title: Control DCs

status: Public on Dec 01 2017

city: nanjing

first: Jian

last: Lin

state: jiangsu

address: tongwei road N0.1

department: Life Science

institute: nanjing agricultural university

description: Total RNA was extracted from cultured DCs for control.

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

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

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

organism: Gallus gallus

source_name: chicken dendritic cells_control

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

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

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

treatment_protocol: At day 6, the non-adherent, relatively immature DCs were harvested and plated in fresh medium (1×10^6 cells/ml). Then, cultured chicken BMDCs were randomly divided into control group and IBV stimulated group. Each group consisted of three wells of BMDCs from three chickens.

value: bone marrow

tag: cell type

value: dendritic cells


title: DCs stimulated with IBV (infectious bronchitis virus)

type: RNA

country: China

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

molecule: total RNA

source_name: chicken dendritic cells_stimulated with IBV

tag: tissue


title: Sample 8338 - Testis - medium boar taint

status: Public on Sep 25 2017

type: SRA

city: Kongens Lyngby

first: Haja

middle: N

last: Kadarmideen

address: Richard Petersens Plads, Building 324

department: Department of Applied Mathematics and Computer Science

country: Denmark

institute: Technical University of Denmark

description: stranded mRNA

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Trimmomatic v.0.33 - trimming for bad reads by standard parameters: PE -phred33 \ ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Cutadapt v.1.8.1 - trimming for adapter sequences: -a TACACTCTTTCCCTACACGACGCTCTTCCGATCT -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -a GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT -A AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC \ -e 0.1 -O 5 -m 15 --minimum-length 1 STAR aligner v. 020201 - aligned by parameters: --runThreadN 10 --outFilterMultimapNmax 3 --outFilterMismatchNmax 8 --readFilesCommand zcat --outSAMunmapped Within --outReadsUnmapped Fastx >> output.log
samtools v. 1.3.1 by parameters: view -h -F 1792
HT-seq count v. 0.6.0 - genes counted by parameters: -m intersection-nonempty -s reverse -r pos -f sam -a 10 -t exon
Genome_build: Sus scrofa 10.2.79
Supplementary_files_format_and_content: HT-seq count file (.txt) - raw gene counts

organism: Sus scrofa

source_name: Testis

extract_protocol:
Following slaughter at 100 kg, the liver was extracted from the carcass and 150 mg of tissue were retrieved by punch biopsy and immediately immersed into 1.5 ml RNAlater (QIAGEN, Hilden, Germany) in 2 ml Eppendorf tubes (Eppendorf, Hamburg, Germany). The carcasses were kept in a cold room at 4°C for approximately 1.5 h before 150 mg testis tissue were retrieved by punch biopsy and immersed into 1.5 ml RNAlater (QIAGEN).
Either TruSeq stranded mRNA (Illumina, San Diego, USA) kit following instructions of the manufacturer or TruSeq total stranded RNA (Illumina) kit following instructions of the manufacturer.

value: Testis

tag: group

value: medium boar taint


title: Sample 8102 - Testis - medium boar taint

description: stranded mRNA


title: Sample 9128 - Testis - high boar taint

description: stranded mRNA

value: high boar taint


title: Sample 1111 - Testis - medium boar taint

description: stranded mRNA


title: Sample 7306 - Testis - high boar taint

description: stranded mRNA


title: Sample 7107 - Testis - high boar taint

description: stranded mRNA


title: Sample 1306 - Testis - high boar taint

description: Total RNA-seq


title: Sample 8325 - Testis - medium boar taint

description: stranded mRNA


title: Sample 9138 - Testis - high boar taint

description: stranded mRNA


title: Sample 9313 - Testis - high boar taint

description: stranded mRNA


title: Sample 7305 - Testis - high boar taint

description: stranded mRNA


title: Sample 7106 - Testis - high boar taint

description: stranded mRNA


title: Sample 3130 - Testis - medium boar taint

description: stranded mRNA


title: Sample 3128 - Testis - medium boar taint

description: stranded mRNA


title: Sample 1331 - Testis - high boar taint

description: Total RNA-seq


title: Sample 7325 - Testis - high boar taint

description: stranded mRNA


title: Sample 7131 - Testis - high boar taint

description: stranded mRNA


title: Sample 9129 - Testis - high boar taint

description: stranded mRNA


title: Sample 8332 - Testis - high boar taint

description: stranded mRNA


title: Sample 1334 - Testis - high boar taint

description: stranded mRNA


title: Sample 9312 - Liver - low boar taint

description: stranded mRNA

source_name: Liver

value: Liver

value: low boar taint


title: Sample 9137 - Liver - low boar taint

description: stranded mRNA


title: Sample 1326 - Testis - high boar taint

description: stranded mRNA


title: Sample 8101 - Liver - low boar taint

description: stranded mRNA


title: Sample 3109 - Liver - low boar taint

description: Total RNA-seq


title: Sample 1338 - Testis - high boar taint

description: stranded mRNA


title: Sample 7312 - Liver - low boar taint

description: stranded mRNA


title: Sample 3309 - Liver - low boar taint

description: stranded mRNA


title: Sample 3114 - Liver - low boar taint

description: stranded mRNA


title: Sample 3102 - Liver - low boar taint

description: stranded mRNA


title: Sample 8311 - Liver - low boar taint

description: stranded mRNA


title: Sample 1325 - Liver - low boar taint

description: stranded mRNA


title: Sample 1314 - Liver - low boar taint

description: stranded mRNA


title: Sample 1101 - Liver - low boar taint

description: stranded mRNA


title: Sample 1127 - Liver - low boar taint

description: stranded mRNA


title: Sample 1137 - Liver - low boar taint

description: stranded mRNA


title: Sample 1105 - Liver - low boar taint

description: stranded mRNA


title: Sample 8338 - Liver - medium boar taint

description: stranded mRNA


title: Sample 9328 - Liver - medium boar taint

description: stranded mRNA


title: Sample 7112 - Liver - medium boar taint

description: stranded mRNA


title: Sample 9135 - Liver - medium boar taint

description: stranded mRNA


title: Sample 8308 - Liver - medium boar taint

description: stranded mRNA


title: Sample 7110 - Liver - medium boar taint

description: stranded mRNA


title: Sample 8106 - Liver - medium boar taint

description: stranded mRNA


title: Sample 8102 - Liver - medium boar taint

description: stranded mRNA


title: Sample 1112 - Liver - low boar taint

description: stranded mRNA


title: Sample 8117 - Liver - medium boar taint

description: stranded mRNA


title: Sample 8325 - Liver - medium boar taint

description: stranded mRNA


title: Sample 9128 - Liver - high boar taint

description: stranded mRNA


title: Sample 9129 - Liver - high boar taint

description: stranded mRNA


title: Sample 1113 - Liver - medium boar taint

description: stranded mRNA


title: Sample 9138 - Liver - high boar taint

description: stranded mRNA


title: Sample 3130 - Liver - medium boar taint

description: stranded mRNA


title: Sample 9313 - Liver - high boar taint

description: stranded mRNA


title: Sample 3128 - Liver - medium boar taint

description: stranded mRNA


title: Sample 8332 - Liver - high boar taint

description: stranded mRNA


title: Sample 2111 - Liver - medium boar taint

description: stranded mRNA


title: Sample 1306 - Liver - high boar taint

description: Total RNA-seq


title: Sample 1111 - Liver - medium boar taint

description: stranded mRNA


title: Sample 7325 - Liver - high boar taint

description: stranded mRNA


title: Sample 7306 - Liver - high boar taint

description: stranded mRNA


title: Sample 9304 - Liver - medium boar taint

description: stranded mRNA


title: Sample 7131 - Liver - high boar taint

description: stranded mRNA


title: Sample 7305 - Liver - high boar taint

description: stranded mRNA


title: Sample 1331 - Liver - high boar taint

description: stranded mRNA


title: Sample 1338 - Liver - high boar taint

description: stranded mRNA


title: Sample 7106 - Liver - high boar taint

description: stranded mRNA


title: Sample 1334 - Liver - high boar taint

description: stranded mRNA


title: Sample 1326 - Liver - high boar taint

description: stranded mRNA


title: Myc-CycGΔP ChIP-seq, replicate 1

status: Public on Jul 01 2017

city: Paris

first: Frédérique

last: Peronnet

address: 9, quai saint-Bernard

department: UMR7622-Developmental biology

country: France

institute: CNRS-SU

library_source: genomic

data_processing:
Quality checking with fastqc
Filtering with fastq_quality_filter (fastx-Toolkit suite). Parameters: p 90, q 20
Alignment with Bowtie2 (v2.1.0). Default parameters
Peak calling with MACS2 (v2.1.0). Fragment sized fixed at 110 bp
Peak reproducibility analysis by the IDR method with the "batch-consistency-analysis" function of the IDR package (v2.0.0)
Reproducible peaks merging with the "merge" function of the BEDtools suite
Generation of bedgraph files from bowtie2 alignement files with the genomeCoverageBed command from the BEDtools suite
Generation of bigWig files from the bedgraph with the bedGraphtoBigWig program from the UCSC binary utilities directory
Genome_build: dm6, r6.07
Supplementary_files_format_and_content: The BED file contains the peaks with IDR score below 0.05, merged from both replicates. bigWig files contain tag density information for individual ChIP and Input experiments.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Third instar female larvae wing imaginal disc

