title: normal 18

city: Homburg

first: Andreas

last: Keller

address: Building 60

institute: Saarland University

hyb_protocol: according to manufacturers instruction (febit biomed)

scan_protocol: Wizard software on standard Microsoft Windows Workstation PC

data_processing: summarizing of technical replica by median and quantile normalization. Following BG correction, negative values were corrected to 1

source_name: RNA from blood

label_protocol: MPEA, microfluidic primer extension assay Biotin labeling

extract_protocol: Blood of patients and volunteers without known disease was extracted in PAXgene Blood RNA tubes (BD, Franklin Lakes, New Jersey USA). For each blood donor, 5 ml of peripheral blood were obtained. The content of blood sampling tubes of each patient and healthy donor was centrifuged at 5000 g for 10 min at room temperature. The supernatant was discarded while the pellet was resuspended in 10 ml RNase free water by vortex. The suspension is again centrifuged at 5000 g for 10 min at RT. Subsequently, the total RNA including the miRNA was isolated using the miRNeasy kit (Qiagen GmbH, Hilden). Therefore the pellet was resuspended in 700 μl QIAzol lysis reagent and incubated for 5 min at RT. Then, 140 μl chloroform were added, vortexed for 15 sec, and incubated for 2-3 min at RT. This was followed by a centrifugation at 14000 rpm and 4°C for 15 min. The upper, watery phase was removed and 1,5 times of its volume added in 100% ethanol (ca. 900 μl). Each 700 μl of this mixture were placed on a column and centrifuged at 13000 rpm at RT for 15 sec. After the mixture had completely passed the column, 700 μl of Buffer RWT were added to each column, and again centrifuged at 13000 rpm at RT for 15 sec. Following this, 500 μl Buffer RPL were added to the column and centrifuged at 13000 rpm at RT for 15 sec. After this, another 500 μl Buffer RPL were added to the column and centrifuged at 13000 rpm at RT for 2 min. The column was then centrifuged at 13000 rpm and RT for 1 min to dry it. The following was the elution step with 40 μl RNase free water, centrifuging at 13000 rpm at RT for 1 min. The eluted RNA was stored at -70°C.

treatment_protocol: stored at -20 degree


title: normal 19

status: Public on Mar 11 2011

type: RNA

country: Germany

label: biotin

molecule: total RNA

organism: Homo sapiens

tag: disease state


title: normal5

city: Seoul

first: Yoosik

last: Yoon

address: 221 HeukSeok-Dong, DongJak-Gu

country: South Korea

institute: Chung-Ang University

description: Gene expression of RNA

hyb_protocol: Labeled cDNAs were hybridized to Agilent’s Human Oligo Microarray (44K) containing probes for 41 000 genes at 65 °C for 17 hrs and washed with Agilent’s Gene Expression Wash Buffer Kit as suggested by the manufacturer’s protocol.

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction software (Agilent Technology).

data_processing: All data normalization was performed using GeneSpring GX 7.3 software (Agilent Technology). The normalization method was quantile.

source_name: Peripheral Blood

label_protocol: One microgram of RNA was reverse transcribed into cDNA and labeled using Agilent’s Low RNA Input Linear Amplification kit (Agilent Technology, Santa Clara, CA, USA).

growth_protocol: To induce an inflammatory response, for in vitro study, the THP1 cells were seeded in 12-well plates at a density of 1 × 106 cells/well in RPMI 1640 medium containing 0.5% fetal bovine serum, and were incubated for 24hr.

extract_protocol: Ten milliliters of peripheral blood of asthma and normal subjects, for in vivo study, were centrifuged at 4000 rpm for 20 min to collect 0.4 mL of the buffy coat fraction, which is mainly composed of peripheral blood nuclear cells. The buffy coat fraction was then mixed with 1.3 ml RNAlater solution (Ambion, Austin, TX, USA) and stored at 4oC until use. For in vitro study, stimulated THP1 cells by LPS or HDM were harvested using a cell scraper and lysed for total RNA extraction. Total RNA was extracted from the buffy coat fractions using a Ribo-pure blood kit (Ambion, Austin, TX, USA).

treatment_protocol: The THP1 cells stimulated for 24 hrs with LPS or HDM extract, in the in vitro study.

value: normal

tag: tissue

value: whole blood

tag: gender

value: male

tag: age


title: CAG 82N1, rep3

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

description:
B286_CAG_82N1
Gene expression of 82N1 (CD82N1-eGFP) transfection.

hyb_protocol: According to the instruction manual, as described in the Affymetrix website.

data_processing: RMA normalization, summarization by mean, done by Partek Genomics suite (version 6.5).

source_name: CAG multiple myeloma (MM) cells, 82N1

extract_protocol: Trizol reagent (Invitrogen).

tag: cell line

value: CAG

tag: cell type

value: multiple myeloma (MM) cells

tag: transfected tetraspanin


title: CAG 81N1, rep3

description:
B285_CAG_81N1
Gene expression of 81N1 (CD81N1-eGFP) transfection.

scan_protocol: According to the instruction manual, as described in the Affymetrix website.

source_name: CAG multiple myeloma (MM) cells, 81N1


title: CAG N1, rep3

description:
B284_CAG_N1
Gene expression of N1 (mock) transfection.

source_name: CAG multiple myeloma (MM) cells, control

label_protocol: According to the instruction manual, as described in the Affymetrix website.

value: mock


title: normal 13


title: normal 15


title: normal 14


title: CAG 81N1, rep1

description:
A907_CAG_81N1
Gene expression of 81N1 (CD81N1-eGFP) transfection.


title: 8226 82N1, rep3

description:
B283_8226_82N1
Gene expression of 82N1 (CD82N1-eGFP) transfection.

source_name: 8226 multiple myeloma (MM) cells, 82N1

value: RPMI 8226


title: CAG 81N1, rep2

description:
B279_CAG_81N1
Gene expression of 81N1 (CD81N1-eGFP) transfection.


title: normal 16


title: CAG 82N1, rep2

description:
B280_CAG_82N1
Gene expression of 82N1 (CD82N1-eGFP) transfection.


title: Y79 cells T1

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

description: Suspension Y79 cells

hyb_protocol: 800ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327) and scanned using the Agilent Microarray Scanner G2505C at 3 micron resolution.

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1)

data_processing: The normalization was done using GeneSpring GX 11 Software.

source_name: Y79 retinoblastoma cell line

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: 1.5x106 Y79 cells were plated in 12 well plates with 1 ml of culture media and incubated at 370C overnight. The next day the fresh media was added to the cells and the cells were exposed to Hydrogen peroxide (H2O2) and incubated.

extract_protocol: RNA was prepared using the Qiagen RNeasy mini kit (Qiagen GmbH, Hilden) following the manufacturer's recommendations. RNA was quantified using NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: After the hydrogen peroxide treatment the Y79 cells (treated/un treated control) were collected and pelleted. The cells were resuspended in RNA Later and processed for Microarray Analysis.

value: Y79 retinoblastoma cell line

tag: stress

value: hydrogen peroxide exposure


title: Y79 cells T2

description: Suspension Y79 cells


title: 8226 N1, rep2

description:
B275_8226_N1
Gene expression of N1 (mock) transfection.

source_name: 8226 multiple myeloma (MM) cells, control


title: CAG N1, rep1

description:
A906_CAG_N1
Gene expression of N1 (mock) transfection.


title: Control Y79 1

description: Suspension Y79 cells

value: control


title: 8226 N1, rep3

description:
B281_8226_N1
Gene expression of N1 (mock) transfection.


title: CAG N1, rep2

description:
B278_CAG_N1
Gene expression of N1 (mock) transfection.


title: lung cancer 28

value: lung cancer


title: normal 12


title: normal 11


title: normal 10


title: lung cancer 27


title: lung cancer 26


title: lung cancer 25


title: normal 6


title: 8226 82N1, rep1

description:
A765 822682N1
Gene expression of 82N1 (CD82N1-eGFP) transfection.


title: 8226 81N1, rep3

description:
B282_8226_81N1
Gene expression of 81N1 (CD81N1-eGFP) transfection.

source_name: 8226 multiple myeloma (MM) cells, 81N1


title: normal 4


title: normal 7


title: normal 9


title: normal 8


title: normal 5


title: normal 17


title: 8226 81N1, rep1

description:
A764 822681N1
Gene expression of 81N1 (CD81N1-eGFP) transfection.


title: CAG 82N1, rep1

description:
A908_CAG_82N1
Gene expression of 82N1 (CD82N1-eGFP) transfection.


title: lung cancer 24


title: Control Y79 2

description: Suspension Y79 cells


title: 8226 N1, rep1

description:
A763 8226N1
Gene expression of N1 (mock) transfection.


title: sham control, biological rep 3

city: Research Triangle Park

first: Michael

middle: Bruce

last: Black

address: 6 Davis Dr., P.O. Box 12137

department: Chemical Safety Sciences

country: USA

institute: The Hamner Institutes for Health Sciences

description: Gene expression data from adult male rat epididymis - sham control

hyb_protocol: Ten micrograms of cRNA were fragmented and hybridized to the RAE230 2.0 array (Affymetrix, Santa Clara, CA), which monitors over 31,000 transcripts. The hybridized arrays were stained in the Fluidics Station 450.

scan_protocol: The hybridized arrays were scanned on the Affymetrix Scanner 3000. All of the array images were visually inspected for defects and quality. Signal values for each array were determined using Gene Chip Operating System 1.0 (GCOS; Affymetrix).

data_processing: Raw signal values were normalized using GCRMA, therefore all subsequent intensity values and odd ratio values are log base 2.  Analyses were performed in R release 2.9 and BioConductor release 2.4

organism: Rattus norvegicus

source_name: rat initial segment of epididymis, sham operation

label_protocol: Five micrograms of total RNA were used to generate biotin-labeled cRNA using an oligo(T7) primer in a reverse transcription reaction, followed by in vitro transcription with biotin-labeled UTP and CTP.

growth_protocol: Normal adult male Sprague-Dawley rats between 275 and 450 grams were maintained on a 12L:12D cycle with free access to food and water in the University of Virginia vivarium.

extract_protocol: The tissue samples stored in RNALater at -20oC were thawed at room temperature and the RNALater was removed. Total RNA was extracted and further purified through RNAeasy columns according to the manufacturer's instructions (Qiagen, Valencia, CA). All samples were treated with DNase on the column and eluted with DEPC-treated water. RNA was quantified by the absorbance at 260 nm and RNA quality was assessed using the Agilent Bioanalyzer (Palo Alto, CA) and spectrophotometric analysis.

