title: wt23h_rep3

city: VTT, Espoo

first: Merja

last: Oja

address: Tietotie 2

country: Finland

institute: VTT Technical Research Centre of Finland

description:
C6-3
23h time point of the cultivation of the control strain (Saccharomyces cerevisiae B67002). It is from cultivation CE6, one of the three biological replicate cultivations of the control strain used in this study.

hyb_protocol: The hybridization, washing and other procedures were performed according to Nimblegen Arrays User’s guide, Gene Expression Analysis, Version 4.0.

scan_protocol: The scanning was performed on the MS 200 Microarray scanner following  Nimblegen Arrays User’s guide, Gene Expression Analysis, Version 4.0.

data_processing: Data was exported from NimbleScan v2.5 Software as X, Y, and Signal report (.xys files) that contains the fluorescence intensity and position of each feature on the array. Data was processed in R, version 2.10.1, (http://www.r-project.org/) using Bioconductor (http://www.bioconductor.org/). Bioconductor package pdInfoBuilder  was used to create a platform design information package for the Nimblegen array, based on the design file (.ndf). Functions read.xysfiles and rma from the oligo package were used to read in and normalize the data. The rma-normalized data is presented as log2 intensities. Each gene was presented by three probesets on the microarray. The signals from the three probesets were averaged after rma normalization.  To retain the information of the three different probesets, the .ndf file provided by NimbleGen was modified by adding an inidicator b1, b2 or b3 to probeset identifiers based on the container (BLOCK1, BLOCK2, or BLOCK3) the probe was located in.

organism: Saccharomyces cerevisiae

source_name: control strain 23h

label_protocol: The cDNA samples were labeled with Cy3 following Nimblegen Arrays User’s guide, Gene Expression Analysis, Version 4.0.

growth_protocol: The industrial strain of S. cerevisiae, B67002 (VTT Culture Collection), containing two copies of  xylB under PGK1 promoter and the control strain without xylB were grown in bioreactions. The yeast was provided 8g/L D-glucose and 21g/L D-xylose at the start of the cultivation. The initial OD600 was ~1. After D-xylose consumption by the xylB-expressing strain at 47 hours, additional D-glucose (4g/l) and D-xylose (~25g/l) were provided to the cultures and the production experiments were carried out for 3 more days.  The cultivations are described in Toivari M, Nygard Y, Kumpula EP, Vehkomaki ML, Bencina M, Valkonen M, Maaheimo H, Andberg M, Koivula A, Ruohonen L et al: Metabolic engineering of Saccharomyces cerevisiae for bioconversion of D-xylose to D-xylonate. Metab Eng 2012, 14(4):427-436 (PMID: 22709678).

extract_protocol: The total RNA was isolated by the RNeasy Plant Mini Kit (QIAGEN) following the glass-bead method. Oligo dT primers were used for the cDNA was synthesis, following Nimblegen Arrays User’s guide, Gene Expression Analysis, Version 4.0. The quality of the RNA and cDNA preparations was assessed by the Bioanalyser 2100 (Agilent Technologies).

treatment_protocol: The cells collected from the bioreactor cultures were harvested by centrifugation, washed, frozen in liquid nitrogen and stored at -80°C.

value: S. cerevisiae B67002

value: hydrolysate tolerant S. cerevisiae strain B67002 (isogenic parental)

tag: time (h)

tag: experimental group; series

value: wt23h; CE6


title: SC-MO/dex_1

status: Public on Nov 18 2014

type: RNA

city: Leiden

first: Marcel

last: Schaaf

address: Einsteinweg 55

department: Institute of Biology

country: Netherlands

institute: Leiden University

description: Biological replicate 1 of 3: SC-MO/dex

hyb_protocol: The dual colour hybridization of the microarray chips was performed at the Microarray Department (MAD) of the University of Amsterdam (Amsterdam, The Netherlands) using the standard Agilent protocol.

scan_protocol: The arrays were scanned with DNA Microarray Scanner G2565CA from Agilent Technologies. The arrays were scanned twice with 10% PMT and 100% PMT laser power.

data_processing: Microarray data was processed from raw data image files with Feature Extraction Software 9.5.3.1 (Agilent Technologies). The XDR function was used to extend the dynamic range. Processed data were subsequently imported into Rosetta Resolver 7.0 (Rosetta Biosoftware, Seattle, Washington) and subjected to default ratio error modelling. The Agilent Feature Extraction files contain the final log ratio data. The algorithms that were used to normalize the feature signal and calculate the log ratios are described in the Reference Guide for Agilent Feature Extraction Software v9.5. The standard settings as described for the GE2-v5_95 protocol in the Reference Guide were used. In order to calculate the normalized signal, the Rank Consistency Probes method was used and the Linear&LOWESSDyeNormFactor (= DyeNormalSignal/(BGSubSignal x LinearDyeNormFactor) was calculated as described on page 231 of the Reference Guide. The dye normalized signal was calculated as follows (page 232): DyeNormSignal = BGSubSignal x DyeNormFactor. The log10 ratio was subsequently calculated as follows (page 232): LogRatio = Log(rProcessedSignal/gProcessedSignal), where rProcessedSignal and gProcessedSignal are signals post dye normalization and post surrogate processing in the red and green channels, respectively. The surrogate values are calculated and used as the lowest limit of detection to replace the dye normalized signal when either the mean feature signal is less than the background signal or not significant when compared to the background signal, or when the mean signal is less than its background standard deviation (page 226).

molecule: total RNA

organism: Danio rerio

source_name: The CR (common reference) was a mixture of all RNA samples from this microarray study.

label_protocol: Amino Allyl modified aRNA was synthesized in one amplification round from 1 ug of total RNA using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion). Subsequently, 6 ug of Amino Allyl modified aRNA was used for coupling of monoreactive Cy3 or Cy5 dye (GE Healthcare) and column purified.

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts).

extract_protocol: Twenty embryos per treatment group were collected in 1 ml of TRIZOL® Reagent (Invitrogen) and stored at -80°C. Embryos were homogenized in TRIZOL® and subsequently total RNA was extracted according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Zebrafish embryos were microinjected at the 1-2 cell stage with 1 nl of 0.05 mM SC-MO, 0.05 mM  MO1, 0.05 mM MO2, or 5 ng/ml zGRb mRNA. At 24 hpf, they were treated with 100 mM dex or vehicle. At 30 hpf, twenty embryos per treatment group were snap-frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent. Three individual experiments were performed, yielding triplicate samples per treatment group.

tag: tissue

value: embryo

source_name: SC-MO-injected at 1-2 cell stage, dex-injected at 24 hpf, RNA isolated from 20 embryos at 30 hpf


title: wt47h_rep3

description:
C6-4
47h time point of the cultivation of the control strain (Saccharomyces cerevisiae B67002). It is from cultivation CE6, one of the three biological replicate cultivations of the control strain used in this study.

source_name: control strain 47h

tag: strain

tag: genotype/variation

value: wt47h; CE6


title: wt00h_rep3

description:
C6-1
0h time point of the cultivation of the control strain (Saccharomyces cerevisiae B67002). It is from cultivation CE6, one of the three biological replicate cultivations of the control strain used in this study.

source_name: control strain 00h

value: wt00h; CE6


title: PNS.HET.1.MEDIP

type: genomic

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

country: Germany

institute: University Hospital Würzburg

description: MeDIP stressed 5Htt +/- mice group 1

hyb_protocol: Approximately 7µg of amplified and terminally labeled DNA was hybridized to tiling arrays at 45°C for 16h at 60 rpm. Washing of arrays and staining of bound DNA was achieved with the GeneChipHWS kit in a Fluidics Station 450 (both Affymetrix) using fluidics script FS450_0001.

scan_protocol: Microarrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Data from MeDIP and input pairs were loess normalized; log2(MeDIP/input) signal log ratios (SLR) were reported in bedGraph files.  Coordinates of genomic probes were mapped to the M. musculus MMv37 sequence assembly. Analyses were performed in R (http://www.r-project.org) with the Bioconductor package Starr (http://www.bioconductor.org).
Raw data from CEL files of MeDIP and input pairs of the same sample were loess normalized, followed by calculation of the MeDIP-input signal log ratio (SLR). SLRs between samples were quantiles normalized, followed by a 300bp sliding-window median smoothing along the genomically ordered probe signals. The preprocessed array signals are reported in the "_smoothed.bedGraph" files. The CMARRT algorithm was employed to define MeDIP-enriched autosomal regions in smoothed SLRs of each sample; the ".cmarrt.bed" files contain genomic coordinates of MeDIP-enriched regions. Analyses were performed in R (http://www.r-project.org) with the Bioconductor package Starr (http://www.bioconductor.org).

label: biotin

molecule: genomic DNA

organism: Mus musculus

source_name: murine hippocampal MeDIP DNA from stressed 5Htt +/- animals

label_protocol: Samples (approximately 7 µg of amplified DNA each) were fragmented and terminally labeled with biotin using the GeneChip Mapping 10K Xba kit (Affymetrix).

growth_protocol: The wt and 5-Htt +/- deficient  mice  ([B6.129(Cg)-Slc6a4tm1Kpl/J]) were housed individually within a temperature-controlled  environment (2161uC) with 12 h light/12 h dark cycle (lights on from 7.00 h) and standard rodent chow and water available ad libitum.

extract_protocol: Genomic DNA was extracted from the tissue using phenol/chloroform/isoamyl alcohol extraction.  300 µl 0.5%-SDS extraction buffer were added to the frozen tissue. The tissue was subsequently homogenized for 30 to 60 sec at 25 Hz at 4°C in the Tissue Lyser (Qiagen, Hilden, Germany) using a metallic bead. After adding 200 µl 0.5%-SDS extraction buffer and 50 µl 10- or 20mg/µl-proteinase K, samples were incubated at 55°C over night/3 h. Following this, samples were incubated with 50 µl 10mg/µl-RNAse A with for 1 h at 37°C and then mixed with 700 µl of phenol/chloroform/isoamyl alcohol mixture (25:24:1). Phases were separated using MaXtract high density tubes (Qiagen) by centrifuging the samples at 14 000 rpm for 5 min at RT. The aqueous phase was then mixed with 700 µl phenol isoamyl alcohol (24:1) and phases were again separated by centrifuging the samples in MaXtract high density tubes as described above. DNA was precipitated with 50 µl sodium acetate and 1000 µl cold absolute ethanol (incubation 10 min at -20°C, centrifugation 20 min at 4°C, 14  000 rpm). The resulting pellet was washed with 500 µl cold 80%-ethanol using the same conditions as for the precipitation, dried at RT for 5 to 30 min and resuspended in 50 µl 1xTE. DNAs of single animals were then pooled, creating 2-3 pools per group. DNA was then  sheared using the BiorupterTM UCD-200 (Diagenode, Liège, Belgium) yielding fragments of 300bp size +/- 200bp.Conditions were 20 KHz, 30 sec ON alternated by 30 sec OFF, for 3 x 5 min at low power

tag: backgroud strain

tag: treatment

value: Prenatal stress group (3 x 45 min/ day, E13-17)


title: PNS.HET.1.INPUT

description: Input stressed 5Htt +/- mice group 1

source_name: murine hippocampal input DNA from stressed 5Htt +/- animals


title: CON.HET.3.INPUT

description: Input unstressed 5Htt +/- mice group 3

source_name: murine hippocampal input DNA from unstressed 5Htt +/- animals

value: control group


title: wt49h_rep3

description:
C6-5
49h time point of the cultivation of the control strain (Saccharomyces cerevisiae B67002). It is from cultivation CE6, one of the three biological replicate cultivations of the control strain used in this study.

source_name: control strain 49h

value: wt49h; CE6


title: wt71h_rep3

description:
C6-6
71h time point of the cultivation of the control strain (Saccharomyces cerevisiae B67002). It is from cultivation CE6, one of the three biological replicate cultivations of the control strain used in this study.

