title: JAZi VIGS floral stage 1_rep1

description:
JAZi VIGS flower, stage 1, replicate 1
Gene expression in developing flower
JAZi VIGS-1-1


title: il7r-/- larvae at 4dpf rep1

status: Public on Jul 12 2017

type: RNA

city: tianjin

first: shijiao

last: cai

address: Qixiangtai road

country: China

institute: Tianjin Medical University

description: Gene expression data from il7r-/- larvae at 4dpf

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on on Zebrafish Gene 1.0 ST Array. GeneChips were washed and stained in GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip2 Scanner 30007G (Affymetrix).

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

molecule: total RNA

organism: Danio rerio

source_name: il7r-/- zebrafish larvae

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

growth_protocol: Zebrafish larvae were raised at 28.5°C under a 10/14h dark/light cycle . Embryos were collected after natural spawning and staged developmentally by hours post fertilization (hpf) or days post fertilization (dpf).

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

treatment_protocol: We generated il7r-/- homozygous mutant by clustered regularly interspaced short palindromic repeats (CRISPR) / Cas9 technology. Tu and il7r-/- larvae at 4dpf were collected and rinsed with E3 medium . They were put in 1.5 mL RNase tube after discarding excess water and stored in liquid nitrogen.

tag: tissue

value: larvae

tag: age

value: 4 days post hybridization (dpf)

tag: genotype


title: LEC1GR DEX br2

city: Davis

first: John

last: Harada

state: CA

address: One Shields Avenue

department: Plant Biology

country: USA

institute: University of California

hyb_protocol: As per manufacturer's protocol for Eukaryotic Sample and Array Processing, using Affymetrix Fluidics Station 450.

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

data_processing: Probe intensities were summarized using the BioConductor package affy (Rafael. A. Irizarry, Benjamin M. Bolstad, Francois Collin, Leslie M. Cope, Bridget Hobbs and Terence P. Speed (2003), Summaries of Affymetrix GeneChip probe level data Nucleic Acids Research 31(4):e15), using the RMA normalization.

organism: Arabidopsis thaliana

source_name: 8d seedling shoot apices, Dex-treated, 1h

label_protocol: Biotinylated cRNA were prepared using the ENZO BioArray High Yield RNA Transcript Labeling Kit (Farmingdale, NY).

growth_protocol: Plants were grown in a Percival cabinet under 16h day/8h night with fluorescent lamps at 20°C.

extract_protocol: Total RNA was extracted using a hot borate procedure (Stones et. al. PNAS vol 98 no 20: 11806-11811 (2001))

treatment_protocol: Eight-day old seedlings were incubated for 1h in liquid GM media (1X MS salts, 1% sucrose, 1X B5 vitamins pH 5.7) with and without 30uM dexamethasone (DEX). Shoot apices were dissected out, frozen in liquid nitrogen and stored at -80°C.

value: Ws-0 35S:LEC1-GR

tag: developmental stage

value: 8d seedling

value: shoot apices

tag: treatment

value: Dex

tag: time


title: JAZi VIGS floral stage 1_rep3

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

country: Germany

institute: Max-Planck-Institute for Chemical Ecology

description:
JAZi VIGS flower, stage 1, replicate 3
Gene expression in developing flower
JAZi VIGS-1-3

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent platform GPL21138 for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and at 37°C with GE Wash buffer 2 (Agilent) as outlined in the One-Color Microarray-Based Gene Expression Analysis manual (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Data was acquired with the Agilent Scan Control software (version A.7.0.1 for the B scanner) and extracted using the Agilent Feature Extraction software (version 9.5). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. 75 percentile normalization was performed for each array of raw data (keeping the controls in the list). Log transformation was done. Controls were removed from the list. All replicated probes were averaged.

organism: Nicotiana attenuata

source_name: JAZi VIGS flower, stage 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp labeling kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Hilden, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: N. attenuata wild type were grown inclimate chamber with a constant temperature of 20ºC set to a 16 h day/8 h night light regime.

extract_protocol: Total RNA was extracted from leaves using the Plant RNeasy kit (Qiagen, Hilden, Germany) and its quality checked by spectrophotometry (NanoDrop, Wilmington, DE). Genomic DNA was removed by DNAse treatment following commercial instructions (Turbo DNase; Ambion, Europe), RNA was cleaned up with RNeasy MinElute columns (Qiagen) and the RNA quality was checked with the RNA 6000 Nano kit (Agilent, Santa Clara, CA) using an Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: Flowers from stage 1 and 3 in JAZi VIGS and control plants were collected at around 10 am.

tag: genotype/variation

value: JAZi VIGS

tag: Stage

value: floral stage 1

value: leaves


title: FL1GR_4hD_INP4

type: genomic

hyb_protocol: Samples were prepared and hybridized to GeneChip Arabidopsis Tiling 1.0R Array, according to Affymetrix specifications.

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G according to manufacturer's instruction.

data_processing:
Probe signal intensity data was processed and standardized using Model-based Analysis of Tiling-array software (MAT; BandWidth=200, MaxGap=150, MinProbe=8, Tvalue=0) to generate the .bar files containing the matscore for each probe on the array.  The bar files were then used as input for CisGenome v1.2 to call significant regions (sample_peaks.bed) using the HMM algorithm and using a posterior probability (PP) > 0.99999 as threshold.
BAR files contain standardized probe intensity generated with Model-based Analysis of Tiling-array software (MAT; BandWidth=200, MaxGap=150, MinProbe=8, Tvalue=0).  BED files contain the peaks called using CisGenome (v1.2) HMM algorithm, posterior probability > 0.99999.  Chromosomal locations refer back to the TAIR8 genome assembly.

molecule: genomic DNA

source_name: 8d sdlg, 4h DEX

label_protocol: ChIP and Input control DNAs were prepared according to O'Geen, Nicolet, Bahnik, Green and Farnham, BioTechniques 41:577-580 (November 2006). 7.5 ug of DNA were fragmented to an average size of 100bp using RQ1 DNAseI (Promega), biotin-labelled using Affymetrix GeneChip WT Double Stranded DNA Terminal Labelling kit and following the manufacturer's instructions.

extract_protocol: Chromatin isolation and immunoprecipitation were performed as described in Gendrel AV, Lippman Z, Martienssen R, Colot V. Nat Methods. 2005;2:213–218, except that the isolated nuclei were resuspended in lysis buffer described in by Johnson et al. (2002) and sonicated to achieve chromatin fragments ranging from 100 to 500 bp.  Nuclear extracts were either set aside for whole genome extracts (input control) or incubated overnight with 10ug of the anti-FLAG (Sigma F1804) antibody.  Crosslinks were reversed and protein digested as in Dahl and Collas, Nat Protoc. 2008;3(6):1032-45, extracted with phenol:chloroform and precipitated using standard procedures.

treatment_protocol: 35S:FLAG-LEC1-GR seedlings were either (1) grown for 8 days on GM media (1X MS salts, 1% sucrose, 1X B5 vitamins, 0.8% Bactoagar, pH 5.7) and incubated for 4h in liquid GM media (same as solid, without Bactoagar) containing 30uM dexamethasone (DEX) or (2) germinated and grown on solid GM media containing 30 uM DEX for 8 days.  Tissues were crosslinked under vaccuum for 10 minutes in Buffer A (0.4M sucrose, 10 mM Tris pH 8.0, 1mM EDTA pH 8.0) containing 1% formaldehyde, at room temperature, then quenched in 100 mM Glycine for 5 minutes.  Crosslinked tissues were rinsed twice with deionized water, ground in liquid nitrogen and stored at -80C until use.

value: Ws-0, 35S:FLAG-LEC1-GR

value: DEX

tag: antibody


title: FL1GR_8dD_FLAG1

source_name: 8d sdlg, 8d DEX, anti-FLAG

value: anti-FLAG


title: FL1GR_4hD_INP3


title: LEC1GR NoDEX br2

source_name: 8d seedling shoot apices, uninduced

value: no Dex


title: Sir3_WT_Expo_Gal_r2

city: Paris

first: Angela

last: Taddei

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: ChIP anti-Sir3 in WT exponentially S.cerevisiae cells growing inYP galactose medium

hyb_protocol: 16 hours at 65°C in the 1X hybridization buffer supplied by Agilent

scan_protocol: Agilent G2565BA microarray scanner. GenePix6.0 software

data_processing: Array was normalized using values corresponding to mitochondrial DNA probes, annotated chrM. .txt files on the sample records contain the normalized Cy5/Cy3 ratios representing ChIP/input.

organism: Saccharomyces cerevisiae

source_name: ChIP anti-Sir3 WT Galactose replicate 2

label_protocol: 4/5 of the immunoprecipitated DNA and 3/5 of the DNA from the whole cell extract were amplified by random primer extension followed by PCR amplification, incorporating amino-allyl dUTP for subsequent dye coupling

growth_protocol: 3 ml YPD culture were inoculated and allowed to grow in YPD for 10 hours. Those cultures were used to inoculate YP Raffinose (3%, i.e 30g/L) at 0.01 O.D. those overnight cultures were used to inoculate 50ml cultures of YP Raffinose 3% at an OD =0.2 . Exponentialy growing cultures were allowed to grow for an additional 2 hours, after which Galactose was added to reach a final concentration of 2 %. Cells were pelleted exactly 2 hours after galactose addition.

extract_protocol: A total of 20 660nm O.D equivalent of cells were fixed in 20 mL with 0.9 % formaldehyde for 15 min at 30°C, quenched with 0.125 M glycine and washed twice in cold TBS 1x pH 7.6. Pellets were suspended in 1mL TBS 1X, centrifuged and frozen in liquid nitrogen for -80°C storage. All following steps were done at 4°C unless indicated. Pellets were re-suspended in 500 µL of lysis buffer (0.01% SDS, 1.1% TritonX-100, 1.2 mM EDTA pH 8, 16.7 mM Tris pH8, 167 mM NaCl, 0.5 % BSA, 0.02 g.L-1 tRNA and 2.5 µL of protease inhibitor from SIGMA P1860) and mechanically lysed by three cycles of 30 s with 710-1.180 µm glass beads followed by two cycles of 30 s with 500 µm zirconium/silica beads (Biospec Products) using a Fastprep instrument (MP Biomedicals). Each bead beating cycle was followed by 5 min incubation on ice. The chromatin was fragmented to a mean size of 500 bp by sonication in the Bioruptor XL (Diagenode) for 14 min at high power with 30 s on / 30 s off and centrifuged 5 min at 13 000 rpm. 10 µL were kept to be used as Input DNA. Cleared lysate was incubated overnight with 1 µL of polyclonal antibody anti-Sir3 (Agro-bio). 50 µL of magnetic beads protein A (NEB) were added to the mixture and incubated for 4h at 4°C. Magnetic beads were washed sequentially with lysis buffer, twice with RIPA buffer (0.1% SDS, 10mM Tris pH7.6, 1mM EDTA pH8, 0,1% sodium deoxycholate and 1% TritonX-100), twice with RIPA buffer supplemented with 300 mM NaCl, twice in LiCl buffer (250 mM LiCl, 0.5% NP40, 0.5 % sodium deoxycholate), with TE 0.2% TritonX-100 and with TE. Input were diluted 10x with elution buffer (50mM Tris, 10mM EDTA pH8, 1%SDS) and beads were re-suspended in 100 µL elution buffer. A reversal cross-linking was performed by heating samples overnight at 65°C. Proteins were digested with proteinase K in presence of glycogen and the remaining DNA was purified on QIAquick PCR purification columns. Finally, samples were treated with 29 µg.mL-1 RNAse A 30 min at 37°C.

tag: strain

source_name: Whole cell extract

growth_protocol: For exponentially growing cells, cells were precultured overnight in YPD, and grown from 0.2 to 1 O.D in rich medium (YPD) at 30°C.