treatment_protocol: Unilateral efferent duct ligation (EDL) surgeries were performed to block lumicrine testicular fluid factors from reaching one side of epididymis. For the control, a sham operation was performed on the contra-lateral side within the same animal.  After 6, 12 and 18 hours of EDL, the most proximal region of the initial segment containing zone 1a and 1b of initial segment was dissected out.

tag: time point

tag: strain

value: Sprague-Dawley

value: initial segment of epididymis

value: adult


title: 8226 81N1, rep2

description:
B276_8226_81N1
Gene expression of 81N1 (CD81N1-eGFP) transfection.


title: HDAC3 fl/fl / Cre3

city: Buffalo

first: Tao

last: Liu

state: NY

address: Elm and Carlton St

department: Biostatistics and Bioinformatics

institute: Roswell Park Comprehensive Cancer Institute

description: Hepatic gene expression data from mice with liver-specific depletion of HDAC5

hyb_protocol: About 2ug cDNA was hybridized at 45°C for 16h to the Mouse Gene 1.0ST array. Arrays were washed and stained using the GeneChIP Hybridization, Wash and Stain Kit (Affymetrix).

scan_protocol: The array was read by GCS3000 laser scanner (Affymetrix).

data_processing: Data analysis was carried out using Partek® Genomics Suite software (Copyright, Partek Inc.).  Data were subjected to background subtraction, quantile normalization, log2 transformation and probeset summarization using RMA (Robust Multichip Average) algorithm. Only the probesets that interrogate genes were retained and those meant for QC and normalization purposes were excluded from further analysis.

label: Biotin

organism: Mus musculus

source_name: liver from HDAC3 fl/fl / Cre mice

label_protocol: Each RNA sample (at least 50ng) was processed with the Ambion WT Expression Kit and the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix). Single strand cDNA is labeled by terminal  deoxynucleotidyl transferase (TdT) with the Affymetrix® proprietary DNA Labeling Reagent that is covalently linked to biotin.

growth_protocol: Male WT C57Bl/6 mice grow in regular 12h light/ 12h dark cycles on normal chow.

extract_protocol: Total RNA was extracted >20mg mouse liver samples using Trizol extraction followed by QIAGEN Rneasy Kit according to the manufacture's instructions.

treatment_protocol: Tail-vein injection of 1.5E11 particles of AAV2/8-Tbg-Cre or AAV2/8-Tbg-GFP virus at 11 week old.

value: Liver

tag: genotype

value: HDAC3 fl/fl

tag: treatment


title: 8226 82N1, rep2

description:
B277_8226_82N1
Gene expression of 82N1 (CD82N1-eGFP) transfection.


title: HDAC3 fl/fl / Cre5

description: Hepatic gene expression data from mice with liver-specific depletion of HDAC7


title: HDAC3 fl/fl / Cre4

description: Hepatic gene expression data from mice with liver-specific depletion of HDAC6


title: lung cancer 23


title: HDAC3 fl/fl / GFP4

description: Hepatic gene expression data from mice with normal liver HDAC6

source_name: liver from HDAC3 fl/fl / GFP mice

value: AAV2/8-Tbg-GFP virus


title: lung cancer 22


title: HDAC3 fl/fl / GFP3

description: Hepatic gene expression data from mice with normal liver HDAC5


title: rss1-2,-NaCl_3 / WT,-NaCl_3

city: Nagoya

first: Daisuke

last: Ogawa

address: Furou-Chou, Chikusa

department: Bioscience and Biotechnology Center

country: Japan

institute: Nagoya University

hyb_protocol: Agilent protocol G4140-90050. 825 ng of each Cy-3- and Cy-5-labeled cRNAs were used for hybridization.

scan_protocol: Agilent scanner model G2505B

data_processing: The scanned images were analyzed with Feature Extraction Software v9.5.3.1 (Agilent) to obtain background-subtracted and spatially detrended Processed Signal intensities. All of raw Cy-3 and Cy-5 signals (gBGSubSignal and rBGSubSignal, respectively) were normalized by variance stabilization normalization method using R software (http://www.r-project.org/). After normalization, the relative expression levels of genes were calculated by dividing the Cy-3 values(test) by Cy-5 values(reference).

organism: Oryza sativa

label_protocol: 400 ng RNAs were labeled by Low RNA input Linear Amplification/Labeling Kit (Agilent).

growth_protocol: Wild type and rss1-2 seedlings were grown on the MS medium in the absence or prescence of 150 mM NaCl for 7 days.

extract_protocol: RNAs were extracted from 1-cm shoot basal tissues by RNeasy mini kit (Qiagen) .

value: rss1 mutant

value: non-stress (-NaCl)

source_name: WT,-NaCl (reference)

value: wild type


title: HDAC3 fl/fl / GFP5

description: Hepatic gene expression data from mice with normal liver HDAC7

value: male


title: HDAC3 fl/fl / Cre2

description: Hepatic gene expression data from mice with liver-specific depletion of HDAC4


title: rss1-2,+NaCl_3 / WT,-NaCl_3

value: salt-stress (+NaCl)


title: HDAC3 fl/fl / Cre1

description: Hepatic gene expression data from mice with liver-specific depletion of HDAC3


title: lung cancer 21


title: normal 3


title: HDAC3 fl/fl / GFP1

description: Hepatic gene expression data from mice with normal liver HDAC3


title: lung cancer 20


title: WT,+NaCl_3 / WT,-NaCl_3

source_name: WT,+NaCl(test)


title: HDAC3 fl/fl / GFP2

description: Hepatic gene expression data from mice with normal liver HDAC4


title: rss1-2,+NaCl_2 / WT,-NaCl_2


title: lung cancer 19


title: day 5 FACS sorted CXCR4+/ FLK+ cells, biological rep3

city: Rochester

first: Anca

last: Chiriac

state: MN

address: Stabile 5, 200 First Street SW

department: Molecular Pharmacology and Experimental Therapeutics

institute: Mayo Clinic

description: Gene expression data from day 5 sorted biomarker positive progenitors

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix 430 2.0 Mouse Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

data_processing:
Analysis was performed using the GeneSpring GX 7.3.1 software (Agilent Technologies). All probe sets were filtered according to chip-specific background noise, and genes expressing signals below threshold were removed. Quality filtering was performed according to an established flag value, with values that are Present (P), Marginal (M) or Absent (A) assigned to the marker. Probe sets from CXCR4+/Flk-1+ and CXCR4-/Flk-1- cells were normalized to gene expression levels from CXCR4-/Flk-1- hybridized arrays.

To ensure that only genes with significant transcriptional changes during cardiogenesis are selected, all probe sets were filtered according to a flag value of Present or Marginal in at least two out of three replicates for one experimental condition. A filter on volcano plot was applied to identify significant changes in gene expression (>1.2 fold, p<0.05) in CXCR4+/Flk-1+ cells compared to their double negative counterparts.
Refined data provided on the Series record were extracted from GeneSpring GX 7.3.1 using a filter on Volcano plot (fold change> 1.2, p value< 0.05)- biomarker positive versus biomarker negative expression values

source_name: CGR8 ES cells differentiated in embryoid bodies, sorted at day 5 according to CXCR4 and FLK-1 cell surface expression

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

extract_protocol: Total RNA was isolated using a combination of gDNA Eliminator and RNeasy columns (Qiagen extraction kit) according to the manufacturer's protocol.

value: embryonic stem cell


title: day 5 FACS sorted CXCR4-/ FLK- cells, biological rep2

description: Gene expression data from day 5 sorted biomarker negative progenitors


title: lung cancer 17


title: lung cancer 18


title: WT,+NaCl_2 / WT,-NaCl_2


title: day 5 FACS sorted CXCR4-/ FLK- cells, biological rep3


title: rss1-2,-NaCl_2 / WT,-NaCl_2


title: day 5 FACS sorted CXCR4+/ FLK+ cells, biological rep2


title: lung cancer 16


title: Blastocysts TCM TCM no11 biologial 1 rep1

city: Quebec

first: Claude

last: Robert

state: Quebec

address: Pavillon Comtois

department: Animal Sciences

country: Canada

institute: Laval University

description: Treatment #11 of publication

hyb_protocol: Labelled samples were concentrated by isopropanol precipitation and pellets were re-suspended in 5 µl of RNAse-free water. The concentrated labeled samples were mixed with 80 µl of hybridization buffer (HybBuffer #1 from Ambion) and deposited on the microarray under a LifterSlip coverslip (Thermo Scientific, Mississauga, ON, Canada). Microarray incubation was conducted for 21 h at 50˚C in an automated station (the Slidebooster apparatus from Advalytix, Danvers, MA).  The coverslips were then gently removed in a low stringency buffer (2X SSC + 0.5X SDS). Slides were washed twice in the low stringency buffer for 15 min at 50˚C, transferred to high stringency buffer (0.5X SSC + 0.5X SDS) and washed twice for 15 min at 50˚C and finally dipped quickly in a 1.25X SSC solution and dried by centrifugation at 1,200xg for 5 min at room temperature.

scan_protocol: Slides were read on a VersArray ChipReader (Bio-Rad, Mississauga, ON, Canada). Image analysis was performed using ArrayPro software version 4.5 (MediaCybernetics, Bethesda, MD). For each spot, background was determined locally. Data tables containing the foreground, background and flagged spot annotation were generated for downstream data processing and

data_processing: Microarray data were pre-processed as follows: 1) background correction was conducted by simple subtraction; 2) mean values were calculated for the technically duplicated arrays; 3) median values were calculated for technically duplicated features spotted on the microarrays; 4) within-array normalization was performed with Loess; 5) Quantile was applied for inter-array normalization; 6) the entire dataset was trimmed according to a cut-off value calculated from the mean values of selected negative control features (Aliens, GFP and Arabidopsis) plus two standard deviations. Steps 3 to 5 as well as the statistical analysis and all downstream steps were conducted in WebArrayDB (Xia et al. 2005, Wang et al. 2009): http://www.webarraydb.org/ webarray/index.html.

label: Alexa 647

organism: Bos taurus

source_name: In vitro produced blastocysts following in vitro maturation, in vitro fertilization and in vitro culture. Blastocysts are collected on day 7.5 of culture.