source_name: control strain 71h

value: wt71h; CE6


title: Treg High Salt_1

city: New Haven

first: Mitja

last: Mitrovic

address: 300 George Street

department: Neurology

country: USA

institute: Yale School of Medicine

description: Gene expression data Tregs

hyb_protocol: Following fragmentation, cDNA was hybridized for 18 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix Gene Chip Scanner 3000

data_processing: LIMMA/Bioconductor

organism: Homo sapiens

source_name: Regulatory T Cells exposed to high salt media

label_protocol: Biotinylated cDNA were prepared using the Encore Biotin Module System from total cDNA following amplification with the Ovation Pico WTA System V2 (standard protocols used).

growth_protocol: For 3 days (72 hours) freshly sorted ex-vivo regulatory T cells (healthy human controls) were incubated in x-vivo media with plate bound anti-CD3 (1ug/mL) and soluble anti-CD28 (1ug/mL).

extract_protocol: Following incubation period, cells were harvested and RNA isolated (Agilent Technologies) prior to being processed for microarray analysis.

treatment_protocol: Throughout this incubation regulatory T cells were either in normal media (x-vivo) or media treated with an additional 40mM NaCl.

tag: cell type

value: regulatory T cell

tag: cellular subset

value: CD4+ lymphocyte

value: high salt media, with anti-CD3/anti-CD28


title: wt07h_rep3

description:
C6-2
7h time point of the cultivation of the control strain (Saccharomyces cerevisiae B67002). It is from cultivation CE6, one of the three biological replicate cultivations of the control strain used in this study.

source_name: control strain 07h

value: wt07h; CE6


title: Treg Normal Salt_2

description: Gene expression data Tregs

source_name: Regulatory T Cells exposed to normal salt media

value: normal salt media, with anti-CD3/anti-CD28


title: Treg High Salt_2

description: Gene expression data Tregs


title: x71h_rep3

description:
C5-6
71h time point of the cultivation of the D-xylonate producing strain (Saccharomyces cerevisiae B67002 expressing XylB gene). It is from cultivation CE5, one of the three biological replicate cultivations of the D-xylonate producing strain used in this study.

source_name: D-xylonate producing strain 71h

value: S. cerevisiae B67002 + xylB

value: D-xylonate producing strain expressing XylB gene from C. crescentus

value: x71h; CE5


title: CON.HET.2.INPUT

description: Input unstressed 5Htt +/- mice group 2


title: Treg Normal Salt_1

description: Gene expression data Tregs


title: CON.HET.2.MEDIP

description: MeDIP unstressed 5Htt +/- mice group 2

source_name: murine hippocampal MeDIP DNA from unstressed 5Htt +/- animals


title: x47h_rep3

description:
C5-4
47h time point of the cultivation of the D-xylonate producing strain (Saccharomyces cerevisiae B67002 expressing XylB gene). It is from cultivation CE5, one of the three biological replicate cultivations of the D-xylonate producing strain used in this study.

source_name: D-xylonate producing strain 47h

value: x47h; CE5


title: x23h_rep3

description:
C5-3
23h time point of the cultivation of the D-xylonate producing strain (Saccharomyces cerevisiae B67002 expressing XylB gene). It is from cultivation CE5, one of the three biological replicate cultivations of the D-xylonate producing strain used in this study.

source_name: D-xylonate producing strain 23h

value: x23h; CE5


title: CON.HET.3.MEDIP

description: MeDIP unstressed 5Htt +/- mice group 3


title: R. sphaeroides 2.4.1 (pBBRSorYi) vs. R. sphaeroides 2.4.1 (pBBR) replicate 2

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

institute: Justus-Liebig University Gießen

description: biological sample 4-6

hyb_protocol: Total RNA of three independent experiments of a SorY overexpressing strain (2.4.1pBBRSorYi) and a control strain harbouring an empty vector (2.4.1pBBR) after 10 min of 1O2 stress, were pooled and hybridized to one array. Two arrays werehybridized with independent experimental runs. Gene chip hybridization and scanning were performed according to the specifications from Agilent.

scan_protocol: Scanned on an Agilent High Resolution Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5)

data_processing: R with Limma package was used for data evaluation. LOESS normalized and background subtracted.

organism: Cereibacter sphaeroides 2.4.1

source_name: R. sphaeroides 2.4.1, 10min 1O2, total cells

label_protocol: The ULSTM Fluorescent Labeling Kit for Agilent arrays (Kreatech) was used for RNA labeling and fragmentation

growth_protocol: R. sphaeroides strains grown aerobically

extract_protocol: Total RNA was isolated by using the hot phenol method (Janzon et al., 1986). After DNase I treatment the RNA was purified by using mixtures of phenol-chloroform-isoamylalcohol and chloroform-isoamylacohol. For microarray analysis the RNA was further purified by RNeasy®MinElute™ spin columns (Qiagen) following the manufacturer’s instructions.

treatment_protocol: R. sphaeroides was grown aerobically. Photooxidative stress conditions were generated by the addition of methylene blue (0.2 µM) and exposure to white light (800wm-2) for 10min

tag: test

value: total RNA isolates of R. sphaeroides 2.4.1 (pBBRSorYi), 10min 1O2

tag: reference

value: total RNA isolates of R. sphaeroides 2.4.1 (pBBR), 10min 1O2


title: R. sphaeroides 2.4.1 (pBBRSorYi) vs. R. sphaeroides 2.4.1 (pBBR) replicate 1

description: biological sample 1-3


title: daf-2;daf-16; starvation; replicate 4

city: Koeln

first: Bjoern

last: Schumacher

address: Zuelpicher Str. 47

institute: University of Cologne

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: Affymetrix Power Tools, 1.14

organism: Caenorhabditis elegans

source_name: daf-2;daf-16; starvation

label_protocol: Affymetrix

growth_protocol: NGM

extract_protocol: Trizol

treatment_protocol: synchronized worms were put on food for 4h, then UV treated and harvested 6h after treatment

tag: genotype

value: Starvation


title: CON.HET.1.INPUT

description: Input unstressed 5Htt +/- mice group 1


title: daf-2;daf-16; replicate 2

value: Untreated


title: x07h_rep3

description:
C5-2
7h time point of the cultivation of the D-xylonate producing strain (Saccharomyces cerevisiae B67002 expressing XylB gene). It is from cultivation CE5, one of the three biological replicate cultivations of the D-xylonate producing strain used in this study.

source_name: D-xylonate producing strain 07h

value: x07h; CE5


title: SC-MO/dex_3

description: Biological replicate 3 of 3: SC-MO/dex

source_name: The CR (common reference) was a mixture of all RNA samples from this microarray study.

value: embryo

source_name: SC-MO-injected at 1-2 cell stage, dex-injected at 24 hpf, RNA isolated from 20 embryos at 30 hpf


title: CON.HET.1.MEDIP

description: MeDIP unstressed 5Htt +/- mice group 1

value: control group


title: daf-2;daf-16; starvation; replicate 3


title: daf-2;daf-16; UV; replicate 1

source_name: daf-2;daf-16; UV

value: UV


title: daf-2;daf-16; starvation; replicate 2


title: x00h_rep3

description:
C5-1
0h time point of the cultivation of the D-xylonate producing strain (Saccharomyces cerevisiae B67002 expressing XylB gene). It is from cultivation CE5, one of the three biological replicate cultivations of the D-xylonate producing strain used in this study.

source_name: D-xylonate producing strain 00h

value: x00h; CE5


title: MD.1

city: Baltimore

first: Saraswati

last: Sukumar

state: MD

address: 1650 Orleans St, CRB 1, Rm 132

department: Breast Cancer Program

institute: Johns Hopkins School of Medicine

description: MDA-MB-231 cells treated with entinostat and doxorubicin

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scan protocol

data_processing: Data was quantile normalized and minimum values were set to 64 using the limma package in R statistical environment.

source_name: MDA-MB-231_Entinostat and Doxorubicin

label_protocol: Biotinylated cRNA were synthesized using Illumina TotalPrep RNA Amplification Kit (AMIL1791, Ambion, Austin, TX) following the standard protocol.

growth_protocol: MDA-MB-231 cells grown in DMEM 10% FBS

extract_protocol: RNA was extracted using RNeasy Mini Kit (Qiagen)

treatment_protocol: MDA-MB-231 cells treated with entinostat (2.5 µM), ATRA (1 µM) and doxorubicin (0.2 µM), single and combinations treatments for 48h

tag: cell line

value: Entinostat and Doxorubicin

tag: replicate


title: PNS.WT.3.MEDIP

description: MeDIP stressed wild type mice group 3

source_name: murine hippocampal MeDIP DNA from stressed wt animals

value: Prenatal stress group (3 x 45 min/ day, E13-17)


title: daf-2;daf-16; replicate 3


title: daf-2;daf-16; UV; replicate 2


title: wt49h_rep2

description:
C4-5
49h time point of the cultivation of the control strain (Saccharomyces cerevisiae B67002). It is from cultivation CE4, one of the three biological replicate cultivations of the control strain used in this study.

source_name: control strain 49h

value: S. cerevisiae B67002

value: hydrolysate tolerant S. cerevisiae strain B67002 (isogenic parental)

value: wt49h; CE4


title: PNS.WT.1.INPUT

description: Input stressed wild type mice group 1

source_name: murine hippocampal input DNA from stressed wt animals


title: daf-2; starvation; replicate 3

source_name: daf-2; starvation


title: daf-2;daf-16; replicate 1


title: PNS.WT.1.MEDIP

description: MeDIP stressed wild type mice group 1


title: wt71h_rep2

description:
C4-6
71h time point of the cultivation of the control strain (Saccharomyces cerevisiae B67002). It is from cultivation CE4, one of the three biological replicate cultivations of the control strain used in this study.

source_name: control strain 71h

value: wt71h; CE4


title: daf-2; starvation; replicate 2


title: CON.WT.3.INPUT

description: Input unstressed wild type mice group 3

source_name: murine hippocampal input DNA from unstressed wt animals


title: SC-MO/dex_2

description: Biological replicate 2 of 3: SC-MO/dex


title: wt23h_rep2

description:
C4-3
23h time point of the cultivation of the control strain (Saccharomyces cerevisiae B67002). It is from cultivation CE4, one of the three biological replicate cultivations of the control strain used in this study.

source_name: control strain 23h

value: wt23h; CE4


title: daf-2;daf-16; starvation; replicate 1


title: daf-2; UV; replicate 2

source_name: daf-2; UV


title: daf-2; starvation; replicate 1


title: wt00h_rep2

description:
C4-1
0h time point of the cultivation of the control strain (Saccharomyces cerevisiae B67002). It is from cultivation CE4, one of the three biological replicate cultivations of the control strain used in this study.

source_name: control strain 00h

value: wt00h; CE4


title: daf-2;daf-16; UV; replicate 3


title: daf-2; UV; replicate 3


title: daf-2; replicate 3


title: wt47h_rep2

description:
C4-4
47h time point of the cultivation of the control strain (Saccharomyces cerevisiae B67002). It is from cultivation CE4, one of the three biological replicate cultivations of the control strain used in this study.

source_name: control strain 47h

value: wt47h; CE4


title: wt07h_rep2

description:
C4-2
7h time point of the cultivation of the control strain (Saccharomyces cerevisiae B67002). It is from cultivation CE4, one of the three biological replicate cultivations of the control strain used in this study.

source_name: control strain 07h

value: wt07h; CE4


title: CON.WT.3.MEDIP

description: MeDIP unstressed wild type mice group 3

source_name: murine hippocampal MeDIP DNA from unstressed wt animals


title: CON.WT.2.INPUT

description: Input unstressed wild type mice group 2


title: CON.WT.1.INPUT

description: Input unstressed wild type mice group 1


title: CON.WT.2.MEDIP

description: MeDIP unstressed wild type mice group 2


title: x71h_rep2

description:
C3-6
71h time point of the cultivation of the D-xylonate producing strain (Saccharomyces cerevisiae B67002 expressing XylB gene). It is from cultivation CE3, one of the three biological replicate cultivations of the D-xylonate producing strain used in this study.

source_name: D-xylonate producing strain 71h

value: S. cerevisiae B67002 + xylB

value: D-xylonate producing strain expressing XylB gene from C. crescentus

value: x71h; CE3


title: CON.WT.1.MEDIP

description: MeDIP unstressed wild type mice group 1


title: x49h_rep2

description:
C3-5
49h time point of the cultivation of the D-xylonate producing strain (Saccharomyces cerevisiae B67002 expressing XylB gene). It is from cultivation CE3, one of the three biological replicate cultivations of the D-xylonate producing strain used in this study.

