title: BY4741

city: Bangalore

first: Malathi

last: Srinivasan

state: Karnataka

address: Allalasandra, GKVK Post, Bellary Road

department: Lipidomic Center

institute: Central Food Technological Research Institute

description:
Stationary phase cells
W1

hyb_protocol: The labeled cRNA samples were hybridized on to a Agilent Platform Custom Saccharomyces cerevisiae 8x15k designed by Genotypic Technology Private Limited.   (AMADID: 016333). 600ng of cy3 labeled samples were fragmented and hybridized .Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Agilent Microarray Scanner G2505C at 5 micron resolution.

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX Version 11.0 software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift . Gene based analysis was perfomred.

source_name: Saccharomyces cerevisiae

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

growth_protocol: cells were grown in synthetic medium(SM) (0.67% yeast nitrogen base, 0.192% drop out) containing uracil (pH 7 – 7.5) and 2% dextrose with aeration at 30°C

extract_protocol: RNA was extracted using the TRIzol (Invitrogen) method with glass beads (Sigma, 425-600um, Cat #G8772) for homogenization following the manufacturer's recommendations.

value: wild type


title: Red sector of colony 15.6 derived from MD556

status: Public on Dec 30 2015

type: genomic

city: Durham

first: Thomas

middle: D

last: Petes

state: NC

address: 213 Research Drive

department: Molecular Genetics and Microbiology

country: USA

institute: Duke University School of Medicine

description: MD556-15.6 R1 WG

hyb_protocol: The hybridization reactions were prepared using an Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit (5188-5220) following kit instructions. Arrays were incubated for 48 hours at 62°. Following hybridization, the arrays were washed for 5 minutes in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent 5188-5221) and 1 minute in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent 5188-5222) that was pre-warmed to 37°. The arrays were then scanned at wavelengths of 635 and 532 nm using the GenePix scanner and the GenePix Pro software using settings recommended by the manufacturer.Microarrays could be re-used approximately 4-6 times by removing the hybridized labeled DNA sequences from the oligonucleotides. Microarrays and gasket slides were stripped separately in 1x stripping buffer (10 mM potassium phosphate, pH6.6). The slides were slowly heated to the boiling point in the stripping buffer for 30-45 minutes. After stripping, they were transferred to deionized water, and then slowly removed and stored in a nitrogen cabinet. The gasket slides were centrifuged at 500 rpm to remove excess liquid. Labels on microarrays were removed prior to stripping.

scan_protocol: The data generated by GenePix Pro were exported to text files and analyzed with Microsoft Excel. Probes that were flagged by the software were deleted from the analysis.

data_processing:
The ratio of the medians (635 nm/532 nm) for each probe was used for analysis, and replicate probe medians were averaged. The data was centered around one by dividing each probe median by the average of all of the probe medians in order to normalize for differences in the hybridization levels for the reference and experimental strain samples. The data were plotted separately for each haploid parental strain and, in plots showing whole chromosomes, the medians were “smoothed” by averaging over nine consecutive probes.
Excel processed data file contents: The sample names (column A) show the name of the strain and isolate, the color of the sector (R1=red, W1=white), whether the strain was a sectored colony (labeled either R1 or W1) or a sub-cultured colony (SC), and the type of microarray used in the analysis. WG indicates that a whole-genome array was used, with densely spaced oligonucleotides located on every chromosome. VA indicates that an array with densely-spaced oligonucleotides on the left arm of chromosome V, the right arm of VIII, and chromosomes I and III was used. Column B has most of the information more explicitly. Column C shows the name of the .gpr files for each strain. All of the other columns are self-explanatory. Column R has the Excel file used to depict the hybridization ratios for our analysis.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Sector of colony grown for two days at 30 degrees C

label_protocol: The methods used to label DNA were described in the Supplementary Information of St, Charles et al. (2012) Genetics 190: 1267-1284. DNA isolated from the experimental samples was labeled with Cy5-dUTP, and DNA from the control strains (PG311 and JSC23) was labed with Cy3-dUTP.

growth_protocol: For analysis of sectored colonies, we grew cells on solid medium lacking arginine and containing 10 micrograms/ml adenine and 120 micrograms/ml of canavanine. Cells were grown for three days at 30 degrees. For sub-culturing experiments, cells were grown from a single cell to a colony on rich solid growth medium (YPD) at 30 degrees.

extract_protocol: We extracted DNA from cultures derived from single colonies by the procedure described in St. Charles et al. (2012) Genetics 190: 1267-1284.

treatment_protocol: For red/white sectored colonies, we re-streaked cells from the sectors and analyzed single colonies derived from either the red or white sectors. The sub-cultured strains were streaked from single colonies, and allowed to form new colonies through 10 cycles of sub-cloning.

tag: color of sector/colony

value: red

tag: growth condition

value: 2 days growth at 30

source_name: PG311 control strain

tag: colony color

value: Pink

tag: sample type

value: Control heterozygous strain


title: Deletion mtf1

type: RNA

country: India

description:
Stationary phase cells
T1

molecule: total RNA

tag: genotype/variation


title: Amur sturgeon Muscle

city: Guangzhou

first: zhang

middle: xiu

last: juan

state: Guangdong province

address: NO.105, Xingang west road, Haizhu district

country: China

institute: Guangdong Entomological institute

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies).

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression).

organism: Acipenser schrenckii

source_name: Amur sturgeon Muscle

label_protocol: The assay started from 2 to 5 ug total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore) and the small RNAs (< 300 nt) isolated were 3'-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.

extract_protocol: Total RNA was extracted using miRNeasy Kit(Qiagen, 217004), following the manufacturer's recommended protocol.

tag: tissue

value: Muscle


title: Amur sturgeon Bain

source_name: Amur sturgeon Bain

value: Bain


title: White sector of colony 12.1 derived from MD556

description: MD556-12.1 W1 WG

value: white


title: Amur sturgeon Spleen

source_name: Amur sturgeon Spleen

value: Spleen


title: Amur sturgeon Liver

source_name: Amur sturgeon Liver

value: Liver


title: SW620 cell line

city: Kyoto

first: Masahiro

last: Inoue

state: Kyoto

address: Med-Pharm Collaboration Bldg 503, Shimoadachi-cho 46, Sakyou-ku, Kyoto, 606-8304, Japan

department: Clinical Bio-resource Research and Development

country: Japan

institute: Kyoto Univ Graduate School of Medicine

description: Gene expression of C45-derived xenograft tumor

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 Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 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: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Homo sapiens

source_name: SW620 cell line, 2D, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: CTOSs were cultured in suspension or embeded in type I collagen gel in StemPro hESC SFM (Life Technologies, Carlsbad, CA).

extract_protocol: Total RNA was extracted from CTOSs with TRIzol reagent (Life Technologies) according to the manufacturer’s instructions.

treatment_protocol: CTOS were cultured under type I collagen gel embeded conditions, and then gel was digested by collagenase and CTOSs were cultured 24h under floating conditions. CTOS were injected into NOD-SCID mice to generate xenograft tumors. RNA was directly extracted from CTOSs and xenotumors. Original patient tumors were formarin fixed, parrafin embeded, and sectioned. RNA was extracted from cancer cell clusters microdissected from the sections.

value: CD cultured cell line


title: Red sector of colony 12.1 derived from MD556

description: MD556-12.1 R1 WG


title: shpkp3-2-2 (HCT116 cell line)

city: navi mumbai

first: Srikanta

last: Basu

state: Maharashtra

address: Kharghar, sector 22

department: Sorab's Lab

institute: TMC-ACTREC

description: Gene expression of HCT116 derived plakophilin3 knockdown clone

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 Whole Human Genome Oligo Microarray ( Design, Agilent-027114; platform GPL13252) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (Agilent SureScan microarray scanner, G2505C US83000164) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm; Scan resolution 5um, Single pass; Dye channel is set to Green and Green PMT is set to XDR High 100% and XDR Low 10%).

data_processing: The scanned images were analyzed using the Automated feature extraction using Agilent Feature Extraction software (9.1). Normalization and statistical analysis, Pathway and Gene Ontology analysis was performed using Agilent's GeneSpring GX v 11.0 and Genotypic's Biointerpreter Software.

source_name: Cells, PKP3 knockdown biological replicate 2

label_protocol: Cy3 Labeling (Single color) was done using Agilent's Quick Amp kit (cDNA synthesis and in vitro transcription)

growth_protocol: cells were grown in Iscove's modified DMEM medium (IMDM) and plasmid encoding shRNA agiainst plakophilin3 was maintained in cells (stable clones) by using 5μg/ml puromycin selection

extract_protocol: RNA was extracted using by column method using the Qiagen Rneasy Plus Mini kit (Cat. No. 74134) in RNase free, Non-DEPC treated water (Invitrogen, Cat#10977015, Ambion).Samples were packed in nuclease-free microtubes secured with parafilm or screw capped tubes.  Samples were sent in dry ice from Dr. Sorab's Lab, TMC-ACTREC, Navi Mumbai, India to Genotypic, Bangalore, India, for further processing of the samples.

treatment_protocol: Plakophilin3 was knocked down using using stable transfection of plasmid encoded shRNA.

tag: cell line

tag: origin

value: colorectal carcinoma derived


title: CB3 CTOS_xenograft tumor

source_name: CB3 CTOS, xenograft tumor, replicate 1

value: xenograft tumor


title: vec2 (HCT116 cell line)

description: Gene expression of HCT116 derived vector control

source_name: Cells, vector control,biological replicate 2


title: CB3 CTOS_in suspension

description: Gene expression of C45 CTOS under floating conditions

source_name: CB3 CTOS, in suspension, replicate 1

value: cultured spheroids (CTOS)


title: vec1 (HCT116 cell line)

source_name: Cells, vector control,biological replicate 1


title: HT29 cell line

source_name: HT29 cell line, 2D, replicate 1


title: CB3 CTOS_in gel

description: Gene expression of C45 CTOS under gel embedded conditions

source_name: CB3 CTOS, in gel, replicate 1


title: White sector of colony 6.1 derived from MD556

description: MD556-6.1 W1 WG


title: shpkp3-2-1 (HCT116 cell line)

source_name: Cells, PKP3 knockdown biological replicate 1


title: C166 CTOS_xenograft tumor

source_name: C166 CTOS, xenograft tumor, replicate 1


title: C166 CTOS_in gel

source_name: C166 CTOS, in gel, replicate 1


title: C138 CTOS_xenograft tumor

source_name: C138 CTOS, xenograft tumor, replicate 1


title: C166 CTOS_in suspension

source_name: C166 CTOS, in suspension, replicate 1


title: C138 CTOS_original tumor

description: Gene expression of C45 original tumor

source_name: C138 CTOS, original tumor, replicate 1

value: patient tumor


title: C138 CTOS_in suspension

source_name: C138 CTOS, in suspension, replicate 1


title: C132 CTOS_in suspension

source_name: C132 CTOS, in suspension, replicate 1


title: Red sector of colony 6.1 derived from MD556

description: MD556-6.1 R1 WG

source_name: Sector of colony grown for two days at 30 degrees C

source_name: PG311 control strain


title: C138 CTOS_in gel

source_name: C138 CTOS, in gel, replicate 1


title: Red sector of colony 5.3 derived from MD556

description: MD556-5.3 R1 WG


title: C132 CTOS_in gel

source_name: C132 CTOS, in gel, replicate 1


title: White sector of colony 5.3 derived from MD556

description: MD556-5.3 W1 WG


title: aladin root, biological rep3

city: Vienna

first: Guillaume

last: Queval

address: Dr Bohr Gasse 3

country: Austria

institute: GMI-Gregor Mendel Institute of Molecular Plant Biology GmbH

description: Gene expression data from aladin root

hyb_protocol: Hybridization was performed as described in the Affymetrix Standard Operating procedures.

