title: Striatum-(PD group)-rep3

city: Wuhan

first: Guiqin

last: Chen

state: Huebei

address: 277 Jiefang Avenue

department: Department of Neurology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by Expression Console.

data_processing: The Expression Console software (Affymetrix, Santa Clara, CA, US) was used to format the raw microarray data. Data pre-processing, including background adjustment, log fold transformation and normalization was completed using the ‘exon level’ option in the software. Moreover, the dataset was normalized using the Robust Multi Array Average (RMA) method to control the inter-array variability. Normalized signal intensities of probes which belong to one transcript of each sample were processed by median for further data analysis. Gene chip and RNA quality were assessed by examining total mRNA expression for each striatum.  R software was used to screen the differential gene expression transcripts (DETs) among these samples. The adjusted P-value <0.05 and fold change (FC) ≥1.2 or ≤ 0.8333 were used as the cut-off criteria. After getting the DETs, we proceeded with the functional analysis, searching the function and signaling pathway of the genes. In this step, we used the known databases mainly, including DAVID Gene Ontology (http://david.abcc.ncifcrf.gov/). Considering the large amount and complex branch structure of Gene ontology (GO) biological processes, we used a significance threshold P-value <0.05 for biological process terms.  The co-expression analysis starts by constructing a matrix of pairwise correlations between all pairs of transcripts across samples of LID+PD98059, LID+Vehicle and LID group. We built an unsigned co-expression network with all the 37177 transcripts in microarray using the Weighted Gene Correlational Network Analysis (WGCNA) package [PMID: 19114008]. GO term enrichment tests were performed for individual gene co-expression modules compared to a background set of all genes expressed in these brain samples using the R packages GOstats (version 2.26.0), biomaRt version (2.14.0), AnnotationDbi (version 1.20.7) and org.Hs.eg.db (version 2.8.0).   To specilize LID+PD98059 from other treatment, unsupervised hierarchical clustering of the candidates in every trait module was performed by bootstrapping analysis using MeV software (http://www.tm4.org/). Bootstrapping analysis provides confidence values for the stability of each cluster derived by hierarchical clustering.

source_name: Striatum-(PD group)

label_protocol: Total RNA were amplified, labeled and purified by using Affymetrix  WT Amplication Kit(Cat#902224， Affymetrix, Santa Clara, CA, US) and GeneChip  WT Terminal Labeling Kit(Cat#900671, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cDNA.

growth_protocol: male Sprague-Dawley rats were housed with free access to food and water, 12 hour light / dark cycle, constant temperature and humidity

extract_protocol: Rats of each group were sacrificed by decapitation. Brain tissues were rapidly removed, dissected for striatum on powdered dry ice. Striatum were immediately incubated in RNAlater (Qiagen) at 4 °C overnight and then stored at − 80 °C for further Microarray analysis.Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Rats with unilateral 6-OHDA lesions of the nigrostriatal pathway received daily L-DOPA treatment for three weeks, and abnormal involuntary movements (AIMs) were assessed every other day. PD98059 was injected in the lateral ventricle daily for 12 days starting from day 10 of L-DOPA treatment

value: Sprague-Dawley

value: brain

tag: tissue region

value: striatum

value: PD


title: Striatum-(Normal group)-rep3

status: Public on Jan 18 2017

type: RNA

country: China

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Striatum-(Normal group)

tag: strain

tag: gender

value: male

tag: tissue

tag: disease state

value: Normal


title: knockout clone 34_2

city: St. Louis

first: Joshua

middle: B

last: Radke

state: Missouri

address: 660 Euclid Ave, CB8230

department: Molecular Microbiology

country: USA

institute: Washington University School of Medicine

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C to the affymetrix U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned by using the Affymetrix GCS3000 scanner.

data_processing: Genespring GX v12.6.1 (Agilent)

organism: Toxoplasma gondii

source_name: tachyzoite (pH 7.0)

label_protocol: Ambion messageAmp premier

growth_protocol: parasites were grown in T175cm flasks in human foreskin fibroblasts

extract_protocol: Qiagen RNA easy, double DNAse digestion

treatment_protocol: in vitro growth at standard tachyzoite conditions, (pH7.0)

tag: genotype/variation

value: knockout clone 34

tag: Stage

value: tachyzoite


title: Striatum-(LID group)-rep2

source_name: Striatum-(LID group)

value: LID


title: Striatum-(LID+PD98059 group)-rep1

source_name: Striatum-(LID+PD98059 group)

tag: agent


title: Striatum-(LID group)-rep1


title: knockout clone 34_1


title: Striatum-(LID+Vehicle group)-rep3

source_name: Striatum-(LID+Vehicle group)

value: Vehicle


title: Striatum-(LID+Vehicle group)-rep1


title: Striatum-(PD group)-rep2


title: Striatum-(Normal group)-rep1


title: Striatum-(Normal group)-rep2


title: Dicer Fx/Fx tamoxifen 3

city: London

first: Tristan

last: Rodriguez

address: Du Cane Road, Hammersmith Hospital Campus

department: National Heart and Lung Institute

country: United Kingdom

institute: NHLI Imperial College London

hyb_protocol: The hybridisation protocols were performed on GeneChip Fluidics Station 450.

scan_protocol: Samples were scanned using the Affymetrix GeneChip Scanner.

data_processing: The data was normalised using the RMA normalisation algorithm in Expression Console 1.2. The array QC was performed using Expression Console first and then Bioconductor.  RMA was used as the standard method for probe summarization (i.e. calculating a transcript signal value from multiple independent probes as on Affy arrays) and normalisation of Affymetrix expression array data. Quality control of Affymetrix expression microarrays involves identifying outlier arrays, rather than setting defined cut-offs for the various quality control metrics that are generated from the various controls and the probe summarization/normalisation. Note that the signal values are all log base 2; this is standard practice for RMA analyzed data. The data was first QC'ed using the Affymetrix Expression console.

label: Biotin

organism: Mus musculus

source_name: Dicer conditional Embryonic stem cell with Dicer deletion

label_protocol: Biotinylated cRNA were prepared using the Affymetrix GeneChip® WT Terminal Labeling Kit (Ambion, Invitrogen).

growth_protocol: Embryonic stem cells (ESCs) were grown in standard ESC conditions

extract_protocol: Cells were pelleted and total RNA was extracted using the Quiagen RNAeasy Kit and then prepared for analysis with the Ambion WT expression kit (Invitrogen)

treatment_protocol: Wild type ES cells (E14) and Dicer Fx/Fx cell lines were grown in ES cell culture conditions and tamoxifen was added for 3 days and cells collected 2 days after that (day 5).

tag: cell type

value: Embryonic Stem Cell


title: Striatum-(LID group)-rep3


title: Striatum-(LID+Vehicle group)-rep2


title: Striatum-(LID+PD98059 group)-rep3


title: Striatum-(PD group)-rep1


title: knockout clone 10_2

value: knockout clone 10


title: Striatum-(LID+PD98059 group)-rep2


title: knockout clone 10_1


title: PruQ parent_2

value: PruQ parent


title: Dicer Fx/Fx tamoxifen 1


title: Data Heifer #10994 [11 vs. 14 months]

city: Quebec

first: David

middle: André

last: Landry

state: Quebec

address: 2440 boul. Hochelaga

department: Animal Science

country: Canada

institute: University Laval

hyb_protocol: The hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects using the expression array protocol.

scan_protocol: Scan on a PowerScanner (Tecan) using the autogain function. Images were quantified using ArrayPro version 6.3 (MediaCybernetics)

data_processing: Background subtracted, Loess and Quantile normalized data obtained from log2 of processed Red signal/processed Green signal. Flexarray software used.

organism: Bos taurus

label_protocol: For each sample, aRNA was labeled using the ULS Fluorescent Labeling Kit for Agilent arrays (Cy3/Cy5) (Kreatech Diagnostics, Amsterdam, Netherlands). The labeled product was then purified with the Pico-Pure RNA Isolation Kit.

extract_protocol:
Total RNA was extracted from the pools using the AllPrep DNA/RNA micro kit, following the Parallel gDNA and total RNA extraction protocol. Total RNA integrity and concentration were evaluated on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) with the RNA PicoLab Chip (Agilent Technologies).
Amp protocol: To generate enough material for hybridization, the samples were linearly amplified. Antisense RNA (aRNA) was produced using the RiboAmp®HSPlus RNA Amplification kit (Thermo fisher Scientific). After two amplification rounds of 6 hr each, the aRNA output was quantified using the NanoDrop ND-1000 (Nano-Drop Technologies, Wilmington, DE).