growth_protocol: Flies were raised on standard yeast-cornmeal medium at 25°C.

extract_protocol:
600 wing imaginal discs were dissected (taking one disc per larva) in Schneider medium and aliquoted per 50 in 1.5 mL microtubes on ice. Discs were fixed at 22°C. 12 sonication cycles were performed (Diagenode Bioruptor sonifier; cycles of 30'' ON, 30'' OFF, high power). After centrifugation, the 12 supernatants were pooled, homogenized, and 2% were removed (Input). The remaining fragmented chromatin was redistributed into 12 tubes and each tube was adjusted to 1 mL with 140 mM NaCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% BSA, Roche complete EDTA-free protease inhibitor cocktail). For immunoprecipitation, 3 µg of anti-Myc antibody (Abcam 9132) were added per tube. The  of water. Two biological replicates were performed.
Library preparation and Illumina sequencing were performed at the Ecole normale superieure Genomic Platform (Paris, France). Libraries were prepared using NEXTflex ChIP-Seq Kit (Bioo Scientific), using 38 ng of IP or Input DNA.
Libraries were multiplexed by 10 on one flowcell run. A 75 bp single read sequencing was performed on a NextSeq 500 device (Illumina).

treatment_protocol: No treatment.

value: Wing imaginal disc

tag: genotype

value: UAS-Myc-CycG^deltaP, da-Gal4/+

tag: age

value: Third instar larvae


title: Input DNA for replicate 1


title: Input DNA for replicate 2


title: Myc-CycGΔP ChIP-seq, replicate 2


title: KO-Brg1 ChIP

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were quality assessed using FastQC v0.11.5 and then quality trimmed using Trimmomatic (parameters used were “trimmomatic_adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36”).
Surviving paired reads were then aligned against the mouse reference genome (GRCm38.p4) using Bowtie2.
Resulting BAM alignments were then processed through PICARD tools (http://broadinstitute.github.io/picard), to clean, sort and deduplicate (PCR and Optical duplicates).
Processed alignments were then used in macs2 with BAM files of ChIP samples as treatments (-t) and the input sample BAM as control.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: bigwig

organism: Mus musculus

source_name: Connective tissue

growth_protocol: Dulbecco’s modified Eagle medium (DMEM) with high glucose (Sigma), 10% fetal bovine serum (Sigma) and 100 units/ml penicillin and 100 µg/ml streptomycin (Sigma), in a humidified incubator with 5% CO2 at 37 Deg.

extract_protocol:
50 ug total fragmented chromatin were mixed with 5 ug antibody overnight at 4 degree with rotation. The chromatin-antibody complex were then precipitated with protein A/G magnetic beads (Thermo Fisher Scientific). After washes with low salt wash buffer (20mM Tris, 2mM EDTA, 50mM NaCl, 0.01% SDS and 1% SDS), high salt wash buffer (same composition, 250 mM NaCl) and LiCL-wash buffer (10mM Tris, 1mM EDTA, 250 mM LiCl, 1% NP40 and 1% sodium deoxycholate), precipitated chromatin was eluted in 200µl of elution buffer (10µl 20% SDS, 20µl 1M NaHCO3 and 170µl dH2O). Reverse cross linking was done by adding 8 ul 5M NaCl and incubate at 65 deg overnight. 1 ul 10 mg/ml RNase A was added to the tube for 30 mins incubation at 37°C. Then 4µl 0.5M EDTA, 8µl 1M Tris-HCl and 1µl 20 mg/ml Proteinase K was added for 2h incubation at 42°C. The released DNA was purified using QIAquick PCR purification kit (Qiagen).
Purified DNA from two replicates were pooled for library preparation using TruSeq Nano DNA Library Prep Kit (Illumina) according to the manufacturer's instructions.

tag: strain/background

value: BALB/c

tag: genotype/variation

value: Actb -/-

value: 10.5 day old embryos

value: Mouse embryonic fibroblast

tag: chip antibody

value: Brg1 (from anki.ostlund Farrant (Stockholm University))


title: KO-Input


title: Sample 7107 - Liver - high boar taint

description: stranded mRNA


title: WT-Brg1 ChIP

value: Actb +/+


title: WT-H3K9Me3 ChIP

value: H3K9Me3 (abcam ab8898)


title: KO-H3K9Me3 ChIP


title: WT-Input


title: H1792 trametinib-treated #2

status: Public on Mar 15 2017

city: Kanazawa

first: Hiromichi

last: Ebi

state: Ishikawa

address: 13-1 Takaramachi

department: Institute for Frontier Science Initiative and Cancer Research Institute

country: Japan

institute: Kanazawa University

description:
Gene expression of H1792 cells treated with 50 nM trametinib for 48 hours
no8_H1792_trametinib_2.txt

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes. On completion of the fragmentation reaction, Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE microarray (G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven at 10 rpm.  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 (G2539A) using one color scan setting (Scan Region 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 039494_D_F_20140813) 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: H1792 trametinib-treated

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

growth_protocol: Cells were cultured in RPMI1640 with 10% FBS.

extract_protocol: RNA was prepared using the RNeasy kit (QIAGEN) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-ND1000 spectrophotometer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: NCI-H358 parental cells were treated with TGFβ1 (4 ng/mL) or PBS for 14 days in order to induce epithelial to mesenchymal transition (EMT). Induction of EMT was confirmed by western blotting with e-cadherin loss and vimentin expression. For NCI-H1792 experiment, 50 nM trametinib were treated for 48 hours.

tag: cell line

tag: origin

value: lung adenocarcinoma

value: Human lung cancer cell line

tag: treated with

value: 50 nM trametinib for 48 hrs

tag: phenotype

value: mesenchymal


title: H1792 trametinib-treated #1

description:
Gene expression of H1792 cells treated with 50 nM trametinib for 48 hours
no7_H1792_trametinib_1.txt


title: H358 TGF-b #1

description:
Gene expression of EMT induced H358 cell line
no3_H358_TGFb_1.txt

source_name: H358 TGF-b

value: TGFβ1 (4 ng/mL) for 14 days

value: EMT induced


title: H2135wtB2M1

status: Public on Feb 27 2017

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

description: B2M gene restituted.

