title: PBS 4


title: Liver, B102_28_L_VC1, replicate 1

status: Public on Sep 30 2016

type: RNA

city: Kitakatsushika-gun

first: Kyosuke

last: Yamashita

state: Saitama

address: Sugito-machi Shimotakano1600

department: Tokyo

country: Japan

institute: Chemicals Evaluation and Research Institute Japan

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60oC for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Rat GE 8x60K Microarray Toxplus for 17 hours at 65ﾂｰC in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37ﾂｰC GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 035170_D_F_20110629) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

organism: Rattus norvegicus

source_name: Liver, B102_28_L_VC1, replicate 1

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

growth_protocol: 5 week-old male Sprague-Dawley (Crl:CD(SD)) Rat were purchased from Charles River Japan. They were housed in an air-conditioned room at 21 to 25 deg C and 40 to 70% humidity, with a 12 h light, 12 h dark cycle. Rats were maintained on a basal diet (Oriental Yeast Co.), with tap water ad libitum.

extract_protocol: RNA was prepared using the miRNA Neasy kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Three animals were administrated corn oil for nine weeks, the other three animals were administrated 1-Amino-2,4-Dibromoanthraquinone (1000 mg/kg/day) for nine weeks.

tag: tissue

value: Liver

tag: treatment

value: Purified Water

tag: strain

value: Sprague-Dawley

tag: gender

value: male


title: WILD TESTIS1

city: Akita

first: Tatsunori

last: Shimizu

address: 1-1-1 Hondo

department: Endocrinology, Diabetes and Geriatric Medicine

institute: Akita University Graduate School of Medicine

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x80k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (GE1_107_Sep09 Protocol). We removed control probe and week signal probes which has gIsWellAboveBG = 0 in all samples. Signal intesity was normalized by Median Normalize method. gProcessedSignal intensity diveded by each sample's median intensity and multipled by 200.

organism: Mus musculus

source_name: Removed testis after anesthetic overdose euthanasia

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: no entry provided by submitter

value: whole testis

tag: age

tag: genotype

value: wild type


title: VEGF-B+DOX 4

city: Helsinki

first: Riikka

last: Kivelä

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki and Wihuri Research Institute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Chipster software (www.chipster.csc.fi)

label: Biotin

source_name: Myocardium

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

extract_protocol: Total RNA was isolated from myocardium with TRIsure reagent (Bioline) and further purified with NucleoSpin RNA II (Macherey-Nagel). Quality control was performed with Agilent Bioanalyser.

value: 10 weeks

value: Male


title: Liver, B93_28_L_H1, replicate 1

source_name: Liver, B93_28_L_H1, replicate 1

treatment_protocol: Three animals were administrated corn oil for nine weeks, the other three animals were administrated Phenolphthalein (1000 mg/kg/day) for nine weeks.

value: Phenolphthalein (1000 mg/kg/day)


title: WILD TESTIS3


title: GIPRKO TESTIS3

value: GIPR KO


title: PBS 3

value: injected with PBS


title: GIPRKO TESTIS2


title: GIPRKO TESTIS1


title: Olfactory placode at HH20, biological rep3

city: London

first: Anthony

last: Graham

address: Guys Campus

department: Developmental Neurobiology

country: United Kingdom

institute: Kings College London

hyb_protocol: Affymetrix manufacturer's recommendation for Chicken Genome Arrays.

data_processing: Affymetrix default CEL file generation & MAS5 for CHP.

label: biotin

organism: Gallus gallus

source_name: Olfactory placode, HH20 embryo

label_protocol: Nugen Ovation V2& Nugen Encore Biotin Module.

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

treatment_protocol: Olfactory placodes were dissected from chick embryos at stages 16, 18 and 20.

value: Olfactory placode

value: HH stage 20 embryo


title: Liver, B92_28_L_H3, replicate 3

source_name: Liver, B92_28_L_H3, replicate 3

treatment_protocol: Three animals were administrated corn oil for nine weeks, the other three animals were administrated Bromodichloromethane (200 mg/kg/day) for nine weeks.

value: Bromodichloromethane (200 mg/kg/day)


title: S. bayanus vs S. cerevisiae 67C, 2 ug

type: genomic

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

country: USA

institute: University of Washington

description: Agilent hybe, short standard washes

hyb_protocol: reference URL : http://dunham.gs.washington.edu/MDhomemadeDNA.pdf

scan_protocol: Pixel Size : 5 Scan Date : 2005-06-24 Scan Time : 11:34:27 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.1.0.10
Datafile type : GenePix Results 3
Image Origin : 0, 0

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: D62 genomic DNA

extract_protocol:
Extracted molecule : Genomic DNA
Extraction method : Hoffman-Winston prep http://dunham.gs.washington.edu/UWyeastDNAprep.pdf

tag: strain name

value: wt S. cerevisiae

source_name: new D67 genomic DNA

value: wt S. uvarum


title: WILD TESTIS2


title: VEGF-B+DOX 3


title: DOX 3

value: doxorubicin


title: Olfactory placode at HH20, biological rep2

scan_protocol: Affymetrix manufacturer's recommendation for Chicken Genome Arrays.


title: Liver, B92_28_L_H2, replicate 2

source_name: Liver, B92_28_L_H2, replicate 2

value: Liver


title: VEGF-B+DOX 2


title: Liver, B92_28_L_VC2, replicate 2

source_name: Liver, B92_28_L_VC2, replicate 2

value: Corn Oil


title: S. bayanus vs S. cerevisiae 67C, 1 ug

description: Agilent hybe, short standard washes

scan_protocol: Pixel Size : 5 Scan Date : 2005-06-24 Scan Time : 11:18:34 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

label_protocol: reference URL : http://dunham.gs.washington.edu/MDhomemadeDNA.pdf


title: Liver, B92_28_L_H1, replicate 1

source_name: Liver, B92_28_L_H1, replicate 1

value: Sprague-Dawley


title: Liver, B92_28_L_VC3, replicate 3

source_name: Liver, B92_28_L_VC3, replicate 3

value: male


title: Liver, B92_28_L_VC1, replicate 1

source_name: Liver, B92_28_L_VC1, replicate 1


title: Olfactory placode at HH18, biological rep3

source_name: Olfactory placode, HH18 embryo

value: HH stage 18 embryo


title: S. bayanus vs S. cerevisiae 65C, 1 ug, normal wash

description: quick washes

scan_protocol: Pixel Size : 5 Scan Date : 2005-06-29 Scan Time : 11:03:28 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: S. cerevisiae 1 ug DNA

source_name: S. bayanus 1 ug DNA


title: DOX 2


title: PBS 1


title: S. bayanus vs S. cerevisiae 65C, 1 ug, long  wash

description: microarray facility long washes, all RT

scan_protocol: Pixel Size : 5 Scan Date : 2005-06-29 Scan Time : 11:39:52 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: S. bayanus vs S. cerevisiae 65C, 1 ug, short 65C  wash

description: quick washes with 65C wash 1

scan_protocol: Pixel Size : 5 Scan Date : 2005-06-29 Scan Time : 11:19:19 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: VEGF-B+DOX 1


title: Olfactory placode at HH20, biological rep1


title: Olfactory placode at HH18, biological rep1


title: S. bayanus vs S. cerevisiae 2 ug DNA 65C

description: Agilent hybe buffer, standard quick washes

scan_protocol: Pixel Size : 5 Scan Date : 2005-06-22 Scan Time : 15:24:34 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: S. cerevisiae (D62) DNA 2 ug

source_name: S. bayanus (D67) DNA 2 ug


title: DOX 1


title: Olfactory placode at HH18, biological rep2


title: S. bayanus vs S. cerevisiae 1 ug DNA 65C

scan_protocol: Pixel Size : 5 Scan Date : 2005-06-22 Scan Time : 15:08:25 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: S. cerevisiae (D62) DNA 1 ug

source_name: S. bayanus (D67) DNA 1 ug


title: M7237_2 22

city: Oak Ridge

first: Dawn

middle: Marie

last: Klingeman

state: TN

address: 1 Bethel Valley Rd building 15056 Rm 366  MS 6038

department: Biosciences Division

institute: Oak Ridge National Lab

hyb_protocol: NimbleGen Hyb Station, 42oC 24hours The labeling, hybridization, and scanning following NimbleGen company's protocols.

scan_protocol: Agilent Scanner_Green_100% The labeling, hybridization, and scanning following NimbleGen company's protocols.

data_processing: Statistical analysis was done with JMP Genomics software (SAS Institute, Cary, NC). The data were subsequently normalized using the Loess normalization algorithm within JMP Genomics. An analysis of variance (ANOVA) was performed to determine differential expression levels between conditions and time points using the FDR testing method (p < 0.05).

label_protocol:
Label with Cy3
The labeling, hybridization, and scanning following NimbleGen company's protocols.

growth_protocol: S. cerevisiae yeast strains M6880 and M7237 were cultured in chemostats using Verdyn’s medium with 10g/L glucose and 2g/L xylose as carbon sources. Chemostat cultures were operated at pH 5.5, 35C

extract_protocol:
Trizol with bead beating extraction followed by DNaseI treatment and Qiagen kit purification
RNA was extracted using a previously described method that involved resuspending previously frozen cells in TRIzol reagent (Invitrogen, CA) and lysis via a bead beating method [23]. Briefly, frozen cell pellets were resuspended into 3 mL TRIzol reagent. Cells were lysed by adding ~1.5 mL of cell pellet/TRIzol mixture to 2 mL screw top tubes containing 0.25 g glass beads (MoBio Laboratories, CA) and bead beating at three 20 second cycles at 6500 rpm for several aliquots. Bead beating was conducted in a Precellys-24 (Bertin Technologies, Montigny-le-Bretonneux, France) bead beater. RNA was treated with DNAse I (Ambion, TX), purified using an RNeasy mini kit (Qiagen, CA), and quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, DE). The quality of extracted RNA was determined with an Agilent BioAnalyzer. Purified RNA of high quality was used as the template to generate ds-cDNA using Invitrogen Superscript double-stranded synthesis kit according to the manufacturers protocols (Invitrogen, CA). ds-cDNA was labeled, hybridized and washed according to the NimbleGen protocols essentially as described previously  ( Yang S, Giannone RJ, Dice L, Yang ZK, Engle NL, Tschaplinski TJ, Hettich RL, Brown SD: Clostridium thermocellum ATCC27405 transcriptomic, metabolomic and proteomic profiles after ethanol stress. BMC Genomics 2012, 13:336.)

treatment_protocol: Two chemostats were used to grow each strain (M6880 and M7237) using growth conditions described above (growth protocol) (i.e. four chemostats in total) and each chemostat was sampled on the following dates; 1/28/14, 1/29/24, 1/30/14, 1/31/14.

