title: PEO4-2

status: Public on Mar 27 2015

city: Dallas

first: Michael

last: White

state: TX

address: 6000 Harry Hines Blvd.

department: Cell Biology

institute: University of Texas Southwestern Medical Center

description: Replicate 3

hyb_protocol: Standard Illumina Hybridization protocol

data_processing: Data were quantile normalized and background subtracted using the previously published MBCB algorithm

label_protocol: Standard Illumina Labeling protocol

growth_protocol: All PEO1 and PEO4 cells were grown in RPMI medium with l-glutamine and 25mM HEPES supplemented with 10% fetal bovine serum and and 100 U/mL penicillin and 100 μg/mL streptomycin. HOSE were grown in Keratinocyte Serum Free Medium with supplements and 100 U/mL penicillin and 100 μg/mL streptomycin.

extract_protocol: RNA was isolated from cells 72 hours after plating using an RNAEasy kit (Qiagen).

tag: cell line


title: PEO1-1.2

type: RNA

country: USA

description: Technical Replicate of Biological Replicate 1

scan_protocol: Standard Illumina scanning protocol

molecule: total RNA

organism: Homo sapiens


title: HOSE-2

description: Replicate 1

source_name: HOSE

value: HOSE


title: PEO4-1

description: Replicate 2


title: Control animal_only vehicle_rep1

status: Public on Mar 28 2015

city: Campinas

first: Rafaela

middle: da Rosa

last: Ribeiro

address: Charles Dawin st, bl.N room 10

department: Structural and functional biology department

country: Brazil

institute: State University of Campinas

description: Gene expression data from ventral prostate colected of control adult rats that received only estrogen vehicle (corn oil)

hyb_protocol: Following fragmentation, 6.75 ug (27 ul at 25ng/ul) of fragmented and labeled single-straded cDNA were hibridized for 18 hrin 45°C hybridization oven, at 60 rpm. GeneChips were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: GeneChip were scanned Affymetrix GeneChip Operating Software v1.3 program.

data_processing: The data were summarized and normalized by Expression Console software (Affymetrix).

label: Biotin

organism: Rattus norvegicus

source_name: Ventral prostate, no-treatment

label_protocol: Biotinylated single-straded cDNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (GeneChip® WT Terminal Labeling and Hybridization User Manual for use with the Ambion® WT Expression Kit, 2009, Affymetrix).

growth_protocol: Male Wistar rats were kept under normal light conditions (12-h light:dark cycle) and received filtered tap water and Purina rodent chow ad libitum

extract_protocol: Ventral prostates were dissected under RNAse-free conditions. Thirty mg of the tissue was used for total RNA extraction. Subsequently, the tissue fragments were extracted using Illustra RNAspin Mini kits (GE Healthcare, Buckinghamshire,UK) according to the manufacturer’s instructions.

treatment_protocol: On the 90th day after birth, the rats were assigned to different treatment groups (n=3): First group were castrated (Cas) by orchiectomy via scrotal incision under ketamine (150 mg/Kg body weight) and xylazin (10 mg/kg body weight) anesthesia; Second group received a 25 mg/Kg body weight dose of 17β-estradiol diluted in corn oil (E2 group);Third group received a combination of both treatments (Cas+E2 group) (combined orchiectomy and 17β-estradiol). In the control group (Ct; normal androgen and estrogen), the animals received only the vehicle.

tag: strain

value: Wistar

tag: tissue

value: Ventral prostate

tag: gender

value: Male

tag: age

value: Adult- 90 days old

tag: protocol

value: Control


title: Unexposed control worker, Control 5

city: Seoul

first: Mi-Kyung

last: Song

address: 39-1 Hwawol-gok-dong, Wolsong-gil5, Seongbuk-gu-seoul

country: South Korea

institute: Korea Institute of Science & Technology

description: miRNA expression of unexposed control worker

hyb_protocol: Labeled total RNA samples were dried completely by using speed-vac, and then hybrized with probes on array slides, accorkding to the manufacture. The hybridization lasted for 20 hours inside 55'C hybridization oven (Agilent). After hybridization, arrays were washed with Gene Expression Wash Buffer 1 (Agilent) at room temperature, and then wahsed with Wash Buffer 2 (Agilent) at 37'C. The washed array were dried and processed to scanning step immediately.

scan_protocol: Slides was scanned immediated after washing step on Agilent G2565CA Microarray Scanner System. (Scan Area is 61x21.6 mm; Scan resolution is 3um; Color channel is Green; Green PMT is 100%)

data_processing: Transformed by using Feature Extraction (V.10.7.3.1) software on default setting. (Protocol is miRNA_107_Sep09, Grid is 031181_D_F_20111226). FRelative signal intensities for each gene were generated using the Robust Multi-Array Average algorithm. Substandard spots, identified by visual examination of each slide, were flagged and excluded from further analysis. Spots harboring dust artifacts or spatial defects were manually flagged and excluded. In an effort to filter out unreliable data, spots with signal-to-noise (signal-background SD) ratios below 10 were not included in the data analysis. Data applied standard normalization methods for one-channel microarrays: quantile normalization using the GeneSpring GX v11.0 (Agilent technologies). The normalized, and log transformed intensity values were then analyzed. Fold change filters included the requirement that the genes be present in at least 150% of controls for up-regulated genes and lower than 67% of controls for down-regulated genes. The statistical significance of the differences was evaluated by using the ANOVA and t-test tool. Differences with P<0.05 were taken as statistically significant. Hierarchical clustering of log ratios was performed to detect clusters of miRNAs and blood samples. In detail, we applied bottom up complete linkage clustering and used the Pearson correlation linkage. In addition, we carried out a standard principal component analysis (PCA), which is dimensionality reduction technique to analysis high-dimensional gene expression dataset using the GeneSpring GX software. PCA was carried out on log-transformed data, using mean centering and scaling.

source_name: Human Whole blood

label_protocol: 100ng Total RNA from each blood case was labeled with Cyanine 3-pCp by using Agilent miRNA labeling kits according to the manufacturer's instructions. Labeled samples were desalted by using MicroBioSpin 6 Columns (Bio-Rad).

extract_protocol: Total RNA containing miRNA from blood samples was extracted using the PAXgene Blood miRNA Kit, including treatment with DNAse I to prevent genomic DNA contamination, strictly following the manufacturer’s instruction (Qiagen)

value: whole blood


title: Drosophila_melanogaster_brat_mutant_0-1.5h_embryos_rep1

city: Toronto

first: Howard

middle: D

last: Lipshitz

state: ON

address: 1 King's College Circle

department: Molecular Genetics

country: Canada

institute: University of Toronto

description: This sample is total RNA isolated from embryos collected from brat mutant females (females with the genotype bratfs1/Df(2L)TE37C-7) 0-1.5 hours post-egglaying. It is the first of three biological replicates.

hyb_protocol: Hybridization was performed following the protocol described in the NimbleGen Array User’s Guide (Gene Expression Arrays, version 6.0).

scan_protocol: Arrays were scanned with a GenePix4000B microarray scanner system (Molecular Devices, Inc., Sunnyvale, CA, USA), and scanned images were initially quantified using Nimblescan (Roche), following the protocol described in the NimbleGen Array User's Guide (Gene Expression Arrays, version 6.0).

data_processing: The raw data (.pair files) were normalized with ArrayStar 12 (DNASTAR) software using the RMA quantile method, and signal intensities were log2-transformed. All samples were normalized together.

organism: Drosophila melanogaster

source_name: 0-1.5 hour embryo from brat mutant female

label_protocol: Labelling was performed following the protocol described in the NimbleGen Array User’s Guide (Gene Expression Arrays, version 6.0).

growth_protocol: The following fly strains were used: w1118, bratfs1/CyO, Df(2L)TE37C-7/CyO. All stocks were maintained at 25˚C.

extract_protocol: Total RNA was extracted using TRI reagent (Molecular Research Center, Inc., Cincinnati, OH) according to the manufacturer’s protocol.

tag: developmental stage

value: 0-1.5 hour embryo

tag: maternal genotype


title: Unexposed control worker, Control 3


title: Drosophila_melanogaster_brat_mutant_0-1.5h_embryos_rep2

description: This sample is total RNA isolated from embryos collected from brat mutant females (females with the genotype bratfs1/Df(2L)TE37C-7) 0-1.5 hours post-egglaying. It is the second of three biological replicates.


title: Drosophila_melanogaster_brat_mutant_1.5-3h_embryos_rep2

description: This sample is total RNA isolated from embryos collected from brat mutant females (females with the genotype bratfs1/Df(2L)TE37C-7) 1.5-3 hours post-egglaying. It is the second of three biological replicates.

source_name: 1.5-3 hour embryo from brat mutant female

value: 1.5-3 hour embryo


title: PEO4 siNC 2

description: Replicate 2

label: biotin

growth_protocol: All PEO4 cells were grown in RPMI medium with l-glutamine and 25mM HEPES supplemented with 10% fetal bovine serum and and 100 U/mL penicillin and 100 μg/mL streptomycin.

extract_protocol: RNA was isolated from cells 72 hours post-transfection using an RNAEasy kit (Qiagen).

treatment_protocol: 10 picomoles of miRNA mimic per well were delivered in 30 μL serum free medium to 96-well microtiter plates.  9.8 μL of serum free medium containing 0.2 μL of DharmaFECT 3 transfection reagent was then added to each well followed by a 20-30 minute incubation at room temperature. Single-cell suspensions were then delivered to each well a total volume of 150 μL.  A total of 10,000 cells/well were added to each well.


title: PEO4 siSIX4 3

description: Replicate 3


title: Drosophila_melanogaster_brat_mutant_1.5-3h_embryos_rep1

description: This sample is total RNA isolated from embryos collected from brat mutant females (females with the genotype bratfs1/Df(2L)TE37C-7) 1.5-3 hours post-egglaying. It is the first of three biological replicates.


title: PEO4 siNC 3

description: Replicate 3


title: Drosophila_melanogaster_brat_mutant_0-1.5h_embryos_rep3

description: This sample is total RNA isolated from embryos collected from brat mutant females (females with the genotype bratfs1/Df(2L)TE37C-7) 0-1.5 hours post-egglaying. It is the third of three biological replicates.


title: Unexposed control worker, Control 2


title: PEO4 miNC 3

description: Replicate 3


title: PEO4 miR-124 3

description: Replicate 3


title: PEO4 miR-124 1

description: Replicate 1


title: PEO4 siSIX4 2

description: Replicate 2


title: HOSE-1

description: Replicate 3


title: Unexposed control worker, Control 4


title: Unexposed control worker, Control 1


title: PEO1-2

description: Replicate 2


title: PEO4 siSIX4 1

description: Replicate 1


title: PEO4 siNC 1

description: Replicate 1


title: PEO4 miR-124 2

description: Replicate 2


title: PEO4 miNC 2

description: Replicate 2


title: PEO1-1

description: Replicate 1


title: PEO4 miNC 1

description: Replicate 1


title: PEO1 siSIX4 3

description: Replicate 3

growth_protocol: All PEO1 cells were grown in RPMI medium with l-glutamine and 25mM HEPES supplemented with 10% fetal bovine serum and and 100 U/mL penicillin and 100 μg/mL streptomycin.

treatment_protocol: 10 picomoles of miRNA mimic per well were delivered in 30 μL serum free medium to 96-well microtiter plates.  9.8 μL of serum free medium containing 0.2 μL of RNAiMax transfection reagent was then added to each well followed by a 20-30 minute incubation at room temperature. Single-cell suspensions were then delivered to each well a total volume of 150 μL.  A total of 10,000 cells/well were added to each well.


title: PEO1 siNC 2

description: Replicate 2

source_name: PEO1_siRNA negative_control


title: Lung-d3_UVSeV-3a

city: St. Louis

first: Anand

middle: Champak

last: Patel

state: MO

address: Campus Box 8116, 660 S. Euclid Ave.

department: Pulmonary/Critical Care Medicine

institute: Washington University School of Medicine

description: Strip A from array and sample B6.3.U.3682.1 each BeadChip consists of two strips (A & B).

