: Root_CW

description: Whitefly infested pepper root

tag: cultivar

tag: infestation

value: whitefly


title: Scrambled 1 (gene)


title: leaf1

description: Whitefly infested pepper leaf

source_name: leaf

value: leaf


title: leaf4

description: BTH + whitefly treated pepper leaf

tag: treatment

value: BTH


title: leaf3

description: BTH treated pepper leaf


title: DS05

description: DS participant

value: DS


title: siEWS 2 (gene)


title: Root_B

description: BTH treated pepper root


title: Root_WB

description: BTH + whitefly treated pepper root


title: leukemiaRNA_ROR1xTCL1_2

city: La Jolla

first: Emanuela

middle: Maria

last: Ghia

state: CA

address: 9310 Athena Circle

department: Center For Novel Therapeutics

institute: University of California San Diego

description: RMA expression value derived from BioConductor Oligo package

hyb_protocol: Samples were hybridized with GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix) and scanned at the UCSD GeneChip Core Facility.

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

data_processing: Raw data were processed with the BioConductor Oligo package for background correction and normalization. Data analysis and statistical evaluations were performed in R (version 2.15.1, R Core Team (2012). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org/).

source_name: ROR1xTCL1 transgenic mouse leukemia RNA

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the Ambion WT Expression Kit (Applied Biosystems) and then fragmented and labeled with the GeneChip WT Terminal Labeling Kit (Affymetrix).

extract_protocol: Total RNA was extracted from leukemia cells using TRIzol® reagent (Life Technologies,Carlsbad, CA) according to the manufacturer’s protocol followed by Turbo DNase treatment (Life Technologies, Carlsbad, CA) to remove trace amounts of genomic DNA.

tag: transgenic mice

value: ROR1xTCL1 mouse


title: leukemiaRNA_TCL1_2

source_name: TCL1 transgenic mouse leukemia RNA

value: TCL1 mouse


title: leukemiaRNA_ROR1xTCL1_4


title: leukemiaRNA_ROR1xTCL1_1


title: leaf2

description: water control treated pepper leaf


title: DS03

description: DS participant

source_name: buccal swab genomic DNA

value: F

tag: age


title: SP Female, replicate 4

city: Shinjukuku

first: Shinji

last: Kasai

state: Tokyo

address: 1-23-1 Toyama

department: Department of Medical Entomology

country: Japan

institute: National Institute of Infectious Diseases

description: Biological replicate 4 of 4.

hyb_protocol: The labeled cRNA were pooled and hybridized to microarray probes in a hybridization oven at 65°C for 17 h under rotation at 10 rpm using a Gene Expression Hybridization Kit (Agilent Technologies, Santa Clara, CA, USA). After hybridization washing, the fluorescent dyes were stabilized against ozone oxidization with the Gene Expression Wash Buffer (Agilent Technologies) and the microarray plate then dried in nitrogen gas.

scan_protocol: The fluorescence of Cy-3 on each spot was scanned using a DNA Microarray Scanner G565BA (Agilent Technologies, Santa Clara, CA, USA). Spot identification and quantification were performed using Feature Extraction Software v. 7.5 (Agilent Technologies, Santa Clara, CA, USA) in the default setting.

data_processing: A linear and LOWESS algorithm (a combination of the linear method and traditional LOWESS method) was used for dye normalization.

organism: Aedes aegypti

source_name: SP, adult females

label_protocol: Fluorescein-labeled cRNA were synthesized via a double-stranded cDNA intermediate using a Low Input Quick Amp Labeling Kit (Agilent Technologies). The cRNA derived from the SP and SMK strains were differentially labeled with cyanine-3 (Cy-3) dye-conjugating CTP (PerkinElmer Inc., Waltham, MA, USA). cRNA was then purified with Qiagen RNeasy Mini Kit (Qiagen, Venlo, Netherlands), and the overall efficacy of cRNA synthesis and fluorescein-labeling was measured using a Nanodrop ND-1000 spectrophotometer.

growth_protocol: Larvae were fed a ground diet of insect food (Oriental Yeast Co., Ltd., Tokyo, Japan), and the adults were maintained on 10% sucrose. Females were given blood meals from a mouse. Both larvae and adults were reared at 27 ± 1°C with a photoperiod of 16:8 (L:D) h.

extract_protocol: Total RNA was extracted from 10 fourth instar larvae or 10 three-day-old adults using ISOGEN (Nippon Gene Co., Ltd., Tokyo, Japan). Genomic DNA was removed by digesting the total RNA samples with DNase I using TURBO DNase (Life Technologies Co., Carlsbad, CA, USA).

tag: strain

value: SP

tag: pyrethroid susceptibility

value: resistant

tag: developmental stage

value: adult

value: 3 days

tag: gender

value: female

value: abdomens


title: DS04

description: DS participant

tag: Sex

tag: down synrome status

tag: brief praxis score


title: SP Female, replicate 3

description: Biological replicate 3 of 4.


title: SP Female, replicate 2

description: Biological replicate 2 of 4.


title: SMK Female, replicate 4

description: Biological replicate 4 of 4.

source_name: SMK, adult females

value: SMK

value: susceptible


title: SP Female, replicate 1

description: Biological replicate 1 of 4.


title: DS01

description: DS participant

value: M


title: siEWS 1 (gene)

value: Female cervix adenocarcinoma

value: HeLa

value: siEWS oligonucleotides


title: leukemiaRNA_TCL1_4


title: leukemiaRNA_ROR1xTCL1_3


title: leukemiaRNA_TCL1_3


title: SP Male, replicate 2

description: Biological replicate 2 of 4.

source_name: SP, adult males

value: male


title: SMK Male, replicate 4

description: Biological replicate 4 of 4.

source_name: SMK, adult males


title: SMK Female, replicate 3

description: Biological replicate 3 of 4.


title: SMK Male, replicate 3

description: Biological replicate 3 of 4.


title: SP Male, replicate 3

description: Biological replicate 3 of 4.


title: SMK Female, replicate 2

description: Biological replicate 2 of 4.


title: 24h Normoxia cultured hESC line H9

source_name: 24h Normoxia cultured hESC line H9

value: normoxia 21 % O2

tag: time


title: SMK Female, replicate 1

description: Biological replicate 1 of 4.