title: Sir3_SIR3oe_Expo_Gal_r2

description: ChIP anti-Sir3 in strain overexpressing SIR3; exponentially S.cerevisiae cells growing inYP galactose medium

source_name: ChIP anti-Sir3 SIR3oe Galactose replicate 2

growth_protocol: For stationnary phase cells, cells were precultured overnight in YPD, and cultures were inoculated at the density of 0.2 OD, for 7 days at 30 °C with shaking (225rpm). The dense fraction was isolated by density gradient fractionnation in Percoll (Sigma Aldrich)


title: Control floral stage 3_rep2

description:
Control flower, stage 3, replicate 2
Gene expression in developing flower
Control-3-2

source_name: Control flower, stage 3

value: Control

value: floral stage 3


title: il7r-/- larvae at 4dpf rep2


title: Control floral stage 1_rep1

description:
Control flower, stage 1, replicate 1
Gene expression in developing flower
Control-1-1

source_name: Control flower, stage 1


title: Sir3_SIR3oe_Expo_Gal_r1

source_name: ChIP anti-Sir3 SIR3oe Galactose replicate 1


title: Control floral stage 3_rep1

description:
Control flower, stage 3, replicate 1
Gene expression in developing flower
Control-3-1


title: JAZi VIGS floral stage 3_rep1

description:
JAZi VIGS flower, stage 3, replicate 1
Gene expression in developing flower
JAZi VIGS-3-1

source_name: JAZi VIGS flower, stage 3


title: Control floral stage 3_rep3

description:
Control flower, stage 3, replicate 3
Gene expression in developing flower
Control-3-3


title: Control floral stage 1_rep2

description:
Control flower, stage 1, replicate 2
Gene expression in developing flower
Control-1-2


title: LEC1GR DEX br1


title: Sir3_WT_Expo_Gal_r1

source_name: ChIP anti-Sir3 WT Galactose replicate 1


title: Tu larvae at 4dpf rep2

description: Gene expression data from  TU larvae at 4dpf

source_name: Tu zebrafish larvae

value: Tu


title: FL1GR_4hD_FLAG3

source_name: 8d sdlg, 4h DEX, anti-FLAG


title: JAZi VIGS floral stage 3_rep2

description:
JAZi VIGS flower, stage 3, replicate 2
Gene expression in developing flower
JAZi VIGS-3-2


title: LEC1GR NoDEX br1


title: FL1GR_4hD_FLAG4


title: RA3

city: liaocheng

first: Min

last: Yuan

address: 67 dongchang xi road

institute: liaocheng people's hospital

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

organism: Homo sapiens

source_name: peripheral blood mononuclear cells, rheumatoid arthritis

label_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: RNA was extracted by TRIzol® Reagent (Invitrogen Life Technologies), and RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

tag: disease state

value: rheumatoid arthritis

tag: cell type

value: peripheral blood mononuclear cells

tag: gender

value: female


title: HC2

source_name: peripheral blood mononuclear cells, healthy control

value: healthy


title: pancreatic ductal adenocarcinoma (PDAC) tumor tissue lncRNA/mRNA 5

status: Public on Jul 11 2017

city: Shanghai

first: Xing

last: Liang

state: Shanghai

address: No.415 Fengyang Road, Shanghai, China

department: Department of Pancreatic-biliary Surgery

institute: Shanghai Changzheng Hospital, China

description: lncRNA and mRNA expression data from pancreatic ductal adenocarcinoma (PDAC) tumor tissue

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x60K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505B

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). GO analysis and Pathway analysis were performed in the standard enrichment computation method.

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: PDAC and matched non-tumor tissues

treatment_protocol: Tissues from PDAC surgury were immediately frozen with TRIzol reagent (Invitrogen) in liquid nitrogen as soon as cutting off at the time of surgery, and then stored at -80℃ until required

value: PDAC tumor tissue


title: HC1


title: pancreatic ductal adenocarcinoma (PDAC) tumor tissue lncRNA/mRNA 4


title: pancreatic ductal adenocarcinoma (PDAC) tumor tissue lncRNA/mRNA 2


title: matched non-tumor tissue of pancreatic ductal adenocarcinoma (PDAC) lncRNA/mRNA 3

description: lncRNA and mRNA expression data from matched non-tumor tissue of pancreatic ductal adenocarcinoma (PDAC)

value: matched non-tumor tissue of PDAC


title: pancreatic ductal adenocarcinoma (PDAC) tumor tissue lncRNA/mRNA 3


title: siRNA-1

city: Guangzhou

first: Dong-liang

last: Chen

address: No.651 Dong Feng East Road

institute: Sun Yat-sen University Cancer Center

description: SW620 cells transfected with siRNA of UICLM

hyb_protocol: cDNA was then labeled and hybridized to the mRNA Expression Microarray (Arraystar 8x60Kv3.0, Rockville, USA) according to the manufacturer’s protocol.

scan_protocol: After hybridization, the arrays were washed, and the slides were scanned with a Agilent Microarray Scanner (Agilent p/n G2565BA).

data_processing: Raw data were extracted as pair files using the Agilent Feature Extraction. The random variance model was used to identify the differentially expressed genes. The threshold set for up and down-regulated genes was a fold change >=4.0 and a p-value <= 0.05, respectively.

label_protocol: not provided.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.

tag: cell line

value: siRNA


title: A549 0Gy for 3days

city: Seoul

first: Su

middle: Jae

last: Lee

state: Haengdang- Dong, Seongdong-Gu

address: 222, Wangsimni-ro

department: Life science

country: South Korea

institute: Hanyang University

description: miRNA

hyb_protocol: Agilent protocol

scan_protocol: Agilent protocol

data_processing: Agilent Feature Extraction

label_protocol: Agilent protocol

growth_protocol: A549 cells was grown in RPMI. RPMI culture media were supplemented with 10% fetal bovine serum, penicillin (100U/mL), and streptomycin (100μg/mL). Cells were passaged at every three days to maintain healthy cell condition.

extract_protocol: Total RNA including miRNAs was extracted from each group of cells using TRIzol reagent (Invitrogen; Thermo Fisher Scientific Incorporation, Waltham, MA, USA).

treatment_protocol: A549 cells was exposed to fractionated dose of radiation (2 Gy x 3; 2 Gy/day for 3 days).

value: Non-small cell lung cancer

value: male


title: matched non-tumor tissue of pancreatic ductal adenocarcinoma (PDAC) lncRNA/mRNA 1


title: siRNA-2


title: HC3


title: pancreatic ductal adenocarcinoma (PDAC) tumor tissue lncRNA/mRNA 1


title: NC-2

description: SW620 cells

value: control


title: 4T1CH9 MURINE TNBC VEH2

city: Melbourne

first: Sathana

last: Dushyanthen

address: 305  Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

description:
Affymetrix MG-430PM
Mouse tumor ex vivo, bulk RNA

hyb_protocol: cDNA was hybridized to Affymetrix Mouse Genome 430PM strip arrays for 16 hours at 45ºC.Washing and staining of microarrays was performed using the GeneAtlas Fluidics Station (Affymetrix, Santa Clara, CA)

scan_protocol: GeneChips were scanned in a GeneAtlas Imaging Station (Affymetrix, Santa Clara, CA)

data_processing: RMA normalization method, GeneGo, GSEA

label: Biotin

organism: Mus musculus

source_name: 4T1CH9 TNBC

label_protocol: BIOTIN, as per manufacturer (Affymetrix)

growth_protocol: MFP injection in vivo 5e4, growth and establishment for 10 days followed by 7 days of treatment.

extract_protocol: RNA extraction,  PureLink RNA Mini Kit

treatment_protocol: Vehicle versus Trametinib (1mg/kg) treatment in  vivo for 7 days

tag: sample type

value: Triple negative breast cancer


title: RA1


title: NC-3

description: SW620 cells


title: siRNA-3


title: RA2


title: matched non-tumor tissue of pancreatic ductal adenocarcinoma (PDAC) lncRNA/mRNA 5


title: 4T1CH9 MURINE TNBC MEK2


title: matched non-tumor tissue of pancreatic ductal adenocarcinoma (PDAC) lncRNA/mRNA 4


title: A549 2Gy for 3days

description: miRNA


title: 4T1CH9 MURINE TNBC VEH1


title: term_amniotic_fluid_MMC 1

city: Boston

first: Tomo

last: Tarui

state: MA

address: 800 Washington St.

department: Pediatric Neurology

institute: Tufts Medical Center

description: gene expression data from control

hyb_protocol: Arrays were washed and stained with streptavidin-phycoerythrin.

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

data_processing: Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method.  Identification of individual differentially-expressed genes was performed via two-sided, paired t-tests using the multtest package in BioConductor, with the Benjamini-Hochberg adjustment for multiple testing.

source_name: cell free mRNA from term amniotic fluid

label_protocol: Samples were labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN, San Carlos, CA).

extract_protocol: RNA was extracted from 10 mL AF with 30 mL TRIzol LS Reagent (Invitrogen, Carlsbad, CA) and 8 mL chloroform. After RNA extraction, RNA was purified and DNA was removed using the RNeasy® Maxi Kit, including the DNase step according to the manufacturer’s protocol (QIAGEN, Valencia, CA).  RNA was precipitated using 3M NaOAc and 100% ethanol, and 80% ethanol was added after 4 hours incubation at -20 °C. cDNA, synthesized from extracted RNA, was amplified and purified using the WT-Ovation™ Pico RNA Amplification System (NuGEN, San Carlos, CA) and the DNA Clean & Concentrator™-25 (Zymo Research, Orange, CA).

tag: gestational age

value: Second Trimester Control


title: second_trimester_amniotic_fluid_control

description: gene expression data from control


title: 4T1CH9 MURINE TNBC MEK1


title: matched non-tumor tissue of pancreatic ductal adenocarcinoma (PDAC) lncRNA/mRNA 2


title: NC-1

description: SW620 cells


title: strainB_refrigerated

city: Ikoma

first: Daisuke

last: Watanabe

state: Nara

address: 8916-5 Takayamacho

country: Japan

institute: Nara Institute of Science and Technology

description: Gene expression during model dough fermentation of strain B cells after refrigerating preservation

hyb_protocol: By using the Gene Expression Hybridization Kit (Agilent), 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 24 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Technologies Yeast (v2) Gene Expression 8x15K Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with Wash Buffer 1and 1 minute at 37°C with Wash Buffer 2 of the Gene Expression Wash Buffer (Agilent), then air-dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (Scan resolution 5 um, TIFF file dynamic change 20 bit).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent). The data were imported to the GeneSpring software and normalized by 75 percentile shift.

source_name: strainB, refrigerated

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini Kit (Qiagen).  Dye incorporation and cRNA yield were checked with the Agilent 2100 BioAnalyzer series II and the NanoDrop 1000 Spectrophotometer.

extract_protocol: Total RNA was prepared from whole cell lysate using the RNeasy Mini Kit (Qiagen). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: Yeast cells were precultured in YPD medium at 30°C and washed with distilled water. Wet yeast pellets were stored in the refrigerator (4°C) or in the freezer (-20°C) for two weeks. Approximately 0.4 g of yeast cells were inoculated into 30 mL of ASF medium, which consists of 23 g of sucrose, 2 g of urea, 1 g of ammonium sulfate, 0.8 g of magnesium sulfate, 1.6 mg of thiamine hydrochloride, 1.6 mg of pyridoxine hydrochloride, 16 mg of nicotinic acid in total 350 mL of 67 mM potassium phosphate buffer (pH 5.6), and incubated at 30°C. After 30 min after inoculation, yeast cells were collected, washed, and immediately frozen using liquid nitrogen.