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol except for adding output of raw array data for beadlevel analyses

data_processing: Hybridization and scanning of BeadChip arrays was performed according to the manufacturer’s instructions, using BeadStudio 3.0 software (Illumina). In order to perform bead-level analysis, raw data is exported from BeadStudio. Microarray normalization and statistical analysis was performed using packages from the Bioconductor project executed in the R programming environment. Raw bead-level intensity data was imported using functions from the beadarray package, including background correction. Each Mouse-WG6 v2 BeadChip array consists of two strips. Due to potential variation in the data from the two different strips (see Shi et al. (2009) [PMID:19903361]), we treated the individual strips from each sample separately through bead-summarization. Thus, for each strip, low-level analysis and quality control was performed using functions from the beadarray package (see Ritchie et al. (2011) [PMID:22144879]). The BASH algorithm was then applied to the raw data to mask beads affected by large spatial artifacts, followed by bead-type summarization, including removal of outlier beads. Summarized data were Log2-transformed, followed by quantile normalization.

organism: Mus musculus

source_name: whole lung, UV-SeV post-infection day 3, rep 3, array strip A

label_protocol: Biotinylated aRNA were prepared using the Illumina TotalPrep Kit (Ambion) per manufacturer's protocol.

growth_protocol: Mice were maintained under pathogen-free conditions, and all study protocols were approved by the Washington University Animal Studies Committee.

extract_protocol: Total RNA was extracted using QIAGEN RNeasy kit per manufacturer's protocol. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Sendai virus (SeV), strain 52, was obtained from American Type Culture Collection and stored at -70°C. Mice were inoculated with SeV or an equivalent amount of UV-inactivated SeV (SeV-UV) intranasally. 3-5 week old male C57BL/6J mice were obtained from Jackson Laboratory. Mice were sacrificed post-infection day 3, and lungs were harvested, right for RNA, left for histology and other studies (see Kim et al, 2008, PMID:18488036).

tag: time

value: 3 days post-infection

tag: infection

value: UV-inactivated Sendai virus


title: PEO1 miR-124 3

description: Replicate 3


title: PEO1 siSIX4 1

description: Replicate 1


title: PEO1 siNC 1

description: Replicate 1


title: PEO1 miR-124 2

description: Replicate 2


title: PEO1 siNC 3

description: Replicate 3


title: Lung-d3_UVSeV-2a

description: Strip A from array and sample B6.3.U.3680.1 each BeadChip consists of two strips (A & B).

source_name: whole lung, UV-SeV post-infection day 3, rep 2, array strip A


title: Lung-d3_SeV-3a

description: Strip A from array and sample B6.3.S.3689.1 each BeadChip consists of two strips (A & B).

source_name: whole lung, SeV post-infection day 3, rep 3, array strip A

value: active Sendai virus


title: TNC-KO ASMCs with exogenous TNC with TNF, #3

city: Kurume

first: Hiroki

last: Aoki

state: Fukuoka

address: 67 Asahimachi

department: Cardiovascular Research Institute

country: Japan

institute: Kurume University

hyb_protocol: We performed the labeling and the hybridization according to the GeneChip 3' IVT Expression Kit User Manual (Affymetrix).

data_processing: The raw data were obtained using Affymetrix GeneChip Command Console Software. The normalized data were obtained using Affymetrix Expression Console Software by scaling the mean signal intensity of each array to 500.

source_name: We cultured TNC-KO ASMCs in the presence or absence of exogenous TNC (10 µg/mL) and stimulated the cells with 10 ng/mL TNF-alpha for 35 h before obtaining total RNA using RNeasy.

extract_protocol: We extracted total RNA using RNeasy (Qiagen)

treatment_protocol: We used periaortic application of 0.5 M CaCl2 to the infrarenal aorta or either wild type (WT) or tenascin C knockout (TNC-KO) mice to create the mouse model for stiffened aorta and infused the mice with AngII (1 µg/min/kg) for 1 week to apply the pathological stress on aorta (Ca+AngII). Mice were then killed with an overdose of pentobarbital to obtain the tissue samples. The suprarenal aortic samples, from the level of right renal artery to 10 mm above the right renal artery, and infrarenal aortic samples, from the level of left renal artery to 10 mm below the left renal artery, were collected and kept in RNAlater (Qiagen) until the extraction of total RNA using RNeasy (Qiagen).

value: male

tag: genotype

value: TNC-KO

tag: cell type

value: aortic smooth muscle cells

tag: treatment

value: exogenous TNC + TNF


title: Lung-d3_UVSeV-3b

description: Strip B from array and sample B6.3.U.3682.2 each BeadChip consists of two strips (A & B).

source_name: whole lung, UV-SeV post-infection day 3, rep 3, array strip B


title: TNC-KO ASMCs with exogenous TNC with TNF, #2

scan_protocol: We performed the labeling and the hybridization according to the GeneChip 3' IVT Expression Kit User Manual (Affymetrix).

source_name: We cultured TNC-KO ASMCs in the presence or absence of exogenous TNC (10 µg/mL) and stimulated the cells with 10 ng/mL TNF-alpha for 34 h before obtaining total RNA using RNeasy.


title: TNC-KO ASMCs with exogenous TNC with TNF, #4

source_name: We cultured TNC-KO ASMCs in the presence or absence of exogenous TNC (10 µg/mL) and stimulated the cells with 10 ng/mL TNF-alpha for 36 h before obtaining total RNA using RNeasy.

label_protocol: We performed the labeling and the hybridization according to the GeneChip 3' IVT Expression Kit User Manual (Affymetrix).


title: Lung-d3_SeV-3b

description: Strip B from array and sample B6.3.S.3689.2 each BeadChip consists of two strips (A & B).

source_name: whole lung, SeV post-infection day 3, rep 3, array strip B


title: TNC-KO ASMCs with exogenous TNC or TNF, #4

source_name: We cultured TNC-KO ASMCs in the presence or absence of exogenous TNC (10 µg/mL) and stimulated the cells with 10 ng/mL TNF-alpha for 32 h before obtaining total RNA using RNeasy.

value: exogenous TNC


title: TNC-KO ASMCs with exogenous TNC or TNF, #3

source_name: We cultured TNC-KO ASMCs in the presence or absence of exogenous TNC (10 µg/mL) and stimulated the cells with 10 ng/mL TNF-alpha for 31 h before obtaining total RNA using RNeasy.


title: TNC-KO ASMCs with exogenous TNC with TNF, #1

source_name: We cultured TNC-KO ASMCs in the presence or absence of exogenous TNC (10 µg/mL) and stimulated the cells with 10 ng/mL TNF-alpha for 33 h before obtaining total RNA using RNeasy.


title: PEO1 miR-124 1

description: Replicate 1


title: Lung-d3_SeV-2b

description: Strip B from array and sample B6.3.S.3690.2 each BeadChip consists of two strips (A & B).

source_name: whole lung, SeV post-infection day 3, rep 2, array strip B


title: TNC-KO ASMCs with exogenous TNC or TNF, #2

source_name: We cultured TNC-KO ASMCs in the presence or absence of exogenous TNC (10 µg/mL) and stimulated the cells with 10 ng/mL TNF-alpha for 30 h before obtaining total RNA using RNeasy.


title: PEO1 miNC 3

description: Replicate 3


title: Lung-d3_UVSeV-2b

description: Strip B from array and sample B6.3.U.3680.2 each BeadChip consists of two strips (A & B).

source_name: whole lung, UV-SeV post-infection day 3, rep 2, array strip B


title: Lung-d3_SeV-2a

description: Strip A from array and sample B6.3.S.3690.1 each BeadChip consists of two strips (A & B).

source_name: whole lung, SeV post-infection day 3, rep 2, array strip A


title: TNC-KO ASMCs with exogenous TNC or TNF, #1

source_name: We cultured TNC-KO ASMCs in the presence or absence of exogenous TNC (10 µg/mL) and stimulated the cells with 10 ng/mL TNF-alpha for 29 h before obtaining total RNA using RNeasy.


title: PEO1 miNC 1

description: Replicate 1


title: genomic DNA from cells stimulated with 10uM OA

type: genomic

city: Leon

first: Silvio

last: Zaina

state: Gto

address: 20 de Enero no. 929

department: Department of Medical Sciences

country: Mexico

institute: University of Guanajuato

description: 10 uM OA

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Infinium HumanMethylation450 BeadChip using standard Illumina protocol

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

data_processing: GenomeStudio (2010.3) Methylation module (1.8.5) software. The non-normalized.txt contains methylated and unmethylated signal intensities.

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from THP-1 monocytes using a standard phenol/chlorophorm extraction and isopropanol precipitation protocol.

value: monocytes

tag: stimulated with

value: 10uM oleic acid (OA)


title: Lung-d3_SeV-1b

description: Strip B from array and sample B6.3.S.3691.2 each BeadChip consists of two strips (A & B).

source_name: whole lung, SeV post-infection day 3, rep 1, array strip B


title: TNC-KO ASMCs without exogenous TNC with TNF, #3

source_name: We cultured TNC-KO ASMCs in the presence or absence of exogenous TNC (10 µg/mL) and stimulated the cells with 10 ng/mL TNF-alpha for 28 h before obtaining total RNA using RNeasy.

value: TNF


title: genomic DNA from cells stimulated with 100uM AA

description: 100 uM AA

value: 100uM arachidonic acid (AA)


title: genomic DNA from cells stimulated with 10uM AA

description: 10 uM AA

value: 10uM arachidonic acid (AA)


title: PEO1 miNC 2

description: Replicate 2


title: genomic DNA from cells stimulated with 100uM OA

description: 100 uM OA

value: 100uM oleic acid (OA)


title: TNC-KO ASMCs without exogenous TNC or TNF, #2

source_name: We cultured TNC-KO ASMCs in the presence or absence of exogenous TNC (10 µg/mL) and stimulated the cells with 10 ng/mL TNF-alpha for 24 h before obtaining total RNA using RNeasy.


title: Lung-d3_UVSeV-1a

description: Strip A from array and sample B6.3.U.3681.1 each BeadChip consists of two strips (A & B).

source_name: whole lung, UV-SeV post-infection day 3, rep 1, array strip A

value: Male


title: TNC-KO ASMCs without exogenous TNC with TNF, #1

source_name: We cultured TNC-KO ASMCs in the presence or absence of exogenous TNC (10 µg/mL) and stimulated the cells with 10 ng/mL TNF-alpha for 26 h before obtaining total RNA using RNeasy.


title: Lung-d3_SeV-1a

description: Strip A from array and sample B6.3.S.3691.1 each BeadChip consists of two strips (A & B).

source_name: whole lung, SeV post-infection day 3, rep 1, array strip A


title: TNC-KO ASMCs without exogenous TNC or TNF, #3

source_name: We cultured TNC-KO ASMCs in the presence or absence of exogenous TNC (10 µg/mL) and stimulated the cells with 10 ng/mL TNF-alpha for 25 h before obtaining total RNA using RNeasy.


title: wildypte RNA 4 [Gene-leve]

city: Nice

first: Andreas

last: Schedl

address: Parc Valrose

department: iBV

country: France

institute: University of Nice

description:
ANS--04-WT1d-251109-MoEX1_0St.CEL
WT1d

hyb_protocol: Fragmented cRNA was hybridized for using the GeneChip Hybridization Oven 645 and washed/stained using  in the Affymetrix Fluidics Station 450

scan_protocol: Arrays were scanned using the AFFYMETRIX GeneChip Scanner 3000 7G.

