title: Lis_KD_2

city: San Francisco

first: Scott

last: Baraban

address: 513 Parnassus Ave

department: Neurosurgery

institute: UCSF

description: gene expression in knock down fish

hyb_protocol: Hybridizations were performed for 14 hrs, according to the manufacturer’s protocol.

scan_protocol: Arrays were scanned using the Agilent microarray scanner and raw signal intensities were extracted with Feature Extraction v10.6 software.

data_processing: Dataset was normalized using the quantile normalization method that is proposed by Bolstad et al (2003).  No background subtraction was performed, and the median feature pixel intensity was used as the raw signal before normalization.

source_name: Lis1MO, 4dpf, pooled RNA

label_protocol: RNA was labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol. Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays.

extract_protocol: RNA was prepared using the RNeasy®Mini Kit (Qiagen) according to 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: 4dpf old zebrafish larvae (WT and Lis1 morphants) were freshly collected and prepared for RNA extraction.

value: whole larvae

tag: age

value: 4 dpf

value: LIS1 KD

tag: genetic background

value: WIK


title: Lis_KD_4

status: Public on Jun 15 2013

type: RNA

state: CA

country: USA

description: gene expression in knock down fish

molecule: total RNA

organism: Danio rerio

tag: tissue

tag: treatment


title: AGS + Hp WT 16h Rep3

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

description: In vitro infection

hyb_protocol: Hybridization using standard hybridization protocols from Illumina

scan_protocol: Standard Illumina protocols for HumanHT-12 chip version from Illumina using the Illumina BeadArray Reader

data_processing: The data were normalized using cubic spline normalization in GenomeStudio from Illumina. The expression at 0h was subtracted and the net expression was obtained after removing the values at NS from the Hp infected samples.

organism: Homo sapiens

source_name: AGS cells infected with WT H. pylori

label_protocol: cRNA was labeled with the Illumina TotalPrep RNA amplification Kit (ambion AMIL1971)

growth_protocol: Low passage AGS (5x) were maintain in regular RPMI. Two days before infection the cells were grown in HAMF12 containing 3% FBS for infection with Hp.

extract_protocol: RNA extracion and DNAseI treatment were done by following the protocols by Invitrogen (Trizol, DNAse I)

treatment_protocol: AGS were infected with the different strains of Hp (WT, rocF, rocF+) during 16h at a 20:1 ratio (bacteria:cell). The wells were washed twice with PBS and 1ml TRIzol was added for RNA extraction.

tag: cell line

value: AGS

tag: cell type

value: gastric epithelial cells

tag: infected with

value: wild type H. pylori strain for 16hrs


title: AGS NS 16h Rep2

description: In vitro infection

source_name: Non-infected AGS cells


title: AGS NS 16h Rep4

description: In vitro infection


title: AGS NS 0h Rep4

description: In vitro infection

source_name: AGS cells before plating


title: Genomic DNA from adenocarcinoma 643

type: genomic

city: Aarhus N.

first: Claus

middle: Lindbjerg

last: Andersen

address: Brenstrupgaardsvej 100

department: Dept. of Molecular Medicine (MOMA)

country: Denmark

institute: Aarhus University Hospital

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchips using the standard Illumina protocol.

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

data_processing: BeadStudio software v3.2. Background-normalized average Beta values were generated.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: adenocarcinoma

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted and purified from serial cryosections using the Puregene DNA purification kit according to standard instructions.

tag: gender

value: female

value: colorectal adenocarcinoma

tag: tissue type

value: fresh frozen


title: AGS NS 0h Rep3

description: In vitro infection


title: Lis_KD_1

description: gene expression in knock down fish


title: AGS NS 0h Rep2

description: In vitro infection


title: Genomic DNA from adenocarcinoma 717

value: male


title: Genomic DNA from adenocarcinoma 959


title: AGS NS 0h Rep1

description: In vitro infection


title: Lis_KD_3

description: gene expression in knock down fish


title: Zea mays_2nd leaf_60min_ rep2 dye-swap

city: San Antonio

first: Jurgen

last: Engelberth

state: Texas

address: One UTSA Circle

department: Biology

institute: University of Texas at San Antonio

description: M.hyb 5

hyb_protocol: Labelled cDNA hybridised using the MWG Gene-Frame system. Slides placed in shaking water bath for 16 h at 42 °C. Arrays then washed in 2x SSC (+0.1 % SDS), 1x SSC, 0.2x SSC and 0.1x SSC, each at 37 °C for 5 min prior to drying and scanning (http://ag.arizona.edu/microarray/Microarraymethod1.doc).

scan_protocol: Arrays were scanned using a GenePix Autoloader 4200AL.

data_processing: Raw data were extracted using GenePix Pro 6.0 program; then saved as gpr and txt files for each block individually (total 4 blocks on the chip resulting in 4 hybridizations). Within arrays, loess normalization was done using the Limma package in R (version R2.5.1) (Yang, Y. H., Dudoit, S., Luu, P., Lin, D. M., Peng, V., Ngai, J., and Speed, T. P. (2002). Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Research 30(4):e15). Between arrays, normalization was also done with the Limma package so that the scale the log-ratios to have the same median-absolute-deviation (MAD) across arrays (Smyth, G. K., and Speed, T. P. (2003). Normalization of cDNA microarray data. In: METHODS: Selecting Candidate Genes from DNA Array Screens: Application to Neuroscience, D. Carter (ed.). Methods Volume 31, Issue 4, December 2003, pages 265-273).

organism: Zea mays

source_name: Zea mays 2nd leaf after 60 min exposure to air (control)

label_protocol: 1 μg RNA samples were used to make Cy3- and Cy5-labeled targets with a three step protocol as follows: 1) cDNA was synthesized using an oligo-(d)T primer that incorporated the T7 promoter; 2) targets were amplified using in vitro transcription to produce aminoallyl-labeled cRNA; and 3) aminoallyl-labeled cRNA was coupled to Cy-labeled dyes. Details of these protocols can be found at: http://www.maizearray.org/files/cRNA_Target_Production_Using_RNA_Amplification.pdf

growth_protocol: Zea mays (inbred line B73) plants were grown in soil (Redi Earth Plug and Seedling Mix, Sun Gro) in a growth chamber with a 12 h photoperiod, 60% relative humidity at 26°C for three weeks (V2 stage). Light intensity was set at app. 150 mmol m2 s-1.

extract_protocol: About 100 mg of leaf material (2nd leaf) was used for RNA extraction. Total RNA was extracted with the Ultra Clean Plant RNA Isolation Kit (MO BIO Laboratories, Carlsbad, CA, USA) according to the manufacturer's instructions with the following modifications. Frozen plant samples were homogenized in 2 ml screw cap FastPrep tubes containing 0.5 g of Zirmil microbeads and 200 ml extraction buffer (PR1) for 20 sec at 6000 rpm in a Precellys tissue homogenizer (MO BIO Laboratories, Carlsbad, CA, USA). After this initial homogenization step the remaining 800 ml of PR1 were added and the sample again homogenized for 10 sec at 6000 rpm. The extract was then further processed as described in the manufacturer's instructions.

treatment_protocol: Zea mays (B73, 3 weeks old) were exposed to 1.5 mM Z-3-hexen-1-ol (Z-3-HOL) in a 10 l glass cylinder for 20 min and 60 min. Controls were treated likewise without the addition of Z-3-HOL. Leaves were cut and frozen in liquid N2 and stored at -80 °C prior to RNA extraction.

tag: line

value: 3 weeks

value: leaf

value: 60 min exposure to air (control)

source_name: Zea mays 2nd leaf after 60 min exposure to Z-3-hexenol (1.5 μM)

value: 60 min exposure to Z-3-hexenol (1.5 μM)


title: Genomic DNA from adenocarcinoma 845


title: Zea mays_2nd leaf_60min_ rep3

description: M.hyb 6


title: Lis_Ctl__2

description: gene expression in control fish

source_name: WT, 4dpf, pooled RNA

value: control


title: Genomic DNA from adenocarcinoma 724


title: Genomic DNA from adenocarcinoma 412


title: Genomic DNA from adenocarcinoma 894


title: Zea mays_2nd leaf_20min_ rep3

description: M.hyb 3

source_name: Zea mays 2nd leaf after 20 min exposure to Z-3-hexenol (1.5 μM)

value: 20 min exposure to Z-3-hexenol (1.5 μM)

source_name: Zea mays 2nd leaf after 20 min exposure to air (control)

value: 20 min exposure to air (control)


title: AGS NS 16h Rep1

description: In vitro infection


title: Lis_Ctl__3

description: gene expression in control fish

value: whole larvae

value: 4 dpf


title: Zea mays_2nd leaf_60min_ rep1

description: M.hyb 4


title: Zea mays_2nd leaf_20min_ rep2 dye-swap

description: M.hyb 2


title: Zea mays_2nd leaf_20min_ rep1

description: M.hyb 1


title: Lis_Ctl__4

description: gene expression in control fish

value: WIK


title: Genomic DNA from adenocarcinoma 424


title: Genomic DNA from adenocarcinoma 347


title: Genomic DNA from adenocarcinoma 294


title: Genomic DNA from adenocarcinoma 133


title: Genomic DNA from adenocarcinoma 346


title: Genomic DNA from adenocarcinoma 11


title: HEK293-YY2

status: Public on Jun 16 2013

city: Berlin

first: David

last: Drews

address: Augustenburger Platz 1

country: Germany

institute: Charite

description: ChIP-chip HEK293 cells YY2

data_processing:
standard NimbleGen protocol, performed by imaGenes GmbH  Campus Berlin-Buch  Robert-Rössle-Str. 10  Erwin-Negelein-Haus (Building 79)  13125 Berlin  Germany
The log2-ratio is computed and scaled to centerthe ratio data around zero. Scaling is performed by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value.

source_name: YY2 ChIP DNA from HEK293 cells

growth_protocol: HEK293 cells were cultured in DMEM media for 3 days

extract_protocol: ChIP was performed with the ChIP Assay Kit (Catalog # 17-295; Upstate) according to manufacturer’s protocol. 10 µg of anti-YY2 (SC-47637; Santa Cruz Biotechnology) antibody was added to immunoprecipitation samples. Incubation with no antibody served as negative control. After ChIP, DNA was purified with the QIAquick PCR Purification Kit (Qiagen). To reach a higher yield of DNA for ChIP-Chip, GenomePlex® Complete Whole Genome Amplification (WGA) Kit was (Catalog # WGA2; SIGMA) used after manufacturer’s recommendations. DNA was purified with the QIAquick PCR Purification Kit.

treatment_protocol: HEK293 cells are an established cell line

tag: chip antibody

tag: chip antibody manufacturer

value: Santa Cruz Biotechnology

tag: chip antibody catalog #

source_name: Input DNA from HEK293 cells

value: none, input DNA


title: DamID H1.2_replicates 1 and 2

city: Oxford

first: Kinga

last: Kamieniarz-Gdula

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

description:
2 biological replicates
DamID H1.2 replicate 1:  raw files CMF_H1.2A_fr_Cy5.pair and CMF_DamH1.2A_fr_Cy3.pair
DamID H1.2 replicate 2:  raw files CMF_H1.2B_fr_Cy3.pair and CMF_DamH1.2B_fr_Cy5.pair

Filename CMF_H1*.pair corresponds to H1-Dam (EXPERIMENTAL).
Filename CMF_DamH1*.pair corresponds to Dam (REFERENCE).

hyb_protocol: 13 µg labeled DNA per, 2.4 µl alignment oligo and 24 µl NimbleGen hybridiziation component A and 1x hybridization buffer in a total volume of 120 µl were heated to 98°C for 5 min and hybridized in a TECAN hybridization station for 16 hrs. at 42°C. Slides were washed sequentially with NimbleGen wash buffers I, II and III with 0.1 mM DTT at 42°C, 25°C, and 23°C, respectively.

scan_protocol: Microarrays were scanned in a DNA Microarray Scanner (Model G2505B, Serial number US22502518) from Agilent Technologies, which uses Scan Control software (Version A.6.11). Slides were first placed in a slide holder before putting it in the Scanner Carousel, which was installed in the scanner. Slides were scanned at multiple PMT (100/70/30/10%) for each channel at 5 um resolution using a suitable scan area.

data_processing: Raw data from each array (2 channels) were loess normalized and median centered. All arrays where then quantile normalized together and the dye-swap arrays were averaged. Software: R/Bioconductor.

source_name: IMR90 human fibroblast cells, expressing H1.2-Dam

label_protocol: 1 µg purified methyl-PCR DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy dye-coupled nonamers (Trilink Biotech) according to NimbleGen Sample Labeling protocol in NimbleGen Array User's Guide, v4.1 (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: IMR90 cells (Coriell) were cultured in DMEM medium (Invitrogen) supplemeted with 15% of FCS (Sigma), non-essential amino-acids (Sigma) and antibiotics.