treatment_protocol:
Ovarian stimulation: Each heifer was first treated with progesterone (CIDR) during the luteal phase. The dominant follicle was aspirated 36 hours prior to administration of hormones. The ovarian stimulation program consisted of 6 injections of 30mg FSH administered at 12h intervals. Ovum pick up was performed 43h after the last FSH injection. Using transvaginal ultrasonography, follicular diameters were then measured and cumulus-oocyte complexes were collected by transvaginal puncture, under epidural, with needle aspiration. COCs and granulosa cells were collected in warm HEPES-buffered Tyrode's medium containing Hepalean and transferred to laboratory for IVM.
Embryo production: In vitro maturation (IVM), in vitro fertilization (IVF), in vitro culture (IVC)

tag: sample type

tag: breed (cattle)

value: holstein

tag: heifers age

value: 14 Months

tag: tissue or cell type

value: Granulosa Cells

value: 11 Months


title: Dicer Fx/Fx 3

source_name: Dicer conditional Embryonic stem cell without deletion


title: Dicer Fx/Fx tamoxifen 2


title: Data Heifer #10995 [11 vs. 14 months]


title: PruQ parent_1


title: PSBM794 complemented clone 30_2

value: PSBM794 complemented clone 30


title: Dicer Fx/Fx 1


title: Data Heifer #10989 [11 vs. 14 months]


title: Data Heifer #10991 [11 vs. 14 months]


title: knockout clone 30_1

value: knockout clone 30


title: HCT116 SH PCAF, rep1

city: Barcelona

first: Oriol

last: bachs

address: Casanova 143

department: Biomedical Sciences

country: Spain

institute: University of Barcelona

hyb_protocol: Samples were hybridized with Affymetrix Humkan Gene 1.0 ST arrays

scan_protocol: Axon 4000B

data_processing: Dataset obtained by Expression Console (Affymetrix) were analyzed by DNA-ChIP analyzer (dChIP) software and tools. Quality control measurements were obtained with ArrayQualityMetrics, while the statistical analysis of significant hits with Limma according to the protocols provided by the manufacturer

organism: Homo sapiens

source_name: HCT116 SH PCAF

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

growth_protocol: Asynchronously growing HCT116 cells

extract_protocol: Total RNA was extracted using the RNeasy Kit (Qiagen, Iberia, Madrid, Spain) according to the manufacturer's instructions. RNA quality control was done with Agilent 2100 bioanalyzer

treatment_protocol: Cells were transfected with shRNA control or shPCAF

tag: cell line

value: PCAF knock-down


title: knockout clone 30_2


title: PSBM794 complemented clone 27_1

value: PSBM794 complemented clone 27


title: PSBM794 complemented clone 30_1


title: knockout clone 27_2

value: knockout clone 27


title: RHCre parent_1

value: RHCre parent


title: PSBM794 complemented clone 27_2


title: knockout clone 27_1


title: Data Heifer #10991 [8 vs. 14 months]

description: Rep 2 of 4

treatment_protocol:
Ovarian stimulation: Each heifer was first treated with progesterone (CIDR) during the luteal phase. The dominant follicle was aspirated 36 hours prior to administration of hormones. The ovarian stimulation program consisted of 6 injections of 30mg FSH administered at 12h intervals. Ovum pick up was performed 43h after the last FSH injection. Using transvaginal ultrasonography, follicular diameters were then measured and cumulus-oocyte complexes were collected by transvaginal puncture, under epidural, with needle aspiration. COCs and granulosa cells were collected in warm HEPES-buffered Tyrode's medium containing Hepalean and transferred to laboratory for IVM.
Embryo production : In vitro maturation (IVM), in vitro fertilization (IVF), in vitro culture (IVC)

value: 8 Months


title: HCT116 SH PCAF, rep2


title: Dicer Fx/Fx 2


title: RHCre parent_2

value: tachyzoite


title: Data Heifer #10995 [8 vs. 14 months]

description: Rep 4 of 4


title: Data Heifer #10989 [8 vs. 14 months]

description: Rep 1 of 4


title: HCT116 SH Ctrl, rep2

source_name: HCT116 SH Ctrl

value: wild-type


title: Data Heifer #10994 [8 vs. 14 months]

description: Rep 3 of 4


title: HCT116 SH Ctrl, rep1


title: Flower AZ_0hr_rep 1

status: Public on Jan 19 2017

city: Bet-Dagan

first: Srivignesh

last: Sundaresan

state: Israel

address: P.O.Box 6, Bet- Dagan

department: Post Harvest Technology

country: Israel

institute: Agricultural Research Organisation, The volcani center, Israel

description: Flower AZ without flower removal_0hr_rep 1

hyb_protocol: The labeled cRNA samples were hybridized on to an Solanum lycopersicum Custom 4x180K Array designed by Genotypic Technology Private Limited. (AMADID: 043310).1650ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Agilent Scanner (Agilent Technologies, Part Number G2565CA).

data_processing: Data extraction from Images was done using Feature Extraction software of Agilent V-10.7.3.1.Feature extracted data was analyzed using GeneSpring GX Version 12 software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift (Percentile shift normalization is a global normalization

organism: Solanum lycopersicum

source_name: flower AZ without flower removal at 0hr

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse transcription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields using Nanodrop-1000 (JH Bio) and specific activity determined based on the concentration of cRNA and dye incorporation.

growth_protocol: Flower bunches of tomato (Solanum lycopersicum c.v. VF 36) were harvested between 10 and 12 AM from a commercial greenhouse in Israel.

extract_protocol: RNA isolation was done using Qiagen method [Qiagen RNeay Plant minikit (Cat. No.74904)] as per the manufacturer protocol with DNAse treatment

treatment_protocol: Bunches containing at least two to four fresh open flowers were brought to the laboratory under high-humidity conditions. Senesced flowers and young (unopened) buds were removed, and the stem ends were trimmed. The flowers were immediately sorted by removing all but two or three fresh flowers from each stem. Bunches of five flower stalks were placed in vials with DDW. They were then placed in an observation room under conditions of 20 ± 1°C, 60 ± 10% RH, and 12 h light at intensity of 14 µmol m-2 s-2, provided by cool white fluorescent tubes. Tissue samples were taken from the AZ, of less than 1 mm thickness for each time point, excised less than 0.5 mm from each side of the visible AZ fracture. The AZ tissue was sampled at five time points (0, 2, 4, 8, and 14 h), following flower removal.

tag: tisssue

value: Whole flower abscission zone (AZ)

tag: nature of the az

value: Attached


title: Primary Breast Cancer4163-250ksty

status: Public on Jan 17 2017

type: genomic

city: Rotterdam

first: Marcel

last: Smid

address: Dr. Molewaterplein 50

department: Medical Oncology

country: Netherlands

institute: Erasmus MC

description: Hybridized to 250K_Sty

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

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

data_processing: The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). .CEL files were imported in Partek Genomics Suite v.6.5. Copy number estimates were calculated in Partek against a reference baseline consisting of 90 female CEPH samples. Copy number segmentation was performed by Parteks Genomic segmentation tool with a minumum number of markers of 20. Threshold for calling gains and losses set to -0.25 < 2 > +25. Signal to noise 0.45.

molecule: genomic DNA

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from fresh frozen primary breast cancer tissue using Qiagen Dneasy kit . DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

value: Primary Breast Cancer

tag: mutation

value: BRCAX


title: Primary Breast Cancer4170-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4155-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4166-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4159-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4165-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4156-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4149-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4160-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4169-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4162-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4161-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4164-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4116-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4172-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4114-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4145-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4158-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4148-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4153-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4147-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4146-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4168-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4127-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4118-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4157-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4113-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4126-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4123-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4122-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4121-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4107-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4103-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4105-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4110-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4101-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4082-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4106-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer2704-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer2879-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4072-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4096-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer2944-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer2875-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer2938-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4079-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4076-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4081-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4087-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4097-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4088-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer2883-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer2877-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4080-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer4075-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer2605-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer2878-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer2676-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer2488-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer2640-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer1944-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer1930-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer1934-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer2268-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer1927-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer1906-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer1889-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer1925-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer1908-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer1885-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer1896-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer1926-250ksty

description: Hybridized to 250K_Sty


title: DMSO control group (replicate 1)

city: Singapore

first: Phillip

middle: H

last: Koeffler

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute

hyb_protocol: standard affymetrix protocol

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

data_processing: Data was processed using Affy Bioconductor package. Briefly CEL files were read using ReadAffy function and rma normalized.

source_name: TC71_DMSO control group

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

growth_protocol: Cells were grown in DMEM medium (Corning) supplemented with 10 % fetal bovine serum (FBS), penicillin, and streptomycin.

extract_protocol: total RNA was extracted by qiagen Rneasy kit according to the manufacturer's instructions.

value: Human sarcoma cell line

tag: condition

value: wildtype cell with DMSO at same concentration


title: Primary Breast Cancer1775-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer1899-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer1913-250ksty

description: Hybridized to 250K_Sty


title: DMSO control group (replicate 2)


title: GS-9972 treatment group (replicate 2)

source_name: TC71_GS-9972 treatment group

value: with SYK inhibitor GS9973 treatment


title: Primary Breast Cancer1820-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer1911-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer1901-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer1514-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer1891-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer1895-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer1028-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer1369-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer2021-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer1897-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer1159-250ksty

description: Hybridized to 250K_Sty


title: GS-9972 treatment group (replicate 1)


title: Primary Breast Cancer1894-250ksty

description: Hybridized to 250K_Sty


title: SYK shRNA infection group (replicate 2)

source_name: TC71_SYK shRNA infection group

value: with SYK shRNA infection


title: Primary Breast Cancer1912-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer1922-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer973-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer1642-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer1275-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer967-250ksty

description: Hybridized to 250K_Sty


title: SYK shRNA infection group (replicate 1)


title: Primary Breast Cancer994-250ksty

description: Hybridized to 250K_Sty


title: shRNA negative control (replicate 2)

source_name: TC71_shRNA negative control

value: with scramble control shRNA infection


title: shRNA negative control (replicate 1)


title: Primary Breast Cancer959-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer957-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer966-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer961-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer951-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer950-250ksty

description: Hybridized to 250K_Sty


title: primary breast cancer, sample_JA-090

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol on Affymetrix scanner 3000

data_processing: mas5 parameters from affy R package, available at www.bioconductor.org using default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: primary breast cancer _Non