tag: biological rep

tag: sample date

tag: tech rep y n

value: Y

tag: parent adapted

value: Adapted

tag: promot sample type

value: cDNA derived from Total RNA

tag: biomaterial provider

value: ORNL

tag: sample

tag: columnname

tag: intensity

value: PM


title: Olfactory placode at HH16, biological rep2

source_name: Olfactory placode, HH16 embryo

value: HH stage 16 embryo


title: MD4:ML5 anergic B cells sort 3

city: Darlinghurst

first: Christopher

middle: Carl

last: Goodnow

state: NSW

address: 384 Victoria Street

department: Immunology

country: Australia

institute: Garvan Institute of Medical Research

description:
Gene expression in anergic B cells coexpressing IgM and IgD
MD4:ML5  mouse 58: 252800516797_S01_GE1_107_Sep09_2_2

hyb_protocol: 600 ng Cy3-labelled fragmented cRNA was hybridized for 17 hrs at 65˚C to Agilent Whole Mouse Genome Oligo Microarrays 8x60K according to the Agilent 60-mer microarray processing protoco using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min.

scan_protocol: After washing, the arrays were scanned on an Agilent Microarray Scanner System G2505C.

data_processing: Using Agilent Feature Extraction Software, protocol GE1_107_Sep09, signal intensities from individual features were normalized by dividing by the median signal of all features on the same array, yielding the relative mRNA units shown

source_name: MD4:ML5 anergic B cells sort 3

label_protocol: Cy3 labelled cRNA was produced by linear T7-based amplification using the Agilent Low Input Quick Amp Labeling Kit following the manufacturer’s protocol, and yields measured with a Nanodrop ND-1000 Spectrophotometer.

growth_protocol: All mice of C57BL/6 background raised in the same room in specific pathogen free environment in microisolator cages with feed and water ad libitum. Where possible, donors of naïve and anergic B cells were siblings.

extract_protocol: Cell pellets were lysed and RNA isolated on NucleoSpin RNA II kits (Macherey-Nagel) using standard protocols. RNA quality was analyzed on an Agilent 2100 Bioanalyzer and samples with RIN >6.4 were used.

treatment_protocol: CD93- CD23+ B220+ HEL-binding kappa light chain+ B cells were sorted from spleen cell suspensions in RPMI 2%FCS on ice. Aliquots comprising 100,000 selected cells were sorted into 15 ml Falcon tubes containing 2 ml fetal calf serum, on ice. The cells were washed in PBS, resuspended in 1400 ul PBS, transferred to 1.5 ml Eppendorf tubes, centrifuged at 900 g for 6 min at 4˚C, supernatants removed, and tubes with cell pellets snap frozen in liquid N2, stored at -80˚C, and all tubes shipped together on dry ice to Miltenyi Biotec, Germany for processing and microarray hybridization as a single batch.

value: 101 days

tag: cell type

value: Spleen mature B cells

tag: sorted cell type

value: anergic B cell

tag: cell expression

value: coexpressing IgM and IgD


title: AAV8-NLS-mCherry (Control)-3

source_name: AAV8-NLS-mCherry (Control)_tibialis anterior muscle

extract_protocol: Total RNA was isolated fromtibialis anterior muscle with TRIsure reagent (Bioline) and further purified with NucleoSpin RNA II (Macherey-Nagel). Quality control was performed with Agilent Bioanalyser.

tag: strain

value: 3 months

value: Male

tag: genotype/variation

value: AAV8-mCherry contro

tag: tissue

value: tibialis anterior muscle


title: Olfactory placode at HH16, biological rep3

value: Olfactory placode

tag: age


title: Olfactory placode at HH16, biological rep1


title: M7237_2 18


title: M7237_2 15

value: N


title: S-BC4-D-g285-pop-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2005-07-16 Scan Time : 17:42:31 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: BC3 genomic DNA

tag: strain name

value: ancestral hybrid strain

source_name: F22 10/31/4 genomic DNA

value: evolved hybrid strain


title: M7237_2 11

tag: biological rep

value: Adapted


title: MD4 naïve B cells sort 3

description:
Gene expression in naïve B cells coexpressing IgM and IgD
MD4  mouse 57: 252800516798_S01_GE1_107_Sep09_1_2

source_name: MD4 naïve B cells sort 3

tag: gender

value: male

value: naïve B cell

tag: genotype


title: M7237_2 7

tag: sample date

tag: tech rep y n

tag: parent adapted

value: cDNA derived from Total RNA

value: ORNL

value: PM


title: DOX 5

source_name: Myocardium

value: 10 weeks

tag: treatment

value: doxorubicin


title: S-BC4-C-g268-pop-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2005-07-16 Scan Time : 17:58:27 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F21 10/31/4 genomic DNA


title: S-BC4-B-g128-c1-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2005-08-05 Scan Time : 16:09:10 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: BC3 DNA


title: Sdelta Evos

description: evolving sul1ko's

hyb_protocol: reference URL : http://dunham.gs.washington.edu/UWAgilentDNA.pdf

scan_protocol: Pixel Size : 5 Scan Date : 2013-03-12 Scan Time : 21:56:27 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 10.5.1.1
Datafile type : Agilent result file

value: wt S. cerevisiae

source_name: evolved sul1ko

value: evolved sul1 S. cerevisiae


title: 7 factors-induced thyroid follicular-like cells

city: Tsukuba city

first: Takaaki

middle: K

last: Noguchi

state: Ibaraki prefecture

department: Life and environmental sciences

institute: The University of Tsukuba

description: Gene expression of Pax8, Nkx2.1, Foxe1, Oct3/4, Sox2, Klf4, and c-Myc induced thyroid follicular-like cells derived from fibroblast cultures.

hyb_protocol: 1.65 μg of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 25x Agilent fragmentation buffer and 10x Agilent gene expression blocking agent following the manufacturers protocols. To stop fragmentation reaction, 2x Hi-RPM hybridization huffer was added, and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4112F) for 18 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 30 sec with Acetonitrile (Wako), and then dried immediately.

scan_protocol: Slides were scanned immediately after wash and dried on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10 μm, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters (protocol: GE1_1105_Oct12, and Grid: 014868_D_F_20131202) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: induced thyroid follicular-like cells, 21 days, 7 factors induced fibroblast cultures

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng-1 μg RNA using the One-Color Quick amp labeling kit (Qiagen) folloowing the manufacturer's instructions, followed by RNeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mouse embryonic fibroblasts were derived from E13.5 ICR mice, and cultured in DMEM low glucose (Wako) containing 10% FBS, and peniciline/streptmycine (Wako). Adult thyroid follicular cells were also derived from adult ICR mice.  ICR mice were grown according to the committee guidelines of the National Institute of Advanced Industrial Science and Technology for animal experiments.

extract_protocol: Total RNA was prepared using RNeasy Mini kit (Qiagen) or Isogen (Nippon Gene) following the manufacturer's instructions. The protocol of RNeasy Mini kit includes DNase digestion. Extratd RNA was qualified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Mouse embryonic fibroblasts were induced with 7 or 8 factors by retro viruses twice, and they were cultured in DMEM low glucose containing 10% FBS, and peniciline/streptmycine for 1 week. After 1 week culture, medium was changed with DMEM/F12 (Wako) containing 10% FBS, 0.1 mM NEAA (Sigma), 100 U/mL penicillin/streptomycin, 1 µg/mL potassium iodide (Wako), and 1 U/mL thyroid stimulating hormone (TSH; Sigma), and supplemented with N2 (Wako)/B27 (Milteny Biotec), and induced fibroblasts were cultured for another 2 weeks. Primary thyroid follicular cells were also cultured in the same medium for 1 week.

value: induced thyroid follicular-like cells

tag: culture day/stage

value: 21 days


title: AAV8-Prox1-2

source_name: AAV8-Prox1_tibialis anterior muscle

value: 3 months

value: Male

value: AAV8-Prox1 overexpression

value: tibialis anterior muscle


title: S-BC4-B-g128-pop-DNA-redo

scan_protocol: Scan Power : 100 PMT Volts : 490 Pixel Size : 5 Laser on time : 4547 Laser Power : 2.47 Scan Date : 2005-07-16 Scan Temperature : 26.06 Scan Time : 20:22:16 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4200A 01 [111967] Scanning software : AxImageIO Scanning software version : 2.0.3.1 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.1.0.10
Datafile type : GenePix Results 3
Image Origin : 1080, 3880

source_name: BC4 genomic DNA

value: ancestral hybrid strain

source_name: F22 8/26/4 genomic DNA

value: evolved hybrid strain


title: Primary thyroid follicular cells

description: Gene expression of primary thyroid follicular cell cultures

source_name: Adult thyroid follicular cells

value: Thyroid follicular cells

value: Adult


title: S-BC4-B-g134-pop-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2005-07-05 Scan Time : 14:11:55 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F22 8/27/4 genomic DNA


title: 8 factors-induced thyroid follicular-like cells

description: Gene expression of Pax8, Nkx2.1, Foxe1, Hhex, Oct3/4, Sox2, Klf4, and c-Myc induced thyroid follicular-like cells derived from fibroblast cultures.

source_name: induced thyroid follicular-like cells, 21 days, 8 factors induced fibroblast cultures


title: M7237_1 23

value: Y

value: Adapted

tag: promot sample type

value: cDNA derived from Total RNA

tag: biomaterial provider

tag: sample

tag: columnname

tag: intensity


title: M7237_1 19

tag: strain

value: ORNL

value: PM


title: Sdelta Evos 8

description: evolving sul1ko's

label_protocol: reference URL : http://dunham.gs.washington.edu/UWAgilentDNA.pdf

value: wt S. cerevisiae


title: S-BC4-A-g132-pop-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2005-07-05 Scan Time : 13:38:54 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F21 8/27/4 genomic DNA


title: AAV8-Prox1-3

scan_protocol: Standard Illumina scanning protocol

tag: genotype/variation

tag: tissue


title: PBS 2

tag: age

value: 10 weeks

value: injected with PBS


title: AAV8-Prox1-1


title: Sdelta Evos 7

description: evolving sul1ko's

tag: strain name

value: evolved sul1 S. cerevisiae


title: M7237_2 3

tag: biological rep

value: N


title: M7237_1 14


title: M7237_1 2


title: M7237_1 6


title: S-BC3-B-g129-c1-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2005-08-05 Scan Time : 13:07:34 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Sdelta Evos 6

description: evolving sul1ko's


title: S-BC3-D-g273-pop-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2005-07-05 Scan Time : 14:27:47 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F20 10/31/4 genomic DNA


title: S-BC3-A-g126-pop-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2005-07-05 Scan Time : 13:04:02 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F19 8/27/4 genomic DNA


title: S-BC3-B-g129-pop-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2005-07-05 Scan Time : 13:20:06 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: BC3 genomic DNA

source_name: F20 8/27/4 genomic DNA


title: ACHN

city: Shanghai

first: le

last: qu

address: 440 North Chengdu Road

department: Department of Urology

country: China

institute: Second Military Medical University

description: Gene expression profiling of ACHN cell lines

hyb_protocol: The labeled RNA was purified and hybridized to microarrays according to the Agilent manufacturer's instructions.