extract_protocol: Genomic DNA was extracted following the manufacture instructions (Dneasy Blood & Tissue, Qiagen)

treatment_protocol: IMR90 cells were transducted with the lentiviruses and harvested after 2 days.

value: IMR90 fibroblast cells

tag: sample type

value: H1.2-Dam (EXPERIMENTAL)

source_name: IMR90 human fibroblast cells, expressing Dam

value: Dam (REFERENCE)


title: DamID H1.1_replicates 1 and 2

description:
2 biological replicates
DamID H1.1 replicate 1:  raw files CMF_H1.1A_fr_Cy3.pair and CMF_DamH1.1A_fr_Cy5.pair
DamID H1.1 replicate 2:  raw files CMF_H1.1B_fr_Cy5.pair and CMF_DamH1.1B_fr_Cy3.pair

Filename CMF_H1*.pair corresponds to H1-Dam (EXPERIMENTAL).
Filename CMF_DamH1*.pair corresponds to Dam (REFERENCE).

source_name: IMR90 human fibroblast cells, expressing H1.1-Dam

value: H1.1-Dam (EXPERIMENTAL)


title: Genomic DNA from adenocarcinoma 479

value: male

value: colorectal adenocarcinoma

value: fresh frozen


title: Genomic DNA from adenocarcinoma 430


title: Genomic DNA from adenocarcinoma 443


title: Genomic DNA from adenocarcinoma 602


title: Genomic DNA from adenocarcinoma 939


title: DamID H1.4_replicates 1 and 2

description:
2 biological replicates
DamID H1.4 replicate 1:  raw files CMF_H1.4A_fr_Cy5.pair and CMF_DamH1.4A_fr_Cy3.pair
DamID H1.4 replicate 2:  raw files CMF_H1.4C_fr_Cy3.pair and CMF_DamH1.4C_fr_Cy5.pair

Filename CMF_H1*.pair corresponds to H1-Dam (EXPERIMENTAL).
Filename CMF_DamH1*.pair corresponds to Dam (REFERENCE).

source_name: IMR90 human fibroblast cells, expressing H1.4-Dam

value: H1.4-Dam (EXPERIMENTAL)


title: FSH_rep4

city: Rochester

first: Stephen

last: Welle

state: NY

address: 601 Elmwood Avenue

institute: University of Rochester

hyb_protocol: The hybridization, washing, and staining methods were those recommended by Affymetrix. After overnight hybridization of target solution with arrays, the arrays were washed and stained with SAPE.

scan_protocol: The stained arrays were scanned with an Affymetrix scanner. Affymetrix Command Console software was used to generate cel files from the pixel-level data.

data_processing:
Cel files were analyzed with Affymetrix Expression Console with the PLIER algorithm. The analysis was limited to the probe sets designated by Affymetrix as 'core' probe sets, i.e. those with the best mapping to known genes.
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label: biotin

source_name: quadriceps muscle biopsy

label_protocol: Biotinylated sense-strand DNA was generated from from 1 microgram total RNA as recommended in the Affymetrix User Manual (GeneChip Whole Transcript Sense Target Labeling Assay). After removal of most of the rRNA with a RiboMinus column, first strand cDNA synthesis introduced a promoter for cRNA synthesis. After second-strand cDNA synthesis, in vitro transcription generated cRNA. The cRNA (10 ug) served as the template for reverse transcription to produce sense-strand DNA, which was fragmented and labeled with biotin.

extract_protocol: Total RNA was extracted from muscle with Trizol reagent (Invitrogen) as recommended by the manufacturer.

value: quadriceps muscle biopsy

tag: muscular dystrophy type

value: facioscapulohumeral


title: Genomic DNA from adenocarcinoma 878

value: female


title: Genomic DNA from adenocarcinoma 569


title: Lis_Ctl__1

description: gene expression in control fish

value: control


title: Genomic DNA from adenocarcinoma 348


title: DamID H1.3_replicates 1 and 2

description:
2 biological replicates
DamID H1.3 replicate 1:  raw files CMF_H1.3A_fr_Cy3.pair and CMF_DamH1.3A_fr_Cy5.pair
DamID H1.3 replicate 2:  raw files CMF_H1.3B_fr_Cy5.pair and CMF_DamH1.3B_fr_Cy3.pair

Filename CMF_H1*.pair corresponds to H1-Dam (EXPERIMENTAL).
Filename CMF_DamH1*.pair corresponds to Dam (REFERENCE).

source_name: IMR90 human fibroblast cells, expressing H1.3-Dam

value: H1.3-Dam (EXPERIMENTAL)


title: Genomic DNA from adenocarcinoma 779


title: Genomic DNA from adenocarcinoma 260


title: FSH_rep6


title: FSH_rep3


title: FSH_rep1


title: Genomic DNA from adenocarcinoma 629


title: DamID H1.5_replicates 1 and 2

description:
2 biological replicates
DamID H1.5 replicate 1:  raw files CMF_H1.5B_fr_Cy5.pair and CMF_DamH1.5B_fr_Cy3.pair
DamID H1.5 replicate 2:  raw files CMF_H1.5C_fr_Cy5.pair and CMF_DamH1.5C_fr_Cy3.pair

Filename CMF_H1*.pair corresponds to H1-Dam (EXPERIMENTAL).
Filename CMF_DamH1*.pair corresponds to Dam (REFERENCE).

data_processing: Raw data from each array (2 channels) were loess normalized and median centered. All arrays where then quantile normalized together and the arrays (not dye-swaps) were averaged. Software: R/Bioconductor.

source_name: IMR90 human fibroblast cells, expressing H1.5-Dam

value: H1.5-Dam (EXPERIMENTAL)


title: Genomic DNA from adenocarcinoma 212


title: FSH_rep8


title: FSH_rep2


title: DM2_rep6

value: myotonic type 2


title: cervical spinal cord-wild-type C

city: Bronx

first: Zaven

last: Kaprielian

address: Kennedy Center RM 616, 1410 Pelham Parkway South

institute: Albert Einstein College of Medicine

hyb_protocol: Hybridization to GeneChip® Mouse Genome 430 2.0 Array (Affymetrix) performed by Einstein’s Affymetrix facility.

scan_protocol: The array image is generated by a high-resolution GeneArray Scanner 3000 7G (Affymetrix, Santa Clara, CA,).

data_processing:
The raw data (CEL files) from each probe set were normalized by RMA methods using GeneSpring GX 10.0 software. The log2 transformed signal intensities were averaged for biological replicates and the mean value was used to compute fold change.
The log2 transformed signal intensities were averaged for biological replicates, and the mean value was used to compute fold change.  We used t-tests to identify these genes with signal levels that were significantely different between tissue derived from Nkx2.9 deficient embryos (experimental) and their WT littermates (control).  Differentially expressed genes were selected with a fold chang >1.5.

organism: Mus musculus

source_name: cervical spinal cord

label_protocol: NuGEN Ovation Pico WTA System (PN 3300) was used to generate sense strand cDNA from total RNA  followed by fragmentation and labeling using Encore® Biotin Module (PN 4200).

extract_protocol: Qiagen Rneasy Micro Kit was used to isolate total RNA from E11.5 cervical spinal cords (excluding dorsal spinal cord and floorplate).

tag: developmental stage

tag: genotype

value: wild type

value: cervical spinal cord


title: FSH_rep7


title: DM2_rep7


title: DM2_rep4


title: FSH_rep5


title: Genomic DNA from adenocarcinoma 584


title: Genomic DNA from adenocarcinoma 759


title: cervical spinal cord Nkx2.9-knockout B

value: Nkx2.9 knockout


title: cervical spinal cord Nkx2.9-knockout C


title: cervical spinal cord-wild-type B


title: Genomic DNA from adenoma 1103

source_name: adenoma

value: colorectal adenoma


title: Genomic DNA from adenoma 1174


title: DM2_rep2


title: DM1_rep7

source_name: diaphragm muscle postmortem

value: diaphragm muscle postmortem

value: myotonic type 1


title: Genomic DNA from adenocarcinoma 763

source_name: adenocarcinoma


title: cervical spinal cord Nkx2.9-knockout A


title: Genomic DNA from adenoma 379


title: Genomic DNA from adenocarcinoma 464


title: Genomic DNA from adenoma 1125

value: male


title: Genomic DNA from adenoma 902


title: Genomic DNA from normal epithelium 1597

source_name: normal epithelium

value: normal colon epithelium


title: Genomic DNA from adenocarcinoma 652

value: colorectal adenocarcinoma

value: fresh frozen


title: DM1_rep8

source_name: quadriceps muscle postmortem

value: quadriceps muscle postmortem


title: DM1_rep5

source_name: biceps brachii muscle postmortem

value: biceps brachii muscle postmortem


title: Genomic DNA from adenoma 1140


title: DM2_rep1

value: quadriceps muscle biopsy


title: cervical spinal cord-wild-type A


title: DM1_rep2


title: DM1_rep4


title: Genomic DNA from normal epithelium 935


title: DM1_rep3


title: DM1_rep6

source_name: tibialis anterior muscle postmortem

value: tibialis anterior muscle postmortem


title: DM1_rep1


title: Normal_rep6


title: Genomic DNA from normal epithelium 1417


title: Genomic DNA from normal epithelium 477

value: female


title: Genomic DNA from normal epithelium 421


title: Sample2_Replicate2

city: Thuwal

first: Alaguraj

last: Veluchamy

address: Thuwal

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

description: Nimblegen tiling array with dye swap

hyb_protocol: Microarray hybridization was performed according to Lippman et al. , following NimbleGen’s 21M “NimbleChip Arrays

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing:
Statistically significant probe bound regions (ChIP-enriched genomic regions) were detected using the RINGO in R Bioconductor package. We used vsn normalization (variance stabilization) in RINGO, recommended for NimbleGen tiling microarray with multiple replicates. The strength of evidence for a ChIP-enriched site i,e Normalization was assessed with a P-value cut-off of 0.02.
VSN-normalized, averaged signal intensity.

organism: Phaeodactylum tricornutum

source_name: McrBC chip on Pt1

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Cultures of P. tricornutum Bohlin clone Pt1 8.6 (CCMP2561) were grown in f/2 medium made with 0.2-μm-filtered and autoclaved seawater supplemented with f/2 vitamins and inorganic filter sterilized nutrients. Cultures were incubated at 19°C under cool white fluorescent lights at approximately 75 μmol.m-2.s-1 in 12h light: 12h dark conditions and maintained in exponential phase in semicontinuous batch cultures.

extract_protocol: Genomic DNA from three P. tricornutum cultures (biological replicates) was sonicated to an average size of 600 nt using the Bioruptor sonicator (UCD-200, Diagenode). After sizeseparation by gel electrophoresis, the gel window corresponding to the 500-700 nt DNA fragments was excised and DNA was recovered using QIAquick Gel Extraction kit. A total of  200 ng of size-filtered DNA was incubated overnight at 37°C in a reaction containing 10 units of McrBC enzyme (New England Biolabs), 1x McrBC buffer, 3 mM GTP , 300 ng/ml BSA, and water. In negative controls, GTP, which is the co-factor required for McrBC activity, was replaced by water. McrBC was then inactivated by heating the reactions for 20 minutes at 65°C. After size-separation by gel electrophoresis, DNA contained in the 500-700 nt gel window was recovered using QIAquick Gel Extraction kit. The efficiency and specificity of DNA digestion by McrBC was verified by semi-quantitative PCR by assessing the amount of DNA from PtC13 CoDi element and from the histone H4 gene which appeared unmethylated in all our set up experiments. For each replicate, we observed a significant and similar exclusion of methylated DNA in the samples compared to negative controls.  Primers: PtC13_Fw 5' TTG-CAA-ATT-TTC-AGC-AGC-AC 3' and PtC13_Rev 5' AGAAGG- CTG-GGA-CAC-AGA-GA 3'; H4_Fw 5' AGG-TCC-TTC-GCG-ACA-ATA-TC 3' and H4_Rev 5' ACG-GAA-TCA-CGA-ATG-ACG-TT 3'.

tag: clone


title: Normal_rep7


title: Sample3_Replicate3

description: Nimblegen tiling array with dye swap


title: Normal_rep8


title: Sample1_Replicate1

description: Nimblegen tiling array with dye swap


title: Genomic DNA from normal epithelium 395


title: Normal_rep5


title: DM2_rep5


title: Normal_rep3


title: VEGF overexp rep 4

status: Public on Jun 14 2013

city: Cincinnati

first: Steven

last: Potter

state: OH

address: 3333 Burnet Ave.