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA was extracted with RNABee (Campro, Veenendaal, the Netherlands) according to the manufacturer procedure

value: snap frozen primary breast tumor

tag: mutation status

value: Non


title: primary breast cancer, sample_JA-081

source_name: primary breast cancer _CHEK2


title: Primary Breast Cancer939-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer956-250ksty

description: Hybridized to 250K_Sty


title: primary breast cancer, sample_JA-121

source_name: primary breast cancer _BRCA1


title: primary breast cancer, sample_JA-038


title: Primary Breast Cancer933-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer942-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer932-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer945-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer941-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer948-250ksty

description: Hybridized to 250K_Sty


title: primary breast cancer, sample_988


title: Primary Breast Cancer927-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer924-250ksty

description: Hybridized to 250K_Sty


title: primary breast cancer, sample_994


title: Primary Breast Cancer920-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer928-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer929-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer930-250ksty

description: Hybridized to 250K_Sty


title: primary breast cancer, sample_975


title: Primary Breast Cancer839-250ksty

description: Hybridized to 250K_Sty


title: G3B_3 [143]

city: Galway

first: Pilib

last: Ó Broin

address: University Rd

country: Ireland

institute: NUI Galway

description: Gene expression data from C4d- / MVI=0/1

hyb_protocol: Total RNA samples hybridized to the Affymetrix Hugene 1.0 st chip according to the protocols provided by the manufacturer.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip 3000 7G scanner, software AGCC v2.0

data_processing: Probe intensities were extracted from Affymetrix CEL files, normalized and summarized at the transcript cluster level using the Robust Multiarray Average method from the R/Bioconductor (http://bioconductor.org) oligo package. Array quality control was performed to remove arrays that significantly differed in initial overall probe intensity. Expression values were analyzed on the log base 2 scale. Significance testing was performed by fitting gene-wise linear models using the limma Bioconductor package, and genes were ranked for differential expression using Benjamini & Hochberg adjusted p-values and log-posterior odds of differential expression. Gene set analysis was performed using the limma romer method. Gene set used were taken from the Molecular Signatures Database (MSigDB) Pathogenesis Based Transcripts (PBT; http://transplants.med.ualberta.ca/Nephlab/data/gene_lists.html) gene sets from the University of Alberta, Edmonton. Analysis for changes in gene expression of Gene Ontology (GO) categories was performed using the GOstats Bioconductor package to calculate Hypergeomtric p-values for over or under-representation of each GO term.

source_name: TGP with C4d negative and MVI=0 or MVI=1

label_protocol: Labelled as per manufacturer's instruction in Ambion Whole Transcript Expression Kit (Catalog Number 4425209, Ambion, Austin, TX) and Affymetix Genechip Whole Transcript Terminal Labeling Kit (Catalog Number 900671, Affymetrix, Santa Clara, CA)

extract_protocol: One biopsy core was collected into a vial containing 1ml of RNALater® (Ambion, Catalog Number AM7023), stored at -20°C for 24 hours and then transferred to -70°C until RNA isolation. Renal tissue and glomerular content in all cores was verified by Pathology department technical personnel using a dissecting microscope and any non-renal tissue was removed.

value: biopsy


title: primary breast cancer, sample_JA-080


title: G3B_4 [154]


title: G3B_2 [101]


title: G3B_5 [181]


title: primary breast cancer, sample_968


title: Primary Breast Cancer838-250ksty

description: Hybridized to 250K_Sty


title: G3B_1 [54]


title: G3A_10 [422V0]

description: Gene expression data from C4d- / MVI=0/1 DSA- Group

source_name: TGP with C4d negative and MVI=0 or MVI=1 and DSA neg


title: G3A_9 [344V0]


title: primary breast cancer, sample_967


title: G3A_8 [244]


title: G3A_7 [155]


title: Primary Breast Cancer804-250ksty

description: Hybridized to 250K_Sty


title: primary breast cancer, sample_966

source_name: primary breast cancer _BRCA2


title: Primary Breast Cancer255-250ksty

description: Hybridized to 250K_Sty


title: Primary Breast Cancer918-250ksty

description: Hybridized to 250K_Sty


title: G3A_4 [52]


title: primary breast cancer, sample_959


title: G3A_6 [149Vex]


title: G3A_3 [49]


title: G3A_2 [27]


title: Primary Breast Cancer461-250ksty

description: Hybridized to 250K_Sty


title: G3A_5 [85]


title: primary breast cancer, sample_950


title: G2_13 [178]

description: Gene expression data from C4d+ / MVI>1 Group

source_name: TGP with C4d+ and/or MVI>1


title: primary breast cancer, sample_962


title: G3A_1 [13]


title: G2_12 [177]


title: G2_14 [231]


title: primary breast cancer, sample_942


title: G2_15 [238]


title: primary breast cancer, sample_951


title: G2_17 [272]


title: primary breast cancer, sample_961


title: G2_9 [152]


title: primary breast cancer, sample_957


title: G2_8 [151]


title: G2_16 [251]


title: G2_5 [118Vex]


title: primary breast cancer, sample_945


title: G2_6 [120]


title: G2_10 [153]


title: G2_2 [21]


title: G2_4 [72Vex]


title: G2_1 [17]


title: G2_11 [176]


title: G2_3 [33]


title: primary breast cancer, sample_939


title: primary breast cancer, sample_937


title: G2_7 [135]


title: Control_5 [246V0]

description: Gene expression data from control group

source_name: control


title: Control_7 [256V0]

description: Gene expression data from control group


title: primary breast cancer, sample_932


title: Control_9 [292V0]

description: Gene expression data from control group


title: Control_11 [311V0]

description: Gene expression data from control group


title: primary breast cancer, sample_973


title: Control_4 [165V0]

description: Gene expression data from control group


title: Control_3 [133V0]

description: Gene expression data from control group


title: G5_13

description: Gene expression data from DSA_IFTA group


title: primary breast cancer, sample_941


title: Control_6 [248V0]

description: Gene expression data from control group


title: primary breast cancer, sample_933


title: Control_12 [322V0]

description: Gene expression data from control group


title: Control_8 [286V0]

description: Gene expression data from control group


title: Control_10 [299V0]

description: Gene expression data from control group


title: primary breast cancer, sample_934


title: Control_2 [97V0]

description: Gene expression data from control group


title: G5_10


title: G5_11


title: G5_9


title: Control_1 [38Vex]

description: Gene expression data from control group


title: primary breast cancer, sample_928


title: G5_8


title: primary breast cancer, sample_929


title: primary breast cancer, sample_927


title: primary breast cancer, sample_930


title: primary breast cancer, sample_924


title: G5_12


title: primary breast cancer, sample_918


title: Experiment 2 - IFNg triple positive

city: La Jolla

first: Bjoern

last: Peters

state: California

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

description: Experiment 2 - CD4 IFNg triple positive

hyb_protocol: 5 ug fragmented, biotin labelled ssDNA was hybridised to an Affymetrix Human Gene 2.0 Array also using the WT plus Reagent kit assay. Arrays were hybridized for 16 hours at 45°C at 60 rpm using an Affymetrix hybridization oven. The arrays were washed according to manufacturer’s instructions on an Affymetrix FS450 fluidics station.

scan_protocol: Arrays were scanned on an Affymetrix Scanner GC3000 7G

data_processing: Data were processed using GeneSpring GX software version 14.8 - Settings used for Experiment 1 and Experiment 2: RMA normalization; transcripts cluster ID filtered on expression (20-100th) percentile in the raw data; Absolute Fold change > 2 in Sample 3 versus Sample 2 (Experiment 1) orin  Sample 6 versus Sample 5 (Experiment 2).

source_name: CD4 T cells from whole blood

label_protocol: 350-1500 pg of RNA was used as input for the amplification and labelling  of samples using the Nugen Ovation Pico WTA System V2 and Encore Biotin Module.

growth_protocol: In vitro stimulation of whole blood with P. falciparum schizont extract for 20h at 37C in 5% C02.

extract_protocol: RNA extracted using RNEasy micro kit (Qiagen) according to manufacturer's instructions

treatment_protocol: FACS sorted CD4 T cells IFNg/IL2/TNF triple positive, IFNg single positive and IFNg negative direclty in RLT buffer

tag: cytokine production pattern

value: IFNg triple positive

tag: experiment

value: Experiment 2


title: primary breast cancer, sample_461

tag: tissue


title: G5_7


title: primary breast cancer, sample_838


title: primary breast cancer, sample_804


title: Experiment 2 - IFNg negative

description: Experiment 2 - CD4 IFNg negative

value: IFNg negative


title: Experiment 2 - IFNg single positive

description: Experiment 2 - CD4 IFNg single positive

value: IFNg single positive


title: G5_6


title: Experiment 1 - IFNg single positive

description: Experiment 1 - CD4 IFNg single positive

value: Experiment 1


title: G5_5


title: Experiment 1 - IFNg triple positive

description: Experiment 1 - CD4 IFNg triple positive


title: G5_2


title: G5_1


title: Experiment 1 - IFNg negative

description: Experiment 1 - CD4 IFNg negative


title: G4_7

description: Gene expression data from IFTA group

source_name: IFTA


title: G4_8

description: Gene expression data from IFTA group


title: primary breast cancer, sample_839


title: G4_12

description: Gene expression data from IFTA group


title: G5_3


title: G4_6

description: Gene expression data from IFTA group


title: G4_9

description: Gene expression data from IFTA group


title: PGC-1alpha WT MEFs

city: New York

first: Neri

last: Minsky

state: NY

address: 1230 York Avenue

institute: Rockefeller University

description: SAMPLE 2

hyb_protocol: Hybridization was performed at 45 degrees celcius for 17 hours. The arrays were washed and stained in the GeneChip Fluidic Station 450 (Affymetrix) by using Hybridization, Wash and Stain kit (Affymetrix).

scan_protocol: The arrays were scanned by the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data expressed as CEL files were normalized by the robust multiarray average (RMA) method with the Expression Console software (Affymetrix).

source_name: PGC-1alpha WT MEFs

label_protocol: Three hundred ng of total RNA was processed for cRNA synthesis with the Ambion WT Expression Kit (PN4411974). Fragmentation and terminal labeling was peformed with the AffymetrixGeneChip WT Terminal Labeling Kit (PN 900671)

growth_protocol: Cells were maintained in DMEM with 10% FCS. For brown adipocytes, differentiation was induced as described (

extract_protocol: Using the Rneasy kit from Qiagen according to manufacturer's protocol

treatment_protocol: In relevant samples, Adenoviruses were added directly to the culture medium and cells were collected 24hr later.