title: SP Male, replicate 1

description: Biological replicate 1 of 4.


title: SP Larvae, replicate 4

description: Biological replicate 4 of 4.

source_name: SP, larvae

value: fourth instar larvae

value: whole body


title: SP Male, replicate 4

description: Biological replicate 4 of 4.


title: SMK Larvae, replicate 3

description: Biological replicate 3 of 4.

source_name: SMK, larvae


title: SMK Larvae, replicate 4

description: Biological replicate 4 of 4.


title: SP Larvae, replicate 2

description: Biological replicate 2 of 4.


title: DS02

description: DS participant

value: F

value: DS


title: SMK Larvae, replicate 2

description: Biological replicate 2 of 4.


title: SP Larvae, replicate 3

description: Biological replicate 3 of 4.

value: SP

value: resistant


title: SP Larvae, replicate 1

description: Biological replicate 1 of 4.


title: SMK Larvae, replicate 1

description: Biological replicate 1 of 4.


title: SMK Male, replicate 2

description: Biological replicate 2 of 4.

value: adult

value: 3 days


title: K4me3_ChIP_24hpi

city: Sacramento

first: Clifford

middle: G.

last: Tepper

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

hyb_protocol: Microarrays were hybridized in a hybridization over for 24 hours at 65C and 20 RPM.  The arrays were washed and scanned in an ozone-free tent.

scan_protocol: Scanned on an Agilent G2539CA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1) with the feature extraction protocol for ChIP-chip experiments (ChIP_107_Sep09).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: KSHV-infected SLK Cells

label_protocol: 1.3 µg of ChIP or Input DNA were labeled according to the manufacturer's protocol (Agilent ChIP-on-chip Analysis, version 11.0).

growth_protocol: SLK cells were maintained in DMEM medium supplemented with 10% FBS, 100 U/ml penicillin and 100 μg/ml streptomycin (P/S).

extract_protocol: ChIP and Input DNA samples were prepared according to previously published protocols Toth, Z. et al.  Epigenetic analysis of KSHV latent and lytic genomes. PLoS pathogens 6:e1001013, 2010).

treatment_protocol: SLK cells were de novo infected by spin-infection (2,000 rpm, 45 min at 30°C) using MOI 1. After infection, the medium was changed and the infected cells were harvested at the indicated time points.

tag: cell line

value: SLK

tag: hrs post kshv infection

tag: antibody


title: SMK Male, replicate 1

description: Biological replicate 1 of 4.

value: SMK

tag: tissue

value: abdomens


title: K4me3_ChIP_4hpi


title: RING1B_ChIP_4hpi


title: K27me3_ChIP_72hpi


title: K4me3_ChIP_72hpi


title: K27me3_ChIP_24hpi


title: K27me3_ChIP_4hpi


title: EZH2_ChIP_72hpi


title: RING1B_ChIP_72hpi


title: EZH2_ChIP_4hpi


title: K27ac_ChIP_72hpi


title: Comparision of the retentostat 2 on day 43 over the retentostat 1 on day 43

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

country: Netherlands

institute: NIZO food research

hyb_protocol: Hybridization buffer (Agilent In Situ Hybridization Kit Plus) was added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers at 65 degrees Celcius for 17 h. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5)

data_processing: Scanned slides were Lowess normalised using Prep (van Hijum, Applied Bioinformatics 2003 2(4):241-244. Interslide scaling was performed using Postprep (van Hijum, Applied Bioinformatics 2003 2(4):241-244).

organism: Lactococcus lactis

label_protocol: Total RNA and enriched mRNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 3 h in the presence of 400 U SuperScript TMIII reverse transcrptase enzyme (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: Lactococcus lactis subsp. lactis strain KF147 were inoculated in 50 ml M17 broth (Terzaghi and Sandine, 1975) complemented with 0.5% glucose (w/v) and grown overnight at 30°C. Overnight cultures were harvested by centrifugation (6,000 g, 10 min., 4°C) and washed twice with physiological salt solution (0.9% NaCl in water). Next, the culture was inoculated into CDM containing 25 mM of glucose (Goffin, et al., 2010). Two independent, carbon source-limited retentostat cultivations with 1.5-l working volume were performed under anaerobic conditions, initiating from chemostat cultivation at dilution rates of 0.025 h-1 as previously described (Ercan, et al., 2013).

extract_protocol: Cultures were lysed by beat-beating and total RNA was isolated by subsequent phenol-chloroform extraction, followed by RNA purification and mRNA enrichment

treatment_protocol: Quenching Buffer 66.7 mM HEPES (pH 6.5) 60%Methanol Extraction Mixture (Prepared in a screw-cap tube) -500 µl phenol/Chloroform -30 µl10% SDS -30 µl 3 M NaAc (pH 5.2) -500 mg glass-beads (75-150 µm) -400 µl TE buffer 1.For each sample prepare a tube with Extraction Mixture

tag: sample

value: day 43


title: Comparision of the retentostat 1 on day 42 over on day 35

value: day 42

value: day 35


title: Comparision of the retentostat 1 on day 43 over retenotstat 1 on day 42


title: Comparision of the retentostat 2 on day 42 over the retentostat 1 on day 42


title: leukemiaRNA_TCL1_1

value: TCL1 mouse


title: Comparision of the retentostat 1 on day 44 over retenotstat 1 on day 43

value: day 44


title: K27ac_ChIP_24hpi


title: Comparision of the retentostat 2 on day 42 over the retentostat 2 on day 43


title: H3_ChIP_ 4hpi


title: Comparision of the retentostat 2 on day 28 over the retentostat 1 on day 28

value: day 28


title: Comparision of the retentostat 2 on day 21 over on day 42

value: day 21


title: Comparision of the retentostat 2 on day 43 over the retentostat 2 on day 44


title: Comparision of the retentostat 1 on day 14 over the chemostat 1

value: day 14

value: day 0


title: H3_ChIP_ 24hpi


title: Comparision of the retentostat 1 on day 7 over the retentostat 2 on day 7

value: day 7


title: H3_ChIP_ 72hpi


title: Comparision of the chemostat 2 over the retentostat 2 on day 2

value: day 2


title: K27ac_ChIP_4hpi


title: Comparision of the retentostat 1 on day 14 over the retentostat 2 on day 14