value: strain B

tag: preservation

value: refrigerated


title: strainB_frozen

description: Gene expression during model dough fermentation of strain B cells after freezing preservation

source_name: strainB, frozen

value: frozen


title: strainA_refrigerated

description: Gene expression during model dough fermentation of strain A cells after refrigerating preservation

source_name: strainA, refrigerated

value: strain A


title: strainA_frozen

description: Gene expression during model dough fermentation of strain A cells after freezing preservation

source_name: strainA, frozen


title: Huh7.5_IRF9_12h_IFNa

status: Public on Jul 08 2017

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

hyb_protocol: Labelled cRNA were hybridized onto Affymetrix Human Gene ST 1.0 chips according to the manufacturer's protocoll

scan_protocol: Arrays were washed and stained with GeneChip Fluidics Station 450 and scanned with GeneChip Scanner 3000 using the GeneChip Operating Software (Affymetrix).

data_processing: R/Bioconductor using oligo package and summarized to transcripts

label_protocol: To generate cDNA, 1 ug of total RNA was transcribed using a QuantiTect reverse transcription kit (Qiagen).

growth_protocol: Huh7.5 cells (a kind gift from C. M. Rice, Laboratory of Virology and Infectious Disease, Rockefeller University, NY) were cultivated in Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (Invitrogen) and 1% penicillin⁄streptomycin (Invitrogen).

extract_protocol: RNeasy Mini Plus Kit (Qiagen, Hilden, Germany)

treatment_protocol: One day before commencement of a time-course experiment, 1.7 · 10^6 cells were seeded into 6 cm dishes. Prior to stimulation with IFNa, the cells were washed three times by removing the culture medium and replacing it with DMEM, and afterwards cultivated in starvation medium for 3 h [DMEM supplemented with 1 mg/mL BSA (Sigma-Aldrich, St Louis, MO, USA) and 25 mm Hepes pH 7.0 (Invitrogen)]. To stimulate cells, human leukocyte IFNa (R&D Systems, Minneapolis, MN, USA) was added to the medium to a final concentration of 500 U/mL. For each time point, the contents of one dish were lysed using 1% Nonidet P-40 lysis buffer (1% Nonidet P-40, 150 mm NaCl, 20 mm Tris pH 7.4, 10mm NaF, 1mm EDTA pH 8.0, 1mm ZnCl2 pH 4.0, 1 mm MgCl2, 1 mm Na3VO4, 10% glycerol, freshly supplemented with 2 ug/mL aprotinin and 200 ug/mL 4-(2-aminoethyl)-benzensulfonylfluoride)

tag: tissue

value: Liver

tag: disease

value: Hepatocellular carcinoma

tag: overexpression

tag: stimulus

value: IFNa


title: Huh7.5_WT_4h_IFNa


title: Huh7.5_IRF9_8h_ctl


title: Huh7.5_IRF9_2h_IFNa


title: Huh7.5_IRF9_8h_IFNa


title: Huh7.5_IRF9_1h_IFNa


title: Huh7.5_WT_3h_IFNa


title: Huh7.5_IRF9_24h_ctl


title: Huh7.5_WT_1h_IFNa


title: Huh7.5_IRF9_3h_IFNa


title: Huh7.5_WT_2h_IFNa


title: Huh7.5_IRF9_24h_IFNa


title: Huh7.5_IRF9_1h_ctl


title: Huh7.5_IRF9_12h_ctl


title: Huh7.5_WT_12h_IFNa


title: Huh7.5_IRF9_4h_ctl


title: Huh7.5_IRF9_4h_IFNa


title: Huh7.5_IRF9_0h_ctl


title: Huh7.5_IRF9_2h_ctl


title: Huh7.5_IRF9_3h_ctl


title: Huh7.5_WT_24h_IFNa


title: Huh7.5_WT_8h_IFNa


title: Huh7.5_WT_12h_ctl


title: Huh7.5_WT_24h_ctl


title: D0-1-249 vs IgG 249_251470710581

status: Public on Jul 10 2017

city: New Orleans

first: HUA

last: LU

state: LA

address: 1430 Tulane Ave

department: Biochemistry and Molecular Biology

institute: TULANE UNIVERSITY

hyb_protocol: Following the Agilent ChIP-on-chip Analysis Protocol Version V11.0

scan_protocol: Scanned on an Agilent G4489A scanner.

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

source_name: reference

growth_protocol: PLC/PRF/5 cells were cultured in DMEM complemented with 10% FBS and under 5% CO2.

extract_protocol: The genomic DNA extraction and ChIP procedures were performed following the Agilent ChIP-on-CHIP analysis protocol Version 11.0.

value: IgG

value: PLC-PRF-5 Human liver hepatoma cell line

source_name: test

value: anti-p53 antibody DO-1


title: D0-1-249 vs IgG 249_251470610638

label_protocol: Following the Agilent ChIP-on-chip Analysis Protocol Version V11.0


title: Huh7.5_WT_3h_ctl


title: Huh7.5_WT_8h_ctl


title: Huh7.5_WT_2h_ctl


title: Huh7.5_WT_1h_ctl


title: Huh7.5_WT_0h_ctl


title: Huh7.5_WT_4h_ctl


title: R.coptidis Shihzu treated vs. DMSO

status: Public on Jul 07 2017

city: Beijing

first: Juan

last: Feng

address: No.30, Shuangqing Road, Haidian District

department: School of Medicine

institute: Tsinghua University

description: Analysis used DMSO-treated RNA as control samples for comparison to the experimental samples treated with R.coptidis from Dayi, Lichuan, Shizhu, Yaan and R.serra from Yunnan.

hyb_protocol: Arrays were hybridized was preformed in a CapitalBio BioMixerTM II Hybridization Station overnight at a rotation speed of 8 rpm and a temperature of 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: confocal LuxScanTM scanner and the images obtained were then analyzed using LuxScanTM 3.0 software (Both from CapitalBio)

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: R.coptidis Shihzu treated

label_protocol: 2 μg amplified RNA was mixed with 4 μg random nanomer, denatured at 65℃ for 5min, and cooled on ice. Then, 5 μL of 4×first-strand buffer, 2 μL of 0.1M DTT, and 1.5 μL CbcScript Ⅱ reverse transcriptase were added. The mixtures were incubated at 25℃ for 10 min, then at 37℃ for 90 min. The cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and vacuum evaporated to 14 μL. The cDNA was mixed with 4 μg random nanomer, heated to 95℃ for 3 min, and snap cooled on ice for 5 min. Then, 5 μL Klenow buffer, dNTP, and Cy5-dCTP or Cy3-dCTP (GE Healthcare) were added to final concentrations of 240 μM dATP, 240 μM dGTP, 240 μM dTTP, 120 μM dCTP, and 40 μM Cy-dCTP. 1.2 μL Klenow enzyme was then added, and the reaction was performed at 37℃ for 90 min. Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer. Labeled controls and test samples were quantitatively adjusted based on the efficiency of Cy5-dCTP or Cy3-dCTP incorporation and dissolved in 80 μl hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray

growth_protocol: HepG2 cells  were maintained in high-glucose Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 units/mL penicillin, and 100 mg/mL streptomycin at 37°C in a humidified incubator under 5% carbon dioxide.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: HepG2 cells  were treated R.coptidis or R.serra extracts for 24 h at a dose of 75 µg/mL. DMSO (1‰）was set as the control group.

source_name: DMSO-treated


title: R.coptidis Dayi treated vs. DMSO

source_name: R.coptidis Dayi treated


title: R.coptidis Lichuan treated vs. DMSO

source_name: R.coptidis Lichuan treated


title: R.coptidis Yaan treated vs. DMSO

source_name: R.coptidis Yaan treated


title: wf#6

city: Koganei

first: Taira

last: Miyahara

state: Tokyo

address: 2-24-16 Nakacho

institute: Tokyo university of agriculture and technology

hyb_protocol: Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent chicken V2 Oligo 4×44K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing: Scanned images are analyzed by Feature extraction 11.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.

organism: Gallus gallus

source_name: leukocyte, wild type, 1-2 old, replicate3

label_protocol: 1.65 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes.

extract_protocol: Total RNA was extracted from leukocyte by using RNeasy ® (QIAGEN) according to the manufacturer’s recommendations. RNA quantity and quality was monitored by 260nm absorption and electrophoresis (Bioanalyzer 2000, Agilent).

treatment_protocol: Chicken blood was collected from the wing vein on 77 mM EDTA-PBS (pH7.4), and collectrd blood was mixed 7.7 mM EDTA-PBS (pH7.4) ar a 1:1 ratio. The blood was then layered on a Ficoll-Paque density rradient (Phamacis Biotech) and centrifuged at 740 xg for 10 min. The cells recovered from interface were washed with PBS and used as chicken leukocytes.

value: female

value: leukocyte

value: wild type


title: wf#4

source_name: leukocyte, wild type, 1-2 old, replicate1


title: tf#1

source_name: leukocyte, transformant, 1-2 old, replicate1

value: hetero GFP transformant


title: R.serra Yunnan treated vs. DMSO

source_name: R.serra Yunnan treated


title: wf#3

description: female

source_name: leukocyte, female, 1-2 old, replicate3


title: wf#5

source_name: leukocyte, wild type, 1-2 old, replicate2


title: wm#1

description: male

source_name: leukocyte, male, 1-2 old, replicate1

value: male


title: wf#2

description: female

source_name: leukocyte, female, 1-2 old, replicate2


title: tf#3

source_name: leukocyte, transformant, 1-2 old, replicate3


title: wm#3

description: male

source_name: leukocyte, male, 1-2 old, replicate3


title: tf#2

source_name: leukocyte, transformant, 1-2 old, replicate2


title: wm#2

description: male

source_name: leukocyte, male, 1-2 old, replicate2


title: MCF7 treated, biological rep 3

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

institute: IGBMC

hyb_protocol: Following fragmentation and end-labeling, 3 μg of cDNAs were hybridized for 16 hours at 45°C on GeneChip® Human Gene 1.0 ST arrays. The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix)

scan_protocol: The chips were scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

data_processing: Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Operating System (GCOS) version 1.4. CEL files were further processed with Affymetrix Expression Console software version 1.1 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings.

source_name: MCF7 cells treated with Delta-2-TGZ treated 25 µM for 12H

label_protocol: Biotinylated single strand cDNA targets were prepared, starting from 250 ng of total RNA, using the Ambion WT Expression Kit (Cat # 4411974) and the Affymetrix GeneChip® WT Terminal Labeling Kit (Cat # 900671) according to Affymetrix recommendations.

growth_protocol: MCF-7 cells were cultured at 37°C under 5% CO2 in DMEM media

extract_protocol: Total RNA were extracted using Rneasy Mini Kit from Qiagen according to manufacturer's intructions

treatment_protocol: MCF-7 cells were culture in 6 well-plated for 12h in presence of DMSO or Delta-2-TGZ


title: Avian  DCs stimulated with AIV

city: nanjing

first: Jian

last: Lin

state: jiangsu

address: tongwei road N0.1

department: Life Science

institute: nanjing agricultural university

description: Total RNA  was extracted from cultured DCs stimulated for IBDV.