value: MEF

tag: genotype/variation

value: PGC-1alpha WT


title: G5_4


title: G4_10

description: Gene expression data from IFTA group


title: primary breast cancer, sample_948


title: G4_11

description: Gene expression data from IFTA group


title: primary breast cancer, sample_633


title: G4_5

description: Gene expression data from IFTA group


title: PGC-1alpha KO MEFs

description: SAMPLE 1

source_name: PGC-1alpha KO MEFs

value: PGC-1alpha KO


title: primary breast cancer, sample_4170


title: primary breast cancer, sample_4172


title: primary breast cancer, sample_4189


title: primary breast cancer, sample_4171


title: G4_3

description: Gene expression data from IFTA group


title: G4_1

description: Gene expression data from IFTA group


title: G4_4

description: Gene expression data from IFTA group


title: G3B_8

description: Gene expression data from TCMR_DSA- group


title: G4_2

description: Gene expression data from IFTA group


title: G3B_9


title: primary breast cancer, sample_4166


title: G3B_3


title: primary breast cancer, sample_4168


title: G3B_7


title: G3B_5


title: G3B_6


title: G3B_10


title: G3B_4


title: primary breast cancer, sample_4169


title: G3B_2


title: G3B_1


title: Primary Breast Cancer4168-250knsp

description: Hybridized to 250K_Nsp

value: Primary Breast Cancer


title: primary breast cancer, sample_4163


title: primary breast cancer, sample_4165


title: primary breast cancer, sample_4162


title: Primary Breast Cancer4172-250knsp

description: Hybridized to 250K_Nsp

value: BRCAX


title: G3A_15

description: Gene expression data from TCMR_IFTA group


title: G3A_16


title: G3A_17


title: Primary Breast Cancer4170-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_4164


title: Primary Breast Cancer4165-250knsp

description: Hybridized to 250K_Nsp


title: G3A_14


title: G3A_13


title: Primary Breast Cancer4166-250knsp

description: Hybridized to 250K_Nsp


title: G3A_9


title: Primary Breast Cancer4169-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer4164-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_4159


title: G3A_11


title: primary breast cancer, sample_4161


title: G3A_10


title: G3A_12


title: G3A_8


title: primary breast cancer, sample_4158


title: G3A_7


title: primary breast cancer, sample_4160


title: G3A_6


title: G3A_5


title: Primary Breast Cancer4161-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_4155


title: Primary Breast Cancer4163-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer4160-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer4162-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_4156


title: G3A_4


title: G3A_2


title: G2_32

description: Gene expression data from cAMR group

source_name: cAMR


title: G2_33

description: Gene expression data from cAMR group


title: primary breast cancer, sample_4149


title: Primary Breast Cancer4159-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_4153


title: Primary Breast Cancer4158-250knsp

description: Hybridized to 250K_Nsp


title: G3A_1


title: G2_28

description: Gene expression data from cAMR group


title: G2_30

description: Gene expression data from cAMR group


title: G2_31

description: Gene expression data from cAMR group


title: G2_29

description: Gene expression data from cAMR group


title: G3A_3


title: G2_27

description: Gene expression data from cAMR group


title: primary breast cancer, sample_4148


title: primary breast cancer, sample_4146


title: G2_26

description: Gene expression data from cAMR group


title: primary breast cancer, sample_4147


title: Primary Breast Cancer4157-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer4156-250knsp

description: Hybridized to 250K_Nsp


title: G2_25

description: Gene expression data from cAMR group


title: primary breast cancer, sample_4145


title: Primary Breast Cancer4153-250knsp

description: Hybridized to 250K_Nsp


title: G2_24

description: Gene expression data from cAMR group


title: primary breast cancer, sample_4127


title: Primary Breast Cancer4149-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer4155-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_4126


title: G2_21

description: Gene expression data from cAMR group


title: Primary Breast Cancer4148-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_4123


title: G2_22

description: Gene expression data from cAMR group


title: G2_17

description: Gene expression data from cAMR group


title: G2_23

description: Gene expression data from cAMR group


title: G2_20

description: Gene expression data from cAMR group


title: G2_18

description: Gene expression data from cAMR group


title: G2_19

description: Gene expression data from cAMR group


title: G2_14

description: Gene expression data from cAMR group


title: G2_15

description: Gene expression data from cAMR group


title: primary breast cancer, sample_4122


title: Primary Breast Cancer4146-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer4147-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_4118


title: G2_16

description: Gene expression data from cAMR group


title: G2_11

description: Gene expression data from cAMR group


title: Primary Breast Cancer4145-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer4127-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer4126-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_4121


title: primary breast cancer, sample_4116


title: G2_12

description: Gene expression data from cAMR group


title: G2_13

description: Gene expression data from cAMR group


title: primary breast cancer, sample_4115


title: G2_10

description: Gene expression data from cAMR group


title: Primary Breast Cancer4123-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_4113


title: G2_9

description: Gene expression data from cAMR group


title: G2_6

description: Gene expression data from cAMR group


title: primary breast cancer, sample_4114


title: G2_7

description: Gene expression data from cAMR group


title: G2_8

description: Gene expression data from cAMR group


title: G2_2

description: Gene expression data from cAMR group


title: G2_3

description: Gene expression data from cAMR group


title: Primary Breast Cancer4122-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer4121-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_4110


title: G2_4

description: Gene expression data from cAMR group


title: G2_5

description: Gene expression data from cAMR group


title: G2_1

description: Gene expression data from cAMR group


title: Primary Breast Cancer4116-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer4118-250knsp

description: Hybridized to 250K_Nsp


title: G1_13

description: Gene expression data from control group


title: primary breast cancer, sample_4106


title: G1_15

description: Gene expression data from control group


title: primary breast cancer, sample_4107


title: G1_14

description: Gene expression data from control group


title: G1_12

description: Gene expression data from control group


title: Primary Breast Cancer4114-250knsp

description: Hybridized to 250K_Nsp


title: G1_11

description: Gene expression data from control group


title: primary breast cancer, sample_4101


title: G1_8

description: Gene expression data from control group


title: primary breast cancer, sample_4099


title: G1_7

description: Gene expression data from control group


title: primary breast cancer, sample_4103


title: Primary Breast Cancer4113-250knsp

description: Hybridized to 250K_Nsp


title: G1_9

description: Gene expression data from control group


title: Primary Breast Cancer4107-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_4105


title: G1_6

description: Gene expression data from control group


title: G1_10

description: Gene expression data from control group


title: G1_16

description: Gene expression data from control group


title: G1_5

description: Gene expression data from control group


title: Primary Breast Cancer4106-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer4110-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer4103-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer4105-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_4097


title: G1_4

description: Gene expression data from control group


title: G1_3

description: Gene expression data from control group


title: Primary human hepatic stellate cells infected with Ad-PGC-1alpha

description: SAMPLE 6

value: primary human hepatic stellate cells

tag: infected with


title: G1_2

description: Gene expression data from control group


title: primary breast cancer, sample_4096


title: G1_1

description: Gene expression data from control group


title: Primary Breast Cancer4101-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_4094


title: primary breast cancer, sample_4093


title: Primary Breast Cancer4097-250knsp

description: Hybridized to 250K_Nsp


title: PGC-1alpha KO differntiated brown adipocytes infected with Ad-Control

description: SAMPLE 7

value: Brown adipocytes

value: Ad-Control


title: PGC-1alpha KO differntiated brown adipocytes infected with Ad-PGC-1alpha

description: SAMPLE 8


title: primary breast cancer, sample_4090


title: LX2 cells infected with Ad-Control

description: SAMPLE 3

source_name: LX2 cells infected with Ad-Control

value: Hepatic stellate cells


title: LX2 cells infected with Ad-PGC-1alpha

description: SAMPLE 4

source_name: LX2 cells infected with Ad-PGC-1alpha


title: Primary human hepatic stellate cells infected with Ad-Control

description: SAMPLE 5


title: Primary Breast Cancer4088-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_4089

value: snap frozen primary breast tumor


title: Primary Breast Cancer4096-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer4087-250knsp

description: Hybridized to 250K_Nsp


title: Kras;p53 lung papillary adenocarcinoma, Ad5-CC10-Cre, biological replicate 1

city: Helsinki

first: Jenni

last: Lahtela

address: Tukholmankatu 8

country: Finland

institute: Institute for Molecular Medicine Finland

description:
3999483029_D
Biological replicate

hyb_protocol: Whole-Genome Gene Expression Direct Hybridization Assay Guide

data_processing: The data were normalised using normaliseIllumina from Package ‘beadarray’

label_protocol: TargetAmp™- Nano Labeling Kit for Illumina® Expression BeadChip®

growth_protocol: Mice were bred on a mixed genetic background.

extract_protocol: Total RNA from snap frozen tumors was extracted using the NucleoSpin RNA II kit (MACHEREY-NAGEL, Duren, Germany). Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cohorts of 8-10 week old mice from multiple litters were intranasally or intratracheally administered with 1 x107 plaque-forming units (pfu) of Ad5-CC10-Cre or 2,5 x 109 pfu of Ad5-SPC-Cre viruses (Viral Vector Core Facility, Unversity of Iowa, USA) under isofluorane anaesthesia.

