title: GMDC_TPT

city: Sapporo

first: Yuichi

last: Kitai

address: N12 W6, Kita-ku

department: Faculty of Pharmaceutical Sciences

institute: Hokkaido University

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

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

data_processing:
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.3.1.187

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

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

value: bone marrow-derived dendritic cells

tag: culture condition

value: cultured with conditioned medium from topotecan-treated E0771 cells


title: GSY122-Rep1-g200-FRY892

status: Public on Dec 01 2016

type: genomic

city: Stanford

first: Barbara

last: Dunn

state: CA

department: Genetics

country: USA

institute: Stanford University

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82588.gif

hyb_protocol: not provided

scan_protocol: Scanner Model: G2505C

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: S cerevisiae + S bayanus genomic DNA sonicated, 300 ng each

label_protocol: not provided

extract_protocol: not provided

tag: reference

source_name: GSY122-Rep1-g200-FRY892-MB2-12 genomic DNA, Hae III cut, 450 ng

tag: strain

tag: genotype

value: whole genome

tag: developmental stage

tag: replicate


title: GSY122-Rep2-g200-FRY994

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82521.gif

value: S cerevisiae + S bayanus genomic DNA sonicated, 300 ng each

source_name: GSY122-Rep2-g200-FRY994-MB2-25 genomic DNA, Hae III cut, 450 ng


title: T3

type: RNA

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

description: Tumor derived from TUBO cells

hyb_protocol: Hybridization and washes were done using a Genechip Affymetrix station (Fluidics station 450) as recommended by manufacturer

scan_protocol: Scanner procedure was done using a Genechip Affymetrix station (GeneChip Scanner 3000) as recommended by manufacturer

data_processing: Laser scanning generated digitized image data files and CEL file that were used for the subsequent statistical analysis. The data were loaded in in oneChannelGUI biocondcutor package version 1.24.0, normalized using sketch-quantile normalization and filtered by IQR > 0.25 to remove unchanged transcripts. To assess differential expression, we used an empirical Bayes method together with a false discovery rate (FDR) correction of the P-value. Genes were selected as differentially expressed if characterized by a FDR ≤ 0.05 and an absolute log2 fold change ≥ 1.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Tumor

label_protocol: cRNA was synthesized using Ambion WT Expression Kit (Ambion) starting from 500 ng of total RNA and following the procedure suggested by the manufacturer.

growth_protocol: For subcutaneous (s.c.) injection, 3-5 x 106 BM cells or 1 x 105  tumor cells were re-suspended in a total of 200 µl PBS with 1 µg murine bFGF (Peprotech, Rocky Hill, NJ, USA) mixed with 400 µl of matrigel (Becton-Dickinson; Franklin Lakes, NY, USA), according to a previously published protocol [17]. We injected a total of 300 µl (cells plus matrigel mix) per mouse in the dorsolateral flank

extract_protocol: tumor masses from primary BALB-neuT breast tumors and DTC tumors grown in NSG mice snap frozen at harvest. Cryostat shavings were used to extract RNA and a representative section was kept for Haematoxylin and Eosin staining in order to evaluate tumor tissue anatomy and to quantify necrotic areas. The quality and quantity of total RNA from samples was determined using Agilent 2100 Bioanalyzer and Nanodrop spectrophotometer.

value: BALB-neuT

tag: cell type

value: Tumor derived from TUBO cells


title: GSY123-Rep2-g150-F06-IX-B-150e

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-02/82901.gif

source_name: GSY123-Rep2-g150-F06-IX-B-150e-MB2-50, genomic DNA, Hae III cut, 400 ng


title: GMDC_ctrl

country: Japan

value: control


title: GSY124-Rep1-g200-FRY996

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82589.gif

source_name: GSY124-Rep1-g200-FRY996-MB2-65 genomic DNA, Hae III cut, 450 ng


title: FRY992-CHEFBand7-b

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83496.gif

source_name: S cerevisiae + S bayanus genomic DNA sonicated, 100 ng each

source_name: FRY992-CHEFBand7-b DNA, 15 ng, HaeIII-cut

value: CHEF


title: GSY144-Rep3-200b

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82597.gif

source_name: GSY144-Rep3-200b-MB1-27 genomic DNA, Hae III cut, 450 ng


title: FRY994-CorrectedCHEFBand4

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82626.gif

source_name: S cerevisiae and S bayanus genomic DNA, sonicated, 100 ng each

source_name: FRY994-CorrectedCHEFBand4 DNA, 6 ng, HAEIII cut


title: T4

description: Tumor derived from TUBO cells


title: GSY123-Rep2-g150-F06-IX-B-150bx

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-02/82941.gif

source_name: S cerevisiae + S bayanus genomic DNA sonicated, 350 ng each

source_name: GSY123-Rep2-g150-F06-IX-B-150bx-MB2-48, genomic DNA, Hae III cut, 500 ng


title: GSY123-Rep2-g150-F06-IX-B-150d

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-02/82943.gif

value: S cerevisiae + S bayanus genomic DNA sonicated, 350 ng each

source_name: GSY123-Rep2-g150-F06-IX-B-150d-MB2-49, genomic DNA, Hae III cut, 500 ng


title: FRY893-CHEFBand2-b

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83469.gif

value: S cerevisiae + S bayanus genomic DNA sonicated, 100 ng each

source_name: FRY893-CHEFBand2-b, 15 ng, HaeIII-cut


title: A23b-CHEFBand4-b

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83624.gif

source_name: A23b-CHEFBand4-b, 15 ng, HaeIII-cut


title: GSY122-Rep1-g100-FRY889

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82596.gif

source_name: GSY122-Rep1-g100-FRY889-MB2-70 genomic DNA, Hae III cut, 450 ng


title: GSY122-Rep1-g150-FRY890

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82585.gif

source_name: S cerevisiae + S bayanus genomic DNA sonicated, 300 ng each

source_name: GSY122-Rep1-g150-FRY890-MB2-8 genomic DNA, Hae III cut, 450 ng


title: A23b-CHEFBand6

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83488.gif

source_name: A23b-CHEFBand6 DNA, 15 ng, HaeIII-cut


title: GSY124-Rep1-g50-9c

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82607.gif

source_name: GSY124-Rep1-g50-9c-PB4-3 genomic DNA, Hae III cut, 450 ng


title: FRY994-CHEFBand2-b

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83472.gif

source_name: FRY994-CHEFBand2-b, 15 ng, HaeIII-cut


title: A23b-CHEFBand3

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-03/83049.gif

source_name: A23b-CHEFBand3, 15 ng, HaeIII-cut


title: T1

description: Tumor derived from TUBO cells

source_name: Tumor


title: T2

description: Tumor derived from TUBO cells


title: FRY994-CHEFBand6-b

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83625.gif

source_name: S cerevisiae + S bayanus genomic DNA sonicated, 100 ng each

source_name: FRY994-CHEFBand6-b, 15 ng, HaeIII-cut


title: GSY122-Rep2-g150-FRY980

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82592.gif

source_name: GSY122-Rep2-g150-FRY980-MB2-21 genomic DNA, Hae III cut, 450 ng


title: FRY891-CHEFBand1

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83633.gif

source_name: FRY891-CHEFBand1, 15 ng, HaeIII-cut


title: GSY123-Rep1-g50-F06-V-E.5d

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-02/82956.gif

source_name: S cerevisiae + S bayanus genomic DNA sonicated, 350 ng each

source_name: GSY123-Rep1-g50-F06-V-E.5d, genomic DNA, Hae III cut, 500 ng


title: FRY892-CHEFBand5

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82623.gif

source_name: S cerevisiae and S bayanus genomic DNA, sonicated, 100 ng each

source_name: FRY892-CHEFBand5 DNA, 6 ng, HAEIII cut


title: GSY123-Rep1-g100-F06-V-E.10c

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-02/82940.gif

source_name: GSY123-Rep1-g100-F06-V-E.10c, genomic DNA, Hae III cut, 500 ng


title: A23b-CHEFBand2-b

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83467.gif

source_name: A23b-CHEFBand2-b, 15 ng, HaeIII-cut


title: DTC2

description: Early disseminated tumor cells

value: Early disseminated tumor cells


title: adrenal cortex-at slaughter 1

city: Dummerstorf

first: Bodo

last: Brand

address: Wilhelm-Stahl-Allee 2

country: Germany

institute: Leibniz Institute of Farm Animal Biology

hyb_protocol: The fragmented cDNA was hybridized to the microarray using the Affymetrix Hyb-WashStain Kit and Affymetrix standard protocols

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000 (Affymetrix, St. Clara, USA)

data_processing:
Gene-level analysis and RMA normalization was performed using Affymetrix Expression Console software based on 147 Microarrays. Filtering of Probesets was performed using the detection above background algorithm. Probe sets that were present in 75% of all samples and transcripts with at least 50% of all probe sets present were included in the final analyses. Two samples (30 and 89) were excluded due to misssing phenotypic data.
BovGene-1_0-v1.pgf
BovGene-1_0-v1.mps

organism: Bos taurus

source_name: adrenal cortex

label_protocol: 5.5 µg of  cDNA was fragmented and labeled using the Affymetrix Terminal Labeling Kit  and Affymetrix standard protocols

extract_protocol: Total RNA was isolated from the adrenal cortex of 147 animals using TRI Reagent (Sigma, Taufkirchen, Germany). After DNaseI treatment the RNA was further purified with the RNeasy Kit (QIAGEN, Hilden, Germany) following the manufacturers recommendations. RNA was quantified using the NanoDrop ND-1000 spectrophotometer (Peqlab, Erlangen, Germany). Integrity of RNA was checked by running 1 μg of RNA on a 1% agarose gel. Absence of DNA contamination was verified by PCR amplifying fragments of GAPDH with RNA as a template.

tag: gender

value: female

tag: age at slaughter in days

tag: year-season of slaughter

tag: tissue

value: adrenal cortex


title: DTC3

description: Early disseminated tumor cells


title: LP-OBP801 TRAP

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: total RNA extracted from rat lateral prostate tissue

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

organism: Rattus norvegicus

source_name: lateral prostate tissus

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: TRAP rats were fed a control diet during experimental periods.

extract_protocol: RNA samples were extracted from prostate tissue using miRNesy mini kit (Quiagen).

treatment_protocol: TRAP rats were intravenously injected with OBP-801 (1mg/kg) or saline 2 times a week.