hyb_protocol: pre-hybridization:  1)Assembled  CustomArray™ microarray with Hybridization Cap and Clips；  2)Fill the hybridization chambers with nuclease-free water.Avoid introducing air bubbles into the chambers. Cover the solution portals with adhesive tape to evaporation.  3)Incubate at 65°C for 10min.  4)Remove the microarray from the incubator and bring to room temperature.Remove the adhesive tape and aspirate the water out of the hybridization chambers.  5)Fill the hybridization chambers with Pre-hybridization Solution.Mix gently by pipetting.A small air bubble can be introduced to improve the mixing process if the arrays are rotated.Wipe the surface clean with a lint-free tissue and cover the solution portals with adhesive tape.  6)Load the microarry onto the rotisserie in the hybridization oven and incubate at 37°C for 60 min with gentle rotation.    Hybridization:  1)Prepare the hybridization solution with labeled mRNA target .  2)Denature the hybridization solution at 95°C for 3 minutes,and then cool for 20 seconds on ice.Remove the hybridization solution from ice and keep it at room temperature.  3)Spin down the hybridization solution in a microcentrifuge for 5 seconds at maximum speed.  4)Remove the adhesive tape and pipet the pre-hybridization solution out of the hybridization chambers.  5)Fill the hybridization chambers with the hybridization solution and mix gently with repeated pipetting.A small air bubble wil form,and it will improve the mixing process if the arrays are rotated in the hybridization rotisserie oven.  6)Carefully wipe excess solution from the surface of the hybridization cap with a lint-free tissue,and cover the solution portals with adhesive tape.  7)Load the microarry onto the rotisserie in the hybridization oven and incubate at 37°C for 16 hours with gentle rotation.    Hybridization washing:  1)Remove the microarray from the hybridization oven.Remove the adhesive tape and pipet the hybridization solution out of the chambers.  2)Using the Wash solution 1,rinse the hybridization chambers,fill the chambers,and incubate the array for 3 minutes at room temperatrue.Remove the Wash solution 1 from the hybridization chambers.  3)Using the Wash solution 2,rinse the hybridization chambers,fill the chambers,and incubate the array for 3 minutes at room temperatrue.Remove the Wash solution 2 from the hybridization chambers.  4)Using the Wash solution 3,rinse the hybridization chambers,fill the chambers,and incubate the array for 3 minutes at room temperatrue.Remove the Wash solution 3 from the hybridization chambers.  5)Repeat step one more time for a total of two washings with the Wash solution 3.

scan_protocol: Imaging is done by laser scanner GenePix4000B(Molecular Device). At first, remove the microarray from the clamp and place it horizontally. Then cover the semiconductor microarray surface with the imaging solution. Using a fresh lifterslip cover it,taking care not to introduce air bubbles. At last, load the microarray into the scanner to scan.

data_processing: Raw signals were normalized with subtract background correction and quantile normalization method, Normalized intensities were transformed to gene expression log2 value. Ratio and log2 ratio of normalized spot intensites between test sample and control sample were calculated. The p-values are calculated with ANOVA Method(O'Mahony, Michael (1986). Sensory Evaluation of Food: Statistical Methods and Procedures. CRC Press. pp. 487. ISBN 0-8247-7337-3). It means the probability of control sample and test sample are no differential expression. So, if p-value (Differentially expressed) is greater than thethreshold it means no differential expression was observed.

source_name: avian dendritic cells

label_protocol: Samples were labled with ULS-Cy5.  The labeling efficiency can be calculated by the concentration of CyDye and RNA measured by spectrophotometer. For good  microarray result, the recommended labeling efficiency is 1.0~3.6.

growth_protocol: Avian BMDCs were generated and expanded in vitro by culturing bone marrow precursors with 50 ng/ml recombinant chicken GM-CSF (Abcam, USA) and 50 ng/ml IL-4（Kingfisher, USA) and in the RPMI 1640 medium supplemented with 10% fetal bovine serum (Gibco), penicillin (100 U/ml), and streptomycin (100 μg/ml) under a humidified atmosphere containing 5% CO2 maintained at 37 ˚C.

extract_protocol: Total RNA was separately isolated using the RNeasy total RNA isolation kit (QIAGEN).  Microarray was hybridized and raw data were normalized using the RMA method

treatment_protocol: At day 6, the non-adherent, relatively immature DCs were harvested and plated in fresh medium (1×106 cells/ml) . Then,cultured avian BMDCs were randomly divided into control group and AIV stimulated group. Each group consisted of three wells of BMDCs from three chickens.

value: chicken dendritic cells


title: Wild-type_4

city: Kiel

first: Ashraf

middle: Yusuf

last: Rangrez

address: Arnold-Heller Str. 3 (Haus 6)

institute: University Medical Center Kiel

description: microRNAs from wild-type mice to be used as control

hyb_protocol: Hybridization is performed at 58°C, in GEX-HCB buffer (Illumina Inc.) at a concentration of 100 ng cRNA/µl, unsealed in a wet chamber for 20h. Spike-in controls for low, medium and highly abundant RNAs were added, as well as mismatch control and biotinylation control oligonucleotides. Microarrays were washed twice in E1BC buffer (Illumina Inc.) at room temperature for 5 minutes. After blocking for 5 min in 4 ml of 1% (wt/vol) Blocker Casein in phosphate buffered saline Hammarsten grade (Pierce Biotechnology, Inc., Rockford, IL), array signals are developed by a 10-min incubation in 2 ml of 1 µg/ml Cy3-streptavidin (Amersham Biosciences, Buckinghamshire, UK) solution and 1% blocking solution. After a final wash in E1BC, the arrays are dried and scanned.

scan_protocol: Microarray scanning was done using a Beadstation array scanner, setting adjusted to a scaling factor of 1 and PMT settings at 430. Data extraction was done for all beads individually, and outliers are removed when > 2.5 MAD (median absolute deviation). All remaining data points are used for the calculation of the mean average signal for a given probe, and standard deviation for each probe was calculated.

data_processing: Data analysis was done by normalization of the signals using the quantile normalization algorithm without background subtraction, and differentially regulated genes are defined by calculating the standard deviation differences of a given probe in a one-by-one comparisons of samples or groups.

source_name: Mouse heart

label_protocol: Biotin-labeled cRNA samples for hybridization on Illumina Mouse Sentrix-6 BeadChip arrays (Illumina, Inc.) were prepared according to Illumina's recommended sample labeling procedure based on the modified Eberwine protocol.

extract_protocol: Total RNA was isolated from the hearts of Calsarcin-1 knockout and wild-type mice using QIAzol lysis reagent accord-ing to the manufacture's instruction (Qiagen).

tag: genotype

value: Calsarcin-1 wild-type

value: heart


title: Calsarcin-1-ko_4

description: microRNAs from Calsarcin-1 knockout mice

value: Calsarcin-1 knockout


title: wf#1

description: female

source_name: leukocyte, female, 1-2 old, replicate1


title: Wild-type_2


title: Wild-type_3


title: MCF7 treated, biological rep 1


title: Wild-type_1


title: Calsarcin-1-ko_2


title: MCF7 control, biological rep 3

source_name: Control MCF7 cells not treated


title: Calsarcin-1-ko_1


title: MCF7 treated, biological rep 2


title: Calsarcin-1-ko_3


title: MCF7 control, biological rep 1


title: MCF7 control, biological rep 2


title: D_TRF+H2O2+TRF_rep3

status: Public on Jul 06 2017

city: CHERAS

first: NORALISA

last: ABDUL KARIM

state: KUALA LUMPUR

address: JALAN YAACOB LATIFF

department: CELL THERAPY CENTRE

country: Malaysia

institute: UKM MEDICAL CENTRE

description: TRF treatment pre- and post- H2O2 induction. TRF treatments were given from hatching until day 3 of adulthood

hyb_protocol: The biotin-labeled amplified RNA (aRNA) was then fragmented before being hybridized onto the genome array. The hybridization controls was used to monitor the hybridization quality, which composed of a mixture of biotinylated and fragmented cRNA of bioB, bioC, bioD and cre prepared in staggered concentrations (1.5, 5, 25, and 100 pM respectively). Using Affymetrix Genechip C. elegans Genome Array, 22 625 transcripts were screened for changes in expression patterns and levels. After 17 hours of hybridization, washing and scanning of the arrays was carried out using GeneChip Hybridization, Wash and Stain Kit (Affymetrix) in GeneChip Fluidics 450 system.

scan_protocol: GeneChips were scanned using the GeneChip 3000 Scanner.

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

organism: Caenorhabditis elegans

label_protocol: Purified total RNA was amplified and labeled with biotinylated nucleotide analog using Affymetrix GeneChip 3’ IVT Express Kit according to the manufacturer’s protocol.

growth_protocol: The wild type C. elegans strain (N2) were grown at 20°C on nematode growth medium (NGM), with E. coli OP50 as food source

extract_protocol: Total RNA from each group was extracted using TRIzol reagent following manufacturer’s instruction (Invitrogen, USA), purified using RNeasy Mini Kit (Qiagen, USA)

treatment_protocol: No specific treatment prior to extraction

value: Wild type (N2)


title: B_H2O2_rep4

description: Nematodes after 2-hours induction with 0.3 mM H2O2 at L4 stage

source_name: H2O2 induction


title: F_TRF_rep2

description: Nematode treated with TRF throughout the life cycle

source_name: TRF treatment


title: B_H2O2_rep1


title: D_TRF+H2O2+TRF_rep2

source_name: TRF treatment pre- and post- H2O2 induction


title: F_TRF_rep1


title: F_TRF_rep4


title: B_H2O2_rep3


title: D_TRF+H2O2+TRF_rep4


title: A_Control_rep2

description: Nematodes at normal development and aging

source_name: Control


title: D_TRF+H2O2+TRF_rep1


title: F_TRF_rep3


title: A_Control_rep3


title: A_Control_rep4


title: CLL60 d1 vs d0

city: Heidelberg

first: Selcen

last: Ozturk

address: Im Neuenheimer Feld 280

department: Molecular Genetics (B060)

institute: German Cancer Research Center (DKFZ)

hyb_protocol: Array platform: 70 mer oligonucleotides (Human Oligo Set 4.0; Operon, Cologne, Germany). Pretreatment of slides: 2 min in 0.2perc SDS; 2 min in ddH2O at RT; 2 min in ddH2O at 95C, followed by 1 min centrifugation at 1000 rpm. Application of preheated (60 min 60C, 10 min 70C), dye-labeled cDNA in Ultra-Hyb hybridization buffer on microarrays in a GeneTAC Hybridization Station. Hybridization for 40h at 42C with gentle agitation. Wash steps: 36C; 5 min 0.5xSSC, 0.1perc SDS; 3 min 0.05xSSC, 0.1perc SDS; 20s 0.05xSSC; 20s 0.05xSSC, 0.1perc Tween20.

scan_protocol: Scanning of hybridized microarrays at 5 um resolution and variable PMT voltage to obtain maximal signal intensities with < 0.1perc probe saturation, a count ratio of 0.8.1.2 (Cy5/Cy3) and maximal congruence of histogram curves using a GenePix 4000B microarray scanner (Axon Instruments, Union City, USA).

data_processing: Spots not recognized by the image analysis software, or not passing the quality criteria were excluded from the calculations. Raw fluorescence intensities were normalized applying the variance stabilization method (W. Huber et al., Bioinformatics 18 Suppl. 1, 2002).

source_name: CLL cells

label_protocol: Sample labelling by Klenow reaction using Cy3- or Cy5-labeld dUTP. Purification of labelled samples on Microcon YM-30 filter columns. Addition of blocking reagents: 25 ug Cot-1 DNA, 25 ug poly-A RNA, and 75 ug yeast tRNA.

growth_protocol: [culture protocol] 1x10^7 cells in 4 ml per well in 6-well plates

extract_protocol: Total RNA isolation by Trizol extraction and purification on RNeasy Mini spin columns. Amplification of RNA by first- and second-strand cDNA synthesis. In vitro transcription of extracted cDNA by RiboMAX Large Scale RNA Production System T7.