label_protocol: RNA samples were amplified using the RiboAmp kit (Molecular Devices). Protocol was performed as recommanded to the exception that  during the second round of amplification, amino-allyl coupled nucleotides were added to the IVT mix. An aliquot of 5 µg of aRNA was labelled by chemical addition of the Alexa 647 dye. Unincorporated dyes were cleaned up using Clean Up RNeasy Minikit columns (Qiagen).

growth_protocol: Bovine ovaries were collected from the slaughterhouse, cumulus-oocyte complexes were aspirated from 3-6 mm follicles. Selection was done on general morphology and only COCs containing at least 5 layers of cumulus cells were kept. The selected COCs were washed in TLH medium and put through in vitro maturation, in vitro fertilization and in vitro culture. Blastocysts were collected on day 7.5 of culture. For in vivo counterparts, the embryos were collected 7.0 days post insemination.  The embryos were washed in PBS, pooled in groups of 10 with mininal volume of liquid and kept à -80C until total RNA extraction.

extract_protocol: Total RNA was extracted using PicoPure columns following the manufacturer's recommandations. A DNAse 1 treatment was performed on column to remove contaminating genomic DNA.

treatment_protocol: Treatments consists of the different in vitro production systems used. Blastocysts were produced in a total of ten different in vitro systems. In vivo blastocysts were also included and used as reference.

tag: source

value: In vitro

tag: time of collection

value: Day 7.5 of culture (post fertilization)

tag: in vitro maturation conditions

value: TCM-Serum

tag: in vitro culture conditions

value: TCM-serum


title: Blastocysts TCM TCM no11 biologial 1 rep2

description: Treatment #11 of publication


title: Blastocysts TCM SOF no10 biologial 3 rep2

description: Treatment #10 of publication

value: SOF-BSA


title: lung cancer 14

value: lung cancer


title: lung cancer 15


title: Blastocysts TCM TCM no11 biologial 2 rep1

description: Treatment #11 of publication


title: Blastocysts TCM TCM no11 biologial 3 rep1

description: Treatment #11 of publication


title: Blastocysts TCM TCM no11 biologial 3 rep2

description: Treatment #11 of publication


title: Blastocysts TCM TCM no11 biologial 2 rep2

description: Treatment #11 of publication


title: lung cancer 13


title: WT,-NaCl_2 / WT,-NaCl_2

source_name: WT,-NaCl(test)


title: day 5 FACS sorted CXCR4-/ FLK- cells, biological rep1


title: lung cancer 12

source_name: RNA from blood


title: day 5 FACS sorted CXCR4+/ FLK+ cells, biological rep1


title: Blastocysts TCM SOF no10 biologial 3 rep1

description: Treatment #10 of publication


title: Blastocysts TCM SOF no10 biologial 2 rep1

description: Treatment #10 of publication


title: WT,-NaCl_1 / WT,-NaCl_1

source_name: WT,-NaCl (test)


title: Blastocysts TCM SOF no10 biologial 1 rep2

description: Treatment #10 of publication


title: Blastocysts TCM SOF no10 biologial 2 rep2

description: Treatment #10 of publication


title: WT,+NaCl_1 / WT,-NaCl_1


title: WT,-NaCl_3 / WT,-NaCl_3


title: rss1-2,+NaCl_1 / WT,-NaCl_1


title: Blastocysts TCM TCM co culture no9 biologial 2 rep2

description: Treatment #9 of publication

value: TCM-Co-culture


title: Blastocysts TCM TCM co culture no9 biologial 3 rep1

description: Treatment #9 of publication


title: Blastocysts TCM TCM co culture no9 biologial 2 rep1

description: Treatment #9 of publication


title: Blastocysts TCM TCM co culture no9 biologial 3 rep2

description: Treatment #9 of publication


title: lung cancer 10


title: rss1-2,-NaCl_1 / WT,-NaCl_1


title: lung cancer 11


title: Blastocysts TCM SOF no10 biologial 1 rep1

description: Treatment #10 of publication


title: Blastocysts TCM TCM co culture no9 biologial 1 rep2

description: Treatment #9 of publication


title: lung cancer 9


title: Blastocysts TCM TCM co culture no9 biologial 1 rep1

description: Treatment #9 of publication


title: Blastocysts SOFno supp no7 biologial 3 rep2

description: Treatment #7 of publication

value: SOF-no protein supplementation


title: lung cancer 7


title: Blastocysts SOFno supp no7 biologial 2 rep1

description: Treatment #7 of publication


title: Blastocysts SOFno supp no7 biologial 1 rep2

description: Treatment #7 of publication


title: Blastocysts SOFno supp no7 biologial 1 rep1

description: Treatment #7 of publication


title: Blastocysts SOFno supp no7 biologial 2 rep2

description: Treatment #7 of publication


title: normal 2


title: Blastocysts SOFno supp no7 biologial 3 rep1

description: Treatment #7 of publication


title: lung cancer 8


title: Blastocysts SOFserum SOFserum no5 biologial 3 rep2

description: Treatment #5 of publication

value: SOF-Serum


title: Blastocysts SOFserum SOFserum no5 biologial 2 rep2

description: Treatment #5 of publication


title: Blastocysts SOFserum SOFserum no5 biologial 3 rep1

description: Treatment #5 of publication


title: Blastocysts SOFser SOF no3 biologial 3 rep1

description: Treatment #3 of publication


title: Blastocysts SOFser SOF no3 biologial 2 rep1

description: Treatment #3 of publication


title: Blastocysts SOFser SOF no3 biologial 3 rep2

description: Treatment #3 of publication


title: lung cancer 6


title: lung cancer 5


title: lung cancer 3


title: Blastocysts SOFserum SOFserum no5 biologial 1 rep1

description: Treatment #5 of publication


title: Blastocysts SOFser SOF no3 biologial 1 rep2

description: Treatment #3 of publication


title: Blastocysts SOFserum SOFserum no5 biologial 2 rep1

description: Treatment #5 of publication


title: Blastocysts SOFserum SOFserum no5 biologial 1 rep2

description: Treatment #5 of publication


title: normal 1


title: Blastocysts SOFser SOF no3 biologial 2 rep2

description: Treatment #3 of publication


title: lung cancer 2


title: lung cancer 4


title: copd 24

value: copd


title: Blastocysts SOF SOFserum no4 biologial 1 rep2

description: Treatment #4 of publication


title: Blastocysts SOF SOFserum no4 biologial 1 rep1

description: Treatment #4 of publication


title: Blastocysts SOFser SOF no3 biologial 1 rep1

description: Treatment #3 of publication


title: Blastocysts SOF SOFserum no4 biologial 2 rep2

description: Treatment #4 of publication


title: Blastocysts SOF SOFserum no4 biologial 2 rep1

description: Treatment #4 of publication


title: Blastocysts SOF SOFserum no4 biologial 3 rep1

description: Treatment #4 of publication


title: Blastocysts SOF SOF no2 biologial 3 rep2

description: Treatment #2 of publication


title: copd 22


title: copd 21


title: Blastocysts SOF SOF no2 biologial 2 rep2

description: Treatment #2 of publication


title: copd 20


title: Blastocysts SOF SOF no2 biologial 2 rep1

description: Treatment #2 of publication


title: copd 19


title: copd 18


title: copd 17


title: Blastocysts SOF SOF no2 biologial 1 rep1

description: Treatment #2 of publication


title: copd 16


title: Blastocysts SOF Coculture no8 biologial 3 rep1

description: Treatment #8 of publication

value: SOF-Co-culture (BRL cells)


title: Blastocysts SOF SOF no2 biologial 1 rep2

description: Treatment #2 of publication


title: genotype:CI 16151 m9472 (mla6)-pathogen infection:non-inoculated-RNA fraction:total RNA-rep2

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description: This sample is of either the incompatible genotype CI 16151 (Mla6), or compatible genotype CI 16151 m9472 (mla6).  Following 7 days of germination the sample was either inoculated with Bgh isolate 5874 (AVRa6), or noninoculated.  32 hours after infection tissue was harvested.  From this tissue either total RNA or polysomal RNA was isolated for hybridization.

hyb_protocol: Affymetrix GeneChip Hyb

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.

organism: Hordeum vulgare

source_name: phyllome (genotype:CI 16151 m9472 (mla6)-pathogen infection:non-inoculated-RNA fraction:total RNA)

label_protocol: Affymetrix one-cycle target labeling

growth_protocol: Growth Description: Plants were grown for 7 days in the greenhouse, then inoculated with Bgh isolate 5874, or non-inoculated and transferred to a growth chamber for 32 hours.  They were then sampled.  Environmental Conditions: Growth chamber:18C; 16hr light, 8hr night; relative humidity set to 65%

extract_protocol: Hot Phenol/Guanidine Thiocyanate and RNeasy Clean up

tag: germplasm name

value: po:0006001 phyllome

tag: developmental stage

value: PO:0007134 A vegetative growth

value: 8.5 days at time of sampling

tag: growth media

value: garden soil


title: copd 15

tag: disease state


title: copd 14


title: genotype:CI 16151 m9472 (mla6)-pathogen infection:non-inoculated-RNA fraction:total RNA-rep1

tag: tissue

tag: age


title: genotype:CI 16151 m9472 (mla6)-pathogen infection:non-inoculated-RNA fraction:polysomal RNA-rep1

source_name: phyllome (genotype:CI 16151 m9472 (mla6)-pathogen infection:non-inoculated-RNA fraction:polysomal RNA)

extract_protocol: polysome isolation followed by phenol/chloroform RNA extraction


title: genotype:CI 16151 m9472 (mla6)-pathogen infection:non-inoculated-RNA fraction:total RNA-rep3


title: Blastocysts SOF Coculture no8 biologial 2 rep2

description: Treatment #8 of publication


title: Blastocysts SOF Coculture no8 biologial 3 rep2

description: Treatment #8 of publication


title: Blastocysts SOF Coculture no8 biologial 1 rep1

description: Treatment #8 of publication


title: genotype:CI 16151 m9472 (mla6)-pathogen infection: Bgh isolate 5874 (AVRa6)-RNA fraction:total RNA-rep2

source_name: phyllome (genotype:CI 16151 m9472 (mla6)-pathogen infection: Bgh isolate 5874 (AVRa6)-RNA fraction:total RNA)


title: genotype:CI 16151 m9472 (mla6)-pathogen infection: Bgh isolate 5874 (AVRa6)-RNA fraction:total RNA-rep3


title: Blastocysts SOF Coculture no8 biologial 2 rep1

description: Treatment #8 of publication


title: genotype:CI 16151 m9472 (mla6)-pathogen infection:non-inoculated-RNA fraction:polysomal RNA-rep3


