title: iCD103 CD103-

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-026655 Whole Mouse Genome Microarray 4x44K v2 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.

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. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Bone marrow dendritic cells, iCD103 CD103-

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

extract_protocol: RNA was prepared using Qiagen RNeasy Kit.

tag: strain/background

value: bone marrow dendritic cells

tag: cell subset


title: drought  overexression, biological rep2

status: Public on Dec 31 2014

type: RNA

city: Shanghai

first: Kai

last: Xu

address: No.2901, Beidi Rd.

country: China

institute: Shanghai Agrobiological Gene Center

description: Gene expression data from leaves after drought treatment

hyb_protocol: Following fragmentation, 10 μg of cRNA were hybridized for 16 hr at 45℃ on  Affymetrix Oryza sativa Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using default analysis settings and global scaling as normalization method by Partek Genomics Suite 6.5.

label: biotin

molecule: total RNA

organism: Oryza sativa

source_name: OsGRAS23 overexpression rice leaves,drought stress conditions, replicate 2

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

growth_protocol: The seedlings were grown with the liquid culture solution in grow chamber with a 16h light (28℃)/8h dark(24℃) photoperiod.

extract_protocol: Total RNA was extracted using TRIZOL Reagent following the manufacturer's instructions.

treatment_protocol: Half of the 21d-old seedlings were sampled as untreated control, and the rest half of these plants were transferred onto the filter papers to induce drought stress, when the leaves of WT plants began to roll, the leaves were collected for RNA isolation. Two biological replicates (20 seedlings for one replicate) were performed.

tag: tissue

value: leaves

tag: cultivar

value: japonica Zhonghua11

tag: genotype

value: OsGRAS23 overexpression

tag: age

tag: stress

value: drought


title: iCD103 CD103+

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

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

organism: Mus musculus

source_name: Bone marrow dendritic cells, iCD103 CD103+

tag: cell type


title: Primary melanoma_225

city: Lund

first: Göran

last: Jönsson

address: Scheelevägen 8

country: Sweden

institute: Lund University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using cubic spline normalisation. Features present in <80% of assays were discarded (presence defined as detection p‐value < 0.01), leaving 12,379 features for further analysis. After log2 transformation, the data were adjusted for plate by median centering each feature to zero.Reporters with standard deviation (SD) across the replicates of at least 0.3 in at least 50% of the replicated samples were excluded (n=3,447). Replicate samples were merged by average. Missing values have been imputed by k‐nearest neighbor imputation (k=10), using the R package impute. Using principal componenet analysis (PCA) the variation of  PC1 and PC3 were removed since these were strongly associated with technical variables. Hence, the processed data represent log(2) values adjusted for technical variation.

organism: Homo sapiens

source_name: Primary melanoma

label_protocol: Standard Illumina labelling protocol

extract_protocol: RNA was extractedusing the FFPE Roche kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: melanoma

tag: mutation status

value: Sporadic

tag: thickness

tag: histology

value: SSM

tag: clark

tag: number of replicates


title: heart/t3

city: Chandigarh

first: madhu

last: khullar

state: Chandigarh

address: Research Block-B

department: Experimental Medicine and Biotechnology

country: India

institute: Postgraduate Institute of Medical Education and Research

hyb_protocol: Following labeling, 21.5 ul of biotin-labeled RNA was hybridized for 16 hr at 48C on Affymetrix miRNA 2.0 Arrays. The miRNA 2.0 Arrays were washed and stained in the Affymetrix Fluidics Station 450 using fludics script FS450_0003.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 30007G..

data_processing: Data files were analyzed with Affymetrix miRNAQCtool using RMA background correction and quantile normalization (Default settings). Further normalized data also analysed follwed by differentiall miRNA expression and cluster analysis using  GeneSpring GX12.0 sofware.

organism: Rattus norvegicus

source_name: left ventrical/heart

label_protocol: FlashTag RNA Labeling with Genisphere RNA Labeling Kit

growth_protocol: Wistar rats were housed in standard polypropylene cages (2 rats/cage) and maintained under controlled room temperature and humidity with 12/12-hour light-dark cycle.

extract_protocol: Total RNA was isolated using RNeasy mini kit Qiagen.

treatment_protocol: Diabetes in Wistar rats was induced by feeding them with high-fat diet for 4 weeks followed by two Intraperitoneal injection of streptozotocin (STZ, 30mg/kg body weight), at one week interval.Non-diabetic rats was be fed with regular chow for 4 weeks followed by two Intraperitoneal injection of citrate buffer (pH 4.4, 0.05 M at a dose of 0.25 ml/kg body weight), as vehicle, at an interval of one week. Then after both Diabetic and non-diabetic rats were fed on high fat and normal chow diet, respectively and  were sacrificed at 12 weeks after the second STZ injection.   Diabetes in Wistar rats was confirmed by increased fasting blood glucose level (556.25±107.68mg/dl), Total Cholesterol (139.63±55.35mg/dl) & Triglycerides (78.93±21mg/dl), at the time of sacrifice. Intraperitoneal glucose tolerance test (IPGTT) and Intraperitoneal insulin resistance test (IPIRT) confirms glucose tolerance and insulin sensitivity in Diabetic rats.    DCM in Wistar rats was confirmed by the 1.6 fold increased heart to body weight ratio and presence of non-ischemic lesions, interstitial and perivascular fibrosis as well as myocytes atrophy and hypertrophy, on gross and microscopic examination of the heart.

value: heart let ventricle

tag: disease state

value: diabetic cardiomyopathy

tag: gender

value: male

tag: strain

value: Wistar

value: adult


title: ATRA_STA-NB10

city: Vienna

first: Maximilian

last: Kauer

address: Zimmermannplatz 10

department: Molecular Biology

country: Austria

institute: CCRI, St.Anna Children Cancer Research Institute

hyb_protocol: 12µg of aRNA were fragmented at 94°C for 35 min, using the Affymetrix fragmentation buffer, mixed with 200µl hybridization buffer containing hybridization controls and hybridized to GeneChip®PrimeView™Human Gene Expression Array microarrays. hybridization was done in the GeneChip Hybridization Oven 640.

scan_protocol: Fluorescence signals were recorded by an Affymetrix scanner 3000 7G

data_processing: The data was analyzed in R statistical environment using Bioconductor packages. Normalization was done using the RMA algorithm

source_name: Neuroblastoma primary cell line, MYCN amplified

label_protocol: Target labeling and hybridization. For Affymetrix GeneChip 3´ PrimeView analysis, 100 ng total RNA was processed to generate a biotinylated hybridization target using the 3' IVT Amplification Kit Module 1 from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer's protocols (Gene Chip 3´´ IVT Expression kit P/N 703210 Rev. 1, by Affymetrix).

growth_protocol: RPMI1640 GlutaMAX medium (Gibco, Life Technologies) supplemented with 1x Penicilin/Streptomycin, Na-Pyruvate, HEPES and 10% FCS (all PAA Laboratories GmbH, Austria) in a CO2 incubator at 37°C

extract_protocol: mRNA-extraction by using the miRNEasy kit (Qiagen)

treatment_protocol: all-trans-retinoic acid 5 µM for 10 days

tag: cell line

value: neuroblastoma


title: ATRA_CLB-Ma

description: CLB-Ma

source_name: Neuroblastoma cell line, MYCN amplified

value: CLB-Ma


title: Primary melanoma_224


title: heart/t2


title: MI IGF-1 oocytes

city: Foshan

first: Chenglai

last: Xia

address: Renming Xi  11#

institute: Affiliated Foshan Maternity & Chlid Healthcare Hospital, Southern Medical University

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.16.0) (Exiqon) according to array manual

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs with statistical significance were identified through Volcano Plot filtering.

source_name: MI oocytes

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling

growth_protocol: After the informed consent approval was obtained, the oocytes were collected from the patients who were explicitly informed about the research aims, their rights and interests in the research. From April to July 2013, a total of 107 oocytes at MI stage were obtained from patients who received intra-cytoplasmic sperm injection (ICSI) treatments at the Reproductive Medical Center of the Third Affiliated Hospital of Guangzhou Medical University.

extract_protocol: Denuded oocytes were stored in Trizol at -80°C prior to RNA purification. RNA from 45 oocytes in each treatment as above was pooled. To satisfy the minimum requirement of 250 ng RNA for microarray analysis, 300–400 ng RNA were used for each analysis.

treatment_protocol: The isolated MI oocytes were cultured at 37°C and 5% CO2 in G-2TM PLUS (Vitrolife, Sweden) treated with (45 oocytes) or without (62 oocytes) 200 ng/ml IGF-1 for 24 h (Peprotech, USA), then covered with ovoil (Vitrolife, Sweden). After 24 h, all oocytes were stored at 80°C until RNA was extracted. The average age of patients without IGF-1 treatment was 31.66 ± 3.90. The average age of patients with IGF-1 treatment was 31.25 ± 3.31. No apparent bias was detected between these two groups.

tag: Sex

value: female

tag: average age

value: 31.26 years old

tag: treatment


title: heart/c1

tag: tissue

value: control


title: MI oocytes

value: 31.66 years old


title: Primary melanoma_226

value: NM


title: heart/c2


title: Primary melanoma_223


title: Primary melanoma_220


title: drought wild type, bological rep1

source_name: wild-type rice leaves,drought stress conditions, replicate1

value: leaves

tag: cultivar

value: japonica Zhonghua11

tag: genotype

value: wild type


title: drought  overexression, biological rep1

source_name: OsGRAS23 overexpression rice leaves,drought stress conditions, replicate 1

value: OsGRAS23 overexpression

tag: age

tag: stress

value: drought


title: drought wild type, bological rep2

source_name: wild-type rice leaves,drought stress conditions, replicate2


title: normal overexression, biological rep1

description: Gene expression data from leaves before drought treatment

source_name: OsGRAS23 overexpression rice leaves,normal conditions, replicate 1


title: heart/t1

value: heart let ventricle


title: normal overexpression, biological rep2

source_name: OsGRAS23 overexpression rice leaves,normal conditions, replicate 2


title: Primary melanoma_217

value: melanoma

tag: mutation status

value: Sporadic


title: Primary melanoma_218

tag: thickness


title: Primary melanoma_214

value: nevus

tag: histology


title: Primary melanoma_221

value: Mucosal

tag: clark


title: Primary melanoma_216

tag: number of replicates


title: normal wild type, bological rep1

source_name: wild-type rice leaves,normal conditions, replicate 1


title: Primary melanoma_215

value: SSM


title: normal wild type, bological rep2

source_name: wild-type rice leaves,normal conditions, replicate 2


title: Primary melanoma_212

value: LMM


title: Lipase/Esterase A treated leaves, biological replicate3 [RMA]

city: Hyderabad

first: Ramesh

middle: V.

last: Sonti

state: Andhra Pradesh

address: Uppal Road

department: Plant Microbe Interactions

institute: Centre for cellular and molecular biology (CCMB)

description:
12hrs LipA-3.CEL
Expression profile of Lipase/Esterase A treated rice leaves, 12 h after infiltration

hyb_protocol: The biotinylated cRNAs were fragmented and 15µg of this sample was hybridized to Gene Chip Rice Genome Array for 16h at 450C and 60rpm. The hybridized gene chips were subjected to washing and staining protocol using an Affymetrix fluidics station 450

scan_protocol: The gene chips were scanned on an Affymetrix Scanner 3000

data_processing: The CEL files generated by the Gene Chip Operating System (Affymetrix) were subjected to GeneSpring 12.6 - GX - PA  (Agilent Technology) for further analysis. The PLIER 16 and RMA algorithms were used for data normalization

label: Biotin

source_name: Lipase/Esterase A treated leaves, 20 days old Taichung Native-1 rice seedlings

label_protocol: 8µg of total RNA were converted into biotinylated cRNA using Affymetrix one cycle labeling kit as per instructions of the manufacturer (Expression analysis technical manual, 2001, Affymetrix)

growth_protocol: TN-1 rice seeds were germinated in petri plates containing moistened filter paper. Three days old seedlings were transferred to plastic pots containing soil and were grown for 15 days in a green house. Two days before the actual treatment, the pots containing the rice seedlings were transferred to a growth chamber (28oC; 80% relative humidity with 12/12h light/dark cycle)

extract_protocol: 20-30 leaf pieces covering the infiltrated zone from each of the treatments were harvested 12h after infiltration and subjected to total RNA isolation using Trizol (Invitrogen)

treatment_protocol: 30-40μl of either Lipase/Esterase A (500μg/ml) purified from the culture supernatant of wild type Xoo or 10mM potassium phosphate buffer (pH 6.0) were infiltrated to the adaxial surfaces of rice leaves with a 1ml hypodermal syringe without the needle (as described in Jha et al. 2007; MPMI vol 20, pp 31-40)

value: Taichung Native 1

tag: cultivar description

value: bacterial blight susceptible rice cultivar

value: 20 days old

tag: developmental stage

value: seedling

tag: agent

value: Lipase/Esterase A

value: leaf


title: Primary melanoma_209


title: Lipase/Esterase A treated leaves, biological replicate2 [RMA]

description:
12hrs LipA-2.CEL
Expression profile of Lipase/Esterase A treated rice leaves, 12 h after infiltration


title: Buffer treated leaves, biological replicate2 [RMA]

description:
12hrs Buffer-2.CEL
Expression profile of buffer treated rice leaves, 12 h after infiltration

source_name: Buffer treated leaves, 20 days old Taichung Native-1 rice seedlings

value: control


title: Lipase/Esterase A treated leaves, biological replicate3 [PLIER]


title: Primary melanoma_210


title: Buffer treated leaves, biological replicate1 [RMA]

description:
12hrs Buffer-1.CEL
Expression profile of buffer treated rice leaves, 12 h after infiltration


title: Primary melanoma_208


title: Primary melanoma_206


title: Primary melanoma_207

value: NM


title: Buffer treated leaves, biological replicate3 [RMA]

description:
12hrs Buffer-3.CEL
Expression profile of buffer treated rice leaves, 12 h after infiltration


title: Lipase/Esterase A treated leaves, biological replicate1 [RMA]

description:
12hrs LipA-1.CEL
Expression profile of Lipase/Esterase A treated rice leaves, 12 h after infiltration


title: CPT_CLB-Ma

description: CLB-Ma

treatment_protocol: captothecin 5 nM for 3 weeks

tag: cell line

value: CLB-Ma

tag: cell type

value: neuroblastoma


title: Primary melanoma_205


title: Lipase/Esterase A treated leaves, biological replicate1 [PLIER]


title: Gene expression in HMEC

city: Shinagawa-ku

first: Hideyuki

last: Takeshima

state: Tokyo

department: Institute for Advanced Life Sciences

country: Japan

institute: Hoshi University

description: Untreated cells

hyb_protocol: 600 ng of labeled cRNA was hybridized to SurePrint G3 Human GE v2 8x60K Microarray for 17 hours at 65℃ and 10 rpm rotation. Microarrays was washed according to Agilent protocol.