value: lateral prostate tissue

tag: agent

value: 1mg of OBP-801

tag: age

value: Six week-old

tag: Sex

value: male


title: FRY893-CHEFBand3

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-03/83050.gif

source_name: FRY893-CHEFBand3, 15 ng, HaeIII-cut


title: DTC4

description: Early disseminated tumor cells


title: FRY892-CHEFBand4-b

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83620.gif

source_name: FRY892-CHEFBand2-b, 15 ng, HaeIII-cut


title: FRY892-CHEFBand6

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83471.gif

source_name: FRY892-CHEFBand6, 15 ng, HaeIII-cut


title: FRY891-CHEFBand5

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82628.gif

value: S cerevisiae and S bayanus genomic DNA, sonicated, 100 ng each

source_name: FRY891-CHEFBand5 DNA, 6 ng, HAEIII cut


title: GSY123-Rep2-g50-FRY1009

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82587.gif

source_name: S cerevisiae + S bayanus genomic DNA sonicated, 300 ng each

source_name: GSY123-Rep2-g50-FRY1009-MB2-44 genomic DNA, Hae III cut, 450 ng


title: LP-control TRAP

value: saline


title: VP-OBP801 TRAP

description: total RNA extracted from rat ventral prostate tissue

source_name: ventral prostate tissue

value: ventral prostate tissue


title: DTC1

description: Early disseminated tumor cells

source_name: Tumor


title: FRY994-CorrectedCHEFBand1

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83477.gif

source_name: S cerevisiae + S bayanus genomic DNA sonicated, 100 ng each

source_name: FRY994-CorrectedCHEFBand1 DNA, 15 ng, HaeIII-cut


title: FRY891-CHEFBand2-b

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83473.gif

source_name: FRY891-CHEFBand2-b, 15 ng, HaeIII-cut


title: FRY893-CHEFBand1

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83632.gif

source_name: FRY893-CHEFBand1, 15 ng, HaeIII-cut


title: GSY122-Rep1-g100-FRY887

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-02/82946.gif

source_name: S cerevisiae + S bayanus genomic DNA sonicated, 350 ng each

source_name: GSY122-Rep1-g100-FRY887-MB2-6, genomic DNA, Hae III cut, 500 ng

value: whole genome


title: VP-control TRAP


title: GSY123-Rep2-150h

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82593.gif

value: S cerevisiae + S bayanus genomic DNA sonicated, 300 ng each

source_name: GSY123-Rep2-150h-MB2-51 genomic DNA, Hae III cut, 450 ng


title: FRY893-CHEFBand5

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82629.gif

source_name: S cerevisiae and S bayanus genomic DNA, sonicated, 100 ng each

source_name: FRY893-CHEFBand5 DNA, 6 ng, HAEIII cut


title: A23b-CHEFBand7-b

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83489.gif

source_name: A23b-CHEFBand7-b DNA, 15 ng, HaeIII-cut


title: GSY123-Rep1-g50-F06-V-E.5c

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-02/82957.gif

source_name: GSY123-Rep1-g50-F06-V-E.5c, genomic DNA, Hae III cut, 500 ng


title: FRY994-CHEFBand3

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-03/83048.gif

source_name: FRY994-CHEFBand3, 15 ng, HaeIII-cut


title: FRY992-CHEFBand3

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-03/83045.gif

source_name: FRY992-CHEFBand3, 15 ng, HaeIII-cut


title: A23b-CHEFBand5

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82675.gif

source_name: A23b-CHEFBand5 DNA, 6 ng, HaeIII-cut


title: FRY892-CHEFBand3

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-03/83047.gif

source_name: FRY892-CHEFBand3, 15 ng, HaeIII-cut


title: FRY992-CHEFBand5

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82627.gif

source_name: FRY992-CHEFBand5 DNA, 6 ng, HAEIII cut


title: GSY124-Rep2-g200-F06-IX-D.24d

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-02/82938.gif

source_name: GSY124-Rep2-g200-F06-IX-D.24d-PB4-36, genomic DNA, Hae III cut, 500 ng


title: FRY893-CHEFBand7-b

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83495.gif

source_name: S cerevisiae + S bayanus genomic DNA sonicated, 100 ng each

source_name: FRY893-CHEFBand7-b DNA, 15 ng, HaeIII-cut


title: GSY124-Rep2-g50-FRY1015

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82598.gif

source_name: S cerevisiae + S bayanus genomic DNA sonicated, 300 ng each

source_name: GSY124-Rep2-g50-FRY1015-MB2-69 genomic DNA, Hae III cut, 450 ng


title: FRY992-CHEFBand1

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83631.gif

source_name: FRY992-CHEFBand1, 15 ng, HaeIII-cut


title: GSY124-Rep2-g50-F06-IX-D-9d

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-02/82900.gif

source_name: GSY124-Rep2-g50-F06-IX-D-9d, genomic DNA, Hae III cut, 400 ng


title: GSY123-Rep1-g150-F06-V-E-150e

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-02/82954.gif

source_name: S cerevisiae + S bayanus genomic DNA sonicated, 350 ng each

source_name: GSY123-Rep1-g150-F06-V-E-150e-MB2-38, genomic DNA, Hae III cut, 500 ng


title: GSY144-Rep1-g200-FRY924

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82591.gif

source_name: GSY144-Rep1-g200-FRY924-MB1-9 genomic DNA, Hae III cut, 450 ng


title: FRY891-CHEFBand7-b

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83491.gif

source_name: FRY891-CHEFBand7-b DNA, 15 ng, HaeIII-cut


title: A23b-CHEFBand1

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83629.gif

source_name: A23b-CHEFBand1, 15 ng, HaeIII-cut


title: FRY992-CHEFBand4-b

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83622.gif

source_name: FRY992-CHEFBand4-b, 15 ng, HaeIII-cut


title: GSY144-Rep2-g200-FRY977

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82599.gif

source_name: GSY144-Rep2-g200-FRY977-MB1-18 genomic DNA, Hae III cut, 450 ng


title: FRY892-CHEFBand7-b

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83490.gif

source_name: FRY892-CHEFBand7-b DNA, 15 ng, HaeIII-cut


title: FRY992-CHEFBand6-b

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83621.gif

source_name: FRY992-CHEFBand6-b, 15 ng, HaeIII-cut


title: GSY122-Rep2-g200-F06-IX-A.23b

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-02/82902.gif

source_name: GSY122-Rep2-g200-F06-IX-A.23b-PB3-79, genomic DNA, Hae III cut, 400 ng


title: FRY891-CHEFBand3

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-03/83046.gif

source_name: FRY891-CHEFBand3, 15 ng, HaeIII-cut


title: PEF1_Ss

city: Tsukuba

first: Hirohide

last: Uenishi

state: Ibaraki

address: 2-1-2 Kannondai

institute: National Institute of Agrobiological Sciences

description:
raw data file: iPSC1.txt
Normalized gProcessed value is used

hyb_protocol: The mixed labelled cRNAs were hybridized overnight to each array at 65 °C under constant rotation in the hybridization buffer supplied with the Gene Expression Hybridization Kit (Agilent).

scan_protocol: Arrays were washed by using a Gene Expression Wash Pack (Agilent) and scanned with a G2505B DNA microarray scanner (Agilent) in accordance with the manufacturer’s protocol.

data_processing: Linear and LOWESS normalized, background subtracted data obtained from log10 of processed Red signal/processed Green signal. Agilent Feature Extraction Software was used. Normalized gProcessed or rProcessed value is reported in data table.

organism: Sus scrofa

source_name: Porcine embryonic fibroblast

label_protocol: Each total RNA (400 ng) was used to synthesize fluorescence-labelled complementary RNA (cRNA) by using a Low RNA Input Fluorescent Linear Amplification Kit (Agilent) in accordance with the manufacturer’s protocol. Total RNAs of differentiated iPS cells and PEF were labelled with cyanine-5 (Cy5) and cyanine-3 (Cy3), respectively. The labelled cRNA was purified by using a QIAGEN RNeasy Mini Kit (Qiagen).

growth_protocol: Cells were grown in a 5% CO2 humidified incubator at 37degreeC in DMEM supplemented with 10% FBS.

extract_protocol: Total RNA was extracted from the cells by using Fast pure RNA kit (Takara) in accordance with the manufacturer's protocol.

tag: cell line

value: parental embryonic fibroblast


title: Liver_PCI_rep.1 (het)

city: Jena

first: Falk

last: Gonnert

state: Thuringen

address: Erlanger Allee 101

department: Department of Anaesthesiology and Intensive Care Medicine

institute: Jena University Hospital

description:
4700303028_G
in vivo

hyb_protocol: Hybridization was in agreement with the Whole-Genome Gene Expression Direct Hybridization Assay protocol from Illumina.

scan_protocol: Arrays were readout with the detection system iScan from Illumina.

data_processing: Raw data were obtained using GenomeStudio (v 1.9.0)  and annotation by MouseRef-8_V2_0_R3_11278551_A.bgx.xml. Robust spline normalization (rsn) and detection filtering were performed via lumi package within Bioconductor and R.

source_name: liver tissue, 6h sepsis (PCI)

label_protocol: Amplification and biotinylation of RNA were carried out using the TargetAmp™-Nano Labeling Kit for Illumina® Expression BeadChip® (Epicentre).

extract_protocol:
RNA was isolated from liver tissue using QIAcubeTM and RNeasy® Mini Kit from Qiagen in accordance to the Purification of Total RNA from Animal Tissues protocol. RNA concentration and purity were determined with the NanoDrop® ND-2000c spectrophotometer and quality control was performed with the automated electrophoresis system ExperionTM (Bio-Rad Laboratories) according to the manufacturer’s specifications using the ExperionTM RNA StdSens Analysis Kit.
RNA was isolated from liver tissue using QIAcubeTM and RNeasy® Mini Kit from Qiagen in accordance to the Purification of Total RNA from Animal Cells Using Spin Technology protocol and the Purification of Total RNA from Animal Tissues protocol, respectively. RNA concentration and purity were determined with the NanoDrop® ND-2000c spectrophotometer and quality control was performed with the automated electrophoresis system ExperionTM (Bio-Rad Laboratories) according to the manufacturer’s specifications using the ExperionTM RNA StdSens Analysis Kit.

treatment_protocol: Animal experiments were carried out after approval of the local ethics committee. Referring to a recently published rodent model (Gonnert et al., J Surg Res. 2011), 12 to 14 weeks old C57BL/6 Jackson mice were subjected to peritoneal contamination and infection (PCI). The animals received an intraperitoneal injection of 5 µl/g BW of a standardized human feces suspension (predicted to be lethal).

tag: treatment

value: 6h sepsis (PCI) induced by injecting human stool suspension into peritoneal cavity of host

value: liver


title: GSY123-Rep1-g100-FRY956

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-02/82959.gif

value: S cerevisiae + S bayanus genomic DNA sonicated, 350 ng each

source_name: GSY123-Rep1-g100-FRY956-MB2-36, genomic DNA, Hae III cut, 500 ng


title: Liver_PCI_rep.4 (het)

description:
4700303052_C
in vivo

growth_protocol: Animal experiments were carried out after approval of the local ethics committee.


title: GSY123-Rep1-g100-FRY954

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82582.gif

source_name: S cerevisiae + S bayanus genomic DNA sonicated, 300 ng each

source_name: GSY123-Rep1-g100-FRY954-MB2-35 genomic DNA, Hae III cut, 450 ng


title: GSY31-Rep2-200b

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82594.gif

source_name: GSY31-Rep2-200b-MB1-45 genomic DNA, Hae III cut, 450 ng


title: Blood_PCI_rep.3 (hom)

description:
7165861065_E
in vivo

source_name: whole blood, 6h sepsis (PCI)

extract_protocol:
RNA was isolated from whole blood using QIAcubeTM and RNeasy® Mini Kit from Qiagen in accordance to the Purification of Total RNA from Animal Tissues protocol. RNA concentration and purity were determined with the NanoDrop® ND-2000c spectrophotometer and quality control was performed with the automated electrophoresis system ExperionTM (Bio-Rad Laboratories) according to the manufacturer’s specifications using the ExperionTM RNA StdSens Analysis Kit.
RNA was isolated from circulating leukocytes from whole blood using QIAcubeTM and RNeasy® Mini Kit from Qiagen in accordance to the Purification of Total RNA from Animal Cells Using Spin Technology protocol and the Purification of Total RNA from Animal Tissues protocol, respectively. RNA concentration and purity were determined with the NanoDrop® ND-2000c spectrophotometer and quality control was performed with the automated electrophoresis system ExperionTM (Bio-Rad Laboratories) according to the manufacturer’s specifications using the ExperionTM RNA StdSens Analysis Kit.