title: Blastocysts Culture 5d BSA 2d serum no6 biologial 3 rep2

description: Treatment #6 of publication

value: SOF-BSA 5 days + SOF-serum 2.5 days


title: copd 12


title: genotype:CI 16151 m9472 (mla6)-pathogen infection: Bgh isolate 5874 (AVRa6)-RNA fraction:total RNA-rep1


title: genotype:CI 16151 m9472 (mla6)-pathogen infection: Bgh isolate 5874 (AVRa6)-RNA fraction:polysomal RNA-rep3

source_name: phyllome (genotype:CI 16151 m9472 (mla6)-pathogen infection: Bgh isolate 5874 (AVRa6)-RNA fraction:polysomal RNA)


title: copd 13


title: Blastocysts SOF Coculture no8 biologial 1 rep2

description: Treatment #8 of publication


title: copd 11


title: copd 10


title: Blastocysts Culture 5d BSA 2d serum no6 biologial 3 rep1

description: Treatment #6 of publication


title: Blastocysts Culture 5d BSA 2d serum no6 biologial 2 rep2

description: Treatment #6 of publication


title: Blastocysts Culture 5d BSA 2d serum no6 biologial 2 rep1

description: Treatment #6 of publication


title: copd 9


title: genotype:CI 16151 m9472 (mla6)-pathogen infection: Bgh isolate 5874 (AVRa6)-RNA fraction:polysomal RNA-rep2


title: genotype:CI 16151 m9472 (mla6)-pathogen infection: Bgh isolate 5874 (AVRa6)-RNA fraction:polysomal RNA-rep1


title: Blastocysts Culture 5d BSA 2d serum no6 biologial 1 rep2

description: Treatment #6 of publication


title: copd 7


title: genotype:CI 16151 (Mla6)-pathogen infection:non-inoculated-RNA fraction:total RNA-rep1

source_name: phyllome (genotype:CI 16151 (Mla6)-pathogen infection:non-inoculated-RNA fraction:total RNA)


title: genotype:CI 16151 (Mla6)-pathogen infection:non-inoculated-RNA fraction:polysomal RNA-rep3

source_name: phyllome (genotype:CI 16151 (Mla6)-pathogen infection:non-inoculated-RNA fraction:polysomal RNA)


title: genotype:CI 16151 (Mla6)-pathogen infection:non-inoculated-RNA fraction:total RNA-rep2


title: copd 8


title: copd 4


title: copd 6


title: copd 5


title: lung cancer 1


title: Blastocysts Culture 5d BSA 2d serum no6 biologial 1 rep1

description: Treatment #6 of publication


title: genotype:CI 16151 (Mla6)-pathogen infection:non-inoculated-RNA fraction:total RNA-rep3


title: genotype:CI 16151 (Mla6)-pathogen infection:non-inoculated-RNA fraction:polysomal RNA-rep2


title: Blastocysts in vivo biologial 2 rep1

description: Treatment #1 of publication

source_name: In vivo collected blastocysts by uterine flushing on day 7.0 post insemination

value: In vivo

value: Day 7.0 post insemination


title: Blastocysts in vivo biologial 3 rep2

description: Treatment #1 of publication


title: Blastocysts in vivo biologial 3 rep1

description: Treatment #1 of publication


title: Blastocysts in vivo biologial 2 rep2

description: Treatment #1 of publication


title: copd 3


title: copd 2


title: copd 1


title: Blastocysts in vivo biologial 1 rep2

description: Treatment #1 of publication


title: genotype:CI 16151 (Mla6)-pathogen infection: Bgh isolate 5874 (AVRa6)-RNA fraction:total RNA-rep2

source_name: phyllome (genotype:CI 16151 (Mla6)-pathogen infection: Bgh isolate 5874 (AVRa6)-RNA fraction:total RNA)


title: genotype:CI 16151 (Mla6)-pathogen infection: Bgh isolate 5874 (AVRa6)-RNA fraction:polysomal RNA-rep3

source_name: phyllome (genotype:CI 16151 (Mla6)-pathogen infection: Bgh isolate 5874 (AVRa6)-RNA fraction:polysomal RNA)


title: genotype:CI 16151 (Mla6)-pathogen infection: Bgh isolate 5874 (AVRa6)-RNA fraction:total RNA-rep3


title: genotype:CI 16151 (Mla6)-pathogen infection:non-inoculated-RNA fraction:polysomal RNA-rep1

growth_protocol: Growth Description: Plants were grown for 7 days in the greenhouse, then inoculated with Bgh isolate 5874, or non-inoculated and transferred to a growth chamber for 32 hours.  They were then sampled.  Environmental Conditions: Growth chamber:18C; 16hr light 8hr dark; relative humidity set to 65%


title: genotype:CI 16151 (Mla6)-pathogen infection: Bgh isolate 5874 (AVRa6)-RNA fraction:total RNA-rep1


title: genotype:CI 16151 (Mla6)-pathogen infection: Bgh isolate 5874 (AVRa6)-RNA fraction:polysomal RNA-rep1

growth_protocol: Growth Description: Plants were grown for 7 days in the greenhouse, then inoculated with Bgh isolate 5874, or non-inoculated and transferred to a growth chamber for 32 hours.  They were then sampled.  Environmental Conditions: Growth chamber:18C; 16hr light 8hr night; relative humidity set to 65%


title: Blastocysts in vivo biologial 1 rep1

description: Treatment #1 of publication


title: genotype:CI 16151 (Mla6)-pathogen infection: Bgh isolate 5874 (AVRa6)-RNA fraction:polysomal RNA-rep2

growth_protocol: Growth Description: Plants were grown for 7 days in the greenhouse, then inoculated with Bgh isolate 5874, or non-inoculated and transferred to a growth chamber for 32 hourse.  They were then sampled.  Environmental Conditions: Growth chamber:18C; 16hr light, 8hr night; relative humidity set to 65%


title: tt16 DPA3, tt16 DPA7 replicate 4

status: Public on Mar 10 2011

city: Saskatoon

first: Raju

last: Datla

state: SK

address: 110 Gymnasium Place

institute: NRC-PBI

description: Biological replicate 4 of 4. tt16 DPA3, tt16 DPA7 seed coat

hyb_protocol: SlideHyb buffer #1 (Ambion, Catalog# 8861) was used. 42°C overnight. After hybridization, slides were washed sequential.

scan_protocol: Hybridized arrays were scanned with a Genepix 4000B microarray scanner (Axon Instruments, CA, USA) at 10µm resolution and 100% laser power using a dual laser scanning system.

data_processing:
The image analysis was performed using GenePix Pro version 6.0 software (Axon Instruments, CA, USA). The local background corrected spot fluorescence intensities for the Cy5 and Cy3 channels were saved as .gpr files. These .gpr files were used as the starting point for statistical analysis and were also analysed using GeneSpring GX 7.3.1 (Agilent Technologies, Inc.) The Cy3 and Cy5 channels within each array were calibrated using Huber's variance stabilization normalization algorithm and a difference statistic was calculated for each gene for each array hybridization (Huber et al., 2002).
Normalized log2 ratio representing two lines in the same development timepoint or two development timepoint in the same line.

organism: Arabidopsis thaliana

source_name: tt16 DPA3 seed coat

label_protocol: RNA amplification was carried out using the MessageAmp aRNA kit (Ambion, Catalog# 1750) according to the supplied protocol. During the second round of in vitro transcription, aminoallyl-UTP was incorporated into the newly synthesized aRNA.Dye molecules were coupled to the amplified RNA, and the dye-labeled RNA was fragmented before hybridization.

growth_protocol: The plants were grown in the chambers at 20°C under continuous light (90 to 120 μmol m-2s-1 photosynthetically active radiation [PAR])

extract_protocol: Total RNA was extracted from each seed coat sample using the RNAqueous Micro kit (Ambion, Catalog# 1927) with a minor modification as follows. The seed coat tissues were crushed completely with a plastic pestle in Eppendorf tubes in 250 μL lysis buffer, then centrifuged at 13200 rpm for 2 minutes. 200 μL of supernatant was removed to a new Eppendorf tube and the extraction was completed according to the kit protocol.

tag: development stage

tag: mutant line

source_name: tt16 DPA7 seed coat


title: tt16 DPA7, tt16 DPA11 replicate 2

description: Biological replicate 2 of 4. tt16 DPA7, tt16 DPA11 seed coat

source_name: tt16 DPA11 seed coat


title: tt16 DPA7, tt16 DPA11 replicate 4

description: Biological replicate 4 of 4. tt16 DPA7, tt16 DPA11 seed coat


title: tt16 DPA7, tt16 DPA11 replicate 3

description: Biological replicate 3 of 4. tt16 DPA7, tt16 DPA11 seed coat


title: copd 23


title: tt16 DPA7, tt16 DPA11 replicate 1

description: Biological replicate 1 of 4. tt16 DPA7, tt16 DPA11 seed coat


title: tt16 DPA3, tt16 DPA7 replicate 2

description: Biological replicate 2 of 4. tt16 DPA3, tt16 DPA7 seed coat


title: ws2 DPA7, ws2 DPA11 replicate 3

description: Biological replicate 3 of 4. ws2 DPA7, ws2 DPA11 seed coat

source_name: ws2 DPA7 seed coat

tag: wild type line

source_name: ws2 DPA11 seed coat


title: ws2 DPA3, ws2 DPA7 replicate 4

description: Biological replicate 4 of 4. ws2 DPA3, ws2 DPA7 seed coat

source_name: ws2 DPA3 seed coat


title: ws2 DPA7, ws2 DPA11 replicate 4

description: Biological replicate 4 of 4. ws2 DPA7, ws2 DPA11 seed coat


title: tt16 DPA3, tt16 DPA7 replicate 3

description: Biological replicate 3 of 4. tt16 DPA3, tt16 DPA7 seed coat


title: ws2 DPA7, ws2 DPA11 replicate 2

description: Biological replicate 2 of 4. ws2 DPA7, ws2 DPA11 seed coat


title: ap2 DPA7, ap2 DPA11 replicate 3

description: Biological replicate 3 of 4. ap2 DPA3, ap2 DPA7 seed coat

source_name: ap2 DPA7 seed coat

source_name: ap2 DPA11 seed coat


title: ap2 DPA7, ap2 DPA11 replicate 4

description: Biological replicate 4 of 4. ap2 DPA3, ap2 DPA7 seed coat


title: ap2 DPA7, ap2 DPA11 replicate 2

description: Biological replicate 2 of 4. ap2 DPA3, ap2 DPA7 seed coat


title: genotype:CI 16151 m9472 (mla6)-pathogen infection:non-inoculated-RNA fraction:polysomal RNA-rep2