scan_protocol: The microarray was scanned with an Agilent G2565BA microarray scanner (Agilent Technologies).

data_processing: Scanned data was analyzed with Feature Extraction Ver.9.1 and analyzed using GeneSpring Ver.12.5 software (Agilent Technologies).

source_name: Normal mammary epithelial cells, HMEC

label_protocol: From 200 ng of total RNA, Cy3-labeled cRNA was synthesized using Low Input Quick Amp Labeling Kit (Agilent technologies).

growth_protocol: Du145, PC3, MCF7, and MDA-MB-231 were maintained in RPMI1640 medium.  RWPE1 was maintained in keratinocyte-SFM.  HMEC was maintained in mammary epithelial cell serum-free growth medium.

extract_protocol: Total RNA was extracted from cancer cell lines and normal cells using ISOGEN (Nippon Gene, Tokyo, Japan).

value: HMEC


title: iPS OX3_9

type: genomic

city: Oxford

first: Sally

middle: A

last: Cowley

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

description: induced pluripotent stem cell line derived from dermal fibroblasts, control donor 'OX3', clone 9

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Standard Illumina scanning protocol for BeadChip Arrays

data_processing: The scanned data files were processed by GenomeStudio Genotyping module v1.9, using the cluster file HumanCytoSNP-12v2-1_H.egt provided by Illumina. Raw data was also uploaded to KaryoStudio (Illumina) for generation of karyotype reports (see publication).

label: Biotin (C, G), Dinitrophenyl (A, T)

molecule: genomic DNA

source_name: control iPSc OX3 clone 1

extract_protocol: genomic DNA was extracted using QIAGEN DNeasy blood and tissue kit

treatment_protocol: untreated cell samples; Fibroblasts grown in ADMEM + 10% FCS; iPSc lines all grown in mTeSR-1 medium + ES-qualified matrigel prior to harvest

tag: gender

value: male

tag: culture conditions

value: mTeSR-1 + matrigel


title: Primary melanoma_204

tag: tissue

value: melanoma

value: Sporadic


title: Lipase/Esterase A treated leaves, biological replicate2 [PLIER]

tag: cultivar


title: SIX2 overexpression, 4TO7 control, replicate 3

city: Salt Lake City

first: Aik Choon

last: Tan

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

country: USA

institute: Huntsman Cancer Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Gene 1.1 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed and normalized by using Affymetrix Power Tools (apt-probeset-summarize) with RMA.

source_name: tumor 4TO7 transduced with pcDNA, replicate 3

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

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


title: SIX2 overexpression, 4TO7 Six2 overexpression, replicate 3

source_name: tumor 4TO7 transduced with Six2 overexpression, replicate 3


title: Buffer treated leaves, biological replicate3 [PLIER]


title: Gene expression in RWPE1

description: Untreated cells

source_name: Normal prostatic epithelial cell line, RWPE1


title: Buffer treated leaves, biological replicate2 [PLIER]


title: 20110303_Blood_VivoSubQ_rAd5_1E8_024hr_3_AgilentV_TopL

status: Public on Dec 30 2014

city: Seattle

first: Daniel

middle: Edward

last: Zak

state: WA

address: 307 Westlake Ave N, Suite 5

institute: Seattle Biomedical Research Institute

hyb_protocol: 600ng of Cy3-labeled cRNA was hybridized in Agilent hybridization chambers for 17 hours at 65 C and 10rpm.  The arrays were washed for 1 minute in Agilent GE Wash Buffer 1 and then for another minute in Agilent GE Wash Buffer 2.

scan_protocol: Scanning was performed using an Agilent High-Resolution DNA Microarray Scanner, with 3 micron resolution and 20-bit dynamic range. The resulting images were processed with Agilent Feature Extraction version 10.7.3.1 to generate raw probe intensity data.

data_processing:
Arrays were normalized using the normalize.quantiles function in the Bioconductor package preprocessCore and then Log2 transformed.  Repeated measurements for a given gene were averaged in the following manner:
(1) Simple averages were computed for repeated measurements of individual sequences, then (2) weighted averages based on 90% expression quantiles were sequentially computed for repeated measures of Agilent SystematicName and then Agilent GeneName.

source_name: mouse PBMCs

label_protocol: Labeling was performed with the One-Color Microarray-Based Gene Expression Analysis protocol version 6.5 (Agilent).  Briefly, double-stranded cDNA was synthesized from 200ng of total RNA using a T7-oligo(dT) primer, followed by in vitro transcription by T7 RNA polymerase with incorporation of Cy3-labeled CTP.

extract_protocol: Draining popliteal lymph nodes were harvested in RNAprotect Cell Reagent (Qiagen). RNA was isolated using the RNAqueous 4PCR kit (Ambion) as per manufacturer instructions and yield and quality was checked using the RNA6000 Chip on a 2100 Bioanalyzer (Agilent)

treatment_protocol: Vectors were grown and purified as described previously (PMID:23390298). rAd5, rAd28, rAd35, sAd11 and sAd16 expressing SIV Gag were obtained from GenVec Inc. (Gaithersburg, MD). chAd3 and chAd63 backbones were obtained from Okairos (Italy). Poly I:C was formulated with poly-lysine and carboxy-methylcellulose and used at a dose of 50 µg.  A dose of 1 x 10^8 particle units (PU) given intramuscularly was chosen to provide a hierarchy of potency at memory. For rAd35, which does not elicit detectable responses at this dose, mice were vaccinated with 1 x 10^9 PU.

value: PBMCs

tag: genotype

value: WT

tag: bioreplicate comparison groups (batches)

value: D

tag: bioreplicate id

tag: stimulation condition

tag: vector dose (particle units)

tag: time post-stimulation

tag: in vivo or in vitro

value: in vivo

tag: array

value: AgilentV

tag: hyb position on 8-plex array

value: TopL


title: Buffer treated leaves, biological replicate1 [PLIER]

value: Taichung Native 1

tag: cultivar description

value: bacterial blight susceptible rice cultivar

tag: age

value: 20 days old

tag: developmental stage

value: seedling


title: SIX2 overexpression, 4TO7 Six2 overexpression, replicate 2

source_name: tumor 4TO7 transduced with Six2 overexpression, replicate 2

tag: cell line


title: 20110303_Blood_VivoSubQ_PBS_NA_024hr_4_AgilentV_BotR

tag: cell type

value: PBS

value: BotR


title: 20110308_Blood_VivoSubQ_rAd5_1E8_024hr_6_AgilentX_MidBotR

value: AgilentX

value: MidBotR


title: 20110303_Blood_VivoSubQ_rAd5_1E8_024hr_4_AgilentV_MidBotL

value: MidBotL


title: SIX2 overexpression, 4TO7 Six2 overexpression, replicate 1

source_name: tumor 4TO7 transduced with Six2 overexpression, replicate 1


title: 20110301_Blood_VivoSubQ_rAd5_1E8_024hr_1_AgilentT_TopR

value: AgilentT

value: TopR


title: 20110308_Blood_VivoSubQ_rAd28_1E8_024hr_6_AgilentX_MidBotL

value: PBMCs


title: 20110308_Blood_VivoSubQ_PBS_NA_024hr_5_AgilentX_MidTopL

value: WT

value: MidTopL


title: 20110303_Blood_VivoSubQ_rAd28_1E8_024hr_4_AgilentV_MidBotR

value: D

value: in vivo


title: 20110308_Blood_VivoSubQ_PBS_NA_024hr_6_AgilentX_BotL

value: BotL


title: 20110308_Blood_VivoSubQ_rAd5_1E8_024hr_5_AgilentX_TopR


title: iPS C9_7245_3

description: induced pluripotent stem cell line derived from dermal fibroblasts, ALS patient [C9orf72 expansion repeat] '7245', clone 3

source_name: ALS C9orf72 7245, iPSc clone 3

tag: gender

value: female

tag: culture conditions

value: mTeSR-1 + matrigel


title: 20110303_Blood_VivoSubQ_PBS_NA_024hr_3_AgilentV_MidTopR

value: AgilentV

value: MidTopR


title: 20110303_Blood_VivoSubQ_rAd28_1E8_024hr_3_AgilentV_TopR


title: HDF OX3

description: dermal fibroblasts, control donor

source_name: control fibroblasts

value: male

value: ADMEM + 10% FCS


title: SIX2 overexpression, 4TO7 control, replicate 1

source_name: tumor 4TO7 transduced with pcDNA, replicate 1


title: 20110301_Blood_VivoSubQ_rAd28_1E8_024hr_2_AgilentT_TopL

value: TopL


title: iPS C9_7245_1

description: induced pluripotent stem cell line derived from dermal fibroblasts, ALS patient [C9orf72 expansion repeat] '7245', clone 1

source_name: ALS C9orf72 7245, iPSc clone 1


title: 20110308_Blood_VivoSubQ_rAd28_1E8_024hr_5_AgilentX_TopL

value: AgilentX


title: 20110301_Blood_VivoSubQ_rAd5_1E8_024hr_2_AgilentT_TopR


title: SIX2 overexpression, 4TO7 control, replicate 2

source_name: tumor 4TO7 transduced with pcDNA, replicate 2


title: 20110301_Blood_VivoSubQ_rAd28_1E8_024hr_1_AgilentT_TopL


title: 20110301_Blood_VivoSubQ_PBS_NA_024hr_1_AgilentT_MidTopL

value: PBS


title: 20110301_Blood_VivoSubQ_PBS_NA_024hr_2_AgilentT_MidTopL

value: AgilentT


title: HDF C9_7245

description: dermal fibroblasts, ALS patient [C9orf72 expansion repeat] '7245'

source_name: ALS C9orf72 7245 fibroblasts


title: iPS C9_T2_7

description: induced pluripotent stem cell line derived from dermal fibroblasts, ALS patient [C9orf72 expansion repeat] 'T2', clone 7

source_name: ALS C9orf72 T2, iPSc clone 7


title: 20130327_popLN_Susp_VivoSubQ_PBS.TMEM173_NA_008hr_3.4F.2.0Mo_AgilentLM

source_name: mouse draining popliteal lymph node suspension

value: C


title: 20130327_popLN_Susp_VivoSubQ_PBS.WT_NA_008hr_5.4F.2.0Mo_AgilentLM

value: draining popliteal lymph node suspension


title: 20130327_popLN_Susp_VivoSubQ_rAd5.WT_3E7_008hr_7.5F.2.0Mo_AgilentLM

value: WT


title: 20130327_popLN_Susp_VivoSubQ_PBS.WT_NA_008hr_5.5F.2.0Mo_AgilentLM


title: 20130327_popLN_Susp_VivoSubQ_rAd5.WT_3E7_008hr_7.4F.2.0Mo_AgilentLM


title: 20130327_popLN_Susp_VivoSubQ_PBS.IFNAR1_NA_008hr_1.4M.5.0Mo_AgilentLM


title: 20130327_popLN_Susp_VivoSubQ_PBS.IFNAR1_NA_008hr_1.3M.5.0Mo_AgilentLM


title: 20130327_popLN_Susp_VivoSubQ_ChAd63.TMEM173_3E7_008hr_4.4F.2.0Mo_AgilentLM


title: 20130325_popLN_Susp_VivoSubQ_PBS.WT_NA_008hr_5.2F.2.0Mo_AgilentLM


title: 20130327_popLN_Susp_VivoSubQ_ChAd63.IFNAR1_3E7_008hr_2.5M.5.0Mo_AgilentLM


title: iPS C9_T2_6

description: induced pluripotent stem cell line derived from dermal fibroblasts, ALS patient [C9orf72 expansion repeat] 'T2', clone 6