source_name: D-xylonate producing strain 49h

value: x49h; CE3


title: x47h_rep2

description:
C3-4
47h time point of the cultivation of the D-xylonate producing strain (Saccharomyces cerevisiae B67002 expressing XylB gene). It is from cultivation CE3, one of the three biological replicate cultivations of the D-xylonate producing strain used in this study.

source_name: D-xylonate producing strain 47h

value: x47h; CE3


title: x23h_rep2

description:
C3-3
23h time point of the cultivation of the D-xylonate producing strain (Saccharomyces cerevisiae B67002 expressing XylB gene). It is from cultivation CE3, one of the three biological replicate cultivations of the D-xylonate producing strain used in this study.

source_name: D-xylonate producing strain 23h

value: x23h; CE3


title: x00h_rep2

description:
C3-1
0h time point of the cultivation of the D-xylonate producing strain (Saccharomyces cerevisiae B67002 expressing XylB gene). It is from cultivation CE3, one of the three biological replicate cultivations of the D-xylonate producing strain used in this study.

source_name: D-xylonate producing strain 00h

value: x00h; CE3


title: daf-2; UV; replicate 1

value: UV


title: x07h_rep2

description:
C3-2
7h time point of the cultivation of the D-xylonate producing strain (Saccharomyces cerevisiae B67002 expressing XylB gene). It is from cultivation CE3, one of the three biological replicate cultivations of the D-xylonate producing strain used in this study.

source_name: D-xylonate producing strain 07h

value: x07h; CE3


title: wt71h_rep1

description:
C2-6
71h time point of the cultivation of the control strain (Saccharomyces cerevisiae B67002). It is from cultivation CE2, one of the three biological replicate cultivations of the control strain used in this study.

value: S. cerevisiae B67002

value: wt71h; CE2


title: daf-2; replicate 2

value: Untreated


title: wt49h_rep1

description:
C2-5
49h time point of the cultivation of the control strain (Saccharomyces cerevisiae B67002). It is from cultivation CE2, one of the three biological replicate cultivations of the control strain used in this study.

source_name: control strain 49h

value: hydrolysate tolerant S. cerevisiae strain B67002 (isogenic parental)

value: wt49h; CE2


title: daf-2; replicate 1


title: daf-16; starvation; replicate 2

source_name: daf-16; starvation

value: Starvation


title: daf-16; UV; replicate 3

source_name: daf-16; UV


title: wt23h_rep1

description:
C2-3
23h time point of the cultivation of the control strain (Saccharomyces cerevisiae B67002). It is from cultivation CE2, one of the three biological replicate cultivations of the control strain used in this study.

value: wt23h; CE2


title: wt00h_rep1

description:
C2-1
0h time point of the cultivation of the control strain (Saccharomyces cerevisiae B67002). It is from cultivation CE2, one of the three biological replicate cultivations of the control strain used in this study.

value: wt00h; CE2


title: daf-16; UV; replicate 1


title: daf-16; UV; replicate 2


title: wt07h_rep1

description:
C2-2
7h time point of the cultivation of the control strain (Saccharomyces cerevisiae B67002). It is from cultivation CE2, one of the three biological replicate cultivations of the control strain used in this study.

value: wt07h; CE2


title: wt47h_rep1

description:
C2-4
47h time point of the cultivation of the control strain (Saccharomyces cerevisiae B67002). It is from cultivation CE2, one of the three biological replicate cultivations of the control strain used in this study.

value: wt47h; CE2


title: daf-16; replicate 3


title: daf-16; starvation; replicate 1


title: N2; starvation; replicate 3

source_name: N2; starvation


title: x49h_rep1

description:
C1-5
49h time point of the cultivation of the D-xylonate producing strain (Saccharomyces cerevisiae B67002 expressing XylB gene). It is from cultivation CE1, one of the three biological replicate cultivations of the D-xylonate producing strain used in this study.

value: S. cerevisiae B67002 + xylB

value: D-xylonate producing strain expressing XylB gene from C. crescentus

value: x49h; CE1


title: N2; UV; replicate 3

source_name: N2; UV


title: N2; starvation; replicate 1


title: N2; starvation; replicate 2


title: daf-16; replicate 2


title: x07h_rep1

description:
C1-2
7h time point of the cultivation of the D-xylonate producing strain (Saccharomyces cerevisiae B67002 expressing XylB gene). It is from cultivation CE1, one of the three biological replicate cultivations of the D-xylonate producing strain used in this study.

value: x07h; CE1


title: N2; replicate 1


title: x23h_rep1

description:
C1-3
23h time point of the cultivation of the D-xylonate producing strain (Saccharomyces cerevisiae B67002 expressing XylB gene). It is from cultivation CE1, one of the three biological replicate cultivations of the D-xylonate producing strain used in this study.

value: x23h; CE1


title: x47h_rep1

description:
C1-4
47h time point of the cultivation of the D-xylonate producing strain (Saccharomyces cerevisiae B67002 expressing XylB gene). It is from cultivation CE1, one of the three biological replicate cultivations of the D-xylonate producing strain used in this study.

value: x47h; CE1


title: x00h_rep1

description:
C1-1
0h time point of the cultivation of the D-xylonate producing strain (Saccharomyces cerevisiae B67002 expressing XylB gene). It is from cultivation CE1, one of the three biological replicate cultivations of the D-xylonate producing strain used in this study.

value: x00h; CE1


title: N2; UV; replicate 2

value: UV


title: N2; UV; replicate 1


title: x71h_rep1

description:
C1-6
71h time point of the cultivation of the D-xylonate producing strain (Saccharomyces cerevisiae B67002 expressing XylB gene). It is from cultivation CE1, one of the three biological replicate cultivations of the D-xylonate producing strain used in this study.

value: x71h; CE1


title: xpa-1 10mJ/cm2; replicate 3

data_processing: Affymetrix Power Tools, version 1.14

source_name: xpa-1 10mJ/cm2


title: x49h_rep3

description:
C5-5
49h time point of the cultivation of the D-xylonate producing strain (Saccharomyces cerevisiae B67002 expressing XylB gene). It is from cultivation CE5, one of the three biological replicate cultivations of the D-xylonate producing strain used in this study.

value: x49h; CE5


title: xpa-1 10mJ/cm2; replicate 2


title: N2; replicate 2

value: Untreated


title: xpa-1 0mJ/cm2; replicate 3

source_name: xpa-1 0mJ/cm2

value: untreated


title: xpa-1 10mJ/cm2; replicate 1


title: xpa-1 0mJ/cm2; replicate 1


title: T2(TangDonggen)

city: Shanghai

first: yong

middle: wei

last: sun

state: Shanghai

address: Road pujian 200

department: Department of General Surgery

country: China

institute: Shanghai Jiao-Tong University School of Medicine, Renji Hospital

description: Development of lncRNA and mRNA expression after pancreaticoduodenectomy

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA.

scan_protocol: The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505B).

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: pancreatic ductal adenocarcinoma

label_protocol: The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen).

value: pancreatic ductal adenocarcinoma

tag: gender

value: male


title: T1(YiChangyin)

value: femal


title: N2; replicate 3


title: N2(ZhangYiting)

source_name: normal pancreatic tissue

value: normal pancreatic


title: N1(ChenGuodong)


title: T3(YangWenru)


title: xpa-1 0mJ/cm2; replicate 2


title: N2 starved; replicate 2

source_name: N2 starved

value: starved


title: N2 starved; replicate 3


title: N2 starved; replicate 1


title: Calu-6

city: Ibbenbüren

first: Dirk

last: Kemming

address: Roggenkampstr.

institute: ELA

description: Gene expression of MDA-MB-231-WT treated with 5-Aza-2'-deoxycytidine  vs untreated

hyb_protocol: Following fragmentation, 825 ng of each cRNA were hybridized for 17 hr at 65C on Agilent 4x44k Whole Human Genome Array. Arrays were washed according to the manufacturer's protocol.

scan_protocol: Agilent Technologies Scanner G2505B; Agilent Scanner protocol GE1-v5_95_Feb07; Scan resolution 5 µm; XDR Hi 100% XDR Lo 10%

data_processing: Data extraction was done using Agilent Feature Extraction Software. Agilent Feature Extraction Software (v 9.5.3.1) was used for extraction, background subtraction and Dye normalization. Replicate features have been averaged.

source_name: Calu-6 treated with 5-Aza-2'-deoxycytidine

label_protocol: Cy3 and Cy5 labeled cRNA were prepared according to the standard Agilent protocol from 500ng total RNA.

growth_protocol: BEAS-2B was cultured in BEBM medium including BEBM Single Quots supplements. H1993 and H1395 were grown in RPMI-1640 medium supplemented with 10% fetal bovine serum and 2 mM glutamine. Calu-6 was cultured in MEM medium containing 10% fetal bovine serum, 2 mM glutamine, 1% sodium pyruvate and 1% essential amino acids. All cell lines were grown in a humidified atmosphere with 5% CO2 at 37 °C. BEAS-2B, H1993, and H1395 cell lines were authenticated using Multiplex Cell Authentication.

extract_protocol: Total RNA of the cells was isolated using RNAeasy kit (Qiagen, Hilden Germany)

treatment_protocol: Cells were seeded at  15% confluence. 5-Aza-2'-deoxycytidine was dissolved in sterile water. After 6 hours of plating the cells were cultured in absence or presence of 1 µM 5-Aza-CdR, and the medium was changed daily until the cells reached a confluence of 90-100%.

value: lung

source_name: Calu-6 untreated

tag: cell lines


title: N2 60mJ/cm2; replicate 3

source_name: N2 60mJ/cm2


title: H1993

description: Gene expression of MDA-MB-231-BR treated with 5-Aza-2'-deoxycytidine  vs untreated

source_name: H1993 treated with 5-Aza-2'-deoxycytidine

source_name: H1993 untreated


title: N2 60mJ/cm2; replicate 2


title: N3(LiuJunhua)


title: N2 0mJ/cm2; replicate 3

source_name: N2 0mJ/cm2


title: H1395

description: Gene expression of MDA-MB-231-SA treated with 5-Aza-2'-deoxycytidine  vs untreated

source_name: H1395 treated with 5-Aza-2'-deoxycytidine

source_name: H1395 untreated


title: N2 60mJ/cm2; replicate 1


title: PNS.WT.3.INPUT

description: Input stressed wild type mice group 3

source_name: murine hippocampal input DNA from stressed wt animals

value: Prenatal stress group (3 x 45 min/ day, E13-17)


title: N2 0mJ/cm2; replicate 2


title: pacific_EB50-rep6

status: Public on Nov 17 2014

city: Victoria

first: Ben

middle: F

last: Koop

state: BC

address: PO Box 3020 STN CSC

department: Biology

country: Canada

institute: The University of Victoria

description:
pacific_EB50
Slide_5_SLICE_Block4.txt

hyb_protocol: Samples were hybridized to oligonucleotide microarrays as per manufacturers' instructions for Low-Input Quick Amp kits (Agilent; v6.5). Arrays were designed using previously annotated ESTs from both Pacific and Atlantic L. salmonis (Yasuike et al. 2012; eArray design ID 024389; Agilent).

scan_protocol: Scanned at 5 micrometer resolution on a ScanArray Express (Perkin Elmer) and quantified on Imagene (v8.1; BioDiscovery).

data_processing: For each probe on the microarray, the background median was subtracted from the foreground median. Data analysis was performed in GeneSpring GX11 (Agilent). Each array was normalized using an intensity-dependent Lowess normalization. All entities on the array are presented in the attached matrix file here, however, for the analysis, quality control filters for each of the three experiments retained probes that pass the following criteria in at least 65% of the samples in any one condition: raw signal ≥ 500 in both channels and no poor quality flags.

organism: Lepeophtheirus salmonis

source_name: Pacific Canada_mixed pool_sensitive

label_protocol: Labeled cRNA was generated from 825ng total RNA using Low-Input Quick Amp kits (Agilent; v6.5). A Cy3-cRNA reference pool to hybridize alongside samples was created for each of the above experiments, ensuring each experimental condition was included in the pool.