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a total volume of 25ul following the manufacturer's instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4851A) 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: Scanner Agilent G2565CA Feature extraction 10.7.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: NSCLC cell line H2135, wtB2M

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 45ng total RNA using a Low Input QuickAmp Labeling Kit (Agilent Technologies, Palo Alto, Calif, USA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).

growth_protocol: Cells grown in HITES with 5% FBS.

extract_protocol: Total RNA were extracted using Trizol Reagent.

treatment_protocol: wtB2M cells were infected with a plasmid carrying B2M gene; mock cells correspond to the infection with the empty vector.

value: non-small cell lung cancer (NSCLC) cell line

tag: plasmid

value: beta-2 microglobulin (B2M)


title: H358 parental #1

description:
Gene expression of NCI-H358 cells
no1_H358_parental_1.txt

source_name: H358 parental

value: PBS for 14 days

value: epihtelial


title: H2009wtB2M2

description: B2M gene restituted.

source_name: NSCLC cell line H2009, wtB2M


title: H2009wtB2M1

description: B2M gene restituted.


title: H2135wtB2M3

description: B2M gene restituted.


title: H1792 parental #1

description:
Gene expression of H1792 cell line
no5_H1792_parental_1.txt

source_name: H1792 parental


title: H358 parental #2

description:
Gene expression of NCI-H358 cells
no2_H358_parental_2.txt


title: H1

status: Public on Mar 26 2017

city: Kyoto

first: Kazuo

last: Takayama

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

institute: Kyoto University

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver2.0 (Agilent) 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 SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was extracted using RNeasy Mini Kit.

treatment_protocol: The human ES cell lines, H1, H9 (WiCell Research Institute), and KhES1 (provided by Dr. Norio Nakatsuji, Kyoto University), were maintained on a feeder layer of mitomycin C-treated EmbryoMax Primary Mouse Embryo Fibroblasts (MEF, Merck Millipore) with ReproStem medium (ReproCELL) supplemented with 5 ng/ml fibroblast growth factor 2 (FGF2, KATAYAMA CHEMICAL INDUSTRIES). Human ES cells were used following the Guidelines for Derivation and Utilization of Human Embryonic Stem Cells of the Ministry of Education, Culture, Sports, Science and Technology of Japan and furthermore, and the study was approved by the Independent Ethics Committee. The human iPS cell lines, Tic and Dotcom (provided by Dr. Akihiro Umezawa, National　Center　for　Child　Health　and　Development), were maintained on a feeder layer of mitomycin C-treated MEF with ReproStem medium supplemented with 10 ng/ml FGF2. Human iPS cell line, YOW-iPS cells, generated from primary human hepatocytes were maintained on a feeder layer of mitomycin C-treated MEF with ReproStem medium supplemented with 10 ng/ml FGF2.


title: H2009mock2

source_name: NSCLC cell line H2009, mock

value: empty vector


title: H1792 parental #2

description:
Gene expression of H1792 cell line
no6_H1792_parental_2.txt


title: MCF10A .WT.vs.H1047R - Replicate 3

status: Public on Feb 28 2017

city: Boston

first: Antoine

middle: Elias

last: Karnoub

state: MA

address: 3 Blackfan Circle

department: Pathology

country: USA

institute: Beth Israel Deaconess Medical Center and Harvard Medical School

description: biological replicate 3 of 3

hyb_protocol: Scanned on an Agilent SureScan Microarray Scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and Linear-Lowess normalization.

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: MCF10A cells expressing JP1520-PIK3CA-WT(Addgene plasmid # 14570) and JP1520-PIK3CA-H1047R (Addgene plasmid # 14572)  were generated and grown as described previously (Debnath et al., 2003; Hutti et al., 2012). Stable pools were generated by selection in 2ug/ml puromycin.

extract_protocol: Total RNA was isolated using RNeasy RNA extraction kit (Qiagen) according to manufacturer's instruction.

value: breast cancer

value: Wild-type

value: activated PIK3CA mutant H1047R


title: MCF10A .WT.vs.H1047R - Replicate 2

description: biological replicate 2 of 3


title: H2135mock1

source_name: NSCLC cell line H2135, mock


title: H2009wtB2M3

description: B2M gene restituted.


title: H2009mock1


title: H2135mock2


title: H2135mock3


title: Tic

description: Tic

source_name: Tic,undifferentiated

value: Tic


title: H358 TGF-b #2

description:
Gene expression of EMT induced H358 cell line
no4_H358_TGFb_2.txt


title: MCF10A .WT.vs.H1047R - Replicate 1

description: biological replicate 1 of 3


title: H9


title: H2009mock3


title: YOW-iPS

description: YOW-iPS

source_name: YOW-iPS,undifferentiated

value: YOW-iPS


title: Dotcom

description: Dotcom

source_name: Dotcom,undifferentiated

value: Dotcom


title: H2135wtB2M2

description: B2M gene restituted.


title: KhES1


title: FUCO2

status: Public on Feb 09 2017

city: Yonago

first: Miwa

last: Yoshimoto

address: 36-1 Nishi-cho

institute: Tottori University

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

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: human gastric cancer in the presence of fucoidan

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

growth_protocol: Cell growth assay was performed by counting cell numbers using a hemocytometer.

extract_protocol: Total RNA was collected from cultured MKN45 cells using the RNeasy mini kit (Qiagen, Hilden, Germany).

treatment_protocol: Cells were cultured in DMEM with 10% FBS. For fucoidan treatment, culture medium was replaced with fresh medium mixed with fucoidan (1 mg/ml), and cells were cultured until the assay.

value: gastric cancer cells

tag: cell line source

value: stomach, liver metastasis, epithelial-like adenocarcinoma in a 62 year-old Japanese female

value: fucoidan


title: CTR1

source_name: human gastric cancer

value: none (control)


title: FUCO1


title: CHC001 PDX ET-743 - replicate 2

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

hyb_protocol: 600 ng of labeled samples were hybridized on 8 x 60K glass array; after 17 hours of incubation at 65°C, the slide was washed following the manufacturers' instructions.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: Raw data were  background corrected (normexp method) and quantile normalized using bioconductor.

source_name: CHC001 PDX ET-743 - replicate 2

label_protocol: 100 ng of mRNA was amplified and labeled using One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling kit (Agilent)

growth_protocol: RPMI + 10%FBS

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. Absolutely RNA miRNA Kit

treatment_protocol: EGI-1 xenografts and CHC001 PDXs were treated  with 0.15 mg/Kg weekly i.v. (three administrations) or with PBS alone

tag: xenograft source

value: patient-derived CHC001 PDX

tag: treatment

value: ET-743 (0.15 mg/Kg weekly i.v., three administrations)


title: CHC001 PDX NT - replicate 1

source_name: CHC001 PDX NT - replicate 1

value: PBS


title: CHC001 PDX ET-743 - replicate 1

source_name: CHC001 PDX ET-743 - replicate 1


title: EGI-1 xenograft ET-743 - replicate 1

source_name: EGI-1 xenograft ET-743 - replicate 1

value: EGI-1 cell line


title: EGI-1 xenograft ET-743 - replicate 2

source_name: EGI-1 xenograft ET-743 - replicate 2


title: HCT116_48h_siRBM39_replicate_1

status: Public on Jan 20 2017

city: Tsukuba-shi

first: Taisuke

last: Uehara

state: Ibaraki

address: Tokodai 5-1-3

department: Oncology Business Group

institute: Eisai Co., Ltd.

description: Gene expression after 48hr treatment with siRBM39

hyb_protocol: Cy3-labeled cRNAs were hybridized to the SurePrint G3 Human Gene Expression 8×60K Microarray (Agilent Technologies) at 65 °C for 17 hours with a Gene Expression Hybridization Kit (Agilent Technologies), according to the manufacturer’s instructions. The arrays were washed with a Gene Expression Wash Pack (Agilent Technologies), according to the manufacturer’s instructions.

scan_protocol: Slides were scanned on a DNA Microarray Scanner (Agilent Technologies), according to the manufacturer’s instructions.

data_processing: The scanned images were then quantified using Feature Extraction software (version 11.5.1.1, Agilent Technologies), and the resulting files were imported and analyzed with GeneSpring (version 12.5, Agilent Technologies).

label_protocol: Total RNA (200 ng) was converted to cyanine-3 (Cy3)-labeled complementary RNA (cRNA) using a Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies), according to the manufacturer’s instructions for single-color 8×60K gene expression arrays. Cy3-labeled cRNAs were purified using an RNeasy Mini purification kit (Qiagen).

growth_protocol: Cells were cultured in RPMI-1640 (Wako) supplemented with 10% fetal bovine serum (FBS; Sigma Aldrich) and 1% penicillin-streptomycin (Wako), and grown at 37 °C in a humidified incubator under 5% CO2.