department: Developmental Biology

institute: Cincinnati Children's Hospital

hyb_protocol: A hybridization cocktail is created as per Affymetrix protocols for each sample. The samples were then hybridized to Affymetrix Mouse Gene 1.0 ST arrays in the GeneChip hybridization oven 640 (Affymetrix) overnight. Probe arrays were then washed and stained using the Fluidics Station 450 (Affymetrix).

scan_protocol: The arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G following manufacturer's instructions. Raw data files were created by command console, the Affymetrix operating software program.

data_processing:
The Affymetrix  Gene 1.0 ST array quality control metrics for the samples were examined using the Affymetrix Expression Console Program. Specific quality control metrics examined included the signal histogram, relative log expression signal, Pearson's correlation coefficients, pm mean (average signal intensity of probes), pos vs neg auc (area under the curve), expression values of spiked in control poly-A controls and values of the spiked in hybridization controls.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm8.mps

source_name: bitransgenic mutant

label_protocol: For each sample the Ambion WT Expression Kit (Life Technologies) synthesizes cDNA target from 120 nanograms of total RNA. Then the GeneChip WT terminal labeling kit (Affymetrix) is used to both chemically fragment and biotin-label the cDNA target.

growth_protocol: E16  E16 GFAP-tTA: TetO-VEGF-A164 bitransgenic embryos compared to wild type (without TetO-VEGF-A164)

extract_protocol: Qiagen Rneasy kit

tag: strain background

value: mixed

tag: genotype/variation

value: induced overexpression of VEGF

tag: age

value: brain cortex


title: control replicate 3

source_name: wild type control

value: wild type

tag: tissue


title: miR-142-/- Qa2- thymocytes

city: Rehovot

first: Alexander

last: Mildner

address: 234 Herzl street

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: Gene expression data of Qa2+ thymocytes isolated from miR-142-/- mice

scan_protocol: According to Affymetrix standard protocols, using Affymetrix GeneChip 3000 7G plus scanner

data_processing: RMA was carried out using Partek Genomic Suite 6.5 (Inc. St. Charles, MO; www.partek.com)

source_name: thymus

growth_protocol: Thymi were removed from 8 weeks old animals and meshed on a 100mm mesh.

extract_protocol: 1x10e6 sorted cells were used for RNA extraction. The microRNA kit from Qiagen was used for RNA preparation in combination with Dnase digest according to manufacturer's instruction.

treatment_protocol: Single cell suspension was enriched for CD4+ cells by depleting CD8+ cells with CD8 MACS beads (Miltenyi). Enriched flow through cell fraction was stained with antibodies against CD4, CD8, CD69 and Qa2 for 25min on ice. After washing, cells were resuspended and sorted with a FACS Aria.

tag: strain

tag: Sex

value: pool of 1 female and 3 male

value: 8 weeks

tag: sorting strategy


title: miR-142-/- Qa2+ thymocytes

hyb_protocol: According to Affymetrix standard protocols


title: Normal_rep1


title: Normal_rep4


title: control replicate 2


title: VEGF overexp rep 3


title: Normal_rep2


title: VEGF overexp rep 1


title: control replicate 4


title: WT Qa2- thymocytes

description: Gene expression data of Qa2- thymocytes isolated from WT mice

label_protocol: According to Affymetrix standard protocols

value: pool of 3 female and 2 male


title: VEGF overexp rep 2


title: control replicate 1


title: IgG_immunoprecipitation_rep1

city: Cambridge

first: Lingbo

last: Zhang

address: Nine Cambridge Center

institute: Whitehead Institute for Biomedical Research and MIT Department of Biology

hyb_protocol: Hybridization follows manufacture instruction of the Affymetrix’s GeneChip WT terminal labeling and hybridization user manual for use with the Ambion WT expression kit.

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

data_processing: Data was extracted from the array images, normalized and processed according to standard protocol.  RMA normalization using bioconductor affy package

source_name: Immunoprecipitation on early erythroid progenitors using IgG_rep1

label_protocol: Label was performed following a two step protocol. The first step follows manufacture instruction of the Ambion WT expression kit for Affymetrix GeneChip Whole Transcript (WT) expression arrays. The second step follows manufacture instruction of the Affymetrix’s GeneChip WT terminal labeling and hybridization user manual for use with the Ambion WT expression kit.

growth_protocol: Early erythroid progenitors were enriched from mouse E14.5 fetal liver. The first step includes a negative selection for erythroid progenitors by magnetic depleting of mature blood cells (lineage positive cells), early multipotent GEMM colony forming cells (Sca-1 positive cells), and myeloid colony-forming cells (CFU-G/M/Mk) (CD16/32 positive, CD41 positive, or CD34 positive cells). The second step includes a FACS based positive selection of early erythroid progenitor process (c-kit positive and CD71 10%low cells).

extract_protocol: RNAs were extracted by using Qiagen RNA extraction kit following the manufacturer's instruction.

treatment_protocol: Early erythroid progenitors were isolated from mouse E14.5 fetal liver and lysed. Control rabbit IgG or RBP specific antibody were incubated with cell lysis, and immunoprecipitation was performed according to manufacture instruction (EZ-Magna RIP RNA-Binding Protein Immunoprecipitation Kit). Microarray experiments were carried out to identify transcripts that are immunoprecipitated by either control IgG or RBP specific antibody.

value: fetal liver

tag: cell type

value: early erythroid progenitors

tag: rip antibody

value: Control rabbit IgG


title: RBP_immunoprecipitation_rep2

source_name: Immunoprecipitation on early erythroid progenitors using RBP antibody_rep2

value: RBP specific antibody (Abcam, Catalog#:ab70775, Lot#:557821)


title: RBP_immunoprecipitation_rep1

source_name: Immunoprecipitation on early erythroid progenitors using RBP antibody_rep1


title: GIST_RNA_32

city: Seoul

first: Kyoung-Mee

last: Kim

address: #50 Irwon-dong

country: South Korea

institute: Samsung Medical Center

description: KIT gene with deletion mutation, WKV557-559C genotype

hyb_protocol: The hybridization was incubated in Agilent SureHyb chambers for 17 hr in a Rotisserie Hybridization Oven set to 65℃ and rotating at 10 rpm.

scan_protocol: Arrays were scanned using an Agilent Technologies Scanner G2505C US84703596 (Agilent Technologies, Inc).

data_processing: Extracted data analyzed with Agilent Genespring GX software 11.5 (Agilent Technologies) and R-programming (Variance Stabilization and Normalization, the VSN package)

source_name: Stomach_GIST_high risk

label_protocol: Total RNA (10-200ng) was reverse transcribed into cDNA by incorporating a T7 promoter primer prior to the generation of ﬂuorescent cRNA using an Agilent Quick Amp Labeling KIT (Agilent Technologies).

extract_protocol: Tumor tissues were extracted from the fresh tissue by QiagenRNeasy Mini KIT (Qiagen, Crawley, UK) according to the manufacturer’s instructions.

tag: gender

value: male

tag: tissue type

value: Gastrointestinal stromal tumor (GIST)


title: GIST_RNA_31

description: KIT gene with insertion mutation, D572-587NPTQLPYDHKWEFPRN genotype


title: WT Qa2+ thymocytes

description: Gene expression data of Qa2+ thymocytes isolated from WT mice


title: GIST_RNA_12

description: KIT and PDGFRA wild-type

source_name: Stomach_GIST_low risk

value: KIT and PDGFRA wild-type


title: REF_RNA

description: mixed schwannoma and leiomyoma total RNA

value: schwannoma and leiomyoma tumor


title: GIST_RNA_25

description: KIT gene with missense mutation, V559D genotype


title: GIST_RNA_24

description: PDGFRA gene with missense mutation, D842V genotype

source_name: Stomach_GIST_moderate risk


title: GIST_RNA_30

description: KIT gene with insertion mutation, 576-579LPYD genotype


title: GIST_RNA_26

value: KIT gene with missense mutation, V559D genotype


title: GIST_RNA_10

description: KIT and PDGFRA wild-type


title: GIST_RNA_27

description: KIT gene with deletion mutation, WKV557-559F genotype


title: GIST_RNA_09

description: KIT and PDGFRA wild-type

value: female


title: GIST_RNA_02

source_name: Stomach_GIST_very low risk


title: GIST_RNA_03

description: KIT gene with missense mutation, V560D genotype


title: DM2_rep3

source_name: quadriceps muscle biopsy

value: quadriceps muscle biopsy

value: myotonic type 2


title: GIST_RNA_08

description: KIT gene with missense mutation, N822K genotype


title: GIST_RNA_07

description: KIT gene with deletion mutation, D579 genotype


title: GIST_RNA_05

value: KIT gene with deletion mutation, WKV557-559F genotype


title: Ryp4 in ryp4-37 ChIP, sample B

first: Mark

last: Voorhies

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

hyb_protocol: Labeled DNA samples were hybridized following Agilent's ChIP-on-chip protocol.

scan_protocol: Slides were scanned with an Agilent scanner and raw ratios were obtained with the Agilent ChIP_107_Sep09 protocol.

data_processing: Background subtracted probe intensities were transformed to log2 (red/green) ratios (M) and log2 (sqrt(red*green)) geometric mean intensities (A), excluding probes with intensities below background. The M,A values were fit using the LOWESS algorithm (The American Statistician 35:54) as implemented in R, and the fit curve was subtracted from the transformed data to yield lowess normalized log2 ratio values.

organism: Histoplasma capsulatum

source_name: Ryp4 in ryp4-37 ChIP, sample B

label_protocol: Both input and output DNA were amplified and labeled with fluorescent dyes (Cy3 and Cy5) using strand displacement amplification following published protocol (Methods in Enzymology 470:737).

extract_protocol: 300 mg of ground samples were vortexed vigorously in lysis buffer [50 mM Hepes/KOH (pH 7.5), 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate supplemented with Halt protease and phosphatase inhibitors (Pierce)] for 3 hrs with 0.5 mm glass beads to lyse the cells. Following cell lysis, lysates were sonicated in a Diagenode Bioruptor for 30 min (30 sec on, 1min off) to shear DNA. Input DNA was collected and rest of the samples was subjected to immunoprecipitation. For filamentous-phase samples (ryp mutants), lysates from three identical tubes were combined prior to antibody incubation. Each sample was incubated overnight at 4C with 20 ug of polyclonal antibodies against portion of Ryp1 (ID:2877, ELDKPFPPGEKKRA), Ryp2 (ID:237, QTNRDYPFYNGPDAKRPR), Ryp3 (ID:338, GIKIPIRKDGVKGPRGGQ), or Ryp4 (ID:8, PPPQQSLQGWSPEEW). Next day, 40 ul of Protein-A Sepharose 4B Fast Flow (Sigma-Aldrich) beads were added lysate-antibody mixture and further incubated for 2 hrs. Then, beads were collected by centrifugation, and washed 9 times. Protein-DNA complexes that are bound to the beads were collected by incubating beads at 65C with elution buffer (50 mM Tris.HCl pH8.0, 10mM EDTA, 1% SDS).  Protein-DNA crosslinks in input and ChIPed samples were reversed overnight at 65C. Proteins were digested with proteinase K and DNA was purified with phenol: chloroform extraction as described (Methods in Enzymology 470:737).

source_name: Input


title: Ryp4 in G217B-37 ChIP, sample A

source_name: Ryp4 in G217B-37 ChIP, sample A


title: GIST_CGH_32

description: KIT with deletion mutation, WKV557-559C genotype

hyb_protocol: Differentially labeled patient and reference DNAs were combined and hybridized to Agilent Human Genome CGH 244A microarrays at 65℃ for 40 hr. Four washing steps were completed with Agilent Oligo CGH washes: Wash Buffer 1 at room temperature for 5 min, Wash Buffer 2 at 37℃ for 1 min, an acetonitrile rinse at room temperature for 1 min and a 30 sec wash at room temperature in Agilent’s Stabilization and Drying Solution.

scan_protocol: Arrays were scanned using an Agilent Technologies Scanner G2505B US45103026 (Agilent Technologies, Inc).

data_processing: Data were obtained using Agilent Feature Extraction Software and analyzed with Agilent Genomic Workbench 6.0 Software using the statistical algorithms z-score and common aberration detection method 2 (ADM-2) with sensitivity thresholds at 2.5 and 6.0, respectively, and a moving average window of 0.2 Mb.

source_name: Normal Human Genomic DNA

label_protocol: Same amounts (1.5㎍) of patient DNA and gender-matched reference DNA were digested. The digested DNAs were labeled by random priming with Cy3-dUTP (reference DNA) and Cy5-dUTP (patient DNA) using Agilent Labeling KIT.