scan_protocol: Scanning was performed as described in the Affimetrix Standard Operating procedures.

data_processing: The Robust Multiarray Averaging (RMA) method of microarray normalization and summarization was used.

label: biotin

organism: Arabidopsis thaliana

source_name: Arabidopsis root

label_protocol: Labeling was performed as described in the Affymetrix Standard Operating Procedures.

growth_protocol: After a stratification period of 3 days, the plants were grown for 10 days on vertical plates containing solidified half strength Murashige and Skoog medium (1/2 MS) supplemented with 1% sucrose, 0.1 g.L-1 myo-inositol, 0.5 g.L-1 MES (pH 5.7) and 1% agar at 16 h photoperiod and 20°C.

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

treatment_protocol: Immediatly after the separation of the roots and the shoots, the samples were frozen in liquid nitrogen.

value: root

tag: genotype

value: aladin

tag: age

value: 10 days


title: White sector of colony 4.3 derived from MD556

description: MD556-4.3 W1 WG


title: aladin root, biological rep2

description: Gene expression data from aladin root


title: C111 CTOS_in suspension

source_name: C111 CTOS, in suspension, replicate 1


title: White sector of colony 4.1 derived from MD556

description: MD556-4.1 W1 WG


title: Red sector of colony 4.3 derived from MD556

description: MD556-4.3 R1 WG

value: red


title: aladin root, biological rep1

description: Gene expression data from aladin root


title: Red sector of colony 4.1 derived from MD556

description: MD556-4.1 R1 WG

value: 2 days growth at 30


title: C97 CTOS_in suspension

source_name: C97 CTOS, in suspension, replicate 1


title: Wassilewskija-4 root, biological rep2

description: Gene expression data from Wassilewskija-4 root


title: White sector of colony 1 derived from MD556

description: MD556-1 W1 WG

value: Pink


title: C97 CTOS_in gel

source_name: C97 CTOS, in gel, replicate 1


title: C75 CTOS_xenograft tumor

source_name: C75 CTOS, xenograft tumor, replicate 1


title: C86 CTOS_in gel

source_name: C86 CTOS, in gel, replicate 1


title: Red sector of colony 1 derived from MD556

description: MD556-1 R1 WG

value: Control heterozygous strain


title: C75 CTOS_in gel

source_name: C75 CTOS, in gel, replicate 1


title: C111 CTOS_in gel

source_name: C111 CTOS, in gel, replicate 1


title: Wassilewskija-4 root, biological rep3


title: C86 CTOS_in suspension

source_name: C86 CTOS, in suspension, replicate 1


title: C86 CTOS_original tumor

description: Gene expression of C45 original tumor

source_name: C86 CTOS, original tumor, replicate 1


title: White sector of colony 23.10 derived from MD555

description: MD555-23.10 W1 WG


title: C48 CTOS_in suspension

source_name: C48 CTOS, in suspension, replicate 1


title: C75 CTOS_original tumor

description: Gene expression of C45 original tumor

source_name: C75 CTOS, original tumor, replicate 1


title: Wassilewskija-4 root, biological rep1


title: C48 CTOS_in gel

source_name: C48 CTOS, in gel, replicate 1


title: C75 CTOS_in suspension

source_name: C75 CTOS, in suspension, replicate 1


title: aladin shoot, biological rep2

description: Gene expression data from aladin shoot

source_name: Arabidopsis shoot

value: shoot


title: Red sector of colony 23.10 derived from MD555

description: MD555-23.10 R1 WG

source_name: Sector of colony grown for two days at 30 degrees C

source_name: PG311 control strain


title: aladin shoot, biological rep3

description: Gene expression data from aladin shoot


title: White sector of colony 23.8 derived from MD555

description: MD555-23.8 W1 WG


title: aladin shoot, biological rep1

description: Gene expression data from aladin shoot


title: C45 CTOS_xenograft tumor

source_name: C45 CTOS, xenograft tumor, replicate 1


title: Red sector of colony 23.9 derived from MD555

description: MD555-23.9 R1 WG


title: C45 CTOS_original tumor

description: Gene expression of C45 original tumor

source_name: C45 CTOS, original tumor, replicate 1


title: Red sector of colony 23.8 derived from MD555

description: MD555-23.8 R1 WG


title: Wassilewskija-4 shoot, biological rep3

description: Gene expression data from Wassilewskija-4 shoot


title: Wassilewskija-4 shoot, biological rep2


title: C45 CTOS_in suspension

source_name: C45 CTOS, in suspension, replicate 1


title: C45 CTOS_in gel

source_name: C45 CTOS, in gel, replicate 1


title: Wassilewskija-4 shoot, biological rep1


title: White sector of colony 23.7 derived from MD555

description: MD555-23.7 W1 WG


title: Red sector of colony 23.7 derived from MD555

description: MD555-23.7 R1 WG


title: C86 CTOS_xenograft tumor

source_name: C86 CTOS, xenograft tumor, replicate 1


title: White sector of colony 23.5 derived from MD555

description: MD555-23.5 W1 WG


title: Red sector of colony 23.5 derived from MD555

description: MD555-23.5 R1 WG


title: White sector of colony 23.4 derived from MD555

description: MD555-23.4 W1 WG


title: Red sector of colony 23.4 derived from MD555

description: MD555-23.4 R1 WG


title: White sector of colony 23.9 derived from MD555

description: MD555-23.9 W1 WG


title: White sector of colony 19.3 derived from MD555

description: MD555-19.3 W1 WG


title: White sector of colony 17.2 derived from MD555

description: MD555-17.2 W1 WG


title: Red sector of colony 15.5 derived from MD555

description: MD555-15.5 R1 WG


title: White sector of colony 15.5 derived from MD555

description: MD555-15.5 W1 WG


title: Red sector of colony 17.2 derived from MD555

description: MD555-17.2 R1 WG


title: White sector of colony 15.1 derived from MD555

description: MD555-15.1 W1 WG


title: Red sector of colony 15.1 derived from MD555

description: MD555-15.1 R1 WG


title: Red sector of colony 19.3 derived from MD555

description: MD555-19.3 R1 WG


title: siNRCP-3

city: allston

first: rajesha

last: rupaimoole

state: ma

address: 1315 commonwealth ave, apt 308

institute: UT MD Anderson Cancer Center

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V3.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing:
Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Sample Gene Profile option of this software was used.
We used Sample Gene Profile option of Illumina BeadStudio software.

label: Biotin

source_name: Ovarian cancer cells

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

growth_protocol: Cells were cultured in 5% CO2 humidified chamber.

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

treatment_protocol: Skov3 cancer cells were treated with siRNA against NRCP and control siRNAs for 48hrs.


title: E8N

city: Bethesda

first: Howard

last: Yang

state: MD

address: 37 CONVENT DR, Room 5120

department: CCR

institute: NCI

description: frozen tissue extracted by Trizol

hyb_protocol: Total RNA was reverse transcripted to cDNA, reverse transcripted to labelled aRNA, purified, fragmented, and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The arrays were then washed using Affymetrix fluidics stations, and scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Microarray data were normalized using the RMA method .

source_name: adjacent normal tissue

label_protocol: As per manufacturer (Affymetrix).

extract_protocol: Total RNA was extracted and purified by standard Trizol method and followed with qualification check by Agilent 2100.

tag: diagnosis

value: esophageal squamous cell carcinoma (ESCC)

tag: tissue type

value: adjacent normal epithelium


title: sicontrol-2


title: E8T

description: frozen tissue extracted by Trizol

source_name: tumor tissue

value: tumor


title: sicontrol-1


title: E9T

description: frozen tissue extracted by Trizol


title: sicontrol-3


title: siNRCP-1


title: E5N

description: frozen tissue extracted by Trizol


title: E9N

description: frozen tissue extracted by Trizol


title: E7T

description: frozen tissue extracted by Trizol


title: siNRCP-2


title: E6N

description: frozen tissue extracted by Trizol


title: Acute TCMR, 6334175099_E

city: Bari

first: Fabio

last: Sallustio

state: Bari

address: Piazza G. Cesare N°11

country: Italy

institute: University of Bari

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

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

source_name: FFPE renal biopsy, acute TCMR

label_protocol: Biotinylated cDNA was prepared with the Illumina WG-DASL asay.

extract_protocol: RNA was extracted with QIAGEN miRNeasy FFPE kit in accordance with the prescribed protocol provided with the kit.