growth_protocol:
Atlantic: L. salmonis individuals were obtained from Atlantic salmon farms in Back Bay, New Brunswick, Canada (high EMB resistance) or near Grand Manan, New Brunswick, Canada (low EMB resistance). Lice collected from salmon farms were grown on fish in house at Atlantic Veterinary College (University of Prince Edward Island) for approximately 80-90 days, after which the third set of egg strings were extruded. Lice hatched from these adults (F1 generation) were grown on Atlantic salmon in house until molt to pre-adult stage. At this point, Atlantic salmon were sedated with Tricaine Methylsulfonate (MS-222) to prevent damage to lice during removal, and lice were collected and placed in Petri dishes with seawater (10 oC, 33 parts per thousand salinity). Petri dishes were swirled and any lice not adhering to the side were not used.
Pacific: L. salmonis egg strings were obtained from adult female lice infecting Atlantic salmon in a salmon farm near Campbell River, British Columbia (BC) in March 2009. Eggs were hatched, grown to copepodids, and then grown on Atlantic salmon in house at Pacific Biological Station, Nanaimo, BC, Canada. Pre-adult lice were removed from Atlantic salmon sedated with Metomidate hydrochloride (Aquacalm, Syndel Laboratories Ltd.) and held briefly in cold seawater for less than 1 hour. Approximately 25 pre-adult I and II stage male and female individuals were randomly distributed into each of 24 beakers containing 500 ml filtered seawater (10 oC; 30 parts per thousand salinity; one air stone per beaker).

extract_protocol: Atlantic: Lice were flash frozen individually and kept at -80 degrees Celcius until RNA extraction (n = 77 individuals). Total RNA was extracted from frozen tissue using TRIzol reagent® (Life Technologies), treated with TURBO™ DNase treatment (Life Technologies) followed by RNEasy column purification as per manufacturers’ instructions (QIAGEN). Purified total RNA was tested by agarose gel and automated electrophoresis (Experion; Bio-Rad) and spec.

treatment_protocol:
Atlantic: Stock emamectin benzoate (EMB; PESTANAL®, Sigma-Aldrich) was prepared to 100 mg/L in methanol, then diluted to working concentrations in seawater. EMB dilutions were prepared to final concentrations of 0, 0.1, 25, 300 or 1000 parts per billion (n = 4 individuals for each population/sex/dose combination). Lice were randomly distributed to beakers containing the above concentrations, and exposed for 24 hours.          Pacific: As with Atlantic, but to final concentrations of 0, 25, or 50 ppb EMB (n = 6 pools per condition).
Pacific: As described for Atlantic, except that lice were flash frozen together and treated with on-column DNase (QIAGEN) instead of TURBO™ DNase, and quality tested with agarose gel electrophoresis and by spectrophotometry (NanoDrop-1000) for purity and quantity.

tag: salmon type

value: Pacific Canada

tag: age

value: pre-adult lice

tag: Sex

value: mixed pool

tag: emb sensitivity

value: sensitive

tag: exposed to emb (ppb)

source_name: all condition pool

tag: sample type

value: reference pool


title: pacific_EB50-rep2

description:
pacific_EB50
Slide_2_SLICE_Block1.txt


title: BEAS-2B

description: Gene expression of MCF_10A treated with 5-Aza-2'-deoxycytidine vs untreated

source_name: BEAS-2B treated with 5-Aza-2'-deoxycytidine

tag: tissue

source_name: BEAS-2B untreated


title: atl_f-res25-rep4

description:
f-res25
10096.4_Block4.txt

source_name: Atlantic Canada_female_resistant

value: Atlantic Canada

value: female

value: resistant


title: pacific_EB25-rep5

description:
pacific_EB25
Slide_4_SLICE_Block2.txt


title: atl_m-res0.1-rep4

description:
m-res0.1
10096.2_Block2.txt

source_name: Atlantic Canada_male_resistant


title: pacific_EB50-rep3

description:
pacific_EB50
Slide_3_SLICE_Block2.txt


title: pacific_EB0-rep2

description:
pacific_EB0
Slide_2_SLICE_Block3.txt


title: pacific_EB50-rep1

description:
pacific_EB50
Slide_1_SLICE_Block3.txt


title: pacific_EB25-rep4

description:
pacific_EB25
Slide_4_SLICE_Block1.txt


title: atl_m-sen0-rep4

description:
m-sen0
10096.3_Block3.txt

source_name: Atlantic Canada_male_sensitive


title: pacific_EB0-rep6

description:
pacific_EB0
Slide_5_SLICE_Block3.txt


title: pacific_EB25-rep1

description:
pacific_EB25
Slide_2_SLICE_Block2.txt


title: pacific_EB25-rep3

description:
pacific_EB25
Slide_3_SLICE_Block3.txt


title: pacific_EB0-rep5

description:
pacific_EB0
Slide_4_SLICE_Block3.txt


title: pacific_EB25-rep6

description:
pacific_EB25
Slide_5_SLICE_Block2.txt


title: N2 0mJ/cm2; replicate 1

tag: treatment


title: atl_m-sen300-rep4

description:
m-sen300
10096.1_Block1.txt


title: pacific_EB25-rep2

description:
pacific_EB25
Slide_2_SLICE_Block4.txt


title: pacific_EB0-rep4

description:
pacific_EB0
Slide_3_SLICE_Block4.txt


title: pacific_EB50-rep4

description:
pacific_EB50
Slide_4_SLICE_Block4.txt


title: pacific_EB0-rep3

description:
pacific_EB0
Slide_3_SLICE_Block1.txt


title: pacific_EB0-rep1

description:
pacific_EB0
Slide_1_SLICE_Block4.txt


title: pacific_EB50-rep5

description:
pacific_EB50
Slide_5_SLICE_Block1.txt


title: atl_m-res1000-rep4

description:
m-res1000
10095.3_Block3.txt


title: atl_f-res0.1-rep4

description:
f-res0.1
10095.4_Block4.txt


title: daf-16; replicate 1

value: Untreated


title: atl_m-res1000-rep3

description:
m-res1000
10095.2_Block2.txt


title: atl_f-res1000-rep4

description:
f-res1000
10093.4_Block4.txt


title: atl_f-sen0.1-rep3

description:
f-sen0.1
10094.4_Block4.txt

source_name: Atlantic Canada_female_sensitive


title: atl_f-res25-rep3

description:
f-res25
10094.2_Block2.txt


title: atl_f-sen0.1-rep4

description:
f-sen0.1
10095.1_Block1.txt


title: atl_f-sen25-rep4

description:
f-sen25
10093.3_Block3.txt


title: atl_m-res300-rep4

description:
m-res300
10093.2_Block2.txt


title: atl_m-res1000-rep2

description:
m-res1000
10094.1_Block1.txt


title: atl_f-res25-rep2

description:
f-res25
10091.3_Block3.txt


title: atl_m-sen300-rep2

description:
m-sen300
10089.4_Block4.txt


title: atl_f-sen0-rep4

description:
f-sen0
10091.2_Block2.txt


title: atl_m-res0.1-rep3

description:
m-res0.1
10092.4_Block4.txt


title: atl_f-sen1000-rep4

description:
f-sen1000
10089.3_Block3.txt


title: atl_f-res0-rep4

description:
f-res0
10090.2_Block2.txt


title: atl_f-res1000-rep3

description:
f-res1000
10093.1_Block1.txt


title: atl_m-sen25-rep2

description:
m-sen25
10090.1_Block1.txt


title: atl_f-sen25-rep3

description:
f-sen25
10091.4_Block4.txt


title: atl_m-sen0-rep3

description:
m-sen0
10092.1_Block1.txt


title: atl_f-sen0-rep3

description:
f-sen0
10091.1_Block1.txt


title: atl_m-res300-rep3

description:
m-res300
10090.3_Block3.txt


title: atl_m-res0-rep4

description:
m-res0
10090.4_Block4.txt


title: atl_m-sen25-rep3

description:
m-sen25
10092.3_Block3.txt


title: atl_m-sen300-rep3

description:
m-sen300
10092.2_Block2.txt


title: atl_f-sen0.1-rep2

description:
f-sen0.1
10089.2_Block2.txt


title: atl_m-sen0.1-rep4

description:
m-sen0.1
10088.2_Block2.txt


title: atl_f-sen0.1-rep1

description:
f-sen0.1
10089.1_Block1.txt


title: atl_m-sen0.1-rep3

description:
m-sen0.1
10087.4_Block4.txt


title: atl_m-res25-rep4

description:
m-res25
10088.4_Block4.txt


title: atl_m-sen1000-rep4

description:
m-sen1000
10088.3_Block3.txt


title: Esg replicate 2

city: London

first: Tony

middle: David

last: Southall

address: South Kensington Campus

department: Life Sciences

country: United Kingdom

institute: Imperial College London

description: Dam-Esg / Dam-control in adult midguts

hyb_protocol: Hybridisation has been done with HX1 mixer following Nimblegen's procedures

scan_protocol: Arrays were scanned by Nimblegen

data_processing: The  Dam-fusion/Dam log2 ratios were median normalised using NimbleScan software (Nimblegen)

organism: Drosophila melanogaster

source_name: Dam-Esg processed DNA from adult midguts

label_protocol: Labeling has been done using the Nimbelgen Dual-Color Labeling Kit based on a Klenow enzymatic reaction following manufacturer's protocol

growth_protocol: Drosophila were reared at 25oC and midguts dissected from 2-5 days old females.

extract_protocol: Tissues were dissected and placed n 180ul of PBS with 100mM EDTA before samples were processed as previously described (Choksi et al., 2006)

treatment_protocol: Midguts were dissected in standard PBS and immediately frozen on dry ice.

value: w-; + ; UAS-Dam-Esg

tag: cell type

value: adult midguts

source_name: Dam processed DNA from adult midguts

value: w-; UAS-Dam; +


title: atl_m-sen300-rep1

description:
m-sen300
10087.2_Block2.txt

value: male


title: atl_m-sen1000-rep3

description:
m-sen1000
10087.3_Block3.txt


title: atl_m-res0-rep2

description:
m-res0
10074.2_Block2.txt


title: atl_m-res25-rep3

description:
m-res25
10076.2_Block2.txt


title: atl_m-sen1000-rep2

description:
m-sen1000
10075.2_Block2.txt


title: atl_f-sen1000-rep2

description:
f-sen1000
10074.3_Block3.txt


title: atl_f-sen1000-rep3

description:
f-sen1000
10076.3_Block3.txt


title: atl_f-sen300-rep4

description:
f-sen300
10075.4_Block4.txt


title: atl_f-sen300-rep2

description:
f-sen300
10073.2_Block2.txt


title: atl_m-sen0-rep2

description:
m-sen0
10074.4_Block4.txt


title: atl_f-sen0-rep2

description:
f-sen0
10076.4_Block4.txt


title: Esg replicate 1

description: Dam-Esg / Dam-control in adult midguts


title: Esg replicate 3

description: Dam-Esg / Dam-control in adult midguts


title: atl_f-res25-rep1

description:
f-res25
10075.1_Block1.txt


title: atl_f-sen300-rep3

description:
f-sen300
10074.1_Block1.txt


title: atl_f-sen0-rep1

description:
f-sen0
10076.1_Block1.txt


title: atl_m-sen1000-rep1

description:
m-sen1000
10073.4_Block4.txt


title: atl_m-res0.1-rep2

description:
m-res0.1
10073.3_Block3.txt


title: atl_f-res1000-rep2

description:
f-res1000
10087.1_Block1.txt


title: atl_m-res0-rep3

description:
m-res0
10075.3_Block3.txt


title: atl_f-res0.1-rep3

description:
f-res0.1
10073.1_Block1.txt


title: atl_f-res0-rep3

description:
f-res0
10071.3_Block3.txt


title: atl_f-res0-rep2

description:
f-res0
10071.1_Block1.txt


title: atl_f-res1000-rep1

description:
f-res1000
10072.4_Block4.txt


title: atl_f-sen25-rep2

description:
f-sen25
10071.4_Block4.txt


title: atl_m-res25-rep1

description:
m-res25
10070.1_Block1.txt


title: atl_f-sen25-rep1

description:
f-sen25
10070.4_Block4.txt


title: atl_f-res0.1-rep1

description:
f-res0.1
10069.3_Block3.txt


title: atl_f-res300-rep2

description:
f-res300
10070.3_Block3.txt


title: atl_m-sen0-rep1

description:
m-sen0
10069.4_Block4.txt


title: atl_m-sen0.1-rep2

description:
m-sen0.1
10071.2_Block2.txt


title: atl_m-res25-rep2

description:
m-res25
10072.2_Block2.txt


title: atl_m-sen25-rep1

description:
m-sen25
10068.4_Block4.txt


title: atl_m-res0-rep1

description:
m-res0
10070.2_Block2.txt


title: atl_f-sen1000-rep1

description:
f-sen1000
10067.4_Block4.txt


title: atl_m-res1000-rep1

description:
m-res1000
10068.1_Block1.txt


title: atl_f-res0.1-rep2

description:
f-res0.1
10072.1_Block1.txt


title: atl_m-res0.1-rep1

description:
m-res0.1
10067.3_Block3.txt


title: atl_f-sen300-rep1

description:
f-sen300
10068.3_Block3.txt


title: Oa labrum;R

city: Ghent

last: Elewaut

state: België

address: de pintelaan 185

department: Rheumatology

country: Belgium

institute: Ghent University

description: SAMPLE 8

hyb_protocol: After fragmentation cDNA was hybridized for 16h on 45°C on Human GeneChip Gene 1.0 ST array system.GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: Scanned by GeneChip Scanner 3000 7G