source_name: ALS C9orf72 T2, iPSc clone 6


title: 20130327_popLN_Susp_VivoSubQ_ChAd63.WT_3E7_008hr_6.4F.2.0Mo_AgilentLM


title: 20130325_popLN_Susp_VivoSubQ_PBS.TMEM173_NA_008hr_3.3F.2.0Mo_AgilentLM


title: 20130325_popLN_Susp_VivoSubQ_rAd5.WT_3E7_008hr_7.3F.2.0Mo_AgilentLM


title: 20130325_popLN_Susp_VivoSubQ_PBS.IFNAR1_NA_008hr_1.5F.10.Mo_AgilentLM


title: 20130327_popLN_Susp_VivoSubQ_ChAd63.TMEM173_3E7_008hr_4.5F.2.0Mo_AgilentLM


title: HDF C9_T2

description: dermal fibroblasts, ALS patient [C9orf72 expansion repeat] 'T2'

source_name: ALS C9orf72 T2 fibroblasts


title: 20130327_popLN_Susp_VivoSubQ_PBS.TMEM173_NA_008hr_3.5F.2.0Mo_AgilentLM


title: 20130327_popLN_Susp_VivoSubQ_ChAd63.IFNAR1_3E7_008hr_2.4F.5.0Mo_AgilentLM


title: 20130325_popLN_Susp_VivoSubQ_PBS.IFNAR1_NA_008hr_1.2F.5.0Mo_AgilentLM


title: 20130325_popLN_Susp_VivoSubQ_ChAd63.TMEM173_3E7_008hr_4.2F.2.0Mo_AgilentLM


title: 20130327_popLN_Susp_VivoSubQ_ChAd63.WT_3E7_008hr_6.5F.2.0Mo_AgilentLM


title: 20130325_popLN_Susp_VivoSubQ_PBS.WT_NA_008hr_5.3F.2.0Mo_AgilentLM


title: 20130325_popLN_Susp_VivoSubQ_ChAd63.WT_3E7_008hr_6.3F.2.0Mo_AgilentLM


title: 20130325_popLN_Susp_VivoSubQ_ChAd63.WT_3E7_008hr_6.2F.2.0Mo_AgilentLM


title: 20130325_popLN_Susp_VivoSubQ_rAd5.WT_3E7_008hr_7.2F.2.0Mo_AgilentLM


title: 20130325_popLN_Susp_VivoSubQ_PBS.TMEM173_NA_008hr_3.2F.2.0Mo_AgilentLM


title: 20130322_popLN_Susp_VivoSubQ_PBS.WT_NA_008hr_5.1F.2.0Mo_AgilentLM


title: 20130325_popLN_Susp_VivoSubQ_ChAd63.IFNAR1_3E7_008hr_2.3F.5.0Mo_AgilentLM


title: 20130322_popLN_Susp_VivoSubQ_PBS.TMEM173_NA_008hr_3.1F.2.0Mo_AgilentLM


title: 20130325_popLN_Susp_VivoSubQ_ChAd63.TMEM173_3E7_008hr_4.3F.2.0Mo_AgilentLM


title: 20130322_popLN_Susp_VivoSubQ_PBS.IFNAR1_NA_008hr_1.1F.5.0Mo_AgilentLM


title: 20130322_popLN_Susp_VivoSubQ_rAd5.WT_3E7_008hr_7.1F.2.0Mo_AgilentLM


title: 20130325_popLN_Susp_VivoSubQ_ChAd63.IFNAR1_3E7_008hr_2.2F.5.0Mo_AgilentLM


title: 20111116_popLN_Susp_VivoSubQ_PolyICLC_NA_072hr_3_AgilentJJ_TopR

value: B

value: PolyICLC

value: AgilentJJ

value: TopR


title: 20130322_popLN_Susp_VivoSubQ_ChAd63.WT_3E7_008hr_6.1F.2.0Mo_AgilentLM

value: in vivo


title: 20111116_popLN_Susp_VivoSubQ_PolyICLC_NA_072hr_4_AgilentJJ_MidTopL

value: MidTopL


title: 20111115_popLN_Susp_VivoSubQ_rAd5_1E8_072hr_2_AgilentII_TopL

value: AgilentII


title: 20111115_popLN_Susp_VivoSubQ_PolyICLC_NA_072hr_1_AgilentII_TopR


title: 20130322_popLN_Susp_VivoSubQ_ChAd63.TMEM173_3E7_008hr_4.1F.2.0Mo_AgilentLM


title: 20130322_popLN_Susp_VivoSubQ_ChAd63.IFNAR1_3E7_008hr_2.1F.5.0Mo_AgilentLM


title: 20111115_popLN_Susp_VivoSubQ_ChAd63_1E8_072hr_2_AgilentII_MidTopR

value: MidTopR


title: 20111115_popLN_Susp_VivoSubQ_PolyICLC_NA_024hr_4_AgilentHH_MidTopL

value: AgilentHH


title: 20111116_popLN_Susp_VivoSubQ_ChAd3_1E8_072hr_4_AgilentJJ_MidTopR


title: 20111115_popLN_Susp_VivoSubQ_rAd5_1E8_072hr_1_AgilentHH_MidBotR

value: MidBotR


title: 20111116_popLN_Susp_VivoSubQ_ChAd63_1E8_072hr_4_AgilentJJ_TopL

value: TopL


title: 20111115_popLN_Susp_VivoSubQ_ChAd3_1E8_072hr_2_AgilentII_MidTopL


title: 20111115_popLN_Susp_VivoSubQ_ChAd63_1E8_024hr_4_AgilentHH_TopL


title: 20111115_popLN_Susp_VivoSubQ_PolyICLC_NA_072hr_2_AgilentII_MidBotL

value: MidBotL


title: 20111115_popLN_Susp_VivoSubQ_ChAd3_1E8_072hr_3_AgilentII_BotL

value: BotL


title: 20111115_popLN_Susp_VivoSubQ_ChAd63_1E8_072hr_1_AgilentHH_MidBotL


title: 20111115_popLN_Susp_VivoSubQ_ChAd63_1E8_072hr_3_AgilentII_BotR

value: BotR


title: 20111115_popLN_Susp_VivoSubQ_PolyICLC_NA_024hr_3_AgilentHH_TopR


title: 20111110_popLN_Susp_VivoSubQ_rAd5_1E8_024hr_1_AgilentFF_MidBotR

value: AgilentFF


title: 20111110_popLN_Susp_VivoSubQ_rAd5_1E8_024hr_2_AgilentGG_TopL

value: draining popliteal lymph node suspension

value: AgilentGG


title: 20111115_popLN_Susp_VivoSubQ_ChAd3_1E8_024hr_4_AgilentHH_MidTopR

value: WT

value: B


title: 20111115_popLN_Susp_VivoSubQ_ChAd3_1E8_072hr_1_AgilentHH_BotR


title: 20111110_popLN_Susp_VivoSubQ_PolyICLC_NA_024hr_1_AgilentGG_TopR

value: PolyICLC


title: 20111110_popLN_Susp_VivoSubQ_rAd5_1E8_008hr_1_AgilentDD_TopR

value: AgilentDD

value: TopR


title: 20111110_popLN_Susp_VivoSubQ_PolyICLC_NA_024hr_2_AgilentGG_MidBotL

value: in vivo


title: 20111110_popLN_Susp_VivoSubQ_PolyICLC_NA_008hr_2_AgilentEE_MidTopR

value: AgilentEE


title: 20111110_popLN_Susp_VivoSubQ_PolyICLC_NA_008hr_3_AgilentEE_BotR


title: 20111110_popLN_Susp_VivoSubQ_rAd5_1E8_008hr_2_AgilentDD_BotR


title: 20111110_popLN_Susp_VivoSubQ_PolyICLC_NA_008hr_1_AgilentDD_MidBotR


title: 20111110_popLN_Susp_VivoSubQ_PBS_NA_008hr_4_AgilentFF_MidTopL

value: PBS

value: MidTopL


title: 20111110_popLN_Susp_VivoSubQ_PolyICLC_NA_008hr_4_AgilentFF_MidTopR

value: MidTopR


title: 20111110_popLN_Susp_VivoSubQ_ChAd63_1E8_024hr_2_AgilentGG_MidTopR


title: 20111110_popLN_Susp_VivoSubQ_ChAd63_1E8_024hr_3_AgilentGG_BotR


title: 20111110_popLN_Susp_VivoSubQ_PBS_NA_008hr_3_AgilentEE_BotL


title: 20111110_popLN_Susp_VivoSubQ_PBS_NA_008hr_1_AgilentDD_MidBotL


title: 20111110_popLN_Susp_VivoSubQ_ChAd63_1E8_008hr_4_AgilentFF_TopR


title: 20111110_popLN_Susp_VivoSubQ_PBS_NA_008hr_2_AgilentEE_MidTopL


title: 20111110_popLN_Susp_VivoSubQ_ChAd3_1E8_024hr_3_AgilentGG_BotL


title: 20111110_popLN_Susp_VivoSubQ_ChAd63_1E8_008hr_3_AgilentEE_MidBotR

value: MidBotR


title: 20111110_popLN_Susp_VivoSubQ_ChAd3_1E8_008hr_3_AgilentEE_MidBotL

value: MidBotL


title: 20111110_popLN_Susp_VivoSubQ_ChAd63_1E8_024hr_1_AgilentFF_MidBotL


title: 20111110_popLN_Susp_VivoSubQ_ChAd3_1E8_008hr_4_AgilentFF_TopL

value: TopL


title: 20110323_popLN_Susp_VivoSubQ_sAd11_1E8_072hr_VI_AgilentAA_MidBotR

value: A

value: AgilentAA


title: 20111110_popLN_Susp_VivoSubQ_ChAd63_1E8_008hr_1_AgilentDD_TopL

value: draining popliteal lymph node suspension


title: 20110323_popLN_Susp_VivoSubQ_sAd16_1E8_072hr_VI_AgilentAA_MidBotL


title: 20111110_popLN_Susp_VivoSubQ_ChAd3_1E8_008hr_1_AgilentDD_MidTopR


title: 20111110_popLN_Susp_VivoSubQ_ChAd3_1E8_024hr_2_AgilentGG_MidTopL

value: AgilentGG


title: 20110323_popLN_Susp_VivoSubQ_rAd35high_1E9_072hr_VI_AgilentAA_MidTopL

value: WT


title: 20111110_popLN_Susp_VivoSubQ_ChAd63_1E8_008hr_2_AgilentDD_BotL

value: B

value: BotL


title: 20110323_popLN_Susp_VivoSubQ_rAd28_1E8_072hr_VI_AgilentAA_TopL


title: 20111110_popLN_Susp_VivoSubQ_ChAd3_1E8_008hr_2_AgilentEE_TopR


title: 20110323_popLN_Susp_VivoSubQ_rAd5_1E8_072hr_VI_AgilentAA_TopR


title: 20110323_popLN_Susp_VivoSubQ_PBS_NA_072hr_VI_AgilentAA_BotL


title: 20110316_popLN_Susp_VivoSubQ_sAd16_1E8_072hr_V_AgilentZ_MidBotL

value: AgilentZ


title: 20110316_popLN_Susp_VivoSubQ_sAd16_1E8_072hr_IV_AgilentY_MidBotL

value: AgilentY


title: 20110316_popLN_Susp_VivoSubQ_sAd11_1E8_072hr_IV_AgilentY_MidBotR

value: in vivo


title: 20111110_popLN_Susp_VivoSubQ_ChAd3_1E8_024hr_1_AgilentFF_BotR

value: AgilentFF

value: BotR


title: 20110316_popLN_Susp_VivoSubQ_sAd11_1E8_072hr_V_AgilentZ_MidBotR


title: 20110316_popLN_Susp_VivoSubQ_rAd5_1E8_072hr_IV_AgilentY_TopR

value: TopR


title: 20110316_popLN_Susp_VivoSubQ_rAd35high_1E9_072hr_IV_AgilentY_MidTopL

value: MidTopL


title: 20110316_popLN_Susp_VivoSubQ_rAd28_1E8_072hr_IV_AgilentY_TopL


title: 20110316_popLN_Susp_VivoSubQ_rAd35high_1E9_072hr_V_AgilentZ_MidTopL


title: 20110316_popLN_Susp_VivoSubQ_PBS_NA_072hr_IV_AgilentY_BotL

value: PBS


title: H9c2 cells pTT vs. pTT-ApoO Transfected DyeSwap, Replicate 5

city: Toulouse

first: Philippe

middle: V

last: Rouet

address: 1 Ave Jean Poulhes

department: Cardiology

country: France

institute: INSERM U1048

description:
H9c2 cardiomyoblast cells are derived from embryonic BD1X rat heart; obtained from EACC.
Biological replicate 5 of 6.

hyb_protocol: Samples were mixed in hybridization buffer (chipHybe from Roche-Ventana) applied to microarrays prehybridized (1%BSA/ 2XSSC,/0.2%SDS) in Ventana Discovery System and hybridized 8 hours at 42°C. After hybridization, slides were washed sequentially in Ribowash buffer from Roche-Ventana (2 times), 0.1X SSC (1 time) and dried on a microcentrifuge.

scan_protocol: Scanned on an 4000B Axon scanner (from Molecular Device). Images were quantified using GenePix Software.

data_processing: LOWESS normalized, background subtracted data obtained from log2 of pTT-ApoO signal/pTT signal. Agilent software was used.

source_name: H9c2 cardiomyoblast, pTT-ApoO

label_protocol: 5µg of total RNA were labeled with the Chipshot Direct Labeling system from Promega.

growth_protocol: ES cells were kept in an undifferentiated, pluripotent state by using 1000 IU/ml leukemia inhibitory factor (LIF; Chemicon, ESGRO, ESG1107), and grown on top of murine embryonic fibroblasts feeder layer inactivated by 10 ug/ml of mitomycin C (Sigma, St. Louis). ES cells were cultured on 0.1% gelatin-coated plastic dishes in ES medium containing Dulbecco modified Eagle medium supplemented with 15% fetal calf serum, 0.1 mM beta-mercaptoethanol, 2 mM glutamine, and 0.1 mN non-essential amino acids.