extract_protocol: Genomic DNAs from tumor tissue was extracted from the fresh tissue by manual microdissection, standard proteinase K digestion, and QIAamp DNA mini KIT according to the manufacturer’s instructions (Qiagen, Hilden, Germany).

value: Human Genomic DNA from multiple anonymous donors (Promega Corporation, Madison, USA)


title: IgG_immunoprecipitation_rep2

source_name: Immunoprecipitation on early erythroid progenitors using IgG_rep2


title: GIST_CGH_31

description: KIT with insertion mutation, D572-587NPTQLPYDHKWEFPRN genotype


title: Ryp4 in ryp4-37 ChIP, sample A

source_name: Ryp4 in ryp4-37 ChIP, sample A


title: Ryp2 in ryp2-37 ChIP, sample B

source_name: Ryp2 in ryp2-37 ChIP, sample B


title: Ryp3 in G217B-37 ChIP, sample C

source_name: Ryp3 in G217B-37 ChIP, sample C


title: protocol (management) biopsy 82

city: Vienna

first: Julia

last: Wilflingseder

address: Währinger Gürtel 18-20

department: Nephrology and Dialysis

country: Austria

institute: Medical University of Vienna

description: miRNA profile of renal graft with perfect function and morphology

hyb_protocol: The complementary RNA hybridization cocktail was incubated overnight at 48°C while rotating in a hybridization oven. After 16 hours of hybridization, the cocktail was removed and the arrays were washed and stained in an Affymetrix GeneChip fluidics station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip 3000G scanner.

data_processing: All ouput files (.cel) were analyzed by the miRNA QC Tool (Affymetrix) to assess data quality. Affymetrix data were preprocessed, normalized, summarized and annotated with the robust multi-average (RMA) method, quantile normalization and corresponding annotation file (.cdf). Only miRNAs with at least 80% of valid entries were considered for successive analysis steps

source_name: kidney allograft biopsy

label_protocol: Total RNA (1µg per sample) was labeled using the FlashTag RNA Labeling Kit (Genisphere, Cat.# FT30AFYB) and hybridized to the arrays as described by the manufacturer (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA from ten slides (5 µm) was isolated and purified using miRNeasy FFPE Kit (Qiagen, Cat.No. 217404)

value: kidney


title: protocol (management) biopsy 80

value: renal graft with perfect function and morphology


title: BMDCs- Helicobacter pylori Ag lysate stimulated 3

city: Baltimore

first: Jessica

last: Shiu

state: MD

address: 655 W Baltimore St

department: Pediatrics

institute: University of Maryland School of Medicine

description: BMDC Helicobacter pylori stimulated, Biological replicate 3

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized by median method implemented in R package beadarray and log2 transformed.

source_name: Mouse bone marrow

label_protocol: Biotinylated cRNA were prepared using the Illumina TotalPrep RNA Amplification Kit from Ambion.

growth_protocol: BMDCs were generated from the bone marrow of WT female C57BL/6 mice using flt3L at 100 ng/mL for 8 days.

extract_protocol: RNA was extracted using Qiagen's Rneasy kit. Quality Control was performed with an Agilent Bioanalyser.

treatment_protocol: BMDCs were either treated with media alone or media with 10 ug/mL of antigen lysate from either E. coli or H. pylori.

value: bone marrow derived Dendritic Cells

tag: stimulated

value: Helicobacter pylori Ag lysate

value: Female

tag: time point

value: 24 hours


title: protocol (management) biopsy 81

tag: sample type


title: GIST_CGH_30

description: KIT with insertion mutation, 576-579LPYD genotype


title: Ryp1 in G217B-37 ChIP, sample B

source_name: Ryp1 in G217B-37 ChIP, sample B


title: Ryp3 in G217B-37 ChIP, sample B

source_name: Ryp3 in G217B-37 ChIP, sample B


title: Ryp1 in G217B-37 ChIP, sample C

source_name: Ryp1 in G217B-37 ChIP, sample C


title: Ryp2 in G217B-37 ChIP, sample B

source_name: Ryp2 in G217B-37 ChIP, sample B


title: Ryp1 in ryp1-37 ChIP, sample A

source_name: Ryp1 in ryp1-37 ChIP, sample A


title: BMDCs- Helicobacter pylori Ag lysate stimulated 1

description: BMDC Helicobacter pylori stimulated, Biological replicate 1


title: Ryp4 in G217B-37 ChIP, sample B

source_name: Ryp4 in G217B-37 ChIP, sample B


title: Ryp2 in ryp2-37 ChIP, sample A

source_name: Ryp2 in ryp2-37 ChIP, sample A


title: BMDCs- Escherichia coli Ag lysate stimulated 3

description: BMDC Escherichia coli stimulated, Biological replicate 3

value: Escherichia coli Ag lysate


title: BMDCs- Escherichia coli Ag lysate stimulated 2

description: BMDC Escherichia coli stimulated, Biological replicate 2


title: GIST_CGH_26

description: KIT with missense mutation, V559D genotype

source_name: Stomach_GIST_high risk

value: male


title: Ryp2 in G217B-37 ChIP, sample C

source_name: Ryp2 in G217B-37 ChIP, sample C

source_name: Input


title: GIST_CGH_29

description: KIT with insertion mutation, G578-592YDHKWEFPRNRLSFD genotype

source_name: Normal Human Genomic DNA

value: Gastrointestinal stromal tumor (GIST)


title: Ryp3 in ryp3-37 ChIP, sample A

source_name: Ryp3 in ryp3-37 ChIP, sample A


title: Ryp4 in G217B-37 ChIP, sample C

source_name: Ryp4 in G217B-37 ChIP, sample C


title: protocol (management) biopsy 52


title: GIST_CGH_24

description: PDGFRA with missense mutation, D842V genotype

source_name: Stomach_GIST_moderate risk


title: protocol (management) biopsy 53


title: GIST_CGH_25

value: KIT with missense mutation, V559D genotype


title: Ryp2 in G217B-37 ChIP, sample A

source_name: Ryp2 in G217B-37 ChIP, sample A


title: Ryp1 in G217B-37 ChIP, sample A

source_name: Ryp1 in G217B-37 ChIP, sample A


title: protocol (management) biopsy 50

source_name: kidney allograft biopsy


title: protocol (management) biopsy 49


title: GIST_CGH_22

description: KIT with deletion mutation, WK557-558 genotype


title: BMDCs- Escherichia coli Ag lysate stimulated 1

description: BMDC Escherichia coli stimulated, Biological replicate 1

source_name: Mouse bone marrow


title: Ryp3 in G217B-37 ChIP, sample A

source_name: Ryp3 in G217B-37 ChIP, sample A


title: protocol (management) biopsy 48


title: BMDCs- unstimulated 2

description: BMDC unstimulated, Biological replicate 2

value: no


title: Ryp3 in ryp3-37 ChIP, sample B

source_name: Ryp3 in ryp3-37 ChIP, sample B


title: BMDCs- unstimulated 1

description: BMDC unstimulated, Biological replicate 1


title: GIST_CGH_28

description: KIT with deletion mutation, WKV557-559F genotype


title: GIST_CGH_19


title: BMDCs- Helicobacter pylori Ag lysate stimulated 2

description: BMDC Helicobacter pylori stimulated, Biological replicate 2


title: GIST_CGH_23

description: KIT with deletion mutation, D579 genotype


title: protocol (management) biopsy 46


title: GIST_CGH_18

description: KIT with missense mutation, V559G genotype


title: protocol (management) biopsy 47

description: miRNA profile of renal graft with perfect function and morphology


title: GIST_CGH_21

description: KIT with insertion mutation, LPYDHKWEFPRNR576-588 genotype


title: GIST_CGH_20

description: KIT with deletion mutation, EVQWK554-558 genotype


title: delayed graf function 83

description: miRNA profile of delayed graft function

value: delayed graft function


title: GIST_CGH_17

description: KIT with missense mutation, V560D genotype


title: GIST_CGH_16

description: KIT with insertion mutation, P577-579PYD genotype

source_name: Stomach_GIST_low risk


title: delayed graf function 76

description: miRNA profile of delayed graft function


title: delayed graf function 77

description: miRNA profile of delayed graft function


title: GIST_CGH_15

description: KIT with missense mutation, V559E genotype


title: Ovules of fuzzless-lintless mutant of G. hirsutum L. cv. MCU5 at 20 dpa, biological replicate 3

city: New delhi

first: Padmalatha

state: Delhi

address: Pusa campus

department: Plant Biotechnology

country: India

institute: NRCPB

description:
Gene expression profiles of fuzzless-lintless ovules of mutant at 20 dpa , biological replicate 3.
Comparative analysis of transcriptome profiles of G. hirsutum L. cv. MCU5 and its fuzzless-lintless mutant at 20 dpa

scan_protocol: The cotton GeneChip Genome arrays were scanned on a GeneChip scanner 3000.

data_processing: After scannig CEL files were analyzed using GeneSpring GX 11.5 software. The Robust Multiarray Average (RMA) algorithm was used for the back ground correction, quantile normalization and median polished probe set summarization to generate single expression value for each probe set. Normalized expression values were log2-transformed and differential expression analysis was performed using unpaired t-test. The p-values were corrected by applying the false discovery rate (FDR) correction (Benjamini and Hochberg, 2000).

organism: Gossypium hirsutum

source_name: ovules of fuzzless-lintless mutant of G. hirsutum L. cv. MCU5 at 20 dpa

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5.0 µg total RNA Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45°C on Affymertix cotton Genechip Genome array. The arrays were washed and stained using streptavidin phycoerythrin on an Affymetrix fluidics station 450.

growth_protocol: The Gossypium hirsutum L. cv. MCU5 (wild-type) and its fuzzless-lintless mutant were grown in normal agronomic field.

extract_protocol: Total RNA was isolated using Spectrum Plant Total RNA Kit (Sigma, USA) from Fiber bearing ovules of wild-type and fuzzless-lintless ovules of mutant.

treatment_protocol: The Gossypium hirsutum L. cv. MCU5 and its fuzzless-lintless mutant were grown under field condition. Flowers were tagged at the day of anthesis and considered as 0 dpa (days post anthesis). Cotton bolls were collected at Fiber initiation (-2, -1, 0, 1 and 2 dpa), elongation (5, 10 and 15 dpa) and secondary cell wall synthesis (20 dpa) stages. The -2 and -1 dpa represents the days before anthesis. Harvested cotton bolls were immediately frozen in liquid nitrogen and stored at -70 oC until used for total RNA extraction.

tag: cultivar

value: fuzzless-lintless mutant

value: ovules

tag: developmental stage

value: 20 dpa


title: GIST_CGH_14

description: KIT with missense mutation, V559A genotype

tag: genotype


title: Ovules of fuzzless-lintless mutant of G. hirsutum L. cv. MCU5 at 20 dpa, biological replicate 2

description:
Gene expression profiles of fuzzless-lintless ovules of mutant at 20 dpa , biological replicate 2.
Comparative analysis of transcriptome profiles of G. hirsutum L. cv. MCU5 and its fuzzless-lintless mutant at 20 dpa

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45°C on Affymertix cotton Genechip Genome array. The arrays were washed and stained using streptavidin phycoerythrin on an Affymetrix fluidics station 450.