scan_protocol: Images were scanned with the Agilent microarray scanner (Agilent 2565CA), gridded, and analyzed using Agilent feature extraction software version 10.10.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parametersto obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Homo sapiens

source_name: renal cancer cell lines_parental

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

growth_protocol: The RCC cell lines 786-O and ACHN (ATCC, USA), as well as 7Su3rd, ACSu3rd were cultured in DMEM (GIBCO, Invitrogen Inc, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS, Gibco). 7Su3rd and ACSu3rd cells were chronically exposed in sunitinib at 5μM

extract_protocol: Total RNA was extracted from the specimens using Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA). RNA purity and concentration were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000) and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

treatment_protocol: For RCC sunitinib resistant xenografts model, 6×10^6 cells of 786-O or ACHN cells were injected subcutaneously into the flanks of nude mice. When the volume of xenografts reached 200 mm3, mice were treated with sunitinib orally (40 mg/kg/day) in a standard 4 weeks on, 2 weeks off treatment schedule. After one cycle of treatment, RCC cells dissociated from xenografts were transplanted into secondary mice followed with the same sunitinib-treatment. Xenografts with sunitinib resistance were defined as unaffected xenograft growth under sunitinib pressure. Freshly isolated RCC cells obtained from the 3rd generation xenografts (termed 7Su3rd and ACSu3rd) were used for subsequent experiment.

tag: cell type

value: renal cancer cell lines


title: GOS2ERF71roots_normal_two week_2

city: Pyeongchang

first: Dong-Keun

last: Lee

address: Pyeongchang Dae-ro, Daehwa-myeon

department: GBST

country: South Korea

institute: Seoul National University

description: This sample is GOS2::OsERF71 Nipponbare rice roots. It is the two of two GOS2::OsERF71 biological replicates used in this experiment, each from separate cultures.

hyb_protocol: 13㎍ of DNA was used for microarray hybridization. The sample was mixed with 19.5㎕ of 2X hybridization buffer (Nimblegen, U.S.A.) and finalized to 39 ㎕ with deionized water. Hybridization was performed with MAUI chamber (Biomicro, U.S.A.) at 42℃ for 16 hours.

scan_protocol: The microarray was scanned with Genepix 4000 B (Axon Instruments) preset with a 5 um resolution and for Cy3 signal. Signals were digitized and analyzed by Nimblescan (Nimblegen, U.S.A.). The grid was aligned to the image with a chip design file, NDF file. The alignment was checked by ensuring that the grid’s corners are overlaid on the images corners. This was further checked by uniformity scores in the program.

data_processing: First pair reports (*.probe.txt) files were generated in which sequence, probe, and signal intensity information for Cy3 channel were collected. Data-based background subtraction using a local background estimator was performed to improve fold change estimates on arrays with high background signal. The data was nomalized and processed with cubic spline normalization using quantiles to adjust signal variations between chips (Workman et al., 2002. Genome Biol. 3: research0048.1 - research0048.16 ).     Probe-level summarization by Robust Multi-Chip Analysis (RMA) using a median polish algorithm implemented in NimbleScan was used producing calls files. The method identifies probes that are outliers in the overall behavior of the expression measured for a given gene and the contribution by those outliers is reduced in the reported gene expression level. This improves the sensitivity and reproducibility of microarray results (Irizarry et al., 2003. Nucleic Acids Research 31:e15).

organism: Oryza sativa

source_name: roots of two-week-old GOS2::OsERF71

label_protocol: For the synthesis of C3-labeled target DNA fragments, 1 ㎍ of double strand cDNA was mixed with 40 ㎕ (1OD) of Cy3-9mer primers(Sigma-Aldrich, U.S.A.) and denatured by heating at 98 ℃ for 10 minute. The reaction was further proceeded by adding 10 ㎕ of 50X dNTP mix (10mM each), 8 ㎕ of deionized water, 2 ㎕ of Klenow fragment(50 U/㎕, NEB, U.S.A.) and incubating at 37 ℃ for 2 hours. DNA was precipitated by centrifugation at 12,000 x g force after adding 11.5 ㎕ of 5M NaCl and adding 110 ㎕ of isopropanol. Precipitated samples were rehydrated with 25 ㎕ of water. The concentration of each sample was determined by using spectrophotometer.

growth_protocol: RCc3::OsERF71 and GOS2::OsERF71 plants and NT controls were grown in greenhouse at 28-30 ºC for 14 days.

extract_protocol: Total mRNAs were extracted from roots of two-week-old RCc3::OsERF71 and GOS2::OsERF71 transgenic and NT plants grown under normal growth conditions and purified with Qiagen Oligotex column system according to the manufacturer’s instructions.

tag: cultivar

value: Nipponbare

tag: genotype

value: roots


title: ACSu3rd

description: Gene expression profiling of ACSu3rd cell lines

source_name: renal cancer cell lines_sunitinib-resistant


title: S-BB-2N-B-g557-pop-DNA

scan_protocol: Scan Power : 100 PMT Volts : 490 Pixel Size : 5 Laser on time : 4611 Laser Power : 2.49 Scan Date : 2005-07-16 Scan Temperature : 26.31 Scan Time : 21:31:15 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4200A 01 [111967] Scanning software : AxImageIO Scanning software version : 2.0.3.1 Focus Position : 0

source_name: BB genomic DNA

value: ancestral S. uvarum strain

source_name: F4 5/31/5 genomic DNA

value: evolved S. uvarum strain


title: M7237_1 10

scan_protocol: Agilent Scanner_Green_100% The labeling, hybridization, and scanning following NimbleGen company's protocols.

tag: sample date

tag: tech rep y n

tag: parent adapted


title: GOS2ERF71roots_normal_two week_1

description: This sample is GOS2::OsERF71 Nipponbare rice roots. It is the first of two GOS2::OsERF71 biological replicates used in this experiment, each from separate cultures.


title: 786-O

description: Gene expression profiling of 786-O cell lines


title: M6880_2 21

value: Parent

tag: promot sample type


title: S. bayanus vs S. cerevisiae 65C, 1 ug, long 65C  wash

description: microarray facility long washes, 65C wash 1

scan_protocol: Pixel Size : 5 Scan Date : 2005-06-29 Scan Time : 11:56:00 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: S. cerevisiae 1 ug DNA

source_name: S. bayanus 1 ug DNA

value: wt S. uvarum


title: 7Su3rd

description: Gene expression profiling of 7Su3rd cell lines


title: M6880_2 17

value: Y

tag: biomaterial provider


title: AAV8-NLS-mCherry (Control)-2

source_name: AAV8-NLS-mCherry (Control)_tibialis anterior muscle

value: 3 months

tag: gender

value: Male

value: AAV8-mCherry contro

value: tibialis anterior muscle


title: S-BC4-A-g132-c1-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2005-08-05 Scan Time : 15:37:43 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: BC3 DNA

value: ancestral hybrid strain

value: evolved hybrid strain


title: M6880_2 12

value: cDNA derived from Total RNA

value: ORNL

tag: sample

tag: columnname

value: PM


title: M6880_2 8

tag: strain

value: N

tag: intensity


title: AAV8-NLS-mCherry (Control)-1

tag: genotype/variation

tag: tissue


title: Liver, B109_28_L_H3, replicate 3

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 045522_D_F_20130222) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Liver, B109_28_L_H3, replicate 3

treatment_protocol: Three animals were administrated corn oil for nine weeks, the other three animals were administrated 4,4'-Thiobis(6-tert-Butyl-m-Cresol) (300 mg/kg/day) for nine weeks.

value: Liver

tag: treatment

value: Sprague-Dawley

value: male


title: S-BB-2N-A-g541-pop-DNA

scan_protocol: Scan Power : 100 PMT Volts : 490 Pixel Size : 5 Laser on time : 4566 Laser Power : 2.47 Scan Date : 2005-07-16 Scan Temperature : 26.13 Scan Time : 20:41:09 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4200A 01 [111967] Scanning software : AxImageIO Scanning software version : 2.0.3.1 Focus Position : 0

tag: strain name

value: ancestral S. uvarum strain

source_name: F3 5/31/5 genomic DNA

value: evolved S. uvarum strain


title: Liver, B109_28_L_H2, replicate 2

source_name: Liver, B109_28_L_H2, replicate 2


title: M6880_1 20

tag: biological rep

value: Parent


title: M6880_2 4


title: Wtroots_normal_two week_2

description: This sample is wild-type Nipponbare rice roots. It is the two of two wild-type biological replicates used in this experiment, each from separate cultures.

source_name: roots of two-week-old WT

tag: cultivar

value: Nipponbare

value: wild type

value: roots


title: RCc3ERF71roots_normal_two week_1

description: This sample is RCc3::OsERF71 Nipponbare rice roots. It is the first of two RCc3::OsERF71 biological replicates used in this experiment, each from separate cultures.

source_name: roots of two-week-old RCc3::OsERF71

tag: genotype


title: RCc3ERF71roots_normal_two week_2

description: This sample is RCc3::OsERF71 Nipponbare rice roots. It is the two of two RCc3::OsERF71 biological replicates used in this experiment, each from separate cultures.


title: Liver, B109_28_L_VC3, replicate 3

source_name: Liver, B109_28_L_VC3, replicate 3

value: Corn Oil


title: S. bayanus vs S. cerevisiae 65C, 1 ug, long 65C wash print 3

scan_protocol: Pixel Size : 5 Scan Date : 2005-08-05 Scan Time : 13:39:21 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: FY DNA DNA

value: wt S. cerevisiae

source_name: YZ DNA

value: wt S. uvarum


title: M6880_2 16

tag: sample date


title: Liver, B109_28_L_H1, replicate 1

source_name: Liver, B109_28_L_H1, replicate 1


title: Liver, B109_28_L_VC2, replicate 2

source_name: Liver, B109_28_L_VC2, replicate 2


title: Wtroots_normal_two week_1

description: This sample is wild-type Nipponbare rice roots. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures.


title: Liver, B108_28_L_H2, replicate 2

source_name: Liver, B108_28_L_H2, replicate 2

treatment_protocol: Three animals were administrated corn oil for nine weeks, the other three animals were administrated Carbon tetrachloride (100 mg/kg/day) for nine weeks.