title: Comparision of the retentostat 2 on day 44 over the retentostat 1 on day 44


title: Comparision of the retentostat 2 on day 14 over the chemostat 2


title: Comparision of the retentostat 1 on day 42 over on day 21


title: Comparision of the retentostat 2 on day 2 over on day 7


title: Comparision of the retentostat 2 on day 35 over the retenotstat 1 on day 35


title: Comparision of the retentostat 2 on day 7 over on day 14


title: Comparision of the retentostat 2 on day 14 over on day 21


title: Comparision of the retentostat 2 on day 21 over on day 28


title: Comparision of the retentostat 1 on day 2 over the retentostat 2 on day 2


title: Comparision of the retentostat 1 on day 21 over the retentostat 2 on day 21


title: Comparision of the retentostat 1 on day 35 over on day 28


title: Comparision of the retentostat 2 on day 35 over on day 42


title: Comparision of the retentostat 1 on day 28 over on day 21


title: Comparision of the retentostat 1 on day 14 over on day 7


title: Comparision of the retentostat 2 on day 28 over on day 35


title: Comparision of the retentostat 1 on day 21 over on day 14


title: Comparision of the retentostat 1 on day 2 over on day 0 (chemostat 1)


title: Comparision of the retentostat 1 on day 7 over on day 2


title: E12.5 Cirh1a+/- rep1

city: Montreal

first: Andrea

last: Richter

state: Quebec

address: 3175 chemin Côte-Ste-Catherine

department: Service de Génétique Médicale

institute: CHU Sainte-Justine

description: replicate 1

data_processing: The data were normalised using quantile normalisation with FlexArray in R (McGill University & Génome Québec Innovation Centre)

source_name: E12.5 Liver

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

extract_protocol: Total RNA was extracted by using RNAeasy mini kit (Qiagen), and subjected for Bioanalyzer analysis first.

value: C57BL/6 JAX

tag: gene targeting

value: Cirh1a β-Geo gene-trap


title: E11.5 Wildtype  rep2

description: replicate 2

source_name: E11.5 Liver


title: E11.5 Cirh1a+/- rep2

description: replicate 2


title: Comparision of the chemostat 1 over the chemostat 2


title: E12.5 Wildtype  rep1

description: replicate 1


title: E12.5 Cirh1a+/- rep2

description: replicate 2


title: E12.5 Cirh1a+/- rep3

description: replicate 3


title: E9.5 Cirh1a+/- rep3

description: replicate 3

data_processing: The data were normalised using quantile normalisation with FlexArray in R(McGill University & Génome Québec Innovation Centre)

source_name: E9.5 whole embryo

extract_protocol: Total RNA was extracted by using RNAeasy mini kit(Qiagen), and subjected for Bioanalyzer analysis first.


title: E11.5 Cirh1a+/- rep1

description: replicate 1


title: E11.5 Cirh1a+/- rep3

description: replicate 3


title: E9.5 Cirh1a+/- rep2

description: replicate 2


title: E9.5 Wildtype  rep3

description: replicate 3


title: E8.5 Cirh1a+/- rep2

description: replicate 2

source_name: E8.5 whole embryo


title: E12.5 Wildtype  rep2

description: replicate 2


title: E12.5 Wildtype  rep3

description: replicate 3


title: E9.5 Cirh1a+/- rep1

description: replicate 1


title: E11.5 Wildtype  rep1

description: replicate 1


title: double_vs_prp28-1_rep2

city: San Francisco

first: Argenta

last: Price

institute: University of California, San Francisco

description: prp28-1/prp8-tes vs. prp28-1, biological replicate 2. Raw data: 0518_014-10.gpr

hyb_protocol: Competitive hybridization at 65oC for 14h

scan_protocol: Images were acquired using an Axon Instruments GenePix 4000B scanner, reading at wavelengths of 635nm and 532nm (Axon Instruments, http://www.axon.com). Image analysis was performed using Axon Instruments GenePix Pro version 5.1.

data_processing: Spot ratio data were log2 transformed and normalized within each array using global loess regression implemented in the Bioconductor marray package

organism: Saccharomyces cerevisiae

source_name: saccharomyces cerevisiae prp28-1/prp8-tes strain

label_protocol: aa-dUTP incorporation during cDNA synthesis

growth_protocol: YEPD at 30oC to OD 0.5, then shift to 16oC for 50min

extract_protocol: Acid phenol

source_name: saccharomyces cerevisiae prp28-1 strain


title: double_vs_prp28-1

description: prp28-1/prp8-tes vs. prp28-1. Raw data: 0412_076_10.gpr


title: E8.5 Wildtype  rep3

description: replicate 3


title: double_vs_prp28-1_rep2_dye-swap

description: prp28-1/prp8-tes vs. prp28-1, biological replicate 2, dye-swap. Raw data: 0518_014-20.gpr


title: E9.5 Wildtype  rep2

description: replicate 2


title: E8.5 Cirh1a+/- rep1

description: replicate 1


title: E9.5 Wildtype  rep1

description: replicate 1


title: E8.5 Wildtype  rep2

description: replicate 2


title: E8.5 Cirh1a+/- rep3

description: replicate 3


title: double_vs_prp28-1_dye-swap

description: prp28-1/prp8-tes vs. prp28-1, dye-swap. Raw data: 0412_076_20.gpr


title: double_vs_wt_rep2

description: prp28-1/prp8-tes vs. wt, biological replicate 2. Raw data: 0518_012-10.gpr

source_name: saccharomyces cerevisiae wild-type strain

value: wild-type


title: double_vs_wt_dye-swap

description: prp28-1/prp8-tes vs. wt, dye-swap. Raw data: 0412_075_20.gpr


title: double_vs_wt

description: prp28-1/prp8-tes vs. wt. Raw data: 0412_075_10.gpr


title: double_vs_wt_rep2_dye-swap

description: prp28-1/prp8-tes vs. wt, biological replicate 2, dye-swap. Raw data: 0518_012-20.gpr


title: prp28-1_vs_wt_rep2-dye-swap

description: prp28-1 vs. wt, biological replicate 2, dye-swap. Raw data: 0518_011-20.gpr