title: delayed graf function 75

description: miRNA profile of delayed graft function


title: GIST_CGH_12

description: KIT and PDGFRA wild-type

value: female

value: KIT and PDGFRA wild-type


title: GIST_CGH_13

value: Human Genomic DNA from multiple anonymous donors (Promega Corporation, Madison, USA)

value: KIT with missense mutation, V560D genotype


title: GIST_CGH_27

value: KIT with deletion mutation, WKV557-559F genotype


description:
Gene expression profiles of Fiber bearing ovules of G. hirsutum L. cv. MCU5 at 20 dpa, biological replicate 3.
Comparative analysis of transcriptome profiles of G. hirsutum L. cv. MCU5 and its fuzzless-lintless mutant at 20 dpa

value: wild type


title: delayed graf function 74

description: miRNA profile of delayed graft function

value: kidney


title: Ovules of fuzzless-lintless mutant of G. hirsutum L. cv. MCU5 at 15 dpa, biological replicate 3

description:
Gene expression profiles of fuzzless-lintless ovules of mutant at 15 dpa , biological replicate 3.
Comparative analysis of transcriptome profiles of G. hirsutum L. cv. MCU5 and its fuzzless-lintless mutant at 15 dpa

source_name: ovules of fuzzless-lintless mutant of G. hirsutum L. cv. MCU5 at 15 dpa

value: 15 dpa


description:
Gene expression profiles of Fiber bearing ovules of G. hirsutum L. cv. MCU5 at 20 dpa, biological replicate 1.
Comparative analysis of transcriptome profiles of G. hirsutum L. cv. MCU5 and its fuzzless-lintless mutant at 20 dpa


description:
Gene expression profiles of Fiber bearing ovules of G. hirsutum L. cv. MCU5 at 20 dpa, biological replicate 2.
Comparative analysis of transcriptome profiles of G. hirsutum L. cv. MCU5 and its fuzzless-lintless mutant at 20 dpa


title: GIST_CGH_08

description: KIT with missense mutation, N822K genotype

source_name: Stomach_GIST_very low risk


title: GIST_CGH_05

description: KIT with deletion mutation, WKV557-559F genotype


title: Ovules of fuzzless-lintless mutant of G. hirsutum L. cv. MCU5 at 15 dpa, biological replicate 2

description:
Gene expression profiles of fuzzless-lintless ovules of mutant at 15 dpa , biological replicate 2.
Comparative analysis of transcriptome profiles of G. hirsutum L. cv. MCU5 and its fuzzless-lintless mutant at 15 dpa


title: GIST_CGH_07

description: KIT with deletion mutation, D579 genotype


title: delayed graf function 73

description: miRNA profile of delayed graft function


title: GIST_CGH_11

description: KIT and PDGFRA wild-type


title: GIST_CGH_06

description: KIT with deletion mutation, NYVYIDPTQL567-576KE genotype


title: Ovules of fuzzless-lintless mutant of G. hirsutum L. cv. MCU5 at 20 dpa, biological replicate 1

description:
Gene expression profiles of fuzzless-lintless ovules of mutant at 20 dpa , biological replicate 1.
Comparative analysis of transcriptome profiles of G. hirsutum L. cv. MCU5 and its fuzzless-lintless mutant at 20 dpa


title: GIST_CGH_02

description: KIT with missense mutation, V559D genotype


title: GIST_CGH_03

description: KIT with missense mutation, V560D genotype


title: GIST_CGH_10

description: KIT and PDGFRA wild-type


title: delayed graf function 72

description: miRNA profile of delayed graft function


title: GIST_CGH_04

description: KIT with deletion mutation, WK557-558 genotype


title: GIST_CGH_09

description: KIT and PDGFRA wild-type


title: GIST_CGH_01


title: PC3-EMT1-Scr

city: ANN ARBOR

first: Hernan

last: Roca

state: MI

address: 1011 N. University Ave.

department: Periodontics and Oral Medicine

institute: University of Michigan

description:
007
Gene expression data from prostate cancer cell line.

hyb_protocol: Following fragmentation, 16 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Human U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

label: Biotin

source_name: PC3-EMT1, scrambled shRNA

label_protocol: Biotinylated aRNA were prepared according to the Ambion Premier kit protocol from 250 ng total RNA (MessageAmp Premier RNA Amplification Kit Instruction Manual, 2008, Ambion).

growth_protocol: Cells were grown in RPMI with 5% FBS.

extract_protocol: RNA was extracted using the Qiagen RNeasy kit following manufacturer specifications and treated with DNase.

treatment_protocol: Transfection of mesenchymal cell lines PC3-EMT1 and PC3-EMT14 with lentiviral ZEB1-shRNA vector sh4 or the scrambled control (Scr).

tag: cell line

value: derived from PC3-Epi human prostate cancer epithelial cells

tag: shRNA

value: scrambled

tag: phenotype

value: mesenchymal


title: Ovules of fuzzless-lintless mutant of G. hirsutum L. cv. MCU5 at 15 dpa, biological replicate 1

description:
Gene expression profiles of fuzzless-lintless ovules of mutant at 15 dpa , biological replicate 1.
Comparative analysis of transcriptome profiles of G. hirsutum L. cv. MCU5 and its fuzzless-lintless mutant at 15 dpa

tag: genotype/variation

tag: tissue


title: PC3-EMT14-sh4

description:
006
Gene expression data from prostate cancer cell line.

source_name: PC3-EMT14, ZEB1 shRNA

value: epithelial


title: delayed graf function 71

description: miRNA profile of delayed graft function


title: PC3-EMT14-Scr

description:
005
Gene expression data from prostate cancer cell line.

source_name: PC3-EMT14, scrambled shRNA


title: PC3-EMT14

description:
004
Gene expression data from prostate cancer cell line.


title: delayed graf function 43

description: miRNA profile of delayed graft function


title: Ryp1 in ryp1-37 ChIP, sample B

city: San Francisco

source_name: Ryp1 in ryp1-37 ChIP, sample B

tag: strain

source_name: Input


title: delayed graf function 41

description: miRNA profile of delayed graft function


title: delayed graf function 70

description: miRNA profile of delayed graft function


title: PC3-EMT12

description:
003
Gene expression data from prostate cancer cell line.


title: delayed graf function 34

description: miRNA profile of delayed graft function


title: delayed graf function 39

description: miRNA profile of delayed graft function


title: delayed graf function 40

description: miRNA profile of delayed graft function


title: Ovules of fuzzless-lintless mutant of G. hirsutum L. cv. MCU5 at 10 dpa, biological replicate 3

description:
Gene expression profiles of fuzzless-lintless ovules of mutant at 10 dpa , biological replicate 3.
Comparative analysis of transcriptome profiles of G. hirsutum L. cv. MCU5 and its fuzzless-lintless mutant at 10 dpa

source_name: ovules of fuzzless-lintless mutant of G. hirsutum L. cv. MCU5 at 10 dpa

value: 10 dpa


title: PC3-EMT1

description:
002
Gene expression data from prostate cancer cell line.


title: acute cellular rejection, BANFF2 68

description: miRNA profile of acute cellular rejection

value: acute cellular rejection


title: PC3-Epi

description:
001
Gene expression data from prostate cancer cell line.

value: derived from PC3 human prostate cancer epithelial cells


description:
Gene expression profiles of Fiber bearing ovules of G. hirsutum L. cv. MCU5 at 15 dpa, biological replicate 1.
Comparative analysis of transcriptome profiles of G. hirsutum L. cv. MCU5 and its fuzzless-lintless mutant at 15 dpa

value: ovules


title: PC3-EMT1-sh4

description:
008
Gene expression data from prostate cancer cell line.

source_name: PC3-EMT1, ZEB1 shRNA


title: Ovules of fuzzless-lintless mutant of G. hirsutum L. cv. MCU5 at 10 dpa, biological replicate 2

description:
Gene expression profiles of fuzzless-lintless ovules of mutant at 10 dpa , biological replicate 2.
Comparative analysis of transcriptome profiles of G. hirsutum L. cv. MCU5 and its fuzzless-lintless mutant at 10 dpa

value: fuzzless-lintless mutant


description:
Gene expression profiles of Fiber bearing ovules of G. hirsutum L. cv. MCU5 at 15 dpa, biological replicate 3.
Comparative analysis of transcriptome profiles of G. hirsutum L. cv. MCU5 and its fuzzless-lintless mutant at 15 dpa


description:
Gene expression profiles of Fiber bearing ovules of G. hirsutum L. cv. MCU5 at 10 dpa, biological replicate 2.
Comparative analysis of transcriptome profiles of G. hirsutum L. cv. MCU5 and its fuzzless-lintless mutant at 10 dpa


description:
Gene expression profiles of Fiber bearing ovules of G. hirsutum L. cv. MCU5 at 10 dpa, biological replicate 3.
Comparative analysis of transcriptome profiles of G. hirsutum L. cv. MCU5 and its fuzzless-lintless mutant at 10 dpa


title: Ovules of fuzzless-lintless mutant of G. hirsutum L. cv. MCU5 at 10 dpa, biological replicate 1

description:
Gene expression profiles of fuzzless-lintless ovules of mutant at 10 dpa , biological replicate 1.
Comparative analysis of transcriptome profiles of G. hirsutum L. cv. MCU5 and its fuzzless-lintless mutant at 10 dpa


description:
Gene expression profiles of Fiber bearing ovules of G. hirsutum L. cv. MCU5 at 15 dpa, biological replicate 2.
Comparative analysis of transcriptome profiles of G. hirsutum L. cv. MCU5 and its fuzzless-lintless mutant at 15 dpa


title: acute cellular rejection, BANFF2 66


description:
Gene expression profiles of Fiber bearing ovules of G. hirsutum L. cv. MCU5 at 10 dpa, biological replicate 1.
Comparative analysis of transcriptome profiles of G. hirsutum L. cv. MCU5 and its fuzzless-lintless mutant at 10 dpa


title: acute cellular rejection, BANFF2 16


title: Ovules of fuzzless-lintless mutant of G. hirsutum L. cv. MCU5 at 5 dpa, biological replicate 3

description:
Gene expression profiles of fuzzless-lintless ovules of mutant at 5 dpa , biological replicate 3.
Comparative analysis of transcriptome profiles of G. hirsutum L. cv. MCU5 and its fuzzless-lintless mutant at 5 dpa

source_name: ovules of fuzzless-lintless mutant of G. hirsutum L. cv. MCU5 at 5 dpa

value: 5 dpa


title: 405623: gastric adenocarcinoma vs matched non-tumor epithelium

city: Nashville

first: Barbara

middle: G

last: Schneider

state: TN

address: 2215 Garland Avenue, 1030C MRB IV

department: Div. of Gastroenterology, Hepatology, & Nutrition

institute: Vanderbilt University Medical Center

hyb_protocol: The labeled Methyl IP DNA (6µg of each test and reference sample) were combined and dried to completion.  The hybridization target was resuspended in 5µL of water and then added to 13µL of Nimblegen hybridization cocktail using reagents from the Nimblegen,  Hyb Kit (KIT#002-2), following Nimblegen Methylation User Guide v2.0, 7 Sept 2007. Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridizations and washes were completed, following Nimblegen Methylation User Guide v2.0, 7 Sept 2007

scan_protocol: Arrays were scanned on an Axon 4000B scanner, following Nimblegen Methylation User Guide v2.0, 7 Sept 2007

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4

source_name: gastric adenocarcinoma

label_protocol: 1 µg MethylIP DNA from each sample was directly labeled by Klenow (New England Biolabs) random priming with Cy5 (Test samples) and Cy3 (Reference or Control samples) nonamers, following Nimblegen Methylation User Guide v2.0, 7 Sept 2007

extract_protocol:
proteinase K digestion, phenol/chloroform extraction, ethanol precipitation
Methylated sequence isolation protocol: MethylIP and Amplification completed by Rubicon (samples 19-30); MethylIP and Amplification completed by GSR Core Lab (Samples 30-42) using Invitrogen MethylMiner Kit and Sigma WGA 4 Kit, following manufacturer's protocol

value: gastric adenocarcinoma

tag: sample description

value: tumor 51584

tag: source

source_name: non-tumor gastric epithelium

value: non-tumor gastric epithelium

value: control 51584

tag: sample source


title: acute cellular rejection, BANFF2 12

source_name: kidney allograft biopsy


title: 405622: gastric adenocarcinoma vs matched non-tumor epithelium

value: tumor 4471

value: control 4470


title: acute cellular rejection, BANFF2 11

value: kidney


title: acute cellular rejection, BANFF2 15


title: acute cellular rejection, BANFF2 13


title: 257014: gastric adenocarcinoma vs matched non-tumor epithelium

value: tumor 4473

value: control 4472


title: 405657: gastric adenocarcinoma vs matched non-tumor epithelium

value: tumor 4477

value: control 4476


title: 258785: metaplasia vs pooled gastritis

description: metaplasia vs pooled gastritis

source_name: metaplasia

value: metaplasia

value: metaplasia 5113

source_name: gastritis

value: gastritis

value: 5082 gastritis


title: 258425: dysplasia vs pooled gastritis

description: dysplasia vs pooled gastritis

source_name: dysplasia

value: dysplasia

value: dysplasia 5094

value: 5088 gastritis


title: Ovules of fuzzless-lintless mutant of G. hirsutum L. cv. MCU5 at 5 dpa, biological replicate 2

description:
Gene expression profiles of fuzzless-lintless ovules of mutant at 5 dpa , biological replicate 2.
Comparative analysis of transcriptome profiles of G. hirsutum L. cv. MCU5 and its fuzzless-lintless mutant at 5 dpa

value: fuzzless-lintless mutant

value: ovules

value: 5 dpa


title: 258480: metaplasia vs pooled gastritis

description: metaplasia vs pooled gastritis

value: metaplasia 5083


title: Control_+DEX_rep2

description: mRNA expression in day3 cultured cells (+DEX) infected with control virus repeat 2

hyb_protocol: Agilent expression arrays were hybridized according to manufacturer instructions and scanned using an Agilent DNA microarray scanner.