value: Carbon tetrachloride (100 mg/kg/day)


title: M6880_1 13

tag: tech rep y n

value: cDNA derived from Total RNA


title: M6880_1 24

value: Y

tag: parent adapted

value: ORNL


title: Liver, B109_28_L_VC1, replicate 1

source_name: Liver, B109_28_L_VC1, replicate 1


title: S-BC4-D-g285-c1-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2005-08-09 Scan Time : 14:30:13 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

value: ancestral hybrid strain

value: evolved hybrid strain


title: Sbay_sul2D_evo_g260_4

scan_protocol: Pixel Size : 5 Scan Date : 2013-07-16 Scan Time : 17:08:43 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

organism: Saccharomyces bayanus

source_name: S.bay ILY444

source_name: evolved strain

value: evolved sul2 S. uvarum


title: Liver, B108_28_L_H1, replicate 1

source_name: Liver, B108_28_L_H1, replicate 1

value: Liver

value: Sprague-Dawley

value: male


title: M6880_1 1

value: N

value: Parent

tag: promot sample type

value: PM


title: Sbay_sul2D_evo_g260_3

value: ancestral S. uvarum strain


title: S-BC3-C-g263-pop-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2005-07-05 Scan Time : 13:56:09 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: BC3 genomic DNA

source_name: F19 10/31/4 genomic DNA


title: S-BC3-D-g273-c1-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2005-08-09 Scan Time : 13:55:00 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: BC3 DNA


title: Liver, B108_28_L_H3, replicate 3

source_name: Liver, B108_28_L_H3, replicate 3


title: M6880_1 5

tag: biomaterial provider


title: Liver, B108_28_L_VC3, replicate 3

source_name: Liver, B108_28_L_VC3, replicate 3

value: Corn Oil

tag: gender


title: Sbay_sul2D_evo_g260


title: Sbay_sul2D_evo_g260_2


title: S-BB-2N-B-g557-c1-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2005-08-09 Scan Time : 11:57:18 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F4 5/31/5 clone1 DNA

value: evolved S. uvarum strain


title: F4_050520_g499

scan_protocol: Pixel Size : 909.090909090909 Scan Date : 2012-10-16 Scan Time : 13:38:53 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1


title: S-BB-2N-A-g541-c1-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2005-08-09 Scan Time : 11:40:16 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F3 5/31/5 clone1 DNA


title: Liver, B108_28_L_VC2, replicate 2

source_name: Liver, B108_28_L_VC2, replicate 2


title: S-BC3-A-g126-c1-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2005-08-05 Scan Time : 13:55:05 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F19 8/27/4 clone1 DNA


title: F3_050531_g541


title: 4_050531_g556

scan_protocol: Pixel Size : 909.090909090909 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

source_name: evolved sbay


title: S-BC3-C-g263-c1-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2005-08-09 Scan Time : 12:13:01 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: F3_050524_g506


title: Liver, B108_28_L_VC1, replicate 1

source_name: Liver, B108_28_L_VC1, replicate 1


title: control 50: KM_D-580169

status: Public on Sep 29 2016

city: Louisville

first: Hongying

last: Hao

state: KY

address: 505 South Hancock Street

department: Surgery

institute: University of Louisville

description: Gene expression data from sentinel lymph node RNA.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome HG-U133Plus2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using Fluidics Protocol FS450-0001.

scan_protocol: GeneChips were scanned using Affymetrix' GeneChip Scanner GCS3000 7G and Command Console Version 1.0

data_processing: A fold change outlier filter (FCO) was applied independently to reduce the dimension of the data before determining differentially expressed genes (DEGs) between the controls and the cases. The Fold Change (FC) was calculated and four filters, T1={μ(FC) ± 1.5σ(FC)}, T2={μ(FC) ± 2σ(FC)}, T3={μ(FC) ± 3σ(FC)} and T4={μ(FC) ± 4σ(FC)}, were used to filter data, where μ(FC) is the mean of fold changes and σ(FC) is the standard deviation of fold changes. The genes that fell inside T1, T2 and T3 were filtered from the differential data respectively. After filtering the data, t-test for normal gene expression data and Wilcoxon test for non-normal expression data were applied. In order to control for multiplicity, the Benjamini-Hochberg method was employed to adjust the p-values.

source_name: sentinel lymph node RNA - non-recurrence

label_protocol: Biotinylated cRNA were prepared according to the standard protocol for Affymetrix' IVT Express kit from 100 ng total RNA.

extract_protocol: Total RNA from cells and exosomes were isolated using TRIREAGENT kit according to the manufacturer’s guidelines.

treatment_protocol: A portion of each sentinel lymph node (SLN) (defined as one fourth of the lymph node or a 2-mm3 portion of the node, whichever was smaller) was snap-frozen on dry ice or liquid nitrogen and stored at -80°C until it was shipped on dry ice. SLNs were processed and analyzed by a central laboratory (National Genetics Institute) that was blinded to clinical and pathologic data.

value: sentinel lymph node

tag: cancer status

value: Melanoma

tag: group

value: non-recurrence


title: control 49: KM_D-567915


title: control 52: KM_D-638104


title: control 55: KM_D-902027


title: control 58: KM_D-AF0455


title: control 48: KM_D-507195


title: control 51: KM_D-587132


title: control 54: KM_D-878037


title: control 57: KM_D-987407


title: control 53: KM_D-782711


title: control 56: KM_D-902047


title: control 47: KM_D-506248


title: control 46: KM_D_AC1114


title: control 43: KM_D_942052


title: control 41: KM_D_618512


title: control 38: KM_D_570581


title: control 44: KM_D_981595


title: control 45: KM_D_AA5640


title: control 42: KM_D_896301


title: control 39: KM_D_601887


title: control 40: KM_D_617522


title: control 36: KM_D_499674


title: control 35: KM_D_499663


title: control 31: D774636


title: control 37: KM_D_502917


title: control 34: D-ab8920


title: control 32: D827797


title: control 33: D951022a


title: control 19: KM_D348286


title: control 24: KM_D403050


title: control 28: D584126


title: control 27: D383674


title: control 18: KM_D343673a


title: control 30: D609721


title: control 20: KM_D355035


title: control 22: KM_D397762


title: control 25: KM_D520986


title: control 23: KM_D400854


title: control 26: D373061


title: M6880_1 9

scan_protocol: Agilent Scanner_Green_100% The labeling, hybridization, and scanning following NimbleGen company's protocols.

tag: strain

value: cDNA derived from Total RNA

tag: sample

tag: columnname


title: control 15: KM_D198049

tag: tissue


title: control 12: KM_D-BS8634


title: control 16: KM_D305110


title: control 13: KM_550255_GD


title: control 7: KM_D-894268


title: control 5: KM_D-864031


title: control 11: KM_D-BQ0815


title: control 21: KM_D355744


title: control 14: KM_D198048


title: control 29: D590457


title: control 8: KM_D-915392


title: control 9: KM_D-AA7800


title: EHEC_wt_anaerobic

city: Dallas

first: Juan

middle: D

last: Hernandez

state: Texas

address: 5349 Amesbury Drive, 2314

department: Microbiology

institute: University of Texas Southwestern medical centre

hyb_protocol: standard Affymetrix protocols

scan_protocol: standard Affymetrix protocols

data_processing: All data processed using GCOS v1.4

organism: Escherichia coli

source_name: wt bacteria

label_protocol: standard Affymetrix protocols

growth_protocol: bacteria were grown for 6 hours anaerobically using Gaspack system in low glucose DMEM

extract_protocol: Ambion RiboPure RNA isolation protocol

treatment_protocol: no treatment

value: EHEC 86-24 strain

tag: genotype/variation

value: WT

tag: growth condition

value: grown in DMEM anaerobically


title: EHEC_∆cro_anaerobic

source_name: cro mutation

value: EHEC {delta}cro strain

value: {delta}cro


title: S-BC4-C-g268-c1-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2005-08-09 Scan Time : 12:28:45 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

tag: strain name

value: ancestral hybrid strain

value: evolved hybrid strain


title: control 4: KM_D-843724


title: control 10: KM_D-AB6381


title: control 6: KM_D-880921


title: spermatogonian stem cell rep2

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

description:
SSC2
replicate 2

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were background corrected and normalized using quantile normalization with lumi package in R

source_name: spermatogonian stem cell

label_protocol: cDNA were prepared with Ambion illumina TotalPrep RNA amplification kits and labeled according standard manufacturer’s instructions.

extract_protocol: Total RNA from germ line stem cells was extracted using Trizol reagent according to the manufacturer’s instructions.RNA that passed the quality check were hybridized to Mouse WG-6 v2.0 (Illumina).

tag: age

value: 6 days

value: testis

tag: cell type

value: spermatogonian stem cell


title: female germline stem cell rep2

description:
FGSC2
replicate 2

source_name: female germline stem cell

value: 3 days

value: ovary

value: female germline stem cell


title: control 2: KM_D-607000

value: sentinel lymph node


title: spermatogonian stem cell rep3

description:
SSC3
replicate 3


title: control 1: KM_D-500741

value: Melanoma


title: female germline stem cell rep1

description:
FGSC1
replicate 1


title: case 38: KM_B-BV2237

source_name: sentinel lymph node RNA - recurrence

value: recurrence


title: F&V Intervention Participant 15 Visit 1

city: New Lambton

first: Evan

middle: James

last: Williams

address: 1 Kookaburra Crt

department: Respiratory

institute: The University of Newcastle, Australia

hyb_protocol: 750 ng cRNA was hybridised to Illumina Sentrix HumanHT-12 Version 4 Expression BeadChip  (Illumina, San Diego, CA, USA) using standard protocols

scan_protocol: Each BeadChip measured the expression of over 31,000 genes and was scanned using the Illumina Bead Station and captured using BeadScan 3.5.11 (Illumina)

data_processing: The data was transformed using the log2 method, then normalised using quantile normalisation with lumi package in R

source_name: Peripheral blood

label_protocol: A total of 500 ng of blood RNA was amplified and labelled with biotin-uridine triphosphate using the Total Prep RNA amplification kit as per manufacture's instructions (Life Technologies)

extract_protocol: Whole blood RNA was extracted from PAXgene tubes using the PAXgene Blood RNA Extraction Kit (Qiagen), as per manufacturer’s instructions. RNA was quantitated and the quality assessed using Bioanalyser and Quant-iT Ribogreen RNA Reagent (Molecular Probes, Invitrogen), the average RNA integrity number was 8.07.

tag: disease state

value: Obese; High Baseline CRP (≥3.0)

tag: ID

tag: bmi

tag: visit


title: spermatogonian stem cell rep1

description:
SSC1
replicate 1


title: female germline stem cell rep3

description:
FGSC3
replicate 3


title: case 39: KM_B-BW2136


title: F&V Intervention Participant 16 Visit 1


title: control 3: KM_D-619894

value: non-recurrence


title: F&V Intervention Participant 14 Visit 1


title: case 35: KM_B-614127


title: F&V Intervention Participant 12 Visit 1


title: case 37: KM_B-782684


title: case 34: KM_B-592603


title: case 36: KM_B-636294


title: F&V Intervention Participant 14 Visit 2


title: F&V Intervention Participant 11 Visit 1


title: F&V Intervention Participant 16 Visit 2


title: case 33: KM_B-BV2236


title: F&V Intervention Participant 13 Visit 1


title: F&V Intervention Participant 10 Visit 2


title: F&V Intervention Participant 12 Visit 2


title: F&V Intervention Participant 11 Visit 2


title: F&V Intervention Participant 13 Visit 2


title: F&V Intervention Participant 10 Visit 1


title: F&V Intervention Participant 15 Visit 2


title: F&V Intervention Participant 19 Visit 2


title: case 30: KM_B-928952


title: F&V Intervention Participant 8 Visit 2


title: case 32: KM_B-954529


title: F&V Intervention Participant 7 Visit 1


title: case 31: KM_B-943369


title: F&V Intervention Participant 8 Visit 1


title: F&V Intervention Participant 9 Visit 1


title: control 17: KM_D321035


title: F&V Intervention Participant 6 Visit 1


title: F&V Intervention Participant 6 Visit 2


title: F&V Intervention Participant 5 Visit 2


title: F&V Intervention Participant 7 Visit 2


title: case 29: KM_B-870309


title: Neural Stem Cells Generated from Human iPSCs [NSC-11T-rep 2]

city: Newcastle upon Tyne

first: LILI

last: ZHU

address: Central Parkway

institute: Newcastle University

description: Biological replicate 2 of 2. Human NSC-11T.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent Gene Expression Hybridization Kit) were added, and samples were applied to microarrays enclosed in Agilent Microarray Hybridization Chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on a Agilent C Scanner

data_processing: Agilent Feature Extraction (FE) software was used for background subtraction and LOWESS normalization.