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions. RNA integrity was tested by capillary electrophoresis on Experion (Bio-Rad).

treatment_protocol: Plasmid transfection by electroporation and cotransfection with pgkneo vector followed by G48 selection of transfectants.

tag: strain

value: cardiomyoblast cells

tag: treatment

value: pTT-ApoO transfected

tag: passage

source_name: H9c2 cardiomyoblast, pTT

value: pTT transfected


title: 20110316_popLN_Susp_VivoSubQ_PBS_NA_072hr_V_AgilentZ_BotL

tag: genotype

tag: bioreplicate comparison groups (batches)

value: A

tag: bioreplicate id


title: H9c2 cells pTT vs. pTT-ApoO Transfected DyeSwap, Replicate 1

description:
H9c2 cardiomyoblast cells are derived from embryonic BD1X rat heart; obtained from EACC.
Biological replicate 1 of 6.


title: 20101214_popLN_Susp_VivoSubQ_sAd16_1E8_072hr_I_AgilentM_MidBotR

value: draining popliteal lymph node suspension

tag: stimulation condition

tag: vector dose (particle units)

tag: time post-stimulation

value: AgilentM

value: MidBotR


title: H9c2 cells pTT vs. pTT-ApoO Transfected DyeSwap, Replicate 2

description:
H9c2 cardiomyoblast cells are derived from embryonic BD1X rat heart; obtained from EACC.
Biological replicate 2 of 6.


title: 20101214_popLN_Susp_VivoSubQ_sAd16_1E8_072hr_II_AgilentN_MidTopL

value: WT

tag: in vivo or in vitro

tag: array

value: AgilentN

tag: hyb position on 8-plex array


title: 20110316_popLN_Susp_VivoSubQ_rAd5_1E8_072hr_V_AgilentZ_TopR

value: AgilentZ


title: H9c2 cells pTT vs. pTT-ApoO Transfected DyeSwap, Replicate 6

description:
H9c2 cardiomyoblast cells are derived from embryonic BD1X rat heart; obtained from EACC.
Biological replicate 6 of 6.


title: 20101214_popLN_Susp_VivoSubQ_sAd16_1E8_072hr_III_AgilentO_TopL

value: AgilentO

value: TopL


title: H9c2 cells pTT vs. pTT-ApoO Transfected DyeSwap, Replicate 3

description:
H9c2 cardiomyoblast cells are derived from embryonic BD1X rat heart; obtained from EACC.
Biological replicate 3 of 6.


title: H9c2 cells pTT vs. pTT-ApoO Transfected DyeSwap, Replicate 4

description:
H9c2 cardiomyoblast cells are derived from embryonic BD1X rat heart; obtained from EACC.
Biological replicate 4 of 6.


title: 20101214_popLN_Susp_VivoSubQ_sAd11_1E8_072hr_II_AgilentN_MidBotR

value: in vivo


title: 20110316_popLN_Susp_VivoSubQ_rAd28_1E8_072hr_V_AgilentZ_TopL


title: MCF-7_scramble transfection, biological rep1

city: CANBERRA

first: Jiayu

last: Wen

state: ACT

address: 133 Garran Rd

department: Department of Genome Science

country: Australia

institute: John Curtin School of Medical Research, The Australian National University

description: Gene expression data: scramble transfection (rep1)

hyb_protocol: The labeled samples were hybridized to the GeneChip Genome U133 plus 2 arrays (Affymetrix, Santa Clara, CA, USA) using standard Affymetrix procedures.

scan_protocol: The arrays were washed and stained with phycoerytrin conjugated streptavidin (SAPE) using the Affymetrix Fluidics Station® 450, and the arrays were scanned in the Affymetrix GeneArray® 2500 scanner to generate fluorescent images, as described in the Affymetrix GeneChip® protocol

data_processing: Affymetrix probeset intensity of miR-95 and scramble transfection experiments were preprocessed using the affy package in BioConductor, including steps of background correction, between-array normalization and transformation by VSN (Variance stabilization and calibration) method, and a summarization step by RMA (Robust Multichip Average) method.

source_name: miR-95, MCF-7, scramble, 24h, rep1

label_protocol: RNA was amplified and labeled using the 3’ IVT Express kit (Affymetrix, Santa Clara, CA, USA) according to manufactures instructions. 250 ng total RNA was used as input.

growth_protocol: MCF-7 cells were seeded in 6-cm plates

extract_protocol: Total RNA was harvested 24 h after transfection using Trizol reagent.

treatment_protocol: miR-9  triplicate transfections were performed the following day with 50 nM miR-95 or scramble control using Lipofectamine 2000

tag: transfection

value: scramble


title: MCF-7_miR95 transfection, biological rep3

description: Gene expression data: miR-95 transfection (rep3)

source_name: miR-95, MCF-7, transfection, 24h, rep3

tag: cell line


title: 20101214_popLN_Susp_VivoSubQ_rAd5_1E8_072hr_III_AgilentO_BotL

tag: cell type

value: BotL


title: MCF-7_scramble transfection, biological rep3

description: Gene expression data: scramble transfection (rep3)

source_name: miR-95, MCF-7, scramble, 24h, rep3


title: 20101214_popLN_Susp_VivoSubQ_sAd11_1E8_072hr_I_AgilentM_TopR

value: TopR


title: MCF-7_miR95 transfection, biological rep2

description: Gene expression data: miR-95 transfection (rep2)

source_name: miR-95, MCF-7, transfection, 24h, rep2


title: MCF-7_scramble transfection, biological rep2

description: Gene expression data: scramble transfection (rep2)

source_name: miR-95, MCF-7, scramble, 24h, rep2


title: MCF-7_miR95 transfection, biological rep1

description: Gene expression data: miR-95 transfection (rep1)

source_name: miR-95, MCF-7, transfection, 24h, rep1


title: 20101214_popLN_Susp_VivoSubQ_rAd5_1E8_072hr_I_AgilentM_MidBotL

value: MidBotL


title: 20101214_popLN_Susp_VivoSubQ_rAd5_1E8_072hr_II_AgilentN_BotR

value: BotR


title: hMSC/inv at T2 S, experimental rep3, Donor 2

city: Natal

first: Joana

middle: Cristina Medeiros

last: Tavares

state: Rio Grande do Norte

address: Rua Trairi, S/N Centro

department: Faculty of Health Sciences Trairi

country: Brazil

institute: Federal university of  Rio Grande do Norte

description: Gene expression data from Cell culture of senescent hMSC with chromosome inversion (46,XY,inv(3)(p13p25))at passage 18 with seven days  culture after being seeded on plate culttura

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16hr at 45C on Affymetrix Human Genome U133 plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Genechip Fluidics Station-450.

scan_protocol: GeneChips were scanned using the HAffymetrix Gene-Chip Scanner-3000-7G (Affymetrix).

data_processing: The data were analyzed with Expression Console Version 1.1 (Affymetrix) using Affymetrix default analysis settings and RMA (Robust Multi-array Analysis) as normalization method. Statistical analysis was performed using the Partek Genomic Suite (version 6.4; Partek Inc., St. Louis, MO) with default RMA as summarization and normalization method using CG background correction. The signal of each transcript was calculated using the average of intensities from each probset corresponding to the same transcript. The correspondence between the experimental replicates was performed using Principal Component Analysis and Pearson Correlation. For the identification of differentially expressed genes, was applied ANOVA (one-way analysis of variance) with Bonferroni Correction. Was considered statistically significant genes with p-value 0.001 ˂ with Bonferroni correction and the fold change ˃ 3.0.

source_name: Human mesenchymal stem cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from  100ng total RNA (GeneChip® 3’ IVT Express Kit manual).

growth_protocol: Cells were seeded at a  cell initial number 6X105 and 2X105 for, respectively, two and seven days of cultive in culture dishes with growth area (60.1 cm2), maintained with alpha-MEM medium (Gibco) supplemented with 10% FBS (Gibco) and 1% solution antibiotic (penicillin and streptomycin - Sigma or Gibco) and maintained at 37 ° C in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted from 1x106 cells using the RNeasy mini kit (Qiagen), following the instructions contained in the kit manual.

tag: tissue

value: Umbilical Cord Vein

value: Donor 2, Karyotype with chromosome inversion (46,XY,inv(3)(p13p25))

tag: age

value: Cell culture of senescent hMSC at passage 18 with seven days  culture after being seeded on plate culttura


title: 20101214_popLN_Susp_VivoSubQ_rAd35high_1E9_072hr_III_AgilentO_MidBotR

value: draining popliteal lymph node suspension

value: A


title: 20101214_popLN_Susp_VivoSubQ_sAd11_1E8_072hr_III_AgilentO_MidTopL

value: MidTopL


title: hMSC/inv at T1 S, experimental rep3, Donor 2

description: Gene expression data from cell culture of senescent hMSC with chromosome inversion (46,XY,inv(3)(p13p25)) at passage 18 with two days  culture after being seeded on plate culttura

value: Cell culture of senescent hMSC at passage 18 with two days  culture after being seeded on plate culttura


title: hMSC/inv at T2 S, experimental rep1, Donor 2


title: hMSC/inv at T1 S, experimental rep1, Donor 2


title: hMSC/inv at T2 S, experimental rep2, Donor 2

description: Gene expression data from Cell culture of senescent hMSC with chromosome inversion (46,XY,inv(3)(p13p25)) at passage 18 with seven days  culture after being seeded on plate culttura


title: Late.High.Rep6

city: Ames

first: Patrick

middle: S.

last: Schnable

state: IA

address: 2035B Roy J Carver Co-Lab

institute: Iowa State University

description: Plants were ground using mortars and pestles. RNA was isolated using Trizol reagent, following manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003). Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. A total of 6 biological replications were perfomred for each treatment at each time point.

hyb_protocol: Fluorescent targets were hybridized as described in the cDNA microarray protocol file at http://schnablelab.plantgenomics.iastate.edu/resources/protocols/

scan_protocol: The arrays for all replications were scanned using a ScanArray 5000 (Packard, Meriden, CT) at 10um resolution for both Cy3 and Cy5 channels. Scans were performed at three intensities (Skibbe, Wang et al. 2006).

data_processing: The lowess normalization method of Dudoit, Yang, Callow, and Speed (2002) was applied to the log of background-corrected raw signal intensities to remove signal-intensity-dependent dye effects from each slide.  Normalization was carried out separately for each slide to avoid introducing dependencies among biological replications. Following lowess normalization, the normalized data for each slide/dye combination were median centered so that expression measures would be comparable across slides.  Median-centering involves subtracting the median value for a particular slide/dye combination from each individual value associated with the particular slide/dye combination. The lowess normalized data from each scan was used for a mixed linear model analysis (Wolfinger et al., 2001).

organism: Zea mays

source_name: Maize root, nitrate-induced, 24 hrs

label_protocol: Targets were synthesized and hybridized as described at http://schnablelab.plantgenomics.iastate.edu/resources/protocols/

growth_protocol: All experiments were conducted using plants of the B73 inbred line of maize (Zea mays sp.). Kernels were disinfected by soaking for 30 minutes in a solution of 10% commercial bleach (containing 5% sodium hypochlorite), then imbibed for 24 hours in aerated distilled water. The imbibed kernels were then wrapped in germination paper soaked in distilled water, placed in a beaker containing distilled water, and germinated in the dark at 28°C. After 72, hours the solution was changed to 5mM calcium sulfate and the beakers transferred to a growth chamber (16 hours light at 25°C and 8 hours dark at 20°C). The solutions were replenished periodically to maintain constant level.

extract_protocol: RNA was extracted by homogenizing roughly 3g of root tissue in 30ml Trizol Reagent (Invitrogen, Catalog No. 15596-026) and subsequently following the manufacturer's protocol adjusted to 3g of tissue. mRNA was isolated using Qiagen Oligotex kits (Catalog No. 70042), following the manufacturer's protocol. Total RNA was reverse transcribed using SuperscriptII (Invitrogen, Catalog No. 18064-022) with poly d(T) primers.

treatment_protocol: Two time points of nitrate exposure were considered in these experiments: 30 minutes (early) and 24 hours (late). Six biological replications were included for each time point, where a replication consisted of a control sample and a nitrate-treated sample. After 10 days of growth on germination paper in 5mM calcium sulfate, six biological replications were chosen at random and placed in either fresh 5mM calcium sulfate or 5mM calcium nitrate, these replications constituted the late treatment groups. On day 11 following imbibition the remaining six biological replications were randomly assigned to either 5mM calcium sulfate or 5mM calcium nitrate for 30 minutes, constituting the early treatment groups. The root tissue was then harvested, frozen with liquid N2, and stored at -80°C.