scan_protocol: Arrays were scanned using an Agilent DNA microarray scanner with SureScan high-resolution technology.

data_processing: Data was extracted from the array images using Agilent’s Feature Extraction software, quantile normalized using limma from Bioconductor in R, and processed.

source_name: Erythroid cells

label_protocol: Label was performed following one-color microarray-based gene expression analysis low input quick amp labeling protocol (Agilent Technologies 'one-color microarray-based gene expression analysis').

treatment_protocol: Early erythroid progenitors were infected with control virus or viruses encoding RBP shRNAs, and cultured in medium for 3 days before mRNA extraction.

tag: age

value: fetal liver

tag: cell type

value: early erythroid progenitors

tag: infection

value: control virus

tag: culture conditions

value: +DEX


description:
Gene expression profiles of Fiber bearing ovules of G. hirsutum L. cv. MCU5 at 5 dpa, biological replicate 1.
Comparative analysis of transcriptome profiles of G. hirsutum L. cv. MCU5 and its fuzzless-lintless mutant at 5 dpa

value: wild type


description:
Gene expression profiles of Fiber bearing ovules of G. hirsutum L. cv. MCU5 at 5 dpa, biological replicate 2.
Comparative analysis of transcriptome profiles of G. hirsutum L. cv. MCU5 and its fuzzless-lintless mutant at 5 dpa


title: 255929: gastric adenocarcinoma vs matched non-tumor epithelium

value: gastric adenocarcinoma

value: tumor 4469

value: non-tumor gastric epithelium

value: control 4468


title: 405690: gastric adenocarcinoma vs matched non-tumor epithelium

value: tumor 4475

value: control 4474


title: shRNA2_+DEX_rep2

description: mRNA expression in day3 cultured cells (+DEX) infected with virus encoding shRNA 2 targeting RBP repeat 2

value: virus encoding shRNA 2 targeting RBP


title: ryp1-RT expression, sample 10

hyb_protocol: Cy5-labeled samples were competitively hybridized against the Cy3-labeled pooled reference sample on custom glass slide 70-mer oligomer microarrays.

scan_protocol: Arrays were scanned on a GenePix 4000B scanner (Axon Instruments/Molecular Devices, www.moleculardevices.com) to determine the intensity units in the 635- and 523-nm channels (detecting Cy5 and Cy3, respectively) for each spot on the microarray.

data_processing: Data were analyzed by using GENEPIX PRO version 6.0, NOMAD (http://nomad2.ucsf.edu/NOMAD/nomad-cgi/login.pl), and MultiExperiment Viewer 4.0 (www.tm4.org/mev.html) (Methods in enzymology 411:134; BioTechniques 34:374). After removal of values for flagged spots and bulk-scale normalization, the ratio of the median Cy5 intensity/median Cy3 intensity for these spots was used for further analysis. Normalized data was analyzed by Bayesian Analysis for Gene Expression Levels (BAGEL) to obtain relative expression ratios for each spot in each condition or mutant (Briefings in bioinformatics 6:318). Using the values obtained by BAGEL, we compared any two samples by dividing the ratio of the first sample by the ratio of the second sample. To determine the number and identity of genes that changed significantly in expression in any given comparison, we used >2.0-fold change in transcript levels and p-value <0.01 as a cutoff criteria. Results of these analyses are given in Tables S1 and S3 of the accompanying publication.  Normalized expression ratios, as submitted to BAGEL, are reported in the VALUE column.

molecule: polyA RNA

label_protocol:
15 ug of total RNA was used to generate amino-allyl labeled cDNA as described previously (Science 278:680) with following modifications: Reverse transcription reaction was performed with Superscript RT II (Life Technologies-Invitrogen), and reactions were cleaned using QIAquick PCR clean-up kit (Qiagen) with phosphate wash buffer (5 mM KPO4, pH 8.0, 80% ethanol). cDNA from each ryp mutants and wild-type controls was labeled with Cy5 (GE Healthcare Life
Sciences-Amersham) as described (Science 278:680).

extract_protocol: For transcriptional profiling experiments, liquid cultures were grown at 120 rpm to minimize growth condition differences with filamentous-phase cultures. Total RNA from H. capsulatum strains was harvested as previously described (Proc Natl Acad Sci. 105:4880).

value: Histoplasma capsulatum G217B

source_name: pooled reference

label_protocol: Reference RNA was generated by mixing total RNA from ryp mutants and wild-type control strains in three different ratios: For microarray experiments with ryp T-DNA mutants, equal amounts of total RNA from each ryp mutant or wild-type were combined. For microarray experiments with ryp1, ryp2, and ryp3 knockdown strains, total RNA from wild-type yeast, wild-type filaments and ryp knockdown strains were mixed in 1:1:2 ratio. For microarray experiments with ryp4 knockdown strains, total RNA from wild-type yeast, wild-type filaments and ryp4 knockdown strains were mixed in 1:1:1 ratio.


title: ryp3-37 expression, sample 7


title: acute cellular rejection, BANFF2 10

description: miRNA profile of acute cellular rejection

value: kidney

tag: sample type

value: acute cellular rejection


description:
Gene expression profiles of Fiber bearing ovules of G. hirsutum L. cv. MCU5 at 5 dpa, biological replicate 3.
Comparative analysis of transcriptome profiles of G. hirsutum L. cv. MCU5 and its fuzzless-lintless mutant at 5 dpa

tag: cultivar

value: ovules

value: 5 dpa


title: ryp3-37 expression, sample 8


title: ryp2-37 expression, sample 8


title: WT-RT expression, sample 12

source_name: WT-RT


title: ryp1-RT expression, sample 9


title: Ovules of fuzzless-lintless mutant of G. hirsutum L. cv. MCU5 at 5 dpa, biological replicate 1

description:
Gene expression profiles of fuzzless-lintless ovules of mutant at 5 dpa , biological replicate 1.
Comparative analysis of transcriptome profiles of G. hirsutum L. cv. MCU5 and its fuzzless-lintless mutant at 5 dpa

value: fuzzless-lintless mutant

tag: developmental stage


title: acute cellular rejection, BANFF2 09


title: shRNA1_+DEX_rep1

description: mRNA expression in day3 cultured cells (+DEX) infected with virus encoding shRNA 1 targeting RBP repeat 1

value: fetal liver

value: early erythroid progenitors

value: virus encoding shRNA 1 targeting RBP


title: WT-RT expression, sample 10


title: ryp2-RT expression, sample 8


title: shRNA1_+DEX_rep2

description: mRNA expression in day3 cultured cells (+DEX) infected with virus encoding shRNA 1 targeting RBP repeat 2

value: +DEX


title: WT-RT expression, sample 11


title: Control_+DEX_rep1

description: mRNA expression in day3 cultured cells (+DEX) infected with control virus repeat 1

value: control virus


title: acute cellular rejection, BANFF2 06


title: acute cellular rejection, BANFF2 05


title: shRNA2_+DEX_rep1

description: mRNA expression in day3 cultured cells (+DEX) infected with virus encoding shRNA 2 targeting RBP repeat 1


title: 258426: metaplasia vs pooled gastritis

description: metaplasia vs pooled gastritis

value: metaplasia

value: metaplasia 5102

value: gastritis

value: 5088 gastritis


title: ryp2-RT expression, sample 7


title: ryp1-RT expression, sample 8


description:
Gene expression profiles of Fiber bearing ovules of G. hirsutum L. cv. MCU5 at 0 dpa, biological replicate 3.
Comparative analysis of transcriptome profiles of G. hirsutum L. cv. MCU5 and its fuzzless-lintless mutant at 0 dpa

value: wild type

value: 0 dpa


title: Ovules of fuzzless-lintless mutant of G. hirsutum L. cv. MCU5 at 0 dpa, biological replicate 1

description:
Gene expression profiles of fuzzless-lintless ovules of mutant at 0 dpa , biological replicate 1.
Comparative analysis of transcriptome profiles of G. hirsutum L. cv. MCU5 and its fuzzless-lintless mutant at 0 dpa

source_name: ovules of fuzzless-lintless mutant of G. hirsutum L. cv. MCU5 at 0 dpa


title: Ovules of fuzzless-lintless mutant of G. hirsutum L. cv. MCU5 at 0 dpa, biological replicate 3

description:
Gene expression profiles of fuzzless-lintless ovules of mutant at 0 dpa , biological replicate 3.
Comparative analysis of transcriptome profiles of G. hirsutum L. cv. MCU5 and its fuzzless-lintless mutant at 0 dpa


title: Control_-DEX_rep1

description: mRNA expression in day3 cultured cells (-DEX) infected with control virus repeat 1

value: -DEX


title: acute cellular rejection, BANFF2 04

value: kidney


title: WT-RT expression, sample 8

value: Histoplasma capsulatum G217B


title: Control_-DEX_rep2

description: mRNA expression in day3 cultured cells (-DEX) infected with control virus repeat 2


title: acute cellular rejection, BANFF2 01

value: acute cellular rejection


title: ryp3-37 expression, sample 6


title: 0 mM Cy5 x Paraq 5 mM Cy3 Repl 2

city: Santo André

first: Luiz

middle: R.

last: Nunes

state: SP

address: Rua Santa Adélia 166

department: Centro de Ciências Naturais e Humanas

country: Brazil

institute: UFABC - Universidade Federal do ABC

description: This hybridization is part of an experiment that aimed at evaluating gene expression modulation in P. brasiliensis yeast cells exposed to oxidative stress conditions induced by paraquat

hyb_protocol: Labelled cDNAs were mixed, dried in a Savant speed vacuum and resuspended in 100 µl of 1X Hybridization buffer, containing 6X SSC, 5X Denhardt´s solution, 0,25 mg/ml salmon sperm DNA, 0,01 % SDS, 50 % formamide and 92,5 ng/ul poly (dT) 25u (Amersham). Arrays were hybridized overnight (42 °C) in a Gene-Tac Hybridization Station (Genomic Solutions, Inc., Ann Arbor, MI) and washed twice (42 °C) in 0.5 X SSC, 0.01 % SDS, followed by two washes in 0.06X SSC, 0.01 % SDS and two final washes in 0.06 X SSC. All washing steps consisted of 1 min of flow, followed by 5 min of incubation. Slides were then dried and subjected to fluorescent detection

scan_protocol: Slides were subjected to fluorescent detection with a GMS (Affymetrix) 418 Array Scanner (Affymetrix Inc., Santa Clara, CA) Cy3 channel was scanned at 100 % laser power and 70 % PMT gain Cy5 channel was scanned at 100 % laser power and 80 % PMT gain

data_processing: Images were analyzed with the TIGR Spotfinder program (v.2.2.4). All spots with less than 50 % of the pixels with values lower than the median local background plus two SD have been flagged and excluded from further analyses. Raw data were submitted to a series of mathematical transformations with the aid of the software TIGR MIDAS v.2.19. These included filtering out all spots whose integrated intensities were below 10,000 a/d units, normalization between the two channels with the aid of the Lowess algorithm and SD regularization of the Cy5/Cy3 ratios across all sectors (blocks) of the array

organism: Paracoccidioides brasiliensis

source_name: P. brasiliensis_5 mM_Paraquat

label_protocol: The RNA sample extracted with Trizol was further purified with aid of the RNA easy kit (Qiagen) and labeled by incorporation of Cy3- or Cy5-dCTP. Briefly, 30 µg of total P. brasiliensis RNA were mixed with 2 µg of oligo(dT)12-18 in 20 µl of water and heated to 65 °C for 10 min. The tube was briefly chilled on ice and mixed with 4 µl of 5 mM dNTPs, 4 µl of 0.1 M DTT, 8 µl of 5X first-strand buffer (Invitrogen) and 1.5 µl of Superscript II (200 units/ml) (Invitrogen). The reaction was then incubated at 42 °C for 1.5 h and terminated by a 15-min incubation at 65 °C. The RNA was degraded by adding 1 µl of 10 mg/ml RNAse A and incubation at 37 °C for 1 hour. The resulting first strand cDNA was purified and concentrated with the aid of a Microcon YM-30 cartridge and final volume was adjusted to 29 µl. One microliter (1 µl) of 4 ug/µl random primer solution (9-mers) and 4 µl of 10X Klenow buffer were then added to the system. The tube was then heated at 65 °C for 5 min and allowed to cool to room temperature for ten min for primer annealing. Finally, fluorescence incorporation was performed by the addition of 4 µl of 10X low dNTP solution (5 mM dATP, 5m M dTTP, 5 mM dGTP and 2 mM dCTP), 1 µl of Cy3-labeled dCTP (1 mM) (Amersham Biosciences) and 1 µl of the Klenow fragment (50 units/µl) (Invitrogen). The reaction was then incubated at 37 °C for 2 h and the final labeled cDNA was purified in a Microcon YM-30 cartridge (3 washes)

growth_protocol:
Paracoccidioides brasiliensis isolate 18, fungal cells were cultivated in ypd medium: 1% yeast extract, 2% casein peptone, 2% glucose, pH 6.5 at 36 °C (yeast phase), liquid cultures were shaken at 120 rpm in a rotatory shaker
P. brasiliensis yeast cells were grown in YPD until an OD600 = 2.15 (late phase of exponential growth). Then, the culture was divided into three equal parts and one of them was treated with paraquat to final concentration of 5 mM. Next, the culture was incubated at 36°C for 5 hours at 120 rpm in a rotatory shaker. Following the paraquat exposure period, yeast cells were harvested by filtration and immediately frozen in liquid nitrogen.