extract_protocol: Total RNA was prepared using RNeasy mini spin columns (Qiagen), according to the manufacturer’s protocol. The yield and quality of each isolated total RNA sample was determined using a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific) and an RNA Nano LabChip(R) kit analyzed on a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: HCT116 cells were seeded in a six-well plate at a density of 1.0 × 105 cells per well with or without the siRNA reverse transfection of the siGENOME SMARTpool of RBM39 (Dharmacon, M-011965) and non-targeting siRNA pool #2 (D-001206-14). Following incubation overnight, DMSO or E7820 were added to the siRNA-free HCT116 plate (final 1 μM of E7820) and incubated for 24 hours.

tag: sample type

value: cultured cell


title: HCT116_24h_E7820_replicate_3

description: Gene expression after 24hr treatment with E7820


title: HCT116_24h_DMSO_replicate_2

description: Gene expression after 24hr treatment with DMSO


title: HCT116_48h_siRBM39_replicate_2


title: HCT116_24h_DMSO_replicate_3


title: HCT116_48h_nontarget_siRNA_replicate_2

description: Gene expression after 48hr treatment with non-target siRNA


title: HCT116_24h_E7820_replicate_2


title: CHC001 PDX NT - replicate 2

source_name: CHC001 PDX NT - replicate 2


title: EGI-1 xenograft NT - replicate 1

source_name: EGI-1 xenograft NT - replicate 1


title: HCT116_48h_nontarget_siRNA_replicate_3


title: HCT116_24h_E7820_replicate_1


title: HCT116_48h_nontarget_siRNA_replicate_1


title: HCT116_48h_siRBM39_replicate_3


title: HCT116 TET1-knockdown #1 with 5-aza-dC

status: Public on Jan 01 2017

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

institute: Sapporo Medical University

description:
HCT116 stable TET1-knockdown clone 1 treated with 5-aza-dC
HCT116_TET1KD1_aza

hyb_protocol: Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v 10.7) was used following default protocol with background subtraction.

source_name: HCT116 TET1-knockdown

label_protocol: Total RNA (100 ng) was labeled using a Low Input Quick Amp Labeling Kit One-Color (Agilent Technologies) according to manufacturer's instruction.

growth_protocol: HCT116 cells were cultured in McCoy's 5A medium supplemented with 10% heat-inactivated fetal bovine serum.  The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using a TRIZOL reagent (Invitrogen).

treatment_protocol: Cells were transfected with each TET1 knockdown vector or a pcDNA6.2-GW/EmGFP-miR-neg control plasmid (Thermo Fisher Scientific), after which they were selected with 0.6 mg/ml G418. Established clones were treated with our without with 1 μM 5-aza-2’-deoxycytidine (5-aza-dC, Sigma-Aldrich) for 72 h, replacing the drug and medium every 24 h.

tag: cell type

value: colorectal cancer (CRC) cells

tag: transfected with

value: TET1 knockdown vector

value: 1 μM 5-aza-2’-deoxycytidine (5-aza-dC) for 72 h


title: EGI-1 xenograft NT - replicate 2

source_name: EGI-1 xenograft NT - replicate 2


title: HCT116_24h_DMSO_replicate_1


title: HCT116 TET1-knockdown #2 with 5-aza-dC

description:
HCT116 stable TET1-knockdown clone 2 treated with 5-aza-dC
HCT116_TET1KD2_aza


title: chitosan

status: Public on Jan 18 2017

city: Chuo-ku

first: Keisuke

last: Sekine

state: Tokyo

address: 5-1-1 Tsukiji

department: Graduate School of Medicine

institute: National Cancer Center Research Institute, Japan

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 High-Resolution Microarray Scanner using one color scan setting for 8x60kv2 array slides.

data_processing: The scanned images were analyzed with R using limma package.

source_name: Cell cultured on Chitosan membrane

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

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

value: colon cancer cell line


title: chitosan_HA

source_name: Cell cultured on HA-grafted Chitosan membrane


title: CTR2


title: HCT116 control #2 with 5-aza-dC

source_name: HCT116 control

value: mock


title: Colo320DM TET1-knockdown #2 with 5-aza-dC

description:
Colo320DM stable TET1-knockdown clone 2 treated with 5-aza-dC
Colo320_TET1KD2_aza

source_name: Colo320DM TET1-knockdown

growth_protocol: Colo320DM cells were cultured in DMEM supplemented with 10% heat-inactivated fetal bovine serum.  The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

treatment_protocol: Cells were transfected with each TET1 knockdown vector or a pcDNA6.2-GW/EmGFP-miR-neg control plasmid (Thermo Fisher Scientific), after which they were selected with 1.0 mg/ml G418. Established clones were treated with our without with 1 μM 5-aza-2’-deoxycytidine (5-aza-dC, Sigma-Aldrich) for 72 h, replacing the drug and medium every 24 h.


title: Colo320DM TET1-knockdown #1 with 5-aza-dC

description:
Colo320DM stable TET1-knockdown clone 1 treated with 5-aza-dC
Colo320_TET1KD1_aza


title: 2D

source_name: Cell cultured on tissue culture polystyrene plates


title: HCT116 TET1-knockdown #1

description:
HCT116 stable TET1-knockdown clone 1
HCT116_TET1KD1


title: Colo320DM control #1 with 5-aza-dC

description:
Colo320DM negative control clone 1 treated with 5-aza-dC
Colo320_CONT1_aza

source_name: Colo320DM control


title: Colo320DM control #2 with 5-aza-dC

description:
Colo320DM negative control clone 2 treated with 5-aza-dC
Colo320_CONT2_aza


title: Colo320DM TET1-knockdown #3

description:
Colo320DM stable TET1-knockdown clone 3
Colo320_TET1KD3


title: Undifferentiated iPSC_donorA_rep1

status: Public on Dec 14 2016

city: Fujisawa

first: Tadahiro

last: Shinozawa

address: Muraokahigashi 2chome

institute: Takeda pharmaceuticals

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 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 SurePrint G3 Human GE v2 8x60K Microarray (G039494) 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 (G2505B) using one color scan setting for 8x60k 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 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 039494_D_F_20140813) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Undifferentiated iPSC_donorA

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Quick Amplification Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was purified with an RNeasy Mini Kit (Qiagen) following the manufacturer's protocol.

value: Undifferentiated iPSC

tag: donor

value: A


title: Colo320DM control #2

description:
Colo320DM negative control clone 2
Colo320_CONT2


title: Colo320DM control #3 with 5-aza-dC

description:
Colo320DM negative control clone 3 treated with 5-aza-dC
Colo320_CONT3_aza


title: HCT116 TET1-knockdown #2

description:
HCT116 stable TET1-knockdown clone 2
HCT116_TET1KD2


title: HCT116 control #1


title: HCT116 control #1 with 5-aza-dC


title: Colo320DM control #1

description:
Colo320DM negative control clone 1
Colo320_CONT1


title: Colo320DM TET1-knockdown #3 with 5-aza-dC

description:
Colo320DM stable TET1-knockdown clone 3 treated with 5-aza-dC
Colo320_TET1KD3_aza


title: Colo320DM TET1-knockdown #2

description:
Colo320DM stable TET1-knockdown clone 2
Colo320_TET1KD2


title: Colo320DM control #3

description:
Colo320DM negative control clone 3
Colo320_CONT3


title: HCT116 control #2


title: Colo320DM TET1-knockdown #1

description:
Colo320DM stable TET1-knockdown clone 1
Colo320_TET1KD1


title: Undifferentiated iPSC_donorE_rep1

source_name: Undifferentiated iPSC_donorE

value: E


title: Undifferentiated iPSC_donorH_rep1

source_name: Undifferentiated iPSC_donorH

value: H


title: T24_gemcitabine-resistant_3

status: Public on Nov 30 2016

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

institute: Toyohashi University of Technology

hyb_protocol: The labeled cRNAs were purified, fragmented, and hybridized to microarrays in a rotating hybridization oven at 10 rpm for 17 h at 65 °C.

scan_protocol: After hybridization, the microarrays were washed according to the manufacturer’s protocol and scanned on an Agilent DNA Microarray Scanner G2505C with the Scan Control software (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 039494_D_F_20140813) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: T24 bladder cancer cells, gemcitabine-resistant, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from cultured cells using the miRNeasy mini kit (Qiagen, Hilden, Germany).