tag: strain

value: Mixed C57Bl/6J;29X1/SvJ;ICR

value: Lung

value: Kras (G12D)+/fl; Trp53fl/fl

tag: virus induction

tag: developmental stage

value: Adult

tag: tumor

value: lung papillary adenocarcinoma


title: Primary Breast Cancer4082-250knsp

description: Hybridized to 250K_Nsp

tag: cell type


title: Kras;p53 lung papillary adenocarcinoma, Ad5-SPC-Cre, biological replicate 2

description:
3999483029_B
Biological replicate

scan_protocol: Whole-Genome Gene Expression Direct Hybridization Assay Guide


title: Kras;p53 lung papillary adenocarcinoma, Ad5-SPC-Cre, biological replicate 3

description:
3999483029_C
Biological replicate


title: primary breast cancer, sample_4087

value: Non


title: Kras;p53 lung papillary adenocarcinoma, Ad5-SPC-Cre, biological replicate 1

description:
3999483029_A
Biological replicate


title: primary breast cancer, sample_4083


title: Kras;p53 lung papillary adenocarcinoma, Ad5-CC10-Cre, biological replicate 2

description:
3999483029_F
Biological replicate


title: primary breast cancer, sample_4088


title: Primary Breast Cancer4081-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_4082


title: Kras;Lkb1 lung papillary adenocarcinoma, biological replicate 3

description:
9977362037_C
Biological replicate

data_processing: The data were normalized using normaliseIllumina from Package ‘beadarray’

source_name: Kras;Lkb1 lung papillary adenocarcinoma, Ad5-SPC-Cre

extract_protocol: Total RNA from snap frozen tumors was extracted using the NucleoSpin RNA II kit (MACHEREY-NAGEL, Duren, Germany). Quality control was performed with Agilent Bioanalyzer.

value: Kras (G12D)+/fl; Lkb1fl/fl


title: Kras;Lkb1 lung adenosquamous carcinoma, biological replicate 4

description:
9977362037_D
Biological replicate

source_name: Kras;Lkb1 lung adenosquamous carcinoma, Ad5-CC10-Cre

value: lung adenosquamous carcinoma


title: primary breast cancer, sample_4081

source_name: primary breast cancer _Non


title: Kras;Lkb1 lung papillary adenocarcinoma, biological replicate 5

description:
9977362037_E
Biological replicate


title: Kras;Lkb1 lung adenosquamous carcinoma, biological replicate 6

description:
9977362037_F
Biological replicate


title: Primary Breast Cancer4080-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer4079-250knsp

description: Hybridized to 250K_Nsp


title: Kras;Lkb1 lung papillary adenocarcinoma, biological replicate 6

description:
9853741072_F
Biological replicate


title: Kras;Lkb1 lung papillary adenocarcinoma, biological replicate 1

description:
9977362037_A
Biological replicate


title: Kras;Lkb1 lung papillary adenocarcinoma, biological replicate 4

description:
9853741072_D
Biological replicate


title: primary breast cancer, sample_4080


title: Kras;Lkb1 lung adenosquamous carcinoma, biological replicate 2

description:
9977362037_B
Biological replicate


title: Primary Breast Cancer4076-250knsp

description: Hybridized to 250K_Nsp


title: Mixture Replicate 3

city: Vicksburg

first: Natalia

last: Vinas

state: MS

address: 3909 Halls Ferry Rd

institute: Mississippi State University

description:
MIX-113
Reference sample: pool of RNA from male and female fathead minnow liver, gonad and brain.

hyb_protocol: Hybridization was performed following the standard Agilent protocol.

scan_protocol: Arrays were scanned with Agilent scanner.

data_processing: Microarray image processing and data pre-processing were performed using Agilent’s Feature Extraction software v 9.5. In brief, log2 transformed signal ratio between the experimental channel and the reference channel was calculated for each spot, followed by within-array LOWESS transformation and between array scale normalization on median intensities (Zahurak, 2007). Two-way ANOVA was performed on the log2 transformed signal ratios of each probe individually, followed by Tukey-HSD pair-wise comparisons to determine genes whose expression was significantly regulated by the treatments.

organism: Pimephales promelas

source_name: Liver tissue exposed to a mixture of EE2/ZM

label_protocol: Array hybridizations were performed using a reference design and Agilent standard protocol. The liver samples were labeled with Cy5, while the reference sample was labeled with Cy3.

extract_protocol: Total RNA was isolated from FHM livers with the RNA Stat-60 reagent (Tel-test, Friendswood, TX).

treatment_protocol: Exposed to estrogen EE2, a mixture of EE2 and the anti-estrogen ZM, or solvent control.

value: Liver

tag: Sex

value: male

tag: treatment

value: mixture of estrogen EE2 and the anti-estrogen ZM

source_name: Reference sample

value: Pool of liver, gonad, and brain

value: Pooled male and female


title: Primary Breast Cancer4072-250knsp

description: Hybridized to 250K_Nsp

value: Primary Breast Cancer

value: BRCAX


title: Mixture Replicate 1

description:
MIX-97
Reference sample: pool of RNA from male and female fathead minnow liver, gonad and brain.


title: Primary Breast Cancer4075-250knsp

description: Hybridized to 250K_Nsp


title: Kras;Lkb1 lung adenosquamous carcinoma, biological replicate 1

description:
9853741072_A
Biological replicate


title: Mixture Replicate 4

description:
MIX-122
Reference sample: pool of RNA from male and female fathead minnow liver, gonad and brain.


title: Kras;Lkb1 lung adenosquamous carcinoma, biological replicate 5

description:
9853741072_E
Biological replicate


title: Kras;Lkb1 lung papillary adenocarcinoma, biological replicate 2

description:
9853741072_B
Biological replicate


title: primary breast cancer, sample_4079


title: Mixture Replicate 2

description:
MIX-108
Reference sample: pool of RNA from male and female fathead minnow liver, gonad and brain.


title: primary breast cancer, sample_4075


title: primary breast cancer, sample_4076


title: primary breast cancer, sample_4074


title: EE2 Replicate 2

description:
EE2-75
Reference sample: pool of RNA from male and female fathead minnow liver, gonad and brain.

source_name: Liver tissue exposed to EE2

value: estrogen EE2


title: Primary Breast Cancer2944-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_4078

value: snap frozen primary breast tumor


title: EE2 Replicate 3

description:
EE2-83
Reference sample: pool of RNA from male and female fathead minnow liver, gonad and brain.


title: EE2 Replicate 4

description:
EE2-91
Reference sample: pool of RNA from male and female fathead minnow liver, gonad and brain.


title: Primary Breast Cancer2883-250knsp

description: Hybridized to 250K_Nsp


title: Kras;Lkb1 lung adenosquamous carcinoma, biological replicate 3

description:
9853741072_C
Biological replicate

value: Mixed C57Bl/6J;29X1/SvJ;ICR


title: Primary Breast Cancer2878-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer2877-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer2879-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_4073


title: Control Replicate 4

description:
TEG-25
Reference sample: pool of RNA from male and female fathead minnow liver, gonad and brain.

source_name: Liver tissue exposed to solvent control

value: solvent control


title: Primary Breast Cancer2938-250knsp

description: Hybridized to 250K_Nsp


title: Control Replicate 2

description:
TEG-9
Reference sample: pool of RNA from male and female fathead minnow liver, gonad and brain.


title: EE2 Replicate 1

description:
EE2-65
Reference sample: pool of RNA from male and female fathead minnow liver, gonad and brain.


title: primary breast cancer, sample_4072


title: Control Replicate 1

description:
TEG-1
Reference sample: pool of RNA from male and female fathead minnow liver, gonad and brain.


title: Control Replicate 3

description:
TEG-18
Reference sample: pool of RNA from male and female fathead minnow liver, gonad and brain.


title: Primary Breast Cancer2875-250knsp

description: Hybridized to 250K_Nsp


title: A549_PSX146 25 mM_24 hours

city: Frankfurt am Main

first: Jose

middle: M.

last: Arencibia

address: Theodor-Stern-Kai 7

department: Medizinische Klinik I

country: Germany

institute: Universitätsklinikum Frankfurt

hyb_protocol: Hybridation performed by Atlas Biolabs GmbH (Berlin, Germany). Six-hundred ng of Cy3-labelled cRNA was fragmented according to the manufacturer´s instructions, and 480 ng of fragmented cRNA were hybridized (conc: 12 ng/μl) to the Human GE 8x60K Microarray. Hybridization conditions: 65°C, 10 rpm, 17 h; in an Agilent hybridization oven.

scan_protocol: Scanning performed by Atlas Biolabs GmbH (Berlin, Germany). Agilent arrays were washed using Agilent´s gene expression wash buffers 1 and 2 according to Agilent´s instructions and scanned using an Agilent DNA Microarray Scanner (Model G2505C) and Agilent´s Scan Control Software (version A.8.3.1). Primary data analysis was performed using Agilent´s Feature Extraction Software (version 10.7.3.1).

data_processing: Files containing raw data were imported and analyzed using BRB-array tools (v4.2.1) developed by Dr. Richard Simon and BRB-ArrayTools Development Team. Replicate spots in the array were averaged, unknown features removed and signal intensity values log2 transformed before normalizing the data relative to the median of a reference array. Spots were excluded if the intensity was <10. Genes were filtered if less than 20% of the samples had at least 1.5 fold change in gene expression and had missing values. Hierarchical clustering was performed using one minus correlation and complete linkage to select differentially expressed gene clusters. GO term analysis of differentially expressed genes was performed using gprofiler and GSEA web based tools.

source_name: A549 human lung cancer cell line_compound concentration_time of treatment

label_protocol: Total RNA labelled by Atlas Biolabs GmbH (Berlin, Germany) using Low Input Quick Amp Labeling Kit, One Color (#5190-2305, Agilent Technologies), using 100 ng of total RNA as starting material, according to the manufacturer´s instructions.

growth_protocol: A549 human lung cancer cells were routinely grown at 37°C in a humidified atmosphere of 5% CO2 using RPMI1640 medium containg 10% Heat Inactivated FBS.

extract_protocol: Medium and cells were recovered together and after washing with PBS, RNA was extracted using RNeasy kit (QIAGEN) following the manufacturer’s instructions. Quality and concentration of RNA was analyzed using a 2100 Bioanalyzer (Agilent).

treatment_protocol: A549 cells were seeded in 100 mm dishes at a density of 1.5 106 per dish and allowed to attach overnight. Next day medium was replaced with medium containing compounds or DMSO as control and further incubated for different times.