data_processing:
Arrays have been quantile-normalize with respect to the probe GC content using the RMA algorithm. Not or low expressed transcripts have been removed by a maximum expression cutoff < 50. The data filtering resulted in 155,619 of 188,590 probe sets and 15,591 meta-probe sets defined in the core dataset and in 375483 of 780,360 probe sets and 93,629 meta-probe sets defined in the full dataset. The analysis on alternative splicing events has been performed using the two way ANOVA approach of the Partek Genomic Suite version 6.4. Resulting interaction p-values indicating the probability of splicing events. They have been multiple testing corrected using the Bejamini Hochberg procedure (Benjamini & Hochberg, 1995). Probe sets with an ANOVA FDR < 0.05 (n = 4383 in the core dataset, n = 7211 in the full dataset) have been selected as a significant differential spliced subset. Log2 splicing indexes have been calculated and used for heatmaps visualization of splice events. The splicing index was defined as the inter-condition ratio of median probe set signals which has been normalized to the meta-probe set intensity (http://www.affymetrix.com/support/ technical/whitepapers/exon_alt_transcript_analysis_whitepaper.pdf).
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps/MoEx-1_0-st-v1.r2.dt1.mm9.full.mps

source_name: E18.5 glomeruli

label_protocol: Labeling was performed using the Affymetrix labeling kit according to manufacturers instructions

growth_protocol: Mice on a mixed genetic background were housed in a conventional animal facility with free access to food and water

extract_protocol: Glomeruli were extracted using a magnetic separation after perfusion with magnetic beads

treatment_protocol: no special treatment

tag: genotype/variation

value: wildypte

tag: genetic background

value: C57Bl6x DBA2 mixed


title: TNC-KO ASMCs without exogenous TNC or TNF, #1

source_name: We cultured TNC-KO ASMCs in the presence or absence of exogenous TNC (10 µg/mL) and stimulated the cells with 10 ng/mL TNF-alpha for 23 h before obtaining total RNA using RNeasy.


title: Lung-d3_UVSeV-1b

description: Strip B from array and sample B6.3.U.3681.2 each BeadChip consists of two strips (A & B).

source_name: whole lung, UV-SeV post-infection day 3, rep 1, array strip B

value: 3 days post-infection


title: Frasier RNA 4 [Gene-leve]

description:
ANS--08-Fras6e-251109-MoEX1_0St.CEL
Frasier6e

value: wt1(+KTS) mutant


title: wildypte RNA 2 [Gene-leve]

description:
ANS--02-WT4C-251109-MoEX1_0St.CEL
WT4C


title: TNC-KO infrarenal aorta with Ca+AngII

source_name: Infrarenal aorta of TNC-KO mice with Ca+AngII treatment

value: Infrarenal aorta

value: Ca+AngII


title: TNC-KO ASMCs without exogenous TNC with TNF, #2

source_name: We cultured TNC-KO ASMCs in the presence or absence of exogenous TNC (10 µg/mL) and stimulated the cells with 10 ng/mL TNF-alpha for 27 h before obtaining total RNA using RNeasy.

value: male

value: TNC-KO


title: Frasier RNA 1 [Gene-leve]

description:
ANS--05-Fras6a-251109-MoEX1_0St.CEL
Frasier6a


title: genomic DNA from cells stimulated with 1uM OA

description: 1 uM OA

value: 1uM oleic acid (OA)


title: Frasier RNA 3 [Gene-leve]

description:
ANS--07-Fras4e-251109-MoEX1_0St.CEL
Frasier4e


title: wildypte RNA 3 [Gene-leve]

description:
ANS--03-WT5C-251109-MoEX1_0St.CEL
WT5C


title: Frasier RNA 2 [Gene-leve]

description:
ANS--06-Fras3e-251109-MoEX1_0St.CEL
Frasier3e


title: genomic DNA from cells stimulated with 1uM AA

description: 1 uM AA

value: 1uM arachidonic acid (AA)


title: TNC-KO infrarenal aorta control

source_name: Infrarenal aorta of TNC-KO mice without treatment


title: IMR32 + Terfilunomide biol repl 03

city: Essen

first: Sven

last: Lindner

address: Hufelandstraße 55

country: Germany

institute: University Hospital Essen

hyb_protocol: Hybridisation to human arrays was performed according to the manufacturers recommendations (Affymetrix)

scan_protocol: Scanning of chips was performed using a GeneArray scanner (Agilent)

data_processing: Data were summarized to gene levels and normalized using gcRMA from the Bioconductor repository of statistical tools. Only probes with the highest mean expression for each gene and with a log2 expression >5 were included in the analysis for differential expression using the Rank Product analysis package v 2.36.0 in R. Samples were clustered by applying hierarchical clustering and dissimilarity based on Manhattan distance

source_name: Human neuroblastoma cell line IMR32

label_protocol: Biotin labelling was performed according the manufacturers recommendations (Affymetrix)

growth_protocol: IMR32 cells were seeded onto 6-well plates (1 x 105 cells/well). Tweleve hours after seeding cells were treated

extract_protocol: Total RNA was extracted using the RNeasyMini kit (Qiagen, Hilden, Germany)

treatment_protocol: Cells were incubated with 118 µM Teriflunomide or DMSO 0.1% for 24h

value: Teriflunomide


title: Primary Hepatocytes_2

city: seoul

first: Jonghun

last: Kim

address: 120 neungdong-ro, Gwangjin-gu

department: school of medicine

institute: Konkuk univ.

description:
control hepatocytes, isolated from mouse liver tissue, were cultured for 6 d in hepatocyte culture medium(HCM).
Primary hepatocytes were isolated from 8 to 10 week-old male C57/B6 mice by 2-step collagenase perfusion method, and then cultured for 6 d in hepatocyte culture medium(HCM).

hyb_protocol: The fragmented cRNA was hybridized to Affymetrix GeneChip arrays for 16 h.

scan_protocol: The Chips were washed and stained using an Affymetrix Fluidics Station and fluorescence was detected using the Affymetrix Imaging Station.

data_processing: Raw data were background-corrected and subsequently normalized using Partek Express Affymetrix Edition under the Robust Microarray Analysis (RMA) algorithm.

source_name: Primary isolated hepatocytes

label_protocol: 100 ng of total RNA undergoes reverse transcription to synthesize first-strand cDNA. This cDNA is then converted into a double-stranded DNA template for transcription. In vitro transcription synthesizes aRNA and incorporates a biotin-congugated nucleotide.

growth_protocol: Primay hepatocytes and all iHeps were cultured in hepatocyte culture medium(HCM): DMEM/F-12 supplemented with 10% FBS (Biowest), 0.1 μM dexamethasone (Sigma), 10 mM nicotinamide (Sigma), 1% ITS (insulin-transferrin-selenium) premix (Gibco), 5 ml of penicillin/streptomycin/glutamine (Invitrogen), 10 ng/ml fibroblast growth factor 4 (Peprotech), and both hepatocyte growth factor (Peprotech) and epidermal growth factor (Peprotech) at a final concentration of 10 ng/ml on Type I collagen-coated dish (Sigma)

extract_protocol: Total RNA was prepared from MEFs, iHeps and primary hepatocytes using the RNeasy Mini Kit (Qiagen)

treatment_protocol: Fibroblasts were transfected with episomal vectoers encoding transcription factors(Gata4, Hnf1a, Foxa3). After 48 h, the transfected fibroblasts were cultured in hepatocyte culture medium(HCM).

value: hepatocyte


title: Primary Hepatocytes_1


title: wildypte RNA 1 [Gene-leve]

description:
ANS--01-WT3C-251109-MoEX1_0St.CEL
WT3C


title: Primary Hepatocytes


title: genomic DNA from unstimulated cells

description: unstimulated control

value: monocytes

value: none (unstimulated control)


title: WT infrarenal aorta control

source_name: Infrarenal aorta of WT mice without treatment

value: WT


title: PEO1 siSIX4 2

description: Replicate 2


title: iHeps_G4H1F3 transduced (viral vector, pMXs)_2

description:
induced hepatocyte-like cells, directly converted from MEFs by viral vectors(pMXs) encoding transcription factors; Gata4, Hnf1a, Foxa3
Epithelial-like colonies appeared on 15 days post-transduction(pMXs). They were picked up and established as expandable iHep lines with several passaging.

source_name: iHeps, G4H1F3-tranduced (viral vectors, pMXs)

value: iHep

value: converted from MEFs by viral vectors


title: WT infrarenal aorta with Ca+AngII

source_name: Infrarenal aorta of WT mice with Ca+AngII treatment


title: IMR32 + Terfilunomide biol repl 02


title: IMR32 + Terfilunomide biol repl 01


title: IMR32 + DMSO biol repl 02

value: DMSO


title: TNC-KO suprarenal aorta control

source_name: Suprarnal aorta of TNC-KO mice without treatment

value: Suprarenal aorta


title: IMR32 + DMSO biol repl 03


title: iHeps_G4H1F3 transfected (Episomal vectors)_2

description:
induced hepatocyte-like cells, directly converted from MEFs by episomal vectors encoding transcription factors; Gata4, Hnf1a, Foxa3
Epithelial-like colonies appeared on 15 days post-transfection(Episomal). They were picked up and established as expandable iHep lines with several passaging.

source_name: iHeps, G4H1F3-transfected (Episomal vectors)

value: converted from MEFs by episomal vectors


title: TNC-KO suprarenal aorta with Ca+AngII

source_name: Suprarnal aorta of TNC-KO mice with Ca+AngII treatment


title: iHeps_G4H1F3 transduced (viral vector, pMXs)_1


title: MEFs

description:
C57/B6 mouse strain embryos at embryonic day (E)13.5 after removing the head and all internal organs including the liver
MEFs are mesenchymal cells

source_name: Primary isolated mouse embryonic fibroblasts

value: MEF


title: WT suprarenal aorta with Ca+AngII

source_name: Suprarnal aorta of WT mice with Ca+AngII treatment


title: IMR32 + DMSO biol repl 01


title: iHeps_G4H1F3 transfected (Episomal vectors)_1


title: WT suprarenal aorta control

source_name: Suprarnal aorta of WT mice without treatment


title: iNSC-Episomal(20), biological rep2

first: sung min

last: kim

address: neudong ro 120

institute: Konkuk university

description: Gene expression data from e-iNSCs at late passage

source_name: iNSCs-episomal vectors

growth_protocol: The MEFs were maintained in DMEM (Biowest) containing 10% FBS (Biowest), 5 ml of penicillin/streptomycin/glutamine (Invitrogen) and 5 ml of MEM NEAA solution (Invitrogen) in 500 ml of MEF medium. The control NSCs and established iNSCs were maintained in NSC culture medium: DMEM/F-12 supplemented with 10 ml of B27 supplements (Gibco), 10 ng/ml EGF (Peprotech), 10 ng/ml bFGF (Peprotech) and 5 ml of penicillin/streptomycin/glutamine (Invitrogen) in 500 ml of NSC medium.

treatment_protocol: MEFs were transduced with either episomal vectors or pMX retroviral vectors encoding Brn4, Sox2, Klf4 and c-Myc cultured in standard NSC medium.

value: induced neural stem cells, directly converted from MEFs by the episomal vectors encoding Brn4, Sox2, Klf4 and c-Myc


title: iNSC-pMX (P10), biological rep1

description: Gene expression data from r-iNSCs at P10

source_name: iNSCs-pMX vectors

value: induced neural stem cells, directly converted from MEFs by the pMX vectors encoding Brn4, Sox2, Klf4 and c-Myc


title: iNSC-Episomal(P5), biological rep2

description: Gene expression data from e-iNSCs at early passage


title: iNSC-Episomal(P5), biological rep1


title: iNSC-Episomal(20), biological rep1


title: iNSC-pMX (P10), biological rep2

description: Gene expression data from r-iNSCs at P11


title: Frasier RNA 4 [Exon-level]

source_name: E18.5 glomeruli

value: wt1(+KTS) mutant

value: C57Bl6x DBA2 mixed


title: MEF

description: Gene expression data from MEFs

value: C3H mouse strain embryos at embryonic day (E)13.5 after removing the head and all internal organs


title: Frasier RNA 3 [Exon-level]


title: Control NSC

description: Gene expression data from brain-derived NSCs

source_name: Primarily isolated neural stem cells

value: control neural stem cells, isolated from mouse brain, were cultured in NSC medium.


title: Gonad of individual 3, triploid beta, stage 3, male

status: Public on Mar 26 2015

city: Caen

first: Nolwenn

middle: Marie

last: Dheilly

address: Esplanade de la Paix

department: Biological sciences

institute: Universite de caen

hyb_protocol: Hybridization was performed using the Agilent’s Gene expression hybridization kit as described by the purchaser with 1.65μg of aRNA samples labeled with Cy3. Subsequently, slides were washed with Gene expression wash buffer kit (Agilent Technologies), dried and stablilized in Stabilization and Drying solution (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565AA) using one color scan setting for 4x44k array slides (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 6.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. A matrix of gene expression levels was generated, where each row corresponds to a different gene and each column to one sample. The expression level of each gene was then logarithmically transformed, centered, and reduced, so that relative variations rather than absolute values were used for interpretation.