treatment_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) in a humidified atmosphere containing 5% CO2. Gemcitabine-resistant T24 cells (T24GR) were established in our laboratory. Briefly, T24 cells were initially cultured in the medium containing 5 nM gemcitabine and the dose was gradually increased over 3 months. Finally, we obtained T24GR cells that were viable in the presence of 50 nM gemcitabine. In specified experiments, cells were cultured in CSS obtained from Thermo Fisher Scientific (Waltham, MA, USA).

value: bladder cancer cells


title: U251-USP22-shRNA

city: Newhaven

first: Jiangbing

last: zhou

address: 310 Cedar Street, Ste LH 412A

institute: Yale university

description: Gene expression after reducing USP22 expression

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human Gene Expression 8x60K v2 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 (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: whole cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg 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: U251MG was grown in the DMEM supplemented with 10% FBS (GIBCO)

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: cells were stably transduced with a lentiviral vector containing the shRNA sequence of BMI1, USP22 and control

value: reduced USP22 expression


title: U251-BMI1-shRNA

description: Gene expression after reducing BMI1 expression

value: reduced BMI1 expression


title: T24_1

source_name: T24 bladder cancer cells, replicate 1


title: T24_2

source_name: T24 bladder cancer cells, replicate 2


title: T24_gemcitabine-resistant_1

source_name: T24 bladder cancer cells, gemcitabine-resistant, replicate 1


title: T24_gemcitabine-resistant_2

source_name: T24 bladder cancer cells, gemcitabine-resistant, replicate 2


title: U251-NC

description: Gene expression as control

value: wild type (control)


title: T24_3

source_name: T24 bladder cancer cells, replicate 3


title: SCC13 TLR4 cells replicate_LPS 1

status: Public on Nov 16 2016

city: Zurich

first: Guergana

last: Iotzova-Weiss

address: Gloriastrasse 31

country: Switzerland

institute: Dermatology Clinic Zurich

description:
gene expression after 24 hours
SCC13 skin tumor cell line stably transfected

hyb_protocol: 600 ng of the obtained Cy3-labeled cRNA was was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Sure Print GE 8x60 K v2 Microarrays (Agilent Technologies)  (G4112A) 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.

scan_protocol: Slides were scanned immediately after washing on the Agilent  G2565CA Microarray Scanner System (Scan Control Software 8.5, Agilent) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: Normalized Signal Intensity

source_name: TLR4  LPS

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng of total RNA using the One-Color Low Input Quick Amp Labeling  kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).Quantification and and quality assessment  were done using Nanodrop spectrophotometer  (Witec)  and Agilent 2100 Bioanalyzer (Agilent Technologies) respectively.

growth_protocol: SCC13 cell lines were grown in conventional DMEM medium supplied with 10% fetal calf serum

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) according to manufacturer's protocol

treatment_protocol: SCC13 tumor cells were stably transfected with control (pUNO, Invivogen) and TLR4 expressing plasmid (pUNO-TLR4GFP, Invivogen) following the manufacturer’s protocol. For the selection of positive clones the transfected cells were further grown in DMEM medium containing blasticidine (10μg/ml) as a selection marker. Afterwards cells were treated with 10μg/ml ultrapure LPS (Sigma) for 24 hours.

tag: transfection agent

value: LPS 10μg/ml replicate 1


title: SCC13 TLR4 cells replicate_LPS 2

value: LPS 10μg/ml replicate 2


title: SCC13 cells control replicate_LPS 3

source_name: control  LPS

value: pUNO

value: LPS 10μg/ml replicate 3


title: SCC13 cells control replicate_LPS 2


title: SCC13 cells control replicate_LPS 1


title: SCC13 TLR4 cells replicate_LPS 3


title: SCC13 cells control replicate_no treatment 2

source_name: control no LPS

value: no treatment replicate 2


title: SW480-KR12-500nM-6h-rep1

status: Public on Nov 01 2016

city: Chiba

first: Jason

last: Lin

state: Chiba

address: 666-2 Nitona-cho, Chuo-ku

institute: Chiba Cancer Center Research Institute

description: RNA Spike-In Kit

hyb_protocol: Sample preparations were performed on SurePrint G3 Human GE 8x60K V2 microarrays per Agilent Technologies’ recommendations.

scan_protocol: Data acquisition was performed on an Agilent SureScan microarray scanner.

data_processing: Differential expressions of microarray data were calculated by the LIMMA package in R. Replicates underwent background correction by the “normexp” method with an offset of 16, and scale-normalized for replicate spots between arrays. After a linear model fit for each gene was determined, statistical evaluations and differential expressions were compiled via the method of empirical Bayes, with fold changes calculated based on difference in responses between DMSO and KR12 treatments. Spots with matching RefSeq mRNA and ncRNA identifiers were filtered and retained for subsequent analyses.

source_name: SW480 cultures, 500 nM biotinylated KR12 incubation, 6 h

label_protocol: Samples at 100 ng were labeled with RNA Spike-In Kit.

growth_protocol: SW480 cultures at 9.6 × (10^4) cells per sample were plated in a 6-well microtiter plate for overnight attachment prior to treatment

extract_protocol: RNA was extracted using the RNeasy Plus Mini Kit (Qiagen).

treatment_protocol: Samples were administered 500 nM KR12 or 0.05% DMSO for 6 h prior to extraction.

tag: tissue

value: colon


title: SCC13 cells control replicate_no treatment 3

value: no treatment replicate 3


title: SCC13 cells control replicate_no treatment 4

value: no treatment replicate 4


title: SCC13 cells control replicate_LPS 4

value: LPS 10μg/ml replicate 4


title: SW480-KR12-500nM-6h-rep2

description: RNA Spike-In Kit


title: LS180-DMSO-6h-sample2-rep2

description: RNA Spike-In Kit

source_name: LS180 cultures, DMSO treatment, 6 h

growth_protocol: LS180 cultures at 9.6 × (10^4)  cells per sample were plated in a 6-well microtiter plate for overnight attachment prior to treatment


title: SW480-DMSO-6h-rep1

description: RNA Spike-In Kit

source_name: SW480 cultures, DMSO treatment, 6 h


title: LS180-KR12-500nM-6h-sample1-rep1

description: RNA Spike-In Kit

source_name: LS180 cultures, 500 nM biotinylated KR12 incubation, 6 h


title: LS180-DMSO-6h-sample2-rep1

description: RNA Spike-In Kit


title: LS180-KR12-500nM-6h-sample1-rep2

description: RNA Spike-In Kit


title: SCC13 TLR4 cells replicate_no treatment 3

source_name: TLR4 no LPS


title: SCC13 cells control replicate_no treatment 1

value: no treatment replicate 1


title: LS180-KR12-500nM-6h-sample2-rep1

description: RNA Spike-In Kit


title: SW480-KR12-500nM-6h-rep3

description: RNA Spike-In Kit


title: LS180-DMSO-6h-sample1-rep1

description: RNA Spike-In Kit


title: 121202-lung carcinoma tissue

status: Public on Oct 22 2016

city: Kunming

first: Yanliang

last: Zhang

state: Yunnan province

address: No. 295, Xichang Road

department: Department of Clinical Laboratory

institute: First Affiliated Hospital of Kunming Medical University

description: Gene expression of 121202-lung carcinoma tissue.