treatment_protocol: Animal experiments were carried out after approval of the local ethics committee. Referring to a recently published rodent model (Gonnert et al., J Surg Res. 2011), 12 to 14 weeks old C57BL/6 Jackson mice were subjected to peritoneal contamination and infection (PCI). The animals received an intraperitoneal injection of 5 µl/g BW of a standardized murine feces suspension (predicted to be lethal).

value: 6h sepsis (PCI) induced by injecting murine stool suspension into peritoneal cavity of host

value: blood

value: circulating leukocytes


title: Liver_PCI_rep.3 (het)

description:
4700303041_D
in vivo


title: Liver_PCI_rep.2 (hom)

description:
7165861078_H
in vivo


title: iPS6FC2_Ss

description:
raw data file: iPSC2.txt
Normalized rProcessed value is used

source_name: iPS cell clone establshed from porcine embryonic fibroblast

value: iPS 6F clone 2


title: GSY123-Rep1-200j-TechRep

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82583.gif

source_name: GSY123-Rep1-200j-MB2-40 genomic DNA, Hae III cut, 450 ng


title: FRY893-CHEFBand6

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83492.gif

source_name: S cerevisiae + S bayanus genomic DNA sonicated, 100 ng each

source_name: FRY893-CHEFBand6 DNA, 15 ng, HaeIII-cut

value: CHEF


title: PEF2_Ss

description:
raw data file: iPSC2.txt
Normalized gProcessed value is used


title: Liver_PCI_rep.3 (hom)

description:
7165861065_C
in vivo


title: GSY123-Rep1-g100-F06-V-E.10b

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-02/82958.gif

source_name: S cerevisiae + S bayanus genomic DNA sonicated, 350 ng each

source_name: GSY123-Rep1-g100-F06-V-E.10b, genomic DNA, Hae III cut, 500 ng


title: Liver_PCI_rep.2 (het)

description:
4700303028_H
in vivo


title: FRY994-CHEFBand7-b

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83493.gif

value: S cerevisiae + S bayanus genomic DNA sonicated, 100 ng each

source_name: FRY994-CHEFBand7-b DNA, 15 ng, HaeIII-cut


title: Blood_PCI_rep.3 (het)

description:
4700303052_D
in vivo


title: Blood_PCI_rep.2 (hom)

description:
7165861065_D
in vivo


title: FRY892-CHEFBand1

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83628.gif

source_name: FRY892-CHEFBand1, 15 ng, HaeIII-cut


title: GSY123-Rep2-g100-F06-IX-B-100a

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-02/82955.gif

source_name: GSY123-Rep2-g100-F06-IX-B-100a-MB2-45, genomic DNA, Hae III cut, 500 ng


title: Blood_PCI_rep.4 (het)

description:
5222622030_F
in vivo


title: Liver_PCI_rep.1 (hom)

description:
7165861078_E
in vivo


title: Blood_PCI_rep.2 (het)

description:
5222622030_G
in vivo


title: C57BL/6J_OVX_L4 (5665159006_H)

city: Charlottesville

first: Charles

middle: R

last: Farber

state: VA

department: Center for Public Health Genomics

institute: University of Virginia

hyb_protocol: cRNA was quantified and normalized to 77 ng/μl, and then 850 ng was hybridized to Beadchips.

scan_protocol: The hybridized Beadchips were scanned by Illumina BeadScan confocal scanner. cRNA synthesis, hybridization and scanning was performed by the Genome Sciences Laboratory in the Center for Public Health Genomics at the University of Virginia.

data_processing: Raw expression values were quantile normalized using the affy R package and log2 transformed.

source_name: lumbar vertebrae (L5)

label_protocol: Biotin-labeled cRNA was synthesized by the total prep RNA amplification kit from Ambion (Austin, TX).

growth_protocol: Female BALBC/J (Stock #000651), C3H/HeJ (Stock #000659) and C57BL6/J (Stock #000664) mice were purchased from the Jackson labs.  At 16 weeks of age females from the three classical inbred strains were randomly assigned to SHAM or OVX surgical groups (N=8/group/strain). Mice were anesthetized with isoflurane. Using sterile technique, surgery was performed using a dorsal approach. Small lateral incisions were made in the abdominal wall to exteriorize and excise the ovaries, and the abdominal and skin incisions were subsequently closed. Analgesia was provided with administration of Bupivacaine and Ketoprofen.  Before and after surgery, mice were given free access to food and water.  Mice were euthanized four weeks post-surgery.

extract_protocol: Dissected L5 vertebras were immediately homogenized in Trizol and lysates were frozen at -80ºC until RNA isolation.  Total RNA was isolated using the Trizol Plus RNA Purification Kit (Invitrogen, Carlsbad, CA).  RNA integrity was confirmed using a 1% agarose gel (Agilent, Palo Alto, CA).

treatment_protocol: At sacrifice, L5 vertebras were dissected and cleared free of soft tissue. The L5 vertebras were immediately homogenized in Trizol for subsequent RNA isolation.

value: Female

tag: surgical group

value: OVX

value: lumbar vertebrae (L5)


title: C3H/HEJ_SHAM_L4 (5665159006_C)

value: SHAM


title: BALB/CJ_SHAM_L4 (5665159015_B)

value: BALB/cJ


title: C3H/HEJ_OVX_L4 (5665159015_G)


title: C57BL/6J_SHAM_L4 (5665159006_E)


title: BALB/CJ_OVX_L4 (5665159006_D)


title: Blood_PCI_rep.1 (hom)

description:
7165861065_A
in vivo


title: C57BL/6J_OVX_L4 (5665159015_C)


title: BALB/CJ_SHAM_L4 (5665159015_D)


title: BALB/CJ_SHAM_L4 (5665159006_A)


title: C3H/HEJ_OVX_L4 (5665159006_B)


title: BALB/CJ_OVX_L4 (5665159015_E)


title: C57BL/6J_SHAM_L4 (5665159015_F)


title: BALB/CJ_OVX_L4 (5665159006_F)


title: BALB/CJ_OVX_L4 (5665159006_G)


title: C57BL/6J_OVX_L4 (5665159026_F)


title: C3H/HEJ_SHAM_L4 (5665159026_H)


title: C3H/HEJ_SHAM_L4 (5665159015_H)


title: Blood_PCI_rep.1 (het)

description:
5222622015_C
in vivo


title: C3H/HEJ_SHAM_L4 (5665159015_A)


title: C57BL/6J_SHAM_L4 (5665159026_B)


title: C57BL/6J_OVX_L4 (5665159026_E)


title: C3H/HEJ_OVX_L4 (5665159026_G)


title: WT_OVX (9380251061_H)

growth_protocol: Sncatm1Rosl/J (Stock #003692) mice were purchased from the Jackson labs. Males homozygous for the Sncatm1Rosl allele (Snca-/-) were bred to C57BL6/J females and Snca+/- mice were intercrossed generating Snca+/+ and Snca-/- littermate females.  At 8 weeks of age Snca+/+ and Snca-/- females were randomly assigned to SHAM or OVX surgical groups (N=4 biological replicates per genotype and surgical group).  Mice were anesthetized with isoflurane. Using sterile technique, surgery was performed using a dorsal approach. Small lateral incisions were made in the abdominal wall to exteriorize and excise the ovaries, and the abdominal and skin incisions were subsequently closed. Analgesia was provided with administration of Bupivacaine and Ketoprofen.  Before and after surgery, mice were given free access to food and water.  Mice were euthanized four weeks post-surgery.

value: Snca wild type


title: MT_SHAM (9380251061_G)

value: Snca knockout


title: C3H/HEJ_OVX_L4 (5665159026_A)


title: C57BL/6J_SHAM_L4 (5665159026_C)


title: MT_OVX (9380251061_F)


title: GSY124-Rep1-g200-FRY998

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82590.gif

value: S cerevisiae + S bayanus genomic DNA sonicated, 300 ng each

source_name: GSY124-Rep1-g200-FRY998-MB2-67 genomic DNA, Hae III cut, 450 ng

value: whole genome


title: WT_SHAM (9380251061_E)


title: WT_SHAM (9380251061_D)


title: WT_OVX (9370680097_E)


title: WT_SHAM (9370680097_G)


title: WT_OVX (9370680097_F)


title: WT_OVX (9380251061_B)


title: MT_OVX (9380251061_C)


title: MT_SHAM (9370680097_C)


title: MT_SHAM (9380251061_A)


title: MT_SHAM (9370680097_B)


title: MT_OVX (9370680097_D)


title: iPS6FC1_Ss

description:
raw data file: iPSC1.txt
Normalized rProcessed value is used

value: iPS 6F clone 1


title: MT_OVX (9370680097_H)


title: WT_SHAM (9370680097_A)


title: HMP358-F2

city: Shanghai

first: hong

last: li

address: 320 Yueyang Road

country: China

institute: SIBS

description: genotyping data from PDX59 F2

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: The CEL files wrere read by R function crlmm. I only keep SNP probes (906600), and removed probes whose chromosomes are "NA". Therefore, the Sample table contains 905422 rows.

organism: Homo sapiens

label_protocol: Affymetrix protocol

growth_protocol: Fresh tumor tissues for engraftment were placed in ice-chilled high glucose DMEM supplemented with 10% FBS, 100 U/mL penicillin, and 100 U/mL streptomycin and rapidly processed for engraftment. After removing necrotic tissue and washing three times in ice-cold PBS, tumor specimens were divided under aseptic sterile conditions using a No.10 scalpel blade to yield 2 × 1 × 1 mm3 pieces. The tissue fragments were then incubated in DMEM supplemented with 10% FBS, 100 U/mL penicillin, and 100 U/mL streptomycin (condition 1), or in DMEM medium supplemented with 50% Matrigel™ (BD; 356234), 10 ng/mL epidermal growth factor (Gibco; PHG0314), 10 ng/ml basic fibroblast growth factor (Gibco; PHG0264), 100 U/mL penicillin, and 100 U/mL streptomycin (condition 2) for 30 min. After sterilizing the dorsal shaved area(s) with Betadine® surgical scrub, followed by 70% ethanol, three or four pieces of tissue were transplanted subcutaneously into the right flanks of NOD/SCID mice (n = 3) with a No.2 trocar.

extract_protocol: DNA from each sample was digested using the NspI (Cat#R0602L, New England BioLabs, Ipswich, MA, US) and StyI (Cat#R0500L, New England BioLabs) restriction enzymes, and two adaptors were ligated to the DNA fragment for PCR amplification. To obtain biotin-labeled DNA, amplified DNA was labeled using the Affymetrix® Genome-Wide Human SNP Nsp/Sty Assay Kit 6.0 (Cat#901015, Affymetrix, Santa Clara, CA, US) according to the manufacturer’s instructions.