tag: time point

value: CLL


title: B_H2O2_rep2


title: PB6 d1 vs d0

source_name: B cells

value: Healthy


title: PB6 d0 vs d1


title: PB9 d0 vs d1


title: PB9 d1 vs d0


title: CLL61 d1 vs d0


title: CLL59 d0 vs d1


title: PB5 d1 vs d0


title: A_Control_rep1


title: PB5 d0 vs d1


title: PB8 d1 vs d0


title: CLL58 d1 vs d0


title: CLL58 d0 vs d1


title: PB8 d0 vs d1


title: CLL60 d0 vs d1


title: PB10 d0 vs d1


title: KoIc6

city: Braunschweig

first: Daniel

last: Goedbloed

address: Mendelssohnstrasse 4

institute: TUBS

description: gene expression from samples in the field

hyb_protocol: Agilent Low Input Quick Amp Labelling kit for ‘One-Color Microarray-Based Gene Expression Analysis’

scan_protocol: Agilent DNA Microarray Scanner (type C)

data_processing: feature extraction software (Agilent)

organism: Salamandra salamandra

source_name: tail-tip

growth_protocol: field samples

extract_protocol: Trizol total RNA extraction

treatment_protocol: tissue samples taken in the field and stored in RNA-later at -20 degrees C

value: tail-tip

tag: site

value: KoIc


title: CLL61 d0 vs d1


title: PB10 d1 vs d0


title: KoB1

value: Katzenlochbach


title: KoB2


title: CLL59 d1 vs d0


title: KoIc5


title: KoV2-4


title: KoV2-1


title: KoV2-3


title: KoIc2


title: KoE5

value: KoE


title: Arm B, Biological rep 17, normal squamous mucosa, T1

city: Cleveland

first: Linda

middle: Cheng

last: Cummings

state: OH

address: 11100 Euclid Avenue Mailstop 5066

department: Medicine/Division of Gastroenterology and Liver Disease

institute: Case Western Reserve University/University Hospitals Cleveland Medical Center

description: Gene expression data from normal squamous mucosa after vitamin D supplementation, no dysplasia/low grade dysplasia arm

hyb_protocol: 45 degrees C x 16 hours, 60 rpm

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Robust Multi-Chip analysis (RMA) was applied to all samples in the dataset using the R package affy

label_protocol: Affymetrix WT Plus Labeling Kit

extract_protocol: RNA was isolated from fresh frozen esophageal biopsies using the mirVana RNA isolation kit (Ambion).

treatment_protocol: Cold forceps biopsies were obtained from Barrett's esophageal and normal squamous mucosa before and after vitamin D supplementation.  Biopsies were flash frozen during endoscopy and stored at -80 C until RNA isolation.

value: Normal esophageal squamous mucosa

tag: arm

value: Arm B

tag: timepoint (t0=before, t1=after)


title: KoE1


title: KoGa6

value: Annabergerbach


title: KoB3


title: Arm B, Biological rep 15, normal squamous mucosa, T1

source_name: normal squamous mucosa after vitamin D supplementation, no dysplasia/low grade dysplasia arm


title: Arm B, Biological rep 17, BE segment, T1

description: Gene expression data from BE segment after vitamin D supplementation, no dysplasia/low grade dysplasia arm

value: Barrett's esophagus segment


title: KoB4


title: Arm B, Biological rep 16, BE segment, T1

source_name: BE segment after vitamin D supplementation, no dysplasia/low grade dysplasia arm


title: KoV2-6


title: KoE2


title: Arm B, Biological rep 17, normal squamous mucosa, T0

description: Gene expression data from normal squamous mucosa before vitamin D supplementation, no dysplasia/low grade dysplasia arm


title: KoIc4


title: Arm B, Biological rep 16, normal squamous mucosa, T1


title: Arm B, Biological rep 15, BE segment, T1


title: Arm B, Biological rep 16, normal squamous mucosa, T0

source_name: normal squamous mucosa before vitamin D supplementation, no dysplasia/low grade dysplasia arm


title: Arm B, Biological rep 17, BE segment, T0

description: Gene expression data from BE segment before vitamin D supplementation, no dysplasia/low grade dysplasia arm


title: Arm B, Biological rep 15, normal squamous mucosa, T0


title: KoGa4


title: KoE4


title: KoGa1


title: KoGa2


title: Arm B, Biological rep 16, BE segment, T0

source_name: BE segment before vitamin D supplementation, no dysplasia/low grade dysplasia arm


title: KoGb6

value: Klufterbach


title: KoH4

value: Hittelbach


title: Arm B, Biological rep 15, BE segment, T0


title: KoH6


title: Arm B, Biological rep 14, BE segment, T1


title: KoGb3


title: Arm B, Biological rep 14, normal squamous mucosa, T1


title: KoGb2


title: KoGc3

value: Vennerbach


title: KoGc4


title: Arm B, Biological rep 12, BE segment, T1


title: KoGb5


title: Arm B, Biological rep 12, normal squamous mucosa, T1


title: Arm B, Biological rep 13, BE segment, T1


title: KoH5


title: KoH2


title: Arm B, Biological rep 13, BE segment, T0


title: KoGc1


title: REIT6

value: Reitlingstal


title: Arm B, Biological rep 11, normal squamous mucosa, T1


title: Arm B, Biological rep 14, BE segment, T0


title: Arm B, Biological rep 12, normal squamous mucosa, T0


title: Arm B, Biological rep 14, normal squamous mucosa, T0


title: Arm B, Biological rep 11, normal squamous mucosa, T0


title: Arm B, Biological rep 11, BE segment, T1


title: Arm B, Biological rep 11, BE segment, T0


title: KoGc6


title: Arm B, Biological rep 12, BE segment, T0


title: REIT2


title: REIT1


title: REIT3


title: WOB3

value: Wolfsburg


title: WOB5


title: WOB1


title: WOB2


title: Arm B, Biological rep 9, normal squamous mucosa, T1


title: Arm B, Biological rep 10, normal squamous mucosa, T1


title: Arm B, Biological rep 9, BE segment, T1


title: S08 L.RCC

city: Salt Lake City

first: Jared

last: Rutter

state: Utah

address: 15 N Medical Drive East, Rm 4100

department: Biochemistry

institute: University of Utah

description:
Test
Nanostring Elements
SAMPLE 20

hyb_protocol: RNA was hybridized to probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol (below). Probes were based on manufacturer's  fourescent barcode system.

scan_protocol: Scanning was carried out according to manufacturer's protocols in conjunsting with the University of Utah Core Facility and ARUP

data_processing: Data was uploaded and visualized in nSolver provided by Nanostring. Positive and negative controls were included as part of the panel as well as 7 normalization genes (ActB, B2m, Cltc, GusB, Rpl19, Tbp, and Ywhaz).

label: Flourescent tag barcode

source_name: Small intestine crypt single cells

label_protocol: Manufacturer designed probes

growth_protocol: Normal mouse protocol and diet. Mice genetically wild-type harboding the Lgr5-EGFP allele and were 6-12 weeks of age, comprised of male and female.

extract_protocol: Single GFP positive cells were extracted directly in RLT buffer by vortexing.

treatment_protocol: Mice and cells were genetically wild-type without any manipulation prior to sorting and lysis.

tag: egfp signature

value: Low


title: S08 H.RCC

description:
Test
Nanostring Elements
SAMPLE 19

value: High


title: S07 L.RCC

description:
Test
Nanostring Elements
SAMPLE 17


title: S08 M.RCC

description:
Test
Nanostring Elements
SAMPLE 21

value: Mid


title: T01 H.RCC

description:
Test
Nanostring Elements
SAMPLE 22


title: T01 L.RCC

description:
Test
Nanostring Elements
SAMPLE 23


title: T01 M.RCC

description:
Test
Nanostring Elements
SAMPLE 24


title: Arm B, Biological rep 10, normal squamous mucosa, T0


title: S07 M.RCC

description:
Test
Nanostring Elements
SAMPLE 18


title: Arm B, Biological rep 8, normal squamous mucosa, T1


title: Arm B, Biological rep 9, normal squamous mucosa, T0


title: Arm B, Biological rep 8, BE segment, T1


title: Arm B, Biological rep 9, BE segment, T0


title: S07 H.RCC

description:
Test
Nanostring Elements
SAMPLE 16


title: S05 M.RCC

description:
Test
Nanostring Elements
SAMPLE 15


title: Arm B, Biological rep 7, BE segment, T1


title: Arm B, Biological rep 7, normal squamous mucosa, T1


title: Arm B, Biological rep 10, BE segment, T1


title: Arm B, Biological rep 8, BE segment, T0


title: Arm B, Biological rep 10, BE segment, T0


title: Arm B, Biological rep 7, normal squamous mucosa, T0


title: Arm B, Biological rep 7, BE segment, T0


title: Arm B, Biological rep 8, normal squamous mucosa, T0


title: Mid - 4.RCC

description:
Test
Nanostring Elements
SAMPLE 9


title: RED L.RCC

description:
Test
Nanostring Elements
SAMPLE 11


title: S05 H.RCC

description:
Test
Nanostring Elements
SAMPLE 13


title: RED H.RCC

description:
Test
Nanostring Elements
SAMPLE 10


title: Mid - 3.RCC

description:
Test
Nanostring Elements
SAMPLE 8


title: Low - 4.RCC

description:
Test
Nanostring Elements
SAMPLE 6


title: Low - 3.RCC

description:
Test
Nanostring Elements
SAMPLE 5


title: Low - 2.RCC

description:
Test
Nanostring Elements
SAMPLE 4


title: High - 4.RCC

description:
Test
Nanostring Elements
SAMPLE 3


title: Arm B, Biological rep 6, normal squamous mucosa, T0


title: Mid - 2.RCC

description:
Test
Nanostring Elements
SAMPLE 7


title: High - 2.RCC

description:
Test
Nanostring Elements
SAMPLE 1


title: Arm B, Biological rep 6, BE segment, T0


title: WENR 3

description:
Group C
Nanostring Elements
SAMPLE 21

source_name: Small intestine Organoid

extract_protocol: Organoids were washed and extracted for total RNA using Qiagen Rneasy kit.

tag: treatment

value: Basal Media


title: Arm B, Biological rep 5, BE segment, T0


title: Arm B, Biological rep 6, BE segment, T1


title: S05 L.RCC

description:
Test
Nanostring Elements
SAMPLE 14


title: Arm B, Biological rep 4, normal squamous mucosa, T0


title: Arm B, Biological rep 6, normal squamous mucosa, T1


title: WENR 2

description:
Group C
Nanostring Elements
SAMPLE 20


title: Arm B, Biological rep 4, BE segment, T0


title: Arm B, Biological rep 3, normal squamous mucosa, T1


title: Arm B, Biological rep 3, BE segment, T1


title: RED M.RCC

description:
Test
Nanostring Elements
SAMPLE 12


title: Arm B, Biological rep 3, BE segment, T0


title: WENR 1

description:
Group C
Nanostring Elements
SAMPLE 19


title: Arm B, Biological rep 3, normal squamous mucosa, T0


title: Arm B, Biological rep 5, BE segment, T1


title: UK-5099 2

description:
Group C
Nanostring Elements
SAMPLE 17


title: UK-5099 1

description:
Group C
Nanostring Elements
SAMPLE 16


title: UK-5099 3

description:
Group C
Nanostring Elements
SAMPLE 18


title: Arm B, Biological rep 2, normal squamous mucosa, T1


title: High - 3.RCC

description:
Test
Nanostring Elements
SAMPLE 2


title: Arm B, Biological rep 2, BE segment, T0


title: Arm B, Biological rep 4, BE segment, T1


title: Arm B, Biological rep 2, normal squamous mucosa, T0


title: ENR 90w 2

description:
Group B
Nanostring Elements
SAMPLE 14

value: EGF + Noggin + RSPO1 + Wnt3A


title: Arm B, Biological rep 1, normal squamous mucosa, T1


title: Arm B, Biological rep 1, BE segment, T1


title: ENR 90w 1

description:
Group B
Nanostring Elements
SAMPLE 13


title: ENR 90w 3

description:
Group B
Nanostring Elements
SAMPLE 15


title: ENR 2

description:
Group B
Nanostring Elements
SAMPLE 11

value: EGF + Noggin + RSPO1


title: Arm B, Biological rep 1, normal squamous mucosa, T0


title: ENR 3

description:
Group B
Nanostring Elements
SAMPLE 12


title: ENR 1

description:
Group B
Nanostring Elements
SAMPLE 10


title: Arm A, Biological rep 4, BE segment, T1

description: Gene expression data from BE segment after vitamin D supplementation, high grade dysplasia arm