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized in an Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2x SSC at 42℃ for 5 min, and 0.2x SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and GeneSpring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: lung carcinoma tissue from 121202

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine's linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

tag: disease status

value: lung cancer

value: lung carcinoma tissue

tag: gender

value: male

tag: geographic location

value: Xuanwei County, China

tag: patient id


title: 110902_lung carcinoma tissue

description: Gene expression of 110902_lung carcinoma tissue.

source_name: lung carcinoma tissue from 110902

value: female


title: 120901_lung carcinoma tissue

description: Gene expression of 120901-lung carcinoma tissue.

source_name: lung carcinoma tissue from 120901


title: 121002-lung carcinoma tissue

description: Gene expression of 121002-lung carcinoma tissue.

source_name: lung carcinoma tissue from 121002


title: SCC13 TLR4 cells replicate_no treatment 2

tag: cell line


title: LS180-DMSO-6h-sample1-rep2

description: RNA Spike-In Kit


title: 121203-lung carcinoma tissue

description: Gene expression of 121203-lung carcinoma tissue.

source_name: lung carcinoma tissue from 121203


title: 110901_lung carcinoma tissue

description: Gene expression of 110901_lung carcinoma tissue.

source_name: lung carcinoma tissue from 110901


title: 120502_lung carcinoma tissue

description: Gene expression of 120502_lung carcinoma tissue.

source_name: lung carcinoma tissue from 120502


title: 120401_lung carcinoma tissue

description: Gene expression of 120401_lung carcinoma tissue.

source_name: lung carcinoma tissue from 120401


title: Human Induced Pluripotent Stem Cells (iPSCs) [19-9-11T-rep 1]

status: Public on Sep 29 2016

city: Newcastle upon Tyne

first: LILI

last: ZHU

address: Central Parkway

country: United Kingdom

institute: Newcastle University

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

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

scan_protocol: Scanned on a Agilent C Scanner

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

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

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

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

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

value: Male

tag: cell lines

value: mixture of 10 human cell lines

tag: reference

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


title: Human Induced Pluripotent Stem Cells (iPSCs) [19-9-11T-rep 2]

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

source_name: Pooled Agilent's Universal Human Reference RNA


title: Human Induced Pluripotent Stem Cells (iPSCs) [19-9-7T-rep 1]

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


title: Human Induced Pluripotent Stem Cells (iPSCs) [NHDF-iPS(S)-rep 1]

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

source_name: HiPSC-NHDF(S)

value: NHDF-iPS(S)


title: Human Embyronic Stem Cell (ESCs) [H1-rep 2]

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


title: Human Induced Pluripotent Stem Cells (iPSCs) [NHDF-iPS(L)-rep 1]

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

source_name: HiPSC-NHDF(L)

value: NHDF-iPS(L)


title: LNCaP(BHC80-2)_3

status: Public on Sep 15 2016

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

description: SAMPLE 9

hyb_protocol: cRNAs were hybridized on Agilent SurePrint G3 Human Gene Expression v2 8x60K Microarray  (AMDID 039494).

scan_protocol: Arrays were scanned with an Agilent DNA Microarray Scanner at a 3 µm scan resolution

data_processing: Data were processed with Agilent Feature Extraction 11.0.1.1. Processed signals were quantile normalized with Agilent GeneSpring 12.0. Raw and normalized data can also be found in the file AgilentHumanv2GE_20Nov14.txt available on the series record.

label_protocol: The quality of the RNA samples was checked with the Agilent 2100 Bioanalyzer and NanoDrop ND-2000 UV-VIS spectrophotometer. Only samples with RNA Integrity Number (RIN) ≥8.0, A260/280 OD values between 1.8 and 2.0 and an A260/A230 OD value of 2.0 were used for one-color labelling using Agilent’s One-Colour Microarray-Based Gene Expression Analysis Low Input Quick Amp Labelling v6.0 (Agilent Technologies, Santa Clara, CA). Total RNA (100 ng) was used to generate cyanine-3-labeled cRNA.

extract_protocol: RNA extraction protocol not provided.

tag: tumor subtype

value: Adenocarcinoma

value: LNCaP

value: BHC80-2 overexpression


title: Human Embyronic Stem Cell (ESCs) [H9-rep 2]

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

value: Female


title: Human Induced Pluripotent Stem Cells (iPSCs) [NHDF-iPS(S)-rep 2]

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


title: LNCaP(BHC80-2)_1

description: SAMPLE 7


title: Human Induced Pluripotent Stem Cells (iPSCs) [NHDF-iPS(L)-rep 2]

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


title: Human Induced Pluripotent Stem Cells (iPSCs) [19-9-7T-rep 2]

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


title: Human Embyronic Stem Cell (ESCs) [H9-rep 1]

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


title: LNCaP(BHC80-2)_2

description: SAMPLE 8


title: LNCaP(BHC80-1)_1

description: SAMPLE 4

value: BHC80-1 overexpression


title: LNCaP(BHC80-1)_3

description: SAMPLE 6


title: LNCaP(control)_1

description: SAMPLE 1

source_name: LNCaP(control)

value: control overexpression


title: SW480-DMSO-6h-rep2

description: RNA Spike-In Kit

value: colon


title: FKB_1

city: Serdang

first: Nadiah

last: Abu

state: Selangor

address: Animal Tissue Culture Lab

department: Faculty of Biotechnology

country: Malaysia

institute: Universiti Putra Malaysia

description: Gene expression in HeLa cells after 48 hours of treatment with FKB

hyb_protocol: 600 ng of Cy3-labeled cRNA (specific activity >6 pmol Cy3/µg cRNA) were fragemnted at 60C for 30 minutes in reaction volume of 25 µl with 1x Agilent Fragmentation Buffer and 2x Agilent blocking agent per manufacturer's protocol

scan_protocol: slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (SureScan Microarray Scanner with the product number: G4900DA) using one color scan setting for 8X60k with scan area 61x21.6 mm and 3µm resolution. We used one color channel for Cy3

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.

source_name: HeLa Cells, 48h FKB-Treated, replicate 1

label_protocol: Cy3labeled cRNA was prepared from 25 ng of total RNA using the Low Input Quick Amp Labelinh One-Color Microarray-Based Gene Expression Analysis

growth_protocol: HeLa cells were grown in RPMI-1640 supplemented with 10%FBS and 1% pennicillin-streptomycin and kept in a humidified 37 C chamber equipped with 5%CO2

extract_protocol: Cells were extracted using the QIAGEN Rneasy Mini Kit as per manufacturer's protocol

treatment_protocol: FKB-treated cells were treated with 7µg/mL of FKB for 48 hours, FIH-treated cells were treated with 15 µg/mL of FIH for 48 hours, the untreated cells were treated with the vehicle.

value: HeLa

value: 48 hours of treatment with FKB:Flavokawain B


title: FKB_3

source_name: HeLa Cells, 48h FKB-Treated, replicate 3


title: FIH_2

description: Gene expression in HeLa cells after 48 hours of treatment with FIH

source_name: HeLa Cells, 48h FIH-Treated, replicate 2

value: 48 hours of treatment with FIH:Diterpene Isopimara-7,15-Dien-19-Oic Acid


title: FKB_2

source_name: HeLa Cells, 48h FKB-Treated, replicate 2


title: LNCaP(control)_3

description: SAMPLE 3


title: FIH_3

source_name: HeLa Cells, 48h FIH-Treated, replicate 3


title: Human Embyronic Stem Cell (ESCs) [H1-rep 1]

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


title: Control (Untreated)_1

description: Gene expression in HeLa cells with no drug treatment

source_name: HeLa Cells, 48h Untreated, replicate 1

value: no treatment


title: H1299_FBS_3

status: Public on Sep 08 2016

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

institute: IDIBELL

description:
sample name: 039_MA__2100253949441025__Cy3_403_2_1
cancer cell line

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a total volume of 25ul following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4851A) 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: Scanner Agilent G2565CA Feature extraction 10.7

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Non Small Cell Lung Cancer (NSCLC)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 45ng total RNA using a LowInput QuickAmp Labeling Kit (Agilent Technologies, Palo Alto, Calif, USA) 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: Cells where growth on RPMI media with 10% FBS, 1% PS

extract_protocol: Total RNA were extracted using Trizol Reagent.