value: liver


title: HMP351-F2

description: genotyping data from PDX52 F2


title: HMP331-F2

description: genotyping data from PDX41 F2


title: HMP347-F2

description: genotyping data from PDX55 F2


title: HMP357-F2

description: genotyping data from PDX69 F2


title: HMP241-F2

description: genotyping data from PDX48 F2


title: HMP332-F2

description: genotyping data from PDX51 F2


title: HMP308-F4

description: genotyping data from PDX8 F4


title: HMR340-F2

description: genotyping data from PDX50 F2


title: HMP308-F2

description: genotyping data from PDX8 F2


title: HMP245-F2

description: genotyping data from PDX54 F2


title: HMP308-F0

description: genotyping data from PDX8 F0


title: HMP224-F2

description: genotyping data from PDX47 F2


title: HMP209-F2

description: genotyping data from PDX9 F2


title: wt_3

city: Bangor

first: Ramsay

last: Mcfarlane

state: Gwynedd

address: Brambell Building, Deiniol Road

department: North West Cancer Research Institute

country: United Kingdom

institute: Bangor University

description: S. pombe wildtype strain

hyb_protocol: Affymetrix Gene Chip Arrays were hybridized following the "GeneChip Whole Transcript (WT) Double-Stranded Target Labeling Assay Manual" (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidiscs protocol FS450_0002 was used for washing.

scan_protocol: Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip Scanner 3000 with autoloader.

data_processing:
CEL files were generated with GeneChip® Command Console® Software; data preprocessing and analysis was performed in R (v3.0.1) and Bioconductor.
additional results files; Expression data for all samples as matrix (expressionDataMatrix.txt) and for each sample as a BED file.
results file descriptions: Preprocessing and analysis was performed in R (v3.0.1) and Bioconductor: The quality of the arrays was assessed with the R packages preprocessCore, oligo, affy and Starr. The R package waveTiling was used for background correction and quantile normalization. A batch effect was identified with PCA and removed using the ComBat function of the R package sva.

label: Biotin

organism: Schizosaccharomyces pombe

source_name: wt strain

label_protocol: Samples were prepared and hybridized to GeneChip® S. pombe Tiling 1.0FR (Affymetrix, Cat. No. 900647) according to Affymetrix specifications.

growth_protocol: All S. pombe strains were grown in yeast extract liquid with supplements (200 mg/liter adenine; 200 mg / liter uracil; 200 mg/liter leucine) at 30oC to an absorbance of 0.5 at 600 nm.

extract_protocol: RNA was extracted using the hot phenol method [Moreno et al. (1991) Molecualr genetic analysis of fission yeast Schizosaccharomyces pombe. Methods Enzymol. 194, 795-823]

treatment_protocol: Cells were harvested and RNA extracted directly (no additional treatment).

tag: strain info.

value: wildtype strain


title: HMP338-F2

description: genotyping data from PDX37 F2


title: HFP343-F2

description: genotyping data from PDX53 F2


title: tsn1ago1_2

description: S. pombe ΔtsnΔago1

source_name: tsn1ago1 strain


title: wt_1

description: S. pombe wildtype strain


title: tsn1ago1_3

description: S. pombe ΔtsnΔago1


title: tsn1ago1_1

description: S. pombe ΔtsnΔago1


title: HMP359-F2

description: genotyping data from PDX40 F2


title: HMP333-F2

description: genotyping data from PDX30 F2


title: HMP328-F2

description: genotyping data from PDX32 F2


title: tsn1_2

description: S. pombe Δtsn1

source_name: tsn1 strain


title: HMP312-F2

description: genotyping data from PDX21 F2


title: tsn1_3

description: S. pombe Δtsn1


title: HMP322-F2

description: genotyping data from PDX19 F2


title: HMP325-F2

description: genotyping data from PDX33 F2


title: tsn1_1

description: S. pombe Δtsn1


title: HMP323-F2-Cryopreserved

description: genotyping data from PDX20 F2


title: HMP321-F2

description: genotyping data from PDX17 F2


title: HMP320-F2

description: genotyping data from PDX16 F2


title: HFP227-F2

description: genotyping data from PDX31 F2


title: HMP136-F2

description: genotyping data from PDX36 F2


title: traxtsn1ago1_3

description: S. pombe ΔtfxΔtsn1Δago1

source_name: traxtsn1ago1 strain


title: traxtsn1ago1_2

description: S. pombe ΔtfxΔtsn1Δago1


title: wt_2

description: S. pombe wildtype strain


title: HMP323-F2

description: genotyping data from PDX20 F2


title: HMP215-F2

description: genotyping data from PDX24 F2


title: taf4bprmcpr5  leaf , biological replicate 3

city: lucknow

first: Samir

middle: V

last: Sawant

address: Rana pratap marg

department: Plant molecular biology

country: India

institute: National Botanical research Institute

description: Arabidopsis Thaliana double mutant leaf

hyb_protocol: According to affymatrix gene chip instruction manual using Fluidisc station 450.

scan_protocol: GeneChips were scanned using Affymatrix gene chip scanner.

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

organism: Arabidopsis thaliana

source_name: Arabidopsis Thaliana double mutant leaf

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

growth_protocol: Four weeks old Arabidopsis plants were used. Plants were grown at 22 0C in a mixture of commercial potting of soil rite (Keltech Energies Ltd., Bengaluru, India) and vermiculite (3:1) in a culture room having 16h-light/8-h-dark photoperiod with 200µmol m-2 s-1 light intensity and 80% relative humidity.

extract_protocol: Total RNA isolated from plant total RNA sigma kit.

treatment_protocol: Plant sample collected under normal and infected (fungal and bacterial) condition.

value: leaf

tag: infection

value: normal condition

tag: condition

value: taf4bprmcpr5 double mutant

tag: genotype/variation


title: traxtsn1_2

description: S. pombe ΔtsnΔago1

source_name: traxtsn1 strain


title: traxtsn1_1

description: S. pombe ΔtsnΔago1


title: traxtsn1_3

description: S. pombe ΔtsnΔago1


title: taf4bprmcpr5  leaf , biological replicate 2

description: Arabidopsis Thaliana double mutant leaf


title: traxtsn1ago1_1

description: S. pombe ΔtfxΔtsn1Δago1


title: traxago1_3

description: S. pombe ΔtfxΔago1

source_name: traxago1 strain


title: traxago1_1

description: S. pombe ΔtfxΔago1


title: ES4 Infected taf4bprm leaf , biological replicate 3

description: Arabidopsis Thaliana leaf in ES4 infected condition

source_name: ES4 Infected Arabidopsis Thaliana mutant leaf

value: bacteria ES4

value: taf4bprm mutant


title: taf4bprmcpr5  leaf , biological replicate 1

description: Arabidopsis Thaliana double mutant leaf


title: HMP326-F2

description: genotyping data from PDX23 F2


title: HMP319-F4

description: genotyping data from PDX14 F4


title: ES4 Infected taf4bprm leaf , biological replicate 1


title: HFP318-F2

description: genotyping data from PDX25 F2


title: HMP322-F3-Cryopreserved

description: genotyping data from PDX19 F3


title: AB Infected taf4bprm leaf , biological replicate 3

description: Arabidopsis Thaliana leaf in AB infected condition

source_name: AB Infected Arabidopsis Thaliana mutant leaf

value: fungi AB


title: ES4 Infected Col-0 leaf , biological replicate 3

source_name: ES4 Infected Arabidopsis Thaliana leaf

tag: ecotype

value: control


title: trax_3

description: S. pombe Δtfx

source_name: trax strain

value: Δtfx


title: HMP319-F3-Cryopreserved

description: genotyping data from PDX14 F3


title: trax_1

description: S. pombe Δtfx


title: ES4 Infected taf4bprm leaf , biological replicate 2


title: AB Infected taf4bprm leaf , biological replicate 2


title: ES4 Infected Col-0 leaf , biological replicate 2


title: AB Infected taf4bprm leaf , biological replicate 1


title: ES4 Infected Col-0 leaf , biological replicate 1


title: ago1_2

description: S. pombe Δago1

source_name: ago1 strain


title: ago1_1

description: S. pombe Δago1


title: trax_2

description: S. pombe Δtfx


title: ago1_3

description: S. pombe Δago1


title: HMP319-F2

description: genotyping data from PDX14 F2


title: AB Infected Col-0 leaf , biological replicate 3

source_name: AB Infected Arabidopsis Thaliana leaf


title: HMR210-F4

description: genotyping data from PDX11 F4


title: HMP319-F0

description: genotyping data from PDX14 F0


title: AB Infected Col-0 leaf , biological replicate 1


title: AB Infected Col-0 leaf , biological replicate 2


title: taf4bint leaf , biological replicate 2

description: Arabidopsis Thaliana mutant leaf

source_name: Arabidopsis Thaliana mutant leaf

value: taf4bint mutant


title: traxago1_2

description: S. pombe ΔtfxΔago1


title: Taf4b_oexp leaf biological replicate 2

description: Arabidopsis Thaliana over-expression transgenic leaf

value: taf4b over-expression


title: Col-0 leaf 10, biological replicate 1

description: Arabidopsis Thaliana leaf in  normal condition were taken as control for taf4bcpr5 double mutant lines

source_name: Arabidopsis Thaliana leaf

value: Col-0_control for taf4bprmcpr5 double mutant lines


title: HMP357-F2

description: gene expression data from PDX69 F2

scan_protocol: Arrays were scanned using the GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix) and Command Console Software 3.1 (Affymetrix) with default settings.

data_processing: The CEL files wrere read by R function ReadAffy, normalized using normalize.quantiles.robust, and do log2 transformation.

extract_protocol: Total RNA was extracted using TRIzol® reagent (Cat#15596-018, Life Technologies, Carlsbad, CA, US) according to the manufacturer’s instructions and the RNA integrity number (RIN) was verified using an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was purified further using an RNeasy micro kit (Cat#74004, Qiagen, Germany) and an RNase-Free DNase Set (Cat#79254, Qiagen).

tag: tisssue


title: pLenti6PPFIA1construct4_UT-SCC-95 Replicate 1

city: Helsinki

first: Outi

last: Monni

address: Haartmaninkatu 8

department: Department of Biomedicine

country: Finland

institute: University of Helsinki

description:
pL6PPFIA1_95_1
110810_1._3_95_PPFIA14_(HuEx-1_0-st-v2)

hyb_protocol: A hybridization cocktail was prepared including the labeled, fragmented target and hybridization controls. The target was then hybridized to GeneChip array in cartridge format during 16-hour incubation at 45˚C.

scan_protocol: Immediately following hybridization, the array was washed and stained with streptavidin phycoerytherin conjugate using an automated protocol on the GeneChip Fluidics 450, followed by scanning on an Affymetrix Gene Scanner 3000 7G.

data_processing: Data was normalized using Affymetrix Gene Expression Console and prosessed using Chipster software. Background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and quantile normalized.

source_name: UT-SCC-95_PPFIA1 open reading frame (ORF)

label_protocol: DNA was labeled by terminal deoxynucleotidyl transferase (TdT) with the Affymetrix proprietary DNA Labeling Reagent that was covalently linked to biotin.

growth_protocol: Cells were grown on Dulbecco's Modified Eagles Medium, supplemented with fetal bovine serum (10%), non essential amino acids, penicillin and streptomycin and L-glutamin.

extract_protocol: RNA was extracted according to miRNA easy Minikit from Qiagen.

treatment_protocol: Cells were transduced with lentiviral particles carrying shScr, shPPFIA1, PPFIA1 ORF or empty vector constructs, selected with puromycin or blastidicin after which cells were harvested and RNA extracted.