value: Root

tag: treatment duration

value: 24 hrs

tag: replicate

tag: scan intensity

value: High

source_name: Maize root, non-induced, 24 hrs


title: Late.Medium.Rep6

tag: genotype

value: Medium


title: Late.Low.Rep6

value: Low


title: Late.Medium.Rep4


title: 20101214_popLN_Susp_VivoSubQ_rAd35high_1E9_072hr_II_AgilentN_TopR

value: WT

tag: bioreplicate comparison groups (batches)

value: in vivo

value: AgilentN


title: hMSC/n at T2 S, experimental rep6, Donor 1

description: Gene expression data from Cell culture of senescent hMSC with  Normal karyotype (46,XX) at passage 18 with seven days  culture after being seeded on plate culttura

value: Donor 1, Normal karyotype (46,XX)


title: 20101214_popLN_Susp_VivoSubQ_rAd28_1E8_072hr_III_AgilentO_MidTopR

tag: bioreplicate id

value: AgilentO

value: MidTopR


title: hMSC/inv at T1 S, experimental rep2, Donor 2

value: Umbilical Cord Vein

value: Donor 2, Karyotype with chromosome inversion (46,XY,inv(3)(p13p25))


title: hMSC/n at T2 S, experimental rep5, Donor 1

value: Cell culture of senescent hMSC at passage 18 with seven days  culture after being seeded on plate culttura


title: Late.High.Rep5


title: Late.Medium.Rep5


title: Late.Low.Rep5


title: 20101214_popLN_Susp_VivoSubQ_rAd35high_1E9_072hr_I_AgilentM_MidTopR

value: draining popliteal lymph node suspension

value: A

tag: stimulation condition

value: AgilentM


title: Late.High.Rep4

value: Root


title: Late.Low.Rep4

value: 24 hrs


title: Late.Medium.Rep3


title: Late.Low.Rep3


title: Late.Low.Rep2


title: Late.Medium.Rep2


title: Late.High.Rep3

value: High


title: hMSC/n at T2 S, experimental rep3, Donor 1


title: 20101214_popLN_Susp_VivoSubQ_rAd28_1E8_072hr_I_AgilentM_BotR

tag: vector dose (particle units)

value: BotR


title: 20101214_popLN_Susp_VivoSubQ_rAd28_1E8_072hr_II_AgilentN_BotL

tag: time post-stimulation

value: BotL


title: 20101214_popLN_Susp_VivoSubQ_PBS_NA_072hr_III_AgilentO_BotR

value: WT

value: PBS

tag: in vivo or in vitro


title: hMSC/n at T2 S, experimental rep4, Donor 1


title: hMSC/n at T2 S, experimental rep2, Donor 1


title: Late.Medium.Rep1

value: Medium


title: Late.Low.Rep1

value: Low


title: Early.Medium.Rep5

source_name: Maize root, nitrate-induced, 30 min

value: 30 min

source_name: Maize root, non-induced, 30 min


title: 20101214_popLN_Susp_VivoSubQ_PBS_NA_072hr_II_AgilentN_MidBotL

value: in vivo

tag: array

value: AgilentN

value: MidBotL


title: Early.High.Rep6


title: Early.Low.Rep6


title: Early.Medium.Rep6


title: Late.High.Rep1


title: hMSC/n at T1 S, experimental rep2, Donor 1

description: Gene expression data from cell culture of senescent hMSC with  Normal karyotype (46,XX) at passage 18 with two days  culture after being seeded on plate culttura

value: Umbilical Cord Vein

value: Donor 1, Normal karyotype (46,XX)

value: Cell culture of senescent hMSC at passage 18 with two days  culture after being seeded on plate culttura


title: hMSC/n at T2 S, experimental rep1, Donor 1

value: Cell culture of senescent hMSC at passage 18 with seven days  culture after being seeded on plate culttura


title: Early.Low.Rep5

value: Root


title: hMSC/n at T1 S, experimental rep3, Donor 1


title: Early.Low.Rep3


title: hMSC/inv at T2 Y, experimental rep3, Donor 2

description: Gene expression data from cell culture of young hMSC with chromosome inversion (46,XY,inv(3)(p13p25)) at passage 9 with seven days  culture after being seeded on plate culttura

value: Donor 2, Karyotype with chromosome inversion (46,XY,inv(3)(p13p25))

value: Cell culture of young hMSC at passage 9 with seven days  culture after being seeded on plate culttura


title: Late.High.Rep2

value: 24 hrs

value: High


title: 20101005_popLN_Susp_VivoSubQ_sAd11_1E8_008hr_VI_AgilentL_MidTopR

value: draining popliteal lymph node suspension

value: WT

value: A

value: AgilentL

tag: hyb position on 8-plex array

value: MidTopR


title: Early.Medium.Rep3

value: 30 min

value: Medium


title: hMSC/n at T1 S, experimental rep1, Donor 1


title: hMSC/inv at T2 Y, experimental rep2, Donor 2


title: 20101214_popLN_Susp_VivoSubQ_PBS_NA_072hr_I_AgilentM_TopL

value: PBS

value: in vivo

value: AgilentM

value: TopL


title: Early.Low.Rep4

value: Low


title: Early.High.Rep5

value: Root


title: Early.Medium.Rep4


title: 20101005_popLN_Susp_VivoSubQ_sAd11_1E8_008hr_V_AgilentK_TopR

value: AgilentK

value: TopR


title: 20101005_popLN_Susp_VivoSubQ_sAd16_1E8_008hr_VI_AgilentL_MidBotR

value: MidBotR


title: Early.High.Rep4

value: High


title: Early.High.Rep3


title: 20101005_popLN_Susp_VivoSubQ_sAd16_1E8_008hr_V_AgilentK_MidTopR

value: draining popliteal lymph node suspension


title: hMSC/inv at T1 Y, experimental rep3, Donor 2

description: Gene expression data from cell culture of young hMSC with chromosome inversion (46,XY,inv(3)(p13p25))at passage 9 with two days  culture after being seeded on plate culttura

value: Umbilical Cord Vein

value: Donor 2, Karyotype with chromosome inversion (46,XY,inv(3)(p13p25))

value: Cell culture of young hMSC at passage 9 with two days  culture after being seeded on plate culttura


title: hMSC/inv at T2 Y, experimental rep1, Donor 2

value: Cell culture of young hMSC at passage 9 with seven days  culture after being seeded on plate culttura


title: 20101005_popLN_Susp_VivoSubQ_rAd5_1E8_008hr_VI_AgilentL_MidTopL

value: WT

value: A

value: AgilentL

value: MidTopL


title: Early.Low.Rep2

value: 30 min


title: Early.Medium.Rep1

value: Medium


title: Early.Low.Rep1

value: Low


title: Early.High.Rep2

value: Root


title: hMSC/n at T1 Y, experimental rep3, Donor 3

description: Gene expression data from cell culture of young hMSC with  Normal karyotype (46,XX) at passage 9 with seven days  culture after being seeded on plate culttura

value: Donor 3, Normal karyotype (46,XX)


title: 20101005_popLN_Susp_VivoSubQ_rAd35high_1E9_008hr_V_AgilentK_BotL

value: in vivo

value: AgilentK

value: BotL


title: hMSC/inv at T1 Y, experimental rep1, Donor 2

description: Gene expression data from cell culture of young hMSC with chromosome inversion (46,XY,inv(3)(p13p25)) at passage 9 with two days  culture after being seeded on plate culttura


title: 20101005_popLN_Susp_VivoSubQ_rAd35high_1E9_008hr_VI_AgilentL_TopR

value: draining popliteal lymph node suspension

value: TopR


title: 11058 6 month 19

city: Research Triangle Park

first: Zongli

address: 111 tw alexander Dr.

institute: NIH/NIEHS

description: microRNA expression analyzed from total RNA extracted from serum

hyb_protocol: RNA was hybridized for 42 hours to the GeneChip miRNA 1.0 array

scan_protocol: The arrays were washed and stained using standard Affymetrix protocols and scanned using the Affymetrix GCS 3000 7G Scanner. Feature intensities were extracted using the miRNA 1.0 array library files.

data_processing: MiRNA expression intensity values were background corrected and normalized across arrays using the Robust Multichip Average (RMA) method. The intensity data used in all analysis were log (2) transformed. For each array the miRNA probe set signals were compared to the distribution of signals for anti-genomic probes that had matching GC content (miRNA QC Tool, Version 1.0.33.0) and following the manufacture’s recommendation, Wilcoxon Rank-Sum test of  p<0.06 was used to identify miRNAs above background. Subsequent analysis was restricted to 307 miRNAs that exceeded background levels in at least 10% of samples. Using R 2.15, paired t-tests were used to identify miRNA probes differentially expressed between the cases and controls or in subsequent analyses between case samples collected at different time points.

source_name: Serum

label_protocol: 8µl of total RNA was directly labeled using The Flash Tag Biotin HSR Labeling kits following the manufacturer’s instructions. RNA was heated at 80° C for 10 min before labeling to inactivate any residual DNase activity.

extract_protocol: Total RNA was extracted in batches using the Total RNA purification kit. Each individual sample was split into four equal aliquots and then processed following the manufacture’s recommended protocol for total RNA purification from serum. An on-column DNase digestion was added before sample elution using the RNase-Free DNase I Kit, following the manufacturer’s instructions.

tag: batch

tag: status

value: 6 month

tag: Sex

value: FEMALE


title: 11057 month 19

value: 1 month


title: Early.Medium.Rep2

tag: tissue


title: 20101005_popLN_Susp_VivoSubQ_rAd5_1E8_008hr_V_AgilentK_TopL

source_name: mouse draining popliteal lymph node suspension

tag: cell type

value: WT

value: TopL


title: 11061 month 20

tag: age


title: 11059 control 19

description: microRNA expression analyzed from total RNA extracted from plasma

source_name: Plasma

value: control


title: 11060 surgery 20

value: surgery


title: 20101005_popLN_Susp_VivoSubQ_rAd28_1E8_008hr_VI_AgilentL_MidBotL

value: A

value: AgilentL

value: MidBotL


title: hMSC/n at T1 Y, experimental rep2, Donor 3

value: Umbilical Cord Vein

value: Cell culture of young hMSC at passage 9 with two days  culture after being seeded on plate culttura


title: hMSC/n at T1 Y, experimental rep1, Donor 3

value: Donor 3, Normal karyotype (46,XX)


title: hMSC/inv at T1 Y, experimental rep2, Donor 2

value: Donor 2, Karyotype with chromosome inversion (46,XY,inv(3)(p13p25))


title: Early.High.Rep1

value: Root

tag: treatment duration

value: 30 min

tag: replicate

value: High


title: 11056 surgery 19


title: 11051 control 17

value: MALE


title: 11054 6 month 18

value: 6 month


title: 20101005_popLN_Susp_VivoSubQ_PBS_NA_008hr_V_AgilentK_BotR

value: draining popliteal lymph node suspension

tag: genotype

value: PBS

value: in vivo

value: AgilentK

value: BotR


title: 11053 month 18

value: 1 month


title: hMSC/n at T2 Y, experimental rep3, Donor 1

value: Donor 1, Normal karyotype (46,XY)

value: Cell culture of young hMSC at passage 9 with seven days  culture after being seeded on plate culttura


title: 11055 control 18

value: control


title: 11052 surgery 18

value: surgery


title: 20101005_popLN_Susp_VivoSubQ_rAd28_1E8_008hr_V_AgilentK_MidTopL

value: WT

tag: bioreplicate comparison groups (batches)

value: A

value: MidTopL


title: 20101005_popLN_Susp_VivoSubQ_PBS_NA_008hr_VI_AgilentL_TopL

tag: bioreplicate id

value: AgilentL

value: TopL


title: 20100930_popLN_Susp_VivoSubQ_sAd16_1E8_008hr_IV_AgilentJ_TopR

tag: stimulation condition

value: AgilentJ

value: TopR


title: 20100930_popLN_Susp_VivoSubQ_sAd16_1E8_008hr_III_AgilentI_BotL

value: draining popliteal lymph node suspension

tag: vector dose (particle units)

value: AgilentI

value: BotL


title: hMSC/n at T2 Y, experimental rep1 Y,  Donor1

value: Umbilical Cord Vein


title: hMSC/n at T2 Y, experimental rep2 Y,   Donor1


title: 11050 6 month 17

value: 6 month

value: FEMALE


title: 11049 month 17

value: 1 month


title: 11048 surgery 17


title: 11045 month 16

value: MALE


title: hMSC/n at T1 Y, experimental rep3 Y,  Donor1

description: Gene expression data from cell culture of young hMSC with  Normal karyotype (46,XX) at passage 9 with two days  culture after being seeded on plate culttura

value: Donor 1, Normal karyotype (46,XY)

value: Cell culture of young hMSC at passage 9 with two days  culture after being seeded on plate culttura


title: 20100930_popLN_Susp_VivoSubQ_sAd11_1E8_008hr_III_AgilentI_MidBotL

value: WT

tag: time post-stimulation

value: in vivo

value: MidBotL


title: hMSC/n at T1 Y, experimental rep1, Donor1


title: hMSC/n at T1 Y, experimental rep2 Y,  Donor1


title: 11043 control 15

value: control


title: 11041 month 15


title: 20100930_popLN_Susp_VivoSubQ_rAd5_1E8_008hr_IV_AgilentJ_BotR

value: A

tag: in vivo or in vitro

value: BotR


title: 20100930_popLN_Susp_VivoSubQ_sAd11_1E8_008hr_IV_AgilentJ_BotL

tag: array

value: AgilentJ


title: 11044 surgery 16

value: surgery


title: 11039 control 14


title: 11042 6 month 15


title: 11046 6 month 16


title: 11047 control 16


title: 20100930_popLN_Susp_VivoSubQ_rAd35high_1E9_008hr_III_AgilentI_MidTopL

value: draining popliteal lymph node suspension

value: AgilentI

tag: hyb position on 8-plex array

value: MidTopL


title: 20100930_popLN_Susp_VivoSubQ_rAd35high_1E9_008hr_IV_AgilentJ_MidBotL


title: 11038 6 month 14

tag: batch

value: 6 month


title: A-Pool 3 P10+12+13 POST

city: Madrid

first: DAVID

last: CALZADA

address: Avenida Reyes Católicos n2

department: Allergy and Immunology

country: Spain

institute: IIS-Fundación Jiménez Díaz

description: PBMCs extracted in Post- polinization period

hyb_protocol: Following fragmentation, 10 µg of cDNA were hybridized for 16 hr at 45C on the GeneChip HuGe U133 plus 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Microarrays were scanned using the GeneChip® Scanner 3000, enabled for High-Resolution Scanning

data_processing: Preliminary microarray analysis included assessment of data quality by standard quality checks and principal component assays. First-line check, background corrections, and quantile normalization of the data were performed by Robust Multiarray Averaging (RMA) method. Data analysis was performed using Partek Genomics Suite software. Affymetrix raw data files (CEL files) where background corrected using RMA methodology. Intensity signal was standardized across arrays via quantile normalization algorithm. Further analyses where carried out using Babelomics web suite.