organism: Magallana gigas

label_protocol: 200 ng of total RNA was indirectly labeled with Cy3 using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions. Qiagen's RNeasy mini spin columns were used for purifying amplified RNA (aRNA) samples. After purification, aRNA amplification and dye incorporation rates were controlled using a ND-1000 spectrophotometer (Nanodrop Technologies) and were comprised respectively between 200 and 500 ng/μL (concentration) and between 20 and 50 pmol/μg aRNA (dye incorporation).

extract_protocol: Total RNA was extracted from the tissues with Tri-Reagent kit (Sigma) and subsequently cleaned with nucleospin RNA Clean-up (Macherev Nagel) isolation columns. After homogenisation of the N2 grinding powder in Tri-reagent and the first centrifugation, the aqueous phase was extracted to directly isolate the tota RNA on the column as described by the provide. RNA concentrations were measured using an ND-1000 spectrophotometer (Nanodrop Technologies) and RNA integrity was controlled on the Agilent bioanalyser using RNA 6000 nano kit (Agilent Technologies)

treatment_protocol: Oysters were sampled in the field and tissues were immediately dissected, snap-frozen in liquid nitrogen, and stored at -80 degrees celcius for total RNA extraction

tag: group

value: 3n beta Stage 3

value: M

tag: array


title: Frasier RNA 2 [Exon-level]


title: wildypte RNA 4 [Exon-level]

description:
ANS--04-WT1d-251109-MoEX1_0St.CEL
WT1d

value: wildypte


title: Gonad of individual 2, triploid beta, stage 3, male


title: wildypte RNA 2 [Exon-level]

description:
ANS--02-WT4C-251109-MoEX1_0St.CEL
WT4C


title: Frasier RNA 1 [Exon-level]


title: wildypte RNA 3 [Exon-level]

description:
ANS--03-WT5C-251109-MoEX1_0St.CEL
WT5C


title: MHCC97HshGP73

city: Beijing

first: Xinxin

last: chen

address: 5 Dong Dan San Tiao

department: Institute of Basic Medical Sciences and School of Basic Medicine

country: China

institute: Peking Union Medical College and Chinese Academy of Medical Sciences

description: GP73 knocked down liver cancer cell

hyb_protocol: Following fragmentation,5.5 ug  of  ss-ccDNA were hybridized for 16hr at 45C on GeneChip Human Transcriptome Array 2.0 .GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the  GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Affymetrix Expression Console Software using Affymetrix default analysis settings and global scaling as normalization method.

source_name: GP73 knock down MHCC97H cell

label_protocol: Biotinglated  ss-ccDNA were prepared according to the standard Affymetrix protocal form 100ng total RNA (Genechip WT PLUS reagent manual 2013)

growth_protocol: Cells were cultured in DMEM, supplemented with 10% FBS and 1% antibiotics in 5% CO2 at 37 °C

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

treatment_protocol: no

tag: cell line

value: liver cancer cell line MHCC97H

value: GP73 knockdown


title: Gonad of individual 1, triploid beta, stage 3, male


title: wildypte RNA 1 [Exon-level]

description:
ANS--01-WT3C-251109-MoEX1_0St.CEL
WT3C


title: MHCC97Hshv

description: the control cell expressed high GP73

source_name: MHCC97H control cell

value: control


title: Gonad of individual R7, triploid beta, stage 1, sex undetermined

value: 3n beta Stage 1

value: NI


title: Gonad of individual 2, triploid beta, stage 3, female

value: F


title: Gonad of individual 15, triploid beta, stage 1, sex undetermined


title: Gonad of individual R21, triploid beta, stage 1, sex undetermined


title: Gonad of individual 8, triploid beta, stage 1, sex undetermined


title: Gonad of individual R22, triploid beta, stage 1, sex undetermined


title: Gonad of individual R6, triploid beta, stage 1, sex undetermined


title: Gonad of individual 3, triploid beta, stage 3, female


title: Gonad of individual 7, triploid beta, stage 1, sex undetermined


title: Gonad of individual 1, triploid alpha, stage 3, male

value: 3n alpha Stage 3


title: Gonad of individual 1, triploid beta, stage 3, female


title: Gonad of individual 4, triploid beta, stage 3, female


title: Gonad of individual 6, triploid beta, stage 1, sex undetermined


title: Gonad of individual 2, triploid alpha, stage 3, female


title: Gonad of individual 2, triploid alpha, stage 3, male


title: Gonad of individual 4, triploid alpha, stage 3, male


title: Gonad of individual 6, triploid alpha, stage 3, female

source_name: Gonad of individual 2, triploid alpha, stage 3, female


title: Gonad of individual 1, triploid alpha, stage 3, female


title: Gonad of individual 3, triploid alpha, stage 3, male


title: Gonad of individual R8, triploid alpha, stage 1, sex undetermined

value: 3n alpha Stage 1


title: Gonad of individual R28, triploid alpha, stage 1, sex undetermined


title: Gonad of individual R9, triploid alpha, stage 1, sex undetermined


title: Gonad of individual 1, triploid alpha, stage 1, sex undetermined


title: Gonad of individual 14, triploid alpha, stage 1, sex undetermined


title: Gonad of individual R18, triploid alpha, stage 1, sex undetermined


title: Gonad of individual 2, triploid, stage 0, sex undetermined

value: 3n stage 0


title: Gonad of individual 1, triploid, stage 0, sex undetermined


title: Gonad of individual 3, triploid, stage 0, sex undetermined


title: Gonad of individual 4, triploid, stage 0, sex undetermined


title: Gonad of individual 12, triploid alpha, stage 1, sex undetermined


title: Gonad of individual 2, triploid alpha, stage 1, sex undetermined


title: IFNb rep1

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Estimated background was subtracted from the foreground for each bead. For replicate beads, outliers greater than 3 median absolute deviations from the median were removed and the average signal was calculated for the remaining intensities. For each probe a detection score was calculated by comparing its average signal with the summarized values for the negative control probes. Non-expressed probes were removed yielding 15978 expressed probes (detection p < 0.05). Expressed probe data were neqc normalized.

label_protocol: standard biotin Ambion labeling - Illumina

growth_protocol: Specific pathogen-free C57Bl/6 mice were purchased from Harlan Sprague-Dawley (Horst, the Netherlands) and housed in a controlled environemt on 12h/12h light/dark cycles.

extract_protocol: Rneasy kit procedures including DNAse digestion.

treatment_protocol: BMDMs were stimulated with 10ng/ul ultrapure Ecoli lipopolysaccharide (LPS).

tag: strain

value: Specific pathogen-free C57Bl/6

value: bone marrow-derived macrophage (BMDM)

tag: stimulated

value: IFNb for 18hrs


title: ML differential expression at HH35

city: Worcester

first: Shweta

last: Kukreja

state: MA

address: Aaron Lazare Medical Research Building (LRB) 364 Plantation Street, LRB 9th Floor

department: Biochemistry and Molecular Pharmacology

institute: University of Massachusetts Medical School

description:
Sample name: 9M vs 9L
one sample from medial and lateral tectum each hybridized in separate channel and compared

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent scanner.

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

organism: Gallus gallus

source_name: brain

label_protocol: Sample labeling, hybridization, scanning and data processing was done by personelle at Agilent microarray facility, Genome technology Acess Centre, Washington University at St. Louis.

growth_protocol: Gallus gallus embryos were incubated at 37 degrees in a humidifies chamber till the mentioned developmental stage, then sacrificed and optic tecta were harvested

extract_protocol: Total RNA was extracted using Trizol according to manufacturers instructions

treatment_protocol: Optic tecta were harvested at desired developmental stage and bisected along the AP or MV axis as mentioned on the sample. Sixty tectal halves were  pooled to get one sample. Tissues were stored in Trizol frozen till all samples were collected

tag: tissue

value: medial tectum

value: lateral tectum


title: IFNb rep2


title: ML differential expression at HH30

description:
Sample name: 7M vs 7L
one sample from medial and lateral tectum each hybridized in separate channel and compared


title: AP differential expression at HH37

description:
Sample name: 11A vs 11P
one sample from anterior and posterior tectum each hybridized in separate channel and compared

value: posterior tectum

value: anterior tectum


title: AP differential expression at HH35

description:
Sample name: 9A vs 9P
one sample from anterior and posterior tectum each hybridized in separate channel and compared


title: IFNg rep3

value: IFNγ for 18hrs


title: Gonad of individual 5, triploid alpha, stage 3, female

tag: gender


title: IFNg rep2


title: IFNg rep1


title: Ctrl rep3

value: none (control)


title: NL55

city: Fuzhou

first: Xiaolong

last: Liu

state: Fujian

address: 312，Xihong Road

department: Mengchao Hepatobiliary Hospital

institute: Fujian Medical University

description:
Invasion and metastasis related long non-coding RNA expression profiles in HCC
molecule: LncRNA

hyb_protocol: Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm and a temperature of 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: the data were scaned using Angilent Scanter G2565CA

data_processing: The lncRNA+mRNA array data were analyzed for data summarization, normalization and quality control by using the GeneSpring software V12.0 (Agilent).

source_name: normal liver tissue

label_protocol: cDNA labeled with a fluorescent dye  Cy3-dCTP was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, 2 and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA

extract_protocol: Trizol reagent (Invitrogen, Carlsbad, CA, USA) was used to extract the total RNAs from tissues

treatment_protocol: Fresh-frozen HCC tissues and normal liver tissue samples were collected during the surgical resection at Mengchao Hepatobiliary Hospital of Fujian Medical University, and stored in the tissue bank for further usage.

value: liver

tag: tumor stage

value: normal control


title: NL43


title: NL802


title: Xenograft_5

city: vancouver

first: Mohammed

last: Alshalalfa

state: bc

address: water st

institute: GenomeDx

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using SCAN software package (Bioconductor)
HuEx-1_0-st-v1.r2.pgf

source_name: Xenograft tumor

label_protocol: RNA was amplified, fragmented and biotinylated using the Ovation FFPE system v 3.0 (NuGEN)

extract_protocol: RNA was extracted using the High Pure RNA Paraffin Kit from Roche (Indianapolis, IN).

tag: pathological stage

value: Xenograf


title: NL44


title: NL45


title: With DETA NONOate treatment

city: Ikoma

first: Daisuke

last: Watanabe

state: Nara

address: 8916-5 Takayamacho

institute: Nara Institute of Science and Technology

description: Gene expression data from cells with 0.5 mM DETA NONOate treatment for 2 h.

hyb_protocol: 4 ug of cRNA were hybridized  for 16 hr at 45C on Affymetrix Yeast Genome 2.0 Array. GeneChips were washed and stained according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

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

organism: Schizosaccharomyces pombe

source_name: Schizosaccharomyces pombe cells with 0.5 mM DETA NONOate treatment for 2 h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

growth_protocol: Cells were grown to mid-log phase in YES medium at 30C.

extract_protocol: Total RNA was isolated by using RNeasy Mini Kit (Qiagen).

treatment_protocol: Cells were treated with 0.5 mM DETA NONOate (Cayman Chemical) for 2 h

value: 0.5 mM DETA NONOate


title: Xenograft_2


title: Xenograft_1


title: Bladder cancer_primary 4

source_name: Bladder tumor

value: Bladder cancer primary


title: Xenograft_4


title: Bladder cancer_primary 3


title: Bladder cancer_primary 5


title: C2-414

source_name: non-invasion and metastasis HCC tissue

value: liver HCC

value: non-invasion and metastasis


title: IFNb_LPS rep1

value: IFNb for 18hrs and LPS for 6hrs


title: C2-426


title: Bladder cancer_primary 1


title: C2-646


title: C1-425

source_name: invasion and metastasis HCC tissue

value: invasion and metastasis


title: Xenograft_3


title: IFNg_LPS rep1

value: Specific pathogen-free C57Bl/6

value: bone marrow-derived macrophage (BMDM)

value: IFNγ for 18hrs and LPS for 6hrs


title: C1-433


title: Mouse_Sca+cell_Cyclin T1_BR1

city: Greifswald

first: Sabine

last: Ameling

address: Felix-Hausdorff.Str 8

department: Interfakultäres Institut für Genetik und Funktionelle Genomforschung

institute: Universitätsmedizin Greifswald

hyb_protocol: Biotin-labeled amplified RNA was hybridized to Affymetrix Mouse430_2 arrays, and the arrays were washed.