tag: tissue source

value: tongue from primary tumor

tag: cell type

value: head and neck squamous cell carcinoma

tag: transduced with

value: pLenti6 PPFIA1 overexpression construct


title: taf4bprm leaf , biological replicate 3

description: Arabidopsis Thaliana mutant leaf


title: pLenti6PPFIA1construct5_UT-SCC-95 Replicate 2

description:
pL6PPFIA1_95_2
110810_2._4_95_PPFIA15_(HuEx-1_0-st-v2)


title: taf4bprm leaf , biological replicate 2

description: Arabidopsis Thaliana mutant leaf


title: Col-0 leaf 11, biological replicate 2


title: Col-0 leaf 9 biological replicate 3

description: Arabidopsis Thaliana leaf in  normal condition were taken as control for Taf4b oexp lines

value: Col-0_control for Taf4b over-expression lines


title: taf4bint leaf , biological replicate 3

description: Arabidopsis Thaliana mutant leaf


title: taf4bprm leaf , biological replicate 1

description: Arabidopsis Thaliana mutant leaf


title: HMP347-F2

description: gene expression data from PDX55 F2

value: liver


title: HMP308-F2

description: gene expression data from PDX8 F2


title: Taf4b_oexp leaf biological replicate 3

source_name: Arabidopsis Thaliana over-expression transgenic leaf


title: HMP308-F4

description: gene expression data from PDX8 F4


title: HMP308-F0

description: gene expression data from PDX8 F0


title: HMP209-F2

description: gene expression data from PDX9 F2


title: HMR210-F0

description: genotyping data from PDX11 F0


title: Ctrl_pLenti6emptyvector_UT-SCC-95 Replicate 1

description:
pL6_95_1
110810_6._18_95_plenti6emptyA_(HuEx-1_0-st-v2)

source_name: UT-SCC-95_ctrl/empty pLenti6 vector

value: pLenti6 empty vector


title: HMR210-F2

description: genotyping data from PDX11 F2


title: HMP245-F2

description: gene expression data from PDX54 F2


title: Col-0 leaf 8 biological replicate 2

value: leaf


title: Taf4b_oexp leaf biological replicate 1

value: normal condition


title: Col-0 leaf 4, biological replicate 1

description: Arabidopsis Thaliana leaf in normal condition were taken as control for taf4bint

value: Col-0_control for taf4bint


title: HFP343-F2

description: gene expression data from PDX53 F2


title: HMP332-F2

description: gene expression data from PDX51 F2


title: Col-0 leaf 6, biological replicate 3


title: HMP351-F2

description: gene expression data from PDX52 F2


title: Col-0 leaf 5, biological replicate 2


title: HMP325-F2

description: gene expression data from PDX33 F2


title: HMR340-F2

description: gene expression data from PDX50 F2


title: HFP227-F2

description: gene expression data from PDX31 F2


title: Col-0l leaf 7 biological replicate 1


title: Col-0 leaf 2, biological replicate 2

description: Arabidopsis Thaliana leaf in normal condition were taken as control for taf4bprm

value: Col-0_control for taf4bprm


title: HMP326-F2

description: gene expression data from PDX23 F2


title: HMP241-F2

description: gene expression data from PDX48 F2


title: HMP224-F2

description: gene expression data from PDX47 F2


title: Col-0 leaf 1, biological replicate 1


title: Col-0 leaf 3, biological replicate 3


title: HMP359-F2

description: gene expression data from PDX40 F2


title: HMP328-F2

description: gene expression data from PDX32 F2


title: HMP338-F2

description: gene expression data from PDX37 F2


title: HMP331-F2

description: gene expression data from PDX41 F2


title: HMP136-F2

description: gene expression data from PDX36 F2


title: HFP318-F2

description: gene expression data from PDX25 F2


title: HMP215-F2

description: gene expression data from PDX24 F2


title: taf4bint leaf , biological replicate 1

description: Arabidopsis Thaliana mutant leaf


title: HMP323-F2-Cryopreserved

description: gene expression data from PDX20 F2


title: HMP312-F2

description: gene expression data from PDX21 F2


title: HMP322-F3-Cryopreserved

description: gene expression data from PDX19 F3


title: HMP323-F2

description: gene expression data from PDX20 F2


title: HMP319-F4

description: gene expression data from PDX14 F4


title: HMP321-F2

description: gene expression data from PDX17 F2


title: HMP322-F2

description: gene expression data from PDX19 F2


title: HMP320-F2

description: gene expression data from PDX16 F2


title: HMP319-F3-Cryopreserved

description: gene expression data from PDX14 F3


title: HMP333-F2

description: gene expression data from PDX30 F2


title: HMP319-F0

description: gene expression data from PDX14 F0


title: HMR210-F0

description: gene expression data from PDX11 F0


title: HMR210-F4

description: gene expression data from PDX11 F4


title: HMP319-F2

description: gene expression data from PDX14 F2


title: Notch Agonism Experiment:agD (SAM613501)

city: South San Francisco

first: Matthew

last: Brauer

state: California

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

description: gene expression from cultured MDA-MB-468 cells 24h after treatment with various Notch agonists

hyb_protocol: Hybridization was performed according to methods developed by Affymetrix, using Human gene U133 Plus 2.0 arrays.

scan_protocol: Samples were scanned on a GeneChip Scanner 3000

data_processing: Probe intensities were normalized using RMA and imported into R version 2.10 (R Development Core Team, 2010) and non-specifically filtered by variance using the nsFilter method from the 'genefilter' package

source_name: Cell culture 24h after post-washout treatment

label_protocol: Labeling was performed according to methods developed by Affymetrix

growth_protocol: For the NOTCH3 antagonism experiment, MDAMB-468 cells were plated at 2.5x10e6 cells/10 cm plate. For the NOTCH3 agonism gene expression experiment, MDA-MB-468 cells were plated at 6.25 x10e6 cells/10 cm plate.

extract_protocol: mRNA extraction and cRNA synthesis were performed according to methods developed by Affymetrix

treatment_protocol: For the NOTCH3 antagonism experiment, after 40h, test articles were added to the medium: 10 ug/ml control anti-gD IgG plus .05% DMSO, 10 ug/ml control IgG plus 5 uM DAPT, or 10 ug/ml anti-N3.A4 plus .05% DMSO. Cells were harvested 24h later. For the NOTCH3 agonism gene expression experiment, DMSO was added to .05% final concentration of one plate, while the rest received 5 uM DAPT to inhibit baseline Notch signaling. After 16h, the DMSO or DAPT was washed out of all plates and replaced with regular growth medium alone, for 2h. Then DMSO was readded to the DMSO plate, while the remaining plates received either 5 uM DAPT, 20 ug/ml control IgG, 20 ug/ml antiN3.A13, JAG1-Fc coated beads, or Fc coated beads. DAPT or DMSO were re-added to their corresponding plates 22h later. Cells were harvested after 6h or 24 h of postwashout treatment.

value: MBA-MB-468 breast cancer cells

value: agD

tag: experiment

value: Notch agonism


title: Notch Agonism Experiment:agD (SAM614979)


title: BIO

type: SRA

city: Lanzhou

first: Y

last: Gao

address: Xujiaping 1

institute: LVRI

description: raw data was lost

library_source: transcriptomic

data_processing:
Basecalls performed using Perl package developed by BGI
We will get rid of some contaminant reads from the fq file and get the final clean reads. And then summarize the length distribution of these clean reads. Normally, length of small RNA is between 18nt and 30nt. The length distribution analysis is helpful to see the compositions of small RNA sample. For example, miRNA is normally 21nt or 22nt, siRNA is 24nt, and piRNA is 30nt.
Getting rid of low quality reads (The criteria for this is listed in the explanation of meaning of each row in the result table).
Getting rid of reads with 5' primer contaminants or without 3' primer.
Getting rid of reads without the insert tag or poly A.
Getting rid of reads shorter than 18nt.
Summarize the length distribution of the clean reads.
Genome_build: mm9
Supplementary_files_format_and_content: abundance measurements

growth_protocol: The J1 mESC was gelatin adapted and plated on 0.2% (w/v) gelatin coated tissue culture plates in Knockout DMEM supplemented with 15% (v/v) Knockout Serum Replacement, 1× non-essential amino acids, 100 μM β-mercaptoethanol, 2 mM glutamine, 50 units/ml Penicillin, 50 μg/ml Streptomycin, 1000 U/ml LIF at condition of 37℃ and 5% CO2.

extract_protocol:
Total cellular RNA was isolated from J1 mESC using TRIzol RNA Isolation Reagent (Invitrogen, USA) following the manufacturer's recommendations.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The J1 mESCs were treated with a final concentration of BIO (1μM), CHIR99021 (3μM), RA (1μM), DMSO (1μL), VC (50μg/ml), ddH2O (1μL)

value: BIO

value: J1 mESC


title: HMR210-F2

description: gene expression data from PDX11 F2


title: Notch Agonism Experiment:aN3 A13 (SAM614981)

value: aN3 A13


title: Notch Agonism Experiment:DAPT (SAM620989)

value: DAPT


title: Notch Agonism Experiment:DAPT (SAM612933)


title: Notch Agonism Experiment:DMSO (SAM613500)

value: DMSO


title: Notch Agonism Experiment:DAPT (SAM620988)


title: Notch Agonism Experiment:Fc-B (SAM614982)

value: Fc-B


title: Notch Agonism Experiment:aN3 A13 (SAM612934)


title: Notch Agonism Experiment:J1-B (SAM612505)


title: Notch Agonism Experiment:J1-B (SAM612506)


title: Notch Agonism Experiment:J1-B (SAM612504)


title: Notch Agonism Experiment:aN3 A13 (SAM614980)


title: Notch Agonism Experiment:agD (SAM612501)


title: Notch Antagonism Experiment:panNotch (SAM618113)

description: gene expression from cultured MDA-MB-468 cells 24h after treatment with various Notch antagonists

source_name: Cell culture 24h after treatment

value: agD/DAPT

value: Notch antagonism


title: Notch Agonism Experiment:Fc-B (SAM612503)


title: Notch Agonism Experiment:Fc-B (SAM612502)


title: Notch Agonism Experiment:DMSO (SAM611943)


title: Notch Antagonism Experiment:CTL (SAM613110)

value: agD/DMSO


title: Notch Agonism Experiment:DMSO (SAM611944)


title: HMP358-F2

description: gene expression data from PDX59 F2

value: liver


title: Notch Antagonism Experiment:panNotch (SAM612175)


title: Notch Antagonism Experiment:CTL (SAM612350)


title: Notch Antagonism Experiment:Notch3 (SAM618110)


title: Notch Antagonism Experiment:panNotch (SAM611723)


title: Notch Antagonism Experiment:CTL (SAM611933)


title: Notch Antagonism Experiment:Notch3 (SAM611722)


title: intracranial aneurysm15

city: Beijing

first: Jia

last: Wang

address: Tian Tan Xili 6#

department: Neurosurgery

institute: Beijing Tian Tan Hospital, Capital Medical University

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

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

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: intracranial aneurysm15

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

extract_protocol: Total RNA was extracted and purified using RNeasy micro kit(Cat#74004, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

tag: tissue

value: intracranial aneurysm

tag: individual


title: intracranial aneurysm15 matched superficial temporal artery

value: superficial temporal artery


title: Transgenic waterlogged

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

description: WL TL

hyb_protocol: 1650ng of labeled cRNA were hybridized on the array using the Hi-RPM large Hybridization Kit (Part No: 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression Wash Buffers Set (Part No: 5188-5327).