title: prp28-1_vs_wt_rep2

description: prp28-1 vs. wt, biological replicate 2. Raw data: 0518_011-10.gpr


title: prp8-tes_vs_wt_rep2_dye-swap

description: prp8-tes vs. wt, biological replicate 2, dye-swap. Raw data: 0518_010-20.gpr

source_name: saccharomyces cerevisiae prp8-tes strain


title: prp28-1_vs_wt

description: prp28-1 vs. wt. Raw data: 0412_074_10.gpr


title: prp28-1_vs_wt_dye-swap

description: prp28-1 vs. wt, dye-swap. Raw data: 0412_074_20.gpr


title: E11.5 Wildtype  rep3

description: replicate 3


title: prp8-tes_vs_wt_dye-swap

description: prp8-tes vs. wt, dye-swap. Raw data: 0412_073_20.gpr


title: E8.5 Wildtype  rep1

description: replicate 1


title: prp8-tes_vs_wt_rep2

description: prp8-tes vs. wt, bioligical replicate 2. Raw data: 0518_010-10.gpr


title: prp8-tes_vs_wt

description: prp8-tes vs. wt. Raw data: 0412_073_10.gpr


title: 1624F LOW liver_rep100

city: Lleida

first: Romi

middle: N

last: Pena

state: Lleida

address: 191 Alcalde Rovira Roure Ave

department: Animal Production

institute: University  of Lleida

description: global gene expression data from liver samples of adult duroc pigs

hyb_protocol: Hybridisation protocol as recommented by Affymetrix using the Porcine Genome Array from Affymetrix.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A, as recommended by Affymetrix

data_processing: CEL files were compiled using the BRB-array tool. Data was normalised with the GCRMA algorithm. Class comparison (HIGH vs LOW) was performed with the Class Comparision option of the  BRB-array tool, with 10000 permutations, and FDR<5%.

organism: Sus scrofa

source_name: liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Duroc pigs were grown in standart commercial condictions, fed a commercial pellet diet and slaughtered at 190 days of age. Tissue samples were collected at slaughter, snap froxen in LN2 and stored at -80ºC until analysis

extract_protocol: total RNA was extracted from gluteus medius muscle using Ribopure kit (AMBION) following the manufacturer's protocol

treatment_protocol: After slaughter, controled animals (n=350) were ranked based in 13 carcass, plasma and muscle fat deposition and fat composition traits. The top amd bottom extreme of this distribution were selected to form the HIGH (n=53) and LOW (n=51) groups.

tag: phenotype

value: low carcass, plasma and muscle fat content

tag: breed

value: duroc

value: male

value: neutered

value: 190 days of age


title: 1602F LOW liver_rep96

tag: age


title: 1903F HIGH liver_rep102

value: high carcass, plasma and muscle fat content


title: 1605F HIGH liver_rep98


title: 1592F HIGH liver_rep94


title: 1910F LOW liver_rep104


title: 1901F LOW liver_rep101


title: 1567F HIGH liver_rep92


title: 1553F LOW liver_rep89


title: 1604F LOW liver_rep97


title: 1906F LOW liver_rep103


title: 1586F HIGH liver_rep93


title: 1559F LOW liver_rep90


title: 1619F HIGH liver_rep99


title: 1563F HIGH liver_rep91


title: 1540F HIGH liver_rep85


title: 1545F LOW liver_rep86


title: 1528F HIGH liver_rep81


title: 1538F HIGH liver_rep83


title: Control: empty vector_rep2

first: Sandra

last: Rodriguez-Perales

address: Melchor Fernandez Almagro,3

institute: CNIO

description: Gene expression after 2 weeks of transduction

hyb_protocol: 1.0 ug of Cy3-labelled cRNA  was fragmented at 60°C for 30 minutes in a reaction containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human SurePrint GE 8x60K Microarrays (GPL16699) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505X) C class using one color scan  (Scan resolution 3mm, Dye channel is set to Cy3 (Green)).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: CD34+ cells isolated from umbilical cord blood

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

extract_protocol: RNA was prepared using the RNeasy Mini Kit (QIAGEN) purification of total RNA from animal cells, following the manufacture's recomendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Total CD34+ cells were purified from normal human cord blood (CB) samples using direct CD34+ MACS magnetic bead separation over two sequential columns (Miltenyi Biotec) according to the manufacturer’s instructions. CD34+ cells were cultured in IMDM media containing 20% FBS, 100 U/mL penicillin/streptomycin and a citokine cocktail of FLT3L (100 ng/mL), SCF (100 ng/mL), TPO (100 ng/mL), IL-6 (20 ng/mL), GM-CSF (20 ng/mL), EPO (6 U/mL) and IL-3 (50 ng/mL) (Peprotech). This was performed at 37ºC in a humidified incubator with an atmosphere of 5% O2.CD34+ cells were pre-stimulated with the cytokine cocktail for 48 h, and infected with concentrated virus in the presence of polybrene (8μg/ml)

value: cord blood

tag: transfection

value: control


title: RUNX1/ETO_rep2


title: 1539F LOW liver_rep84


title: 1503F LOW liver_rep79


title: 1513F LOW liver_rep80


title: 1497F LOW liver_rep76


title: RUNX1/ETO_rep1


title: RUNX1a_rep1


title: RUNX1a_rep2


title: RUNX1/TMEM48_rep2


title: 1496F HIGH liver_rep75


title: 1533F HIGH liver_rep82


title: 1594F LOW liver_rep95


title: 1551F LOW liver_rep88


title: 1502F HIGH liver_rep78


title: 1550F LOW liver_rep87


title: 1498F HIGH liver_rep77


title: 1487F HIGH liver_rep72


title: RUNX1/TMEM48_rep1


title: Control: empty vector_rep1


title: AML Patient 48hrs Dar first cycle

city: Lausanne

first: Eric

middle: R

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

country: Switzerland

institute: EPFL

description: Sensitivity

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing: Raw text files for the one-color Agilent array were imported in R version 2.14.0 using the package limma(PMID 16646809). We processed the data by first subtracting the background using normexp,  took the log2 of the remaining intensity and applied quantile normalization to the entire set of arrays. Differential expression of genes was computed using limma(PMID 16646809). We considered genes as differentially expressed if the mean normalized signal of the two conditions is higher than 5 and the differential expression is greater than two fold change.