extract_protocol: Yeast cells were disrupted with glass beads and by grinding in liquid nitrogen, respectively, and immediately mixed with Trizol (Invitrogen) for RNA extraction following the supplier’s recommendations.

treatment_protocol: 5-hour incubation at 36 °C in YPD supplemented with paraquat (5 mM), at 120 rpm in a rotatory shaker

tag: treatment

value: 5 mM Paraquat

source_name: P. brasiliensis_0 mM_Paraquat

growth_protocol:
Paracoccidioides brasiliensis isolate 18, fungal cells were cultivated in ypd medium: 1% yeast extract, 2% casein peptone, 2% glucose, pH 6.5 at 36 °C (yeast phase), liquid cultures were shaken at 120 rpm in a rotatory shaker
Fungal cells were cultivated in YPD medium (1% yeast extract, 2% casein peptone, 2% glucose, pH 6.5) at 36 °C (yeast phase); liquid cultures were shaken at 120 rpm in a rotatory shaker.

value: 0 mM Paraquat


title: 0 mM Cy3 x Paraq 5 mM Cy5 Repl 2


title: 0 mM Cy5 x Paraq 5 mM Cy3 Repl 1


description:
Gene expression profiles of Fiber bearing ovules of G. hirsutum L. cv. MCU5 at 0 dpa, biological replicate 2.
Comparative analysis of transcriptome profiles of G. hirsutum L. cv. MCU5 and its fuzzless-lintless mutant at 0 dpa

value: ovules


title: ryp3-RT expression, sample 9


title: 0 mM Cy3 x Paraq 5 mM Cy5 Repl 1


title: acute cellular rejection, BANFF2 03


title: acute cellular rejection, BANFF1 65


title: WT-RT expression, sample 7


title: ryp1-37 expression, sample 9


title: acute cellular rejection, BANFF1 64


title: acute cellular rejection, BANFF1 62


title: acute cellular rejection, BANFF1 60


description:
Gene expression profiles of Fiber bearing ovules of G. hirsutum L. cv. MCU5 at 0 dpa, biological replicate 1.
Comparative analysis of transcriptome profiles of G. hirsutum L. cv. MCU5 and its fuzzless-lintless mutant at 0 dpa


title: 0 mM Cy3 x Paraq 0.5 mM Cy5 Repl 2

source_name: P. brasiliensis_0.5 mM_Paraquat

growth_protocol:
Paracoccidioides brasiliensis isolate 18, fungal cells were cultivated in ypd medium: 1% yeast extract, 2% casein peptone, 2% glucose, pH 6.5 at 36 °C (yeast phase), liquid cultures were shaken at 120 rpm in a rotatory shaker
P. brasiliensis yeast cells were grown in YPD until an OD600 = 2.15 (late phase of exponential growth). Then, the culture was divided into three equal parts and one of them was treated with paraquat to final concentration of 0.5 mM. Next, the culture was incubated at 36°C for 5 hours at 120 rpm in a rotatory shaker. Following the paraquat exposure period, yeast cells were harvested by filtration and immediately frozen in liquid nitrogen

treatment_protocol: 5-hour incubation at 36 °C in YPD supplemented with paraquat (0.5 mM), at 120 rpm in a rotatory shaker

value: 0.5 mM Paraquat


title: WT-37 expression, sample 13


title: acute cellular rejection, BANFF1 58


title: ryp1-RT expression, sample 7


title: WT-RT expression, sample 16


title: 0 mM Cy5 x Paraq 0.5 mM Cy3 Repl 1

growth_protocol:
Paracoccidioides brasiliensis isolate 18, fungal cells were cultivated in ypd medium: 1% yeast extract, 2% casein peptone, 2% glucose, pH 6.5 at 36 °C (yeast phase), liquid cultures were shaken at 120 rpm in a rotatory shaker
P. brasiliensis yeast cells were grown in YPD until an OD600 = 2.15 (late phase of exponential growth). Then, the culture was divided into three equal parts and one of them was treated with paraquat to final concentration of 0.5 mM. Next, the culture was incubated at 36°C for 5 hours at 120 rpm in a rotatory shaker. Following the paraquat exposure period, yeast cells were harvested by filtration and immediately frozen in liquid nitrogen.


title: 0 mM Cy5 x Paraq 0.5 mM Cy3 Repl 2


title: WT-RT expression, sample 15


title: acute cellular rejection, BANFF1 29


title: ryp2-RT expression, sample 5


title: ryp2-RT expression, sample 6


title: 0 mM Cy3 x Paraq 0.5 mM Cy5 Repl 1


title: ryp3-RT expression, sample 8


title: fat-high oleic-animal7

city: Madrid

first: Cristina

last: Ovilo

address: Ctra Coruña km 7.5

country: Spain

institute: INIA-CSIC

description: Gene expression data from adipose tissue of male Iberian pig fed a oleic acid enriched diet.

hyb_protocol: Standard Affymetrix hybridization protocol.

scan_protocol: Standard Affymetrix scanning protocol using GCOS.

data_processing: Expression data were generated with GeneChip Operating Software (GCOS, Affymetrix) and GCRMA normalization was carried out with BRB-Array Tools (v.3.6.0), by filtering out those probes with minimal variation across the set of arrays. Only genes displaying more than 20% of expression values over ± 1.5 times the median expression of all arrays were used for further analysis (3272 probes).

organism: Sus scrofa

source_name: adipose tissue, inner layer, high oleic diet

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

growth_protocol: The energy content per kg of feed was 3,130 Kcal of crude energy for the C diet, and 3,360 Kcal for the HO diet. Animals were fed twice a day according to scale based on average live weight. The daily feed supplied for pig of the HO group increased from 1.0 to 3.3 kg during the 24 weeks of treatment. A 10% greater quantity of feed was supplied to the other group in order to match the lower energy and protein content of C feed and provide isoenergetic and isoproteic rations to the pigs of both groups. Fresh water was provided ad libitum.

extract_protocol: RiboPure RNA isolation kit.

treatment_protocol: Adipose tissue samples obtained at slaughter were mantained at -80ºC until processing for RNA extraction.

tag: breed

value: Iberian

tag: gender

value: castrated male

tag: live weight

value: adipose

value: high oleic diet


title: fat-high oleic-animal8


title: acute cellular rejection, BANFF1 28


title: ryp4-RT expression, sample 3


title: ryp3-RT expression, sample 7


title: acute cellular rejection, BANFF1 27


title: fat-high oleic-animal6


title: fat-high oleic-animal5


title: acute cellular rejection, BANFF1 26


title: WT-RT expression, sample 6


title: ryp4-37 expression, sample 4


title: acute cellular rejection, BANFF1 25


title: WT-37 expression, sample 11


title: fat-high oleic-animal4


title: ryp3-RT expression, sample 6


title: fat-high oleic-animal3


title: WT-RT expression, sample 13


title: WT-37 expression, sample 12


title: WT-RT expression, sample 14


title: ryp3-37 expression, sample 5


title: acute cellular rejection, BANFF1 24


title: fat-high oleic-animal2


title: ryp4-37 expression, sample 3


title: ryp1-37 expression, sample 8


title: WT-37 expression, sample 10


title: acute cellular rejection, BANFF1 22


title: acute cellular rejection, BANFF1 23


title: WT-37 expression, sample 9


title: acute cellular rejection, BANFF1 20


title: fat-high oleic-animal1


title: ryp4-37 expression, sample 2


title: fat-control-animal7

description: Gene expression data from adipose tissue of male Iberian pig fed a standard diet.

source_name: adipose tissue, inner layer, control

value: standard diet


title: acute cellular rejection, BANFF1 17

description: miRNA profile of acute cellular rejection


title: ryp1-RT expression, sample 6


title: WT-37 expression, sample 8


title: ryp1-37 expression, sample 7


title: ryp2-37 expression, sample 6


title: fat-control-animal4


title: fat-control-animal3


title: ryp4-RT expression, sample 2


title: acute cellular rejection, BANFF2 07


title: ryp2-37 expression, sample 5


title: fat-control-animal5


title: ryp2-37 expression, sample 7


title: ryp4-37 expression, sample 1


title: fat-control-animal2


title: WT-37 expression, sample 7


title: antibody mediated rejection 97

description: miRNA profile of acute humoral rejection

value: acute humoral rejection


title: antibody mediated rejection 99


title: antibody mediated rejection 100


title: fat-control-animal1


title: WT-RT expression, sample 5


title: ryp1-37 expression, sample 6


title: ryp1-RT expression, sample 5


title: antibody mediated rejection 96


title: ryp4-RT expression, sample 1


title: ryp3-RT expression, sample 5


title: WT-RT expression, sample 9


title: Ovules of fuzzless-lintless mutant of G. hirsutum L. cv. MCU5 at 0 dpa, biological replicate 2

description:
Gene expression profiles of fuzzless-lintless ovules of mutant at 0 dpa , biological replicate 2.
Comparative analysis of transcriptome profiles of G. hirsutum L. cv. MCU5 and its fuzzless-lintless mutant at 0 dpa

tag: genotype/variation

value: fuzzless-lintless mutant


title: fat-control-animal6

tag: tissue


title: antibody mediated rejection 90


title: antibody mediated rejection 92


title: antibody mediated rejection 94


title: antibody mediated rejection 93


title: antibody mediated rejection 87


title: antibody mediated rejection 91


title: Soft Palate_NSCP patient_male,3 years,I degree_rep 1 (252182713706_S01_2_1_GeneView)

city: Shanghai

first: Huijun

last: Wang

state: Shanghai

address: 399 Wanyuan Road,

department: Translational Research Center for Development and Disease

country: China

institute: Children Hospital of Fudan University

description:
miRNA expression
252182713706_S01_2_1_GeneView

hyb_protocol: Resuspend the dried labeled miRNA sample in 17 μL of nuclease-free water when the Spike-In solution is used. Add 4.5 μL of the 10X GE Blocking Agent and 22.5 μL of 2X Hi-RPM Hybridization Buffer to each sample for a total of 45μl.. Incubate at 100°C for 5 minutes and then immediately transfer to an ice water bath for 5 minutes.Quickly spin in a centrifuge to collect any condensation at the bottom of the tube. On completion of preparing the hybridization assembly, 45μl of 1X hybridization buffer was added and hybridized to Agilent Microarray Hybridization Chamber Kit (G2534A) for 55°C for 20 hours in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100% for XDR Hi and 5% for XDR Lo).

data_processing:
The scanned images were analyzed with Agilent Feature Extraction Software 10.7 following the manufacturers instructions .
The normalization is achieved by Agilent Feature Extraction Software (v10.7).
The dye- normalized signal is calculated by multiplying the background- subtracted signal by the dye normalization factor: DyeNormSignal =BGSubSignal x DNF where DNF = LinearDyeNormFactor, when linear dye normalization method is used and where: DNF=LinearDyeNormFactor x LOWESSDyeNormFactor when LOWESS dye normalization method is used.

source_name: Soft Palate,NSCP patient,male,3 years,I degree,replicate 1

label_protocol: Agilent’s miRNA Complete Labeling and Hyb Kit (p/n 5190- 0456) generates fluorescent miRNA with a sample input of 100ng of total RNA. This method involves the ligation of one Cyanine 3- pCp molecule to the 3' end of a RNA molecule by using the Micro Bio- spin 6 columns for purification of the labeled miRNA. The sample must be completely dried after labeling.

extract_protocol: Total RNA was extracted using TRIzol® Reagent (Ambion®, Invitrogen, USA) according to the manufacturer instructions. RNA concentration was assessed with NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, USA) and RNA integrity was verified using an Agilent 2100 bioanalyzer (Agilent, USA).

treatment_protocol: All samples were cut off into small pieces and immediately transferred to RNA Later (Ambion, USA). After disposing in room temperature for 12hrs, samples were stored at -80℃ until the total RNA extraction.