value: Arm A


title: EN 1

description:
Group B
Nanostring Elements
SAMPLE 7

value: EGF + Noggin


title: C line KO 3

description:
Group A
Nanostring Elements
SAMPLE 6

value: TAM Treated MPC1 KO


title: Arm A, Biological rep 4, BE segment, T0

description: Gene expression data from BE segment before vitamin D supplementation, high grade dysplasia arm


title: Arm A, Biological rep 4, normal squamous mucosa, T1

description: Gene expression data from normal squamous mucosa after vitamin D supplementation, high grade dysplasia arm

value: Normal esophageal squamous mucosa


title: Arm A, Biological rep 4, normal squamous mucosa, T0

description: Gene expression data from normal squamous mucosa before vitamin D supplementation, high grade dysplasia arm


title: Arm B, Biological rep 1, BE segment, T0

value: Arm B


title: EN 2

description:
Group B
Nanostring Elements
SAMPLE 8


title: Arm A, Biological rep 3, normal squamous mucosa, T1

source_name: normal squamous mucosa after vitamin D supplementation, high grade dysplasia arm


title: C line KO 2

description:
Group A
Nanostring Elements
SAMPLE 5


title: C line KO 1

description:
Group A
Nanostring Elements
SAMPLE 4


title: C line 2

description:
Group A
Nanostring Elements
SAMPLE 2

value: Wild-type Untreated


title: Arm A, Biological rep 3, BE segment, T0

source_name: BE segment before vitamin D supplementation, high grade dysplasia arm

value: Barrett's esophagus segment


title: C line 3

description:
Group A
Nanostring Elements
SAMPLE 3


title: C line 1

description:
Group A
Nanostring Elements
SAMPLE 1


title: EN 3

description:
Group B
Nanostring Elements
SAMPLE 9


title: Arm A, Biological rep 3, normal squamous mucosa, T0

source_name: normal squamous mucosa before vitamin D supplementation, high grade dysplasia arm


title: Arm A, Biological rep 3, BE segment, T1

source_name: BE segment after vitamin D supplementation, high grade dysplasia arm


title: Arm A, Biological rep 2, normal squamous mucosa, T1


title: Arm A, Biological rep 2, normal squamous mucosa, T0


title: Arm A, Biological rep 1, BE segment, T1


title: Arm A, Biological rep 1, BE segment, T0


title: Hep_RetSat_kd_rep3

status: Public on Jul 05 2017

city: Berlin

first: Michael

last: Schupp

address: Hessische Str. 3-4

department: Institute of Pharmacology

institute: Charite Universitätsmedizin Berlin

description: Gene expression data from primary mouse hepatocytes with RetSat knockdown

hyb_protocol: Five and a half micrograms of labeled cDNA were added to Affymetrix  hybridization cocktails, heated at 99 C for 5 min and hybridized for 16h at 45 C to Mouse Gene 1.0 ST GeneChips (Affymetrix Inc., Santa Clara CA). The microarrays were then washed at low (6X SSPE) and high (100 mM MES, 0.1 M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A GeneChip 3000 7G scanner was used to collect fluorescence signal.

data_processing: Probe intensity (.cel) data was normalized using RMA as implemented in Partek Genomics Suite (v6.6, Partek, Inc., St. Louis, MO).

source_name: primary hepatocyte

label_protocol: 100 ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated the T7 promoter sequence. Second-strand cDNA synthesis was followed by in vitro transcription with T7 RNA polymerase for linear amplification of each transcript, and the resulting cRNA was converted to cDNA, fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling

growth_protocol: Livers of anesthetized male wt C57BL/6J mice were perfused with digestion buffer containing 5000 U collagenase (Worthington). After filtration and separation by a Percoll gradient (Biochrome), cells were seeded on collagen-coated 12-well plates in Dulbecco’s modified Eagle’s medium (DMEM) without pyruvate containing 25 mM glucose, 10% FBS (Invitrogen) and 1% penicillin/streptomycin (GIBCO).

extract_protocol: 48 hours later, culture media was aspirated, lysis buffer added directly to the cells, and total RNA isolated using RNeasy (Qiagen) and according to the manufacturer's instructions.

treatment_protocol: After the attachment of hepatocytes to the cell culture plate, media was replaced by 500 µl of DMEM without supplements, and cells transfected with 1 nmol of siRNA (Dharmacon) and 4 µl of Lipofectamine 2000 (Invitrogen) per 12 well overnight. The next morning, media was replaced by DMEM containing 10% FBS and 1% penicillin/streptomycin.

tag: strain

tag: primary cell type

value: hepatocytes

tag: genotype/variation

value: RetSat knockdown


title: Hep_RetSat_kd_rep2


title: Hep_control_kd_rep3

description: Gene expression data from primary mouse hepatocytes with control knockdown

value: control knockdown


title: Hep_control_kd_rep2


title: Hep_RetSat_kd_rep1


title: Hep_control_kd_rep1


title: OA_28_PB

first: Biljana

last: Smiljanovic

address: Charitéplatz 1

department: Department of Rheumatology and Clinical Immunology

institute: Charité - Universitätsmedizin Berlin

hyb_protocol: 50µg/ml of labeled cRNA was hybridized at 45°C for 16h using the Affymetrix GeneChip hybridization oven. Washing and staining was performed on the Affymetrix Fluidics 450 using the EukGE-WS2v4 protocol.

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

data_processing: Data were processed with GCOS 1.4 (TGT = 150) and subsequently imported and further analyzed in the online database (www.bioretis.de)

source_name: Peripheral blood Monocytes from OA patient

label_protocol: 100 ng of total RNA was amplified and labelled using the GeneChip® one-cycle target labelling and control reagents (Affymetrix)

extract_protocol: Total RNA was extracted with Rneasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

tag: diagnosis

value: Osteoarthritis (OA)

value: Peripheral blood

tag: gender

value: male


title: RA_93_PB

source_name: Peripheral blood Monocytes from RA patient

value: Rheumatoid arthritis (RA)


title: OA_80_PB


title: OA_75_PB


title: RA_1_PB

description: Already integrated into GEO as a part of GSE38351 accession, with sample number: GSM940484

value: female


title: RA_98_PB

description: Already integrated into GEO as a part of GSE38351 accession, with sample number: GSM940487


title: OA_101_PB


title: OA_7_BM

source_name: Bone marrow Monocytes from OA patient

value: Bone marrow


title: OA_2_PB


title: RA_88_PB

description: Already integrated into GEO as a part of GSE38351 accession, with sample number: GSM940486


title: OA_1_PB


title: OA_62_BM


title: OA_202_BM


title: OA_39_BM


title: RA_18_PB

description: Already integrated into GEO as a part of GSE38351 accession, with sample number: GSM940485


title: Arm B, Biological rep 4, normal squamous mucosa, T1


title: OA_2_BM


title: RA_93_BM

source_name: Bone marrow Monocytes from RA patient


title: OA_1_BM


title: OA_50_BM


title: OA_23_BM


title: Il15ra KO pre-osteoblasts, rep5

city: Philadelphia

first: Emanuele

last: Loro

state: PA

address: 415 Curie Boulevard

department: Physiology

institute: University of Pennsylvania

description:
Il15raKO pre-osteoblast_5
Transcriptome analysis data from Il15ra null murine primary pre-osteoblasts at 5 days of osteogenic differentiation.

hyb_protocol: Five and a half micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Mouse Transcriptome 1.0 ST GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

data_processing:
Affymetrix Command Console and Expression Console were used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters.
Supplementary CHP files include RMA values.

source_name: Primary pre-osteoblasts from tibia bone marrow compartment

label_protocol: Second-strand cDNA synthesis was followed by in vitro transcription with T7 RNA polymerase for linear amplification of each transcript, and the resulting cRNA was converted to cDNA, fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling.

growth_protocol: BMSC were obtained according to Soleimani, Nat. Protoc. (2009) and cultured in MEMalpha supplemented with 10% fetal bovine serum and antibiotics.

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

treatment_protocol: Osteogenic differentiation was obtained by adding 10 mM β-glycerophosphate (Sigma) and 50 µg/ml ascorbic acid to the culture medium, with daily changes for 5 days.

tag: strain/background

value: Il15ra null

tag: cell type

value: pre-osteoblasts

tag: differentiation

value: 5 days osteogenic differentiation


title: RA_92_PB

tag: tissue


title: Il15ra KO pre-osteoblasts, rep4

description:
Il15raKO pre-osteoblast_4
Transcriptome analysis data from Il15ra null murine primary pre-osteoblasts at 5 days of osteogenic differentiation.


title: Il15ra KO pre-osteoblasts, rep3

description:
Il15raKO pre-osteoblast_3
Transcriptome analysis data from Il15ra null murine primary pre-osteoblasts at 5 days of osteogenic differentiation.


title: Il15ra KO pre-osteoblasts, rep6

description:
Il15raKO pre-osteoblast_6
Transcriptome analysis data from Il15ra null murine primary pre-osteoblasts at 5 days of osteogenic differentiation.


title: Control pre-osteoblasts, rep6

description:
Ctrl pre-osteoblast_6
Transcriptome analysis data from control murine primary pre-osteoblasts at 5 days of osteogenic differentiation.

value: Ctrl


title: Control pre-osteoblasts, rep3

description:
Ctrl pre-osteoblast_3
Transcriptome analysis data from control murine primary pre-osteoblasts at 5 days of osteogenic differentiation.


title: RA_68_BM


title: RA_83_BM


title: RA_56_BM


title: Control pre-osteoblasts, rep5

description:
Ctrl pre-osteoblast_5
Transcriptome analysis data from control murine primary pre-osteoblasts at 5 days of osteogenic differentiation.


title: Arm B, Biological rep 2, BE segment, T1

description: Gene expression data from BE segment after vitamin D supplementation, no dysplasia/low grade dysplasia arm


title: Control pre-osteoblasts, rep2

description:
Ctrl pre-osteoblast_2
Transcriptome analysis data from control murine primary pre-osteoblasts at 5 days of osteogenic differentiation.


title: Il15ra KO pre-osteoblasts, rep1

description:
Il15raKO pre-osteoblast_1
Transcriptome analysis data from Il15ra null murine primary pre-osteoblasts at 5 days of osteogenic differentiation.


title: Control pre-osteoblasts, rep4

description:
Ctrl pre-osteoblast_4
Transcriptome analysis data from control murine primary pre-osteoblasts at 5 days of osteogenic differentiation.


title: RA_33_BM


title: RA_13_BM


title: Il15ra KO pre-osteoblasts, rep2

description:
Il15raKO pre-osteoblast_2
Transcriptome analysis data from Il15ra null murine primary pre-osteoblasts at 5 days of osteogenic differentiation.


title: Control pre-osteoblasts, rep1

description:
Ctrl pre-osteoblast_1
Transcriptome analysis data from control murine primary pre-osteoblasts at 5 days of osteogenic differentiation.