label_protocol: The total RNA were labled with Cy3 (Samples) or Cy5 (References) by following the protocol of Two-Color Microarray-Based Gene Expression Analysis from Agilent.

growth_protocol: Human ESCs and iPSCs were maintained on Matrigel (growth-factor-reduced; BD Biosciences)-coated plates with mTeSR1 (Stemcell Technologies) according to Wicell protocols. Cells were passaged every 4-5 days at ~80% confluence by using 0.02% EDTA (Versene). The NSCs were maintained on Poly-L-ornithine/ Laminin (Sigma) coated flasks with the N2B27 medium containing: DMEM/F12, N2 supplement (1:100), B27 supplement (1:50, Invitrogen), 100 mM nonessential amino acids (Invitrogen) plus 10 ng/mL FGF2 (R&D Systems), 10 ng/mL EGF (R&D Systems). The cells were passaged every 4-6 days at ~90% confluence by using Accutase. All NSCs used in this study were between passage 6-10.

extract_protocol: Total RNA isolated was done using the ReliaPrep™ RNA Cell Minprep System (Promega);

treatment_protocol: The cells were cultured in normal condition and were collected for microarray untill they were 70% confluency.

tag: cell line

value: Male

tag: cell lines

value: mixture of 10 human cell lines

tag: reference

value: Pooled Agilent's Universal Human Reference RNA, catalog#740000


title: case 27: KM_B_AG2163

tag: cancer status

tag: group


title: case 25: KM_B_927148


title: HCT116_siH19-2, biological rep2 (06_GAC-MO-6)

city: Houston

first: HUI

last: LING

state: TX

address: 1901 east road

department: Experimental Therapeutics

institute: The University of Texas MD Anderson Cancer Center

description: Gene expression data from HCT116 siH19-2 cells

hyb_protocol: Fragmented and labeled ss-cDNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the affymetrix Scanner 7G.

data_processing: The data were analyzed with Affymetrix® Expression Console™ Software  using Affymetrix default analysis settings. The Robust Multi-array Averaging (RMA) background correction, median polish probe summarization, and quantile normalization were applied as standard method.

label_protocol: RNA samples were processed according to the GeneChip® WT PLUS Reagent Kit. A total of 500 ng RNA was used for a double-round of cDNA synthesis. After fragmentation of 2nd-cycle single-stranded cDNA (ss-cDNA), sample was labeled with biotin by terminal deoxynucleotidyl transferase (TdT).

growth_protocol: The human colon cancer cell line HCT116 was obtained from the American Type Culture Collection (Manassas, VA, USA) and grown as suggested by the supplier. Cells were cultured at 37oC in 5% CO2.

treatment_protocol: Cells were transfected for 48 hr with a final concentration of 50 nM siRNA with Lipofectamine RNAiMAX reagent (Invitrogen) in Opti-MEM medium (Thermo Fisher Scientific) according to the manufacture’s protocol.

value: HCT116 cell line

tag: treatment


title: F&V Intervention Participant 5 Visit 1


title: HCT116_si(-), biological rep2 (04_GAC-MO-4)

description: Gene expression data from HCT116 si(-) cells

value: control


title: F&V Intervention Participant 4 Visit 2


title: case 28: KM_B-374859


title: HCT116_siH19-1, biological rep2 (05_GAC-MO-5)

description: Gene expression data from HCT116 siH19-1 cells


title: case 26: KM_B_AB3897


title: HCT116_siH19-2, biological rep1 (03_GAC-MO-3)


title: Neural Stem Cells Generated from Human iPSCs [NSC-11T-rep 1]

description: Biological replicate 1 of 2. Human NSC-11T.

tag: gender

source_name: Pooled Agilent's Universal Human Reference RNA


title: HCT116_si(-), biological rep1 (01_GAC-MO-1)


title: HCT116_siH19-1, biological rep1 (02_GAC-MO-2)


title: F&V Intervention Participant 4 Visit 1


title: Neural Stem Cells Generated from Human iPSCs [NSC-7T-rep 2]

description: Biological replicate 2 of 2. Human NSC-7T.


title: case 24: KM_B_556673

tag: tissue


title: F&V Intervention Participant 3 Visit 2


title: HCT116_siCTNNB1, biological rep2 (F_GAC-MO-F)

description: Gene expression data from HCT116  siCTNNB1 cells

growth_protocol: The human colon cancer cell line HCT116 was obtained from the American Type Culture Collection (Manassas, VA, USA) and grown as suggested by the supplier. Cells were cultured at 37°C in 5% CO2.


title: F&V Intervention Participant 2 Visit 2


title: Neural Stem Cells Generated from Human iPSCs [NSC-NHDF(S)-rep 2]

description: Biological replicate 2 of 2. Human NSC-NHDF(S).

source_name: NSC-NHDF(S)

value: NSC-NHDF(S)


title: F&V Intervention Participant 1 Visit 2


title: Neural Stem Cells Generated from Human iPSCs [NSC-7T-rep 1]

description: Biological replicate 1 of 2. Human NSC-7T.


title: F&V Intervention Participant 2 Visit 1


title: Neural Stem Cells Generated from Human iPSCs [NSC-NHDF(L)-rep 1]

description: Biological replicate 1 of 2. Human NSC-NHDF(L).

source_name: NSC-NHDF(L)

value: NSC-NHDF(L)


title: case 21: B646825


title: case 16: B525328


title: case 19: B583442


title: case 22: B697046a


title: HCT116_si(-), biological rep1 (A_GAC-MO-A)


title: HCT116_si(-), biological rep2 (E_GAC-MO-E)


title: HCT116_siCTNNB1, biological rep1 (B_GAC-MO-B)

description: Gene expression data from HCT116 siCTNNB1 cells


title: HCT116_si(-), biological rep2 (GAC-MO-3)


title: HCT116_si(-), biological rep1 (GAC-MO-1)


title: Neural Stem Cells Generated from Human iPSCs [NSC-NHDF(S)-rep 1]

description: Biological replicate 1 of 2. Human NSC-NHDF(S).


title: HCT116_siCDK8, biological rep1 (GAC-MO-2)

description: Gene expression data from HCT116 siCDK8 cells


title: F&V Intervention Participant 3 Visit 1


title: HCT116_siCDK8, biological rep2 (GAC-MO-4)


title: DLD1_siH19-2 (GAC-MO-D3)

description: Gene expression data from DLD1 siH19-2 cells

growth_protocol: The human colon cancer cell line DLD1 was obtained from the American Type Culture Collection (Manassas, VA, USA) and grown as suggested by the supplier. Cells were cultured at 37°C in 5% CO2.

value: DLD1 cell line


title: Neural Stem Cells Generated from Human ESCs [NSC-H9-rep 1]

description: Biological replicate 1 of 2. Human NSC-H9.

value: Female


title: case 17: B527465


title: case 20: B634744


title: Neural Stem Cells Generated from Human ESCs [NSC-H1-rep 2]

description: Biological replicate 2 of 2. Human NSC-H1.


title: case 18: B531976

description: Gene expression data from sentinel lymph node RNA.


title: F&V Intervention Participant 1 Visit 1


title: case 23: KM_B_502921


title: Neural Stem Cells Generated from Human iPSCs [NSC-NHDF(L)-rep 2]

description: Biological replicate 2 of 2. Human NSC-NHDF(L).


title: Neural Stem Cells Generated from Human ESCs [NSC-H9-rep 2]

description: Biological replicate 2 of 2. Human NSC-H9.


title: case 13: B305108


title: DLD1_siH19-1 (GAC-MO-D2)

description: Gene expression data from DLD1 siH19-1 cells


title: case 14: B355711


title: DLD1_si(-) (GAC-MO-D1)

description: Gene expression data from DLD1 si(-) cells


title: case 15: B495538


title: Atrazine 1000µg/L exposure [Ta-4]

city: Stoneville

first: JIANXIU

last: YAO

state: Mississippi

address: 141 Experiment station Rd

institute: USDA-ARS

description: gene expression after 48-hr insecticide exposure

hyb_protocol: Cyanine-3 labeled cRNAs (600 ng) of each sample was hybridized to the microarray chip (six samples, including 3 from the control diet and 3 from the protoxin diet, and were hybridized on six individual microarray chips) and incubated at 65˚С for 17 h

scan_protocol: Slides were scanned using an Axon GenePix 4000B (Molecular Devices Inc. Sunnyvale, CA) with default value based on Aglient's recommendation microarray scanner at a 532 nm wavelength

data_processing:
The signal intensity of each hybridized spot was qualified and quantified with Agilent Feature Extraction Ver. 9.5 software (Agilent). 15 raw data files with 13,674 customer designed probes and control probes extracted by Agilent Feature Extraction software were imported to GeneSpring GX11 and were applied ‘75% percentile shift’ normalization algorithm. Fifteen samples were grouped into our groups (three controls and four treatments of each insecticide exposure). The analysis was performed individually to identified significantly differentially expressed genes by comparing to control treatment.
The quality control was assessed by examining principal components analysis (PCA) plots and correlation analysis of sample replicates. The correlation coefficients within transgenic corn feeding treatment or non-transgenic corn leaves feeding control group were larger than 97% indicating the high quality control.  Analysis of variance (one-way ANOVA, p<0.05) was performed to test the variation between two groups (one insecticide  treatment and control). The Benjamini-Hochberg multiple testing correction (q<0.05) was also employed after ANOVA to identify the transcripts that were differentially expressed when the cutoff of the fold change was set at ≥2.0. The expression differences with p <0.05 and with expression ratios ≥2.0 were considered significantly different between one treatment and control, respectively. In this analyses, 146, 435 and 244 genes were significantly differentially expressed (p-value ≤0.05 with expression ratios ≥2.0) after 48-hr of 0.1 µg/L, 0.5 µg/L chlorpyrifos, and 1000 µg/L atrazine exposure, respectively. They included 46 down-regulated and 103 up-regulated transcripts in chlorpyrifos 0.1 µg/L treatment, 158 down-regulated and 276 up-regulated transcripts in chlorpyrifos 0.5 µg/L treatment, and 100 down-regulated and 143 up-regulated transcripts in atrazine 1000 µg/L exposure.  Finally, gene ontologies of all significantly different expressed gut genes were analyzed by using Blast2go (http://www.blast2go.org) at level 2.