scan_protocol: Arrays were scanned using a GeneChip System Confocal Scanner 3000 (Affymetrix). Image processing was done in GCOS (Affymetrix).

data_processing:
Raw data files (CEL) were exported to Rosetta Resolver 7.2 (Ceiba Solutions, Seattle, U.S.A.) for probe set extraction and normalization.
First, the pipeline calculates expression summaries from scans using both the perfect-match (PM) and mis-match (MM) probes. It returns both reporter and sequence-level results. The resulting P-values may be used as a guideline to decide expression presence or absence if negative controls are available and correctly identified.
In a second step, the pipeline combines the expression values for individual profiles using an error-weighted average in a transformed space and calculates the error of the result. Reporter-level data are used to impute missing reporters, if any, and to increase robustness by calculating the averages in a transformed space at the more granular reporter-level. All profiles in the experiment definition are normalized together.

source_name: Sca+ cells, Cyclin T1/Gq overexpressing transgenic

label_protocol: Linear amplification of total RNA (250ng) was performed using T7-RNA Polymerase following the GeneChip 3'IVT Express Kit protocol (Affymetrix, Santa Clara, CA, USA). Size distribution and concentration of biotin-labeled amplified RNA was analyzed using Nanodrop ND-1000.

growth_protocol: Freshly isolated undifferentiated Sca-1 progenitor cells derived either from heart failure transgenic αMHC-CyclinT1/Gαq overexpressing mice or wildtype littermates.

extract_protocol: Total RNA was extracted from freshly isolated Cyc and Wt cells of two independent experiments using Trizol reagent. Concentration and quality were assessed using a Nanodrop ND-1000 (NanoDrop Technologies, Inc. Wilmington, USA) and a RNA 6000 Pico LabChip® on a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA).

treatment_protocol: Adult Sca-1 positive progenitor cells (Sca-1 cells) were isolated from age-matched wildtype (Wt cells) and double-transgenic mice (Cyc cells) as described previously. Freshly isolated cells or minimally cultured for up to 4-5 days to attain cell adhesion were used to represent the undifferentiated state and to avoid cell culture-triggered alterations.

tag: strain/background

value: FVB

tag: age

value: 6 weeks

value: undifferentiated Sca-1 progenitor cells

tag: disease state

value: heart failure


title: Ctrl_LPS rep1

tag: cell type

value: LPS for 6hrs


title: KO2-NC

city: Boston

first: Kun Ping

last: Lu

address: 330 Brookline Ave

institute: Beth Israel Deaconess Medical Center

description: From Pin1 KO mouse

hyb_protocol: Hybridazations were performed according to the standard Affymetrix protocol

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

data_processing: Raw expression data were normalized and summarized using the Robust Multichip Analysis (RMA) method along with log2 transformation using the BRB-Array Tools.

source_name: NC

label_protocol: cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Cells were isolated from mouse tissues without culturing

extract_protocol: Total RNA was isolated using Agilent Total RNA Isolation Kit

value: brain

value: Pin1 KO


title: WT2-NC

description: From Pin1 WT mouse

value: Pin1 WT


title: Bladder cancer_primary 2


title: C1-421


title: C2-368


title: Beko_Notch1ER_OHT

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

institute: Philipps University of Marburg

hyb_protocol: Standard Affymetrix hybridization protocol onto GeneChip® Mouse Gene 1.0 ST Arrays (1,102,500 probes; Affymetrix) for 16 hours at 45°C. Staining and washing using the Fludics Station 450 instrument (Affymetrix)

scan_protocol: Standard Affymetrix scanning protocol with GeneChip(R) 3000 laser confocal slide scanner.

data_processing: Data were RMA normalized via Bioconductor.using the CDF package mogene10stmmensgcdf_18.0.0.zip

label_protocol: Biotin is added with an Affymetrix Labeling Reagent

growth_protocol: Beko cells were grown in IMDM, 2% FCS, 1 x MEM nonessential amino acids, 3 mg/L Primtone, 5 mg/L Insuline

extract_protocol: Cells were collected after 24 or 48h treatment and total RNA was isolated by RNAeasy column.

treatment_protocol: Cell were treated with 10 μM DAPT, or 0.75 μg/mL 5-OHT (for DNMAML-ER and NOTCH1-ER)

value: Beko


title: Ctrl rep1

value: none (control)


title: Beko_Notch1ER_Eth


title: WT1-NC

description: From Pin1 WT mouse


title: C1-298

value: liver HCC


title: WT2-MEC

description: From Pin1 WT mouse

source_name: MEC

value: mammary gland


title: KO1-NC

description: From Pin1 KO mouse


title: C1-415


title: Mouse_Sca+cell_Cyclin T1_BR2


title: Beko_DNMAML_Eth


title: KO2-MEC

description: From Pin1 KO mouse


title: Beko_DAPT


title: 2103AN 3

status: Public on Mar 25 2015

city: Monterrey

first: Roberto

last: Portillo Lara

state: Nuevo León

address: Ave. Eugenio Garza Sada 2501 Sur Col. Tecnológico

department: División de Biotecnología y Alimentos

institute: Tecnológico de monterrey

description: Total RNA was isolated from cell samples and hybridized at 60 degrees celcius for 16 hours. Two sets of probes (CodeSets) were used in this study: the GX Cancer Reference Kit and the custom made ITESM CodeSet containing 14 genes associated with prostate cancer. After hybridization to the cartridge, data resolution was set at high on the Digital Analyzer. This corresponds to 600 fields of view (FOV).

hyb_protocol: Hybridization to the NanoString cartridge is performed at the automated PrepStation without manipulation from the user.

scan_protocol: Microscopic imaging of the NanoString cartridge is performed at the automated Digital Analyzer without manipulation from the user. Data resolution was set at high (600 FOV)

data_processing: Raw counts were normalized using the geometric mean of six internal positive controls. Background noise was removed using the average of eight negative controls. Data normalization was carried out using the nSolver Analysis Software from NanoString Technologies.

label: EPI_N REP2

molecule: polyA RNA

source_name: Prostate carcinoma

label_protocol: Purified RNA was hybridized for 16 hours in a Axygen thermal cycler at 60 degrees celcius using one of two sets of probes: GX Cancer Reference Kit or ITESM

growth_protocol: PC3 cells were grown in T25 tissue culture treated flasks with DMEM-FBS: monolayer cultures in DMEM-F12 (Gibco) supplemented with 5% fetal bovine serum (FBS, Invitrogen) and 100 U/100 μg/ml penicillin-streptomycin (Gibco)

extract_protocol: Total RNA was extracted using the Rneasy mini or micro kits (depending on the amount of starting material), according to instructions from the manufacturer.

treatment_protocol: PC3 cells were grown in 6-well ultra-low attachment culture plates with EpiGRO human Prostate Complete Media Kit (hPCM, Millipore) for 12 days

tag: experimental condition

value: Magnetically sorted CD133-negative prostasphere cells

value: PC3 Prostate cancer cell line


title: 2103AN 2

label: EPI_N REP1


title: 2103AP 1

label: EPI_P REP1

value: Magnetically sorted CD133-possitive prostasphere cells


title: 2103A 3

label: EPI_4 REP3

value: Day 12 prostaspheres


title: IFNb_LPS rep2

value: Specific pathogen-free C57Bl/6

value: bone marrow-derived macrophage (BMDM)

value: IFNb for 18hrs and LPS for 6hrs


title: Beko_DNMAML_OHT


title: Beko_DMSO


title: KO1-MEC

description: From Pin1 KO mouse


title: WT1-MEC

description: From Pin1 WT mouse


title: Adult testis gene expression

city: Madrid

first: Jesus

last: Garcia Lopez

address: C/Ramiro de Maeztu 9

department: Cellular and Molecular Biology

country: Spain

institute: Cib (CSIC)

description:
Analysis using gonad-less embryos at 13.5 dpc  as control sample for comparison to the PGCs, SPG and adult testis samples.
Series README.txt file includes description of contents of GPR files

hyb_protocol: Labeled targets were resuspended in hybridization buffer and applied to glass microarrays. Hybridizations were performed overnight at 42°C. Washed and dried slides were imaged in an Axon GenePix 4000A scanner.

scan_protocol: Arrays scanned using an GenePix 4000B scanner.

data_processing: Raw data were normalized using limma package and R Bioconductor open software. The background was subtracted from each individual hybridization and they were Lowess normalized. For each condition, a technical replicate was performed by dye-swapping (two hybridizations) in order to minimize a possible bias in the labeling process. Gene expression values are showed as log2FC (fold change). Clustering analysis was performed using to define the expression profiles of genes involved in germ cell differentiation; we applied the intensity, fold change, and pair-wise P values as additional filters.

source_name: Adult testis

label_protocol: For each sample, 2.5 μg of aRNA was labeled with Cy3 or Cy5 and it was purified with the Amino Allyl MessageAmp aRNA kit® (Ambion) as manufacturers instructions. Samples purified using QIAGEN PCR purification kit before hybridization.

extract_protocol: Total RNA from adult testis, gonad-less embryos, Spermatogonia and Primordial Germ Cells (PGCs) was isolated using TRIzol® Reagent (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: To purify fetal PGCs and postnatal SPGs, a cell suspension was prepared from 13.5 dpc male gonads and 8.5 dpn testes, respectively. The PGCs were purified from the cell suspension by immunopurification using anti-CD15 (anti-SSEA-1 in mouse) magnetic beads and the purity of the cells was validated by alkaline phosphatase staining. The SPGs were purified from the cell suspension by performing a short cell culture discrimination procedure (3-4 hours) that promotes the sedimentation and adhesion of somatic cells. Accordingly, the SPGs suspended in the supernatant can be readily recovered. The purity of the SPGs was validated by the presence of Stra8 (germline-specific gene) and the absence of Fn1 (soma-specific gene). For comparative purposes, total RNA from both: whole adult testis, as source of tissue expressing all male germ cells, and 13.5 dpc embryos, that were depleted of their gonads before to RNA isolation (“gonad-less” embryos)

value: Adult testis

value: gonad-less 13.5 dpc embryos


title: Spermatogonia cells gene expression

source_name: Spermatogonia cells (SPG) 8.5 dpn (days postnatal)

growth_protocol: The SPGs were purified from the cell suspension by performing a short cell culture discrimination procedure (3-4 hours) that promotes the sedimentation and adhesion of somatic cells. Accordingly, the SPGs suspended in the supernatant can be readily recovered.

value: Spermatogonia cells 8.5 dpn

source_name: 13.5 dpc embryos, that were depleted of their gonads before to RNA isolation


title: PGCs gene expression

source_name: Primordial Germ Cells (PGCs) 13.5 dpc (days poscoitum)

value: Primordial Germ Cells 13.5 dpc


title: 2103A 1

label: EPI_4 REP1


title: 2103A 2

label: EPI_4 REP2


title: 1703 3

label: EPI_3 REP3

value: Day 8 prostaspheres


title: 1403 3

label: EPI_2 REP3

value: Day 4 prostaspheres


title: 1703 2

label: EPI_3 REP2


title: 1703 1

label: EPI_3 REP1


title: 1403 2

label: EPI_2 REP2


title: IFNg_LPS rep3

value: IFNγ for 18hrs and LPS for 6hrs


title: 1403 1

label: EPI_2 REP1


title: 503 3

label: EPI_1 REP3

value: Day 0 parental monolayers


title: 503 2

label: EPI_1 REP2


title: Cb_OD 5.0_FA, rep2

city: Ulsan

first: Siseon

last: Lee

address: UNIST-gil 50

institute: Ulsan National Institute of Science and Technology

description: CbN8052_FA 0.5_16

hyb_protocol: After quantification, 600 ng of the cRNA was used for hybridization with the Gene Expression Hybridization Kit (Agilent Technologies, USA). Hybridization was conducted at 65 °C for 17 h, followed by washing and drying of the chip using the Gene Expression Wash Buffer Kit (Agilent Technologies, USA).