treatment_protocol: GCRA: Dexamethasone (1uM) + Retinoic Acid (1uM) 120hours; COMB: Dexamethasone (1uM) + Retinoic Acid (1uM) + Aza (0.2uM) + SAHA (0.2uM) 120 hours

tag: individual

value: Diseased donor

tag: cell line type

value: BRG1 mutant

value: FBS


title: FIH_1

source_name: HeLa Cells, 48h FIH-Treated, replicate 1

tag: treatment


title: H1299_GCRA_2

description:
sample name: 041_MA__2300253949441027__Cy3_412_2_3
cancer cell line

value: GCRA


title: LNCaP(BHC80-1)_2

description: SAMPLE 5


title: DMS114_GCRA_3

description:
Sample name: DMS114_P_GC_RA_4023
Cancer cell line

source_name: Lung

value: SCLC cell line DMS114


title: LS180-KR12-500nM-6h-sample2-rep2

description: RNA Spike-In Kit

source_name: LS180 cultures, 500 nM biotinylated KR12 incubation, 6 h


title: DMS114_COMB_2

description:
Sample name: DMS114_P_COMB_4032
Cancer cell line

value: COMB


title: DMS114_COMB_3

description:
Sample name: DMS114_P_COMB_4033
Cancer cell line


title: DMS114_FBS_3

description:
Sample name: DMS114_P_FBS_4013
Cancer cell line


title: DMS114_GCRA_2

description:
Sample name: DMS114_P_GC_RA_4022
Cancer cell line


title: H460_GCRA_3

description:
Sample name: H460_Sc_GC_RA_2123
Cancer cell line

value: NSCLC cell line H460

value: MYC amplified


title: H1299_FBS_1

description:
sample name: 037_MA__1300253949437761__Cy3_401_1_3
cancer cell line


title: H1299_COMB_3

description:
sample name: 045_MA__2100253949441026__Cy3_423_2_1
cancer cell line


title: DMS114_FBS_2

description:
Sample name: DMS114_P_FBS_4012
Cancer cell line


title: DMS114_GCRA_1

description:
Sample name: DMS114_P_GC_RA_4021
Cancer cell line


title: SCC13 TLR4 cells replicate_LPS 4

description:
gene expression after 24 hours
SCC13 skin tumor cell line stably transfected

source_name: TLR4  LPS

value: LPS 10μg/ml replicate 4


title: DMS114_COMB_1

description:
Sample name: DMS114_P_COMB_4031
Cancer cell line


title: H1299_COMB_2

description:
sample name: 044_MA__1200253949441025__Cy3_422_1_2
cancer cell line


title: SW480-DMSO-6h-rep3

description: RNA Spike-In Kit

source_name: SW480 cultures, DMSO treatment, 6 h


title: H1299_GCRA_3

description:
sample name: 042_MA__1400253949437761__Cy3_413_1_4
cancer cell line


title: H1299_COMB_1

description:
sample name: 043_MA__1100253949437762__Cy3_421_1_1
cancer cell line


title: H1299_FBS_2

description:
sample name: 038_MA__1400253949437762__Cy3_402_1_4
cancer cell line


title: DMS114_FBS_1

description:
Sample name: DMS114_P_FBS_4011
Cancer cell line


title: A549_COMB_2

description:
Sample name: A549_P_COMB_3042
Cancer cell line

value: NSCLC cell line A549


title: A549_COMB_3

description:
Sample name: A549_P_COMB_3043
Cancer cell line


title: A549_GCRA_1

description:
Sample name: A549_P_GC_RA_3021
Cancer cell line


title: H460_shBRG1_COMB_2

description:
Sample name: H460_Sh_COMB_2232
Cancer cell line


title: A549_FBS_1

description:
Sample name: A549_P_FBS_3011
Cancer cell line


title: A549_FBS_2

description:
Sample name: A549_P_FBS_3012
Cancer cell line


title: A549_GCRA_2

description:
Sample name: A549_P_GC_RA_3022
Cancer cell line


title: H460_shBRG1_GCRA_3

description:
Sample name: H460_Sh_GC_RA_2223
Cancer cell line


title: H460_shBRG1_GCRA_2

description:
Sample name: H460_Sh_GC_RA_2222
Cancer cell line


title: H460_shBRG1_COMB_1

description:
Sample name: H460_Sh_COMB_2231
Cancer cell line


title: H460_shBRG1_FBS_1

description:
Sample name: H460_Sh_FBS_2211
Cancer cell line


title: H460_shBRG1_FBS_3

description:
Sample name: H460_Sh_FBS_2213
Cancer cell line


title: A549_FBS_3

description:
Sample name: A549_P_FBS_3013
Cancer cell line


title: H460_shBRG1_GCRA_1

description:
Sample name: H460_Sh_GC_RA_2221
Cancer cell line


title: H460_COMB_1

description:
Sample name: H460_Sc_COMB_2131
Cancer cell line


title: H460_shBRG1_COMB_3

description:
Sample name: H460_Sh_COMB_2233
Cancer cell line


title: H460_GCRA_2.2

description:
Sample name: H460_Sc_GC_RA_2122_rep2
Cancer cell line


title: H460_FBS_3

description:
Sample name: H460_Sc_FBS_2113
Cancer cell line


title: H460_COMB_2

description:
Sample name: H460_Sc_COMB_2132
Cancer cell line


title: H460_shBRG1_FBS_2

description:
Sample name: H460_Sh_FBS_2212
Cancer cell line


title: H460_FBS_2

description:
Sample name: H460_Sc_FBS_2112
Cancer cell line


title: H460_GCRA_2

description:
Sample name: H460_Sc_GC_RA_2122
Cancer cell line


title: H82_shBRG1_COMB_3

description:
Sample name: H82_Sh_COMB_1233
Cancer cell line

value: SCLC cell line H82


title: A549_COMB_1

description:
Sample name: A549_P_COMB_3041
Cancer cell line


title: H82_shBRG1_GCRA_2

description:
Sample name: H82_Sh_GC_RA_1222
Cancer cell line


title: H460_GCRA_1

description:
Sample name: H460_Sc_GC_RA_2121
Cancer cell line


title: H460_COMB_3

description:
Sample name: H460_Sc_COMB_2133
Cancer cell line


title: A549_GCRA_3

description:
Sample name: A549_P_GC_RA_3023
Cancer cell line


title: H460_FBS_1

description:
Sample name: H460_Sc_FBS_2111
Cancer cell line


title: H82_shBRG1_COMB_2

description:
Sample name: H82_Sh_COMB_1232
Cancer cell line


title: H82_shBRG1_GCRA_3

description:
Sample name: H82_Sh_GC_RA_1223
Cancer cell line


title: H82_shBRG1_COMB_1

description:
Sample name: H82_Sh_COMB_1231
Cancer cell line


title: H82_shBRG1_GCRA_1

description:
Sample name: H82_Sh_GC_RA_1221
Cancer cell line


title: H82_COMB_2

description:
Sample name: H82_Sc_COMB_1132
Cancer cell line


title: H82_COMB_3

description:
Sample name: H82_Sc_COMB_1133
Cancer cell line


title: H82_GCRA_3

description:
Sample name: H82_Sc_GC_RA_1123
Cancer cell line


title: H82_shBRG1_FBS_3

description:
Sample name: H82_Sh_FBS_1213
Cancer cell line


title: H82_GCRA_2

description:
Sample name: H82_Sc_GC_RA_1122
Cancer cell line


title: H82_shBRG1_FBS_2

description:
Sample name: H82_Sh_FBS_1212
Cancer cell line


title: H82_COMB_1

description:
Sample name: H82_Sc_COMB_1131
Cancer cell line


title: H82_shBRG1_FBS_1

description:
Sample name: H82_Sh_FBS_1211
Cancer cell line


title: C_59934_87

status: Public on Aug 31 2016

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

hyb_protocol: cRNA samples were hybridized to an Agilent Technologies Human Gene Expression 8x60K Microarray Agilent Technologies). The hybridization slides were washed, stabilized, dried, and immediately scanned.

scan_protocol: Scanned with an Agilent Technologies Microarray Scanner using default parameters. Each sample represents one channel of a dual-channel array.

data_processing: Expression arrays were processed using BioConductor (one color arrays, Quantile normalization). Also we combated the dataset by patient (as the “batch” variable).

source_name: prostate cancer

label_protocol: The cRNA labeling was performed according to Protocol from Agilent Technologies Inc. (Santa Clara, CA) using the Agilent Quick Amp Labeling Kit (Agilent Technologies, Palo Alto, CA) following the two-colour manufacturer's protocol.

extract_protocol: RNA was extracted following the manufacturer's recommendations.