organism: Chironomus tentans

source_name: hemogenized 4th instar larvae whole body

label_protocol: Cyanine-3 labeled cRNAs were synthesized from Agilent single-color microarray-based gene expression kit. Dye-incorporation ratio was determined using NanoDrop 2000 spectrophotometry. The cRNA samples with the ratio cyanine-3 labeled cRNA ≥10 pmol/µg were used for hybridization

growth_protocol: An aquatic midge, C. tentans, colony was maintained in a culture tank contained fresh water and silica sand substrate at 25±1℃ with a 16L:8D photoperiod according to the standard midge culturing procedures (USEPA, 1994) with slight modifications.

extract_protocol: The total RNA were extracted from all collected samples using Trizol reagent (Invitrogen, Carlsbad, CA). The total RNA quantity and quality were measured by NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific Inc. USA) and Agilent 2100 bioanalyzer (Agilent, Palo Alto, CA, USA).

treatment_protocol: The appropriate dilutions of each pesticide were prepared in acetone. The concentrations of chlopyrifos (0.1 µg/L and 0.5 µg/L), and atrazine (1000 µg/L) were prepared in glass beakers by adding the appropriate dilutions of each pesticides into 1 L reconstituted water containing 10 mL of fine silica sand, respectively, acetone was used as control. Fifteen fourth-instar larva were placed into each glass beaker and the alive midges from each glass beaker were collected at 48-hr exposure under 25±1℃ with a 16L:8D photoperiod. Sixteen beakers were used in this experiment with 4 glass beakers per treatment. Five alive larvae were collected from each beaker and pooled as one sample. Totally, four samples of each treatment were collected for total RNA extraction, except control has three samples.

value: whole body

tag: developmental stage

value: 4th instar larvae


title: Neural Stem Cells Generated from Human ESCs [NSC-H1-rep 1]

description: Biological replicate 1 of 2. Human NSC-H1.


title: Atrazine 1000µg/L exposure [Ta-2]


title: Atrazine 1000µg/L exposure [Ta-3]


title: Chlorpyrifos 0.5µg/L exposure [T2-4]


title: Atrazine 1000µg/L exposure [Ta-1]


title: case 12: B157754


title: Chlorpyrifos 0.5µg/L exposure [T2-3]


title: case 11: B145823


title: case 10: KM_B957417b


title: case 9: KM_B933308


title: Chlorpyrifos 0.5µg/L exposure [T2-2]


title: Chlorpyrifos 0.1µg/L exposure [T1-4]


title: Chlorpyrifos 0.1µg/L exposure [T1-3]


title: case 8: KM_B773011


title: case 7: KM_B742344


title: case 5: KM_B637712


title: case 6: KM_B655192


title: case 4: KM_B581473


title: control [C3]


title: Chlorpyrifos 0.5µg/L exposure [T2-1]


title: Chlorpyrifos 0.1µg/L exposure [T1-1]


title: control [C1]


title: control [C2]


title: case 3: KM_B580518


title: case 2: KM_B312117


title: case 1: KM_B179109


title: Chlorpyrifos 0.1µg/L exposure [T1-2]


title: 3-4 R-strain fed on non-trangenic corn leaves

status: Public on Sep 28 2016

description: gene expression after 6-hrs feeding

data_processing:
The signal intensity of each hybridized spot was qualified and quantified with Agilent Feature Extraction Ver. 9.5 software (Agilent). Six raw data files with 12,972 customer designed probes and control probes extracted by Agilent Feature Extraction software were imported to GeneSpring GX11 and were applied ‘75% percentile shift’ normalization algorithm. Six samples were grouped into two groups (three controls and three treatments).
The quality control was assessed by examining principal components analysis (PCA) plots and correlation analysis of sample replicates. The correlation coefficients within transgenic corn feeding treatment or non-transgenic corn leaves feeding control group were larger than 97% indicating the high quality control.  Analysis of variance (one-way ANOVA, p<0.05) was performed to test the variation between two groups. The Benjamini-Hochberg multiple testing correction (q<0.05) was also employed after ANOVA to identify the transcripts that were differentially expressed when the cutoff of the fold change was set at ≥2.0. The expression differences with p <0.05 and with expression ratios ≥2.0 were considered significantly different. In strain larvae guts, 398 out of 2,895 gut genes showed significantly different expression,while only 264 gut genes showed significantly different expression in the R-strain (expression ratio ≥2.0 with p value <0.05). Finally, gene ontologies of all significantly different expressed gut genes were analyzed by using Blast2go (http://www.blast2go.org) at level 2.

organism: Ostrinia nubilalis

source_name: hemogenized whole gut tissue

growth_protocol: The Bt-susceptible and resistant strains of O. nubilalis was obtained from the University Nebraska-Lincoln. Larvae were reared at 26ºC using artificial diet (Bio-Service Inc. NJ), and adults were reared in a metal cage under long-day conditions (L: D =16: 8) and 70% humidity, and routinely fed 2% sucrose water to provide supplementary reproductive nutrition.

extract_protocol: Total RNA was prepared independently for each replicate (a group of five larvae) using TRIzol reagent (Invitrogen Inc. Frederick, MD). The quantity and quality of the total RNA were determined by NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific Inc. Waltham, MA) and Agilent 2100 bioanalyzer (Agilent Technologies Inc. Santa Clara, CA).

treatment_protocol: In these experiments, 40 third-instar larvae of each strain were first starved for 24 h to ensure that they would feed immediately when placed on transgenic corn leaves, respectively. In each strains, 40 larvae were divided into two groups (control and treated) and each group consisted of four replicates (5 individuals in each replicate). Twenty larvae of each strain were fed transgenic corn leaves and 20 larvae were fed on non-transgenic corn leaves as control.

value: whole gut

value: 3rd instar larvae


title: 4-1 R-strain fed on non-trangenic corn leaves

description: gene expression after 6-hrs feeding


title: 3-3 R-strain fed on trangenic corn leaves

description: gene expression after 6-hrs feeding


title: 3-2 R-strain fed on non-trangenic corn leaves

description: gene expression after 6-hrs feeding


title: 4-3 R-strain fed on non-trangenic corn leaves

description: gene expression after 6-hrs feeding


title: 4-4 R-strain fed on trangenic corn leaves

description: gene expression after 6-hrs feeding


title: 4-2 R-strain fed on trangenic corn leaves

description: gene expression after 6-hrs feeding


title: 2-4 S-strain fed on non-transgenic corn leaves

description: gene expression after 6-hrs feeding


title: 2-2 S-strain fed on non-transgenic corn leaves

description: gene expression after 6-hrs feeding


title: 1-4 S-strain fed on transgenic corn leaves

description: gene expression after 6-hrs feeding


title: 2-3 S-strain fed on non-transgenic corn leaves

description: gene expression after 6-hrs feeding


title: 3-1 R-strain fed on trangenic corn leaves

description: gene expression after 6-hrs feeding


title: 1-1 S-strain fed on transgenic corn leaves

description: gene expression after 6-hrs feeding


title: 1-3 S-strain fed on transgenic corn leaves

description: gene expression after 6-hrs feeding


title: 2-1 S-strain fed on non-transgenic corn leaves

description: gene expression after 6-hrs feeding


title: 1-2 S-strain fed on transgenic corn leaves

description: gene expression after 6-hrs feeding


title: CorpusLuteum_large-luteal-cells_2

city: Lincoln

first: Sarah

last: Romereim

state: NE

address: 3940 Fair Street

department: Animal Science

institute: University of Nebraska-Lincoln

description: Luteal cells were isolated by elutriation from the corpora lutea of ovaries collected at a local abattoir (JBSSA, Omaha, NE) as described previously for tissue from both sheep and cattle (Fitz et al., 1982; Mao et al., 2013). Each corpus luteum (n = 3 for both LLC and SLC) was digested with collagenase to dissociate the cells, which were then suspended in a solution of DMEM (calcium free, 3.0 g/L glucose, 25 mM HEPES, 3.8g/L sodium bicarbonate; 0.1 % BSA, 0.02 mg/mL deoxyribonuclease, pH 7.2) to a total volume of 30 mL. Elutriation was then performed with a Beckman Coulter Avanti-J20X centrifuge with a JE 5.0 rotor. The cells were applied to a Sanderson (Beckman) elutriation chamber and the eluates were collected with continuous flow with each fraction comprising 100 mL of eluate. As described previously, the second and third collected fractions contained ≥95% SLCs, while the fourth fraction contained a majority of LLCs (≥80%) along with some SLC and endothelial cells (Mao et al., 2013). SLCs and LLCs were concentrated with additional centrifugation of the relevant fractions.

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 42C on Bovine GeneChip Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G using the Affymetrix GeneChip Command Console Software

data_processing: Affymetrix Expression Console software was used to perform GC-RMA normalization and export the linear expression data.

organism: Bos taurus

source_name: bovine corpus luteum, large luteal cells isolated by elutriation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Homogenized in Tri-Reagent (Sigma-Aldrich) for total RNA extraction according to the manufacturer's instructions.

tag: Stage

value: luteal


title: CorpusLuteum_small-luteal-cells_3

source_name: bovine corpus luteum, small luteal cells isolated by elutriation


title: DominantFollicle_granulosa-cells_2

description: Isolated from estrogen-active dominant follicles in ovaries of beef cows (75% Red Angus, 25% MARC III) from the physiology herd located at the University of Nebraska Agricultural Research and Development Center. The University of Nebraska-Lincoln Institutional Animal Care and Use Committee approved all procedures and facilities used in this experiment. Estrous cycles of cows were synchronized with a modified Co-Synch protocol using gonadotropin releasing hormone (GnRH) and a controlled internal drug release device (CIDR; 1.38 g progesterone, Zoetis) for 7 days with a PGF2α (25 mg/mL; Lutalyse, Pfizer Animal Health) injection at CIDR removal (Summers et al., 2014). Ovariectomy was performed approximately 36 hours after CIDR removal (Youngquist et al., 1995). Upon ovariectomy, each dominant antral follicle was aspirated/dissected and the granulosa cells (≥ 94% purity), theca cells (≥ 82% purity), and follicular fluid were isolated as described previously (Summers et al., 2014).

source_name: bovine ovarian dominant follicle, mural and cumulus granulosa cells

value: follicular


title: CorpusLuteum_small-luteal-cells_2


title: DominantFollicle_theca-cells_2

source_name: bovine ovarian dominant follicle, theca interna cells


title: DominantFollicle_theca-cells_3


title: CorpusLuteum_small-luteal-cells_1


title: D10 pool2

city: worcester

first: yukiko

last: maeda

state: massachusetts

address: 364 Plantation Street

department: Medicine

institute: Umass Medical School

description:
Gene expression data from Arthritic synovium at peak inflammation pooled from 10 mice
D10p2_(MoGene-2_0-st).CEL

hyb_protocol: cDNA was hybridized for 16hr at 45C on  Mouse Gene 2.0 ST array (Affymetrix).  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:
Quality control was performed using Expression Console (Affymetrix). Expression values were RMA normalized and detection p-values for each probeset determined with the detectable above background (DABG) algorithm using apt-probeset-summarize in Affymetrix Power Tools.
All values were read into R and probesets with a DABG p-value < 0.05 in both replicates of at least one condition were called present. Genes with less than 50% of the probesets called present or undetected in all  conditions were removed.