tag: patient type

value: acute T-cell mediated rejection (TCMR)

value: renal biopsy


title: E3N

description: frozen tissue extracted by Trizol


title: E3T

description: frozen tissue extracted by Trizol


title: E30T

description: frozen tissue extracted by Trizol


title: E4T

description: frozen tissue extracted by Trizol


title: E30N

description: frozen tissue extracted by Trizol


title: E6T

description: frozen tissue extracted by Trizol


title: Acute TCMR, 6334175099_C


title: E7N

description: frozen tissue extracted by Trizol


title: E4N

description: frozen tissue extracted by Trizol


title: E5T

description: frozen tissue extracted by Trizol


title: Red sector of colony 14.4 derived from MD555

description: MD555-14.4 R1 WG


title: E2T

description: frozen tissue extracted by Trizol


title: White sector of colony 13.8 derived from MD555

description: MD555-13.8 W1 WG

value: white


title: Red sector of colony 13.8 derived from MD555

description: MD555-13.8 R1 WG


title: White sector of colony 14.4 derived from MD555

description: MD555-14.4 W1 WG


title: White sector of colony 13.7 derived from MD555

description: MD555-13.7 W1 WG


title: Red sector of colony 13.7 derived from MD555

description: MD555-13.7 R1 WG


title: White sector of colony 13.4 derived from MD555

description: MD555-13.4 W1 WG


title: E2N

description: frozen tissue extracted by Trizol


title: E29T

description: frozen tissue extracted by Trizol


title: E27N

description: frozen tissue extracted by Trizol


title: Acute TCMR, 6334175132_G


title: Acute TCMR, 6334175099_A


title: Acute TCMR, 6334175132_I


title: E28T

description: frozen tissue extracted by Trizol


title: E29N

description: frozen tissue extracted by Trizol


title: E26T

description: frozen tissue extracted by Trizol


title: E27T

description: frozen tissue extracted by Trizol


title: Acute TCMR, 6334175132_E


title: Acute TCMR, 6334175132_K


title: E25T

description: frozen tissue extracted by Trizol


title: Red sector of colony 13.4 derived from MD555

description: MD555-13.4 R1 WG


title: E26N

description: frozen tissue extracted by Trizol


title: Acute TCMR, 6334175132_C


title: E25N

description: frozen tissue extracted by Trizol


title: E24N

description: frozen tissue extracted by Trizol


title: Acute TCMR, 6334175132_A


title: E24T

description: frozen tissue extracted by Trizol


title: White sector of colony 12.1 derived from MD555

description: MD555-12.1 W1 WG


title: Acute TCMR, 6334175132_B


title: E28N

description: frozen tissue extracted by Trizol


title: E23T

description: frozen tissue extracted by Trizol


title: E23N

description: frozen tissue extracted by Trizol


title: Red sector of colony 12.1 derived from MD555

description: MD555-12.1 R1 WG


title: E22N

description: frozen tissue extracted by Trizol


title: E21T

description: frozen tissue extracted by Trizol


title: White sector of colony 6.1 derived from MD555

description: MD555-6.1 W1 WG


title: Cadaveric Donor, 5937329086_I

source_name: FFPE renal biopsy, cadaveric donor

value: cadaveric donor


title: White sector of colony 5.5 derived from MD555

description: MD555-5.5 W1 WG


title: Red sector of colony 6.1 derived from MD555

description: MD555-6.1 R1 WG


title: White sector of colony 5.2 derived from MD555

description: MD555-5.2 W1 WG


title: E21N

description: frozen tissue extracted by Trizol


title: Red sector of colony 5.2 derived from MD555

description: MD555-5.2 R1 WG


title: White sector of colony 5.1 derived from MD555

description: MD555-5.1 W1 WG


title: Red sector of colony 5.5 derived from MD555

description: MD555-5.5 R1 WG


title: Red sector of colony 5.1 derived from MD555

description: MD555-5.1 R1 WG


title: E1T

description: frozen tissue extracted by Trizol


title: E22T

description: frozen tissue extracted by Trizol


title: Cadaveric Donor, 5937329086_F


title: E20T

description: frozen tissue extracted by Trizol


title: E20N

description: frozen tissue extracted by Trizol


title: Cadaveric Donor, 5937329086_G


title: E1N

description: frozen tissue extracted by Trizol


title: Cadaveric Donor, 5937329086_E


title: E18N

description: frozen tissue extracted by Trizol


title: Cadaveric Donor, 5937329086_A


title: E15T

description: frozen tissue extracted by Trizol


title: E18T

description: frozen tissue extracted by Trizol


title: Cadaveric Donor, 5937329086_K


title: Cadaveric Donor, 5937329086_D


title: E17T

description: frozen tissue extracted by Trizol


title: White sector of colony 2.1 derived from MD555

description: MD555-2.1 W1 WG


title: E19T

description: frozen tissue extracted by Trizol


title: E15N

description: frozen tissue extracted by Trizol


title: Cadaveric Donor, 5937329086_B


title: Cadaveric Donor, 5937329086_C


title: E17N

description: frozen tissue extracted by Trizol


title: E19N

description: frozen tissue extracted by Trizol


title: E16T

description: frozen tissue extracted by Trizol


title: E14T

description: frozen tissue extracted by Trizol


title: E16N

description: frozen tissue extracted by Trizol


title: Cadaveric Donor, 5993419094_I


title: E14N

description: frozen tissue extracted by Trizol


title: Cadaveric Donor, 5993419094_G


title: E13T

description: frozen tissue extracted by Trizol


title: Red sector of colony 2.1 derived from MD555

description: MD555-2.1 R1 WG


title: E13N

description: frozen tissue extracted by Trizol


title: Cadaveric Donor, 5993419094_E


title: Cadaveric Donor, 5993419094_A


title: E12T

description: frozen tissue extracted by Trizol


title: E11N

description: frozen tissue extracted by Trizol


title: E12N

description: frozen tissue extracted by Trizol


title: Chronic TCMR, 5993419100_L

source_name: FFPE renal biopsy, chronic TCMR

value: chronic T-cell mediated rejection (TCMR)


title: E11T

description: frozen tissue extracted by Trizol


title: Cadaveric Donor, 5993419094_C


title: Cadaveric Donor, 5993419100_K


title: HCT_Dox2

city: Sevilla

first: Jose

middle: C.

last: Reyes

address: Av. Américo Vespucio

department: Genome biology

country: Spain

institute: CABIMER

description: Gene level transcriptome

hyb_protocol: GeneChip® HTA Arrays (GeneChip® Human Transcriptome Array 2.0) were hybridized for 16 hours in a 45°C oven, rotated at 60 rpm. According to the GeneChip® Expression Wash, Stain and Scan Manual (PN 702731 Rev 3, Affymetrix Inc., Santa Clara, CA) the arrays were then washed and stained using the Fluidics Station 450

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix), using standard parameters.

data_processing: Raw data were extracted from the scanned images and analyzed with the Affymetrix Command Console® 2.0 Software (AGCC). The raw array data were preprocessed and normalized using the Robust Multichip Average (RMA) method (5). Data were further processed using Trancriptome Analysis Console (TAC) Software from Affymetrix

source_name: HCT-shSLBP + DOX

label_protocol: 250 nanograms of total RNA from each sample were used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the GeneChip® WT PLUS Reagent Kit User Manual (P/N 703174 Rev 1 Affymetrix Inc., Santa Clara, CA).

growth_protocol: HCT-shSLBP cells were cultured in McCoy’s 5A-modified. Medium was supplemented with 10% fetal bovine serum , 100 units/ml penicillin and 100 µg/ml streptomycin, and cells were cultivated in a 37°C incubator with 5% CO2.

extract_protocol: Total RNA was isolated in triplicate from HCT-shSLBP cells using RNeasy Mini Kit (Qiagen)

treatment_protocol: Three cultures (replicates)  were not treated. Three cultures (replicates) were treated with 2 μg/ml Doxycycline

value: HCT-shSLBP derived from HCT116

tag: cell type

value: colon cancer


title: Cadaveric Donor, 5993419100_G


title: Cadaveric Donor, 5993419100_H


title: CON3

city: TianJin

first: Ding

last: Yahui

address: Nanjing Road 288

institute: Institute of Hematology & Hospital of Blood Diseases

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 12.6.1 (Agilent technologies, Santa Clara, CA, US).

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-026，Life technologies, Carlsbad, CA, US)/TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: KG1a cells were cultured in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum. MCL induced gene expression in KG1a cell was measured at 8 hours after exposure to doses of 10µM. Each sample was performed in triplicate.

tag: agent

value: control


title: Cadaveric Donor, 5993419100_I


title: MCL1

value: MCL


title: HCT_Control3

description: Gene level transcriptome

source_name: HCT-shSLBP


title: MCL3


title: E10T

description: frozen tissue extracted by Trizol


title: MEP control rep3

city: Fukuoka

first: Hirofumi

last: Tsuzuki

address: 3-1-1 Maidashi, Higashi-Ku

department: Department of Medicine and Biosystemic Science

institute: Kyushu University

description: replicate 3

data_processing: The data were normalized using quantile normalization with BeadStudio (Illuumina).

organism: Mus musculus

label_protocol: Biotinylated cRNA samples were prepared with MessageAmp II aRNA Kit (Life Technologies) and Illumina TotalPrep RNA Amplification Kit (Illumina) for Illumina microarrays.

growth_protocol: EoPs, BaPs or MCPs were cultured for 48 hours in the presence of IL-3 (1ng/ml) with or without IL-33 (50ng/ml). MEPs were cultured for 48 hours in the presence of SCF (1ng/ml), IL-3 (2ng/ml), IL-11 (1ng/ml), Tpo (1ng/ml) and human Epo (0.5U/ml) with or without IL-33 (50ng/ml).

extract_protocol: RNA samples were extracted with TRIzol reagent following to the manufacture's guideline.

tag: strain

value: 12 weeks

tag: tissue/cell source

value: bone marrow

tag: stimulated with

value: none (control)


title: MCL2


title: CON1


title: HCT_Dox1

description: Gene level transcriptome


title: E10N

description: frozen tissue extracted by Trizol


title: CON2


title: HCT_Dox3

description: Gene level transcriptome


title: HCT_Control1

description: gene level transcriptome


title: MEP IL-33 rep3

description: replicate 3

value: IL-33 (50ng/ml) for 48hrs


title: HCT_Control2

description: Gene level transcriptome


title: MEP control rep2

description: replicate 2


title: Cadaveric Donor, 5993419100_C


title: MEP IL-33 rep2

description: replicate 2


title: MCP control rep2

description: replicate 2

value: isolated from day4 granulocyte/monocyte progenitor (GMP) cultured in the presence of IL-3

value: mast cell progenitors (MCPs)


title: BaP control rep2

description: replicate 2

value: basophil progenitors (BaPs)


title: MCP IL-33 rep2

description: replicate 2


title: Cadaveric Donor, 5993419100_E


title: Islets of Langerhans _48hrs in culture 2

first: Renjitha

last: Gopurappilly

address: GKVK PO, Bellary Rd, Allalasandra, Yelahanka

department: Regenerative Medicine

institute: SORM, Manipal University

description: Gene expression of freshly isolated pancreatic islets

hyb_protocol: 600ng of labeled cRNA were hybridized on the array using the Gene Expression Hybridization kit (Part Number 5188-6420; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).  The hybridized, washed microarray slides were then scanned on a G2600D scanner (Agilent Technologies)

scan_protocol: Microarray slides were then scanned on a G2600D scanner (Agilent Technologies)

data_processing: Images were quantified using Agilent Feature Extraction Software and   Normalization of the data was done in GeneSpring GX using the 75th percentile shift (Percentile shift normalization)

source_name: Pancreas

label_protocol: The samples were labeled using Agilent Quick Amp Kit (Part number: 5190-0424). 500ng of total RNA was reverse transcribed using oligodT primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106). Concentration and amount of dye incorporated was determined using Nanodrop. Samples that pass the QC for specific activity were taken for hybridization.