scan_protocol: The microarray slide was scanned using Agilent Scanner (Agilent Technologies, Part Number G2600D).

data_processing: The scanned images were analyzed using Agilent  Feature Extraction Software  and Normalization of the data was done in GeneSpring GX using the 75th percentile shift.

organism: Arabidopsis

source_name: Transgenic waterlogged plants

label_protocol: The samples were labeled using Agilent Quick Amp Labeling Kit one color (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using oligodT primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using  RNeasy Mini Kit(Qiagen, Cat No: 74106). Concentration and amount of dye incorporated was determined using Nanodrop. Samples that pass the Quality Control for specific activity were taken for hybridization

growth_protocol: Arabidopsis thaliana ecotype Columbia-0 seedlings were grown in a climate-controlled chamber with an 8-h light period initially. After 2 weeks, seedlings were transferred to a 16-h light period growth chamber. For waterlogging experiments, 30-d-old plants were used.

extract_protocol: RNA extraction was done by using Trizol method.

treatment_protocol: Plants grown individually in pots with organic potting mix were placed inside plastic tanks and were exposed to waterlogging by filling up to a level such that the upper water level always remained below the pot upper edge. For control, plants were put inside the tank without flooding.

value: overexpressing waterlogging-inducible-AP2 family of transcription factor

tag: growth condition

value: after 4 days of waterlogging stress


title: EW8 siControl 24h rep3

city: Iowa City

first: David

middle: Jon

last: Gordon

state: Iowa

address: 25 S Grand Ave

department: Pediatric Hematology/Oncology

institute: University of Iowa

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation with GenomeStudio.

source_name: EW8 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from 1 mcg total RNA.

growth_protocol: Cell were cultured for 24 hours in the presence of ciclopirox, DMSO, RRM2 siRNA and non-targeting siRNA

extract_protocol: Total RNA was collected using a Qiagen RNeasy kit according to the manufacturer's directions.

value: Ewing sarcoma

value: siControl


title: Transgenic control

description: TLC

source_name: Transgenic plants

value: control condition


title: EW8 siRRM2 24h rep2

description: replicate 2


title: Wild type waterlogged

description: WL WT

source_name: Wild type waterlogged plants

value: wild type


title: Wild type control

description: WTC

source_name: Wild type plants


title: intracranial aneurysm13

source_name: intracranial aneurysm13


title: intracranial aneurysm12 matched superficial temporal artery

description: 431010 ST


title: intracranial aneurysm14 matched superficial temporal artery


title: intracranial aneurysm14

source_name: intracranial aneurysm14


title: intracranial aneurysm13 matched superficial temporal artery


title: intracranial aneurysm10 matched superficial temporal artery


title: intracranial aneurysm10

source_name: intracranial aneurysm10


title: EW8 siRRM2 24h rep3

description: replicate 3


title: EW8 siControl 24h rep1

description: replicate 1


title: intracranial aneurysm12

description: 431010 An

source_name: intracranial aneurysm12


title: intracranial aneurysm11 matched superficial temporal artery

description: 428592 ST


title: A673 siRRM2 24h rep3

description: replicate 3

source_name: A673 cells


title: intracranial aneurysm11

description: 428592 An

source_name: intracranial aneurysm11


title: EW8 siRRM2 24h rep1

description: replicate 1


title: A673 siControl 24h rep3

description: replicate 3


title: A673 siRRM2 24h rep1

description: replicate 1


title: EW8 siControl 24h rep2

description: replicate 2


title: A673 siRRM2 24h rep2

description: replicate 2


title: intracranial aneurysm9 matched superficial temporal artery


title: 53691602

city: Rockville

first: Rose

last: Yang

state: MD

address: 9609 Medical Center Dr

department: Division of Cancer Epidemiology and Genetics

institute: National Cancer Institute

hyb_protocol: The reference sample was a pool of six male individuals (Promega, Madison, WI) provided by Nimblegen. 2.5 μg of test and reference DNA were labeled with Cy3 and Cy5 respectively and co-hybridized to the array slides. The intensity of the two fluorescent dyes that reflects chromosomal imbalances between test and reference samples was extracted using NimbleScan software, and SignalMap™ was employed to visualize the array-CGH data. The Cy3 and Cy5 signal intensities on each array were normalized to one another using the qspline normalization. The log2 ratio was then created for each probe and was used as input to the segment-calling algorithm (SegMNT) to identify copy number changes and breakpoints. The hybridization, normalization, window-averaging, and segmentation analyses were performed by Nimblegen.

source_name: Germline DNA from Blood

extract_protocol: Standard DNA extraction protocol

tag: affection status (melanoma)

value: Unaffected

tag: age

tag: gender

value: M

tag: cdkn2a mutation status

value: Negative

tag: sample type

value: Pooled from 6 healthy individuals


title: intracranial aneurysm9

source_name: intracranial aneurysm9


title: intracranial aneurysm7 matched superficial temporal artery


title: 53696702

data_processing: The Cy3 and Cy5 signal intensities on each array were normalized to one another using the qspline normalization. The log2 ratio was then created for each probe and was used as input to the segment-calling algorithm (SegMNT) to identify copy number changes and breakpoints.

label_protocol: 2.5 μg of test and reference DNA were labeled with Cy3 and Cy5 respectively and co-hybridized to the array slides. The intensity of the two fluorescent dyes that reflects chromosomal imbalances between test and reference samples was extracted using NimbleScan software, and SignalMap™ was employed to visualize the array-CGH data.

value: Affected


title: intracranial aneurysm8

source_name: intracranial aneurysm8


title: A673 siControl 24h rep2

description: replicate 2

tag: cell line

tag: treatment


title: intracranial aneurysm7

source_name: intracranial aneurysm7


title: 53645302

scan_protocol: The intensity of the two fluorescent dyes that reflects chromosomal imbalances between test and reference samples was extracted using NimbleScan software, and SignalMap™ was employed to visualize the array-CGH data.

value: F


title: U2OS DMSO 24h rep1

description: replicate 1

source_name: U2OS cells

value: DMSO


title: A673 siControl 24h rep1

description: replicate 1


title: U2OS DMSO 24h rep3

description: replicate 3


title: U2OS ciclopirox 24h rep2

description: replicate 2

value: ciclopirox


title: intracranial aneurysm4

source_name: intracranial aneurysm4


title: BJ ciclopirox 24h rep3

description: replicate 3

source_name: BJ cells

value: BJ


title: intracranial aneurysm4 matched superficial temporal artery


title: intracranial aneurysm8 matched superficial temporal artery


title: U2OS ciclopirox 24h rep3

description: replicate 3


title: intracranial aneurysm6

source_name: intracranial aneurysm6

value: intracranial aneurysm


title: U2OS ciclopirox 24h rep1

description: replicate 1


title: intracranial aneurysm5 matched superficial temporal artery

value: superficial temporal artery


title: U2OS DMSO 24h rep2

description: replicate 2


title: 53693702


title: intracranial aneurysm6 matched superficial temporal artery


title: 53757102


title: intracranial aneurysm5

source_name: intracranial aneurysm5


title: intracranial aneurysm3

source_name: intracranial aneurysm3


title: intracranial aneurysm2

source_name: intracranial aneurysm2


title: BJ ciclopirox 24h rep1

description: replicate 1


title: BJ DMSO 24h rep3

description: replicate 3


title: 53659502


title: 53645402


title: 53694202


title: 53698302


title: intracranial aneurysm2 matched superficial temporal artery


title: intracranial aneurysm3 matched superficial temporal artery


title: BJ ciclopirox 24h rep2

description: replicate 2


title: BJ DMSO 24h rep2

description: replicate 2


title: BJ DMSO 24h rep1

description: replicate 1


title: 53694302


title: intracranial aneurysm1

source_name: intracranial aneurysm1


title: intracranial aneurysm1 matched superficial temporal artery


title: EW8 ciclopirox 24h rep3

description: replicate 3

source_name: EW8 cells


title: 53757002


title: 53659302


title: 53677602


title: 53672302


title: 53667702


title: EW8 ciclopirox 24h rep2

description: replicate 2


title: EW8 ciclopirox 24h rep1

description: replicate 1


title: 53683302


title: 53664202


title: Urothelial  cell Passage 8 replicate 3

first: Clara Ibel

last: Chamorro Jimenez

address: Center for Molecular Medicine (CMM) Karolinska University Hospital L8:02 Sweden

department: Department of Women's and Children's Health

country: Sweden

institute: Karolinska Institute

description:
Gene expression of primary human  urothelila cells at passage 8
FELA_8

hyb_protocol: The labeled cDNA probes were in then hybridized to the gene chip and scanned. Hybridization was performed in a GeneChip Hybridization Oven 640 and washing and staining in a GeneChip Fluidic Station 450 according to standard Affymetrix protocols.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G.

data_processing:
Scanned images were preprocessed in Affymetrix GeneChip Operating Software (GCOS) to obtain quantitative signals and qualitative detection calls for each gene and sample. In order to investigate differentially expressed genes, pairwise comparisons of the early and late passage were performed for each of the three cultures, generating quantitative signal log ratios and qualitative change calls.
Affymetrix Microarray Suite (MAS5) was used for the pre-processing, including an all probe set scaling to TGT = 100.

source_name: Human donor 3

label_protocol: Twenty micrograms of total RNA was used to prepare cDNA probes labeled with biotin. Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Urothelial cells were harvested from bladder washing as described previously(1). The cells were seeded in one well of a 6-well plastic cell culture plate (approximately 10 sqcm, company name, city) on a feeder cell layer consisting J2 3T3 cells that had been treated with mitomicyn C (brand and city of manufacture) and cultured in epithelial cell culture medium consisting of DMEM and Ham’s F12 in a 4:1 mixture (Gibco, Scotland) containing 10% fetal bovine serum (Gibco, Scotland), insulin (5 mg/ml), hydrocortisone (0.4 mg/ml), adenine (24 µg/ml, Sigma, MO), cholera toxin (10-7mmol/l), triiodothyronine (2 x106mmol/l), transferrin (5 mg/ml), and antibiotics (penicillin 50 U/ml and streptomycin 50 mg/ml) under standard cell culture conditions. Epidermal growth factor (concentration) (10ng/ml, Sigma, MO) was added to the cell culture medium 24 hours after plating. After approximately two weeks, when the colonies achieved about 50% confluence, cells were de-attached with trypsin and split (passage 1) into two 25 sqcm flasks containing culture medium without feeder cells layer for further propagation. The cells from passage 1 were harvested once the culture flask reached 70-80% confluence.  The cells from one of the 25 sqcm bottles were isolated and re-suspended in freezing medium in -180°C as described previously [3]. The other 25 sqcm bottle was passaged and split 1:3 (passage 2) for future propagation until passage 8.    Rerence:M. Fossum, C.J. Gustafson, A. Nordenskjold, G. Kratz, Isolation and in vitro cultivation of human urothelial cells from bladder washings of adult patients and children, Scandinavian journal of plastic and reconstructive surgery and hand surgery / Nordisk plastikkirurgisk forening [and] Nordisk klubb for handkirurgi, 37 (2003) 41-45

extract_protocol: We used the RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions

treatment_protocol: Total RNA was prepared and analyzed separately from three independent samples of primary urothelial cell cultures (three different donors) in passage 2 and 8 by using RNeasy Mini Kit (Qiagen, Valencia, CA, USA).