source_name: RNA from PBMCs stimulated with P10+12+13 of 2 allergic patients (J4.1 and J4.6)  in post pollination period

label_protocol: Microarray targets were prepared from 200 ng of total RNA using the Affymetrix (Santa Clara, CA, USA) kit for reverse transcription and a double round of in vitro transcription. Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 10 µg of cDNA.

growth_protocol: PBMCs isolated from peripheral blood by density gradient

extract_protocol: Total RNA was isolated from PBMCs (10^6 cells) using Trizol (Invitrogen, Carlsbad, CA, USA) extraction and isopropyl alcohol precipitation. RNA was quantified by spectrophotometry in a nanodrop, and integrity was confirmed with the Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).We utilized an RNA-pooling strategy to maximize the number of individuals in the microarray study to increase statistical power and representation of intra-individual variability in gene expression.Three independent pools were created for each experimental conditions and two different pollen exposition condition (during and outside pollen season).  A total of 96 RNAs samples were studied (12 subjects x 2 exposure moments x 4 experimental conditions)

treatment_protocol: PBMCs from 6 controls subjects and 6 Olive pollen–allergic patients (1,000,000 cls) were cultured with and without olive pollen stimuli (olive pollen extract (Olea), peptide 2+3 and peptide 10+12+13) during 24 hours.

value: Peripheral blood mononuclear cells

tag: diagnosis

value: allergic


title: 11040 surgery 15

tag: status

tag: Sex

value: FEMALE


title: 11037 month 14

value: 1 month

value: MALE


title: A-Pool 1 P10+12+13 PRE

description: PBMCs extracted in Polinization period

source_name: RNA from PBMCs stimulated with P10+12+13 of 2 allergic patients (S4.5 and G4.4) in polinization period

tag: cell type


title: 11036 surgery 14

tag: age


title: A-Pool 2 P10+12+13 POST

source_name: RNA from PBMCs stimulated with P10+12+13 of 2 allergic patients (J4.5 and J4.8) in post pollination period


title: 11035 control 13


title: 20100930_popLN_Susp_VivoSubQ_rAd5_1E8_008hr_III_AgilentI_MidBotR

value: WT

value: MidBotR


title: A-Pool 3 P10+12+13 PRE

description: PBMCs extracted in Polinization period

source_name: RNA from PBMCs stimulated with P10+12+13 of 2 allergic patients (J4.1 and J4.6) in polinization period


title: 11032 surgery 13


title: 20100930_popLN_Susp_VivoSubQ_rAd28_1E8_008hr_IV_AgilentJ_TopL

value: in vivo

value: TopL


title: 11034 6 month 13


title: 20100930_popLN_Susp_VivoSubQ_rAd28_1E8_008hr_III_AgilentI_BotR

value: A


title: 10944 month 12


title: 11033 month 13


title: A-Pool 3 P2+3 PRE

description: PBMCs extracted in Polinization period

source_name: RNA from PBMCs stimulated with P2+3 of 2 allergic patients (J4.1 and J4.6) in pollination period


title: A-Pool 1 P10+12+13 POST

source_name: RNA from PBMCs stimulated with P10+12+13 of 2 allergic patients (S4.5 and G4.4) in post pollination period


title: 10945 6 month 12


title: 10943 surgery 12


title: A-Pool 1 P2+3 PRE

description: PBMCs extracted in Polinization period

source_name: RNA from PBMCs stimulated with P2+3 of 2 allergic patients (S4.5 and G4.4)  in pollination period


title: 20100930_popLN_Susp_VivoSubQ_PBS_NA_008hr_III_AgilentI_MidTopR

value: PBS

value: MidTopR


title: A-Pool 2 P2+3 PRE

description: PBMCs extracted in Polinization period

source_name: RNA from PBMCs stimulated with P2+3 of 2 allergic patients (J4.5 and J4.8)  in pollination period


title: 10941 6 month 11


title: 10940 month 11


title: 20100930_popLN_Susp_VivoSubQ_PBS_NA_008hr_IV_AgilentJ_MidBotR

value: AgilentJ


title: 10942 control 11

value: control


title: 20100927_popLN_Susp_VivoSubQ_sAd11_1E8_008hr_II_AgilentH_MidTopL

value: draining popliteal lymph node suspension

value: AgilentH


title: A-Pool 2 P2+3 POST

source_name: RNA from PBMCs stimulated with P2+3 of 2 allergic patients (J4.5 and J4.8)    in post pollination period


title: 20100927_popLN_Susp_VivoSubQ_sAd16_1E8_008hr_II_AgilentH_MidBotL

value: MidBotL


title: A-Pool 3 P2+3 POST

source_name: RNA from PBMCs stimulated with P2+3 of 2 allergic patients (J4.1 and J4.6) in post pollination period

value: Peripheral blood mononuclear cells


title: 20100927_popLN_Susp_VivoSubQ_sAd11_1E8_008hr_I_AgilentG_TopL

value: AgilentG


title: 10939 surgery 11

value: surgery


title: 10938 control 10

value: FEMALE


title: A-Pool 1 P2+3 POST

source_name: RNA from PBMCs stimulated with P2+3 of 2 allergic patients (S4.5 and G4.4) in post pollination period

value: allergic


title: 20100927_popLN_Susp_VivoSubQ_sAd16_1E8_008hr_I_AgilentG_MidTopL

value: WT

value: MidTopL


title: 10936 month 10

value: 1 month


title: 10937 6 month 10

value: 6 month


title: 10933 6 month 9

value: MALE


title: 10932 month 9


title: 10935 surgery 10


title: A-Pool 3 olea PRE

description: PBMCs extracted in Polinization period

source_name: RNA from PBMCs stimulated with Olea of 2 allergic patients (J4.1 and J4.6)  in pollination period


title: A-Pool 2 olea PRE

description: PBMCs extracted in Polinization period

source_name: RNA from PBMCs stimulated with Olea of 2 allergic patients (J4.5 and J4.8)  in pollination period


title: 10931 surgery 9


title: 10930 control 8


title: 20100927_popLN_Susp_VivoSubQ_rAd5_1E8_008hr_II_AgilentH_MidTopR

value: A

value: in vivo


title: 20100927_popLN_Susp_VivoSubQ_rAd35high_1E9_008hr_I_AgilentG_BotR

value: BotR


title: 20100927_popLN_Susp_VivoSubQ_rAd35high_1E9_008hr_II_AgilentH_TopL

value: TopL


title: 10929 6 month 8


title: 10927 surgery 8


title: 10934 control 9

value: control


title: 10928 month 8


title: A-Pool 1 olea POST

source_name: RNA from PBMCs stimulated with Olea of 2 allergic patients (S4.5 and G4.4)  in post pollination period


title: 20100927_popLN_Susp_VivoSubQ_rAd5_1E8_008hr_I_AgilentG_TopR

value: draining popliteal lymph node suspension

value: TopR


title: 10946 control 12


title: 10926 control 7


title: A-Pool 3 olea POST

source_name: RNA from PBMCs stimulated with Olea of 2 allergic patients (J4.1 and J4.6)  in post pollination period

value: Peripheral blood mononuclear cells


title: 20100927_popLN_Susp_VivoSubQ_rAd28_1E8_008hr_I_AgilentG_MidTopR

source_name: mouse draining popliteal lymph node suspension

value: AgilentG

value: MidTopR


title: A-Pool 1 olea PRE

description: PBMCs extracted in Polinization period

source_name: RNA from PBMCs stimulated with Olea of 2 allergic patients  (S4.5 and G4.4)  in pollination period


title: 10925 6 month 7

source_name: Serum

value: FEMALE


title: 10921 6 month 6


title: 10922 control 6

source_name: Plasma


title: 20100927_popLN_Susp_VivoSubQ_PBS_NA_008hr_II_AgilentH_TopR

value: PBS

value: AgilentH


title: 10920 month 6


title: A-Pool 2 olea POST

source_name: RNA from PBMCs stimulated with Olea of 2 allergic patients (J4.5 and J4.8) in post pollination period

value: allergic


title: 20100927_popLN_Susp_VivoSubQ_rAd28_1E8_008hr_II_AgilentH_MidBotR

value: WT

value: MidBotR


title: 10924 month 7

value: 1 month


title: A-Pool 2 basal PRE

description: PBMCs extracted in Polinization period

source_name: RNA from PBMCs without stimulation of 2 allergic patients (J4.5 and J4.8) in pollination period


title: 20100927_popLN_Susp_VivoSubQ_PBS_NA_008hr_I_AgilentG_BotL

value: A

value: BotL


title: A-Pool 3 basal PRE

description: PBMCs extracted in Polinization period

source_name: RNA from PBMCs without stimulation of 2 allergic patients (J4.1 and J4.6)  in pollination period


title: 10918 control 5


title: A-Pool 2 basal POST

source_name: RNA from PBMCs without stimulation of 2 allergic patients  (J4.5 and J4.8)   in post pollination period


title: 10917 6 month 5

value: 6 month


title: A-Pool 1 basal PRE

description: PBMCs extracted in Polinization period

source_name: RNA from PBMCs without stimulation of 2 allergic patients (S4.5 and G4.4)   in pollination period


title: 10916 month 5


title: 10919 surgery 6

value: surgery


title: 9967 month 4


title: 10915 surgery 5


title: 20100901_popLN_Susp_VivoSubQ_sAd16_1E8_024hr_VI_AgilentF_MidTopR

value: in vivo

value: AgilentF


title: C-Pool 3 P10+12+13 PRE

description: PBMCs extracted in Polinization period

source_name: RNA from PBMCs stimulated with P10+12+13 of 2 healthy controls (S1.1 and J1.2) in polinization period

value: healthy


title: 20100901_popLN_Susp_VivoSubQ_sAd11_1E8_024hr_VI_AgilentF_TopL

value: draining popliteal lymph node suspension

value: TopL


title: A-Pool 3 basal POST

source_name: RNA from PBMCs without stimulation of 2 allergic patients (J4.1 and J4.6)  in post pollination period

value: Peripheral blood mononuclear cells


title: 20100901_popLN_Susp_VivoSubQ_sAd16_1E8_024hr_V_AgilentE_TopL

value: AgilentE


title: 9969 control 4

value: control

value: FEMALE


title: 9968 6 month 4


title: A-Pool 1 basal POST

source_name: RNA from PBMCs without stimulation of  2 allergic patients (S4.5 and G4.4)  in post pollination period

value: allergic


title: 10923 surgery 7


title: 20100901_popLN_Susp_VivoSubQ_sAd11_1E8_024hr_V_AgilentE_TopR

value: WT

value: TopR


title: 9966 surgery 4


title: 9961 control 2


title: 9965 control 3


title: C-Pool 1 P10+12+13 PRE

description: PBMCs extracted in Polinization period

source_name: RNA from PBMCs stimulated with P10+12+13 of 2 healthy controls (S1.4 and S1.5) in polinization period


title: 9962 surgery 3


title: C-Pool 2 P10+12+13 PRE

description: PBMCs extracted in Polinization period

source_name: RNA from PBMCs stimulated with P10+12+13 of 2 healthy controls (S1.7 and G1.2) in polinization period


title: 9963 month 3

value: 1 month


title: 9960 6 month 2


title: 9964 6 month 3


title: 9959 month 2


title: C-Pool 2 P10+12+13 POST

source_name: RNA from PBMCs stimulated with P10+12+13 of 2 healthy controls (S1.7 and G1.2) in post pollination period