growth_protocol: Groups of two to four mice were killed by cervical dislocation, and pancreata were removed aseptically without ductal injection and distension.  The pancreata were cut into small pieces and washed thrice with HBSS. The resulting pieces were subjected to collagenase digestion using a magnetic stirrer. The dissociation medium consisted of Dulbecco’s modified minimum essential medium (DMEM) supplemented with 1 mg/mL collagenase type V (Sigma) and 2% BSA fraction V (Sigma). The tissue digest was then transferred to 50 ml conical flask, and digestion was stopped by addition of chilled DMEM with 10% fetal calf serum. The mixture was then centrifuged at 1000 rpm for 10 min, vortexed and the pellet was seeded in T25 culture flasks. DMEM Knockout media (Invitrogen) with 10% FBS (Hyclone) was used for the isolation procedure. The cells seeded in T25 flasks were incubated at 37°C in an atmosphere comprising of 5% CO2 for 48 h. The flasks were rinsed by removing the supernatant and flushing out the islets with media. The islets were purified and used as REFERENCE.                                                                                Fibroblastoid-like cells seen attached to the surface were passaged every 3rdto 4th day once they acquired 80-90% confluency. These MSC-like cells were thereafter maintained under similar conditions.For differentiation into ISLET-LIKE CLUSTERS MSCs were re-suspended in serum free (SFM) medium containing 1% BSA and 1X insulin transferrin selenium (ITS) in low adherent dishes. On day 3 cells were allowed to settle in sterile centrifuge tube and reseeded in above medium with addition of 0.3 mM taurine. On day 7, the cell clusters were fed with SFM containing 1.5% BSA, 100 mM nicotinamide, 3 mM taurine and 100 mM GLP-1. A progressive cell clustering from day 2 onwards which led to typical islets like clusters (ILCs) formation at the end of day 10 was seen.

extract_protocol: RNA was prepared using the RNeasy Lipid Tissue Kit (Catlog No : 74804)  following the manufacturer's recommendations.

value: Swiss albino

tag: weight

value: 10-12 weeks

tag: gender

value: Male

value: freshly isolated pancreatic islets


title: EoP control rep2

description: replicate 2

value: eosinophil progenitors (EoP


title: Islets of Langerhans _48hrs in culture 1


title: MEP control rep1

description: replicate 1


title: Cadaveric Donor, 5993419100_B

value: cadaveric donor

value: renal biopsy


title: Cadaveric Donor, 5937329079_K


title: EoP IL-33 rep2

description: replicate 2


title: Cadaveric Donor, 5993419100_F


title: MEP IL-33 rep1

description: replicate 1


title: Chronic TCMR, 5937329079_H

value: chronic T-cell mediated rejection (TCMR)


title: Cadaveric Donor, 5937329079_I


title: Transcriptomic profiling in the heart of C57BL/6J mice at age of 2 weeks

city: Gdansk

first: Pawel

last: Sachadyn

address: Narutowicza 11/12

department: Molecular Biotechnology and Microbiology

country: Poland

institute: Gdansk University of Technology

description: transcriptomic profiling performed for the pool of three total RNA samples extracted from three hearts

hyb_protocol: Probe labeling and hybridization was performed with Roche NimbleGen kit using the standard protocol for eukaryotic RNA samples and NimbleGen mouse gene expression 12x135K array (Roche, cat. no. 05543797001). The cDNA samples were labeled with Cy3 using a NimbleGen One-Color DNA labeling kit (Roche, cat. no. 06370411001), and hybridized to slides using a NimbleGen hybridization system (Roche, cat. no. 05583683001).

scan_protocol: The slides were scanned using MS200 Scanner (Roche, NimbleGen) at 2 µm resolution by using high-sensitivity and autogain settings.

data_processing: The data from scanned images were processed and normalized using a robust multi-chip average (RMA) algorithm using NimbleScan (2.6.0.0) software with default settings (Roche)

source_name: whole heart

label_protocol: First strand cDNA synthesis was performed with Maxima Reverse Transcriptase (ThermoScientificBio. cat. no. EP0742) using 3 µg of total RNA, 400 U of the Maxima Reverse Transcriptase (200 U/ul), 5 x reaction buffer (250 mM Tris-HCl, 375 mM KCl, 15 mM MgCl, 50 mM DTT) and oligo dT15.(200 pmoles) in a total volume of 40 µl. Second strand cDNA was synthesized using cDNA Synthesis System (Roche, cat. no. 11 117 831 001) according to the second strand synthesis manufacturer's protocol.

extract_protocol: The solid tissues were disrupted in liquid nitrogen prior RNA extraction. Total RNAs was purified using the RNeasy Mini Kit (QIAGEN. cat. no. 74104) coupled with on-column DNA digestion following the manufacturer’s protocols.

treatment_protocol: Tissue samples from C56BL/6J mice from the Tri-City Academic Laboratory Animal Centre – Research and Services Centre, Medical University of Gdańsk for hearts form embryonic day 15, 16, 17, 19, 1 day, 7 day and 2 week old mice. Tissue samples form C56BL/6J mice from Jackson Laboratories for hearts fro 8 week old mice.  All tissues were collected in RNAlater stabilization reagent (QIAGEN. cat. no. 76104), transported on dry ice and stored at -80 C.

value: heart

value: 2 weeks


title: Chronic TCMR, 5937329079_L


title: MCP control rep1

description: replicate 1

value: 12 weeks


title: Transcriptomic profiling in the heart of C57BL/6J mice at age of 8 weeks

value: 8 weeks


title: Transcriptomic profiling in the heart of C57BL/6J mice at age of 1 day

value: 1 day


title: Insulin producing clusters _in vitro_ pancreatic MSC-like cells 2

description: Gene expression of islet like clusters generated from MSCs after 10day culture with induction cocktail


title: Transcriptomic profiling in the heart of C57BL/6J mice at age of 7 days

value: 7 days


title: Cadaveric Donor, 5937329079_G


title: BaP IL-33 rep2

description: replicate 2

value: bone marrow

value: IL-33 (50ng/ml) for 48hrs


title: Transcriptomic profiling in the heart of C57BL/6J mice at embryonic day 18

value: embryonic day 18


title: BaP control rep1

description: replicate 1

value: basophil progenitors (BaPs)

value: none (control)


title: Chronic TCMR, 5937329079_F


title: Transcriptomic profiling in the heart of C57BL/6J mice at embryonic day 19

value: embryonic day 19


title: Transcriptomic profiling in the heart of C57BL/6J mice at embryonic day 16

value: embryonic day 16


title: Insulin producing clusters _in vitro_ pancreatic MSC-like cells 1

value: Swiss albino

value: 10-12 weeks

value: Male

value: islet like clusters generated from MSCs after 10day culture with induction cocktail


title: MCP IL-33 rep1

description: replicate 1

value: isolated from day4 granulocyte/monocyte progenitor (GMP) cultured in the presence of IL-3

value: mast cell progenitors (MCPs)


title: ASC 1HR LL-37

city: Seoul

first: Sa Ik

last: Bang

address: Ilwon-dong 50 cancer center

department: Plastic Surgery

country: South Korea

institute: Samsung Medical Center

description: Gene expression after 1hr in ll-37 treat

hyb_protocol: The Cy5-labeled aRNAs were resuspended in 100 ㎕ of hybridization solution (GenoCheck, Korea). After labeled aRNAs were placed on Agilent Human whole genome 4x44K array (Agilent technologies, CA) and covered by a NimbleGen A4 mixer (Biomicro systems, Inc. UT). The slides were hybridized for 12 hr at 42 ℃ MAUI system (Biomicro systems, Inc. UT). The hybridized slides were washed in 2 X SSC, 0.1 % SDS for 2 min, 1 X SSC for 3 min, and then 0.2 X SSC for 2 min at room temperature. The slides were centrifuged at 3000 rpm for 20 sec to dry.

scan_protocol: The arrays were analyzed using an Agilent scanner with associated software. Gene expression levels were calculated with Feature Extraction v10.7.3.1 (Agilent technologies, CA) Relative signal intensities for each gene were generated using the Robust Multi-Array Average algorithm.

data_processing: The data were processed based on median polish normalization method using the GeneSpring GX 11.0 (Agilent technologies, CA). This normalization method aims to make the distribution of intensities for each array in a set of arrays the same. The normalized, and log transformed intensity values were then analyzed using GeneSpring GX 11.0 (Agilent technologies, CA). Fold change filters included the requirement that the genes be present in at least 200% of controls for up-regulated genes and lower than 50% of controls for down-regulated genes. Hierarchical clustering data were clustered groups that behave similarly across experiments using GeneSpring GX 7.3.1 (Agilent technologies, CA). Clustering algorithm was Euclidean distance, average linkage.

source_name: Adiopse derived stem cell, 6hr, ll-38 no treatment

label_protocol: Each total RNA sample (2ug) was labeled and amplified using ULS aRNA labeling kit (Kreatech diagnostics, Netherlands)

extract_protocol: Total RNA was extracted from the human stem cell using the TRI REAGENT (MRC, OH) according to the manufacturer’s instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Freshly adipose derived stem cells (ASCs) from healthy volunteers was treated with LL-37 20 μg/ml for 1 hr with low glucose DMEM medium supplemented with 10% heat-inactivated fetal bovine serum.   The cells were incubated for 1 hours at 37 ºC in a humidified incubator with 5% CO2.

value: adipose tissue

value: female


title: Cadaveric Donor, 5937329079_E

value: cadaveric donor

value: renal biopsy


title: EoP IL-33 rep1

description: replicate 1

value: 12 weeks

value: bone marrow

value: eosinophil progenitors (EoP


title: White sector of colony 1-16 derived from SLA64

description: SLA64.1-16 W1 VA

source_name: Sector of colony grown for two days at 30 degrees C

tag: color of sector/colony

value: white

tag: growth condition

value: 2 days growth at 30

source_name: JSC23 control strain

tag: colony color

value: Pink

tag: sample type

value: Control heterozygous strain


title: BaP IL-33 rep1

description: replicate 1

value: basophil progenitors (BaPs)

value: IL-33 (50ng/ml) for 48hrs


title: Chronic TCMR, 5937329079_D

value: chronic T-cell mediated rejection (TCMR)

tag: tissue


title: ShamPOD7, biological rep4

first: Seog Bae

last: Oh

address: 101 Daehakro, Jongno-Ku

institute: Seoul National University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse gene 1.0 ST Array as described in the Gene Chip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Genechip Array scanner 3000 7G (Affymetrix).

data_processing: Expression data were generated by Affymetrix Expression Console software version1.1. We normalized the arrays using Robust Multichip Average (RMA) normalization. we summarized perfect match (PM) probes on the array by specifically taking the log of the second highest PM probe intensity. In addition, we removed batch effects using a two-stage least squares method.