source_name: Human PBMCs

label_protocol: standard Agilent protocol

extract_protocol: Peripheral blood was collected in heparin tubes. PBMCs were isolated using Ficoll gradient separation. RNA was isolated using Qiagen AllPrep Mini kit.

treatment_protocol: Darinaparsin (300mg/m2) was administered by intravenous infusion on five consecutive days followed by 16 days off drug. Following the end of the first 21-day cycle, this protocol was repeated for cycle 2.

tag: genotype

tag: disease state

value: AML

tag: cell type

value: PBMC

tag: treatment

value: 48hrs darinaparsin first cycle


title: AML Patient Pre-treatment first cycle

description: Sensitivity

value: Pre-treatment first cycle


title: 1495F LOW liver_rep74

tag: Sex


title: Tibialis Anterior Muscle_Ctrl_ZT20_replicate B

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova

hyb_protocol: Fragmented and biotin-labeled sense strand DNA were hybridized for 16 hr at 45C on Affymetrix Mouse Gene 1.0 ST arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

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

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

source_name: Control_Tibialis Anterior_ZT20

label_protocol: 5.5μg sense strand DNA was prepared from 250ng total RNA using the Ambion® WT Expression Kit for Affymetrix® GeneChip® Whole Transcript (WT) Expression Arrays, and was fragmented and biotin-labeled using the GeneChip® WT Terminal Labeling Kit according to manufacturer's intructions.

growth_protocol: Animals: Conditional muscle-specific inactivation of Bmal1 (mKO) was obtained by crossing a mouse line with floxed Bmal1 (Storch et al., Cell, 2007) with mouse line carrying a Cre recombinase transgene under control of the Mlc1f promoter (Mlc1f-Cre) (Bothe et al., Genesis, 2000). 5 month old adult male mKO mice and Cre negative littermates (Ctrl) were used for microarray experiments.

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

treatment_protocol: Animals were housed in an isolated temperature controlled room (22°C) under a 12-h light-dark regimen, with lights on at ZT0 (Zeitgeber Time 0, or 6am), lights off at ZT12 (Zeitgeber Time 12, or 6pm), with standard chow and water provided ad libitum. Soleus (SOL) and Tibialis Anterior (TA) were collected immediately after cervical dislocation at ZT0, 4, 8, 12, 16, and 20, snap frozen in liquid nitrogen and stored at -80°C until subsequent use.

tag: strain background

tag: genotype/variation

value: control Cre- littermates (Ctrl)

tag: gender

value: 5 months

value: tibialis anterior skeletal muscle

tag: time point

value: Zeitgeber Time 20

tag: source animal id


title: AML Patient 48hrs Dar second cycle

description: Resistance

value: 48hrs darinaparsin second cycle


title: AML Patient Pre-treatment second cycle

description: Resistance

value: Pre-treatment second cycle


title: Tibialis Anterior Muscle_mKO_ZT20_replicate B

source_name: mKO_Tibialis Anterior_ZT20

value: muscle-specific Bmal1 knockout (mKO)

tag: tissue


title: 1488F LOW liver_rep73

value: low carcass, plasma and muscle fat content

value: duroc

value: male


title: Tibialis Anterior Muscle_Ctrl_ZT20_replicate C


title: 1469F HIGH liver_rep70

value: high carcass, plasma and muscle fat content

value: neutered

value: 190 days of age


title: 1467F LOW liver_rep68


title: 1483F HIGH liver_rep71


title: 1456F LOW liver_rep67


title: Tibialis Anterior Muscle_Ctrl_ZT20_replicate A


title: Tibialis Anterior Muscle_mKO_ZT20_replicate A


title: Tibialis Anterior Muscle_mKO_ZT20_replicate C


title: 1452F HIGH liver_rep66


title: Tibialis Anterior Muscle_Ctrl_ZT16_replicate B

source_name: Control_Tibialis Anterior_ZT16

value: Zeitgeber Time 16


title: 1468F HIGH liver_rep69


title: Tibialis Anterior Muscle_Ctrl_ZT16_replicate A


title: 1450F LOW liver_rep65


title: Tibialis Anterior Muscle_mKO_ZT16_replicate C

source_name: mKO_Tibialis Anterior_ZT16


title: Tibialis Anterior Muscle_mKO_ZT16_replicate B


title: 1444F LOW liver_rep63


title: 1446F LOW liver_rep64


title: Tibialis Anterior Muscle_Ctrl_ZT16_replicate C


title: Tibialis Anterior Muscle_Ctrl_ZT12_replicate C

source_name: Control_Tibialis Anterior_ZT12

value: Zeitgeber Time 12


title: Tibialis Anterior Muscle_mKO_ZT16_replicate A


title: Tibialis Anterior Muscle_Ctrl_ZT12_replicate A


title: Tibialis Anterior Muscle_mKO_ZT12_replicate C

source_name: mKO_Tibialis Anterior_ZT12


title: 1431F HIGH liver_rep61


title: 1429F HIGH liver_rep60


title: Tibialis Anterior Muscle_mKO_ZT12_replicate B


title: 1443F HIGH liver_rep62


title: Tibialis Anterior Muscle_Ctrl_ZT12_replicate B


title: Tibialis Anterior Muscle_mKO_ZT12_replicate A


title: Tibialis Anterior Muscle_Ctrl_ZT8_replicate B

source_name: Control_Tibialis Anterior_ZT8

value: Zeitgeber Time 8


title: Tibialis Anterior Muscle_Ctrl_ZT4_replicate A

source_name: Control_Tibialis Anterior_ZT4

value: Zeitgeber Time 4


title: Tibialis Anterior Muscle_Ctrl_ZT8_replicate C

value: control Cre- littermates (Ctrl)