title: tt16 DPA3, tt16 DPA7 replicate 1

description: Biological replicate 1 of 4. tt16 DPA3, tt16 DPA7 seed coat


title: ap2 DPA7, ap2 DPA11 replicate 1

description: Biological replicate 1 of 4. ap2 DPA7, ap2 DPA11 seed coat


title: ap2 DPA3, ap2 DPA7 replicate 3

source_name: ap2 DPA3 seed coat


title: ws2 DPA3, ws2 DPA7 replicate 3

description: Biological replicate 3 of 4. ws2 DPA3, ws2 DPA7 seed coat


title: ws2 DPA7, ws2 DPA11 replicate 1

description: Biological replicate 1 of 4. ws2 DPA7, ws2 DPA11 seed coat


title: col2 DPA7, col2 DPA11 replicate 1

description: Biological replicate 1 of 4. col2 DPA7, col2 DPA11 seed coat

source_name: col2 DPA7 seed coat

tag: wildtype line

source_name: col2 DPA11 seed coat


title: tt16 DPA11, ap2 DPA11 replicate 2

description: Biological replicate 2 of 4. tt16 DPA11, ap2 DPA11 seed coat


title: tt16 DPA3, ap2 DPA3 replicate 4

description: Biological replicate 4 of 4. tt16 DPA3, ap2 DPA3 seed coat


title: col2 DPA3, col2 DPA7 replicate 1

description: Biological replicate 1 of 4. col2 DPA3, col2 DPA7 seed coat

source_name: col2 DPA3 seed coat


title: col2 DPA3, col2 DPA7 replicate 3

description: Biological replicate 3 of 4. col2 DPA3, col2 DPA7 seed coat


title: tt16 DPA7, ap2 DPA7 replicate 3

description: Biological replicate 3 of 4. tt16 DPA7, ap2 DPA7 seed coat


title: ws2 DPA3, ws2 DPA7 replicate 2

description: Biological replicate 2 of 4. ws2 DPA3, ws2 DPA7 seed coat


title: tt16 DPA7, ap2 DPA7 replicate 1

description: Biological replicate 1 of 4. tt16 DPA7, ap2 DPA7 seed coat


title: ap2 DPA3, ap2 DPA7 replicate 2


title: tt16 DPA11, ap2 DPA11 replicate 3

description: Biological replicate 3 of 4. tt16 DPA11, ap2 DPA11 seed coat


title: ap2 DPA3, ap2 DPA7 replicate 4


title: tt16 DPA7, ap2 DPA7 replicate 4

description: Biological replicate 4 of 4. tt16 DPA7, ap2 DPA7 seed coat


title: col2 DPA7, col2 DPA11 replicate 3

description: Biological replicate 3 of 4. col2 DPA7, col2 DPA11 seed coat


title: ws2 DPA11, tt16 DPA11 replicate 3

description: Biological replicate 3 of 4. ws2 DPA11, tt16 DPA11 seed coat


title: tt16 DPA3, ap2 DPA3 replicate 2

description: Biological replicate 2 of 4. tt16 DPA3, ap2 DPA3 seed coat


title: ws2 DPA11, tt16 DPA11 replicate 4

description: Biological replicate 4 of 4. ws2 DPA11, tt16 DPA11 seed coat


title: tt16 DPA7, ap2 DPA7 replicate 2

description: Biological replicate 2 of 4. tt16 DPA7, ap2 DPA7 seed coat


title: tt16 DPA11, ap2 DPA11 replicate 1

description: Biological replicate 1 of 4. tt16 DPA11, ap2 DPA11 seed coat


title: col2 DPA7, col2 DPA11 replicate 4

description: Biological replicate 4 of 4. col2 DPA7, col2 DPA11 seed coat


title: col2 DPA3, col2 DPA7 replicate 2

description: Biological replicate 2 of 4. col2 DPA3, col2 DPA7 seed coat


title: tt16 DPA11, ap2 DPA11 replicate 4

description: Biological replicate 4 of 4. tt16 DPA11, ap2 DPA11 seed coat


title: ws2 DPA11, tt16 DPA11 replicate 2

description: Biological replicate 2 of 4. ws2 DPA11, tt16 DPA11 seed coat


title: col2 DPA7, col2 DPA11 replicate 2

description: Biological replicate 2 of 4. col2 DPA7, col2 DPA11 seed coat


title: tt16 DPA3, ap2 DPA3 replicate 3

description: Biological replicate 3 of 4. tt16 DPA3, ap2 DPA3 seed coat


title: ws2 DPA7, tt16 DPA7 replicate 4

description: Biological replicate 4 of 4. ws2 DPA7, tt16 DPA7 seed coat


title: ws2 DPA11, tt16 DPA11 replicate 1

description: Biological replicate 1 of 4. ws2 DPA11, tt16 DPA11 seed coat


title: Blastocysts SOF SOF no2 biologial 3 rep1

description: Treatment #2 of publication

source_name: In vitro produced blastocysts following in vitro maturation, in vitro fertilization and in vitro culture. Blastocysts are collected on day 7.5 of culture.

value: In vitro

value: Day 7.5 of culture (post fertilization)


title: ws2 DPA7, tt16 DPA7 replicate 3

description: Biological replicate 3 of 4. ws2 DPA7, tt16 DPA7 seed coat


title: tt16 DPA3, ap2 DPA3 replicate 1

description: Biological replicate 1 of 4. tt16 DPA3, ap2 DPA3 seed coat


title: col2 DPA3, col2 DPA7 replicate 4

description: Biological replicate 4 of 4. col2 DPA3, col2 DPA7 seed coat


title: ws2 DPA3, ws2 DPA7 replicate 1

description: Biological replicate 1 of 4. ws2 DPA3, ws2 DPA7 seed coat


title: ap2 DPA3, ap2 DPA7 replicate 1

description: Biological replicate 1 of 4. ap2 DPA3, ap2 DPA7 seed coat


title: ws2 DPA3, tt16 DPA3 replicate 2

description: Biological replicate 2 of 4. ws2 DPA3, tt16 DPA3 seed coat


title: ws2 DPA7, tt16 DPA7 replicate 1

description: Biological replicate 1 of 4. ws2 DPA7, tt16 DPA7 seed coat


title: ws2 DPA7, tt16 DPA7 replicate 2

description: Biological replicate 2 of 4. ws2 DPA7, tt16 DPA7 seed coat


title: ws2 DPA3, tt16 DPA3 replicate 4

description: Biological replicate 4 of 4. ws2 DPA3, tt16 DPA3 seed coat


title: ws2 DPA3, tt16 DPA3 replicate 1

description: Biological replicate 1 of 4. ws2 DPA3, tt16 DPA3 seed coat


title: ws2 DPA3, tt16 DPA3 replicate 3

description: Biological replicate 3 of 4. ws2 DPA3, tt16 DPA3 seed coat


title: col2 DPA11, ap2 DPA11 replicate3

description: Biological replicate 3 of 4. col2 DPA11, ap2 DPA11 seed coat


title: col2 DPA11, ap2 DPA11 replicate4

description: Biological replicate 4 of 4. col2 DPA11, ap2 DPA11 seed coat


title: col2 DPA11, ap2 DPA11 replicate2

description: Biological replicate 2 of 4. col2 DPA11, ap2 DPA11 seed coat


title: col2 DPA11, ap2 DPA11 replicate1

description: Biological replicate 1 of 4. col2 DPA11, ap2 DPA11 seed coat


title: col2 DPA7, ap2 DPA7 replicate 1

description: Biological replicate 1 of 4. col2 DPA7, ap2 DPA7 seed coat


title: col2 DPA7, ap2 DPA7 replicate 3

description: Biological replicate 3 of 4. col2 DPA7, ap2 DPA7 seed coat


title: col2 DPA7, ap2 DPA7 replicate 4

description: Biological replicate 4 of 4. col2 DPA7, ap2 DPA7 seed coat


title: Neutrophils rep2

city: Tampa

first: Je-In

last: Youn

state: FL

address: 12902 Magnolia Drive

institute: H. Lee. Moffitt Cancer Center

description: Gene expression data from neutrophils

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scanner.

data_processing: The data were analyzed with the Affymetrix GCOS 1.4 software using the MAS 5.0 algorithm with default analysis settings and global scaling as the normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Ascitic fluids

label_protocol: Biotinylated cRNA were prepared according to the Ambion Message Amp Premier protocol using 100 ng of total RNA (Ambion).

growth_protocol: C57BL/6 mice were injected with EL4 cells subcutaneously and its spleen was used for isolation of G-MDSC 3.5 weeks after tumor injection.C57BL/6 mice received two intraperitoneal injections of 12% casein (1.5 ml) with 16 hr interval and were sacrificed 3 hr later. Cells were collected by peritoneal lavage with PBS and neutrophils were isolated using microbeads.

extract_protocol: Isolation of total RNA was performed using the Qiagen RNEasy column according to the manufacturer's instructions.

treatment_protocol: The red blood cells were removed using ACK lysis buffer.

tag: gender

value: Female

tag: strain

value: Ascitic fluids

tag: cell type

value: neutrophils


title: G-MDSC rep2

description: Gene expression data from G-MDSC

source_name: Splenocytes

value: Spleen

value: G-MDSC


title: Neutrophils rep1

description: Gene expression data from neutrophils


title: col2 DPA7, ap2 DPA7 replicate 2

description: Biological replicate 2 of 4. col2 DPA7, ap2 DPA7 seed coat


title: G-MDSC rep1

description: Gene expression data from G-MDSC


title: col2 DPA3, ap2 DPA3 replicate 2

description: Biological replicate 2 of 4. col2 DPA3, ap2 DPA3 seed coat


title: col2 DPA3, ap2 DPA3 replicate 1

description: Biological replicate 1 of 4. col2 DPA3, ap2 DPA3 seed coat


title: DPI + DNFB rep3

city: Toledo

first: masaaki

last: miyazawa

state: OH

address: 3000 Arlington Ave

department: Medical Microbiology and Immunology

institute: University of Toledo College of Medicine

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45 degrees C on GeneChip 430 2.0 arrays. GeneChips were washed and stained with streptavidin-phycoerythrin using the Affymetrix Fluidics Station 450, according to the manufacturer's recommended protocol.