source_name: spinal microglia 7day after sham surgery

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

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

tag: genotype

value: Cx3cr1 hetero

value: spinal cord microglia

value: 8-10 weeks


title: ASC 1HR CONTROL

description: Gene expression after 1hr in ll-37 no treat

source_name: Adiopse derived stem cell, 6hr, ll-37 treatment

value: adipose tissue


title: Cadaveric Donor, 5937329057_I


title: Cadaveric Donor, 5937329079_C


title: Cadaveric Donor, 5937329079_A


title: Cadaveric Donor, 5937329057_E


title: Phosphor4_04

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

country: Germany

institute: FBN Dummerstorf

description:
Gene expression data from PBMCs isolated from whole blood
Snowball arrays (Freeman et al. in BMC Biol 2012, 10:90), see the ArrayExpress database, accession no. A-AFFY-189

hyb_protocol: Labelled DNA was hybridized for 16 hr at 42°C on Snowball Arrays. Chips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500 and BioConductor.

organism: Sus scrofa

source_name: PBMC

label_protocol: Each RNA sample was transcribed to DNA using the Ambion WT Expression Kit (Ambion, Austin, TX, USA). DNA preparations were fragmented and labelled with the WT Terminal Labeling Kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated using Qiazol reagent (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was column-purified using the RNeasy Kit (Qiagen, Hilden, Germany).

treatment_protocol: Diets varying in phosphate content

value: PBMC

tag: dietary group

value: low-intake

value: w

tag: age (days post natum)


title: Cadaveric Donor, 5937329057_K

value: cadaveric donor

value: renal biopsy


title: ShamPOD7, biological rep3

tag: age


title: Cadaveric Donor, 5937329057_G

tag: patient type


title: Cadaveric Donor, 5937329057_C


title: ShamPOD7, biological rep5


title: ShamPOD7, biological rep6


title: EoP control rep1

description: replicate 1

value: 12 weeks

value: bone marrow

tag: cell type

value: eosinophil progenitors (EoP

value: none (control)


title: ShamPOD7, biological rep2


title: ShamPOD7, biological rep1


title: Phosphor4_02

value: medium-intake

value: m


title: Phosphor4_05


title: Phosphor1_20


title: Phosphor1_18

value: high-intake


title: Chronic TCMR, 5993419042_L

value: chronic T-cell mediated rejection (TCMR)


title: Red sector of colony 1-16 derived from SLA64

description: SLA64.1-16 R1 VA

value: red

value: 2 days growth at 30

value: Pink

value: Control heterozygous strain


title: POD7, biological rep5

source_name: spinal microglia 7day after L4 SNT

value: Cx3cr1 hetero

value: spinal cord microglia

value: 8-10 weeks


title: POD7, biological rep6


title: Phosphor4_03

value: PBMC


title: Phosphor1_19

value: w


title: Phosphor4_01

value: low-intake


title: White sector of colony 1-15 derived from SLA64

description: SLA64.1-15 W1 VA

value: white


title: Red sector of colony 1-15 derived from SLA64

description: SLA64.1-15 R1 VA


title: Phosphor1_17


title: White sector of colony 1-13 derived from SLA64

description: SLA64.1-13 W1 VA


title: Red sector of colony 1-14 derived from SLA64

description: SLA64.1-14 R1 VA


title: Cadaveric Donor, 5993419042_K

value: cadaveric donor

value: renal biopsy


title: White sector of colony 1-14 derived from SLA64

description: SLA64.1-14 W1 VA


title: Red sector of colony 1-13 derived from SLA64

description: SLA64.1-13 R1 VA


title: POD7, biological rep4


title: White sector of colony 1-12 derived from SLA64

description: SLA64.1-12 W1 VA


title: Phosphor1_15


title: Chronic TCMR, 5993419042_J


title: ShamPOD1, biological rep5

source_name: spinal microglia 1day after sham surgery


title: Phosphor1_16

value: medium-intake


title: POD7, biological rep2


title: Cadaveric Donor, 5993419042_I


title: Chronic TCMR, 5993419042_F


title: Cadaveric Donor, 5993419042_G


title: Red sector of colony 1-12 derived from SLA64

description: SLA64.1-12 R1 VA


title: Phosphor1_14


title: POD7, biological rep1


title: Cadaveric Donor, 5993419042_E


title: Chronic TCMR, 5993419042_D


title: POD7, biological rep3


title: Cadaveric Donor, 5993419042_C


title: ShamPOD1, biological rep4


title: Phosphor1_13


title: Phosphor1_11

value: m


title: Phosphor1_12

value: high-intake


title: ShamPOD1, biological rep3


title: White sector of colony 1-8 derived from SLA64

description: SLA64.1-8 W1 VA


title: Red sector of colony 1-6 derived from SLA64

description: SLA64.1-6 R1 VA


title: Phosphor1_10


title: White sector of colony 1-5 derived from SLA64

description: SLA64.1-5 W1 VA


title: Red sector of colony 1-8 derived from SLA64

description: SLA64.1-8 R1 VA


title: White sector of colony 1-6 derived from SLA64

description: SLA64.1-6 W1 VA


title: Red sector of colony 1-5 derived from SLA64

description: SLA64.1-5 R1 VA


title: Cadaveric Donor, 5993419042_A


title: Chronic TCMR, 5993419042_B

value: chronic T-cell mediated rejection (TCMR)


title: POD1, biological rep5

source_name: spinal microglia 1day after L4 SNT


title: Phosphor1_09


title: ShamPOD1, biological rep1


title: Phosphor1_06


title: Phosphor1_08


title: Cadaveric Donor, 5993419039_I


title: Cadaveric Donor, 5993419039_K


title: ShamPOD1, biological rep2


title: Phosphor1_05


title: Cadaveric Donor, 5993419039_G


title: Phosphor1_04


title: Cadaveric Donor, 5993419039_F


title: POD1, biological rep3


title: Phosphor1_03


title: POD1, biological rep6


title: POD1, biological rep1


title: Cadaveric Donor, 5993419039_E


title: POD1, biological rep4


title: POD1, biological rep2


title: Phosphor1_02


title: Phosphor1_01


title: Ovarian Tumor tissue R14

description: noncoding RNA expression

hyb_protocol: Superscript Plus Indirect cDNA labelling system from Lifetechnologies

scan_protocol: Agilent Scanner G2505B at 5 um in cy3 and cy5

data_processing: Agilent FE v 9.5.3.1

source_name: ovarian cancer tumor tissue

extract_protocol: RNA was isolated using Trizol RNA isolation method (Lifetechnologies). RNA qulaity was meassured using Agilent Bioanalsyer, with atleast RIN<8.

value: Ovarian Tumor tissue

value: Female


title: Transcriptomic profiling in the heart of C57BL/6J mice at embyronic day 15

value: heart

value: embryonic day 15


title: Cadaveric Donor, 5993419039_C


title: Ovarian Tumor tissue R13

description: noncoding RNA expression

label_protocol: Superscript Plus Indirect cDNA labelling system from Lifetechnologies


title: mammary_gland_tumor-Elf5_Metastasis rep3

city: Sydney

first: Daniel

last: Roden

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute

description:
Lung metastasis, Elf5 dox induced EGFP positive
Met_3

hyb_protocol: Labeled, fragmented cDNA hybridized to Affymetrix Mouse Gene 1.0 ST Gene Arrays at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.

scan_protocol: Arrays were scanned at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.

data_processing: Data was RMA normalized using NormalizeAffymetrixST (version 2.0) GenePattern module from the Peter Wills Bioinformatics Centre's GenePattern Server: http://pwbc.garvan.unsw.edu.au/gp

label_protocol: Total RNA was converted to cDNA. The cDNA was fragmented, biotin labeled at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.

growth_protocol: MMTV-PyMT mouse mammary tumor samples  (and metastasis) were processed for single cell suspension and FACS sorted based on Lin- CD24+ markers. RNA was extracted from these populations straight after FACS sorting.

extract_protocol: Total RNA was extracted by using the Qiagen RNeasy minikit (Qiagen, Doncaster, Vic, Australia) according to manufacturer’s protocol. Following extraction, RNA concentration and purity were analyzed using the NanoDrop® ND-1000 Spectrophotometer (Nano-Drop Technologies, Wilmington, DE, USA). For Affymetrix GeneChip® analysis, the integrity of RNA was analyzed using the Agilent Bioanalyser 2100 6000 Nano Assay (Agilent Technologies, Palo Alto, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Mice were exposed continuosly to a diet containing 700mg/Kg of Doxocyclin (Gordon’s Specialty Stockfeeds) from week 6 of age until the ethical endpoint (8 weeks total treatment)

value: female

value: lung metastasis

value: FBV/N

tag: genotype/variation

value: chronic (8 weeks) Elf5 induced expression


title: Cadaveric Donor, 5993419039_B


title: Phosphor4_19

value: PBMC

value: w


title: Phosphor4_20

value: low-intake


title: Ovarian Tumor tissue R11

description: noncoding RNA expression


title: Cadaveric Donor, 5993419039_A

value: cadaveric donor


title: Phosphor4_18


title: Phosphor4_17


title: Cadaveric Donor, 5993419039_D

value: renal biopsy


title: Ovarian Tumor tissue R10

description: noncoding RNA expression


title: mammary_gland_tumor-Elf5_Metastasis rep2

description:
Lung metastasis, Elf5 dox induced EGFP positive
Met_2

tag: strain


title: Ovarian Tumor tissue R12

description: noncoding RNA expression


title: mammary_gland_tumor-Elf5_EGFP_pos rep1

description:
Mammary gland tumor, Elf5 dox induced EGFP positive
GFP_Pos_1

value: mammary gland tumor


title: mammary_gland_tumor-Elf5_EGFP_pos rep3

description:
Mammary gland tumor, Elf5 dox induced EGFP positive
GFP_Pos_3


title: Ovarian Tumor tissue R8

description: noncoding RNA expression


title: mammary_gland_tumor-Elf5_Metastasis rep1

description:
Lung metastasis, Elf5 dox induced EGFP positive
Met_1


title: Chronic TCMR, 5937345100_G


title: Chronic TCMR, 5937345100_J


title: mammary_gland_tumor-Elf5_EGFP_pos rep2

description:
Mammary gland tumor, Elf5 dox induced EGFP positive
GFP_Pos_2


title: Chronic TCMR, 5937345100_I


title: mammary_gland_tumor-Elf5_EGFP_neg rep3

description:
Mammary gland tumor, EGFP negative control
GFP_Neg_3

value: control


title: Phosphor4_14


title: Phosphor4_16

value: medium-intake

value: m


title: Ovarian Tumor tissue R9

description: noncoding RNA expression

value: Ovarian Tumor tissue


title: Ovarian Tumor tissue R6

description: noncoding RNA expression

value: Female


title: Ovarian Tumor tissue R7

description: noncoding RNA expression


title: mammary_gland_tumor-Elf5_EGFP_neg rep2

description:
Mammary gland tumor, EGFP negative control
GFP_Neg_2


title: mammary_gland_tumor-Elf5_EGFP_neg rep1

description:
Mammary gland tumor, EGFP negative control
GFP_Neg_1


title: Chronic TCMR, 5937345100_F

value: chronic T-cell mediated rejection (TCMR)


title: Phosphor4_12

value: high-intake


title: Cadaveric Donor, 5937345100_D


title: Ovarian Tumor tissue R5

description: noncoding RNA expression


title: Cadaveric Donor, 5937345100_C


title: Ovarian Tumor tissue R2

description: noncoding RNA expression


title: Cadaveric Donor, 5937345100_B


title: Ovarian Tumor tissue R1

description: noncoding RNA expression


title: Bone marrow MRL/MpJ

description: transcriptomic profiling performed for the pool of three total RNA samples extracted from bone marrow collected from three 2-month old females of the MRL/MpJ mouse and powdered prior RNA extraction

data_processing: The data from scanned images were processed and normalized using a robust multi-chip average (RMA) algorithm using DEVA 1.0.2 software with default settings (Roche)

source_name: bone marrow

treatment_protocol: Tissue samples (hearts, livers, spleens, ears and bone marrow) from 2-month-old females of the MRL/MpJ (stock #000486), C57BL/6J (stock #000664) strains were purchased from the Jackson Laboratory and those of 2-month-old females of the BALB/c strain were prepared in the Tri-City's Academic Animal Experiment Centre of the Medical University of Gdańsk. All tissues were collected in RNAlater stabilization reagent (QIAGEN. cat. no. 76104), transported on dry ice and stored at -80 C.