title: 20100901_popLN_Susp_VivoSubQ_rAd5_1E8_024hr_VI_AgilentF_MidBotL

value: A

value: MidBotL


title: C-Pool 3 P10+12+13 POST

source_name: RNA from PBMCs stimulated with P10+12+13 of 2 healthy controls  (S1.1 and J1.2)  in post pollination period


title: 9958 surgery 2


title: 20100901_popLN_Susp_VivoSubQ_rAd35high_1E9_024hr_V_AgilentE_BotL

value: BotL


title: 9932 control 1

value: MALE


title: 20100901_popLN_Susp_VivoSubQ_rAd5_1E8_024hr_V_AgilentE_MidBotR

value: in vivo

value: MidBotR


title: 9931 6 month 1

value: 6 month


title: 20100901_popLN_Susp_VivoSubQ_rAd35high_1E9_024hr_VI_AgilentF_TopR

value: draining popliteal lymph node suspension

value: AgilentF


title: 20100901_popLN_Susp_VivoSubQ_rAd28_1E8_024hr_VI_AgilentF_BotR

value: BotR


title: C-Pool 1 P10+12+13 POST

source_name: RNA from PBMCs stimulated with P10+12+13 of 2 healthy controls (S1.4 and S1.5) in post pollination period

value: Peripheral blood mononuclear cells

value: healthy


title: 20100901_popLN_Susp_VivoSubQ_rAd28_1E8_024hr_V_AgilentE_MidBotL

source_name: mouse draining popliteal lymph node suspension

value: AgilentE


title: C-Pool 2 P2+3 PRE

description: PBMCs extracted in Polinization period

source_name: RNA from PBMCs stimulated with P2+3 of 2 healthy controls (S1.7 and G1.2)  in pollination period


title: C-Pool 3 P2+3 PRE

description: PBMCs extracted in Polinization period

source_name: RNA from PBMCs stimulated with P2+3 of 2 healthy controls (S1.1 and J1.2) in pollination period


title: C-Pool 1 P2+3 PRE

description: PBMCs extracted in Polinization period

source_name: RNA from PBMCs stimulated with P2+3 of 2 healthy controls (S1.4 and S1.5)  in pollination period


title: 11077 month 24

source_name: Serum


title: 11079 control 24

source_name: Plasma

value: control


title: 11078 6 month 24


title: 11076 surgery 24

value: surgery


title: 9929 surgery 1


title: C-Pool 3 P2+3 POST

source_name: RNA from PBMCs stimulated with P2+3 of 2 healthy controls (S1.1 and J1.2) in post pollination period


title: 11075 control 23

value: FEMALE


title: 20100901_popLN_Susp_VivoSubQ_PBS_NA_024hr_V_AgilentE_MidTopL

value: WT

value: PBS

value: MidTopL


title: 9930 month 1

value: 1 month


title: 20100831_popLN_Susp_VivoSubQ_sAd16_1E8_024hr_III_AgilentC_BotL

value: A

value: AgilentC

value: BotL


title: C-Pool 2 P2+3 POST

source_name: RNA from PBMCs stimulated with P2+3 of 2 healthy controls (S1.7 and G1.2)    in post pollination period


title: 11074 6 month 23

value: 6 month


title: 11070 6 month 22

value: MALE


title: 11068 surgery 22


title: 11069 month 22


title: 11072 surgery 23


title: 11071 control 22


title: 20100831_popLN_Susp_VivoSubQ_sAd11_1E8_024hr_IV_AgilentD_BotL

value: draining popliteal lymph node suspension

value: in vivo

value: AgilentD


title: 20100901_popLN_Susp_VivoSubQ_PBS_NA_024hr_VI_AgilentF_MidBotR

value: AgilentF

value: MidBotR


title: 11073 month 23


title: 11067 control 21

value: control


title: 20100831_popLN_Susp_VivoSubQ_sAd11_1E8_024hr_III_AgilentC_BotR

value: BotR


title: C-Pool 3 olea PRE

description: PBMCs extracted in Polinization period

source_name: RNA from PBMCs stimulated with Olea of 2 healthy controls (S1.1 and J1.2)  in pollination period

value: Peripheral blood mononuclear cells

value: healthy


title: C-Pool 1 P2+3 POST

source_name: RNA from PBMCs stimulated with P2+3 of 2 healthy controls (S1.4 and S1.5) in post pollination period


title: 20100831_popLN_Susp_VivoSubQ_rAd5_1E8_024hr_III_AgilentC_MidTopR

value: WT

value: MidTopR


title: C-Pool 1 olea PRE

description: PBMCs extracted in Polinization period

source_name: RNA from PBMCs stimulated with Olea of 2 healthy controls  (S1.4 and S1.5)  in pollination period


title: 20100831_popLN_Susp_VivoSubQ_rAd5_1E8_024hr_IV_AgilentD_MidTopL

value: MidTopL


title: C-Pool 2 olea POST

source_name: RNA from PBMCs stimulated with Olea of 2 healthy controls (S1.7 and G1.2) in post pollination period


title: 20100831_popLN_Susp_VivoSubQ_rAd35high_1E9_024hr_IV_AgilentD_BotR

value: A


title: 11066 6 month 21

value: FEMALE


title: 11064 surgery 21

value: surgery


title: C-Pool 1 olea POST

source_name: RNA from PBMCs stimulated with Olea of 2 healthy controls (S1.4 and S1.5)  in post pollination period


title: 20100831_popLN_Susp_VivoSubQ_rAd35high_1E9_024hr_III_AgilentC_MidBotL

value: AgilentC

value: MidBotL


title: 11063 control 20


title: 11065 month 21

value: 1 month


title: C-Pool 2 olea PRE

description: PBMCs extracted in Polinization period

source_name: RNA from PBMCs stimulated with Olea of 2 healthy controls (S1.7 and G1.2)  in pollination period


title: keratinocytes_pre-miR-Ctrl_rep3

city: Stockholm

first: Ning

address: CMM L8:02

institute: Karolinska Institutet

description:
Gene expression data from keratinocytes transfected with control oligos with scrambled sequence.
pre-miR-Ctrlc

hyb_protocol: The samples were hybridized to a Human Gene 1.1 ST Array Plate according to standard Affymetrix GeneTitan protocol.

scan_protocol: The array plate was scanned using the Affymetrix GeneTitan Scanner.

data_processing: Generated CEL files were analyzed using Affymetrix Expression Console v. 1.1 and the RMA method

label_protocol: Total RNA was labeled using the Whole Transcript (WT) Sense Target Labeling Assay according to the manufacturer’s (Affymetrix) instructions.

growth_protocol: Human adult epidermal keratinocytes were purchased from Cascade Biologics and cultured in EpiLife® serum-free keratinocyte growth medium including Human Keratinocyte Growth Supplement at a final Ca2+ concentration of 0.06mM (Cascade Biologics) at 37°C in 5% CO2.

extract_protocol: 48 hours after transfection, the total RNA was extracted with miRNeasy Mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: The third passage keratinocytes at 30-50% confluence were transfected with 10 nM miR-132 mimics or control oligos (Ambion) using Lipofectamine 2000 (Invitrogen).

tag: tissue

value: skin

value: primary human keratinocytes

tag: transfected with

value: control oligos (pre-miR-Ctrl)


title: 11062 6 month 20

value: 6 month


title: 20100831_popLN_Susp_VivoSubQ_rAd28_1E8_024hr_IV_AgilentD_MidBotR

value: draining popliteal lymph node suspension

tag: genotype

value: in vivo

value: AgilentD

value: MidBotR


title: 20100831_popLN_Susp_VivoSubQ_rAd28_1E8_024hr_III_AgilentC_MidTopL

value: WT

tag: bioreplicate comparison groups (batches)


title: keratinocytes_pre-miR-132_rep1

description:
Gene expression data from keratinocytes with miR-132 overexpression.
pre-miR-132a

value: 10nM miR-132 mimics (pre-miR-132)


title: C-Pool 1 basal PRE

description: PBMCs extracted in Polinization period

source_name: RNA from PBMCs without stimulation of 2 healthy controls (S1.4 and S1.5)    in pollination period

value: Peripheral blood mononuclear cells

value: healthy


title: keratinocytes_pre-miR-132_rep2

description:
Gene expression data from keratinocytes with miR-132 overexpression.
pre-miR-132b


title: C-Pool 3 basal PRE

description: PBMCs extracted in Polinization period

source_name: RNA from PBMCs without stimulation of 2  (S1.1 and J1.2)  in pollination period


title: keratinocytes_pre-miR-Ctrl_rep2

description:
Gene expression data from keratinocytes transfected with control oligos with scrambled sequence.
pre-miR-Ctrlb


title: keratinocytes_pre-miR-132_rep3

description:
Gene expression data from keratinocytes with miR-132 overexpression.
pre-miR-132c


title: C-Pool 3 basal POST

source_name: RNA from PBMCs without stimulation of 2 healthy controls (S1.1 and J1.2)  in post pollination period


title: keratinocytes_pre-miR-Ctrl_rep1

description:
Gene expression data from keratinocytes transfected with control oligos with scrambled sequence.
pre-miR-Ctrla


title: 20100831_popLN_Susp_VivoSubQ_PBS_NA_024hr_IV_AgilentD_MidTopR

source_name: mouse draining popliteal lymph node suspension

value: A

tag: bioreplicate id

value: PBS

value: MidTopR


title: C-Pool 2 basal POST

source_name: RNA from PBMCs without stimulation of 2 healthy controls  (S1.7 and G1.2)   in post pollination period


title: C-Pool 2 basal PRE

description: PBMCs extracted in Polinization period

source_name: RNA from PBMCs without stimulation of 2 healthy controls (S1.7 and G1.2) in pollination period


title: 20100831_popLN_Susp_VivoSubQ_PBS_NA_024hr_III_AgilentC_TopL

tag: stimulation condition

value: AgilentC

value: TopL


title: 20100830_popLN_Susp_VivoSubQ_sAd16_1E8_024hr_I_AgilentA_MidBotL

tag: vector dose (particle units)

value: AgilentA

value: MidBotL


title: WT embryo, biological rep2

city: New York,

first: Shugaku

last: Takeda

state: NY

department: Human Oncology & Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: Following fragmentation, 5.5 ug of ssDNA were hybridized for 16 hr at 45C on GeneChip Mouse ST 1.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: Mouse E10.5 embryo

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: Tasp1+/- mice were intercrossed to generate E10.5 WT and Tasp1-/- embryos.

extract_protocol: The samples were homogenized in TRIzol reagent (Invitrogen) using FastPrep-24 and Lysing Matrix D (MP Biomedicals) and total RNA was harvested according to the manufacturer's instructions.

treatment_protocol: E10.5 embryos were collected from the uterus and dissected to collect head tissue (prosencephalon and mesencephalon) in ice-cold PBS using tweezers.

tag: background strain

value: head (prosencephalon and mesencephalon)

value: Wild type


title: Tasp1 KO embryo, biological rep1

value: Taspase1 knock-out


title: Tasp1 KO embryo, biological rep3


title: 20100830_popLN_Susp_VivoSubQ_sAd16_1E8_024hr_II_AgilentB_BotR

value: draining popliteal lymph node suspension

tag: time post-stimulation

tag: in vivo or in vitro

value: in vivo

value: AgilentB

value: BotR


title: Tumor_Dnmt3a-deficient 1

city: Omaha

first: Rene

last: Opavsky

state: NE

address: 985040 Nebraska Medical Center

institute: University of Nebraska Medical Center

description: Dnmt3a-deficient tumor thymocytes

hyb_protocol: cRNA probes were hybridized to the Affymetrix GeneChip Mouse Gene 1.0 ST Array per the manufacture’s instructions

scan_protocol: GeneChip 3,000 6G scanner was used to scan chips.

data_processing: Intensities were imported into Expression Console using Robust Multi-chip Averaging (RMA)

source_name: Thymus

label_protocol: 200 ng RNA was reverse transcribed and cRNA was generated per the manufacturer’s instructions using the Ambion WT Expression Kit

extract_protocol: Total RNA was isolated using Trizol and repurified using RNAeasy kit from Qiagen.