title: Tibialis Anterior Muscle_mKO_ZT8_replicate C

source_name: mKO_Tibialis Anterior_ZT8

value: 5 months


title: 1412F HIGH liver_rep59


title: 1403F LOW liver_rep57


title: Tibialis Anterior Muscle_mKO_ZT8_replicate B

value: tibialis anterior skeletal muscle


title: Tibialis Anterior Muscle_mKO_ZT8_replicate A


title: 1402F LOW liver_rep56


title: 1404F LOW liver_rep58


title: Tibialis Anterior Muscle_Ctrl_ZT8_replicate A


title: 8697F HIGH liver_rep54


title: 8700F LOW liver_rep55


title: Tibialis Anterior Muscle_mKO_ZT4_replicate B

source_name: mKO_Tibialis Anterior_ZT4

value: BM3     7


title: Tibialis Anterior Muscle_Ctrl_ZT4_replicate C


title: Tibialis Anterior Muscle_Ctrl_ZT4_replicate B


title: Tibialis Anterior Muscle_mKO_ZT4_replicate C

value: BM3     8


title: Tibialis Anterior Muscle_mKO_ZT4_replicate A

value: BM3     3


title: 8695F HIGH liver_rep53


title: 8694F LOW liver_rep52


title: Tibialis Anterior Muscle_Ctrl_ZT0_replicate C

source_name: Control_Tibialis Anterior_ZT0

value: Zeitgeber Time 0


title: Tibialis Anterior Muscle_Ctrl_ZT0_replicate B


title: Tibialis Anterior Muscle_mKO_ZT0_replicate B

source_name: mKO_Tibialis Anterior_ZT0

value: muscle-specific Bmal1 knockout (mKO)


title: 8693F LOW liver_rep51

value: low carcass, plasma and muscle fat content

value: duroc


title: Tibialis Anterior Muscle_Ctrl_ZT0_replicate A

value: male


title: 8688F HIGH liver_rep48

value: high carcass, plasma and muscle fat content

value: neutered


title: 8692F LOW liver_rep50

value: 190 days of age


title: Tibialis Anterior Muscle_mKO_ZT0_replicate C


title: Soleus Muscle_mKO_ZT20_replicate C

value: soleus skeletal muscle

value: Zeitgeber Time 20


title: Soleus Muscle_Ctrl_ZT20_replicate C


title: Soleus Muscle_Ctrl_ZT20_replicate B


title: Soleus Muscle_Ctrl_ZT20_replicate A


title: 8689F HIGH liver_rep49


title: Soleus Muscle_mKO_ZT20_replicate B


title: Tibialis Anterior Muscle_mKO_ZT0_replicate A


title: Soleus Muscle_mKO_ZT20_replicate A


title: 2823F HIGH liver_rep47


title: Soleus Muscle_Ctrl_ZT16_replicate C

value: Zeitgeber Time 16


title: Soleus Muscle_Ctrl_ZT16_replicate A

value: control Cre- littermates (Ctrl)


title: 2820F HIGH liver_rep46


title: 2817F LOW liver_rep45


title: Soleus Muscle_mKO_ZT16_replicate B

value: 5 months


title: 2809F LOW liver_rep44


title: Soleus Muscle_mKO_ZT16_replicate C


title: 2807F HIGH liver_rep42


title: Soleus Muscle_mKO_ZT16_replicate A


title: Soleus Muscle_mKO_ZT12_replicate C

value: Zeitgeber Time 12


title: Soleus Muscle_Ctrl_ZT12_replicate C


title: Soleus Muscle_Ctrl_ZT12_replicate A


title: 2808F HIGH liver_rep43


title: SSSE_28d_S_28D_rep_8

city: Bonn

first: Khalid

middle: A.

last: Abnaof

state: North Rhine-Westfalina

address: Dahlmann Straße 2

department: Algorithmic Bioinformatics

country: Germany

institute: Bonn-Aachen International Centre for Information Technology (B-IT)

description: S24H 7. Group

hyb_protocol: Tecan hybridization stations with fully automated washing steps according to manufacturer instructions

scan_protocol: Imagene Scanner according to manufacturer instructions

data_processing:
norm exponential convulsion method was used for background correction and loess normalization for within array normalization and quantile normalization for between array normalization, spot quality weights are consided
Series supplementary file normalized.txt includes background-corrected and normalized log2 ratio (Cy5/Cy3)
miRBase 15.0

source_name: Hippocampal cells (SSSE Triggered mouse C57BI/6J)

label_protocol: miRCURY LNATM microRNA Hi-Power Labeling Kit according to manufacturer instructions

extract_protocol: Total RNA was isolated from the sonicated tissue using miRVANA miRNA isolation kit According to manufacturer instructions

treatment_protocol: Status Epilepticus (SE) is induced in mice  through electrical stimulation (90min, 100 ms trains of 1 ms, 2 trains per 1 s, 250 μA peak current intensity)

tag: replicate

tag: strain

value: hippocampal cells

source_name: Total RNA from pooled hippocampal cells (SSSE triggered mouse C57BI/6J)


title: Soleus Muscle_Ctrl_ZT12_replicate B


title: Soleus Muscle_Ctrl_ZT16_replicate B


title: Soleus Muscle_mKO_ZT12_replicate B


title: 2805F HIGH liver_rep41

source_name: liver

tag: phenotype


title: SSSE_28d_S_28D_rep_7

description: S18H 7. Group


title: Soleus Muscle_Ctrl_ZT8_replicate C

value: Zeitgeber Time 8


title: SSSE_28d_S_28D_rep_6

description: S16H 7. Group


title: Soleus Muscle_Ctrl_ZT8_replicate A


title: Soleus Muscle_Ctrl_ZT8_replicate B


title: 2801F HIGH liver_rep40

tag: breed


title: Soleus Muscle_mKO_ZT12_replicate A

tag: age


title: SSSE_28d_S_28D_rep_5

description: S15H 7. Group


title: Soleus Muscle_mKO_ZT8_replicate C


title: Soleus Muscle_Ctrl_ZT4_replicate C

value: Zeitgeber Time 4


title: 2734F HIGH liver_rep38


title: 2737F HIGH liver_rep39


title: Soleus Muscle_mKO_ZT8_replicate B


title: Soleus Muscle_mKO_ZT8_replicate A


title: 2731F LOW liver_rep37


title: SSSE_28d_S_28D_rep_4

description: S11H 7. Group


title: SSSE_28d_S_28D_rep_3

description: S8H 7. Group


title: Soleus Muscle_Ctrl_ZT4_replicate A


title: Soleus Muscle_Ctrl_ZT4_replicate B


title: SSSE_28d_S_28D_rep_2

description: S2H 7. Group


title: 2716F LOW liver_rep35


title: Soleus Muscle_mKO_ZT4_replicate A

value: BM3     3


title: SSSE_28d_S_28D_rep_1

description: S1H 7. Group


title: SSSE_24h_S_24H_rep_8

description: S29H 3. Group


title: Soleus Muscle_mKO_ZT4_replicate C

value: muscle-specific Bmal1 knockout (mKO)