tag: donor

value: primary urothelial cell

tag: passage


title: 53662602


title: Urothelial  cell Passage 8 replicate 1

description:
Gene expression of primary human  urothelila cells at passage 8
LIJA_8

source_name: Human donor 1


title: A673 ciclopirox 24h rep3

description: replicate 3

source_name: A673 cells


title: EW8 DMSO 24h rep2

description: replicate 2


title: Urothelial  cell Passage 8 replicate 2

description:
Gene expression of primary human  urothelila cells at passage 8
STIS_8

source_name: Human donor 2


title: 53662502

source_name: Germline DNA from Blood


title: EW8 DMSO 24h rep1

description: replicate 1


title: Urothelial  cell Passage 2 replicate 3

description:
Gene expression of primary human urothelial cells at passage 2
FELA_2


title: Urothelial  cell Passage 2 replicate 1

description:
Gene expression of primary human urothelial cells at passage 2
LIJA_2


title: A673 ciclopirox 24h rep1

description: replicate 1


title: EW8 DMSO 24h rep3

description: replicate 3


title: Urothelial  cell Passage 2 replicate 2

description:
Gene expression of primary human urothelial cells at passage 2
STIS_2


title: 53678102


title: A673 DMSO 24h rep3

description: replicate 3


title: 53665402


title: A673 ciclopirox 24h rep2

description: replicate 2


title: 53663502


title: A673 DMSO 24h rep2

description: replicate 2


title: A673 DMSO 24h rep1

description: replicate 1


title: 53664002


title: control 48 hours experiment c

city: Roseworthy

first: Ruijie

last: Liu

state: South Australia

address: Mudla Wirra Rd

country: Australia

institute: the university of Adelaide

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol with iScan instrument.

data_processing: The scanner operating software, GenomeStudio, converts the signal on the array into a TXT file for analysis. The data were then calibrated and quantile normalized using the neqc method of Shi et al. (2010) [PMID:20929874]. This analysis was was carried out in R using the limma package.

source_name: SGBS adipocytes

label_protocol: Biotinylated cRNA were prepared with the ® TotalPrep™ RNA Amplification Kit   for Illumina arrays

extract_protocol: RNA was extracted using QIAGEN RNeasy micro kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: adipocytes

value: control

value: c


title: 53694002


title: 53663702


title: 53689202


title: DCM_human endomyocardIA/IgGl biopsy P55  IA/IgG_follow up

city: Greifswald

first: Sabine

last: Ameling

address: Felix-Hausdorff.Str 8

department: Interfakultäres Institut für Genetik und Funktionelle Genomforschung

institute: Universitätsmedizin Greifswald

description: P55  IA_FU

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip System Confocal Scanner 3000.

data_processing: Expression raw data were transferred to Rosetta Resolver 7.2 (Rosetta Inpharmatics LLC) and MAS 5.0 extraction algorithm was performed. For further analyses probe sets  exhibiting p<0.05 were used. The pipeline calculates expression summaries using MAS5 via Affymetrix Power Tools from scans using both the perfect-match (PM) and mis-match (MM) probes. It returns only sequence-level results. The resulting P-values may be used as a guideline to decide expression presence or absence. This pipeline combines the expression values for individual profiles using an arithmetic average and computes the error of the result. P-value is the geometric mean of the profile-level P-values. Results are computed from sequence-level data using group processing. All profiles in the experiment definition are normalized together.

label_protocol: Two round T7 RNA polymerase mediated linear amplification was performed with 14-25ng RNA starting amount according to the Affymetrix manufacturers Two Cycle Target Labelling protocol

extract_protocol: Column based RNA extraction (Qiagen) was performed following the manufacturers instructions for total RNA isolation from fibrous tissues, including purifications step using Charge Switch Total RNA Cell Kit. RNA integrity was checked using RNA 6000 Pico LabChip on a Bioanalyzer 2100 (Agilent)

value: endomyocardial biopsy

tag: lvef

tag: lvidd

value: male

tag: virus

value: HHV6 B

tag: inflammation (cd68+ + cd3+)

tag: bmi


title: 53663602


title: active 24 hours experiment c

tag: cell type

value: active

tag: experiment


title: active 48 hours experiment c


title: DCM_human endomyocardIA/IgGl biopsy P54  IA/IgG_follow up

description: P54  IA_FU

value: negative


title: DCM_human endomyocardIA/IgGl biopsy P56  IA/IgG_follow up

description: P56  IA_FU

value: female


title: DCM_human endomyocardIA/IgGl biopsy P53  IA/IgG_follow up

description: P53  IA_FU


title: DCM_human endomyocardIA/IgGl biopsy P52  IA/IgG_follow up

description: P52  IA_FU


title: DCM_human endomyocardIA/IgGl biopsy P50  IA/IgG_follow up

description: P50  IA_FU


title: active 48 hours experiment b

value: b


title: active 24 hours experiment b


title: control 24 hours experiment c


title: DCM_human endomyocardIA/IgGl biopsy P45  IA/IgG_follow up

description: P45  IA_FU


title: control 48 hours experiment b


title: DCM_human endomyocardIA/IgGl biopsy P48  IA/IgG_follow up

description: P48  IA_FU


title: DCM_human endomyocardIA/IgGl biopsy P46  IA/IgG_follow up

description: P46  IA_FU


title: 48127302

value: Unaffected

value: F

value: Negative

value: Pooled from 6 healthy individuals


title: control 24 hours experiment b


title: 53661902

value: Affected

value: M


title: DCM_human endomyocardIA/IgGl biopsy P47  IA/IgG_follow up

description: P47  IA_FU


title: active 48 hours experiment a

value: a


title: 53683102


title: DCM_human endomyocardIA/IgGl biopsy P43  IA/IgG_follow up

description: P43  IA_FU


title: DCM_human endomyocardIA/IgGl biopsy P51  IA/IgG_follow up

description: P51  IA_FU


title: 53667602


title: DCM_human endomyocardIA/IgGl biopsy P44  IA/IgG_follow up

description: P44  IA_FU


title: 53683202


title: 53689502


title: 48149502


title: active 24 hours experiment a

value: adipocytes


title: 48219302


title: 53648302


title: 53663802


title: 53689302


title: control 24 hours experiment a

value: control


title: 53648802


title: Obinutuzumab1

city: Valhalla

first: Sanghoon

last: Lee

state: NY

address: 40 Sunshine Cottage Road, Vos 145

department: Pediatrics

institute: New York Medical College

description: Rep 1

scan_protocol: Standard Illumina scanning protocol

data_processing:
Standard data processing by GenomeStudio version 1.0.6
Note from submitter: both (normalized and non-normalized) are the identical; based on the distribution of signal intensity on QC data, we observed that identical result between normalized and non-normalized data.

source_name: Karpas PMBL cell line

label_protocol: Biotin-labeled RNA was prepared using 200ug of total RNA by MessageAmp™ Premier RNA Amplification Kit for Illumina arrays

growth_protocol: The Karpas-1106P cell lines were cultured in RPMI 1640 medium supplemented with 20% heat-inactivated fetal bovine serum (GIBCO BRL, Gaithersburg, MD, USA) and 1% Glutamine and penicillin-streptomycin in a humid environment of 5% CO2 at 37C.

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 Nanodrop and Agilent Bioanalyser.

treatment_protocol: 10ug/ml of obinutuzumab was treated into cells for 48 hours

tag: agent

value: Obinutuzumab

value: Karpas-1106P PMBL


title: Obinutuzumab2

description: Rep 2


title: control 48 hours experiment a


title: DCM_human endomyocardIA/IgGl biopsy P39  IA/IgG_follow up

description: P39  IA_FU

value: endomyocardial biopsy


title: DCM_human endomyocardIA/IgGl biopsy P36  IA/IgG_follow up

description: P36  IA_FU


title: DCM_human endomyocardIA/IgGl biopsy P37  IA/IgG_follow up

description: P37  IA_FU

value: male


title: IgG1

description: Rep 1

value: IgG


title: DCM_human endomyocardIA/IgGl biopsy P40  IA/IgG_follow up

description: P40  IA_FU

value: negative


title: DCM_human endomyocardIA/IgGl biopsy P38  IA/IgG_follow up

description: P38  IA_FU


title: IgG2

description: Rep 2


title: PBS2

description: Rep 2

value: PBS


title: 54552402

tag: affection status (melanoma)


title: PBS1

description: Rep 1


title: 53697702

tag: age


title: DCM_human endomyocardIA/IgGl biopsy P35  IA/IgG_follow up

description: P35  IA_FU

tag: gender


title: 53688002

tag: cdkn2a mutation status


title: DCM_human endomyocardIA/IgGl biopsy P30  IA/IgG_follow up

description: P30  IA_FU

tag: sample type

value: female


title: 53662102


title: DCM_human endomyocardIA/IgGl biopsy P31  IA/IgG_follow up

description: P31  IA_FU


title: 53661802

value: Unaffected


title: DCM_human endomyocardIA/IgGl biopsy P27  IA/IgG_follow up

description: P27  IA_FU


title: DCM_human endomyocardIA/IgGl biopsy P34  IA/IgG_follow up

description: P34  IA_FU


title: DCM_human endomyocardIA/IgGl biopsy P32  IA/IgG_follow up

description: P32  IA_FU


title: 53648502


title: Healthy Ctrl NCH 666

city: Columbus

first: Santiago

last: Lopez

state: OH

address: 700 Children's dr.

department: Center for Vaccines & Immunity

institute: The Research Institute at the Nationwide Children's Hospital

hyb_protocol: Standard Illumina hybridization protocol .

scan_protocol: Standard Illumina scanning protocol .

data_processing: The data were normalized using average normalization in GenomeStudio’s gene expression module.

label: Total RNA

source_name: Nasal Wash

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep kit for Illumina arrays.

extract_protocol: Total Nasal Wash cell was resuspended in 0.3 or 0.6mL of 2-mercaptoethanol as a lysing buffer and stored at -80C until further processing. Total RNA extraction was performed using PureLink™ RNA Mini Kit (Invitrogen; Catalog No.: 12183018A) per manufacture’s instructions. Briefly, RNA extraction was performed at room temperature, once thaw, samples were transferred into a homogenization tube, centrifuge and proceed to RNA purification. For RNA purification, the sample was transferred into RNase-free tube and added an equal volume of 70% ethanol; subsequently the sample was added into a spin cartridge to bind the RNA to a membrane. After washing the sample (x3), we added a volume of 30-100 uL of RNase-free water to elute the RNA into a recovery tube. RNA integrity was assessed using NanoDrop® sample Spectrophotometers and a Bioanalyzer.