source_name: Arthritic Sybovium at peak inflammation

label_protocol: cDNA was generated from 500 ng of total RNA using the Ambion WT Expression Kit and Affymetrix GeneChip WT Terminal Labeling Kit.

extract_protocol: Synovial samples were isolated from the region of the tibiotalar joint and processed for RNA. Extraction of total RNA was performed according to the manufacturer's instructions for mirVaNa miRNA isolation kit (Ambion, AM1560)

treatment_protocol: Serum transfer arthritis was induced in 12-week-old male C57BL/6J mice by intraperitoneal injection of 150 μl of arthritogenic serum on days 0, 2, and 7. Nonarthritic mice received 150 μl of sterile phosphate buffered saline at each time point.

tag: host strain

tag: serum source strain

value: K/BxN

tag: mouse model

value: serum transfer arthritis (STA) model

tag: time point

value: day 10 (Peak Inflammation)

value: synovium


title: DominantFollicle_granulosa-cells_3


title: NA pool1

description:
Gene expression data from Non-arthritic synovium pooled from 3 mice
NAp1 (2)_(MoGene-2_0-st).CEL

source_name: Nonarthritic Synovium

value: day 0  (Non Arthritic)


title: CorpusLuteum_large-luteal-cells_1


title: CorpusLuteum_large-luteal-cells_3


title: DominantFollicle_granulosa-cells_4


title: DominantFollicle_theca-cells_1


title: NA pool2

description:
Gene expression data from Non-arthritic synovium pooled from 3 mice
NAp2_(MoGene-2_0-st).CEL


title: Wild-type_mouse_DMBA-untreated_rep1

city: Hiroshima

first: Shinji

last: Mii

address: 1-2-3, Kasumi, Minami-ku

department: Department of Molecular Pathology

institute: Hiroshima University Graduate School of Biomedical and Health Sciences

description: Gene expression after 24hr in acetone-treated mouse skin

hyb_protocol: Fragmentation of Cy3-labeled cRNA and hybridization to SurePrint G3 Mouse GE 8×60K Microarray were performed by CDM Center (Takara Bio Inc., Kusatsu, Japan).

scan_protocol: One color scan setting for SurePrint G3 Mouse GE 8x60K Microarray.

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

source_name: Skin of wild-type mouse, DMBA-untreated, replicate 1

label_protocol: Cyanine-3 (Cy3)-labeled cRNA was prepared from 100 ng total RNA using a Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies).

extract_protocol: Total RNA was extracted from the skins of the untreated and DMBA-treated CD109+/+ and CD109-/- mice using TRIzol (Thermo Fisher Scientific) and an RNeasy Mini Kit (Qiagen).

treatment_protocol: DMBA-treatment was performed 24h before RNA extraction.

tag: genotype/variation

value: skin

value: female


title: Wild-type_mouse_DMBA-untreated_rep2

source_name: Skin of wild-type mouse, DMBA-untreated, replicate 2


title: D10 pool1

description:
Gene expression data from Arthritic synovium at peak inflammation pooled from 10 mice
D10p1_(MoGene-2_0-st).CEL


title: DominantFollicle_granulosa-cells_1


title: Liver_CLA_5

city: Gießen

first: Robert

last: Ringseis

address: Heinrich-Buff-Ring 26-32

department: Institute of Animal Nutrition and Nutrition Physiology

country: Germany

institute: JLU Gießen

hyb_protocol: After checking the quality and quantity of the labeled cRNA, cRNA was fractionated and hybridized with the Affymetrix GeneChips. GeneChips were washed and stained with the Affymetrix GeneChip Fluidics station 450. The GeneChips were then scanned with an Affymetrix GeneChip scanner 3000. All procedures were performed according to Affymetrix protocols (GeneChip expression analysis, Technical manual from Affymetrix). The quality of hybridization was assessed in all samples following the manufacturer´s recommendations.

scan_protocol: After scanning the gene chips, cell intensity (CEL) files containing a single intensity value for each probe cell were generated from the raw image data with GeneChip Operating Software v1.2 (Affymetrix).

data_processing: CEL files were imported into Expression Console v1.1 (Affymetrix) and subjected to global normalization using the Robust Multiarray Average (RMA) algorithm.

source_name: Liver CLA

label_protocol: The cRNA was labeled with biotin using the Affymetrix GeneChip labeling kit.

growth_protocol: A total of 40 primi- and multiparous Holstein cows with an average parity number of 2.6 were used for this study. The study was carried out at the Agricultural Experimental Station Hirschau of the Technical University of Munich (Germany) and was approved by the Bavarian state animal care and use committee. The experimental period lasted from wk 3 prepartum to wk 14 postpartum. Details on feeding regimen and husbandry conditions can be found in a recent publication (Schlegel et al., J Dairy Sci. 2012;95:3905-18). In brief, the cows were allotted to two groups of 20 cows each: control group and CLA group. Cows of both groups received an identical partial mixed ration (PMR) ad libitum, which was calculated to meet the energy and protein demand of a cow weighing 650 kg and producing 21 kg milk/d. In addition, cows of both groups were individually offered a limited amount of concentrate via transponder-access feeding stations in order to cover the individual extra requirements for milk production. Calculations for energy and protein supply followed the recommendations of the German Society of Nutrition Physiology (2001). The composition and the nutrient and energy concentrations of both, PMR and concentrate, and the amount of concentrate offered are shown in (Schlegel et al., J Dairy Sci. 2012;95:3905-18). The rumen-protected fat supplements, either control fat or CLA fat, were fed via an extra portion of concentrate (supplemental concentrate) containing 27.3 % fat supplement (either control fat or CLA fat) for both groups. The supplemental concentrate was fed during the experimental period at a constant amount of 630 g of DM/d and cow by hand once daily. The composition and the nutrient and energy concentrations of the supplemental concentrate and the contents of major fatty acids in the fat supplements are also given in (Schlegel et al., J Dairy Sci. 2012;95:3905-18).

extract_protocol: Total RNA was isolated from liver samples using Trizol® according to the manufacturer’s protocol and stored at -80 °C. Concentration and purity of the RNA were estimated from the optical density at 260 and 280 nm, respectively, using a NanoQuant plateTM (Infinite® 200, Tecan).

treatment_protocol: Cows were milked twice daily and milk yields of each cow were recorded automatically. Data on milk yield and milk composition have been reported in (Schlegel et al., J Dairy Sci. 2012;95:3905-18). At wk 1, 5 and 14 of lactation, blood samples and liver biopsies were taken. The liver biopsy procedure has been described in detail in (Schlegel et al., J Dairy Sci. 2012;95:3905-18). The liver biopsy samples were immediately snap-frozen in liquid nitrogen and stored at -80°C until analysis. In the present study, transcript profiling was carried out in the liver samples from wk 5 of lactation in order to identify genes and pathways regulated by rumen-protected CLA during early lactation. The first wks after parturition represent a critical phase in the productive cycle of high-yielding dairy cows because the liver experiences pronounced metabolic and inflammatory stress which increases the risk to develop liver-associated diseases, such as fatty liver and ketosis.

tag: breed

value: Holstein

tag: condition

value: conjugated linoleic acid (CLA)

value: liver

value: week 5 of lactation


title: CD109-deficient_mouse_DMBA-treated_rep2

description: Gene expression after 24hr in DMBA-treated mouse skin

source_name: Skin of CD109-deficient mouse, DMBA-treated, replicate 2


title: Liver_control_5

source_name: Liver control

value: control


title: CD109-deficient_mouse_DMBA-untreated_rep2

source_name: Skin of CD109-deficient mouse, DMBA-untreated, replicate 2


title: Wild-type_mouse_DMBA-treated_rep2

source_name: Skin of wild-type mouse, DMBA-treated, replicate 2


title: Liver_control_4


title: Liver_CLA_2


title: Liver_CLA_1


title: Liver_control_3


title: Liver_CLA_4


title: Liver_CLA_3


title: CD109-deficient_mouse_DMBA-untreated_rep1

source_name: Skin of CD109-deficient mouse, DMBA-untreated, replicate 1


title: CD109-deficient_mouse_DMBA-treated_rep1

source_name: Skin of CD109-deficient mouse, DMBA-treated, replicate 1


title: Liver_control_1


title: Wild-type_mouse_DMBA-treated_rep1

source_name: Skin of wild-type mouse, DMBA-treated, replicate 1


title: Liver_control_2


title: set2_Fc

city: Kobe

first: Kei

last: Enomoto

state: Hyogo

address: Chuo-ku, Minatojima-Minamimachi

institute: ASUBIO PHARMA CO., LTD.

description: Gene expression of mouse microglia treated with Fc

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 mouse GE 8x60K Microarrays (G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 028005_D_F_20140728) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: mouse microglia, Fc, 3h, replicate2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from mouse microglia using the TRIzol Plus RNA Purification System (Invitrogen) following the manufacturer's recommendations. Purified RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: strain

tag: cell type

value: primary microglia cells

value: Fc


title: set2_Ecrg4(71-132)

description: Gene expression of mouse microglia treated with Ecrg4(71-132)

source_name: mouse microglia, Ecrg4(71-132), 3h, replicate2

value: Fc-fused Ecrg4(71-132)


title: set1_Ecrg4(133-148)

description: Gene expression of mouse microglia treated with Ecrg4(133-148)

source_name: mouse microglia, Ecrg4(133-148), 3h, replicate1

value: Fc-fused Ecrg4(133-148)


title: set2_Ecrg4(133-148)

source_name: mouse microglia, Ecrg4(133-148), 3h, replicate2


title: set2_PBS

description: Gene expression of mouse microglia treated with PBS

source_name: mouse microglia, PBS, 3h, replicate2

value: PBS


title: set1_Ecrg4(71-132)

source_name: mouse microglia, Ecrg4(71-132), 3h, replicate1


title: set1_Fc

source_name: mouse microglia, Fc, 3h, replicate1


title: set1_PBS

source_name: mouse microglia, PBS, 3h, replicate1


title: N990275

city: Singapore

first: Aditi

last: Qamra

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: GIS

scan_protocol: BeadChips were scanned using the iScan system

data_processing:
Methylation β-values were calculated and background corrected using the methylumi R BioConductor package.
Normalization was performed using the BMIQ method (watermelon package in R).

label: Cy3 and Cy5

source_name: Gastric Primary Tissue

label_protocol: Standard Illumina protocol - Infinium HD Methylation protocol  Hybridization Protocol: Standard Illumina protocol - Infinium HD Methylation protocol

extract_protocol: Genomic DNA was isolated using Qiagen Blood & Cell Culture DNA Mini Kit according to the manufacturer's protocol

tag: tissue subtype

value: Gastric primary non-malignant tissue


title: N20021007

hyb_protocol: Hybridization Protocol: Standard Illumina protocol - Infinium HD Methylation protocol


title: N980436


title: T990275

value: Gastric primary tumor tissue


title: T20020720


title: T2001206


title: N980417


title: T980417


title: N980447


title: T980319


title: N2001206


title: T980447


title: N980401


title: N990489


title: N990068


title: T980401


title: T2000877


title: T990068


title: N980319


title: T76629543


title: T980436


title: N20020720


title: N20020720 [SNP]

description: The SNP6 profile of this sample was used to generate the reference model for normalizing the following cancer profiles: T20020720, T2001206. The normalized cancer profiles were subsequently used to detect copy number changes, reported in P20020720_cna.bed and P2001206_cna.bed, respectively.