value: BM3     8


title: 2723F HIGH liver_rep36

value: duroc


title: Soleus Muscle_mKO_ZT4_replicate B

value: male

value: BM3     7


title: Soleus Muscle_Ctrl_ZT0_replicate C

value: Zeitgeber Time 0


title: Soleus Muscle_Ctrl_ZT0_replicate B


title: F (BLOOD)

city: Rio de Janeiro

first: Tatiana

middle: Vaz de

last: Carvalho

state: Rio de Janeiro

address: Andre Cavalcanti 37

department: Genetica

country: Brazil

institute: INCA

hyb_protocol: PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: Analysis were performed using Affymetrix® Chromosome Analysis Suite (ChAS) software. Gains and losses in tumour and blood samples from each patient were estimated with 95% confidence intervals. Map position was based on the UCSC Genome Browser, February 2009, gh19  (NCBI Build 37 reference sequence).

source_name: Blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA from blood was extracted from lymphocytes of peripheral blood at diagnosis using the Qiagen DNA Blood Mini Kit. Genomic DNA from tumour was extracted from tissue of pieces of neuroblastoma tumour at diagnosis using the Qiagen DNA Blood Mini Kit, as well. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

value: Lymphocytes

value: Female


title: Soleus Muscle_Ctrl_ZT0_replicate A

value: soleus skeletal muscle


title: SSSE_24h_S_24H_rep_7

description: S28H 3. Group


title: 2705F HIGH liver_rep33

value: high carcass, plasma and muscle fat content

value: neutered

value: 190 days of age


title: Soleus Muscle_mKO_ZT0_replicate C

value: 5 months


title: SSSE_24h_S_24H_rep_6

description: S27H 3. Group

value: hippocampal cells


title: SSSE_24h_S_24H_rep_5

description: S25H 3. Group


title: Soleus Muscle_mKO_ZT0_replicate A


title: 2709F HIGH liver_rep34


title: Soleus Muscle_mKO_ZT0_replicate B


title: 2701F HIGH liver_rep31


title: 2561F LOW liver_rep30

value: low carcass, plasma and muscle fat content


title: 2704F HIGH liver_rep32


title: SSSE_24h_S_24H_rep_4

description: S23H 3. Group


title: 2557F LOW liver_rep29


title: HUVECs3

city: Vienna

first: Klemens

last: Vierlinger

address: Giefinggasse 4

department: HMD

country: Austria

institute: AIT

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 50 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters  to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: endothelial cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNeasy AllPrep column extraction (Qiagen) using the manufacturers protocols

tag: celltype

value: HUVECs


title: SSSE_24h_S_24H_rep_2

description: S6H 3. Group


title: HUVECs2


title: 2556F HIGH liver_rep28


title: SSSE_24h_S_24H_rep_1

description: S5H 3. Group


title: HUVECs1


title: G (TUMOUR)

source_name: Tumour

value: Neuroblastoma

value: Male


title: SSSENaive_SN_rep_7

description: S66H 4. Group

source_name: Hippocampal cells (wild-type mouse C57BI/6J)

value: Naive

source_name: Total RNA from pooled hippocampal cells (wild-type mouse C57BI/6J)


title: SVPs2

source_name: pericytes

value: SVPs


title: C (BLOOD)


title: D (BLOOD)


title: G (BLOOD)


title: E (TUMOUR)


title: SSSE_24h_S_24H_rep_3

description: S22H 3. Group


title: SSSENaive_SN_rep_6

description: S65H 4. Group


title: SSSENaive_SN_rep_5

description: S64H 4. Group


title: SSSENaive_SN_rep_4

description: S63H 4. Group


title: 2551F LOW liver_rep26

value: duroc

value: male


title: E (BLOOD)


title: D (TUMOUR)


title: 2552F HIGH liver_rep27


title: 2546F HIGH liver_rep23


title: SSSENaive_SN_rep_3

description: S62H 4. Group


title: B (TUMOUR)


title: SVPs1


title: 2550F HIGH liver_rep25


title: SSSENaive_SN_rep_2

description: S61H 4. Group


title: Pilocarpine_28 _d_rep8

source_name: Hippocampal cells (Pilocarpne treated mouse NMRI)

treatment_protocol: SE was induced in mice (NMRI) chemically by a single dose of Pilocarpine (300mg/kg;i.p.).

value: Treated (Pilocarpine)

tag: time

value: NMRI

source_name: Total RNA from pooled hippocampal cells (single dose Pilocarpine treated mouse NMRI)


title: 2542F LOW liver_rep21


title: 2189F LOW liver_rep19


title: 2187F LOW liver_rep18


title: Pilocarpine_28 _d_rep7


title: C (TUMOUR)


title: Pilocarpine_28 _d_rep5


title: F (TUMOUR)

value: Female


title: SSSENaive_SN_rep_1

description: S60H 4. Group


title: Pilocarpine_28 _d_rep1


title: Pilocarpine_28 _d_rep2


title: B (BLOOD)

value: Lymphocytes


title: Pilocarpine_28 _d_rep4


title: A (TUMOUR)


title: Pilocarpine_28 _d_rep3


title: Naive_28 _d_rep8

source_name: Hippocampal cells (wild-type mouse NMRI)

source_name: Total RNA from pooled hippocampal cells (wild-type mouse NMRI)