value: Terminal

value: Dnmt3a-deficient tumor thymocytes

tag: genetic background

value: FVB/N


title: Tasp1 KO embryo, biological rep2


title: WT embryo, biological rep3


title: 20100830_popLN_Susp_VivoSubQ_sAd11_1E8_024hr_II_AgilentB_MidBotL

value: WT

value: A

tag: array

tag: hyb position on 8-plex array


title: Tumor_Dnmt3a-deficient 4

description: Dnmt3a-deficient tumor thymocytes


title: 20100830_popLN_Susp_VivoSubQ_sAd11_1E8_024hr_I_AgilentA_MidBotR

value: MidBotR


title: Tumor_Dnmt3a-deficient 2

description: Dnmt3a-deficient tumor thymocytes


title: WT embryo, biological rep1


title: Tumor_Dnmt3a-deficient 3

description: Dnmt3a-deficient tumor thymocytes


title: C-Pool 1 basal POST

source_name: RNA from PBMCs without stimulation of  2 healthy controls (S1.4 and S1.5)  in post pollination period

value: Peripheral blood mononuclear cells

tag: diagnosis

value: healthy


title: 20100830_popLN_Susp_VivoSubQ_rAd5_1E8_024hr_II_AgilentB_TopL

value: TopL


title: Tumor 4

description: Tumor thymocytes

value: Tumor thymocytes

value: wild type


title: Tumor 3

description: Tumor thymocytes


title: 20100830_popLN_Susp_VivoSubQ_rAd35high_1E9_024hr_II_AgilentB_MidBotR


title: 20100830_popLN_Susp_VivoSubQ_rAd5_1E8_024hr_I_AgilentA_TopR

value: AgilentA

value: TopR


title: Tumor 2

description: Tumor thymocytes


title: Tumor 5

description: Tumor thymocytes


title: Thymocytes_normal 3

description: Non-tumor wild-type Thymocytes

value: 24 dpn

value: Non-tumor wild-type Thymocytes


title: Thymocytes_normal 1

description: Non-tumor wild-type Thymocytes


title: 20100830_popLN_Susp_VivoSubQ_rAd35high_1E9_024hr_I_AgilentA_MidTopL

value: draining popliteal lymph node suspension

value: in vivo

value: MidTopL


title: Tumor 1

description: Tumor thymocytes

value: Terminal


title: 20100830_popLN_Susp_VivoSubQ_rAd28_1E8_024hr_I_AgilentA_TopL


title: NY236

city: Yangling

first: Liangzhi

last: Zhang

state: Shaanxi

address: No.22 Xinong Road

department: College of Animal Science and Technology

institute: Northwest A&F University

description: Hybridization of test sample and reference sample

hyb_protocol: Equal amounts of Cy3 labeled test sample and Cy5 labeled reference sample were mixed and hybridized to tiling array, by NimbleGen commercial service

scan_protocol: performed by NimbleGen

data_processing:
NimbleScan2.6 was used to analyze the data with qspline normalization . The high confidence calls are filtered and merged according to the following criteria: we merged overlapping CNV coordinates across hybridizations to form unique CNV regions using the 40% overlapping threshold as previously described. For cattle CNV calling, we tested the false discovery rate (FDR) in the self-self control hybridizations.
We selected a set of conservative calling criteria for the final set of high confidence CNVs, requiring that alternations of *0.5* log2 ratios over *5* neighboring probes (0.5_5), under no false positive was found for self-self control hybridizations

organism: Bos taurus

source_name: blood from Nanyang 236 #

label_protocol: 1 ug of test DNA were labeled with Cy3, and 1 ug of reference DNA were labeled with Cy5, using NimbelGen commercial service

extract_protocol: Blood DNA was extracted from whole blood anticoagulent 0.5 M EDTA. Samples were stored at -80 ℃until DNA isoaltion.500 ul of whole blood were mixed with lysis buffer (10 mmol/LxTris, 0.1 mol/L EDTA, 0.5% SDS), digested with protease K, then extracted twice times with Tris-saturated phenol, phenol /chloroform, once with chloroform. then separate out DNA using frezon absolute ethyl alcohol , finally wash three times with 70% lcohol

treatment_protocol: Wizard@ Genomic DNA purification Kit

tag: breed

value: Nanyang

tag: gender

value: male

value: blood

source_name: blood from Angus

value: Angus

value: female


title: Mus ZM-1 rep2

city: beijing

first: wenqiang

last: liu

address: 7 Science Park Rd., ZGC life science park, Beijing

institute: National Institute of Biological Sciences

hyb_protocol: Hybridization, Wash and Stain Kit(Affymetrix, Inc.)

scan_protocol: GeneChip® Scanner 3000 7G3000 (Affymetrix, Inc.)

data_processing: GCOS 1.4 software provided by Affymetrix

source_name: mouse chromosome transfer embryonic stem  cells

label_protocol: WT Terminal Labeling Kit (Affymetrix, Inc.)

growth_protocol: ES cells were cultured on 0.1% gelatin coated plates in DMEM medium supplemented with the MEK inhibitor PD0325901 , and the GSK3β inhibitor CHIR99021 , and LIF.

extract_protocol: following manufacturer’s recommendation using Trizol reagent (Invitrogen)

tag: cell line


title: MN7

organism: Bos grunniens

source_name: blood from Yak 7 #

value: yak

tag: tissue


title: NY9172

source_name: blood from Nanyang 9172 #


title: AX22

source_name: blood from Anxi 22 #

value: Anxi


title: BH931

source_name: blood from Bohaihei 931#

value: Bohaihei


title: BH803

source_name: blood from Bohaihei 803 #


title: 20100830_popLN_Susp_VivoSubQ_PBS_NA_024hr_I_AgilentA_BotL

tag: cell type

value: WT

value: A

value: PBS

value: BotL


title: NY140

source_name: blood from Nanyang140 #


title: Mus ♂M-1 rep2


title: Mus ♂M-3 rep2


title: 20100830_popLN_Susp_VivoSubQ_rAd28_1E8_024hr_II_AgilentB_MidTopR

tag: genotype

value: AgilentB

value: MidTopR


title: Mus ZM-1 rep1


title: 20100830_popLN_Susp_VivoSubQ_PBS_NA_024hr_II_AgilentB_TopR

value: draining popliteal lymph node suspension

tag: bioreplicate comparison groups (batches)

value: in vivo

value: TopR


title: Mus ♂M-3 rep1


title: Thymocytes_normal 2

description: Non-tumor wild-type Thymocytes

tag: age

value: 24 dpn

value: Non-tumor wild-type Thymocytes

value: wild type

value: FVB/N


title: 20100831_popLN_Susp_VivoSubQ_sAd16_1E8_024hr_IV_AgilentD_TopR

tag: bioreplicate id

tag: stimulation condition

value: AgilentD


title: MG1

source_name: blood from Menggu 1#

value: Mengu

value: male

value: blood

value: Angus

value: female


title: MG8

source_name: blood from Menggu 8#


title: HN2

source_name: blood from Leiqiong2#

value: Leiqiong

value: skin


title: JX1

source_name: blood from Jiaxian 1#

value: Jiaxian


title: JX21

source_name: blood from Jiaxian 21#


title: HN1

source_name: blood from Leiqiong1#


title: QQ63319

source_name: blood from Qinchuan 63319 #

value: Qinchuan


title: JX19

source_name: blood from Jiaxian 19#


title: QQ63307

source_name: blood from Qinchuan 63307 #


title: QQ63306

source_name: blood from Qinchuan 63306 #

source_name: blood from Angus


title: MN20

source_name: blood from Yak 20 #

value: yak


title: HD

source_name: blood from Chinese Holstein

value: Chinese Holstein


title: 817 CS2_vs_817 CD82

city: Nankoku

first: Chie

last: Nishioka

address: Oko-cho, Nankoku, Kochi

institute: Kochi University

description: control shRNA-transduced CD34+CD38- AML (817) cells (CS2) vs CD82 shRNA-transduced CD34+CD38- AML (817) cells (CD82)

hyb_protocol: Equal amounts of corresponding Cy3- and Cy5- labeled cDNAs were combined and  hybridized overnight (17 hours, 65°C) to Agilent Whole Human Genome Oligo Microarrays (8x60K, Design ID 028004) using Agilent’s recommended hybridization chamber and oven. Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1) was used to read out and process the microarray image files.

molecule: polyA RNA

label_protocol: 250 ng of each of the amplified cDNAs were used as template for Cy3 and Cy5 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

growth_protocol: CD34+/CD38− AML cells isolated from 3 patients (case No 817, 908, 927) were purified by magnetic cell sorting utilizing MicroBead kits (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany).Lentiviral CD82 shRNA particles or STAT5A shRNA particles were added to CD34+/CD38− AML cells being cultured in serum free IMDM. On the following day, 1 ml of methylcellulose medium H4034 (StemCell Technologies, Vancouver, BC, Canada) was added to this culture and cells were incubated for 7 days.

extract_protocol: RNA was extracted using the RNA II kit (Macherey & Nagel) following manufacturer's instructions. SuperAmplification was performed according to Miltenyi Biotec’s undisclosed protocol. Briefly, the amplification is based on a global PCR protocol of mRNA-derived cDNA. mRNA was isolated via magnetic bead technology.

value: PBMCs


title: WN1

source_name: blood from Wanan 1#

value: Wannan


title: 908 CS2_vs_908 00-2

description: control shRNA-transduced CD34+CD38- AML (908) cells (CS2) vs STAT5A shRNA-transduced CD34+CD38- AML (908) cells (00-2)


title: Mus ♂M-1 rep1

source_name: mouse chromosome transfer embryonic stem  cells


title: 817 CS2_vs_817 00-2

description: control shRNA-transduced CD34+CD38- AML (817) cells (CS2) vs STAT5A shRNA-transduced CD34+CD38- AML (817) cells (00-2)


title: 927 CS2_vs_927 CD82

description: control shRNA-transduced CD34+CD38- AML (927) cells (CS2) vs CD82 shRNA-transduced CD34+CD38- AML (927) cells (CD82)


title: 927 CS2_vs_927 00-2

description: control shRNA-transduced CD34+CD38- AML (927) cells (CS2) vs STAT5A shRNA-transduced CD34+CD38- AML (927) cells (00-2)


title: 908 CS2_vs_908 CD82

description: control shRNA-transduced CD34+CD38- AML (908) cells (CS2) vs CD82 shRNA-transduced CD34+CD38- AML (908) cells (CD82)


title: JN16

source_name: blood from Jinnan 16#

value: Jinnan


title: Angus

source_name: blood from Augus


title: JN14

source_name: blood from Jinnan 14#


title: JN2

source_name: blood from Jinnan 2#


title: ZS48

source_name: blood from Zaosheng 48 #

value: Zaosheng


title: LC14

source_name: blood from Luxi 14#

value: Luxi


title: LC12

source_name: blood from Luxi 12#


title: SN18

organism: Bubalus bubalis

source_name: blood from bufflo 18#

value: bufflo


title: SN21

source_name: blood from bufflo 21#


title: SN8

source_name: blood from bufflo 8#


title: SP CD8+ technical replicate 2

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

institute: CIC bioGUNE

hyb_protocol: Whole-Genome Gene Expression Direct Hybridization Illumina Inc.'s protocol

scan_protocol: BeadScan Illumina Inc.

data_processing: Raw data were decoded by GenomeStudio Illumina Inc. And normalization was done (1) forcePositive background correction, (2) log2 transformation and (3) quantile normalization

source_name: thymus biopsy

label_protocol: TargetAmp™ Nano-g™ Biotin-aRNA Labeling Kit for the Illumina® System, Epicentre (Cat.Num. TAN07924)

extract_protocol: Normal human postnatal thymocytes were isolated by Ficoll-Hypaque centrifugation and magnetic cell sorting from thymus fragments removed during corrective cardiac surgery

tag: Sex

value: mixed

value: 1-24 months

value: SP CD8+


title: SP CD4+ technical replicate 2

value: SP CD4+


title: SP CD8+ technical replicate 1


title: DP TCR α/β+ technical replicate 2

value: DP TCR α/β+


title: Neurons overexpressing GFP, biological rep1

city: Seville

first: Pedro

middle: Jose

last: Chacon

state: Seville

address: Americo Vespucio s/n

department: Cell Signaling

institute: Andalusian Center of Molecular Biology and Regenerative Medicine (CABIMER).

description: Gene expression data from neuron overexpressing GFP

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45ºC on GeneChip® Mouse Genome 430_2.0 (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station FS450 according to the GeneChip® Expression Analysis Technical Manual, Affymetrix, 2004

scan_protocol: Microarrays were scanned using the GeneChip® Scanner 3000 7G of Affymetrix

data_processing:
CEL files were processed using the Robust Multichip Average (RMA) normalization
Fold-change (log2) values (M) and their FDR-adjusted p-values were calculated with LIMMA (Linear Models for Microarray Analysis) using the affylmGUI interface. All the statistical analysis was performed using R language and the packages freely available from the “Bioconductor Project” (http://www.bioconductor.org)

source_name: Neurons overexpressing GFP

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1.5 µg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix). The products of reaction were purified and then fragmented at 94ºC during 35 min to obtain fragments between 35 and 200 bp.

growth_protocol: Neurons were plated for 6 days on 60mm-diameter dishes plates coated with poly-L-lysine at a density of 350,000 neurons/cm2, and they were cultured in Neurobasal supplemented with B-27 and GlutaMAX I.

extract_protocol: Cells were lysed and total RNA was extracted using illustra RNAspin Mini RNA isolation kit from GE Healthcare. RNA quality was analyzed using a BioAnalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Neurons were transduced at 6 DIV using Sindbis virus expressing myc-tagged Hes1 and GFP or GFP alone as control. After 6h viral particles were removed and proteins were allowed to express during 16h.

tag: strain

value: FVB

value: 6 DIV cultured hippocampal neurons

tag: transfected with

value: Sindbis virus expressing GFP alone


title: Neurons overexpressing GFP, biological rep2


title: SP CD4+ technical replicate 1


title: Neurons overexpressing Hes1 and GFP, biological rep1

description: Gene expression data from neuron overexpressing GFP and Hes-1

source_name: Neurons overexpressing Hes1 and GFP

value: Sindbis virus expressing myc-tagged Hes1 and GFP


title: DP TCR α/β+ technical replicate 1


title: Neurons overexpressing GFP, biological rep3


title: Pre-TCR+ technical replicate 2

value: Pre-TCR+


title: Neurons overexpressing Hes1 and GFP, biological rep3