value: MRL/MpJ

value: bone marrow


title: Ovarian Tumor tissue R3

description: noncoding RNA expression


title: Phosphor4_09


title: Phosphor4_10


title: mammary_gland_tumor-WT rep1

description:
Mammary gland tumor, WT PyMT
WT_1

source_name: Mammary gland tumor, WT PyMT

value: female

value: FBV/N

value: WT PyMT


title: Ovarian Tumor tissue R4

description: noncoding RNA expression


title: mammary_gland_tumor-WT rep3

description:
Mammary gland tumor, WT PyMT
WT_3


title: mammary_gland_tumor-Elf5_EGFP_pos-rep2

description:
Mammary gland tumor, Elf5 dox induced EGFP positive
Elf5_512

hyb_protocol: Labeled, fragmented cDNA hybridized to Affymetrix Human Gene 1.0 ST Gene Arrays at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.

data_processing: Data was RMA normalized using NormalizeAffymetrixST (version 1) GenePattern module from the Peter Wills Bioinformatics Centre's GenePattern Server: http://pwbc.garvan.unsw.edu.au/gp

growth_protocol: MMTV-PyMT mouse mammary tumor samples were processed for single cell suspension and FACS sorted based on Lin- CD24+ markers. RNA was extracted from these populations straight after FACS sorting.

treatment_protocol: Mice were exposed continuosly to a diet containing 700mg/Kg of Doxocyclin (Gordon’s Specialty Stockfeeds) for 1 week at 12-13 weeks old.

value: acute (1 week) Elf5 induced expression


title: Phosphor4_11

value: PBMC


title: Ovarian Tumor tissue S15

description: noncoding RNA expression


title: Phosphor4_06

value: w


title: Bone marrow C57BL/6J

description: transcriptomic profiling performed for the pool of three total RNA samples extracted from bone marrow collected from three 2-month old females of the C57BL/6J mouse and powdered prior RNA extraction


title: Ovarian Tumor tissue S14

description: noncoding RNA expression


title: Bone marrow Balb/c

description: transcriptomic profiling performed for the pool of three total RNA samples extracted from bone marrow collected from three 2-month old females of the Balb/c mouse and powdered prior RNA extraction

value: Balb/c


title: Cadaveric Donor, 5937345100_A

source_name: FFPE renal biopsy, cadaveric donor

value: cadaveric donor

value: renal biopsy


title: Spleen MRL/MpJ

description: transcriptomic profiling performed for the pool of three total RNA samples extracted from three spleens collected from three 2-month old females of the MRL/MpJ mouse and powdered prior RNA extraction

source_name: whole spleen

value: whole spleen


title: mammary_gland_tumor-WT rep2

description:
Mammary gland tumor, WT PyMT
WT_2

value: mammary gland tumor


title: mammary_gland_tumor-Elf5_EGFP_pos-rep1

description:
Mammary gland tumor, Elf5 dox induced EGFP positive
Elf5_496


title: mammary_gland_tumor-Elf5_EGFP_neg-rep2

description:
Mammary gland tumor, EGFP negative control
Control_512

value: control


title: Ovarian Tumor tissue S13

description: noncoding RNA expression

value: Ovarian Tumor tissue

value: Female


title: Spleen C57BL/6J

description: transcriptomic profiling performed for the pool of three total RNA samples extracted from three spleens collected from three 2-month old females of the C57BL/6J mouse and powdered prior RNA extraction


title: Ovarian Tumor tissue S12

description: noncoding RNA expression


title: mammary_gland_tumor-Elf5_EGFP_neg-rep1

description:
Mammary gland tumor, EGFP negative control
Control_496


title: Ovarian Tumor tissue S11

description: noncoding RNA expression


title: Ovarian Tumor tissue S10

description: noncoding RNA expression


title: Ovarian Tumor tissue S9

description: noncoding RNA expression


title: Liver MRL/MpJ

description: transcriptomic profiling performed for the pool of three total RNA samples extracted from three livers collected from three 2-month old females of the MRL/MpJ mouse and powdered prior RNA extraction

source_name: whole liver

value: whole liver


title: mammary_gland_tumor-Elf5_EGFP_neg-rep3

description:
Mammary gland tumor, EGFP negative control
Control_514


title: Spleen Balb/c

description: transcriptomic profiling performed for the pool of three total RNA samples extracted from three spleens collected from three 2-month old females of the Balb/c mouse and powdered prior RNA extraction


title: Liver C57BL/6J

description: transcriptomic profiling performed for the pool of three total RNA samples extracted from three livers collected from three 2-month old females of the C57BL/6J mouse and powdered prior RNA extraction


title: Ovarian Tumor tissue S7

description: noncoding RNA expression


title: Ovarian Tumor tissue S8

description: noncoding RNA expression


title: mice heart MI_rep-2

city: Harbin

first: Xuefeng

last: Qu

state: Heilongjiang

address: 157 Baojian Road

department: Department of Pharmacology

institute: Harbin Medical University

description: Gene expression data from the heart performed the ligating coronary artery

hyb_protocol: Following fragmentation, 5.5μg of ss-ccDNA were hybridized for 16hr at 45C GeneChip transcriptome assays 1.0. Genechips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Genechip Scanner 3000 7G.

data_processing: The data were analyzed with Affymetrix Expression Console Software using Affymetrix default analysis settings and global scaling as normalization method.

source_name: C57BL/6 mice' heart was performed to ligate the coronary artery for 4 weeks

label_protocol: Biotinglated ss-ccDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Genechip WT PLUS reagent manual 2013)

growth_protocol: The heart tissues were collected and stored in liquid nitrogen.

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

value: heart


title: Ovarian Tumor tissue S6

description: noncoding RNA expression


title: Heart Balb/c

description: transcriptomic profiling performed for the pool of three total RNA samples extracted from three hearts collected from three 2-month old females of the Balb/c mouse and powdered prior RNA extraction

source_name: whole heart

value: whole heart


title: mice heart MI_rep-1

treatment_protocol: The heart tissues were collected and stored in liquid nitrogen.


title: Ear MRL/MpJ

description: transcriptomic profiling performed for the pool of three total RNA samples extracted from three pairs of ears collected from three 2-month old females of the MRL/MpJ mouse and powdered prior RNA extraction

source_name: external ears

value: MRL/MpJ

value: external ears


title: mice heart ctl_rep-2

description: Gene expression data from the heart performed the sham operation

source_name: C57BL/6 mice' heart was performed sham operation for 4 weeks


title: Heart MRL/MpJ

description: transcriptomic profiling performed for the pool of three total RNA samples extracted from three hearts collected from three 2-month old females of the MRL/MpJ mouse and powdered prior RNA extraction


title: Liver Balb/c

description: transcriptomic profiling performed for the pool of three total RNA samples extracted from three livers collected from three 2-month old females of the Balb/c mouse and powdered prior RNA extraction


title: Heart C57BL/6J

description: transcriptomic profiling performed for the pool of three total RNA samples extracted from three hearts collected from three 2-month old females of the C57BL/6J mouse and powdered prior RNA extraction


title: mice heart ctl_rep-1


title: mice heart MI_rep-3


title: Ovarian Tumor tissue S4

description: noncoding RNA expression


title: Ear C57BL/6J

description: transcriptomic profiling performed for the pool of three total RNA samples extracted from three pairs of ears collected from three 2-month old females of the C57BL/6J mouse and powdered prior RNA extraction


title: Ovarian Tumor tissue S3

description: noncoding RNA expression


title: mice heart ctl_rep-3


title: Ear Balb/c

description: transcriptomic profiling performed for the pool of three total RNA samples extracted from three pairs of ears collected from three 2-month old females of the Balb/c mouse and powdered prior RNA extraction


title: mammary_gland_tumor-Elf5_EGFP_pos-rep3

description:
Mammary gland tumor, Elf5 dox induced EGFP positive
Elf5_514

value: female

value: FBV/N


title: Ovarian Tumor tissue S1

description: noncoding RNA expression


title: Ovarian Tumor tissue S5

description: noncoding RNA expression


title: Ovarian Tumor tissue S2

description: noncoding RNA expression


title: Normal ovarian tissue N10

description: noncoding RNA expression

source_name: Normal ovarian tissue

value: Normal ovarian tissue


title: Re-differentiated hUC-MSCs, biological rep1

city: Chongqing

first: xiaoqin

last: zhou

address: Zhongshan Er Road

institute: Children's hospital of Chongqing medical university

description: Gene expression data from four stages of hUC-MSCs

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: Human umbilical cord derived mesenchymal stem cells induced re-differentiation for 24h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: hUC-MSCs at passage 5 were seeded at 4x105/well in a 6-well culture plate.

extract_protocol: Total RNA of parietal cortex of the patient was extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction.

treatment_protocol: Cells were pre-induced in all-trans-retinoic acid (ATRA) (1μmol/L) for 24 hours, the undifferentiated hUC-MSCs were induced using MNM for 24 hours to achieve a neuronal differentiation status (Dif). The MNM was replaced with complete culture medium (DMEM/F12 containing 10% FBS) for 24 hours following neuronal differentiation to achieve a neuronal dedifferentiation status（De-Dif）. Then, cells were transferred to MNM for another 24 hours to achieve neuronal redifferentiation status (Re-Dif).