value: PSX146 25 mM 24 hours

tag: cell line


title: A549_PSX626 50 mM_24 hours

value: PSX626 50 mM 24 hours


title: primary breast cancer, sample_2879

source_name: primary breast cancer _BRCA2


title: primary breast cancer, sample_2883

source_name: primary breast cancer _BRCA1


title: Primary Breast Cancer2704-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_2885

source_name: primary breast cancer _CHEK2


title: A549_PSX626 25 mM_24 hours

value: PSX626 25 mM 24 hours


title: A549_PSX706 50 mM_24 hours

value: PSX706 50 mM 24 hours


title: primary breast cancer, sample_2882

value: Non


title: Primary Breast Cancer2676-250knsp

description: Hybridized to 250K_Nsp


title: A549_PS432 10 mM_24 hours

value: PS432 10 mM 24 hours


title: primary breast cancer, sample_2877


title: A549_DMSO_48 hours

value: DMSO 48 hours


title: A549_PS432 50 mM_24 hours

value: PS432 50 mM 24 hours


title: Primary Breast Cancer2488-250knsp

description: Hybridized to 250K_Nsp


title: A549_PSX706 25 mM_24 hours

value: PSX706 25 mM 24 hours


title: A549_DMSO_24 hours

value: DMSO 24 hours


title: primary breast cancer, sample_2875


title: Primary Breast Cancer2268-250knsp

description: Hybridized to 250K_Nsp


title: A549_DMSO_8 hours

value: DMSO 8 hours


title: primary breast cancer, sample_2873


title: A549_DMSO_4 hours

value: DMSO 4 hours


title: primary breast cancer, sample_2878


title: A549_PS432 25 mM_24 hours

value: PS432 25 mM 24 hours


title: Primary Breast Cancer2640-250knsp

description: Hybridized to 250K_Nsp

value: Primary Breast Cancer

value: BRCAX


title: Primary Breast Cancer2605-250knsp

description: Hybridized to 250K_Nsp


title: A549_PS432 25 mM_8 hours

value: PS432 25 mM 8 hours


title: A549_Untreated_0 hours

value: Untreated 0 hours


title: A549_PS432 25 mM_4 hours

value: PS432 25 mM 4 hours


title: A549_PS432 25 mM_48 hours

value: PS432 25 mM 48 hours


title: Primary Breast Cancer1944-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_2640

value: snap frozen primary breast tumor


title: Primary Breast Cancer2021-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_2676


title: primary breast cancer, sample_2455


title: primary breast cancer, sample_2704


title: primary breast cancer, sample_2482


title: Primary Breast Cancer1930-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_2488


title: primary breast cancer, sample_255


title: Primary Breast Cancer1934-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_2605


title: primary breast cancer, sample_2428


title: primary breast cancer, sample_2268


title: primary breast cancer, sample_2021


title: Primary Breast Cancer1922-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer1926-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer1925-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer1927-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer1911-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer1912-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer1906-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_1949


title: primary breast cancer, sample_1944


title: Primary Breast Cancer1901-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_1927


title: primary breast cancer, sample_1934


title: primary breast cancer, sample_1930


title: primary breast cancer, sample_1925


title: primary breast cancer, sample_1922


title: Primary Breast Cancer1913-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_1929


title: Primary Breast Cancer1908-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_1926


title: primary breast cancer, sample_1917


title: primary breast cancer, sample_1913


title: Primary Breast Cancer1897-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer1899-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_1916


title: Primary Breast Cancer1894-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_1912


title: Primary Breast Cancer1891-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer1885-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer1895-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer1820-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_2724


title: Primary Breast Cancer1889-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_1911


title: Primary Breast Cancer1896-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer1514-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer1642-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_1908


title: Primary Breast Cancer1775-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer1369-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_1897


title: primary breast cancer, sample_1899


title: primary breast cancer, sample_1906


title: Primary Breast Cancer1275-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_1901


title: primary breast cancer, sample_1895


title: primary breast cancer, sample_1886


title: Primary Breast Cancer967-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer994-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_1896


title: Primary Breast Cancer1028-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_1894


title: primary breast cancer, sample_1891


title: primary breast cancer, sample_1885


title: Primary Breast Cancer1159-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer973-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_1775


title: Primary Breast Cancer959-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_1820


title: Primary Breast Cancer961-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_1642


title: Primary Breast Cancer966-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer957-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer956-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer948-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_1439


title: primary breast cancer, sample_1514


title: Primary Breast Cancer951-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer942-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_1275


title: primary breast cancer, sample_1339


title: Primary Breast Cancer945-250knsp

description: Hybridized to 250K_Nsp


title: primary breast cancer, sample_1222


title: primary breast cancer, sample_1195


title: Primary Breast Cancer950-250knsp

description: Hybridized to 250K_Nsp


title: D. shibae_ΔdnrF_60_min_anaerob_rep3

city: Braunschweig

first: Matthias

last: Ebert

address: Spielmannstraße 7

department: Institute of Microbiology

institute: Technical University Braunschweig

description: Gene expression of D. shibae ΔdnrF after 60 min of anaerobiosis, Biological replicate 3 of 3.

hyb_protocol: 600 ng of labeled RNA were pooled, fragmented and hybridized according to the “one-color microarray” protocol from Agilent.

scan_protocol: The DNA microarrays were scanned using a Agilent C scanner and the Agilents scan control 8.4.1 software as well as the feature extraction 10.7.3.1 software.

data_processing: Data processing was performed in the R environment (http://www.cran.r-project.org/) using the limma package (Smyth, 2005), BioBASE package (Miller, 1996.) and the GPLOTS package (Warnes, 2012) of the BioConductor project (http:// www.bioconductor.org/). For analyses only genes with an absolute 2 fold logarithmic change (FC) >0.8 expression and a P-value <0.05 were considered in subsequent analyses.

organism: Dinoroseobacter shibae DFL 12 = DSM 16493

source_name: Dinoroseobacter shibae,ΔdnrF, anaerob

label_protocol: Two µg of isolated total cellular RNA was labeled with Cy3, using the ULSTM Fluorescent Labeling Kit for Agilent arrays (Kreatech, Amsterdam, The Netherlands) according to the manufacturers manual.

growth_protocol: For the shift experiment Dinoroseobacter shibae DFL12T wild type and generated mutant strains were grown in artificial saltwater minimal medium (SWM) supplemented with 16.9 mM succinate. For aerobic cultivation 125 ml of cell culture was inoculated with a grown pre-culture to an OD578 nM of 0.05 in a baffled flasks shaking at 200 rpm at 30°C in dark. After reaching an OD578 nM of 0.5 cells were shifted to serum flasks with rubber stoppers and 25 mM nitrate was added. Incubation occurred at 100 rpm and 30°C in dark, to avoid aerobic anoxygenic photosynthesis of D. shibae during the experiment

extract_protocol: A 2 ml volume of a D. shibae culture was used for RNA isolation using RNA protect and RNeasy mini Kit (Qiagen, Hilden, Germany) according to the manufactures manual. Thereby, 1 µl of isolated RNA was analyzed using the Agilent RNA 6000 Nano Kit and the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, USA).

treatment_protocol: An anaerobic shift was performed after reaching an OD578 nM of 0.5 by shifted cells to serum flasks. Oxygen was consumed within 30 min by D. shibae itself. The investigated time points were directly before shift and 60 min after shift.

tag: age

value: exponential phase


title: primary breast cancer, sample_1181


title: primary breast cancer, sample_1028


title: primary breast cancer, sample_1159

value: Non


title: Primary Breast Cancer930-250knsp

description: Hybridized to 250K_Nsp

tag: mutation


title: D. shibae_ΔdnrF_60_min_anaerob_rep2

description: Gene expression of D. shibae ΔdnrF after 60 min of anaerobiosis, Biological replicate 2 of 3.


title: D. shibae_ΔdnrF_60_min_anaerob_rep1

description: Gene expression of D. shibae ΔdnrF after 60 min of anaerobiosis, Biological replicate 1 of 3.


title: Primary Breast Cancer933-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer939-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer929-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer941-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer932-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer927-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer928-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer920-250knsp

description: Hybridized to 250K_Nsp


title: D. shibae_ΔdnrF_aerob_rep3

description: Gene expression of D. shibae ΔdnrF, aerob, Biological replicate 3 of 3.

source_name: Dinoroseobacter shibae,ΔdnrF, aerob


title: Primary Breast Cancer924-250knsp

description: Hybridized to 250K_Nsp


title: D. shibae_ΔdnrE_60_min_anaerob_rep3

description: Gene expression of D. shibae ΔdnrE after 60 min of anaerobiosis, Biological replicate 3 of 3.

source_name: Dinoroseobacter shibae,ΔdnrE, anaerob


title: D. shibae_ΔdnrE_60_min_anaerob_rep2

description: Gene expression of D. shibae ΔdnrE after 60 min of anaerobiosis, Biological replicate 2 of 3.


title: D. shibae_ΔdnrF_aerob_rep2

description: Gene expression of D. shibae ΔdnrF, aerob, Biological replicate 2 of 3.


title: Primary Breast Cancer918-250knsp

description: Hybridized to 250K_Nsp


title: D. shibae_ΔdnrE_60_min_anaerob_rep1

description: Gene expression of D. shibae ΔdnrE after 60 min of anaerobiosis, Biological replicate 1 of 3.


title: D. shibae_ΔdnrE_aerob_rep3

description: Gene expression of D. shibae ΔdnrE, aerob, Biological replicate 3 of 3.

source_name: Dinoroseobacter shibae,ΔdnrE, aerob


title: Primary Breast Cancer839-250knsp

description: Hybridized to 250K_Nsp


title: 6C+4CP_2

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

country: Japan

institute: Hirosaki University

hyb_protocol: Following fragmentation, 12.5 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: CEL files were quantified with the Factor Analysis for Robust Microarray Summarization (FARMS) method, using the statistical language R (R-2.7.2) and Bioconductor 2.2.