data_processing: standard affymetrix expression console software (v.1.1) was used for QC and to generated RMA

source_name: healthy labrum cells

label_protocol: Biotinylation was performed using GeneChip WT sense target labelling assay and reagents according to the manufacturer's instructions.

growth_protocol: Cultured for 7 days in alginate beads system in RPMI medium completed with serum and antibiotics

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

tag: subject id

value: patient R

tag: health condition

value: Healthy

value: acetabular labrum

value: labrum cells

tag: culture age

value: 7 days


title: Control YS-I

city: Des Moines

first: Chunfa

last: Jie

state: IA

address: 3200 Grand Ave

institute: Des Moines University

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using the default quantile normalisation with R/bioconductor package lumi version 2.15.1

source_name: E9.5 Yolk sac

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

growth_protocol: Embryos at day 9.5 of gestation were prepared from a scheduled mating.

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

treatment_protocol: ETV2 was inactivated in FLK1+ cells by a loxP-Cre recombination approach.

tag: strain

value: Embryonic day 9.5

value: Yolk sac


title: atl_m-res300-rep2

description:
m-res300
10069.2_Block2.txt

value: pre-adult lice


title: atl_f-res0-rep1

description:
f-res0
10067.2_Block2.txt

value: reference pool


title: Control YS-II


title: Flk1Cre;ETV2 CKO YS-II


title: Oa labrum;Q

description: SAMPLE 7

value: patient Q


title: atl_m-sen0.1-rep1

description:
m-sen0.1
10068.2_Block2.txt

value: Atlantic Canada

value: sensitive


title: Oa labrum;H

description: SAMPLE 4

source_name: osteoarthritic labrum cells

value: patient H

value: Osteoarthritic


title: Oa labrum;L

description: SAMPLE 6

value: patient L


title: atl_f-res300-rep1

description:
f-res300
10067.1_Block1.txt

value: female

value: resistant


title: control2

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description: sham amputation

hyb_protocol: RNA was hybridized using GeneChip reagents (Affymetrix) and protocols as indicated by the manufacturer

scan_protocol: Expression signals were scanned on an Affymetrix GeneChip Scanner 3000 7G.

data_processing: The CEL files were analyzed using the affy package from R/Bioconductor

source_name: zebrafish heart

label_protocol: Small RNA labeling was performed using FlashTag HSR labeling kit (Genesphere) using 200 ng of small RNA, which was polyA-tailed and biotin conjugated.

growth_protocol: Zebrafish were maintained at 28.5 C following standard methods

extract_protocol: Small RNA (<200 bp) was obtained employing the miRNeasy mini kit (Qiagen)

treatment_protocol: Adult fish were anaesthetized in 0.4% Tricaine and secured, ventral side uppermost, in a slotted sponge. Watchmaker forceps were used to remove the surface scales and penetrate the skin, muscle and pericardial sac. Once exposed, the ventricle was gently pulled at the apex and cut with iridectomy scissors. After surgery, fish were immediately returned to system water.

value: heart


title: Oa labrum;G

description: SAMPLE 3

value: patient G


title: Oa labrum;D

description: SAMPLE 1

value: patient D

value: acetabular labrum


title: amputation1

description: 3 days post-amputation

value: ventricular apex amputation


title: control1

description: sham amputation


title: Oa labrum;E

description: SAMPLE 2

value: patient E

value: labrum cells

value: 7 days


title: Flk1Cre;ETV2 CKO YS-I

value: Embryonic day 9.5

value: Yolk sac


title: Hep3B_shRNA_749

first: Long

last: Yu

address: No.2005, Songhu Road

institute: Fudan University

description: log2 transformed intensity

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028004 SurePrint G3 Human GE 8x60K array(Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: Purified Hep3B cells transfected with shRNA expression plasmid shR-749 targeting UNC50 mRNA (NM_014044.5) at 749bp

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

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's instructions

tag: cell line


title: R_H001

city: Taipei

first: George

last: Hsiao

address: No. 250, Wu-Hsing Str

department: Pharmacology

country: Taiwan

institute: Taipei Medical University

hyb_protocol: Fluorescent targets were hybridized to the Human Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50 ℃, non-speciﬁc binding targets were washed away by three different washing steps (WashⅠ 42 ℃ 5 mins；Wash Ⅱ 42 ℃, 5 mins, 25 ℃ 5 mins; Wash Ⅲ rinse 20 times)

scan_protocol: The arrays were scanned by G2505C (ScanPower=100 n/a, PMTGain=0 n/a) and quantify the fluoresence intensity.

data_processing:
The signal intensity of each spot was loaded into Rosetta Resolver System® (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System® could remove both systematic and random errors form the data. We ﬁltered out spots that the ﬂag is less than 0. Spots that passed the criteria were normalized by 50% media scaling normalization method.Normalize intensities: Median scaling performed on data set without flagged and control data. Merge technical replicate data: Average intensity values calculated on technical replicates.
Calculate average ratios of the hybridization replicates and find significant values for each gene by pairwise comparision (Ranking and hypothesis testing).

source_name: Human THP-1 cells

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (Amersham Pharmacia, Piscataway, NJ, USA).

growth_protocol: Human monocytic cells (THP-1, ATCC) were cultured in RPMI medium 1640 supplemented with 10% heat-inactivated fetal bovine serum (FBS), 100 U/ml penicillin, 100 microg/ml streptomycin and 18 mM HEPES, pH 7.4. Cells were used at 90% confluence, and following treatments were handled in the same medium with 0.5% FBS (Chou et al., 2011).

extract_protocol: RNA extraction by RNeasy Mini kit (Qiagen, Valencia, CA, USA). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧8).

treatment_protocol: Human THP-1 cells were pretreated with vehicle or PBHA (10 μM) before LPS stimulation (50 ng/ml). After 8 hours, the total cellular RNAs were manipulated for microarray assay.

value: treatment with DMSO


title: Oa labrum;I

description: SAMPLE 5

value: patient I


title: KO liver, biological rep3

city: Ann Arbor

first: Jiandie

last: Lin

state: MI

address: 210 Washtenaw Avenue

department: Life Sciences Institute

institute: University of Michigan

description:
Gene expression data from Nrg4 knockout liver, pool 3
Wild type and Neuregulin 4 (Nrg4) knockout mice were fed high-fat diet starting at 3 months of age for eight weeks.

hyb_protocol: Following fragmentation, 7.5 ug of aRNA were hybridized for 16 hr at 45C on MG-430 PM Strip Arrays using the Affymetrix Gene Atlas system (software version 1.0.4.267).

scan_protocol: Strip Arrays were scanned using the Affymetrix Gene Atlas system.

data_processing: Data was analyzed using the limma and affy Bioconductor packages implemented in the R-statistical environment version 2.15.1. RMA was used to normalize the data and fit log2 transformed expression values.

source_name: Nrg4 KO mouse liver

label_protocol: Biotinylated aRNA were prepared according to the Affymetrix GeneChip 3' IVT Express kit protocol from 250 ng total RNA (Affymetrix GeneChip 3' IVT Express kit Instruction Manual, P/N 702646 Rev. 5).

treatment_protocol: Liver tissues were harvested under random fed condition.

value: liver

tag: genotype/variation

value: Nrg4 knockout

tag: diet

value: high-fat diet fed starting at 3 months of age for eight weeks.


title: amputation2

description: 3 days post-amputation


title: Hep3B_shRNA_554

description: log2 transformed intensity

source_name: Purified Hep3B cells transfected with shRNA expression plasmid shR-554 targeting UNC50 mRNA (NM_014044.5) at 554bp


title: V_H004

value: treatment with DMSO and LPS stimulation


title: amputation3

description: 3 days post-amputation


title: V_H003


title: Hep3B_shRNA_mock

description: log2 transformed intensity

source_name: Purified Hep3B cells transfected with mock shRNA expression plasmid


title: P_H008

value: treatment with PBHA and LPS stimulation


title: R_H002


title: Hep3B_shRNA_467

description: log2 transformed intensity

source_name: Purified Hep3B cells transfected with shRNA expression plasmid shR-467 targeting UNC50 mRNA (NM_014044.5) at 467bp


title: P_H007


title: KO liver, biological rep2

description:
Gene expression data from Nrg4 knockout liver, pool 2
Wild type and Neuregulin 4 (Nrg4) knockout mice were fed high-fat diet starting at 3 months of age for eight weeks.


title: Irf8KO_Flt3+ GPs_exp2

city: Yokohama

first: Tomohiko

last: Tamura

address: 3-9 Fukuura, Kanazawa-ku

department: Department of Immunology

country: Japan

institute: Yokohama City University

hyb_protocol: Slides were hybridized according to the manufacturer's protocol (One-Color Microarray-Based Gene Expression Analysis Protocol, Product # G4140-90040, Version 6.5, May 2010).

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-60502) at 100% in Green channel, with a scan resolution of 3 um.

data_processing: Data are extracted with Agilent Feature Extraction Software and normalized.

source_name: Irf8KO Flt3+ GPs, isolated from bone marrow cells, experiment 2

label_protocol: Total RNA was labeled using the Agilent Low Input Quick Amp Labeling Kit according to the manufacturer's instructions.

growth_protocol: GPs were isolated from bone marrow cells.

extract_protocol: Total RNA was extracted using RNeasy Micro Kit (Qiagen) according to the manufacturers' instructions.

value: Bone marrow derived Flt3+ GPs

value: Primary isolated cells


title: WT liver, biological rep3

description:
Gene expression data from wild type liver, pool 3
Wild type and Neuregulin 4 (Nrg4) knockout mice were fed high-fat diet starting at 3 months of age for eight weeks.

source_name: Wild type mouse liver

value: wild type


title: Irf8KO_Flt3- GPs_exp2

source_name: Irf8KO Flt3- GPs, isolated from bone marrow cells, experiment 2

value: Bone marrow derived Flt3- GPs


title: Irf8KO_Flt3- GPs_exp1

source_name: Irf8KO Flt3- GPs, isolated from bone marrow cells, experiment 1


title: Irf8KO_Flt3+ GPs_exp1

source_name: Irf8KO Flt3+ GPs, isolated from bone marrow cells, experiment 1


title: atl_m-res300-rep1

description:
m-res300
10069.1_Block1.txt

source_name: Atlantic Canada_male_resistant

value: Atlantic Canada

value: pre-adult lice

value: male

value: resistant

source_name: all condition pool

value: reference pool


title: KO liver, biological rep1

description:
Gene expression data from Nrg4 knockout liver, pool 1
Wild type and Neuregulin 4 (Nrg4) knockout mice were fed high-fat diet starting at 3 months of age for eight weeks.