value: umbilical cord

tag: origin

value: yellow and Chongqing, China parents

tag: cell stage

value: induced re-differentiation for 24h


title: Re-differentiated hUC-MSCs, biological rep3


title: Normal ovarian tissue N7

description: noncoding RNA expression


title: Normal ovarian tissue N11

description: noncoding RNA expression


title: Normal ovarian tissue N4

description: noncoding RNA expression


title: Re-differentiated hUC-MSCs, biological rep2


title: Normal ovarian tissue N6

description: noncoding RNA expression


title: [LBH589]

city: suzhou

first: Jian

last: Pan

address: Jingde road 303

department: Department of Hematology and Oncology

institute: Children's Hospital of Soochow University

hyb_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology)

scan_protocol: The hybridized arrays were washed, fixed, and scanned using the Agilent DNA Microarray 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 using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, lncRNAs and mRNAs that at least 3 out of 15 samples had flagged as “Present” or “Marginal” were chosen for further data analysis. Differentially expressed lncRNAs and mRNAs were identified through fold change (FC) filtering. Differentially expressed lncRNAs and mRNAs with statistical significance (as determined by two-tailed student’s t-test < 0.05) were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). *The Sample data table contains the quantile-normalized intensity from all probes that were detected in at least 3/15 samples prior to any data processing (e.g. prior to fold-change filtering). There was a considerable number of probes not detected in this experiment.

source_name: SK-NEP-1 cells

growth_protocol: SK-NEP-1  Human kidney (Wilm's Tumor) cell line obtained from the American Type Culture Collection (ATCC) was maintained in the Maccyo’5 (Life Technologies Inc., Gaithersburg, MD, USA) supplemented with 20% heat-inactivated fetal bovine serum (Invitrogen Co., NY, USA) in a humidified incubator with 5% CO2 at 37℃. LBH589 (Cat: S1030 Selleck Chemicals, West Paterson, NJ, USA) was dissolved in DMSO (Cat: D4540 Sigma–Aldrich, St. Louis, MO, USA)

extract_protocol: Briefly, RNA purified from total RNA after removal of rRNA was amplified and transcribed into fluorescent cRNA and cDNA was labeled and hybridized to the Human LncRNA Array v3.0 (8660 K, Arraystar). 30,586 LncRNAs and 26,109coding transcripts which collected from the most authoritative databases such as RefSeq, UCSC Knowngenes, Ensembl and many related literatures can be detected by the microarray.

treatment_protocol: SK-NEP-1 cells were treated with 100nM LBH589 and control group cells were treated with the same volume of DMSO 24 hours later.

tag: cell line

tag: treatment

value: treated with 100nM LBH589


title: De-differentiated hUC-MSCs, biological rep1

source_name: Human umbilical cord derived mesenchymal stem cells induced de-differentiation for 24h

value: induced de-differentiation for 24h


title: Normal ovarian tissue N5

description: noncoding RNA expression

tag: gender


title: Normal ovarian tissue N9

description: noncoding RNA expression


title: hUC-MSCs, biological rep2

source_name: Human umbilical cord derived mesenchymal stem cells

value: baseline


title: Differentiated hUC-MSCs, biological rep1

source_name: Human umbilical cord derived mesenchymal stem cells induced differentiation for 24h

value: induced differentiation for 24h


title: De-differentiated hUC-MSCs, biological rep2


title: Differentiated hUC-MSCs, biological rep2


title: Normal ovarian tissue N1

description: noncoding RNA expression


title: [Blank]

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology)

value: treated with DMSO


title: hUC-MSCs, biological rep1


title: hUC-MSCs, biological rep3


title: Normal ovarian tissue N2

description: noncoding RNA expression

value: Female


title: Normal ovarian tissue N3

description: noncoding RNA expression


title: Normal ovarian tissue N8

description: noncoding RNA expression


title: De-differentiated hUC-MSCs, biological rep3


title: Phosphor4_13

description:
Gene expression data from PBMCs isolated from whole blood
Snowball arrays (Freeman et al. in BMC Biol 2012, 10:90), see the ArrayExpress database, accession no. A-AFFY-189

source_name: PBMC

value: PBMC

value: medium-intake

value: w


title: L406-1(HFD+5%fucoidan 12week fed)

status: Public on Dec 29 2015

city: Kawasaki

first: takashi

last: yokota

address: 1-396,Kosugi-cho, Nakahara-ku

institute: Nippon medical shool

description:
Barcode=MM02012
Gene expression after fed HFD+5% fucoidan

hyb_protocol: The microarray slides were first pretreated with blocking solution consisting of 4X standard saline citrate (SSC), 0.5%SDS, and 1%bovine serum albumin at 42°C for 45min. The labeled cDNA in hybridization buffer [consisting of 2X SSC, 4X Denhardt’s solution (Sigma-Aldrich,St.Louis,MO), and salmon sperm DNA (Invitrogen,Carlsbad,CA) were denatured at 95°C for 2min and cooled to room temperature. Then, cDNA were applied to each individual array window and hybridized at 65°C for 16h. After hybridization, the solutions of labeled cDNA on the microarray slides were flushed away by a solution containing 2X SSC and 0.1%SDS, and then the microarray slide was immediately washed in following solutions; 2X SSC and 0.1% SDS at room temperature for 5min, 0.2X SSC and 0.1% SDS at room temperature for 5min, 0.2X SSC and 0.1% SDS at 55°C for 5min, 0.2X SSC at room temperature for 1min, and 0.05X SSC at room temperature for 2min.

scan_protocol: The images for the hybridized array was captured by GenePix4000B microarray scanner (MolecularDevices,Sunnyvale,CA), and quantified by using the Genepix Pro 6.0 software (Molecular Devices).

data_processing: The adjusted intensity equals the intensity of each gene minus the background value. The genes with an adjusted intensity of less than 2-fold the background value were not detected. The normalized intensity to GAPDH gene were calculated by the following formula and compared with other treatment:normalized intensity = (X - Z)/(Y - Z) X 10000, where X is the adjusted intensity of target gene, Y is the adjusted intensity of GAPDH gene, and Z is the median of adjusted intensities of the negative controls.

label: Alexa Fluor555

source_name: HFD+5%fucoidan group

label_protocol: Alexa Fluor555-lebelled cDNA was prepared from each 10micro gram of total RNA through cDNA synthesis using GeneSQUARE cDNA Direct labeling System (Kurabo Industries Ltd., #MADL-01) according to manufacture’s protocol.

growth_protocol: Mice were fed ad libitum and housed in a temperature-controlled room (22–24 °C) under a 12-hour light/dark cycle.

extract_protocol: Total RNA was extracted using an RNeasy Mini Kit according to the manufacturers’ protocol (Qiagen, Valencia, CA, USA).  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The mice were fed a normal diet (NFD) or high fat diet for 12 weeks. Moreover,　to examine the effects of fucoidan, the mice in the HFD group were fed into HFD + 1% fucoidan (1%fuc) or HFD + 5% fucoidan (5%fuc) for 12 weeks.

value: ApoEshl mice

value: male

value: liver

value: 7-8 weeks-old


title: L405-1(HFD+5%fucoidan 12week fed)


title: L206-1(HFD 12week fed)

description:
Barcode=MM02012
Gene expression after fed HFD

source_name: HFD group


title: L404-1(HFD+5%fucoidan 12week fed)


title: L402-1(HFD+5%fucoidan 12week fed)


title: L403-1(HFD+5%fucoidan 12week fed)


title: L205-1(HFD 12week fed)


title: L201-1(HFD 12week fed)


title: L202-1(HFD 12week fed)


title: L203-1(HFD 12week fed)


title: BEL cells transduced w/ BCR-ABL1-GFP (B/A) + 2 mmol/l Imatinib (IM), then washout of Im, and then re-addition of Im

city: San Francisco

first: Huimin

last: Geng

state: CA

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

hyb_protocol: Standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual)

data_processing: RMA

source_name: acute lymphoblastic leukemia (ALL)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual)

extract_protocol: Extraction Method: Qiagen RNeasy Kit

value: BEL

value: transduced with BCR-ABL1-GFP (B/A) in the presence of 2 mmol/l Imatinib (IM), then washout of Imatinib, and then subsequent re-addition of Imatinib

value: MLL/AF4 ALL


title: BEL cells transduced w/ BCR-ABL1-GFP (B/A) + 2 mmol/l Imatinib (IM)

scan_protocol: Standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual)

value: transduced with BCR-ABL1-GFP (B/A) in the presence of 2 mmol/l Imatinib (IM)


title: 697 cells transduced w/ BCR-ABL1-GFP (B/A) + 2 mmol/l Imatinib (IM), then washout of Im, and then re-addition of Im

value: E2A/PBX1 ALL


title: SEM cells transduced w/ BCR-ABL1-GFP (B/A) + 2 mmol/l Imatinib (IM), then washout of Im, and then  re-addition of Im

value: SEM


title: SEM cells transduced w/ BCR-ABL1-GFP (B/A) + 2 mmol/l Imatinib (IM)


title: SEM cells transduced w/ BCR-ABL1-GFP (B/A) + 2 mmol/l Imatinib (IM) and then washout of Im

value: transduced with BCR-ABL1-GFP (B/A) in the presence of 2 mmol/l Imatinib (IM) and then washout of Imatinib


title: 697 cells transduced w/ BCR-ABL1-GFP (B/A) + 2 mmol/l Imatinib (IM)


title: 697 cells transduced w/ BCR-ABL1-GFP (B/A) + 2 mmol/l Imatinib (IM) and then washout of Im


title: BEL cells transduced w/ BCR-ABL1-GFP (B/A) + 2 mmol/l Imatinib (IM) and then washout of Im


title: L401-1(HFD+5%fucoidan 12week fed)


title: ofr1 null mutant opaque cells vs. ofr1 null mutant white cells on glucose medium Replicate 1

city: Montreal

first: Yuan

last: Sun

state: Quebec

address: 7141 Sherbrooke Street West

department: Biology Department

country: Canada

institute: Concordia University

hyb_protocol: Microarray slides were hybridized with labeled cDNAs overnight at 42°C DIG easy Hyb solution (Roche) containing 0.5 ug/ul of Bakers tRNA and 0.5 ug/ul of salmon sperm DNA. The slides were washed twice with 1X SSC/0.1% SDS and 3 times with 0.1X SSC and spin dry.

scan_protocol: The scanning was done using GenePix4000B microarray scanner Images were quantified using GenePix Pro 7

data_processing: Lowess normalized, background subtracted data obtained from log2 of normalized Red signal/normalized Green signal. GenePix Pro 7 software was used for image normalization and final Lowess normalization and inspection of the data was done with Microsoft Excel 2013 and MultiExperiment Viewer.