source_name: Liver

label_protocol: Biotinylated aRNA was obtained from 100 ng of purified total RNA using a GeneChip 3’ IVT Express Kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated using ISOGEN (Nippon Gene Co., Toyama, Japan), then purified with an RNeasy mini kit (Qiagen K.K., Tokyo, Japan).

treatment_protocol: Excised liver sample was immediately immersed in RNAlater and treated according to the manufacturer's protocol.

tag: diet

value: fed AIN-93M-based low-protein diet containing 6% casein plus 4% collagen peptide for 10 weeks

tag: gender

value: Male

value: BALB/cCrSlc

value: Liver

value: 17 weeks


title: 6C+4CP_1


title: Primary Breast Cancer838-250knsp

description: Hybridized to 250K_Nsp


title: D. shibae_ΔdnrE_aerob_rep1

description: Gene expression of D. shibae ΔdnrE, aerob, Biological replicate 1 of 3.


title: D. shibae_ΔdnrF_aerob_rep1

description: Gene expression of D. shibae ΔdnrF, aerob, Biological replicate 1 of 3.


title: Primary Breast Cancer461-250knsp

description: Hybridized to 250K_Nsp


title: Primary Breast Cancer255-250knsp

description: Hybridized to 250K_Nsp


title: D. shibae_ΔdnrD_60_min_anaerob_rep2

description: Gene expression of D. shibae ΔdnrD after 60 min of anaerobiosis, Biological replicate 2 of 3.

source_name: Dinoroseobacter shibae,ΔdnrD, anaerob


title: D. shibae_ΔdnrE_aerob_rep2

description: Gene expression of D. shibae ΔdnrE, aerob, Biological replicate 2 of 3.


title: D. shibae_ΔdnrD_60_min_anaerob_rep3

description: Gene expression of D. shibae ΔdnrD after 60 min of anaerobiosis, Biological replicate 3 of 3.


title: D. shibae_ΔfnrL_60_min_anaerob_rep3

description: Gene expression of D. shibae ΔfnrL after 60 min of anaerobiosis, Biological replicate 3 of 3.

source_name: Dinoroseobacter shibae,ΔfnrL, anaerob


title: D. shibae_ΔdnrD_aerob_rep1

description: Gene expression of D. shibae ΔdnrD, aerob, Biological replicate 1 of 3.

source_name: Dinoroseobacter shibae,ΔdnrD, aerob


title: 10C_1

value: fed control AIN-93M-based low-protein diet containing 10% casein for 10 weeks


title: 10C_3


title: 10C_2


title: 6C+4CP_3


title: D. shibae_ΔdnrD_aerob_rep3

description: Gene expression of D. shibae ΔdnrD, aerob, Biological replicate 3 of 3.


title: D. shibae_ΔfnrL_60_min_anaerob_rep2

description: Gene expression of D. shibae ΔfnrL after 60 min of anaerobiosis, Biological replicate 2 of 3.


title: D. shibae_ΔdnrD_aerob_rep2

description: Gene expression of D. shibae ΔdnrD, aerob, Biological replicate 2 of 3.


title: D. shibae_ΔdnrD_60_min_anaerob_rep1

description: Gene expression of D. shibae ΔdnrD after 60 min of anaerobiosis, Biological replicate 1 of 3.


title: D. shibae_ΔfnrL_aerob_rep3

description: Gene expression of D. shibae ΔfnrL, aerob, Biological replicate 3 of 3.

source_name: Dinoroseobacter shibae,ΔfnrL, aerob


title: D. shibae_wt_60_min_anaerob_rep3

description: Gene expression of D. shibae after 60 min of anaerobiosis, Biological replicate 3 of 3.

source_name: Dinoroseobacter shibae, anaerob


title: D. shibae_ΔfnrL_60_min_anaerob_rep1

description: Gene expression of D. shibae ΔfnrL after 60 min of anaerobiosis, Biological replicate 1 of 3.


title: D. shibae_ΔfnrL_aerob_rep1

description: Gene expression of D. shibae ΔfnrL, aerob, Biological replicate 1 of 3.


title: D. shibae_ΔfnrL_aerob_rep2

description: Gene expression of D. shibae ΔfnrL, aerob, Biological replicate 2 of 3.


title: D. shibae_wt_60_min_anaerob_rep2

description: Gene expression of D. shibae after 60 min of anaerobiosis, Biological replicate 2 of 3.


title: D. shibae_wt_60_min_anaerob_rep1

description: Gene expression of D. shibae after 60 min of anaerobiosis, Biological replicate 1 of 3.


title: D. shibae_wt_aerob_rep3

description: Gene expression of D. shibae, aerob, Biological replicate 3 of 3.

source_name: Dinoroseobacter shibae, aerob


title: Primary Breast Cancer804-250knsp

description: Hybridized to 250K_Nsp


title: D. shibae_wt_aerob_rep2

description: Gene expression of D. shibae, aerob, Biological replicate 2 of 3.


title: D. shibae_wt_aerob_rep1

description: Gene expression of D. shibae, aerob, Biological replicate 1 of 3.


title: MEF-SGCF-0day-rep2

city: Hangzhou

first: Guoji

last: Guo

state: Zhejiang

address: Yuhangtang Road 866

department: School of Medicine

institute: Zhejiang University

hyb_protocol: Labeled cRNA was fragmented and then hybridized to GeneChip Mouse Genome 430A 2.0 Arrays (Affymetrix).

scan_protocol: Washing, detection, and scanning were performed as described by manufacturer protocols (Affymetrix). Signal intensities of genes for each genechip were computed using the Affymetrix Microarray Suite 5.0.

data_processing: The raw data were firstly summarized, and then processed using the standard RMA algorithm with quantile normalization. The signal intensities for all probes of each gene were averaged and Log2 transformed. The transformed data were subjected to one-factor analysis of variance using Limma package in R. For differentially expressed genes, the false positives were controlled by a cut-off value of false discovery rate (FDR) <=0.001. PCA projection analysis  and Clustering heatmap were generated with differentially expressed genes between each two groups from days 0, 5 and 10 samples for 6TCF or SGCR treatment (FDR<=0.01). PCA were performed using prcomp function; Clustering heatmap were made using pheatmap package. .chp files contain MAS5.0 data.

source_name: mouse embryonic fibroblasts (MEFs)

label_protocol: biotin were labeled according to manufacturer protocols(Affymetrix GeneChip Mouse Genome 430A 2.0 Array)

growth_protocol: MEFs from each embryo were plated onto a 15cm tissue culture dish in MEF medium containing DMEM (Life Technologies) and 10% fetal bovine serum (FBS, Gemini). MEFs were seeded at a density of 20000 cells per 35mm dish. The next day, MEF medium was replaced with the iMT media containing DMEM (Life Technologies) supplemented with 15% FBS (Gemini), 2mM GlutaMax-I (Life Technologies), 1% nonessential amino acids (Life Technologies), 0.1mM β-mercaptoethanol (Sigma) and 40ng/ml basic fibroblast growth factor (bFGF, Stemgent)

extract_protocol: Total RNA was extracted with the Rneasy Mini Kit (Qiagen). cDNA was synthesized and then amplified through in vitro transcription(Affymetrix).

treatment_protocol: MEFs were treated by chemical combinations 6TCF and SGCF respectively on Day 0, Day 5 and Day 10.

value: mouse embryonic fibroblasts (MEFs)

value: SGCF

tag: timepoint

value: Day 0


title: MEF-SGCF-10day-rep1

value: Day 10


title: MEF-SGCF-5day-rep2

value: Day 5


title: MEF-SGCF-0day-rep1


title: MEF-SGCF-10day-rep2


title: Slide US45102948_256525610001_S01.6

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

description: Sample 2

hyb_protocol: The protocol was performed as described in Kloosterman et al., 2006 and Shafeeq et al., 2011.

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner.

data_processing: Dual-channel array images were analyzed with Genepix 6.  Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP software. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets. Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios  were calculated. Further analysis was performed with a Cyber-T Student T-test for paired data.

organism: Streptococcus pneumoniae D39

source_name: F650 Mean

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).

growth_protocol: Cells were grown CDM medium with 0.03 mM and 50mM cysteine and harvested at respective mid-exponential phase.

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Kloosterman et al., 2006). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

value: 0.03 mM cysteine

value: 50 mM cysteine


title: MEF-SGCF-5day-rep1


title: Slide US45102948_256525610001_S01.5

description: Sample 1

source_name: F550 Mean


title: MEF-6TCF-0day-rep2


title: MEF-6TCF-10day-rep2


title: MEF-6TCF-10day-rep1


title: MEF-6TCF-0day-rep1


title: ocm1-340_rep2

status: Public on Jan 16 2017

city: Shanghai

first: Yue

last: Xing

state: Shanghai

address: Zhizaoju Road No.639, Huangpu District

department: Department of Ophthalmology

institute: Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix Human Prime view array in Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: UM cell line with CANT1 overexpression (experimental group)

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

growth_protocol: cells are cultured with DMEM with 10%FBS

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

treatment_protocol: control groups are wild type UM cells, experimental groups are UM cells with CANT1 lncRNA overexpression

value: CANT1 lncRNA overexpression


title: mum-340_rep2


title: MEF-6TCF-5day-rep2


title: 4-week-old WT mice PDL

city: TOKYO

first: Naoki

last: Koda

address: 1-5-45 Yushima, bunkyo-dist.

department: systems biomedicine

institute: TMDU

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to 8x60K Microarray (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: 4-week-old WT mice PDL

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling 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-2000 Spectrophotometer.