scan_protocol: The microarray slides were scanned with an Agilent G2565CA Microarray Scanner System (Agilent Technologies, USA).   The features were scanned at a 5-micron pixel size.

data_processing: The features were extracted and analyzed with the Agilent Feature Extraction software v10.5. The data obtained was then normalized using the 75th percentile value of non-control signals on each array as provided by the program.

organism: Clostridium beijerinckii NCIMB 8052

source_name: Cb_OD 5.0_ferulic acid

label_protocol: All microarray experiments were performed according to the protocol provided for the Agilent One-Color Microarray-Based Exon Analysis. Fluorescent cRNA for each sample was generated using 100 ng of RNA using a Low Input Amp WT Labeling Kit, One color (Agilent Technologies, USA), and then purified using the RNeasy Mini Kit (Qiagen, USA). When the labeling reaction was prepared, the RNA Spike-In Kit, One color (Agilent Technologies, USA) was also used as an internal control.

extract_protocol: For RNA isolation, the culture was harvested by centrifugation at 4,000 rpm for 10 min at 4 °C. The cell pellet was resuspended and treated with 20 mg/mL lysozyme at 37 °C for 4 min in SET buffer (25% sucrose, 50mM EDTA pH 8.0, 50mM Tris-HCl pH 8.0) [49]. To each sample, 1 mL of Trizol (Ambion, USA) and 200 μL of chloroform-isoamylalcohol (Sigma, USA) were added and the samples were incubated at room temperature. After centrifugation at 12,000g for 15 min at 4 °C, the upper aqueous phase was transferred to new tubes containing an equal volume of 70% ethanol. To purify the RNA from the sample, this mixture was transferred to a spin column (RNeasy Mini Kit, Qiagen, USA) and further purification steps were performed according to the manufacturer’s protocol. The RNA samples were then treated with DNase I (Thermo Scientific, USA) to completely remove any genomic DNA remaining. The RNA quality was assessed using a Bioanalyzer 2100 (Agilent Technologies, USA) while the quantity and concentration of RNA was determined with a NanoDrop 2000 (Thermo Scientific, USA).

tag: sample optical density

tag: ferulic acid conc.


title: 503 1

label: EPI_1 REP1


title: Cb_OD 1.4_FA, rep1

description: CbN8052_FA 0.5_10

source_name: Cb_OD 1.4_ferulic acid


title: Cb_OD 1.4_FA, rep2

description: CbN8052_FA 0.5_11


title: Cb_OD 1.4_Ctrl, rep3

description: CbN8052_FA 0.5_09

source_name: Cb_OD 1.4_control

value: 0 g/L


title: Cb_OD 1.4_Ctrl, rep2

description: CbN8052_FA 0.5_08


title: Cb_OD 1.4_Ctrl, rep1

description: CbN8052_FA 0.5_07


title: Cb_OD 1.4_FA, rep3

description: CbN8052_FA 0.5_12


title: IFNg_LPS rep2

label: biotin


title: Cb_OD 0.3_FA, rep2

description: CbN8052_FA 0.5_05

source_name: Cb_OD 0.3_ferulic acid


title: Cb_OD 0.3_FA, rep3

description: CbN8052_FA 0.5_06


title: Cb_OD 5.0_FA, rep1

description: CbN8052_FA 0.5_15


title: Cb_OD 0.3_FA, rep1

description: CbN8052_FA 0.5_04


title: Cb_OD 0.3_Ctrl, rep3

description: CbN8052_FA 0.5_03

source_name: Cb_OD 0.3_control


title: Cb_OD 5.0_Ctrl, rep1

description: CbN8052_FA 0.5_13

source_name: Cb_OD 5.0_control


title: Cb_OD 5.0_Ctrl, rep2

description: CbN8052_FA 0.5_14


title: Cb_OD 0.3_Ctrl, rep2

description: CbN8052_FA 0.5_02


title: Ctrl_LPS rep2

value: LPS for 6hrs


title: Plasma sample from Puerto Rico, S5

city: San Francisco

first: Charles

last: Chiu

state: CA

address: 185 Berry Street, Box 0134

department: Laboratory Medicine

institute: University of California, San Francisco

description: amplified cDNA

hyb_protocol: microarrays were hybridized overnight according to the manufacturer's protocol (Agilent Technologies) using the Agilent Gene Expression Hybridization kit

scan_protocol: microarrays were scanned at 3 um resolution on an Agilent DNA Microarray Scanner

data_processing: Background normalized output intensities from Agilent's Feature Extraction from 37,432 V3 / V4 viral probes (Matrix (Raw)) were used for cluster and Z-score analysis (Eisen, et al., 1998; Chiu, et al., 2006; Chen, et al., 2011)

source_name: Plasma Sample

label_protocol: randomly amplified cDNA was labelled using a Cy3 fluorescent dye via aa-dNTP incorporation (Wang, et al, 2002; Chiu, et al, 2006; Chiu, et al, 2008)

extract_protocol: Nucleic acid extraction was performed from 400 uL of TRIzol-inactivated donor plasma using the Direct-zol RNA MiniPrep Kit (Zymo Technologies) and on-column treatment with Turbo DNase (Life Technologies).

tag: sample type

value: plasma


title: Plasma sample from Puerto Rico, S1

description: amplified cDNA


title: Plasma sample from Puerto Rico, S3

description: amplified cDNA


title: C2-452

source_name: non-invasion and metastasis HCC tissue

value: liver HCC

value: non-invasion and metastasis


title: Plasma sample from Puerto Rico, S2

description: amplified cDNA


title: Cb_OD 0.3_Ctrl, rep1

description: CbN8052_FA 0.5_01


title: Plasma sample from Puerto Rico, S4

description: amplified cDNA


title: Plasma sample from Puerto Rico, S6

description: amplified cDNA


title: dVIN_Sample9

description: amplified cDNA

data_processing: Background normalized output intensities from Agilent's Feature Extraction Software corresponding to 19,058 70-mer viral probes (Matrix) were used for cluster analysis (Eisen, et al., 1998)

source_name: FFPE Tissue

extract_protocol: total nucleic acid was extracted from FFPE 10 uM sections using EZ1 DNA tissue kit (Qiangen), prospectively collected samples were polyA purified using Oligotex kits (Qiagen)

value: differentiated vulvar intraepithelial neoplasia


title: Mouse_Sca+cell_WT_BR2

source_name: Sca+ cells, WT

value: FVB

tag: genotype/variation

value: wildtype

value: 6 weeks

value: undifferentiated Sca-1 progenitor cells

value: healthy


title: dVIN_Sample2

description: amplified cDNA


title: dVIN_Sample10

description: amplified cDNA


title: Normal_Vulvar_Skin_Biopsy

description: amplified cDNA

value: normal vulvar skin biopsy


title: Mouse_Sca+cell_WT_BR1


title: dVIN_Sample4

description: amplified cDNA


title: HPV_Positive_Control

description: amplified cDNA

value: HPV-positive metastatic cervical cancer tissue


title: dVIN_Sample3

description: amplified cDNA


title: Ctrl rep2

value: Specific pathogen-free C57Bl/6

value: bone marrow-derived macrophage (BMDM)

value: none (control)


title: dVIN_Sample7

description: amplified cDNA


title: dVIN_Sample5

description: amplified cDNA


title: dVIN_Sample8

description: amplified cDNA


title: dVIN_Sample6

description: amplified cDNA


title: leaf-Cd-3

city: Tianjin

first: Guo

last: Jun kang

address: Fu kang Road No.31

institute: Agro-Environmental Protection Institute, Ministry of Agriculture

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and RMA as normalization method.

organism: Solanum lycopersicum

source_name: tomato leaf without Cd treated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

extract_protocol: Total RNA of tomato root and leaves were extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction.

value: leaf


title: leaf-Cd-2


title: leaf-ck-1


title: leaf-ck-2


title: leaf-ck-3


title: leaf-Cd-1


title: Without DETA NONOate treatment

description: Gene expression data from cells without DETA NONOate treatment

source_name: Schizosaccharomyces pombe cells without DETA NONOate treatment

tag: treatment


title: dVIN_Sample1

description: amplified cDNA


title: TU_BREAST11_FFPEr_REP1

city: maastricht

first: Tim

middle: C.

last: de Ruijter

address: universiteitssingel 40

department: Medical Oncololgy

country: Netherlands

institute: Maastricht University

hyb_protocol: Illumina protocol

scan_protocol: Chips were scanned using the iScan system (Illumina). iScan data was extracted to GenomeStudio software v2011.1 using default analysis settings. No normalisation was performed on sample data.

data_processing: A detection p-value based on the fluorescence intensity was calculated for all probes. Probes that did not yield a significant intensity over background (p-value ≥0.01) were excluded from the analysis.

label: Cy5 and Cy3

source_name: Breast Tumour, FFPEr

label_protocol: Illumina protocol

extract_protocol: FFPE DNA was extracted using the Maxwell FFPE CSC automated DNA extraction kit (Promega Corporation, Madison, USA) according to the manufacturer’s instructions. FF DNA was extracted using using the Nucleospin Tissue kit (Macherey-Nagel, Düren, Germany) according to the manufacturer’s instructions.

tag: sample age (years)

value: Breast

value: Tumour

tag: fixation

value: FFPEr


title: TU_BREAST10_FFPEr_REP1


title: root-Cd-2

source_name: tomato root with Cd treated

value: root


title: TU_BREAST8_FFPEr_REP2


title: TU_BREAST5_FFPEr_REP2


title: TU_BREAST11_FFPEr_REP2


title: 393P Zeb1 vector rep3

city: Houston

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: 393P cells with Zeb1 induction, sample 3

hyb_protocol: Following fragmentation, cRNA was hybridized on Mouse430 2.0 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-WS2v5 (for FS400) or FS450_0001 (for FS450).

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner (Agilent).

data_processing: The image signal quantification data were generated by Affymetrix software utilizing Affymetrix’ Statistical Algorithm (MAS 5).

source_name: 393P lung cancer cell line

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

growth_protocol: All cell lines were maintained in RPMI supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was isolated by the Ambion kit. RNA quality and quantity were evaluated on a NanoDrop spectrophotometer and the Agilent 2100 Bioanalyzer.

treatment_protocol: Lung cancer cells were made to have stable constitutive expression of either pCDNA vector or Zeb1. DNA transfections were performed with Lipofectamine-2000 or Lipofectamine-LTX reagents (Life technologies, Grand Island, NY) as per manufacturer’s protocol.

tag: cell line

value: Zeb1 vector


title: root-Cd-1

tag: tissue


title: root-Cd-3


title: TU_BREAST6_FFPEr_REP1


title: SeV1.5 24h rep4

city: Bethesda

first: Luna

middle: A

last: Zaritsky

state: MD

address: 50 South Drive

institute: NIH

description:
rep 4
_9967453010_J

hyb_protocol: Standard Illumina hybridization protocol

data_processing: Data extraction was performed using Illumina Genome Studio software without background subtraction or normalization.  Signal levels for each array were normalized using quantile normalization after transforming to log base 2 (JMP/Genomics v7.0). Please note that the probe sets with no detectable signal  were exclued from the data analysis, resulting a reduced data set of 28372 rows.

label_protocol: Biotinylated aRNA was hybridized to the Illumina HumanHT-12 Expression BeadChip

growth_protocol: Cells were grown in RPMI 1640 media + 10% FBS at a concentration of 5 x 10^5 cells/mL

extract_protocol: RNA was isolated using the Rneasy minikit (Qiagen)  according to the manufacturer's instructions with a DNAse cleanup step

treatment_protocol: Cells were left uninfected or infected with either 1.5 or 150 HA u/mL of SeV for 24 h

value: monocytoid

tag: infected with

value: 1.5 HA u/mL of SeV


title: root-ck-3

source_name: tomato root without Cd treated


title: SeV150 24h rep4

description:
rep 4
_9967453010_K

scan_protocol: Standard Illumina hybridization protocol

value: 150 HA u/mL of SeV


title: TU_BREAST9_FFPEr_REP2


title: TU_BREAST10_FFPEr_REP2


title: UI 24h rep4

description:
rep 4
_9967453010_L

value: none (uninfected control)


title: TU_BREAST3_FFPEr_REP2


title: TU_BREAST6_FFPEr_REP2


title: TU_BREAST7_FFPEr_REP2


title: Paf1mut8_spb2013_2

city: Basel

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

hyb_protocol: hybridization was performed for 16h at 45°C and 60rpm in an Affymetrix hybridization oven; washing steps were done in an Affymetrix Fluidics station with the Affymetrix protocol FS450_0002

scan_protocol: GeneChips were scanned with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip® Scanner 3000 with autoloader.