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

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

data_processing:
Data in .CEL format was processed in the following order (Deng et. al., 2012): (1) Normalization: Raw .CEL files were processed using Affymetrix Genotyping Console 4.2. Reference models were created from SNP6.0 profiles of normal gastric tissues according to the hybridization batch. Copy number changes in cell lines and primary tumor samples were determined by using the reference model from primary normal samples. (2) Segmentation:  Copy number segmentation data was produced using the circular binary segmentation (CBS) algorithm implemented in the DNAcopy R package.
copy number altered regions followed by the copy number alteration status

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from flash-frozen gastric tumors and matched non-maligant gastric tissues using a Qiagen genomic DNA extraction kit.

tag: tissuetype

tag: histology

value: not applicable


title: N2000085


title: T990489


title: T2000085


title: N2000877 [SNP]


title: N20021007 [SNP]

description: The SNP6 profile of this sample was used to generate the reference model for normalizing the following cancer profiles: T2000639, T990068, T2000877. The normalized cancer profiles were subsequently used to detect copy number changes, reported in P2000639_cna.bed, P990068_cna.bed and P2000877_cna.bed, respectively.


title: T20020720 [SNP]

description: copy number altered regions followed by the copy number alteration status

value: intestinal


title: T2000877 [SNP]


title: N2000721 [SNP]


title: T990068 [SNP]

value: diffuse


title: N980097 [SNP]


title: N76629543


title: T2001206 [SNP]


title: T20021007


title: N2000639 [SNP]


title: N2001206 [SNP]


title: T980097


title: YCC-7 [SNP]

source_name: Gastric cancer cell line

value: Gastric cancer cell line

value: Adenocarcinoma


title: N2000986 [SNP]


title: T2000639 [SNP]


title: N2000877


title: miRNA expression data from Arthritic synovium at peak inflammation pooled from 10 mice 1

description: Day10 pool1

hyb_protocol: Prior to PCR, cDNA samples were pre-amplified using Megaplex Primer Pools, Rodent Pools Set v3.0 and TaqMan PreAmp Master Mix (Life Technologies, Foster City, CA). PreAmp Master Mix and 0.2x Primers were added to the cDNA samples and pre-amplified as follows: 95°C for 10 min once, 95°C for 15 sec, 60°C for 4 min, (final two steps repeated for 14 cycles). Quantitative Real-Time PCR reactions (qRT-PCR) were performed using the high-throughput BioMark Real-Time PCR system (Fluidigm, South San Francisco, CA). Pre-amplified cDNA samples were diluted with 0.1 mM EDTA in TE Buffer (1:5) and mixed with TaqMan Gene Expression Master Mix (Life Technologies, Foster City, CA), and Sample Loading Reagent (Fluidigm), then pipetted into sample inlets of Dynamic Array 96.96 chips (Fluidigm). Assay Loading Reagent (Fluidigm) and TaqMan miRNA Assays (Fluidigm, South San Francisco, CA) were mixed and pipetted into assay inlets of Dynamic Array 96.96 chips. This platform allows PCR reactions for 96 samples and 96 primers simultaneously.  The IFC Controller HX (Fluidigm) was used to distribute primers and samples into chip reaction wells for qRT-PCR by microfluidic delivery. Real-Time PCR reactions are performed in BioMark System and PCR protocols was 95°C for 10 min denaturation 95°C for 15 seconds and 60°C for 1 min for 30 cycles.

data_processing:
The raw data was normalized by global normalization method (Mestdagh et al., 2009).
Prior to normalization, those miRNA assays with poor or no amplification across all samples were removed. The mean Ct values across all detectable miRNAs for each sample were subtracted from individual miRNA assay Ct values to generate normalized ΔCt values.
The quality of the data was assessed using Principal component Analysis and Pearson correlation to determine replicate efficacy (Spotfire DecisionSite).

label: Rox

source_name: Arthritic Sybovium at peak inflammation

label_protocol: 500ng of RNA samples were converted to cDNA using TaqMan MicroRNA Reverse Transcription Kit (Life Technologies, Foster City, CA). The RNA was converted to cDNA using the following conditions: 16°C for 20 min, 42°C for 1 min, and 50°C for 1 second total 40 cycles. Then, 85°C for 5 min and 4°C hold until further processing or storage.

value: K/BxN

value: serum transfer arthritis (STA) model

value: day 10 (Peak Inflammation)

value: synovium


title: miRNA expression data from Non-arthritic synovium pooled from 3 mice 2

description: Non-Art pool2

source_name: Nonarthritic Synovium

value: day 0  (Non Arthritic)


title: miRNA expression data from Non-arthritic synovium pooled from 3 mice 1

description: Non-Art pool1


title: YCC-21 [SNP]


title: FU97 [SNP]

value: Diffuse adenocarcinoma;poorly differentiated; Lymph node metastasis and pancreatic metastasis were observed


title: NCC-59 [SNP]

value: Moderately differentiated tubular adenocarcinoma


title: miRNA expression data from Arthritic synovium at peak inflammation pooled from 10 mice 2

description: Day10 pool2


title: N980437


title: RPMI_CPI 0.01uM + LENA 5uM/Dexa 0.05uM 6h

city: Barcelona

first: Patricia

last: Pérez-Galán

state: Barcelona

address: Centre Esther Koplowitz, Hemato-oncology dept, Rosello 149-153, 2nd floor

department: Hemato-oncology

country: Spain

institute: IDIBAPS

description:
RPMI_COMBO
Gene expression data in treated RPMI-8226 cells.

hyb_protocol: RNA samples were processed to Affymetrix GeneChip HT HG-U219 arrays.

scan_protocol: Scanning was processed in the GeneTitan instrument.

data_processing:
Determination of the signal value for each probe set of the array were obtained with GeneChip® Command Console® Software (AGCC) (Affymetrix).
Raw data were normalized using the Robust Multichip Analysis (RMA) algorithm implemented in the Expression Console Software v1.1 (Affymetrix).

source_name: RPMI-8226 multiple myeloma cell line, COMBO

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150ng total RNA.

growth_protocol: MM cells at exponential phase were set at 5x10^5 cells/ml for the experiment.

extract_protocol: Total RNA was extracted using the Trizol reagent.

treatment_protocol: MM cells were treated with 0.01uM CPI203 +/- 5uM LENA and 0.05uM Dexa for 6h.

tag: cell line

value: multiple myeloma cell line

tag: treatment

value: CPI203 plus lenalidomide plus dexamethasone


title: IFN neg signature 1

city: Rotterdam

first: Arne

last: IJpma

address: Dr. Molewaterplein 50

department: Bioinformatics

country: Netherlands

institute: Erasmus MC

hyb_protocol: After fragmentation the chips were hybridized for 18h at 45°C. 5ug biotinylated cDNA was hybridized on Human Genome U133 plus 2.0 Array Gene Chips (Affymetrix, High Wycombe, UK) according to the manufacturer's protocols.

scan_protocol: Chips were scanned on a Affymetrix GeneChip Scanner 3000 7G according to the manufacturers protocol using the GeneChip® Command Console® Software (AGCC) v3.2.4

data_processing: The data were analyzed with Partek Genomics Suite version 6.6 using GCRMA with default settings and quantile normalization method. The data is log2 transformed.

source_name: IFN neg signature

label_protocol: The RNA (RIN≥8) was reverse transcribed, amplified, biotinylated and fragmented with the Ovation® Pico WTA system and EncoreTM Biotin Module (NuGEN Technologies, Leek, The Netherlands)

growth_protocol: Plasmacytoid dendritic cells were obtained from peripheral blood using ficoll peripheral blood mononuclear cell isolation.  FACS sorting was used to select BDCA4+CD123+ pDCs.

extract_protocol: Total RNA was isolated from purified CD123+BDCA4+ sorted cell-populations with the PicoPure RNA isolation kit (Arcturus®, Applied Biosystem, CA, USA) according to the manufacturers protocol, including a DNase I treatment (Qiagen, Venlo, The Netherlands) to remove genomic DNA contamination.

treatment_protocol: Steady-state (no treatment)

tag: disease state

value: IFNneg pSS

tag: gender

value: female

tag: age at inclusion

value: purified CD123+BDCA4+ plasmacytoid dendritic sorted cell-population


title: Healthy Control 2

description: ConMV

source_name: Healthy Control

value: control


title: IFN pos signature 2

source_name: IFN pos signature

value: IFNpos pSS


title: placenta_standard_uninfected, JC65

city: Durham

first: Cody

middle: Shaw

last: Nelson

state: NC

address: 2 Genome Ct

department: MGM

institute: Duke University

hyb_protocol: Targets were hybridized to Affymetrix GeneChip® Rhesus Macaque Genome arrays in Affymetrix GeneChip® Hybridization Oven 645, then washed in Affymetrix GeneChip® Fluidics Station 450 according to standard Affymetrix GeneChip® Hybridization and Wash protocols.

scan_protocol: Chip was scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® protocols.

data_processing: Affymetrix microarray data was initially processed, underwent QC, and was normalized with the robust multi-array average method using the affy Bioconductor package from the R statistical programming environment (R studio version 0.99.902). Differential expression was carried out using a moderated t-statistic from the limma package. The false discovery rate was used to control for multiple hypothesis testing.

organism: Macaca mulatta

source_name: fetal placenta from standard HIG group, not CMV-infected

label_protocol: Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion) from total RNA. Biotin labeling.

extract_protocol: Tissue sections weighing approximately 30mg were obtained from flash frozen rhesus placenta, lysed using a TissueLyser LT (Qiagen), then total RNA extracted using an RNeasy Mini Kit (Qiagen). RNA was assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies) and NanoDrop 8000 spectrophotometer (Thermo Scientific/NanoDrop) and confirmed to have: A260/A280>1.8, A260/A230>1.0, and RIN>7.0.

treatment_protocol: Placentas were flash frozen upon fetal abortion or fetal harvest, then stored at -80C.

tag: tissue

value: Fetal placenta

tag: rhcmv infection

value: Not infected

tag: hig tx

value: Standard


title: T980437

value: Gastric primary tumor tissue