title: WT liver, biological rep1

description:
Gene expression data from wild type liver, pool 1
Wild type and Neuregulin 4 (Nrg4) knockout mice were fed high-fat diet starting at 3 months of age for eight weeks.


title: WT_Flt3- GPs_exp2

source_name: WT Flt3- GPs, isolated from bone marrow cells, experiment 2


title: WT_Flt3- GPs_exp1

source_name: WT Flt3- GPs, isolated from bone marrow cells, experiment 1


title: WT_Flt3+ GPs_exp2

source_name: WT Flt3+ GPs, isolated from bone marrow cells, experiment 2


title: RAS-OFF_96_hr_2

status: Public on Nov 16 2014

city: Minneapolis

first: Rebecca

last: LaRue

state: MN

address: 117 Pleasant St SE

department: Department of Lab medicine and Pathology

institute: University of Minnesota

description: Gene expression data from NRASG12V/Mll-AF9 Primary AML, doxcycline-treated (NRASG12V off) 96 hours replicate 2

hyb_protocol: 15 mg labeled cRNA under standard conditions (Affymetrix, Santa Clara, CA)

scan_protocol: Standard (Affymetrix, Santa Clara, CA)

data_processing: Normalization of data and generation of values was performed using Genedata Expressionist software package. Normalization was performed using the Bioconductor RMA method using the Genedata Refiner Array 7.6.

label_protocol: MessageAmpTM III RNA Amplification Kit (Ambion, Austin, TX)

growth_protocol: SCID/Beige mice were injected with NRASG12V/Mll-AF9 leukemia cells via tail vein and aged to develop full blown leukemia (20 days, WBC > 100,000/ul)

extract_protocol: Qiagen Rnesay RNA extraction (QIAGEN, Valencia, CA)

treatment_protocol: Doxycycline intraperitoneal injections at time 0 and doxycycline drinking water at time 0 until sacrifice.

value: Primary AML cells extracted from leukemic spleens

tag: genotype


title: RAS-OFF_60_hr_2

description: Gene expression data from NRASG12V/Mll-AF9 Primary AML, doxcycline-treated (NRASG12V off) 60 hours replicate 2


title: RAS-OFF_72_hr_1

description: Gene expression data from NRASG12V/Mll-AF9 Primary AML, doxcycline-treated (NRASG12V off) 72 hours replicate 1


title: RAS-OFF_96_hr_1

description: Gene expression data from NRASG12V/Mll-AF9 Primary AML, doxcycline-treated (NRASG12V off) 96 hours replicate 1


title: RAS-OFF_72_hr_2

description: Gene expression data from NRASG12V/Mll-AF9 Primary AML, doxcycline-treated (NRASG12V off) 72 hours replicate 2


title: WT_Flt3+ GPs_exp1

source_name: WT Flt3+ GPs, isolated from bone marrow cells, experiment 1


title: RAS-OFF_60_hr_1

description: Gene expression data from NRASG12V/Mll-AF9 Primary AML, doxcycline-treated (NRASG12V off) 60 hours replicate 1


title: RAS-OFF_84_hr_2

description: Gene expression data from NRASG12V/Mll-AF9 Primary AML, doxcycline-treated (NRASG12V off) 84 hours replicate 2


title: RAS-OFF_48_hr_1

description: Gene expression data from NRASG12V/Mll-AF9 Primary AML, doxcycline-treated (NRASG12V off) 48 hours replicate 1


title: RAS-OFF_48_hr_2

description: Gene expression data from NRASG12V/Mll-AF9 Primary AML, doxcycline-treated (NRASG12V off) 48 hours replicate 2


title: RAS-ON_0_hr_5

description: Gene expression data from NRASG12V/Mll-AF9 Primary AML, vehicle-treated 0 hour replicate 5


title: RAS-ON_0_hr_3

description: Gene expression data from NRASG12V/Mll-AF9 Primary AML, vehicle-treated 0 hour replicate 3


title: RAS-OFF_84_hr_1

description: Gene expression data from NRASG12V/Mll-AF9 Primary AML, doxcycline-treated (NRASG12V off) 84 hours replicate 1


title: RAS-ON_0_hr_4

description: Gene expression data from NRASG12V/Mll-AF9 Primary AML, vehicle-treated 0 hour replicate 4


title: RAS-ON_0_hr_1

description: Gene expression data from NRASG12V/Mll-AF9 Primary AML, vehicle-treated 0 hour replicate 1


title: WT liver, biological rep2

description:
Gene expression data from wild type liver, pool 2
Wild type and Neuregulin 4 (Nrg4) knockout mice were fed high-fat diet starting at 3 months of age for eight weeks.


title: RAS-ON_0_hr_2

description: Gene expression data from NRASG12V/Mll-AF9 Primary AML, vehicle-treated 0 hour replicate 2


title: MP2816

status: Public on Nov 15 2014

city: Boston

first: Daria

last: Van Tyne

address: 243 Charles Street

institute: Harvard Medical School

hyb_protocol: Nanostring standard protocols for processing cell lysate and total RNA samples (proprietary)

scan_protocol: nCounter prep station and nCounter digital analyzer

data_processing: Raw counts from the nCounter machine are reported; no normalization or scaling has been done

source_name: in vivo human blood

tag: experiment

value: in vivo peripheral blood sample


title: MP2781

label_protocol: Nanostring standard protocols for processing cell lysate and total RNA samples (proprietary)


title: MP2785

extract_protocol: Nanostring standard protocols for processing cell lysate and total RNA samples (proprietary)


title: MP2798


title: MP2783


title: MP2801


title: MP2797


title: MP2713


title: MP2712B


title: MP2712C


title: MP2786


title: MP2820


title: MP2760


title: MP2789


title: MP2809


title: MP2931


title: MP2782


title: MP2788


title: MP2791


title: MP2826


title: MP2790


title: MP2759


title: MP2745


title: MP2708


title: IVF-2

city: Setagaya-ku

first: Atsushi

last: Fukuda

state: Tokyo

department: Reproductive biology

institute: National Center for Child Health and Development

description: Gene expression at late blastocyst stage in mice

hyb_protocol: For each hybridization, 1.3μg of Cy3 labeled cDNA were fragmented, and hybridized at 65 ℃ for 17 hours to an Agilent SurePrint G3 Mouse GE 8x60K Microarray.

scan_protocol: Microarrays were scanned using an Agilent DNA microarray scanner.

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software and further analyzed using GeneSpring GX software version 12.5. Data were normalized to the 75 th percentile (median).

source_name: in vitro fertilized blastocysts

label_protocol: 5μl of total RNA was amplified using Ovation® RNA Amplification System V2 (NuGEN Technologies, Inc.) following the manufacturer's instructions. Amplified cDNA were labeled with Cy3 using Agilent SureTag DNA Labeling Kit (Agilent Technologies) following the manufacturer's instructions.

growth_protocol: Ca2+ free M16 medium containing 8 mM SrCl2 and 5 µg/ml cytochalasin B 5μg/ml were used to generate parthenogetic embryos. All embryos used in this study were culutured in KSOM medium at 37°C in 5% CO2.

extract_protocol: The total RNA was isolated from cells using the Isogen reagent (NipponGene) following the manufacturer's recommendations.

treatment_protocol: in vitro synthesised mRNA with poly A were injected into MII oocytes and then activated for 6 hours.

value: BDF1 hybrid

value: in vitro fertilized blastocysts

tag: developmental stage

value: pooled blastocysts (day 5)

tag: age

value: 8-10 weeks


title: MP2825


title: IVF-1


title: MP2824


title: MP2821


title: MP2815


title: MP2800


title: MP2784


title: MP2775


title: MP2807


title: MP2763


title: Egfp-PEs-3

source_name: Egfp overexpressed parthenogenetic blastocysts


title: MP2794


title: MP2777


title: Egfp-PEs-2

value: Egfp overexpressed parthenogenetic blastocysts


title: Kdm4b-PEs-3

source_name: Kdm4b overexpressed parthenogenetic blastocysts


title: Egfp-PEs-1


title: MP2762


title: Kdm4b-PEs-1

value: Kdm4b overexpressed parthenogenetic blastocysts


title: MP2754


title: MP2755


title: MP2761


title: MP2753


title: MP2749


title: embryonic secondary neurospheres, WT genotype 4

city: Toronto

first: Freda

last: Miller

state: Ontario

address: 686 Bay Street

department: Neurosciences and Mental Health

institute: Hospital for Sick Children

hyb_protocol: 5.5ug of labeled cDNA was hybridized onto Mouse Gene ChIP 2.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000

data_processing: The data was analyzed using Partek Genomics Suite 6.6 using default settings

label: Biotin

source_name: WT_E14.5 cortical secondary neurospheres

label_protocol: biotinylated cDNA was generated using standard Affymetrix protocol and Ambion WT kit from 250ng of total RNA.

growth_protocol: The E14 neocortex was triturated in serum-free medium containing 20 ng/mL EGF (Sigma), 10 ng/mL FGF2 (Sigma), and 2 mg/mL heparin (Sigma). Cells were plated at 50 cells/ul for 6 days. After 6 days in culture, primary neurospheres were triturated and plated at 50 cells/ul for additional 5 days. Seconday neurospheres 5 days post passage were used to extract RNA.

extract_protocol: Total RNA was extracted using E.Z.N.A. total RNA or MicroElute Total RNA kit (Omega Biotek).

treatment_protocol: Cells were grown as neurospheres using a standard protocol (Coles-Takabe et al., 2008) in 20 ng/mL EGF (Sigma), 10 ng/mL FGF2 (Sigma), and 2 mg/mL heparin (Sigma), except at density 50 cells/ul

tag: strain background

value: WT

tag: embryonic age

value: cortex

value: embryonic secondary neurospheres


title: embryonic secondary neurospheres, WT genotype 1


title: embryonic secondary neurospheres, Ankrd11Yod/+ genotype 3

source_name: Ankrd11Yod/+_E14.5 cortical secondary neurospheres


title: MP2743


title: MP2741


title: MP2728


title: MP2724


title: MP2733


title: MP2747


title: embryonic secondary neurospheres, Ankrd11Yod/+ genotype 2


title: MP2717


title: embryonic secondary neurospheres, WT genotype 3


title: embryonic secondary neurospheres, Ankrd11Yod/+ genotype 4


title: embryonic secondary neurospheres, Ankrd11Yod/+ genotype 1


title: Kdm4b-PEs-2


title: MP2707


title: MP2729


title: 4 Brain

source_name: in vivo human brain

value: in vivo tissue sample


title: 4 Heart

source_name: in vivo human heart


title: MP2720


title: 2E Gut

source_name: in vivo human gut


title: 2D Heart


title: 2E Heart


title: 2D Gut


title: MP2793


title: 4 Gut


title: 2C Heart


title: 2C Lung

source_name: in vivo human lung


title: 2D Brain


title: 2C Gut


title: 2B Brain


title: 3D7 Schiz rep2

type: other

description: crude cell lysate

molecule: other

source_name: in vitro human blood

value: in vitro time course schizont


title: 3D7 Schiz rep1

description: crude cell lysate


title: 2C Brain


title: 2B Blood


title: 2B Heart


title: 2B Gut


title: embryonic secondary neurospheres, WT genotype 5


title: 3D7 Ring rep2

description: crude cell lysate

value: in vitro time course ring


title: 2E Brain


title: 3D7 Ring rep1

description: crude cell lysate


title: Endogenous beta cell_3

city: Cambridge

first: Kendell

last: Clement

state: MA

address: 7 Divinity Ave.

institute: Harvard University

description: replicate 3

hyb_protocol: Hyb protocol for Illumina MouseRef-8 v2.0 expression beadchip

scan_protocol: Scan protocol for Illumina MouseRef-8 v2.0 expression beadchip

data_processing: The raw signal was transformed to logarithm scale (log10).

source_name: Pancreas_endogenous beta cell

label_protocol: label protocol for Illumina MouseRef-8 v2.0 expression beadchip

growth_protocol: Rag1-/- were obtained from Jackson Labs.  For β- cell induction, 100ul (>1x 109 pfu) of purified adenovirus was directly injected into the splenic lobe of the dorsal pancreas.