title: 5294271028_C: O14 + INH-2

status: Public on Jul 04 2017

city: Singapore

first: Vivek

last: Tanavde

state: Singapore

address: 30 Biopolis Street, #07-01, Matrix

department: Genome and Gene Expression Data Analysis Division

country: Singapore

institute: Bioinformatics Institute, A*STAR, Singapore

description:
Not used in  this study
Replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: After 16hr of hybridization, the Beadchips were washed, Cy3-labeled, and scanned with an Illumina Bead array reader confocal scanner.

data_processing: The data was then uploaded to GenomeStudio (Illumina, CA, USA) for background subtraction and conversion into Partek file for data analysis on Partek Genomic Suite. The data was then quantile normalised for further downstream analysis.

source_name: Fetal limb MSCs (Flb-MSCs)

label_protocol: RNA amplification was done using Illumina TotalPrepTM RNA amplification kit (Ambion, TX, USA), according to manufacturer’s instructions. 750ng of biotin-labelled cRNA for hybridization was randomly loaded on to Illumina Sentrix BeadChip Array human Ref-8v3 bead chips (Illumina, San Diego, CA)

growth_protocol: Cell culture: Human fetal limb derived MSCs (Flb-MSCs) was a gift from Lim SK, who derived and characterized the cells. The fetal limb derived MSC cell line was the F3lb cell line. Cells were received at passage 10 and expanded for 2 passages in MSCGM BulletKit (Lonza, MD, USA), with medium change every 3-4 days, and passage during 90% confluency (4-5 days) using TryPLE (Invitrogen, CA, USA) before differentiation. Flb-MSCs were seeded at 5000 cells per cm2 in polystyrene cell culture flask (NUNC, NY, USA) and grown in 5% CO2, 370C incubator.

extract_protocol: Total RNA of the undifferentiated MSC, adipocytes, and osteocytes of Flb-MSCs was harvested using 1ml of Trizol (Invitrogen, CA, USA)/ 10 cm2 area. Chondrocyte pellets were treated with 0.25% of collagenase type II in DMEM high glucose medium (Invitrogen, CA, USA) for 1-2 hr at 370C, centrifuged at 1200g for 5min, and the supernatant replaced with 300ul of Trizol per pellet. All samples were stored in Trizol at -800C until RNA extraction.  RNA extraction from samples in Trizol was done using chloroform and purified with RNeasy kit (Qiagen, Netherlands). Concentration of RNA was determined using Nanodrop (Agilent Technologies, CA, USA) and the RNA integrity measured using RNA Nano LabChip on Agilent Bioanalyzer (Agilent Technologies, CA, USA). Only high quality total RNA samples of OD260/OD280 >1.8 and RNA Integrity Number (RIN) of >8, were used for microarray.

treatment_protocol: MSC differentiation: After expansion, Flb-MSCs were seeded in T75 culture flasks for RNA extraction and in 12-well plates for staining during differentiation of adipocytes, and osteocytes, and in pellet form in 15ml polypropylene tubes for chondrocytes differentiation. Adipocytes and osteocytes grown in 12-well plates were used for Oil Red O and Von Kossa Staining respectively, while Alcian blue staining was done for chondrocytes pellet grown in polypropylene tube.  MSCs were seeded at 1.8 x 104 cells per cm2 for adipogenic differentiation, 0.27 x 104 cells per cm2 for osteogenic differentiation, and in pellet size of 50 x 104 cells for chondrogenic differentiation. Trilineage differentiation was done using hMSC adipogenic, osteogenic, and chondrogenic differentiation BulletKits with recombinant human TGF-B3 (Lonza, MD, USA), according to manufacturer’s protocol. Media was changed every 2-4 days.

value: Osteocytes Day 14 with inhibitor


title: RA_2_BM


title: 5294271029_F: O7+inh-1

description:
Not used in  this study
Replicate 1

value: Osteocytes Day 7 with inhibitor


title: 5294271029_C: O7-1

description: Replicate 1

value: Osteocytes Day 7


title: 5294271028_E: C14+INH-2

description:
Not used in  this study
Replicate 2

value: Chondrocytes Day 14 with inhibitor


title: 5294271027_E: C14-2

description: Replicate 2

value: Chondrocytes Day 14


title: 5294271029_G: A7+inh-1

description:
Not used in  this study
Replicate 1

value: Adipocytes Day 7 with inhibitor


title: 5294271027_H: A14-1

description: Replicate 1

value: Adipocytes Day 14


title: 5294271029_H: C7+inh-2

description:
Not used in  this study
Replicate 2

value: Chondrocytes Day7 with inhibitor


title: 5294271028_H: O14-2

description: Replicate 2

value: Osteocytes Day 14


title: 5294271028_A: A14-2

description: Replicate 2


title: 5294271029_A: A14+inh-2

description:
Not used in  this study
Replicate 2

value: Adipocytes Day 14 with inhibitor


title: 5294271029_B: B0-1

description: Replicate 1

value: Undifferentiated MSCs


title: 5294271029_D: A7-1

description: Replicate 1

value: Adipocytes Day 7


title: 5294271028_D: A14 + INH-2

description:
Not used in  this study
Replicate 2


title: 5294271027_F: B0-1

description: Replicate 1


title: 5294271028_G: B0-2

description: Replicate 2


title: RA_1_BM

value: Rheumatoid arthritis (RA)

value: Bone marrow

value: female


title: 5294271027_C: A14+INH-1

description:
Not used in  this study
Replicate 1


title: 5294271027_G: O14-1

description: Replicate 1


title: 5294271028_B: C14-2

description: Replicate 2


title: 5294271027_D: C14+inh-2

description:
Not used in  this study
Replicate 2


title: 5294271028_F: C14-2

description: Replicate 2


title: 5294271020_G: A14-1

description: Replicate 1


title: 5294271027_A: C14-1

description: Replicate 1


title: 5294271020_H: C14-1

description: Replicate 1


title: 5294271020_D: C14+INH-2

description:
Not used in  this study
Replicate 2


title: 5294271020_F: O14-1

description: Replicate 1


title: 5294271027_B: O14+INH-1

description:
Not used in  this study
Replicate 1


title: 5294271029_E: C7-2

description: Replicate 2

value: Chondrocytes Day7


title: 5294271005_A: B0-1

description: Replicate 1


title: 5294271005_D: C7-2

description: Replicate 2


title: 5294271005_E: O7+inh-1

description:
Not used in  this study
Replicate 1


title: 5294271020_A: O14+INH-1

description:
Not used in  this study
Replicate 1


title: 5267177034_H: O7+inh-2

description:
Not used in  this study
Replicate 2


title: 5294271005_H: O14+inh-2

description:
Not used in  this study
Replicate 2


title: 5294271020_E: B0-1

description: Replicate 1


title: 5294271020_B: A14+INH-1

description:
Not used in  this study
Replicate 1


title: 5294271005_G: C7+inh-2

description:
Not used in  this study
Replicate 2


title: 5267177034_A: A7+inh-2

description:
Not used in  this study
Replicate 2


title: 5267177034_G: C7-2

description: Replicate 2


title: 5267177034_E: O7-2

description: Replicate 2


title: 5267177034_D: B0-2

description: Replicate 2


title: 5267177034_B: C7+inh-2

description:
Not used in  this study
Replicate 2


title: 5267177017_E: A7-2

description: Replicate 2


title: 5294271020_C: C14+INH-2

description:
Not used in  this study
Replicate 2


title: 5294271005_C: A7-1

description: Replicate 1


title: 5267177017_D: O7-2

description: Replicate 2


title: 5267177034_C: A14-2

description: Replicate 2


title: 5267177017_F: C7-2

description: Replicate 2


title: 5267177034_F: A7-2

description: Replicate 2


title: 5267177017_A: C7+inh-2

description:
Not used in  this study
Replicate 2


title: 5267177017_G: O7+inh-2

description:
Not used in  this study
Replicate 2


title: 4958460012_G: A21

growth_protocol: Cell culture: Human embryonic stem cell derived MSCs (hES-MSCs) were a gift from Choo A and Lim SK. Cells were received at passage 11 and expanded for 2 passages in MSCGM BulletKit (Lonza, MD, USA). The hES-MSCs were seeded at 5000 cells per cm2 in polystyrene cell culture flask (NUNC, NY, USA) and grown in 5% CO2, 370C incubator.

treatment_protocol: MSC differentiation: After expansion, hES-MSCs were seeded in T75 culture flasks for RNA extraction and in 12-well plates for staining during differentiation of adipocytes, and osteocytes, and in pellet form in 15ml polypropylene tubes for chondrocytes differentiation. Adipocytes and osteocytes grown in 12-well plates were used for Oil Red O and Von Kossa Staining respectively, while Alcian blue staining was done for chondrocytes pellet grown in polypropylene tube.  MSCs were seeded at 1.8 x 104 cells per cm2 for adipogenic differentiation, 0.27 x 104 cells per cm2 for osteogenic differentiation, and in pellet size of 50 x 104 cells for chondrogenic differentiation. Trilineage differentiation was done using hMSC adipogenic, osteogenic, and chondrogenic differentiation BulletKits with recombinant human TGF-B3 (Lonza, MD, USA), according to manufacturer’s protocol. Media was changed every 2-4 days.

value: Adipocytes Day 21


title: 4958460012_H: O21

source_name: Human embryonic stem cell derived MSCs (hES-MSCs)

value: Osteocytes Day 21


title: 5267177017_H: A7+inh-2

description:
Not used in  this study
Replicate 2


title: 5267177017_B: O14-2

description: Replicate 2


title: 5267177017_C: B0-2

description: Replicate 2


title: 4958460012_E: A7


title: 4958460012_F: O7


title: 4958460012_D: B0


title: 4954581003_H: A7


title: 4954581003_F: A21


title: 4958460012_C: O21


title: 4954581003_E: O7


title: 4958460012_B: A21


title: 4954581003_G: O21


title: 4954581003_D: A7


title: 4954581003_C: B0


title: 4801420006_A: C21

value: Chondrocytes Day 21


title: 4954581003_A: A21


title: 4801420006_G: C21


title: 4801420006_D: A7


title: 4801420006_E: O7

value: Osteocytes Day 7


title: 4801420006_H: C21


title: 4634625076_H: O21


title: 4801420006_F: C21


title: 4954581003_B: O21


title: 4634625076_E: A7


title: 4634625076_D: B0


title: 4801420006_C: C21


title: 4801420006_B: C21


title: 4634625076_F: O7


title: 4634625076_G: A21


title: 4634625076_C: O21


title: 4634625076_B: A21


title: 4634625071_E: O7


title: 4634625071_G: O21


title: 4634625071_F: A21


title: 4634625071_B: O21


title: 4958460012_A: O7


title: 4634625071_D: A7


title: 4634625071_H: A7


title: 4634625071_A: A21


title: 4521621174_H: NA

value: Not used in this study


title: 4634625076_A: O7


title: 4521621170_G: NA


title: 4521621174_B: B0


title: 4634625071_C: B0


title: 4521621174_F: O21


title: 4521621174_G: C7

value: Chondrocytes Day 7


title: 4521621170_C: O7


title: 4521621174_D: O7


title: 4521621170_D: A21


title: 4521621170_B: A7


title: 4521621174_E: A21


title: 4521621170_H: C7


title: 4521621174_C: NA


title: 4474300054_H: C7


title: 4474300054_F: B0


title: 4521621170_E: O21


title: 4474300054_D: A21


title: 4521621174_A: A7


title: 4474300054_C: O7


title: 4521621170_F: C7


title: 4474300033_H: A21


title: 4521621170_A: B0


title: 4474300054_A: B0


title: 5294271005_B: O7-1

description: Replicate 1


title: 5294271005_F: A7+inh-1

description:
Not used in  this study
Replicate 1

value: Adipocytes Day 7 with inhibitor


title: 4474300033_F: A7


title: 4474300054_G: C7


title: 4474300054_E: O21


title: 4474300054_B: A7


title: 4474300033_G: O7


title: 4474300033_E: B0


title: 4474300033_D: C7


title: 4474300033_B: B0


title: 4403835055_F: C7


title: 4403835055_H: A7


title: 4403835055_D: B0


title: 4474300033_C: C7


title: 4403835055_E: C7


title: 4403835055_G: B0


title: 4474300033_A: O21


title: 4403835055_A: O7


title: 4403835055_C: O21


title: 549616A07 - SXB139_58 vs SXB139_59

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

description: The objective is to better understand the adaptive response of the wheat plant to an elevated mean temperature. Besides the morphological and ecophysiological responses, the changes in the expression of genes are investigated. Two genotypes (SxB49 and SxB139) are subjected to two different temperature regimes during the lag-phase of the developing grains. The profiling of the accumulation of gene transcripts throughout 12 developmental stages is carried out using a custom-designed 12x135K Roche NimbleGen gene expression microarray comprising the most recent NCBI wheat contig assembly and annotation (about 45 000 unigenes). This should permit both the identification of differentially expressed genes after heat treatment and the comparison of the behaviours of two wheat genotypes (SxB139 and SxB49).