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

data_processing: The data were analyzed with AGCC and MAS 5.0 in Expression Console using Affymetrix default analysis settings.

source_name: DPI+DNFB

label_protocol: Biotinylated cRNA were prepared by a modified Eberwine procedure using the 3' IVT Express kit (Affymetrix), according to the manufacturer's instructions.

extract_protocol: Extraction of total RNA was performed using TRIzol reagent (Invitrogen) and Rneasy Plus Mini Kit (Qiagen) according to the manufacturer's instructions.

tag: sample type

value: cell line derived from epidermis of newborn A/J mice

value: dendritic cell

tag: genetic background

value: A/J


title: H2O2 rep1


title: col2 DPA3, ap2 DPA3 replicate 4

description: Biological replicate 4 of 4. col2 DPA3, ap2 DPA3 seed coat


title: DPI rep3

source_name: diphenyl iodonium (DPI)


title: DNFB rep2

source_name: dinitrofluorobenzene (DNFB)


title: DPI + DNFB rep1


title: DPI + DNFB rep2


title: DPI rep1


title: H2O2 rep2


title: DPI rep2


title: DNFB rep1


title: BAC, rep3

source_name: benzalkonium chloride

treatment_protocol: CL57BL/6 mice received topical application of a chemical allergen (DNFB), a skin irritant (BAC) on the right ear or vehicle (acetone/olive oil) alone on the left ear fro 6 hours.

value: skin


title: DNFB rep3


title: non-treated rep2


title: DNFB, rep3

source_name: dinitrofluorobenzene


title: non-treated rep3


title: H2O2 rep3


title: col2 DPA3, ap2 DPA3 replicate 3

description: Biological replicate 3 of 4. col2 DPA3, ap2 DPA3 seed coat


title: DNFB, rep2


title: BAC, rep2


title: non-treated rep1


title: DNFB, rep1


title: vehicle, rep3

source_name: vehicle


title: vehicle, rep2


title: BAC, rep1


title: DFOG, biological rep3

city: Mishima

first: Hiromasa

last: Ono

state: Shizuoka

address: National Institute of Genetics, Yata 1111

department: Database Center for Life Science (DBCLS)

institute: Research Organization of Information and Systems

description: Gene expression data from DFOG grew to semiconfluence

hyb_protocol: Biotin labeled cRNA samples were fragmented and then hybridized to the Affymetrix GeneChip® Porcine Genome Array.

scan_protocol: The data from microarrays was obtained by scanning microarrays using GeneChip® Scanner 3000.

data_processing: The data were analyzed with RMA using R/Bioconductor.

organism: Sus scrofa

source_name: GC were dedifferentiated during culture in vitro, and grown to semiconfluence.

label_protocol: 5 µg each of high quality total RNA was used in double stranded cDNA synthesis and labeling reactions using the GeneChip® Expression 3’-Amplification IVT Labelling Kit (Affymetrix).

extract_protocol: RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions. As a last step of the extraction procedure, the RNA was purified with RNeasy Mini Kit (Qiagen).

value: Dedifferentiated porcine follicular granulosa cells (DFOG)


title: DFAT, biological rep3

description: Gene expression data from DFAT grew to semiconfluence

source_name: MA were dedifferentiated during ceiling culture, and grown to semiconfluence.

value: Dedifferentiated porcine mature adipocytes (DFAT)


title: MA, biological rep2

description: Gene expression data from MA derived from fat tissue

source_name: MA derived from fat tissue of porcine

value: Porcine mature adipocytes


title: vehicle, rep1


title: GC, biological rep1

description: Gene expression data from GC derived from ovarian follicles

source_name: GC derived from ovarian follicles of porcine

value: Porcine follicular granulosa cells


title: GC, biological rep2


title: DFOG, biological rep1


title: DFAT, biological rep2


title: GC, biological rep3


title: MA, biological rep1


title: MA, biological rep3


title: DFAT, biological rep1


title: DFOG, biological rep2


title: wt  vs. Mock

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

hyb_protocol: After precipitation, purification and quantification, 1.25 µg of each labeled cRNA was fragmented and subsequent hybridized to whole human genome 44k microarrays according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Hybridized microarrays were washed using the SSC washing protocol (Agilent Technologies). Scanning of microarrays was performed with extended mode (100% and 10%) at 5 µm resolution using a DNA microarray laser scanner (Agilent Technologies).

data_processing: The extracted MAGE-ML files were further analyzed with the Rosetta Resolver Biosoftware, Build 7.2 (Rosetta Biosoftware, Seattle, WA, USA). Ratio profiles comprising single hybridizations were combined in an error-weighted fashion to create ratio experiments. A 1.5–fold change expression cut-off for ratio experiments was applied together with anti-correlation of ratio profiles rendering the microarray analysis highly significant (P-value > 0.01), robust and reproducible.

source_name: wt

label_protocol: RNA labeling was performed with the Quick Amp Labeling Kit (Agilent Technologies). In brief, mRNA was reverse transcribed and amplified using an oligo-dT-T7-promotor primer and resulting cRNA was labeled with either Cyanine 3-CTP according the suppliers instructions

extract_protocol: total RNA was extracted with Trizol (Invitrogen) according the suppliers instructions using Glycogen as carrier

tag: treatment

value: endotoxin-tolerant RAW 264.7 by pre-exposure to heat-killed Salmonella typhimurium SL1344 ("HKS") at an MOI of 10 for 20 h

tag: infection

value: wild-type Salmonella typhimurium SL1344

tag: cell line

source_name: Mock

label_protocol: RNA labeling was performed with the Quick Amp Labeling Kit (Agilent Technologies). In brief, mRNA was reverse transcribed and amplified using an oligo-dT-T7-promotor primer and resulting cRNA was labeled with either Cyanine 5-CTP according the suppliers instructions

value: mock


title: 24wt vs. 24C

value: untreated RAW 264.7


title: 24SPI1/2 vs. 24C

value: wild-type Salmonella typhimurium SL1344 knockout strain lacking both major genomic loci associated with Salmonella pathogenicity ("SPI1" and "SPI2")


title: Ovine_Shunt7

city: Augusta

first: Jing

last: Tian

state: GA

address: 1459 Laney Walker BLVD

department: Vascular Biology Center

institute: Medical College of Georgia

hyb_protocol: Fragmented cRNA was hybridized for 16 h at 45°C to the array chips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Microarray data were processed and normalized using RMA.

organism: Ovis aries

source_name: lung, shunt

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Lambs at 3 days of age.

extract_protocol: Total RNA was extracted using the Qiagen Rneasy Mini kit.

treatment_protocol: Pregnant ewes underwent sham or in utero surgery (9 ± 6 days before term) to anastomose an 8.0-mm Gore-tex vascular graft ( 2-mm length; W. L. Gore and Assos., Milpitas, CA) between the ascending aorta and main pulmonary artery of the fetus. The incisions in the uterus and the abdomen were closed, and the sheep were allowed to deliver normally.Three days after spontaneous delivery, lambs were anesthetized, hemodynamic variables measured, peripheral lung tissues taken, and sacrificed with a lethal injection of potassium chloride (40 ml KaCl 7,45%). All protocols and procedures were approved by the Committees on Animal Research at the German Heart Centre, Munich, Germany; the University of California, San Francisco; and Medical College of Georgia, Augusta, Georgia.

value: lung

value: 3 days

value: shunt

tag: disease model

value: congenital heart disease (CHD) with increased pulmonary blood flow (PBF)


title: Ovine_Shunt8


title: Ovine_Shunt6


title: Ovine_Shunt5


title: 24C vs. 24wt


title: SPI1/2 vs. wt


title: Ovine_Shunt3


title: Ovine_Shunt2


title: 24C vs. 24SPI1/2


title: Ovine_Shunt4


title: wt  vs. SPI1/2


title: HAC1 3'UTR mRNA(3)

city: Stanford

first: Dan

last: Klass

state: CA

address: 259 Campus Drive Beckman Rm 439

department: Biochemistry

institute: Stanford University

description:
Simple annotation: mRNA vs Total RNA Comparison, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82619.gif

hyb_protocol: not provided

scan_protocol: GenePix 4000B

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

organism: Saccharomyces cerevisiae

source_name: HAC1 3'UTR mRNA

label_protocol: not provided

extract_protocol: not provided

tag: experiment

value: HAC1 3'UTR mRNA

source_name: Total mRNA

tag: reference

value: Total mRNA


title: Ovine_Control7

source_name: lung, control

tag: tissue

value: sham

value: control


title: Mock vs. wt


title: HAC1 complete in Cy3(2)

description:
Simple annotation: mRNA vs Total RNA Comparison, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82620.gif

source_name: HAC1 mRNA

value: HAC1 mRNA

value: Total-mRNA


title: Ovine_Control6

tag: age


title: Ovine_Control8


title: Ovine_Control4


title: Ovine_Shunt1


title: Ovine_Control5


title: Ovine_Control2


title: Ovine_Control1


title: HAC1 3'UTR mRNA(4)

description:
Simple annotation: mRNA vs Total RNA Comparison, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82621.gif


title: Ovine_Control3


title: Effect of Conjugated linoleic acid at 37℃ rep4

city: Montreal

first: Andre

last: Nantel

state: QC

address: 6100 Royalmount

department: Biotechnology Research Institute

institute: National Research Council of Canada

hyb_protocol: The microarray slides were pre-hybridized for 2 hours at 42°C with DIGeasy hybridization buffer (Roche) containing 0.5 ug/ul of yeast tRNA (Roche) and 0.5 ug/ul of salmon sperm DNA (Invitrogen) and subsequently washed with 0.1X SSC and air dried. The slides were then hybridized with labeled cDNAs overnight at 42°C in DIGeasy hybridization buffer with yeast tRNA and salmon sperm DNA. Hybridization was done with an Advalytix SlideBooster. The slides were washed twice with SSC-0.2% SDS, once with 0.1X SSC-0.2% SDS and 3 times with 0.1X SSC. A final wash with isopropanol was performed and slides were air-dried.

scan_protocol: Slides were scanned with a ScanArray 5000 scanner (Perkin Elmer) at 10-µm resolution.

data_processing: Signal intensity was quantified with QuantArray software (Perkin Elmer) and final Lowess normalization and inspection of the data was done with the GeneSpring package GX v.7.3 (Agilent Technologies).