extract_protocol: Cherry+  induced beta cells were isolated by fluorescent activated cell sorting (FACS) with FACSaria (BD Bioscience), RNA samples were extracted by Trizol

treatment_protocol: Pancreata were perfused through the common bile duct.  After removing endogenous islets, the acinar fraction was digested with liberase and Elastase (Roche) into single cells.

value: Pancreas

value: Endogenous beta cell


title: 3D7 FFPE Processed

description: crude cell lysate

value: mock in vitro FFPE sample processed


title: Induced beta cell 7m_1

description: replicate 1

source_name: Pancreas_induced beta cell_7m

value: Induced beta cell 7m


title: 3D7 FFPE Lysate

description: crude cell lysate

value: mock in vitro FFPE sample lysate


title: Induced beta cell d60_3

description: replicate 3

source_name: Pancreas_induced beta cell_d60

value: Induced beta cell d60


title: Endogenous beta cell_1

description: replicate 1


title: Induced beta cell 7m_3

description: replicate 3


title: 3D7 Schizont 400000

description: crude cell lysate

value: in vitro dilution for platform limit of detection


title: 3D7 Schizont 100000

description: crude cell lysate


title: 3D7 Filter paper Lysate

description: crude cell lysate

value: mock in vitro filter paper sample lysate


title: Induced beta cell 7m_2

description: replicate 2


title: Induced beta cell d10_1

description: replicate 1

source_name: Pancreas_induced beta cell_d10

value: Induced beta cell d10


title: 3D7 Schizont 25000

description: crude cell lysate


title: Induced beta cell d10_2

description: replicate 2


title: Endogenous beta cell_2

description: replicate 2


title: Induced beta cell d10_3

description: replicate 3


title: Induced beta cell d60_1

description: replicate 1


title: Induced beta cell d30_1

description: replicate 1

source_name: Pancreas_induced beta cell_d30

value: Induced beta cell d30


title: embryonic secondary neurospheres, Ankrd11Yod/+ genotype 5


title: Induced beta cell d60_2

description: replicate 2


title: Induced beta cell d30_3

description: replicate 3


title: embryonic secondary neurospheres, Ankrd11Yod/+ genotype 6


title: Acinar_1

description: replicate 1

value: Acinar


title: embryonic secondary neurospheres, WT genotype 2

value: WT


title: Acinar_3

description: replicate 3


title: 3D7 Filter paper Processed

description: crude cell lysate

value: mock in vitro filter paper sample processed


title: Acinar_2

description: replicate 2


title: Induced beta cell d30_2

description: replicate 2


title: 3D7 Schizont 6250

description: crude cell lysate


title: 3D7 Schizont 1563

description: crude cell lysate


title: 3D7 Ring 400000

description: crude cell lysate


title: 3D7 Schizont 390

description: crude cell lysate


title: 3D7 Ring 100000

description: crude cell lysate


title: 3D7 Ring 25000

description: crude cell lysate


title: LTR-12-3

city: Beijing

first: Huifen

last: Xi

address: Nanxincun 20, Xiangshan Southern Road

department: Institute of Botany

institute: Chinese Academy of Sciences

hyb_protocol: A 10 μg fragmented cRNA with control was hybridized to each GeneChip array at 45°C for 16 h (Affymetrix Gene Chip Hybridization Oven 640) according to the manufacturer’s instructions

scan_protocol: After hybridization, the GeneChip arrays were washed, and then stained with streptavidin phycoerythrinonan (SAPE) with an Affymetrix Fluidics Station 450 followed by scanning with an Affymetrix GeneChip Scanner 3000 7 G.

data_processing: Microarray data processing produced microarray image files (CEL). The signal intensities of each feature were backgroud adjusted and normalized via the quantile normalization performed by Robust Multichip Analysis（RMA). For defining differentially expressed probe sets, two unpaired two group comparisons for all probe sets between 0 and 6 h as well as between 0 and 12 h were performed via significance analysis of microarrays (SAM 2.10)

organism: Vitis vinifera

source_name: leaves

label_protocol: Briefly, 200 ng of total RNA was used for cDNA synthesis, and produced biotin-tagged cRNA with MessageAmpTM Premier RNA Amplification Kit (Ambion)

growth_protocol: Vines of V. vinifera ‘Hongbaladuo’ were used in the experiments, and were grown in the vineyard at the Institute of Botany, Chinese Academy of Sciences, Beijing. Mature (30-day old), healthy leaves with similar size were detached from the shoot at 08:00-09:00, the leaf petioles were immediately inserted into water in the bucket, and re-cut under water to about 6 cm, then rapidly transferred from water bucket to triangular flasks containing ddH2O.

extract_protocol: Total RNA were extracted from grape leaves using Trizol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions, and digested with DNase I at 37°C for 15 min to remove any contaminating DNA. The RNA was cleaned up with RNeasy Kit (Qiagen, Hilden, Germany), and the quantities and qualities were determined by spectrophotometry and 1% formaldehyde denaturing gel electrophoresis. The samples with bright bands of ribosomal 28S to 18S RNA in a ratio >1.5:1 were used for microarray analysis.

treatment_protocol: All leaves were incubated in the dark at 25oC for half an hour, then the leaf abaxial surfaces were exposed for 10 min to 6 W•m-2 UV-C irradiation provided by a UV-C lamp (Model ZW30S26W, Beijing Lighting Research Institute, China) , then the leaves remained in the flasks until sampling. Samples were collected at 0,6 and 12 h after the initiation of treatment, respectively. All treatments and controls were replicated 3 times, and each replicate consisted of 6 leaves

value: 12 h after the initiation of treatment

value: 30 days old, detached


title: 3D7 Ring 6250

description: crude cell lysate


title: 3D7 Ring 1563

description: crude cell lysate


title: LTR-6-2

value: 6 h after the initiation of treatment


title: Embryonic_day15_DS6_Ts1Cje

city: Medford

first: Heather

middle: C

last: Wick

address: 161 College Ave

department: Department of Computer Science

institute: Tufts University

hyb_protocol: Arrays were washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Hybridization, Wash and Stain Kit according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).

scan_protocol: Arrays were scanned on a GeneArray Scanner 3000 7G, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).

data_processing: Quality control and normalization were performed using the pipeline at the www.arrayanalysis.org website (Maastricht University, the Netherlands). Normalization was done using the Robust Multichip Average (RMA) algorithm and the MBNI custom CDF (http://brainarray.mbni.med.umich.edu/) version #14 for the mouse gene 1.0 ST array. Normalization output consisted of data for 21225 probe sets each corresponding to unique Entrez Gene IDs. Embryonic brain gene expression changes were compared to our previously published adult cerebral cortex and hippocampus dataset (GSE49635).

label_protocol: Samples were labeled with Biotin Allonamide Triphosphate according to the GeneChip Whole Transcriptome Labeling and Hybridization protocol (http://www.affymetrix.com) combining the Ambion WT Expression kit (Life Technologies, Grand Island, NY) and the Affymetrix GeneChip Terminal Labeling Kit (Affymetrix, Santa Clara, CA).

growth_protocol: Mice were housed in standard cages with food and water ad libitum under a controlled environment (temperature = 20°C; humidity = 60%) and a light/dark cycle of 12h. Ts1Cje males were backcrossed to C57Bl/6J females for several generations before experiments started. Ts1Cje males were crossed with C57Bl/6J females (Jackson Laboratories, Bar Harbor, ME) and the presence of a vaginal plug was defined as embryonic day 0.5 (E0.5) and 10-15% weight gain at embryonic day 10 as described previously (Kirby et al,2010). Pregnant females were anesthetized with 2.5% isoflurane in a 3/7 02/N2O mixture and euthanized by decapitation at embryonic day E15.5 (E15.5). Embryos were extracted and decapitated in ice-cold phosphate-buffered-saline (PBS1X). Embryonic brains were rapidly removed and brain hemispheres dissected on a cold platform and snap frozen in liquid nitrogen before storage at -80°C.

extract_protocol: On embryonic day 15, Ts1Cje embryos (N=5) and their wild-type littermates (N=5) were extracted and decapitated in ice cold PBS containing RNA later stanilization solution. Embryonic forebrain was dissected and snap frozen in liquid nitrogen before storage at -80°C. Total RNA was isolated using the NucleoSpin RNA II kits following the manufacturer’s instructions (Macherey-Nagel, Bethlehem, PA). RNA concentrations were measured as absorbance at 260 nm on the Nanodrop instrument (Thermo Fisher Scientific, Waltham, MA). RNA quality was analyzed with the Bioanalyzer (Agilent Biotechnologies, Santa Clara, CA) using the RNA 6000 Nano kit according to the manufacturer’s instructions. Only samples displaying an A260/A280 ratio of 2.0-2.1 and a RIN (RNA Integrity Number) > 9 were used for hybridization to the arrays.

value: Ts1Cje male crossed with C57Bl/6J female

tag: gender

value: Male

value: embryonic day 15

value: forebrain


title: 3D7 Ring 390

description: crude cell lysate


title: Embryonic_day15_DS4_Ts1Cje

value: Female

tag: tissue


title: Embryonic_day15_DS12_Ts1Cje


title: LCK-0-3

tag: treatment

value: 0 h after the initiation of treatment


title: LCK-0-1


title: Embryonic_day15_DS1_Ts1Cje


title: LTR-6-3


title: LTR-12-1


title: Embryonic_day15_WT15_Ts1Cje

value: wild type


title: LTR-6-1


title: Embryonic_day15_WT5_Ts1Cje


title: Embryonic_day15_WT11_Ts1Cje


title: Embryonic_day15_DS14_Ts1Cje


title: LCK-0-2


title: Embryonic_day15_WT9_Ts1Cje


title: Embryonic_day15_WT7_Ts1Cje


title: MUO7

status: Public on Nov 14 2014

city: Guelph

first: David

middle: M

last: Mutch

address: 50 Stone Road East

department: Human Health & Nutritional Sciences

institute: University of Guelph

description:
Gene expression data from human periumbilical subcutaneous tissue
DRA_26

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 20 hr on Human Gene 2.1 ST arrays incubated at 48C. GeneChips were washed and stained using the Gene Atlas Fluidics Station.

scan_protocol: HuGene 2.1 ST arrays were scanned using the Gene Atlas Imaging Station.

data_processing: Data was analyzed with R/Bioconductor software and normalized using RMA. An ANOVA was used to identify differentially expressed genes. An FDR of 0.05 was used to account for multiple testing.

source_name: Subcutaneous adipose fasting

label_protocol: Biotinylated cRNA was prepared from 100 ng total RNA according to the standard Affymetrix protocol (WT Expression Kit User Manual, 2010, Affymetrix).

extract_protocol: Total RNA was extracted after homogenisation in TRIzol with a tissue homogenizer and using the Qiagen RNeasy Mini Kit (Qiagen, Mississauga, ON, Canada), according to manufacturer's instruction.