tag: age (month)

value: F

tag: infection

value: healthy

value: Nasal wash


title: Healthy Ctrl NCH 656


title: Healthy Ctrl NCH 681


title: Healthy Ctrl NCH 657


title: 48135102

value: Affected

value: Negative

value: Pooled from 6 healthy individuals


title: DCM_human endomyocardIA/IgGl biopsy P23  IA/IgG_follow up

description: P23  IA_FU


title: 53694402


title: DCM_human endomyocardIA/IgGl biopsy P25  IA/IgG_follow up

description: P25  IA_FU


title: DCM_human endomyocardIA/IgGl biopsy P18  IA/IgG_follow up

description: P18  IA_FU


title: Healthy Ctrl NCH 674

value: M


title: 53662002


title: DCM_human endomyocardIA/IgGl biopsy P22  IA/IgG_follow up

description: P22  IA_FU


title: DCM_human endomyocardIA/IgGl biopsy P16  IA/IgG_follow up

description: P16  IA_FU


title: DCM_human endomyocardIA/IgGl biopsy P21  IA/IgG_follow up

description: P21  IA_FU


title: Healthy Ctrl NCH 684


title: 52977302


title: 53696802


title: DCM_human endomyocardIA/IgGl biopsy P15  IA/IgG_follow up

description: P15  IA_FU


title: 53694602


title: 53698202


title: Healthy Ctrl NCH 678


title: DCM_human endomyocardIA/IgGl biopsy P11  IA/IgG_follow up

description: P11  IA_FU


title: DCM_human endomyocardIA/IgGl biopsy P13  IA/IgG_follow up

description: P13  IA_FU


title: Healthy Ctrl NCH 659


title: 53691902


title: Healthy Ctrl NCH 672


title: 53677702


title: 48219402


title: RSV NCH 652

value: RSV


title: Healthy Ctrl NCH 688


title: 53697402


title: 53668502


title: 53665702


title: RSV NCH 651


title: 53711402


title: 53697302


title: 48140902


title: RSV NCH 648


title: RSV NCH 645


title: RSV NCH 643


title: RSV NCH 638


title: RSV NCH 632


title: 53693802


title: RSV NCH 644


title: 53692002


title: RSV NCH 628


title: 53694502


title: 48149402


title: RSV NCH 630


title: RSV NCH 639


title: RSV NCH 637


title: RSV NCH 636


title: 53693302


title: 53698402


title: 54552602


title: 53671702


title: RSV NCH 623


title: 52977402


title: 53693402


title: RSV NCH 624


title: 53677502


title: 53694702


title: 53711602


title: RSV NCH 625


title: RSV NCH 622


title: RSV NCH 621


title: RSV NCH 617


title: 48135002


title: RSV NCH 618


title: RSV NCH 626


title: 53693502


title: 53696902


title: RSV NCH 613


title: RSV NCH 611


title: RSV NCH 619


title: 48149602


title: 53693902


title: 53672202


title: RSV NCH 607


title: RSV NCH 609


title: RSV NCH 612


title: RSV NCH 602


title: 53697502


title: 53678002


title: RSV NCH 605


title: RSV NCH 601


title: RSV NCH 597


title: RSV NCH 610


title: RSV NCH 595


title: 48219202


title: 53659402


title: RSV NCH 598


title: 53689102


title: RSV NCH 600


title: 52977202


title: 48144502


title: 53665502


title: RSV NCH 592


title: 53678202


title: 53693602


title: 53665902


title: 53688202


title: RSV NCH 589


title: 53665802


title: RSV NCH 590


title: RSV NCH 593


title: 53697202


title: RSV NCH 587


title: RSV NCH 588


title: RSV NCH 582


title: 48195602


title: 53711502


title: 53697802


title: 53691802


title: 53668802


title: RSV NCH 574


title: RSV NCH 581


title: RSV NCH 578


title: RSV NCH 584


title: 53648402


title: 48195702


title: 53663402


title: 53648702


title: 53689402


title: 53668702


title: 53693102


title: 53697602


title: RSV NCH 572


title: 53677802


title: RSV NCH 576


title: RSV NCH 570


title: RSV NCH 569


title: 53669002


title: RSV NCH 561


title: 53663902


title: RSV NCH 563


title: 53662402


title: RSV NCH 556


title: RSV NCH 573


title: RSV NCH 568


title: RSV NCH 555


title: RSV NCH 554


title: RSV NCH 560


title: RSV NCH 571


title: 53668602


title: RSV NCH 549


title: 53678302


title: 48127402


title: 53662202


title: 53671602


title: RSV NCH 552


title: 53671802


title: RSV NCH 562


title: 53688102


title: 53667802


title: 53694102


title: 53645502


title: 53672402


title: 53693202


title: 53691702


title: 53662302


title: RSV NCH 548


title: RSV NCH 547


title: RSV NCH 553


title: RSV NCH 546


title: RSV NCH 550


title: 53697102


title: 53665602


title: RSV NCH 535


title: RSV NCH 538


title: 53677902


title: 48140802


title: 54552502


title: bdf1Δhda1Δ vs bdf1Δ-2

city: Jinan

first: Xiaoming

last: Bao

state: Shandong

address: Shanda Nan Road 27

department: State Key Laboratory of Microbial Technology

institute: Shandong University

description: For each test and control sample, two hybridizations were performed by using a reversal fluorescent strategy. Only genes whose alteration tendency kept consistency (  >2-fold) in both microarray were selected as differentially expressed genes

hyb_protocol: Labeled control and test samples were quantitatively adjusted based on the efficiency of Cy5-dCTP or Cy3-dCTP incorporation and mixed into 80uL hybridization solution (3×SSC, 0.2%SDS, 5×Denhart’s, 25%  formamide). DNA in hybridization solution was denatured at 95°C for 3 min before loading onto a microarray. The array was hybridized at 42°C overnight and washed with two consecutive washing solutions (0.2% SDS，2×SSC at 42°C for 5 min, and 0.2×SSC for 5 min at room temperature).

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a LuxScan3.0 fluorescent scanner (Capital Bio Corp. Beijing, China), and image intensity data were extracted and analyzed with a GenePix Pro 4.0 (Axon Instruments, Foster City, CA).

data_processing: A space and intensity-dependent normalization based on a LOWESS program was employed. For each test and control sample, two hybridizations were performed by using a reversal fluorescent strategy. Only genes whose alteration tendency kept consistency (both above 2-fold) in both microarray were selected as differentially expressed genes.

source_name: bdf1Δhda1Δ under salt treatment

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, GE Healthcare Bio-Sciences, Piscataway, NJ, USA) labeled DNA was produced through Eberwine's linear RNA amplification method.and subsequent enzymatic reaction. The total RNA was purified using NucleoSpin® RNA clean-up kits (MACHEREY-NAGEL, Germany). Because  oligonucleotide arrays were used here, we took a cDNA labeling approach with Klenow enzyme after reverse transcription.

extract_protocol: Total yeast RNA was isolated using NucleoSpin® RNA clean-up kits (MACHEREY-NAGEL, Germany).

tag: strain

tag: stress

value: salt

source_name: bdf1∆ under salt treatment


title: RSV NCH 534


title: 53697002


title: RSV NCH 522


title: RSV NCH 157


title: RSV NCH 503


title: 48129902


title: RSV NCH 530


title: bdf1Δhda1Δ vs bdf1Δ-1


title: RSV NCH 520


title: 53689002


title: 54552902


title: 48195502


title: 37996302

value: Positive


title: bdf1Δ vs W303

description: For each test and control sample, two hybridizations were performed by using a reversal fluorescent strategy. Only genes whose alteration tendency kept consistency ( > 2-fold) in both microarray were selected as differentially expressed genes

source_name: W303 under salt treatment


title: 37947702


title: 37996602


title: 37979202


title: 37947202


title: bdf1Δ+HAL2 vs bdf1Δ-1

source_name: bdf1Δ+HAL2 under salt treatment


title: bdf1Δ+HAL2 vs bdf1Δ-2


title: 37894702


title: 37947402


title: RSV NCH 599


title: Control 2

city: Los Angeles

first: Brendan

middle: H

last: Grubbs

address: 4661 W. Sunset Blvd.

department: Obstetrics and Gynecology

institute: University of Southern California

description: ERCC ExFold mix 1

hyb_protocol: Affymetrix standard

scan_protocol: Affymetrix standard

data_processing: R/bioconductor software xps with vsn usng the ERCC controls as a subset for normalization. Data was summarized by the median-polish method of xps. Statistical analysis was performed with limma using empirical Bayes.

label_protocol: Affymetrix standard

extract_protocol: Total RNA from flow sorted cell suspensions was extracted with standard Ambion trizol reagent.

treatment_protocol: Pregnant Rat Dams were gavage fed all-trans retinoic acid 60mg/kg in ultra pure olive oil. Control animals were gavage fed an equivalent amount of olive oil only.

tag: developmental stage

tag: treatment

value: control

value: neuroepithelial progenitor cells


title: Control 1

description: ERCC ExFold mix 1


title: 37937202


title: Retinoic Acid 3

description: ERCC ExFold mix 2

value: Retinoic acid


title: Retinoic Acid 2

description: ERCC ExFold mix 2


title: Retinoic Acid 1

description: ERCC ExFold mix 2


title: mRNA_OE-SSZ1Δire1Δscj1-rep3

city: Zhenjiang

first: Huang

last: Guoping

state: Jiangsu province

address: Xuefu Road 301#

department: Institute of Life Sciences

institute: Jiangsu University

hyb_protocol: 600ng of labeled cRNA was hybridized onto Agilent SurePrint G3 GE 8x60K Microarray for 17 hours at 65°C, 10 rpm in Agilent hybridization oven.

scan_protocol: After hybridization, the microarray slide was washed in gene expression wash buffer 1 for one minute at room temperature and another minute in gene expression wash buffer 2 at 37°C before scanning on Agilent High Resolution Microarray Scanner (C-model).

data_processing:
Raw signal data were extracted from the TIFF image with Agilent Feature Extraction Software (V10.7.1.1). The raw data were imported into GeneSpring GX 13.0 (Agilent Technologies) for the analysis. Source technology Agilent.SingleColor.31120 was used and saccharomyces cerevisiae was chosen as source organism.
After removed control probes, filtered on flags[detected], and filtered on expression (20.0-673749.438) with entities where at least 100 percent of samples in any 1 out of 3 conditions have values within cut-off, retained values were analyzed using one-way ANOVA with corrected p-value cut-off 0.05 and multiple testing corrections by the Benjamini and Hochberg method (Benjamini and Hochberg, 1995) to correct false discovery rate, and asymptotic P value computation was performed to determine differential expression of genes.

label: cyanine 3-CTP

label_protocol: 100 ng of total RNA was labeled with Low Input Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-2305) following manufacturer instruction (One-Color Microarray-Based Gene Expression, Analysis Low Input Quick Amp Labeling, version 6.5). Briefly, 100 ng of total RNA was converted into double-stranded cDNA by priming with an oligo-dT primer containing the recognition site for T7 RNA polymerase. In vitro transcription with T7 RNA polymerase was used to produce cyanine 3-CTP labeled cRNA.

growth_protocol: Cultures of samples were grown to an OD600 of 0.2-0.3 at 30 °C in synthetic media with shaking at 200 rpm.

extract_protocol: Total RNA of samples was extracted by using the RNeasy Mini Kit (Qiagen).

treatment_protocol: Cells of samples were harvested from cultures with a concentration of less than 0.3 OD/mL.

tag: growth phase

value: early log phase

tag: genotype

value: OE SSZ1Δire1Δscj1


title: 37924302


title: Control 3

description: ERCC ExFold mix 1


title: 37924502


title: 39280402


title: 37927102


title: 37937502


title: 37924102


title: mRNA_Δire1-rep1


title: 37894802


title: mRNA_Δire1-rep2


title: mRNA_OE-SSZ1Δire1-rep1

value: OE SSZ1Δire1


title: mRNA_OE-SSZ1Δire1Δscj1-rep2


title: mRNA_Δire1-rep3


title: 37991202