hyb_protocol: SXB139_59 Cy5 / SXB139_58 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)

scan_protocol: Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Triticum aestivum

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, total RNA  . (PT-SIGMA-01_30-10-2012_T.pdf)

growth_protocol: seed - Plants were grown under semi-controlled conditions in containers 2m2 and 0.5 m deep each, covered by transparent enclosures under natural light. Water was daily supplied but the water statute of the plants was not measured. The mean temperature of one container was set at 19°C and corresponded to the control samples. The mean temperature of a second container was set at 27°C and corresponded to the heat-treated samples. The elevated temperature was applied at Anthesis and lasted for 15 days after anthesis (15DAA), then it was lowered back to 19°C as for the control samples. To obtain a mean temperature of 19 °C on a daily basis, the temperature of the container was set at 21°C between 6am30 and 10pm30 and 15°C otherwise. To obtain a mean temperature of 27°C during the lag-phase, the containers were maintained at 29°C from 6am30 to 10pm30 and 23°C for the rest.

treatment_protocol: no treatment

tag: triticum aestivum (serix babax rils)  -  dev.stage (boyes et al. plant cell 2001)

treatment_protocol: Name:Heat-treated - environmental treatment - temperature,temperature:time 250day . 250°Cd, see Table “RNA extracted”


title: 4403835055_B: A21


title: 549619A12 - SXB49_23 vs SXB49_22

hyb_protocol: SXB49_22 Cy5 / SXB49_23 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549418A07 - SXB49_13 vs SXB49_16

hyb_protocol: SXB49_16 Cy5 / SXB49_13 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549616A12 - SXB139_67 vs SXB139_66

hyb_protocol: SXB139_66 Cy5 / SXB139_67 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549616A05 - SXB139_57 vs SXB139_60

hyb_protocol: SXB139_60 Cy5 / SXB139_57 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549616A11 - SXB139_66 vs SXB139_67

hyb_protocol: SXB139_67 Cy5 / SXB139_66 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549619A06 - SXB139_35 vs SXB139_34

hyb_protocol: SXB139_34 Cy5 / SXB139_35 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549418A06 - SXB139_36 vs SXB139_33

hyb_protocol: SXB139_33 Cy5 / SXB139_36 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549616A08 - SXB139_59 vs SXB139_58

hyb_protocol: SXB139_58 Cy5 / SXB139_59 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549418A05 - SXB139_33 vs SXB139_36

hyb_protocol: SXB139_36 Cy5 / SXB139_33 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549619A05 - SXB139_34 vs SXB139_35

hyb_protocol: SXB139_35 Cy5 / SXB139_34 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549652A12 - SXB49_47 vs SXB49_46

hyb_protocol: SXB49_46 Cy5 / SXB49_47 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549652A08 - SXB49_39 vs SXB49_38

hyb_protocol: SXB49_38 Cy5 / SXB49_39 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549616A06 - SXB139_60 vs SXB139_57

hyb_protocol: SXB139_57 Cy5 / SXB139_60 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549652A11 - SXB49_46 vs SXB49_47

hyb_protocol: SXB49_47 Cy5 / SXB49_46 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549619A11 - SXB49_22 vs SXB49_23

hyb_protocol: SXB49_23 Cy5 / SXB49_22 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549652A09 - SXB49_45 vs SXB49_48

hyb_protocol: SXB49_48 Cy5 / SXB49_45 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549418A08 - SXB49_16 vs SXB49_13

hyb_protocol: SXB49_13 Cy5 / SXB49_16 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549652A10 - SXB49_48 vs SXB49_45

hyb_protocol: SXB49_45 Cy5 / SXB49_48 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549652A03 - SXB49_30 vs SXB49_31

hyb_protocol: SXB49_31 Cy5 / SXB49_30 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549649A12 - SXB49_71 vs SXB49_70

hyb_protocol: SXB49_70 Cy5 / SXB49_71 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549652A02 - SXB49_32 vs SXB49_29

hyb_protocol: SXB49_29 Cy5 / SXB49_32 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549652A07 - SXB49_38 vs SXB49_39

hyb_protocol: SXB49_39 Cy5 / SXB49_38 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549652A05 - SXB49_37 vs SXB49_40

hyb_protocol: SXB49_40 Cy5 / SXB49_37 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549652A06 - SXB49_40 vs SXB49_37

hyb_protocol: SXB49_37 Cy5 / SXB49_40 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549649A10 - SXB49_72 vs SXB49_69

hyb_protocol: SXB49_69 Cy5 / SXB49_72 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549652A01 - SXB49_29 vs SXB49_32

hyb_protocol: SXB49_32 Cy5 / SXB49_29 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549649A11 - SXB49_70 vs SXB49_71

hyb_protocol: SXB49_71 Cy5 / SXB49_70 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549652A04 - SXB49_31 vs SXB49_30

hyb_protocol: SXB49_30 Cy5 / SXB49_31 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549649A07 - SXB49_62 vs SXB49_63

hyb_protocol: SXB49_63 Cy5 / SXB49_62 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549649A01 - SXB49_53 vs SXB49_56

hyb_protocol: SXB49_56 Cy5 / SXB49_53 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549649A02 - SXB49_56 vs SXB49_53

hyb_protocol: SXB49_53 Cy5 / SXB49_56 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549626A07 - SXB139_10 vs SXB139_11

hyb_protocol: SXB139_11 Cy5 / SXB139_10 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549626A10 - SXB139_20 vs SXB139_17

hyb_protocol: SXB139_17 Cy5 / SXB139_20 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549649A09 - SXB49_69 vs SXB49_72

hyb_protocol: SXB49_72 Cy5 / SXB49_69 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549649A08 - SXB49_63 vs SXB49_62

hyb_protocol: SXB49_62 Cy5 / SXB49_63 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549626A12 - SXB139_19 vs SXB139_18

hyb_protocol: SXB139_18 Cy5 / SXB139_19 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549649A05 - SXB49_61 vs SXB49_64

hyb_protocol: SXB49_64 Cy5 / SXB49_61 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549649A04 - SXB49_55 vs SXB49_54

hyb_protocol: SXB49_54 Cy5 / SXB49_55 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549626A04 - SXB139_3 vs SXB139_2

hyb_protocol: SXB139_2 Cy5 / SXB139_3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549649A06 - SXB49_64 vs SXB49_61

hyb_protocol: SXB49_61 Cy5 / SXB49_64 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549649A03 - SXB49_54 vs SXB49_55

hyb_protocol: SXB49_55 Cy5 / SXB49_54 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549626A09 - SXB139_17 vs SXB139_20

hyb_protocol: SXB139_20 Cy5 / SXB139_17 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549626A06 - SXB139_12 vs SXB139_9

hyb_protocol: SXB139_9 Cy5 / SXB139_12 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549626A03 - SXB139_2 vs SXB139_3

hyb_protocol: SXB139_3 Cy5 / SXB139_2 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549626A11 - SXB139_18 vs SXB139_19

hyb_protocol: SXB139_19 Cy5 / SXB139_18 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549619A08 - SXB49_15 vs SXB49_14

hyb_protocol: SXB49_14 Cy5 / SXB49_15 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549626A01 - SXB139_1 vs SXB139_4

hyb_protocol: SXB139_4 Cy5 / SXB139_1 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549619A02 - SXB49_8 vs SXB49_5

hyb_protocol: SXB49_5 Cy5 / SXB49_8 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: Identification of miR-455-5p target genes in PC3.

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

institute: Chiba University

hyb_protocol: Agilent two-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution. Images were quantified using Agilent Feature Extraction software version 10.7.3.1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

source_name: mock

label_protocol: Agilent two-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: Normal cell culture medium RPMI 1640 or DMEM.

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions.

treatment_protocol: microRNA or siRNA transfection using Lipofectamine RNAiMAX (Invitrogen).

tag: cell line

value: prostate cancer

tag: transfection

value: no transfection

source_name: miR-455-5p transfected cell lines


title: 549619A07 - SXB49_14 vs SXB49_15

hyb_protocol: SXB49_15 Cy5 / SXB49_14 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549626A08 - SXB139_11 vs SXB139_10

hyb_protocol: SXB139_10 Cy5 / SXB139_11 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549626A05 - SXB139_9 vs SXB139_12

hyb_protocol: SXB139_12 Cy5 / SXB139_9 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549626A02 - SXB139_4 vs SXB139_1

hyb_protocol: SXB139_1 Cy5 / SXB139_4 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549619A03 - SXB49_6 vs SXB49_7

hyb_protocol: SXB49_7 Cy5 / SXB49_6 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: Identification of miR-455-3p target genes in PC3.

source_name: miR-455-3p transfected cell lines


title: 549618A10 - SXB49_96 vs SXB49_93

hyb_protocol: SXB49_93 Cy5 / SXB49_96 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549619A04 - SXB49_7 vs SXB49_6

hyb_protocol: SXB49_6 Cy5 / SXB49_7 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549619A09 - SXB49_21 vs SXB49_24

hyb_protocol: SXB49_24 Cy5 / SXB49_21 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: Differentially expressed genes by knocking down of MMP14-2 in EBC-1

value: lung squamous cell carcinoma

source_name: si-MMP14-2 transfected cell line


title: 549619A10 - SXB49_24 vs SXB49_21

hyb_protocol: SXB49_21 Cy5 / SXB49_24 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549618A09 - SXB49_93 vs SXB49_96

hyb_protocol: SXB49_96 Cy5 / SXB49_93 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: Identification of miR-149-5p target genes in A498

value: renal cell carcinoma

source_name: miR-149-5p transfected cell lines


title: Differentially expressed genes by knocking down of MYO1B-1 in SAS

value: SAS

value: oral squamous cell carcinoma

source_name: si-MYO1B-1 transfected cell line


title: 549618A03 - SXB49_78 vs SXB49_79

hyb_protocol: SXB49_79 Cy5 / SXB49_78 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549618A06 - SXB49_88 vs SXB49_85

hyb_protocol: SXB49_85 Cy5 / SXB49_88 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: Identification of miR-149-3p target genes in A498

source_name: miR-149-3p transfected cell lines


title: 549618A04 - SXB49_79 vs SXB49_78

hyb_protocol: SXB49_78 Cy5 / SXB49_79 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549618A01 - SXB49_77 vs SXB49_80

hyb_protocol: SXB49_80 Cy5 / SXB49_77 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549618A07 - SXB49_86 vs SXB49_87

hyb_protocol: SXB49_87 Cy5 / SXB49_86 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 549619A01 - SXB49_5 vs SXB49_8

hyb_protocol: SXB49_8 Cy5 / SXB49_5 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)