title: Naive_28 _d_rep7


title: Naive_28 _d_rep6


title: 2178F LOW liver_rep16


title: 2172F LOW liver_rep13


title: 2157F LOW liver_rep10


title: 2176F LOW liver_rep15


title: Naive_28 _d_rep5


title: 2168F LOW liver_rep12


title: 2549F LOW liver_rep24


title: 2174F LOW liver_rep14


title: Naive_28 _d_rep4


title: Naive_28 _d_rep3


title: 2152F HIGH liver_rep9

value: high carcass, plasma and muscle fat content


title: A (BLOOD)


title: SVPs3


title: 2164F LOW liver_rep11

value: neutered


title: Naive_28 _d_rep1


title: 2144F HIGH liver_rep6

value: 190 days of age


title: SSSENaive_SN_rep_8

description: S67H 4. Group


title: 2151F HIGH liver_rep8


title: Pilocarpine_24_h_rep7


title: Naive_28 _d_rep2


title: 2149F HIGH liver_rep7


title: 2196F HIGH liver_rep20


title: 1917F LOW liver_rep2


title: Pilocarpine_24_h_rep6


title: 2179F HIGH liver_rep17


title: 1919F LOW liver_rep4


title: 2142F HIGH liver_rep5


title: Pilocarpine_24_h_rep8


title: RU109_1223_mammary

first: David

last: Quigley

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

institute: UCSF

hyb_protocol: 90uL of hybridization sample were incubated in the Affymetrix GeneTitan Oven instrument for 17 hours at 48C. Arrays were processed with the Affymetrix GeneTitan Fluidics Station instrument, using the 550039 fluidics script and the GeneTitan Hybridization Module for WT Array Plates.

scan_protocol: An Affymetrix GeneTitan instrument was used to acquire the microarray image data

data_processing: CEL files were background corrected and normalized with RMA using the oligo package. Batch effects for array plate and lymph node cluster were corrected using ComBat, using covariates described in sample metadata

source_name: Mammary fat pad

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

growth_protocol: Mice were housed in standard conditions with chow and water ad libitum.

extract_protocol: Trizol followed by Qiagen RNEasy clean-up

treatment_protocol: Mice were not treated

value: mammay fat pads

tag: genetic background

value: [FVB/N x Spret/Ei] x FVB/N Backcross

value: female

value: 8 wk


title: RU109_1222_mammary


title: 2545F HIGH liver_rep22


title: RU109_1213_mammary


title: 1918F LOW liver_rep3

value: low carcass, plasma and muscle fat content


title: RU109_1219_mammary


title: 1911F HIGH liver_rep1


title: RU109_1212_mammary


title: Pilocarpine_24_h_rep5

tag: cell type

value: hippocampal cells


title: RU109_1211_mammary


title: RU109_1203_mammary


title: Pilocarpine_24_h_rep4


title: RU109_1210_mammary


title: Pilocarpine_28 _d_rep6


title: RU109_1221_mammary


title: Pilocarpine_24_h_rep1


title: Naive_24_h_rep8

value: Naive


title: Pilocarpine_24_h_rep3


title: Naive_24_h_rep7


title: RU109_1194_mammary


title: RU109_1202_mammary


title: mammary gland_four times daily milking 21 d_rep 1

city: Burlington

first: Emma

middle: Hull

last: Wall

state: VT

address: 89 Beaumont Ave

department: Medicine

institute: University of Vermont

description: Cow 1 4X time 1

hyb_protocol: The biotinylated cRNAs were fragmented into 50- to 200-base fragments and then hybridized to GeneChip Bovine Genome Arrays for 16h at 45°C in a rotating Affymetrix GeneChip Hybridization Oven 320.  After hybridization, arrays were washed and stained with streptavidin-phycoerythrin on an automated Affymetrix GeneChip Fluidic Station F450.

scan_protocol: The arrays were scanned with an Affymetrix GeneChip Scanner 2700 and the images quantified using Affymetrix GeneChip Operating Software.

data_processing: The signal intensity for each probe on each chip was calculated from scanned images using GeneChip Operating Software (Affymetrix), and signal intensities were analyzed using BioConductor (http://www.bioconductor.org).  Probe intensities were background corrected, normalized, and summarized using the Robust Multichip Average method described by Speed and coworkers (Bolstad et al., 2003; Irizarry et al., 2003).  An alternative normalization method based on housekeeping genes did not significantly change the results.  The false discovery rate (FDR) was calculated by performing distinct permutations of the sample labels (Benjamini et al., 2001; Storey and Tibshirani, 2003; Storey et al., 2005).  In experiment 1, probe sets were considered differentially expressed when the signed fold change (4X vs. 2X) was ≥ 2, the P-value was < 0.05, and the FDR was < 0.20.  In experiment 2, probe sets were considered differentially expressed when the signed fold change was ≥ 1.2 and the P-value was < 0.10.  The less stringent signed fold change and P-value cutoffs for experiment 2 were used to allow for identification of genes that were differentially expressed in experiment 1 and may have been differentially expressed in experiment 2, but to a lesser degree.  To protect against false positives, the results of experiment 1 were used as a filter and only those genes differentially expressed in that experiment were investigated for differential expression in experiment 2.

organism: Bos taurus

source_name: bovine mammary gland, 4X milking

label_protocol: RNA amplification and microarray analysis for both experiments was performed at the University of Vermont microarray core facility using previously described protocols (Affymetrix, 2005-2006).  Briefly, 2 ug of total RNA from each tissue sample were reverse transcribed to the single stranded cDNA using a T7-oligo(dT) primer.  T4 DNA polymerase was used to synthesize double-stranded cDNA, which served as a template for in vitro transcription using T7 RNA polymerase to produce biotinylated cRNA.

extract_protocol: Total RNA was isolated from each biopsy sample using Trizol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.  The RNA was purified using the RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.

value: Lactating mammary gland

tag: group

value: four times daily milking


title: RU109_1200_mammary

tag: Sex


title: mammary gland_control_21 d_rep1

description: Cow 1 2X time 1

source_name: bovine mammary gland, control

value: control


title: Pilocarpine_24_h_rep2

value: Treated (Pilocarpine)


title: RU109_1190_mammary


title: RU109_1192_mammary


title: mammary gland_control_23 d_rep1

description: Cow 1 2X time 2


title: RU109_1183_mammary


title: RU109_1185_mammary


title: Naive_24_h_rep6

value: NMRI


title: RU109_1177_mammary