data_processing:
oligo-level data was rma background corrected, quantile normalized and log2 transformed using Bioconductor packages tilingArray and preprocessCore on R and the probe annotation in the file Sp20b_M_v04_probes_to_sPombe.tab
RMA normalized log2 expression values are available in the file Normalized_data.txt on the series level.

label_protocol: 200ng total RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix (GeneChip Whole Transcription Sense Target Labeling technical manual, Rev. 2).

growth_protocol: Strains grown at 30 degress in YES medium to OD600=0.5

extract_protocol: Total RNA was isolated using the hot phenol method

tag: strain

value: Paf-1Q264Stop, ade6-hp+


title: TU_BREAST5_FFPEr_REP1


title: UI 24h rep3

description:
rep 3
_9967453010_I


title: TU_BREAST9_FFPEr_REP1


title: TU_BREAST2_FFPEr_REP2


title: TU_BREAST4_FFPEr_REP2


title: TU_BREAST1_FFPEr_REP2


title: root-ck-2


title: TU_BREAST4_FFPEr_REP1


title: TU_BREAST3_FFPEr_REP1


title: TU_BREAST2_FFPEr_REP1


title: TU_BREAST8_FFPEr_REP1


title: Leo1mut_spb2012_2

value: Leo1-W157Stop, ade6-hp+


title: TU_BREAST7_FFPEr_REP1


title: root-ck-1


title: SeV1.5 24h rep3

description:
rep 3
_9967453010_G


title: 393P Zeb1 vector rep1

description: 393P cells with Zeb1 induction, sample 1


title: Rot1mut_spb2011_2

value: Rot1-Q472Stop, ade6-hp+


title: SeV150 24h rep3

description:
rep 3
_9967453010_H


title: TU_BREAST1_FFPEr_REP1


title: Paf1mut3_spb2009_2

value: Paf1-G104R, ade6-hp+


title: Cdc73mut_spb2010_2

value: Cdc73-G313R, ade6-hp+


title: 393P pcDNA control vector rep3

description: 393P cells with control vector, sample 3

value: control vector


title: Leo1D_spb1955_2

value: Leo1Δ, ade6-hp+


title: UI 24h rep2

description:
rep 2
_9967453010_F


title: SeV150 24h rep2

description:
rep 2
_9967453010_E


title: wt_spb464_2


title: 393P pcDNA control vector rep2

description: 393P cells with control vector, sample 2


title: SeV150 24h rep1

description:
rep 1
_9967453010_B


title: Paf1D_spb1953_2

value: Paf1Δ, ade6-hp+


title: NL_COLON9_FFPE

source_name: Normal colon Mucosa, FFPE

value: colon

value: Normal

value: FFPE


title: UI 24h rep1

description:
rep 1
_9967453010_C


title: Paf1mut8_spb2013_1


title: Sev1.5 24h rep1

description:
rep 1
_9967453010_A


title: NL_COLON9_FF

source_name: Normal colon Mucosa, FF

value: FF


title: 393P pcDNA control vector rep1

description: 393P cells with control vector, sample 1


title: Root Reduced N, biological rep2

city: Guelph

first: JOSE

last: CASARETTO

address: 50 Stone Road E

department: MCB

institute: University of Guelph

description: Gene expression data from roots from plants shifted form normal to low nitrate.

hyb_protocol: After fragmentation, cRNA were equilibrated at 45 °C for 5 min. The hybridization mix was then transferred to the rice GeneChip microarray cartridge and hybridized at 45 °C for 16 h on a rotisserie at 60 r.p.m. The hybridized arrays were then rinsed and stained in a fluidics station (Affymetrix) as described in Zhu et al, Plant Biotechnology Journal (2003), 1, 59–70.

scan_protocol: Array images were acquired with the GeneChip scanner 3000 and the hybridization signals were quantified using the GCOS software (Affymetrix, Inc.).

data_processing: Data from the CEL files generated were condensed to probe set level approximating genes and transcripts using this custom file with robust multichip analysis (RMA) using an implementation of the algorithm in the Refiner Array tool in the Expressionist software suite from Genedata (Basel, Switzerland). A threshold was applied to the normalized condensed data so that a probe set was excluded if it did not have a detectable signal in at least one experiment (3 replicates). A detectable signal was defined as 2 standard deviations above average background signal. Background signal was defined by unutilized spike in controls.

organism: Oryza sativa Japonica Group

source_name: all roots

label_protocol: Biotinylated cRNA were prepared from 5 ug total RNA that were transcribed in vitro from synthesized cDNA using T7 RNA Polymerase and ENZO BioArray High Yield RNA Transcript Labelling Kit (Enzo).

growth_protocol: Rice plants were germinated and grown in growth chambers with a 16 h light cycle, at 29°C during the day and 23°C during the night and constant relative humidity of 65%. Plants were grown in a hydroponic system for four weeks in normal (3 mM KNO3) or limiting (0.3 mM KNO3) nitrogen conditions. The nutrient solution also contained 4 mM MgSO4, 5 mM KCl, 5 mM CaCl2, 1mM KH2PO4, 0.1 mM Fe–ethylenediaminetetraacetic acid (EDTA), 0.5 mM MES (pH 6.0), 9 mM MnSO4, 0.7 mM ZnSO4, 0.3 mM CuSO4, 46 mM NaB4O7 and 0.2 mM Na2MoO4. Twenty four seedlings were planted in a 35-L container with 25 L of the nutrient solution.

extract_protocol: Total RNA from each sample were isolated using total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen, Chatsworth, CA) according to the manufacturer's instructions.

treatment_protocol: 4-week-old plants grown in low N (0.3 mM NO3) conditions were transferred to a normal (high, 3 mM NO3) N condition (induction treatment) and those grown at normal N conditions moved to a low N system (reduction). Samples (three biological replicates) of leaves and roots were taken separately at 0 h (11 am; normal and low N conditions) and 2 h after induction and reduction treatments (1 pm) and frozen immediately and stored at -80 ºC until further analysis

tag: cultivar

value: Kaybonnet

value: 4 week-old


title: BM_MSCs-RAEB-rep2

city: Daejeon

first: Seungwoo

last: Hwang

address: 52 Eoeun-dong Yuseong-gu

department: Korean Bioinformation Center

institute: Korea Research Institute of Bioscience and Biotechnology

description: Bone marrow mesenchymal stromal cells (BM MSCs) from RAEB group

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with lumi R package

source_name: Bone marrow mesenchymal stromal cells (BM MSCs), RAEB

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina RNA amplification kit

extract_protocol: Total RNA was extracted with Trizol and purified with Qiagen RNeasy columns according to the manufacturers' protocols. Quality control was performed with Agilent 2100 Bioanalyzer.

value: bone marrow mesenchymal stromal cells

tag: diagnosis

value: MDS (RAEB-1)


title: BM_MSCs-RAEB-rep3


title: Rot1mut_spb2011_1


title: Leo1mut_spb2012_1


title: Root Reduced N, biological rep3

tag: age


title: BM_MSCs-RAEB-rep4

value: MDS (RAEB-2)


title: Cdc73mut_spb2010_1


title: NL_COLON8_FFPEr

source_name: Normal colon Mucosa, FFPEr

tag: disease state

value: FFPEr


title: Leo1D_spb1955_1


title: Paf1mut3_spb2009_1


title: Root Reduced N, biological rep1


title: NL_COLON8_FF


title: NL_COLON9_FFPEr


title: BM_MSCs-RAEB-rep1

tag: cell type


title: NL_COLON7_FF


title: Root Induced N, biological rep2

description: Gene expression data from roots from plants shifted form low to normal nitrate.


title: NL_COLON7_FFPE


title: Root Normal N, biological rep3

description: Gene expression data from roots from plants grown under normal nitrate.


title: Paf1D_spb1953_1


title: NL_COLON7_FFPEr


title: Root Induced N, biological rep3


title: Root Induced N, biological rep1


title: BM_MSCs-Control-rep7

description: Bone marrow mesenchymal stromal cells (BM MSCs) from Control group

source_name: Bone marrow mesenchymal stromal cells (BM MSCs), Control

value: Lymphoma with no evidence of BM involvement


title: BM_MSCs-RCMD-rep2

description: Bone marrow mesenchymal stromal cells (BM MSCs) from RCMD group

source_name: Bone marrow mesenchymal stromal cells (BM MSCs), RCMD

value: MDS (RCMD)


title: BM_MSCs-RCMD-rep3


title: Root Normal N, biological rep2


title: BM_MSCs-Control-rep6


title: 393P Zeb1 vector rep2

description: 393P cells with Zeb1 induction, sample 2

value: Zeb1 vector


title: BM_MSCs-RCMD-rep1


title: wt_spb464_1


title: Root Normal N, biological rep1


title: NL_COLON6_FFPEr_62.5NG_REP2


title: NL_COLON6_FFPEr_62.5NG_REP1


title: NL_COLON6_FFPEr_125NG_REP2


title: Root Low N, biological rep3

description: Gene expression data from roots from plants grown under low nitrate.


title: BM_MSCs-Control-rep4


title: BM_MSCs-Control-rep5


title: Root Low N, biological rep1


title: Root Low N, biological rep2


title: BM_MSCs-Control-rep3


title: Leaf Reduced N, biological rep3

description: Gene expression data from leaves from plants shifted form normal to low nitrate.

source_name: leaves from main tiller


title: Leaf Reduced N, biological rep2


title: BM_MSCs-Control-rep2


title: BM_MSCs-Control-rep1


title: Leaf Reduced N, biological rep1


title: NIDF-infected BM cells, biological rep1

city: Cho-ku

first: yoko

last: ogawara

state: Tokyo

address: 5-1-1, Tsukiji

institute: National Cancer Center Research Institute

description: Gene expression data from NPMc, IDH2/R140Q, DNMT3A/R882H and FLT3-ITD-infected BM cells

hyb_protocol: Labeled cDNA were hybridized  on GeneChip Mouse Gene 1.0 ST Array according to the manufacturer's instructions (GeneChip® WT Terminal  Labeling and Hybridization  User Manual, Affymetrix)

data_processing: The data were analyzed with Gene Sping GX Version12.5. Summarization Algorithm: RMA16, Confidence level: All,Baseline Options: Do not perform baseline transformation

label_protocol: Biotinylated cDNA were prepared using a GeneChip WT Terminal Labeling kit (Affymetrix).