organism: Candida albicans

source_name: 90 min in Spider Media at 37℃ + 100 uM CLA

label_protocol: 20 µg of total RNA was reverse transcribed using oligo(dT)21 in the presence of Cy5-dCTP (Perkin-Elmer-Cetus/NEN) and Superscript III reverse transcriptase (Invitrogen). Thereafter, template RNA was degraded by adding 2.5 units of RNase H (USB) and 1 ug of RNase A (Pharmacia) followed by incubation for 15 min at 37°C. The labeled cDNAs were purified with QIAquick PCR Purification Kit (Qiagen).

extract_protocol: Total RNA was isolated from quadruplicate independent biological samples using the RNeasy mini kit (Qiagen). Briefly, frozen cells were thawed out in RNeasy buffer RLT at a ratio of 3:1 [vol/vol] buffer/pellet. Resuspended cells were divided into 1 ml aliquots in 2 ml screw cap microcentrifuge tubes containing 0.6 ml of 0.5 mm diameter acid-washed glass beads. Samples were homogenized 6 times, for 5 minutes each, in a BeadBeater set at maximum speed.

treatment_protocol: C. albicans cells grown overnight in YPD at 30°C (OD600 of ~12-14) were washed in sterile distilled water and diluted to 5 X 106 cells ml-1 (OD600 of 0.1) in Spider medium supplemented with ethanol or CLA (100 μM). Cultures were incubated with shaking at either 30°C or 37°C for 90 minutes.

value: 37℃ + 100 uM CLA

source_name: 90 min in Spider Media at 30℃


title: Effect of Conjugated linoleic acid at 37℃ rep3


title: Estimating GST-protein on Protoarrays (1)

type: protein

description:
Simple annotation: Protein array, Antibody
Image: http://smd.stanford.edu/MicroArray/gifs/2010-05/88125.gif

molecule: protein

source_name: Nothing

value: Nothing

source_name: Anti-GST antibody

value: Anti-GST


title: Effect of Conjugated linoleic acid at 37℃ rep1


title: Effect of Conjugated linoleic acid at 37℃ rep2


title: Estimating GST-protein on Protoarrays (2)

description:
Simple annotation: Protein array, Antibody
Image: http://smd.stanford.edu/MicroArray/gifs/2010-05/88126.gif

source_name: anti-GST antibody

value: anti-GST antibody


title: ARC15_RNA coimmunoprecipitation_Identify Target Genes_CPCE_041_30510

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88928.gif

source_name: Total RNA from lysate after IP

value: Total RNA from lysate after IP

source_name: RNA that co-purified with an RBP


title: MTQ2_RNA coimmunoprecipitation_Identify Target Genes_CPCE_043_30510

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88930.gif


title: HSP26_RNA coimmunoprecipitation_Identify Target Genes_CPCE_063_30710

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88949.gif


title: GUS1_MG_RNA coimmunoprecipitation_Identify Target Genes_CPCE_034_30510

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88919.gif


title: Effect of Conjugated linoleic acid at 30℃ rep4

source_name: 90 min in Spider Media at 30℃ + 100 uM CLA

value: 30℃ + 100 uM CLA


title: 37℃ vs 30℃ rep3

source_name: 90 min in Spider Media at 37℃


title: Effect of Conjugated linoleic acid at 30℃ rep1


title: PAD1_RNA coimmunoprecipitation_Identify Target Genes_CPCE_057_30710

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88943.gif


title: Effect of Conjugated linoleic acid at 30℃ rep3


title: 37℃ vs 30℃ rep1


title: ARF3_RNA coimmunoprecipitation_Identify Target Genes_CPCE_067_30710

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88953.gif


title: Effect of Conjugated linoleic acid at 30℃ rep2


title: SCD6_RNA coimmunoprecipitation_Identify Target Genes_CPCE_031_30510

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88917.gif


title: 37℃ vs 30℃ rep4


title: GIS2_RNA coimmunoprecipitation_Identify Target Genes_CPCE_044_30510

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88931.gif


title: GUS1_EDTA_RNA coimmunoprecipitation_Identify Target Genes_CPCE_037_30510

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88922.gif


title: BUB1_RNA coimmunoprecipitation_Identify Target Genes_CPCE_054_030510

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88940.gif


title: 37℃ vs 30℃ rep2


title: ARC15_RNA coimmunoprecipitation_Identify Target Genes_CPCE_040_30510

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88926.gif


title: SLE-193_Fresh_Neutro

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

description: Fresh neutrophils isolated from this SLE patient

hyb_protocol: Hybridize 6-Sample Beadchip

scan_protocol: SentrixScanVersion 2.3.0.13

data_processing: The data were analyzed using BeadStudio version 1.5.1.3 using the average chip normalization method.

source_name: Neutrophils from SLE Patient

label_protocol: Biotynlated cRNA were generated following manufacturer protocols using the Illumina TotalPrep Amplification Kit from Ambion.

extract_protocol: RNeasy Mini

value: Neutrophil

tag: disease state

value: SLE

value: F

tag: race

value: African American


title: SLE-158_Fresh_Neutro

value: Hispanic


title: SCD6_RNA coimmunoprecipitation_Identify Target Genes_CPCE_033_30510

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88918.gif


title: LYS1_RNA coimmunoprecipitation_Identify Target Genes_CPCE_048_30510

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88935.gif


title: SMY1_RNA coimmunoprecipitation_Identify Target Genes_CPCE_064_30710

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88950.gif


title: CRG1_RNA coimmunoprecipitation_Identify Target Genes_CPCE_039_30510

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88924.gif


title: MOCK_RNA coimmunoprecipitation_Identify Target Genes_CPCE_069_30710

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88955.gif

value: MOCK


title: MOCK_RNA coimmunoprecipitation_Identify Target Genes_CPCE_073_30710

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88959.gif


title: GUS1_EDTA_RNA coimmunoprecipitation_Identify Target Genes_CPCE_036_30510

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88921.gif


title: H204_Fresh_Neutro

description: Fresh neutrophils isolated from this healthy donor

source_name: Neutrophils from Healthy control

value: Caucasian


title: SLE-79_Fresh_Neutro


title: HSP26_RNA coimmunoprecipitation_Identify Target Genes_CPCE_062_30710

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88948.gif


title: VTC1_RNA coimmunoprecipitation_Identify Target Genes_CPCE_061_30710

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88947.gif


title: SLE-114_Fresh_Neutro


title: SLE-55_Fresh_Neutro


title: SLE-202_Fresh_Neutro


title: VTC1_RNA coimmunoprecipitation_Identify Target Genes_CPCE_060_30710

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88946.gif


title: SLE-201C_Fresh_Neutro


title: SLE-65_Fresh_Neutro


title: MOCK_RNA coimmunoprecipitation_Identify Target Genes_CPCE_070_30710

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88956.gif


title: UBP3_RNA coimmunoprecipitation_Identify Target Genes_CPCE_047_30510

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88934.gif


title: SLE-169_Fresh_Neutro


title: SLE-201B_Fresh_Neutro


title: SLE-170_Fresh_Neutro


title: MTQ2_RNA coimmunoprecipitation_Identify Target Genes_CPCE_042_30510

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88929.gif


title: SLE-176_Fresh_Neutro


title: PCS60_RNA coimmunoprecipitation_Identify Target Genes_CPCE_052_30510

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88938.gif


title: SLE-206_Fresh_Neutro


title: SMY1_RNA coimmunoprecipitation_Identify Target Genes_CPCE_065_30710

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88951.gif


title: CRG1_RNA coimmunoprecipitation_Identify Target Genes_CPCE_038_30510

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88923.gif


title: MOCK_RNA coimmunoprecipitation_Identify Target Genes_CPCE_072_30710

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88958.gif


title: GCY1_RNA coimmunoprecipitation_Identify Target Genes_CPCE_050_30510

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88936.gif


title: UBP3_RNA coimmunoprecipitation_Identify Target Genes_CPCE_046_30510

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88933.gif


title: ARF3_RNA coimmunoprecipitation_Identify Target Genes_CPCE_066_30710

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88952.gif


title: SLE-203_Fresh_Neutro

description: Fresh neutrophils isolated from this SLE patient

value: M


title: SLE-80_Fresh_Neutro


title: PAD1_RNA coimmunoprecipitation_Identify Target Genes_CPCE_056_30710

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88942.gif


title: BUB1_RNA coimmunoprecipitation_Identify Target Genes_CPCE_055_030510

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88941.gif


title: SLE-205_Fresh_Neutro


title: SLE-201A_Fresh_Neutro


title: RCR2_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_206_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88965.gif


title: ARP8_RNA coimmunoprecipitation_Identify Target Genes_CPCE_059_30710

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88945.gif


title: SLE-150_Fresh_Neutro


title: MOCK_RNA coimmunoprecipitation_Identify Target Genes_CPCE_068_30710

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88954.gif


title: YEL1_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_211_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88970.gif


title: ABP140_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_204_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88963.gif


title: H195_Fresh_Neutro

description: Fresh neutrophils isolated from this healthy donor

value: control


title: MOCK_RNA coimmunoprecipitation_Identify Target Genes_CPCE_071_30710

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88957.gif


title: STP4_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_235_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88991.gif


title: VTC1_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_220_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88977.gif


title: GUS1_MG_RNA coimmunoprecipitation_Identify Target Genes_CPCE_035_30510

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88920.gif


title: H19_Neutro + IFNa_1000U

description: Neutrophils isolated from healthy donor was cultured with 1000U Unterferon for 6 hours

source_name: Neutrophils from Healthy control cultured with Interferon alpha for 6 hours

value: Interferon alpha


title: H19_Neutro + IFNa_100U

description: Neutrophils isolated from healthy donor was cultured with 100U Unterferon for 6 hours


title: PCS60_RNA coimmunoprecipitation_Identify Target Genes_CPCE_053_30510

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88939.gif


title: GUS1_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_224_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88981.gif


title: KHD1_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_245_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/89001.gif


title: H190_Fresh_Neutro


title: DFR1_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_223_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88980.gif


title: RAS1_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_209_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88968.gif


title: SCD6_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_248_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/89004.gif


title: ARP8_RNA coimmunoprecipitation_Identify Target Genes_CPCE_058_30710

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88944.gif


title: BRR6_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_207_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88966.gif


title: H19_Neutro + SLE-249_serum

description: Neutrophils isolated from healthy donor was cultured with serum from a SLE patient for 6 hours

source_name: Neutrophils from Healthy control cultured with SLE serum for 6 hours

value: SLE Patient serum


title: MTQ2_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_222_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88979.gif


title: MOCK_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_243_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88999.gif


title: INP54_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_217_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88974.gif


title: GIS2_RNA coimmunoprecipitation_Identify Target Genes_CPCE_045_30510

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88932.gif


title: H19_Neutro + SLE-243_serum


title: GLO3_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_214_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88973.gif


title: KHD1_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_246_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/89002.gif


title: APL1_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_238_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88994.gif


title: H19_Neutro + SLE-226_serum


title: GCY1_RNA coimmunoprecipitation_Identify Target Genes_CPCE_051_30510

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88937.gif


title: SMY1_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_205_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88964.gif


title: H19_Neutro + SLE-121_serum


title: H19_Neutro + SLE-80_serum


title: SPT5_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_225_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88982.gif


title: H19_Neutro + SLE-205_serum


title: UBP3_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_228_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88985.gif


title: ASF2_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_232_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88988.gif


title: YAP6_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_219_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88976.gif


title: HBS1_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_203_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88962.gif


title: H19_Neutro + Autologous_serum

description: Neutrophils isolated from healthy donor was cultured with autologous serum for 6 hours

source_name: Neutrophils from Healthy control cultured with Autologous serum for 6 hours

value: Autologous serum


title: ACK1_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_233_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88989.gif


title: 663LNA LS3

city: Atlanta

first: Hanjoong

last: Jo

department: Biomedical Engineering

institute: Emory University

description: replicate 3

hyb_protocol: According to Illumina protocol.