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions.(ISOGEN, Nippon gene)

value: PDL

value: WT


title: MEF-6TCF-5day-rep1


title: ocm1-340_rep3


title: 4-week-old Mkx-KO mice PDL

source_name: 4-week-old Mkx-KO mice PDL

value: Mkx-KO


title: 10-week-old Mkx-KO mice PDL

source_name: 10-week-old Mkx-KO mice PDL


title: ocm1_rep3

source_name: wild type UM cell line (control group)

value: control


title: 10-week-old WT mice PDL

source_name: 10-week-old WT mice PDL


title: mum_rep3


title: mum_rep2


title: uveal melanoma OCM1 cells-CANT1 lncRNA overexpressed-rep1

description: Gene expression data from CANT1 lncRNA overexpressed human uveal melanoma cell line OCM1

source_name: human uveal melanoma cell line OCM1 with CANT1 lncRNA overexpressed

growth_protocol: control groups are wild type human uveal melanoma cells, experimental groups are CANT1 lncRNA overexpressed uveal melanoma cells cultured and selected in DEME with puromycin before RNA extracted.

treatment_protocol: The medium was discarded. Cells were rinsed with PBS and placed on ice in the Trizol solution (Invitrogen).


title: ocm1_rep2


title: uveal melanoma MUM2B cells-CANT1 lncRNA overexpressed-rep1

description: Gene expression data from CANT1 lncRNA overexpressed human uveal melanoma cell line MUM2B

source_name: human uveal melanoma cell line MUM2B with CANT1 lncRNA overexpressed


title: uveal melanoma MUM2B cells-wild type-rep1

description: Gene expression data from wild type human uveal melanoma cell line MUM2B

source_name: human uveal melanoma wild type cell line, MUM2B


title: mum-340_rep3


title: uveal melanoma OCM1 cells-wild type-rep1

description: Gene expression data from wild type human uveal melanoma cell line OCM1

source_name: human uveal melanoma wild type cell line, OCM1


title: 32B_F_HDID1

city: Portland

first: Priscila

last: Darakjian

state: OR

address: 3181 SW Sam Jackson Park Road, L470

department: Behavioral Neuroscience

institute: Oregon Health and Science University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: brain striatum

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

extract_protocol: Frozen brains were slightly thawed and dissected by hand under RNAse-free conditions. Using the optic chiasm as the rostral marker, a 2-mm coronal slice of brain tissue was isolated. Following the partial cone shape of the striatum, the dissection moved dorsal 1 mm, followed by a cut to the lateral boundary of the striatum, with a final cut following the lateral-ventral boundary. The isolated tissue was immediately placed in 100 ml of Trizol  (Invitrogen, Carlsbad, CA). On average, the isolated striatal tissue samples weighed 3 mg.

treatment_protocol: Mice were euthanized, and brains were removed and immediately frozen on dry ice.

tag: sex (f=female, m=male)

value: F

tag: behavioral phenotype

value: Drinker

tag: selection


title: 106B_M_HSNPT

value: M

value: Control


title: 63B_F_HDID2


title: 54B_F_HDID2


title: 126B_M_HSNPT


title: 16B_F_HDID1


title: 80B_F_HDID2


title: 12B_M_HDID1


title: 3B_F_HDID1


title: 10B_F_HDID1


title: 52A_M_HDID1


title: 44A_M_HDID1


title: 8B_M_HDID1


title: 28B_F_HDID1


title: 89B_M_HDID2


title: 24B_M_HDID1


title: 1B_F_HDID1


title: 152B_M_HSNPT


title: 115B_M_HSNPT


title: 22amcA__


title: 97A_F_HDID2


title: 154A_F_HSNPT


title: 151A_M_HSNPT


title: 98B_M_HDID2


title: 51A_M_HDID1


title: 42A_F_HDID1


title: 43A_F_HDID1


title: 20B_F_HDID1


title: 96A_M_HDID2


title: LMNA flx/flx; Alb-cre+ [I1]

city: Ann Arbor

first: Raymond

last: Kwan

state: MI

address: 7720 Med Sci II

department: Molecular and Integrative Physiology

institute: University of Michigan, Ann Arbor

description:
Sample name: I1
Gene expression data from livers.

hyb_protocol: Following labeling procedure, 2.53 ug of cDNA were hybridized at 48 degrees C on Mouse Gene ST 2.1 plates, and were washed and stained using the Affymetrix GeneTitan system (software version 3.2.4.1515).

scan_protocol: Arrays were scanned using the Affymetrix GeneTitan system (software version 3.2.4.1515).

data_processing: Statistical analysis for microarray data was performed using the Oligo and Limma packages of Bioconductor implemented in the R statistical environment. Expression values for each probeset in the microarray was calculated using a robust multi-array average (RMA) (Irizarry et al., 2003). Probesets with a variance over all samples less than 0.05 were filtered out. p-values were adjusted for multiple comparisons using false discovery rate (FDR) (Benjamini and Hochberg, 1995).

source_name: Liver, LMNA flx/flx; Alb-cre+, Normal Chow

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA.

growth_protocol: All mice were C57BL/6 background and were maintained in standard cages in a light- and temperature-controlled room and were allowed chow and water ad libitum.

extract_protocol: Total RNA purification was performed using the Qiagen RNeasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: Normal Chow (NC) mice were fed standard chow for 14 weeks. High Fat Diet (HFD) mice were fed the Surwit Diet plus 42 g/L of carbohydrate in drinking water at a 55% fructose and 45% sucrose for 14 weeks.

tag: strain/background

tag: genotype/variation

value: LMNA flx/flx; Alb-cre+

value: male

tag: tissue

value: Liver

value: 38.9 weeks

value: Normal Chow


title: 95A_M_HDID2


title: LMNA flx/flx; Alb-cre+ [C3]

description:
Sample name: C3
Gene expression data from livers.

source_name: Liver, LMNA flx/flx; Alb-cre+, High Fat Diet

value: 35.3 weeks

value: High Fat Diet


title: LMNA flx/flx; Alb-cre+ [C2]

description:
Sample name: C2
Gene expression data from livers.


title: LMNA flx/+; Alb-cre+ [B2]

description:
Sample name: B2
Gene expression data from livers.

source_name: Liver, LMNA flx/+; Alb-cre+, High Fat Diet

value: LMNA flx/+; Alb-cre+

value: 30 weeks


title: 103A_M_HDID2


title: LMNA flx/flx; Alb-cre+ [C4]

description:
Sample name: C4
Gene expression data from livers.


title: 45B_M_HDID1


title: 49A_F_HDID1


title: 102B_M_HDID2


title: LMNA flx/flx; Alb-cre+ [H2]

description:
Sample name: H2
Gene expression data from livers.


title: 47B_M_HDID1


title: LMNA flx/flx; Alb-cre+ [H1]

description:
Sample name: H1
Gene expression data from livers.


title: 48A_F_HDID1


title: 104A_M_HDID2


title: LMNA flx/+; Alb-cre+ [P1]

description:
Sample name: P1
Gene expression data from livers.

source_name: Liver, LMNA flx/+; Alb-cre+, Normal Chow

value: 24 weeks


title: 46A_M_HDID1


title: LMNA flx/+; Alb-cre+ [B1]

description:
Sample name: B1
Gene expression data from livers.


title: LMNA flx/+; Alb-cre+ [F1]

description:
Sample name: F1
Gene expression data from livers.

value: 26.4 weeks


title: 100A_M_HDID2


title: 155A_F_HSNPT


title: 101A_M_HDID2


title: 158A_M_HSNPT


title: LMNA flx/+; Alb-cre+ [A2]

description:
Sample name: A2
Gene expression data from livers.

value: 30.4 weeks


title: LMNA +/+; Alb-cre+ [N1]

description:
Sample name: N1
Gene expression data from livers.

source_name: Liver, LMNA +/+; Alb-cre+, Normal Chow

value: LMNA +/+; Alb-cre+

value: 24.6 weeks


title: CD133-positive (C68+)

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

hyb_protocol: Labeled RNAs were heat denatured and hybridized to Agilent 8x15k miRNA microarray V19 comprised of 2006 miRNAs from Sanger miRBase (release 19) at 55°C for 20 hours.

scan_protocol: After hybridization, slides were immediately washed and scanned in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA). Feature Extraction v10.7.3.1 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images.

data_processing: Data (intensity signal) were normalized by quantile normalization, using Bioconductor 2.10 with R version 2.15.  ''signal' is  a measure of the abundance of a transcript.

label_protocol: 100 ng of total RNA from each sample were labeled with Cy3 by using Agilent miRNA labeling kit following manufacturer’s instructions.

extract_protocol: Genome wide microRNA profiling of 12 CD133high and 12 CD133low tumor samples were performed using Agilent Human miRNA Microarray (V19).  CD133 positive cells were isolated from freshly resected and physically/enzymatically dissociated tumor tissue samples using Magnetic-activated Cell Sorting (MACS) technique (Miltenyi Biotech, Bergisch Gladbach, Germany) and “EasySep Positive Selection Human PE Selection Kit (StemCell Technologies, (Vancouver, BC, Canada)” following the manufacturer’s protocol. Shortly, fresh tumor tissue samples were physically minced with a scalpel and exposed to enzymatic dissociation using 400 μg/ml Collagenase enzyme (GIBCO, New York, USA) at 37C for 3 hours. Dissociated cells were filtered using a 70-μm cell strainer to get a single cell suspension. Cells were labeled with CD133/2-PE (Miltenyi Biotech clone AC133) antibody. After magnetic sorting, CD133 enriched (CD133high) and remaining (CD133low) cell populations were immediately washed and homogenized in “Lysis/Binding Buffer” of “mirVana miRNA Isolation Kit” (Ambion, Darmstadt, Germany) for further RNA isolation.

tag: cell marker

value: larynx cancer

tag: surgery

value: Total Laryngectomy

tag: grade

value: II

tag: Stage


title: 150A_M_HSNPT

value: M

value: Control


title: LMNA flx/+; Alb-cre+ [F2]

description:
Sample name: F2
Gene expression data from livers.

value: male

value: Liver


title: 148A_F_HSNPT

value: F


title: LMNA +/+; Alb-cre+ [G1]

description:
Sample name: G1
Gene expression data from livers.

value: 27 weeks

value: Normal Chow


title: CD133-positive (C67+)

tag: Sex

value: Supraglottic Laryngectomy

value: III