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

treatment_protocol: Bone marrow cells were isolated from mice.

value: bone marrow


title: NL_COLON6_FFPEr_125NG_REP1


title: Leaf Induced N, biological rep3

description: Gene expression data from leaves from plants shifted form low to normal nitrate.


title: NL_COLON6_FFPEr_250NG_REP2


title: NL_COLON8_FFPE


title: NIF-infected BM cells, biological rep2

description: Gene expression data from NPMc, IDH2/R140Q and FLT3-ITD-infected BM cells


title: NL_COLON6_FFPEr_250NG_REP1


title: NIF-infected BM cells, biological rep1

source_name: NPMc, IDH2/R140Q and FLT3-ITD-infected BM cells


title: NID-infected BM cells, biological rep1

description: Gene expression data from NPMc, IDH2/R140Q and DNMT3A/R882H-infected BM cells


title: NID-infected BM cells, biological rep2

source_name: NPMc, IDH2/R140Q and DNMT3A/R882H-infected BM cells


title: Leaf Normal N, biological rep2

description: Gene expression data from leaves from plants grown under normal nitrate.


title: Leaf Normal N, biological rep1


title: Leaf Induced N, biological rep2


title: NL_COLON6_FFPE_REP2


title: NL_COLON6_FFPEr_500NG_REP1


title: Leaf Normal N, biological rep3


title: NI-infected BM cells, biological rep1

description: Gene expression data from NPMc and IDH2/R140Q-infected BM cells

source_name: NPMc and IDH2/R140Q-infected BM cells

value: NPMc and IDH2/R140Q-infected BM cells


title: NL_COLON6_FF_REP2


title: NL_COLON6_FFPE_REP1


title: NL_COLON6_FF_REP1


title: Leaf Low N, biological rep3

description: Gene expression data from leaves from plants grown under low nitrate.


title: NL_COLON6_FFPEr_500NG_REP2


title: NL_COLON5_FFPEr_50NG_REP2


title: vector-infected BM cells, biological rep1

description: Gene expression data from vector-infected BM cells

source_name: vector-infected BM cells

value: vector-infected BM cells


title: NI-infected BM cells, biological rep2


title: NL_COLON5_FFPEr_175NG_REP1


title: wild-type Mo6 vs varA mutant replicate 4

city: Seoul

first: Juri

last: Kim

address: 50-1, Yonsei-ro, Seodaemun-gu

department: Environmental Medical Biology

institute: Yonsei University

description:
Biological replicate 4 of 5.
Mo6 vs varA_4

hyb_protocol: After checking labeling efficiency, cyanine 3-labeled and cyanine 5-labeled cRNA target were combined and fragmented by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60 oC for 30min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Vibrio vulnificus MO6-24_30K microarray (MYcroarray.com, USA). The arrays hybridized at 57oC for 17 h using Agilent Hybridization oven (Agilent Technology, USA).

scan_protocol: The hybridization images were visualized with Axon GenePix 4000B Scanner (Axon Instrument, CA)

data_processing:
The average fluorescence intensity for each spot was calculated and local background was subtracted. All data normalization and selection of fold-changed genes were performed using GenoWiz 4.0 (Ocimumbiosolutions, India).
Gene Pix Pro 6.0 (Axon Instruments, CA) was used for background subtraction and GenoWiz 4.0 (Ocimumbiosolutions, India) was used Loess normalization.

organism: Vibrio vulnificus

label_protocol: The synthesis of target cRNA probes and hybridization were performed using Agilent’s Low Input Quick Amp WT Labeling kit, two color (Agilent Technology, USA) according to the manufacturer’s instructions. Briefly, each 0.2 ug total RNA was mixed with WT primer mix and incubated at 65 oC for 10min. cDNA master mix (5X First strand buffer, 0.1M DTT, 10mM dNTP mix, RNase-Out, and MMLV-RT) was prepared and added to the reaction mixer. The samples were incubated at 40 oC for 2 hours and then the RT and dsDNA synthesis was terminated by incubating at 70 oC for 15min.   The transcription master mix was prepared as the manufacturer’s protocol (4X Transcription buffer, 0.1M DTT, NTP mix, 50% PEG, RNase-Out, Inorganic pyrophosphatase, T7-RNA polymerase, and Cyanine 3/5-CTP). Transcription of dsDNA was performed by adding the transcription master mix to the dsDNA reaction samples and incubating at 40 oC for 2 hours.

growth_protocol: V. vulnificus strains were cultured at 30°C in LB medium supplemented with an additional 2% NaCl (LBS).

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

value: wild type

value: MO6-24/O, ΔvarA


title: wild-type Mo6 vs varA mutant replicate 5

description:
Biological replicate 5 of 5.
Mo6 vs varA_5


title: vector-infected BM cells, biological rep2


title: NL_COLON5_FF

value: colon

value: Normal


title: NL_COLON5_FFPEr_50NG_REP1


title: Leaf Low N, biological rep1


title: NL_COLON5_FFPEr_100NG_REP1


title: NL_COLON5_FFPEr_100NG_REP2


title: IDH2/R140Q-infected BM cells, biological rep2

description: Gene expression data from IDH2/R140Q-infected BM cells

source_name: IDH2/R140Q-infected BM cells

value: IDH2/R140Q-infected BM cells


title: normal BM, biological rep2

description: Gene expression data from normal BM cells

source_name: normal BM cells

value: normal BM cells


title: NIDF-infected BM cells, biological rep2

source_name: NPMc, IDH2/R140Q, DNMT3A/R882H and FLT3-ITD-infected BM cells


title: NL_COLON5_FFPE

value: FFPE


title: wild-type Mo6 vs varA mutant replicate 3

description:
Biological replicate 3 of 5.
Mo6 vs varA_3


title: Leaf Induced N, biological rep1

value: Kaybonnet

value: 4 week-old


title: IDH2/R140Q-infected BM cells, biological rep1


title: NL_COLON5_FFPEr_250NG_REP1


title: NL_COLON5_FFPEr_175NG_REP2


title: wild-type Mo6 vs varA mutant replicate 2

description:
Biological replicate 2 of 5.
Mo6 vs varA_2


title: NL_COLON5_FFPEr_250NG_REP2


title: wild-type Mo6 vs acsR mutant replicate 4

description:
Biological replicate 4 of 4.
Mo6 vs acsR_4

value: MO6-24/O, ΔacsR


title: wild-type Mo6 vs varA mutant replicate 1

description:
Biological replicate 1 of 5.
Mo6 vs varA_1


title: wild-type Mo6 vs acsR mutant replicate 3

description:
Biological replicate 3 of 4.
Mo6 vs acsR_3


title: Nf(I)DF-AML, biological rep2

description: Gene expression data from NPMc, floxed-IDH2/R140Q, DNMT3A/R882H and FLT3-ITD-mediated AML cells

source_name: floxed-IDH2/R140Q, NPMc, DNMT3A/R882H and FLT3-ITD induced AML cells


title: wild-type Mo6 vs acsR mutant replicate 2

description:
Biological replicate 2 of 4.
Mo6 vs acsR_2


title: Leaf Low N, biological rep2


title: wild-type Mo6 vs acsR mutant replicate 1

description:
Biological replicate 1 of 4.
Mo6 vs acsR_1


title: Nf(I)DF-AML deleted of IDH2/R140Q, biological rep3

description: Gene expression data from NPMc, floxed-IDH2/R140Q, DNMT3A/R882H and FLT3-ITD-mediated AML cells, deleted with IDH2/R140Q

source_name: floxed-IDH2/R140Q, NPMc, DNMT3A/R882H and FLT3-ITD induced AML cells, deleted of IDH2/R140Q


title: NL_COLON4_FFPEr_75NG_REP1

value: FFPEr


title: NL_COLON4_FFPEr_75NG_REP2


title: NL_COLON2_FFPEr_70NG_REP1


title: SJINF020

status: Public on Mar 24 2015

city: Memphis

first: Steven

middle: William

last: Paugh

state: TN

address: 262 Danny Thomas Place

department: Pharmaceutical Sciences Department

institute: St. Jude Children's Research Hospital

description: Gene expression data

hyb_protocol: Affymetrix U133A

scan_protocol: Affymetrix U133A

data_processing: R/Bioconductor MAS5

source_name: Leukemia cells

label_protocol: Affymetrix U133A

extract_protocol: Trisol

value: #N/A

tag: lin


title: Nf(I)DF-AML deleted of IDH2/R140Q, biological rep2

value: NPMc, floxed-IDH2/R140Q, DNMT3A/R882H and FLT3-ITD-mediated AML cells, deleted with IDH2/R140Q


title: SJMLL023

description: Gene expression data


title: Patient576

description: Gene expression data


title: SJETV087

description: Gene expression data

value: SEN

value: B


title: SJMLL032

description: Gene expression data

value: RES


title: Patient577

description: Gene expression data


title: SJHYPER090

description: Gene expression data


title: NL_COLON2_FFPEr_100NG_REP2


title: NL_COLON2_FFPEr_70NG_REP2


title: Patient574

description: Gene expression data


title: Patient573

description: Gene expression data


title: NL_COLON2_FFPEr_100NG_REP1


title: Patient572

description: Gene expression data


title: normal BM, biological rep1

value: bone marrow


title: SJTALL005

description: Gene expression data

value: T


title: NL_COLON1_FFPEr_250NG_REP2


title: SJHYPER047

description: Gene expression data


title: SJHYPER008

description: Gene expression data


title: NL_COLON1_FFPEr_250NG_REP1


title: SJBALL022430

description: Gene expression data


title: NL_COLON1_FFPEr_100NG_REP1


title: NL_COLON2_FFPE

source_name: Normal colon mucosa, FFPE


title: Nf(I)DF-AML, biological rep1

source_name: floxed-IDH2/R140Q, NPMc, DNMT3A/R882H and FLT3-ITD-induced AML cells

value: NPMc, floxed-IDH2/R140Q, DNMT3A/R882H and FLT3-ITD-mediated AML cells


title: SJBALL063

description: Gene expression data


title: SJPHALL005

description: Gene expression data


title: SJBALL196

description: Gene expression data


title: NL_COLON1_FFPEr_100NG_REP2

value: colon


title: SJHYPER054

description: Gene expression data


title: SJBALL272

description: Gene expression data


title: REH

description: Gene expression data

tag: source

value: REH cell line


title: SJETV054

description: Gene expression data


title: SJTALL066

description: Gene expression data


title: SJHYPER052

description: Gene expression data


title: Nf(I)DF-AML deleted of IDH2/R140Q, biological rep1


title: SJHYPO108

description: Gene expression data


title: SJBALL006

description: Gene expression data


title: SJTALL067

description: Gene expression data


title: SJTALL018

description: Gene expression data


title: SJHYPER007

description: Gene expression data


title: SJINF069

description: Gene expression data


title: SJETV053

description: Gene expression data


title: SJHYPER003

description: Gene expression data


title: SJHYPER057

description: Gene expression data


title: SJBALL191

description: Gene expression data


title: SJTALL049

description: Gene expression data


title: SJMLL026

description: Gene expression data


title: SJPHALL004

description: Gene expression data


title: SJTALL213

description: Gene expression data


title: Patient539

description: Gene expression data


title: Patient538

description: Gene expression data


title: SJETV004

description: Gene expression data


title: SJETV050

description: Gene expression data


title: Patient540

description: Gene expression data


title: SJHYPER001

description: Gene expression data


title: SJE2A012

description: Gene expression data


title: SJMLL039

description: Gene expression data


title: Patient534

description: Gene expression data


title: Patient535

description: Gene expression data


title: Patient531

description: Gene expression data


title: Patient530

description: Gene expression data


title: Patient537

description: Gene expression data


title: Patient536

description: Gene expression data


title: Patient525

description: Gene expression data


title: Patient528

description: Gene expression data


title: Patient527

description: Gene expression data


title: Patient526

description: Gene expression data


title: Patient522

description: Gene expression data


title: Patient521

description: Gene expression data


title: Patient532

description: Gene expression data


title: SJPHALL013

description: Gene expression data


title: Patient529

description: Gene expression data


title: SJHYPER055

description: Gene expression data


title: Patient520

description: Gene expression data


title: Patient519

description: Gene expression data


title: NL_COLON1_FFPE

value: Normal


title: Patient514

description: Gene expression data


title: Patient517

description: Gene expression data


title: Patient513

description: Gene expression data


title: Patient511

description: Gene expression data


title: Patient509

description: Gene expression data


title: Patient508

description: Gene expression data


title: Patient518

description: Gene expression data


title: Patient503

description: Gene expression data


title: Patient512

description: Gene expression data


title: Patient507

description: Gene expression data


title: Patient515

description: Gene expression data


title: Patient505

description: Gene expression data


title: Patient506

description: Gene expression data


title: Patient499

description: Gene expression data


title: Patient500

description: Gene expression data


title: Patient524

description: Gene expression data


title: Patient510

description: Gene expression data


title: Patient497

description: Gene expression data


title: Patient504

description: Gene expression data


title: Patient498

description: Gene expression data


title: SJERG003

description: Gene expression data


title: Patient495

description: Gene expression data


title: Patient502

description: Gene expression data


title: Patient494

description: Gene expression data


title: Patient496

description: Gene expression data


title: Patient501

description: Gene expression data


title: Patient493

description: Gene expression data


title: Patient489

description: Gene expression data


title: Patient490

description: Gene expression data


title: Patient487

description: Gene expression data


title: Patient488

description: Gene expression data


title: SJERG025

description: Gene expression data


title: SJPHALL020

description: Gene expression data


title: Patient479

description: Gene expression data