scan_protocol: According to Illumina protocol.

data_processing: The miRNA data were quantile-normalized within Illumina GenomeStudio.

source_name: 663LNA LS

label_protocol: According to Illumina protocol.

growth_protocol: HUVEC were cultured and used between passage 5-6.

extract_protocol: Total RNA were extracted from HUVEC using miReasy kit (QIAQEN)

treatment_protocol: HUVEC were transfected with control or miR-663 LNA (100uM) and then subjected to shear stress (oscillatory or laminar shear stress) for one day

value: HUVEC

tag: transfection protocol

value: miR-663 knockdown

tag: shear stress

value: LS


title: LYS1_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_226_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88983.gif

value: Total RNA from lysate after IP


title: H34_Neutro + SLE-150_serum

description: Neutrophils isolated from healthy donor was cultured with serum from a SLE patient for 6 hours

tag: gender


title: 663LNA LS2

description: replicate 2


title: H34_Neutro + SLE-214_serum


title: SSA3_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_227_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88984.gif


title: Control LS3

description: replicate 3

source_name: control LNA LS

value: Control


title: Control LS2

description: replicate 2


title: APL2_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_239_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88995.gif


title: LEU3_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_202_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88961.gif


title: 663LNA LS1

description: replicate 1


title: H34_Neutro + SLE-80_serum

value: Neutrophil


title: HSP26_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_242_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88998.gif


title: H34_Neutro + SLE-60_serum


title: APL4_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_241_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88997.gif


title: Control LS1

description: replicate 1


title: SLK19_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_201_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88960.gif


title: MOCK_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_244_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/89000.gif


title: BUB1_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_229_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88986.gif


title: CRG1_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_218_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88975.gif


title: H235_Fresh_Neutro


title: YER156C_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_213_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88972.gif


title: SNX3_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_212_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88971.gif


title: PAD1_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_221_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88978.gif


title: 663LNA OS3

description: replicate 3

source_name: 663LNA OS

value: OS


title: ARC15_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_208_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88967.gif


title: 663LNA OS1

description: replicate 1


title: H189_Fresh_Neutro

description: Fresh neutrophils isolated from this healthy donor

value: F


title: H234_Fresh_Neutro


title: APL3_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_240_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88996.gif


title: RRI1_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_231_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88987.gif


title: UBC6_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_210_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88969.gif


title: H188_Fresh_Neutro


title: NFS1_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_234_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88990.gif


title: RCA EC 48h rep3

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: mouse RCA endothelium 48hr after-ligation

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

extract_protocol: Total RNA from intima were separately obtained from LCA and RCA at 48 hr post-ligation by quickly flushing QIAzol lysis reagent and miRNeasy mini kit  was used to RNA extration in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Mice were partially ligated in three of four caudal branches of left common carotid artery (LCA). High-resolution in vivo micro-imaging ultrasound was used to examined the induction of low and oscillatory shear stress in LCA with the contralateral RCA as a control.

tag: strain

value: Male

value: endothelium of carotid, contralateral right common carotid artery (RCA)

tag: stress

tag: time

value: 48 hr


title: LCA EC 48h rep1

description: replicate 1

source_name: mouse LCA endothelium 48hr after-ligation

value: endothelium of carotid, left common carotid artery (LCA)

value: flow-disturbed (partial ligation)


title: H92_Fresh_Neutro

tag: cell type

value: control

value: Caucasian


title: H186_Fresh_Neutro

value: African American

tag: treatment


title: RFS1_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_236_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88992.gif


title: LCA EC 48h rep2

description: replicate 2


title: RCA EC 12h rep1

description: replicate 1

source_name: mouse RCA endothelium 12hr after-ligation

extract_protocol: Total RNA from intima were separately obtained from LCA and RCA at 12 hr or 48 hr post-ligation by quickly flushing QIAzol lysis reagent and miRNeasy mini kit  was used to RNA extration in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: 12 hr


title: H187_Fresh_Neutro

value: M


title: RCA EC 48h rep2

description: replicate 2


title: LCA EC 12h rep3

description: replicate 3

source_name: mouse LCA endothelium 12hr after-ligation


title: RCA EC 12h rep3

description: replicate 3


title: RCA EC 12h rep2

description: replicate 2


title: Control OS1

description: replicate 1

source_name: control LNA OS

value: HUVEC


title: Control OS2

description: replicate 2


title: LCA EC 48h rep3

description: replicate 3


title: Control OS3

description: replicate 3


title: LCA EC 12h rep1

description: replicate 1


title: ASH1-Cy5 labeled (1)

description:
Simple annotation: mRNA vs Total RNA Comparison, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78602.gif

source_name: Total mRNA

value: Total mRNA

source_name: ASH1 IVT mRNA

value: ASH1 IVT mRNA


title: H34_Neutro + Autologous_serum

description: Neutrophils isolated from healthy donor was cultured with autologous serum for 6 hours

value: Hispanic

value: Autologous serum


title: RDS2_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_237_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/88993.gif

source_name: Total RNA from lysate after IP

value: Total RNA from lysate after IP

source_name: RNA that co-purified with an RBP


title: H229_Fresh_Neutro

value: Neutrophil


title: P19_neuronal_rep2

city: Nomi

first: Hitoshi

last: Suzuki

state: Ishikawa

address: 1-1 Asahidai

department: CNMT

institute: JAIST

description: Day 07

hyb_protocol: Samples were hybridized with GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix) and scanned at the Kanazawa Medical University.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
RMA expression value derived from Expression Console software; core-exon analysis
program-name = Expression Console
affymetrix-algorithm-name = plier-exon-core : dabg
affymetrix-algorithm-version = 2.0
Probe group file used in analysis = MoEx-1_0-st-v1.r2.pgf

source_name: P19 neuronal cell, Day 7

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: cells were culture in alpha-MEM with 10% FBS under the 5% CO2 condition. cells were treated with 1 µM RA by aggregation culture for 4 days, and were cultured additional 3 days for neuright growth

extract_protocol: total RNA was isolated from P19 cells with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

value: embryonic carcinoma (EC) P19 cell line

tag: agent

value: retinoic acid (RA)

value: Day 7

value: P19 neuronal cell


title: RCA EC 48h rep1

description: replicate 1

value: Male

value: endothelium of carotid, contralateral right common carotid artery (RCA)

value: 48 hr


title: LCA EC 12h rep2

description: replicate 2

value: endothelium of carotid, left common carotid artery (LCA)

value: flow-disturbed (partial ligation)


title: SDP1_RNA coimmunoprecipitation_Identify Target Genes_CPBZ08_247_091809

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2010-07/89003.gif

tag: cell line


title: ASH1-Cy3 labeled (1)

description:
Simple annotation: mRNA vs Total RNA Comparison, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78731.gif

source_name: IVT ASH1 mRNA

value: IVT ASH1 mRNA


title: 663LNA OS2

description: replicate 2

value: HUVEC

value: miR-663 knockdown

value: OS


title: expt.935 extraction2_array1

status: Public on Mar 09 2011

type: genomic

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

description: channel ch1 is input DNA;

hyb_protocol: 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation.   2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization.   3. Hybridize 18hr at 450C with 45 rpm rotation.   4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.

scan_protocol: Standard Affymetrix Array Scanning Protocol was used

data_processing: M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: expt.935 extraction2_array1 channel_1

extract_protocol:
1. Grow cell cultures in large T-flasks (175-225cm2) to a density of~5x106 cells/ml. Combine the content of 2-3 flasks in one. Immediately proceed with the following steps.   2. Add 37% formaldehyde (Sigma) to final concentration 1.8% directly to the culture incubate for 10min at 250C on a rotating or rocking platform.   3. Stop reaction by adding 1.25M glycine pH 7.0 to each culture to the final concentration of 125mM. Mix well, within next 5 min aliquot cell suspension into 50ml falcon tubes and accumulate them on ice.   4. Pellet fixed cells by spinning for 2? at 1500g, +40C. Use swinging bucket rotor.   5. Resuspend each pellet in 5ml of sterile 1xPBS, pool suspensions together.   6. Pellet the cells by spinning for 2? at 1500g, +40C.   7. Resuspend the cells in 10ml of ChIP wash A solution. Transfer suspension to a new 15ml Falcon tube. Wash fixed cells for 10min at +40C using rotating wheel. Pellet as above.   8. Thoroughly resuspend fixed cells in 10ml of  ChIP wash B solution, wash for 10min at +40C. Use rotating wheel.
After treatment with formaldehyde, Drosophila tissue culture cells were lysed with SDS and sonication (on ice) in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.  Ribonucleic acid was removed by RNAse A, and the DNA was purified using SDS, proteinase K, and organic extraction, followed by ethanol precipitation.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

value: CNS-derived cell-line

tag: developmental stage

value: third instar larval stage

tag: genotype

value: y v f mal

tag: Sex

value: Unknown


title: expt.423 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.423 extraction2_array1 channel_1

label_protocol: 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation.   2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization.   3. Hybridize 18hr at 450C with 45 rpm rotation.   4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.

tag: tissue


title: expt.391 extraction5_array1

description: channel ch1 is input DNA;

source_name: expt.391 extraction5_array1 channel_1