treatment_protocol: Samples were collected after an overnight fast (12h)

value: Subcutaneous adipose

tag: disease state

value: metabolically unhealthy obese MUO


title: MUO4

description:
Gene expression data from human periumbilical subcutaneous tissue
DRA_15


title: MUO9

description:
Gene expression data from human periumbilical subcutaneous tissue
DRA_28


title: MUO10

description:
Gene expression data from human periumbilical subcutaneous tissue
DRA_31


title: MUO2

description:
Gene expression data from human periumbilical subcutaneous tissue
DRA_7


title: MUO1

description:
Gene expression data from human periumbilical subcutaneous tissue
DRA_1


title: MUO6

description:
Gene expression data from human periumbilical subcutaneous tissue
DRA_18


title: MHO9

description:
Gene expression data from human periumbilical subcutaneous tissue
DRA_29

value: metabolically healthy obese MHO


title: MHO7

description:
Gene expression data from human periumbilical subcutaneous tissue
DRA_21


title: MHO6

description:
Gene expression data from human periumbilical subcutaneous tissue
DRA_20


title: LTR-12-2


title: MUO8

description:
Gene expression data from human periumbilical subcutaneous tissue
DRA_27


title: LH6

description:
Gene expression data from human periumbilical subcutaneous tissue
DRA_16

value: lean healthy LH


title: LH1

description:
Gene expression data from human periumbilical subcutaneous tissue
DRA_2


title: MHO1

description:
Gene expression data from human periumbilical subcutaneous tissue
DRA_3


title: LH2

description:
Gene expression data from human periumbilical subcutaneous tissue
DRA_4


title: MHO2

description:
Gene expression data from human periumbilical subcutaneous tissue
DRA_5


title: LH5

description:
Gene expression data from human periumbilical subcutaneous tissue
DRA_14


title: LH9

description:
Gene expression data from human periumbilical subcutaneous tissue
DRA_23


title: MHO3

description:
Gene expression data from human periumbilical subcutaneous tissue
DRA_6


title: MHO4

description:
Gene expression data from human periumbilical subcutaneous tissue
DRA_8


title: LH4

description:
Gene expression data from human periumbilical subcutaneous tissue
DRA_13


title: MHO10

description:
Gene expression data from human periumbilical subcutaneous tissue
DRA_30


title: LH7

description:
Gene expression data from human periumbilical subcutaneous tissue
DRA_19


title: Colorectal cancer tissue sample (FFPE) 348

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

description:
CAIRO2 arm A: capecitabine, oxaliplatin and bevacizumab
Normal colon mucosa from the same patient as the tumor was used as reference in the aCGH experiments.

hyb_protocol: Hybridization protocol available via www.agilent.com.

scan_protocol: Slides were scanned using the Agilent microarray scanner, protocol according to Agilent.

data_processing: The profiles were dewaved (van de wiel et al., Bioinformatics. 2009 (PMID 19276148)), median normalized and corrected for tumor cell percentage by using the R package CGHcall (van de Wiel et al., Bioinformatics. 2007 (PMID 17267432)).

source_name: colorectal cancer, CAIRO2 arm A

label_protocol: DNA labeling protocol according to Enzo Life Sciences.

extract_protocol: DNA isolation protocol available via www.vumc.nl/microarrays. Also described in Brosens et al., J Pathol. 2010 (PMID 20593488).

value: colorectal cancer (FFPE)

tag: study

tag: study arm

value: A

tag: progression-free survival first line (days)

tag: progression

value: yes

source_name: normal colorectum mucosa

value: normal colon mucosa

tag: patient

value: same patient as in ch1

tag: sample type

value: reference


title: Colorectal cancer tissue sample (FFPE) 345


title: Colorectal cancer tissue sample (FFPE) 336


title: Colorectal cancer tissue sample (FFPE) 339


title: Colorectal cancer tissue sample (FFPE) 341


title: Colorectal cancer tissue sample (FFPE) 346


title: Colorectal cancer tissue sample (FFPE) 344


title: Colorectal cancer tissue sample (FFPE) 333


title: Colorectal cancer tissue sample (FFPE) 337


title: Colorectal cancer tissue sample (FFPE) 338


title: Colorectal cancer tissue sample (FFPE) 329


title: Colorectal cancer tissue sample (FFPE) 326


title: Colorectal cancer tissue sample (FFPE) 332

value: no


title: Colorectal cancer tissue sample (FFPE) 321


title: Colorectal cancer tissue sample (FFPE) 327


title: Colorectal cancer tissue sample (FFPE) 325


title: Colorectal cancer tissue sample (FFPE) 334


title: Colorectal cancer tissue sample (FFPE) 343


title: Colorectal cancer tissue sample (FFPE) 342


title: Colorectal cancer tissue sample (FFPE) 340


title: Colorectal cancer tissue sample (FFPE) 349


title: Colorectal cancer tissue sample (FFPE) 322


title: Colorectal cancer tissue sample (FFPE) 330


title: Colorectal cancer tissue sample (FFPE) 347


title: Colorectal cancer tissue sample (FFPE) 328


title: Colorectal cancer tissue sample (FFPE) 320


title: Colorectal cancer tissue sample (FFPE) 323


title: Colorectal cancer tissue sample (FFPE) 335


title: Colorectal cancer tissue sample (FFPE) 331


title: Colorectal cancer tissue sample (FFPE) 324


title: Colorectal cancer tissue sample (FFPE) 319


title: Colorectal cancer tissue sample (FFPE) 313


title: Colorectal cancer tissue sample (FFPE) 310


title: Colorectal cancer tissue sample (FFPE) 314


title: Colorectal cancer tissue sample (FFPE) 307


title: Colorectal cancer tissue sample (FFPE) 317


title: Colorectal cancer tissue sample (FFPE) 304


title: Colorectal cancer tissue sample (FFPE) 316


title: Colorectal cancer tissue sample (FFPE) 298


title: Colorectal cancer tissue sample (FFPE) 299


title: Colorectal cancer tissue sample (FFPE) 303


title: Colorectal cancer tissue sample (FFPE) 306


title: Colorectal cancer tissue sample (FFPE) 311


title: Colorectal cancer tissue sample (FFPE) 308


title: Colorectal cancer tissue sample (FFPE) 295


title: Colorectal cancer tissue sample (FFPE) 300


title: Colorectal cancer tissue sample (FFPE) 302


title: Colorectal cancer tissue sample (FFPE) 296


title: Colorectal cancer tissue sample (FFPE) 309


title: Colorectal cancer tissue sample (FFPE) 292


title: Colorectal cancer tissue sample (FFPE) 305


title: Colorectal cancer tissue sample (FFPE) 301


title: Colorectal cancer tissue sample (FFPE) 294


title: Colorectal cancer tissue sample (FFPE) 293


title: Colorectal cancer tissue sample (FFPE) 291


title: Colorectal cancer tissue sample (FFPE) 297


title: Colorectal cancer tissue sample (FFPE) 290


title: Colorectal cancer tissue sample (FFPE) 288


title: Colorectal cancer tissue sample (FFPE) 289


title: Colorectal cancer tissue sample (FFPE) 284


title: Colorectal cancer tissue sample (FFPE) 287


title: Colorectal cancer tissue sample (FFPE) 286


title: Colorectal cancer tissue sample (FFPE) 278


title: Colorectal cancer tissue sample (FFPE) 272


title: Colorectal cancer tissue sample (FFPE) 273


title: Colorectal cancer tissue sample (FFPE) 285


title: Colorectal cancer tissue sample (FFPE) 283


title: Colorectal cancer tissue sample (FFPE) 275


title: Colorectal cancer tissue sample (FFPE) 263


title: Colorectal cancer tissue sample (FFPE) 280


title: Colorectal cancer tissue sample (FFPE) 282


title: Colorectal cancer tissue sample (FFPE) 276


title: Colorectal cancer tissue sample (FFPE) 279


title: Colorectal cancer tissue sample (FFPE) 265


title: Colorectal cancer tissue sample (FFPE) 277


title: Colorectal cancer tissue sample (FFPE) 266


title: Colorectal cancer tissue sample (FFPE) 274


title: Colorectal cancer tissue sample (FFPE) 264


title: Colorectal cancer tissue sample (FFPE) 269


title: Colorectal cancer tissue sample (FFPE) 281


title: Colorectal cancer tissue sample (FFPE) 270


title: Colorectal cancer tissue sample (FFPE) 267


title: Colorectal cancer tissue sample (FFPE) 262


title: Colorectal cancer tissue sample (FFPE) 271


title: Colorectal cancer tissue sample (FFPE) 268


title: Colorectal cancer tissue sample (FFPE) 315


title: Colorectal cancer tissue sample (FFPE) 261


title: Colorectal cancer tissue sample (FFPE) 312


title: Colorectal cancer tissue sample (FFPE) 258


title: Colorectal cancer tissue sample (FFPE) 255


title: Colorectal cancer tissue sample (FFPE) 254


title: Colorectal cancer tissue sample (FFPE) 256


title: Colorectal cancer tissue sample (FFPE) 249


title: Colorectal cancer tissue sample (FFPE) 251


title: Colorectal cancer tissue sample (FFPE) 252


title: Colorectal cancer tissue sample (FFPE) 253


title: Colorectal cancer tissue sample (FFPE) 242


title: Colorectal cancer tissue sample (FFPE) 250


title: Colorectal cancer tissue sample (FFPE) 247


title: Colorectal cancer tissue sample (FFPE) 244


title: Colorectal cancer tissue sample (FFPE) 248


title: Colorectal cancer tissue sample (FFPE) 238


title: Colorectal cancer tissue sample (FFPE) 246


title: Colorectal cancer tissue sample (FFPE) 257


title: Colorectal cancer tissue sample (FFPE) 245


title: Colorectal cancer tissue sample (FFPE) 241


title: Colorectal cancer tissue sample (FFPE) 260


title: Colorectal cancer tissue sample (FFPE) 240


title: Colorectal cancer tissue sample (FFPE) 239


title: Colorectal cancer tissue sample (FFPE) 235


title: Colorectal cancer tissue sample (FFPE) 237


title: Colorectal cancer tissue sample (FFPE) 318


title: Colorectal cancer tissue sample (FFPE) 234


title: Colorectal cancer tissue sample (FFPE) 230


title: Colorectal cancer tissue sample (FFPE) 229


title: Colorectal cancer tissue sample (FFPE) 231


title: Colorectal cancer tissue sample (FFPE) 243


title: Colorectal cancer tissue sample (FFPE) 227


title: Colorectal cancer tissue sample (FFPE) 236


title: Colorectal cancer tissue sample (FFPE) 228


title: Colorectal cancer tissue sample (FFPE) 232


title: Colorectal cancer tissue sample (FFPE) 233


title: Colorectal cancer tissue sample (FFPE) 222


title: Colorectal cancer tissue sample (FFPE) 219


title: Colorectal cancer tissue sample (FFPE) 226


title: Colorectal cancer tissue sample (FFPE) 220


title: Colorectal cancer tissue sample (FFPE) 216

description:
CAIRO arm A: capecitabine first line
Normal colon mucosa from the same patient as the tumor was used as reference in the aCGH experiments.

source_name: colorectal cancer, CAIRO arm A

value: CAIRO


title: Colorectal cancer tissue sample (FFPE) 225


title: Colorectal cancer tissue sample (FFPE) 215


title: Colorectal cancer tissue sample (FFPE) 224


title: Colorectal cancer tissue sample (FFPE) 214


title: Colorectal cancer tissue sample (FFPE) 221


title: Colorectal cancer tissue sample (FFPE) 209


title: Colorectal cancer tissue sample (FFPE) 217


title: Colorectal cancer tissue sample (FFPE) 212

description:
CAIRO arm B: capecitabine and irinotecan first line
Normal colon mucosa from the same patient as the tumor was used as reference in the aCGH experiments.

source_name: colorectal cancer, CAIRO arm B

value: B


title: Colorectal cancer tissue sample (FFPE) 211


title: Colorectal cancer tissue sample (FFPE) 213


title: Colorectal cancer tissue sample (FFPE) 207


title: Colorectal cancer tissue sample (FFPE) 210


title: Colorectal cancer tissue sample (FFPE) 259


title: Colorectal cancer tissue sample (FFPE) 206


title: Control 9

first: Yidan

last: Zhao

address: 101 College Street

institute: University Health Network

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

scan_protocol: GeneChips were scanned using the HuGene-1_0-st-v1 GeneArray Scanner G2500A.

data_processing: The data were analyzed with Partek Genomics Suite 6.6 using Affymetrix default analysis settings and global scaling as normalization method.

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

treatment_protocol: Global profiles were determined in human lung tissue and compared across 11 normal and 12 severe pulmonary arterial hypertension patients.

tag: sample group

value: normal control

value: lung


title: Control 11


title: Control 10


title: Control 8


title: Colorectal cancer tissue sample (FFPE) 200


title: Colorectal cancer tissue sample (FFPE) 192


title: Colorectal cancer tissue sample (FFPE) 205


title: Colorectal cancer tissue sample (FFPE) 203


title: Colorectal cancer tissue sample (FFPE) 194


title: Colorectal cancer tissue sample (FFPE) 197


title: Colorectal cancer tissue sample (FFPE) 204


title: Colorectal cancer tissue sample (FFPE) 191


title: Colorectal cancer tissue sample (FFPE) 198


title: Colorectal cancer tissue sample (FFPE) 208