tag: individual

value: NSCP patient

value: Soft Palate

value: male

tag: degree

value: I degree


title: Soft Palate_NSCP patient_female,3 years,II degree_rep 1 (252182713706_S01_2_3_GeneView)

description:
miRNA expression
252182713706_S01_2_3_GeneView

source_name: Soft Palate,NSCP patient,female,3 years,II degree,replicate 1

value: female

value: II degree


title: Soft Palate_NSCP patient_female,3 years,II degree_rep 1 (252182713706_S01_2_2_GeneView)

description:
miRNA expression
252182713706_S01_2_2_GeneView


title: Soft Palate_control_female,1 year_rep 1 (252182713706_S01_1_3_GeneView)

description:
miRNA expression
252182713706_S01_1_3_GeneView

source_name: Soft Palate,control,female,1 year,replicate 1

value: control


title: Soft Palate_NSCP patient_male,3 years,I degree_rep 1 (252182713706_S01_1_4_GeneView)

description:
miRNA expression
252182713706_S01_1_4_GeneView


title: Soft Palate_NSCP patient_male,3 years,I degree_rep 1 (252182713706_S01_2_4_GeneView)

description:
miRNA expression
252182713706_S01_2_4_GeneView


title: ryp3-RT expression, sample 4

tag: strain

value: Histoplasma capsulatum G217B


title: Soft Palate_control_male,2 years_rep 1 (252182713706_S01_1_2_GeneView)

description:
miRNA expression
252182713706_S01_1_2_GeneView

source_name: Soft Palate,control,male,2 years,replicate 1


title: ryp3-37 expression, sample 4


title: ryp1-37 expression, sample 5


title: ryp2-RT expression, sample 4


title: ryp3-37 expression, sample 3


title: WT-37 expression, sample 6


title: antibody mediated rejection 85

source_name: kidney allograft biopsy

value: kidney


title: ryp1-RT expression, sample 4


title: Soft Palate_control_male,27 years_rep 1 (252182713713_S01_2_2_GeneView)

description:
miRNA expression
252182713713_S01_2_2_GeneView

source_name: Soft Palate,control,male,27 years,replicate 1


title: Soft Palate_control_male,5 years_rep 1 (252182713706_S01_1_1_GeneView)

description:
miRNA expression
252182713706_S01_1_1_GeneView

source_name: Soft Palate,control,male,5 years,replicate 1


title: Soft Palate_control_female,17 years_rep 1 (252182713713_S01_2_4_GeneView)

description:
miRNA expression
252182713713_S01_2_4_GeneView

source_name: Soft Palate,control,female,17 years,replicate 1


title: Soft Palate_control_male,23 years_rep 1 (252182713713_S01_2_3_GeneView)

description:
miRNA expression
252182713713_S01_2_3_GeneView

source_name: Soft Palate,control,male,23 years,replicate 1


title: ryp1-37 expression, sample 2

source_name: pooled reference


title: WT-RT expression, sample 4

source_name: WT-RT


title: ryp2-37 expression, sample 2


title: ryp2-RT expression, sample 2


title: ryp2-37 expression, sample 4


title: WT-37 expression, sample 2


title: WT-RT expression, sample 2


title: WT-37 expression, sample 5


title: ryp3-37 expression, sample 2


title: ryp2-37 expression, sample 3


title: ryp3-RT expression, sample 2


title: ryp1-RT expression, sample 3


title: ryp2-RT expression, sample 1


title: Soft Palate_NSCP patient_female,1 year,III degree_rep 1 (252182713713_S01_2_1_GeneView)

description:
miRNA expression
252182713713_S01_2_1_GeneView

source_name: Soft Palate,NSCP patient,female,1 year,III degree,replicate 1

value: III degree


title: WT-37 expression, sample 1


title: ryp1-37 expression, sample 3


title: Soft Palate_NSCP patient_male,2 years,III degree_rep 1 (252182713713_S01_1_4_GeneView)

description:
miRNA expression
252182713713_S01_1_4_GeneView

source_name: Soft Palate,NSCP patient,male,2 years,III degree,replicate 1


title: Soft Palate_NSCP patient_male,3 years,I degree_rep 1 (252182713713_S01_1_3_GeneView)

description:
miRNA expression
252182713713_S01_1_3_GeneView


title: ryp1-37 expression, sample 4


title: Soft Palate_NSCP patient_male,5 years,III degree_rep 1 (252182713713_S01_1_2_GeneView)

description:
miRNA expression
252182713713_S01_1_2_GeneView

source_name: Soft Palate,NSCP patient,male,5 years,III degree,replicate 1


title: Soft Palate_NSCP patient_male,3 years,III degree_rep 1 (252182713713_S01_1_1_GeneView)

description:
miRNA expression
252182713713_S01_1_1_GeneView

source_name: Soft Palate,NSCP patient,male,3 years,III degree,replicate 1


title: ryp2-RT expression, sample 3


title: ryp1-RT expression, sample 2


title: WT-RT expression, sample 1


title: ryp3-RT expression, sample 1


title: WT-RT expression, sample 3


title: ryp3-37 expression, sample 1


title: ryp3-RT expression, sample 3


title: WT-37 expression, sample 4


title: ryp1-RT expression, sample 1


title: WT-37 expression, sample 3


title: ryp2-37 expression, sample 1


title: Sham, LV, rep 5

status: Public on Jun 13 2013

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

description: Gene expression data from left ventricle of sham operated dog, 12 weeks after surgery

hyb_protocol: Standard Affymetrix protocol, 16 h hyb @45 degrees C; wash protocol FS450_0001

scan_protocol: Standard Affymetrix scan protocol

data_processing: The data were analyzed using the Mayo Clinic developed microarray analysis pipleine, MAPP, using fastlo normalization method. MAPP calculates individual mRNA expression profile and eliminates background noise present in raw data as well.

organism: Canis lupus

source_name: Heart tissue from Sham operated dog

label_protocol: Standard Affymetrix IVT Express Labeling with 100 ng total RNA as input.

growth_protocol: Normal dogs

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

treatment_protocol: Dogs were assigned to right sided uninephrectomy operation or sham operation, heart tissue was harvested at sacrifice 12 weeks after surgery.

value: Heart, left ventricle

tag: group

value: sham operated


title: Sham, LV, rep 3


title: Uninephrectomy, LV, rep 1

description: Gene expression data from left ventricle of uninephrectomized dog, 12 weeks after surgery

source_name: Heart tissue from Uninephrectomized dog

value: uninephrectomized surgery


title: Sham, LV, rep 4


title: Uninephrectomy, LV, rep 4


title: Sham, LV, rep 2


title: Uninephrectomy, LV, rep 2


title: ryp1-37 expression, sample 1


title: Sham, LV, rep 1


title: Uninephrectomy, LV, rep 5


title: Uninephrectomy, LA, rep 4

description: Gene expression data from left atrium of uninephrectomized dog, 12 weeks after surgery

value: Heart, left atrium


title: Uninephrectomy, LA, rep 5


title: Uninephrectomy, LA, rep 3


title: Uninephrectomy, LV, rep 3


title: Lewis Lung Carcinoma Cells_Technical Control_batch1, rep3

city: Boston

first: christine

middle: elaine

last: briggs

state: MA

address: 736 Cambridge Street

department: Center for Cancer Systems Biology

institute: christine briggs

description: LLC p4 (3) Batch1

hyb_protocol: Following hybridization at 55C, the chips were washed.

scan_protocol: Standard Illumina scanning protocol using Illumina iScan.

data_processing: The data was checked with GenomeStudio (Illumina) for quality control. In GenomeStudio, data was background subtracted and rank invariant normalization was applied.

source_name: LLCp4 control 1

label_protocol: Total RNA of 500ng per sample was amplified using Ambion TotalPrep (Ambion), and 1.5µg of the product was loaded onto the chips.

extract_protocol: RNA was isolated from mouse tumor tissue. Tumor chunks of 1 to 2mm in diameter were placed in TRIzol (Invitrogen, Carlsbad, CA) and homogenized using a Tissue Lyser II (Qiagen, Valencia, CA). Tissue with TRIzol was centrifuged at 1200g and 0.2ml of chloroform was added for 5min. Samples were centrifuged at 10,000g for 15min at 4°C. The aqueous phase with RNA was transferred to a 1.5ml eppendorf tube. Isopropyl alcohol (0.5ml) was added to each sample (room temperature) for 10min and samples were centrifuged at 10,000g for 10min at 4°C. RNA pellets were washed once with 75% ethanol and resuspended in 100μl RNase-free water. Quality and quantity of RNA were measured by an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA).

tag: cell line

value: Lewis lung carcinoma (LLC) cells

value: technical chip control


title: Sham, LA, rep 4

city: Rochester

description: Gene expression data from left atrium of sham operated dog, 12 weeks after surgery


title: Uninephrectomy, LA, rep 2


title: Lewis Lung Carcinoma Cells_Technical Control_batch1, rep1

description: LLC p4 (1) Batch1


title: Lewis Lung Carcinoma Cells_Technical Control_batch2, rep2

description: LLC p4 (2) Batch2

source_name: LLCp4 control 2


title: Lewis Lung Carcinoma Cells_Technical Control_batch2, rep3

description: LLC p4 (3) Batch2


title: Sham, LA, rep 2


title: Sham, LA, rep 1


title: Sham, LA, rep 5


title: Uninephrectomy, LA, rep 1


title: Sham, LA, rep 3


title: Lewis Lung Carcinoma Cells_Technical Control_batch2, rep1

description: LLC p4 (1) Batch2


title: LLC Tumor_Young, rep10

description: Young 0Gy Fe LLC (531)

source_name: Young 0Gy Fe LLC tumor tissue

value: Lewis lung carcinoma (LLC)  tumor

tag: age

value: young


title: LLC Tumor_Young, rep8

description: Young 0Gy Fe LLC (537)


title: Lewis Lung Carcinoma Cells_Technical Control_batch1, rep2

description: LLC p4 (2) Batch1


title: LLC Tumor_Young, rep9

description: Young 0Gy Fe LLC (539)


title: LLC Tumor_Young, rep6

description: Young 0Gy Fe LLC (532)


title: LLC Tumor_Young, rep4

description: Young 0Gy Fe LLC (538)


title: LLC Tumor_Young, rep7

description: Young 0Gy Fe LLC (535)


title: LLC Tumor_Young_0.2Gyx5Fe, rep8

description: Young 0.2Gyx5 Fe LLC (555)

source_name: Young 0.2Gyx5 Fe LLC tumor tissue

value: 0.2Gyx5 56Fe irradiation


title: LLC Tumor_Young, rep2

description: Young 0Gy Fe LLC (533)

value: male


title: LLC Tumor_Young, rep3

description: Young 0Gy Fe LLC (534)


title: LLC Tumor_Young_0.2Gyx5Fe, rep6

description: Young 0.2Gyx5 Fe LLC (553)


title: LLC Tumor_Young_0.2Gyx5Fe, rep3

description: Young 0.2Gyx5 Fe LLC (559)


title: LLC Tumor_Young, rep5

description: Young 0Gy Fe LLC (530)


title: LLC Tumor_Young_0.2Gyx5Fe, rep4

description: Young 0.2Gyx5 Fe LLC (560)


title: LLC Tumor_Young_0.2Gyx5Fe, rep2

description: Young 0.2Gyx5 Fe LLC (551)


title: LLC Tumor_Young_0.2Gyx5Fe, rep1

description: Young 0.2Gyx5 Fe LLC (558)


title: LLC Tumor_Young_0.2Gyx5Fe, rep7

description: Young 0.2Gyx5 Fe LLC (554)


title: LLC Tumor_Young, rep1

description: Young 0Gy Fe LLC (536)


title: LLC Tumor_Middle-Aged, rep5

description: Old 0Gy Fe LLC (717)

source_name: Middle-Aged 0Gy Fe LLC tumor tissue

value: middle-age


title: LLC Tumor_Middle-Aged, rep7

description: Old 0Gy Fe LLC (719)


title: LLC Tumor_Middle-Aged, rep3

description: Old 0Gy Fe LLC (715)


title: LLC Tumor_Middle-Aged, rep1

description: Old 0Gy Fe LLC (712)


title: LLC Tumor_Middle-Aged_0.2Gyx5Fe, rep4

description: Old 0.2Gyx5 Fe LLC (595)

source_name: Middle-Aged 0.2Gyx5 Fe LLC tumor tissue


title: LLC Tumor_Young_0.2Gyx5Fe, rep5

description: Young 0.2Gyx5 Fe LLC (552)


title: LLC Tumor_Middle-Aged, rep6

description: Old 0Gy Fe LLC (711)