organism: Candida albicans

source_name: mRNA extracted from ofr1 null mutant opaque cells on glucose

label_protocol: Indirect cDNA labelling with amino-allyl dUTP

growth_protocol: glucose medium

extract_protocol: Total RNA extracted using hot phenol; polyA Spin mRNA Isolation kit for mRNA isolations

tag: mating type

value: MTLa/α

value: opaque form cells

value: ofr1 mutant

source_name: mRNA extracted from ofr1 null mutant white cells on glucose

value: white form cells

tag: genotype/variatoin


title: ofr1 null mutant opaque cells vs. ofr1 null mutant white cells on GlcNAc medium Replicate 1

source_name: mRNA extracted from ofr1 null mutant opaque cells on GlcNAc

growth_protocol: GlcNAc medium

source_name: mRNA extracted from ofr1 null mutant white cells on GlcNAc


title: ofr1 null mutant opaque cells vs. ofr1 null mutant white cells on glucose medium Replicate 2


title: L204-1(HFD 12week fed)


title: 697 cells transduced w/ GFP empty vectors (EV)

value: transduced with GFP empty vectors (EV)


title: BEL cells transduced w/ GFP empty vectors (EV)


title: SEM cells transduced w/ GFP empty vectors (EV)


title: ofr1 null mutant opaque cells vs. ofr1 null mutant white cells on GlcNAc medium Replicate 2


title: Phosphor4_15

value: PBMC

value: high-intake

value: m


title: ofr1 null mutant white cells vs. wild type yeast cells on glucose medium Replicate 2

source_name: mRNA extracted from wild type white cells on glucose

value: wild type


title: ofr1 null mutant white cells vs. wild type yeast cells on GlcNAc medium Replicate 2

source_name: mRNA extracted from wild type white cells on GlcNAc


title: ofr1 null mutant white cells vs. wild type yeast cells on glucose medium Replicate 1


title: ofr1 null mutant white cells vs. wild type yeast cells on GlcNAc medium Replicate 1


title: ofr1 null mutant white cells vs. wild type yeast cells on GlcNAc medium Replicate 3


title: ko_3

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

hyb_protocol: labeled samples were hybridized to Mouse Gene 1.0  ST Array (Affymetrix) using standard protocol

scan_protocol: The arrays were scanned on a GCS3000 7G scanner using standard Affymetrix protocols

data_processing: The CEL files were converted to Chp files using PLIER in Expression Console v1.4. Further statistical analysis was done using GeneSpring GXv12.6

source_name: osteocyte-enriched bone

label_protocol: 30ng total RNA was converted to fragmented biotinylated cDNA using the standard NuGEN WT pico v2 protocol

extract_protocol: total RNA was isolated from frozen tissues using RNEasy protocol with an oncolumn DNase step. The RNA was checked for quality using a nanodrop and a bioanalyzer nanochip (Agilent).

treatment_protocol: Male mice 39-41 weeks of age were sacrificed and long bones dissected free of soft tissues.  Following removal of marrow tissue, bone tissues were cut into small pieces and alternately digested with cdigested with bacterial collagenase and extracted with 5 mM EDTA/0.1% BSA in PBS at 37 C.  This sequential treatment was repeated four times prior to isolation of mRNA.

value: DMP1 cre Mbtps1 knockout

value: 39-41 weeks

value: male


title: ko_2


title: UTI89 6Hrs Replicate 4

city: Columbus

first: Ashley

middle: R

last: Jackson

state: OH

address: 700 Children's Dr

department: Molecular and Human Genetics

institute: Nationwide Children's Hospital

description: Gene expression after 6Hr infection with UTI89

hyb_protocol: Sample labeling and hybridization was performed according to the manufacturer’s protocols using the One-Color Microarray-Based Gene Expression Analysis Manual (Low Input Quick Amp Version). Samples were hybridized to the SurePrint G3 Mouse GE 8x60K Microarray (AMADID 028005).

scan_protocol: Microarray slides were hybridized overnight, washed and then scanned with Agilent G2505C Microarray Scanner. This high resolution scanner represents the very latest technology from Agilent for Arrays and features an industry-leading extended dynamic range of 106 (20-bits) for high sensitivity scanning without saturation, low-level detection resulting from optimized precision optics, broad dynamic range, minimal spectral cross talk that enables detection of weak features. The information about each probe on the array was extracted from the image data using Agilent Feature Extraction 10.10 (FE). This data is stored in the FE “.txt” files. The raw intensity values from these files is imported into the mathematical software package “R”, which is used for all data input, diagnostic plots, normalization and quality checking steps of the analysis process using scripts developed in-house by Peter White specifically for this analysis.

data_processing: Preprocessing refers to the procedures used to convert raw probe intensities into useful gene expression measurements. For analysis of Agilent Expression data this process consists of  1. Reading in the FE extraction files and extraction the median intensity values for each probe on the array. These intensities are not background corrected (this has been shown to only introduce noise), but are corrected for any scanner offset that was added to the original raw values (see Analysis Log file for details).  2. The dataset is filtered to remove positive control elements and any elements that have been flagged as outliers.  3. Present (P), Marginal (M) or Absent (A) calls are made for each element on the array using in-house methodologies that take into account both the results of FE probe detection statistics and the intensities of the negative controls elements on the array.  4. Data normalization is the process of removing unwanted non-biological variation that might exist between arrays in a microarray experiment. Sources of such variation might include scanner-setting differences, the quantities of mRNA hybridized, processing order and many other factors. Regardless of the normalization approach used, the underlying assumption of the normalization algorithm is that the number of genes changing expression between conditions is relatively small or that an equivalent number of genes increase and decrease in expression. The algorithm for normalization is depending upon whether the design of the experiment was a one-color or two-color approach:  a. Agilent One-Color Analysis: The median green (Cy3) intensities are normalized between the arrays using the Quantile Normalization package in “R” (Bolstad et al., 2003). Quantile normalization is a non-linear probe-level normalization that results in the same empirical distribution of intensities for each array This is a significantly more robust approach than simply normalizing to the median value of each array.

source_name: Bladder, UTI89, 6Hr

extract_protocol: Total RNA was prepared using the the mirVanaTM kit (Life Technologies, ThermoFisher Scientific) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Animals were housed in ventilated cages and transferred to a Biosafety Level 2 room one day prior to inoculation.  Uropathogenic bacteria were inoculated from glycerol stocks into LB medium and expanded statically for 16 hours at 37°C.  Next, the culture was centrifuged and washed with phosphate buffered saline, then resuspended at 2x109 CFU/ml. Urine was manually expressed from bladder prior to infection. 50 µl (108 CFU) was inoculated transurethrally into isoflurane-anesthetized females. Experimental conditions involved collection of bladders at baseline, 2, 6 and 48 hours after infection.

value: female

value: bladder

tag: developmental stage

value: adult

tag: time point

value: after 6Hr infection with UTI89


title: UTI89 48Hrs Replicate 3

description: Gene expression after 48Hr infection with UTI89

source_name: Bladder, UTI89, 48Hr

label_protocol: Sample labeling and hybridization was performed according to the manufacturer’s protocols using the One-Color Microarray-Based Gene Expression Analysis Manual (Low Input Quick Amp Version). Samples were hybridized to the SurePrint G3 Mouse GE 8x60K Microarray (AMADID 028005).

tag: tissue

value: after 48Hr infection with UTI89


title: UTI89 48Hrs Replicate 2


title: control_4

value: wildtype


title: UTI89 48Hrs Replicate 4


title: UTI89 6Hrs Replicate 2


title: UTI89 6Hrs Replicate 3


title: UTI89 48Hrs Replicate 1


title: cKO_3

hyb_protocol: labeled samples were hybridized to Mouse Transcriptome1.0 Array (Affymetrix) using standard protocol

data_processing: The CEL files were converted to CHP files using Expression Consolev 1.4. Further statistical analysis was done using Affymetrix Transcriptome Console v3 and GeneSpring GXv13

source_name: cKO mouse 780

label_protocol: 100ng total RNA was converted to fragmented biotinylated cDNA using the standard WT Plus protocol (Affymetrix)

treatment_protocol: 39-41 week old male mice were euthanized with carbon dioxide gas and then soleus muscles were removed from each leg and flash frozen.

value: DMP1 Cre Mbtps1 knockout

value: soleus muscles


title: control_2


title: UTI89 2Hrs Replicate 3

description: Gene expression after 2Hr infection with UTI89

source_name: Bladder, UTI89, 2Hr

value: after 2Hr infection with UTI89


title: control_3


title: ko_1


title: UTI89 2Hrs Replicate 4


title: cKO_1

source_name: cKO mouse 733


title: cKO_2

source_name: cKO mouse 779


title: Fetal Liver, bio rep 3

city: Providence

first: Jennifer

middle: Ann

last: Sanders

state: RI

address: 593 Eddy Street

department: Pediatric Endocrinology

institute: Rhode Island Hospital

description:
Gene expression from Affymetrix Human Gene 1.0 ST Array.
SAPE (streptavidin-conjugated Phycoerythrin)

hyb_protocol: After fragmentation, 2.475ug cRNA was hybridized for 17 h at 45 C, 60rpm, on a GeneChip Human Gene 1.0 ST Array. Then, washing and staining were done according to manufacturer's instructions using the Fluidics recommended for the arrays and Affymetrix Wash/Stain/Hyb kit.

scan_protocol: The arrays were scanned with a Affymetrix 3000 7G scanner using manufacturer's instructions.

data_processing: RMA algorithm.

source_name: Fetal liver

label_protocol: Samples (100ng total RNA) were labeled with biotin using the Affymetrix WT labeling kit (Cat#900670) according to manufacturer's instructions.

growth_protocol: Normal adult liver was obtained through The Liver Tissue Cell Distribution System is funded by NIH Contract #HHSN276201200017C. Fetal liver was obtained from spontaneous stillbirths.

extract_protocol: Nucleic acids were extracted from liver using the All prep kit (Qiagen) according to the manufacturer's directions.

treatment_protocol: Samples were flash frozen in liquid nitrogen at the time of harvest and stored at -80 until use.

value: liver

value: 22 wk gestation


title: Control_2

source_name: Control mouse 716


title: Control_3

source_name: Control mouse 776


title: UTI89 6Hrs Replicate 1


title: Control_1

source_name: Control mouse 715


title: control_1


title: UTI89 2Hrs Replicate 1


title: Adult Liver, bio rep 3

source_name: Adult liver

value: 65 yrs


title: Control Bladder Replicate 4

description: Gene expression at baseline

source_name: Bladder, Baseline

value: at baseline


title: Control Bladder Replicate 2

description: Gene expression at baseline


title: Control Bladder Replicate 1

description: Gene expression at baseline


title: Adult Liver, bio rep 1

value: 55 yrs


title: Fetal Liver, bio rep 1

value: 21wk gestation


title: Control Bladder Replicate 3

description: Gene expression at baseline


title: Fetal Liver, bio rep 2

value: 20 wk gestation


title: UTI89 2Hrs Replicate 2