tag: ethnicity

value: African-American


title: C_59702_85


title: C_59473_83


title: H82_FBS_2

description:
Sample name: H82_Sc_FBS_1112
Cancer cell line


title: C_59138_71


title: C_53745_61


title: C_53248_59


title: C_53132_57


title: C_47603_33


title: C_55081_65


title: C_59315_81


title: H82_FBS_3

description:
Sample name: H82_Sc_FBS_1113
Cancer cell line


title: C_52014_55


title: C_50738_91


title: H82_FBS_1

description:
Sample name: H82_Sc_FBS_1111
Cancer cell line


title: C_47163_31_R1


title: C_58659_35


title: C_53984_63


title: C_56767_67


title: H82_GCRA_1

description:
Sample name: H82_Sc_GC_RA_1121
Cancer cell line


title: C_58130_69


title: C_36849_21


title: C_37977_93


title: C_46702_89


title: C_32776_49


title: C_32842_51


title: C_40814_95


title: C_42793_37


title: C_37689_25


title: C_36914_79


title: C_39436_29


title: C_37655_23


title: C_31704_19


title: C_30385_47


title: C_32594_77


title: C_19204_11


title: C_14671_75


title: C_23977_15


title: C_19053_43


title: C_36668_53


title: C_21275_45


title: C_10227_7


title: C_22694_13


title: C_10184_39


title: C_8680_73


title: C_6313_1


title: C_14471_41


title: C_10525_9


title: B_59314_82

source_name: benign


title: B_59704_86


title: C_25540_17


title: C_10050_5


title: B_59139_72


title: B_56766_68


title: B_55083_66


title: B_53983_64


title: B_53748_62


title: C_9660_3


title: B_59936_88


title: B_59474_84


title: B_58131_70


title: B_53132_58


title: B_58655_36


title: B_52013_56


title: B_50741_92


title: B_47159_32_R1


title: B_47605_34


title: B_38738_28_R1


title: B_53247_60


title: B_42792_38


title: B_37687_26


title: B_36916_80


title: B_39437_30_R1


title: B_37654_24


title: B_37975_94


title: B_46701_90


title: B_32845_52


title: B_31703_20_R1


title: B_36848_22


title: B_32777_50


title: B_32592_78


title: B_21274_46


title: B_23979_16


title: B_19051_44


title: B_10522_10


title: B_14469_42


title: B_14670_76


title: B_22693_14


title: B_10236_8


title: B_30380_48


title: hiPS_Lu99B_rep1

status: Public on Aug 16 2016

city: Okayama

first: Akimasa

last: Seno

state: Okayama

address: 1-1, Tsushima-Naka, 1-chome, Kita-Ku

department: Applied Chemistry and Biotechnology

institute: Okayama University

description:
Gene expression of induced cancer stem cell established from human iPS cell with Lu99B cell culture medium
OCC-hiPS-27

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver2.0 (Agilent) 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).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Normalized signal intensity by Agilp in series supplementary file.

source_name: Cancer Stem Cell, induced from human iPS cell with culture medium of Lu99B, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Human iPS cells kept undifferentiated were cultured in induction medium to allow differentiation. During the induction of differentiation, half of the medium was exchanged every day and the cells were passaged once or twice every two weeks. The period of induction of differentiation was at least 28 days, and at most two months. The cells were cultured at 37 °C under the atmosphere of 2% CO2.

extract_protocol: Total RNA was prepared with the RNeasy column purification (QIAGEN) according to the manufacturer's instructions

tag: cell type

value: Female

tag: age


title: hiPS_Li-7_rep1

description:
Gene expression of induced cancer stem cell established from human iPS cell with Li-7 cell culture medium
OCC-hiPS-25

source_name: Cancer Stem Cell, induced from human iPS cell with culture medium of Li-7, replicate 1


title: hiPS_ECC4_rep1

description:
Gene expression of induced cancer stem cell established from human iPS cell with ECC4 cell culture medium
OCC-hiPS-16

source_name: Cancer Stem Cell, induced from human iPS cell with culture medium of ECC4, replicate 1


title: hiPS_CW-2_rep1

description:
Gene expression of induced cancer stem cell established from human iPS cell with CW-2 cell culture medium
OCC-hiPS-17

source_name: Cancer Stem Cell, induced from human iPS cell with culture medium of CW-2, replicate 1


title: hiPS_HT-29_rep1

description:
Gene expression of induced cancer stem cell established from human iPS cell with HT-29 cell culture medium
OCC-hiPS-10

source_name: Cancer Stem Cell, induced from human iPS cell with culture medium of HT-29, replicate 1


title: hiPS_MOLT4_rep1

description:
Gene expression of induced cancer stem cell established from human iPS cell with MOLT4 cell culture medium
OCC-hiPS-20

source_name: Cancer Stem Cell, induced from human iPS cell with culture medium of MOLT4, replicate 1


title: hiPS_MY_rep1

description:
Gene expression of induced cancer stem cell established from human iPS cell with MY cell culture medium
OCC-hiPS-19

source_name: Cancer Stem Cell, induced from human iPS cell with culture medium of MY, replicate 1


title: hiPS_ZR-75-1_rep1

description:
Gene expression of induced cancer stem cell established from human iPS cell with ZR-75-1 cell culture medium
OCC-hiPS-6

source_name: Cancer Stem Cell, induced from human iPS cell with culture medium of ZR-75-1, replicate 1


title: hiPS_SKOV3_rep1

description:
Gene expression of induced cancer stem cell established from human iPS cell with SKOV3 cell culture medium
OCC-hiPS-12

source_name: Cancer Stem Cell, induced from human iPS cell with culture medium of SKOV3, replicate 1


title: B_25537_18


title: B_10042_6


title: B_8689_74_R2


title: B_36673_54


title: B_6316_2


title: B_9667_4


title: B_40813_96


title: 253949423953_2_3

status: Public on Jul 31 2016

city: Novato

first: Christina

last: Yau

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute of Age Research

description: Gene expression from patient sample in MK2206 phase 1b study

hyb_protocol: Cy3-labeled cRNA was hybridized to Agilent HD arrays containing ~60K probes (Agilent-039494) as per manufacturer's protocol.

scan_protocol: Slides were scanned after washing on Agilent DNA Microarray scanner (G2505C) using one color scan setting

data_processing: For each array, the green channel mean (gMean) signal was log2-tranformed and centered within array to its 75th quantile as per manufacturer’s data processing recommendations.  A fixed value of 9.5 was then added to avoid negative values

label_protocol: RNA labeling and hybridization was performed by LabCorp. Extracted RNA was labeled using the Sigma WTA kit and Agilent tag labeling protocol as per manufacturer's instruction.

extract_protocol: RNA extraction was performed by Almac Diagnostics.  RNA was isolated using the Ambion RecoverAll Extraction Kit using an optimised Almac procedure.

treatment_protocol: 27 pre-treatment FFPE biopsy samples from 16 unique patients in our MK2206 phase 1b trial collected and sent for gene expression profiling.

tag: patientid

tag: tumor type

value: Breast

tag: primary/metastatic biopsy

value: Metastatic

tag: biopsy site

value: Right Lung

tag: best response

value: SD

value: Pass


title: 253949423926_2_3

value: Liver

value: PR


title: 253949423953_2_4

value: Lung


title: 253949423926_2_2

value: Fail


title: 253949423953_2_2

value: CR


title: 253949423953_1_1

value: Esoph

value: Primary

value: Esophagus


title: 253949423926_2_4

value: Left frontal mass, brain


title: 253949423953_1_3

value: Chest wall

value: nonCR/nonPD


title: 253949423925_2_4

value: Left breast


title: 253949423953_1_2


title: 253949423926_1_3

value: Breast


title: 253949423926_1_1

value: Left Breast


title: 253949423925_1_3

value: Right breast


title: 253949423926_1_4

value: Metastatic

value: Left supraclavicular lymph node


title: 253949423953_2_1

value: Anterior mediastinum

value: Pass


title: 253949423925_2_2

value: Gastric

value: Gastric distal body

value: PD


title: 253949423925_1_2

value: Left lung

value: PR


title: 253949423926_2_1

value: CR


title: 253949423926_1_2

value: Primary


title: 253949423953_1_4

value: Liver mass


title: 253949423925_1_4


title: 253949423924_1_1

value: SD

value: Fail


title: 253949423925_2_3

value: Esophagus and proximal stomach


title: 253949423925_1_1

value: Breast

value: Left breast


title: 253949423925_2_1

value: Omentum


title: 253949423924_1_3

value: Metastatic

value: Soft tissue


title: Tumor sample obtained from patient 4

status: Public on Jul 26 2016

city: Shanghai

first: Jianjun

state: Shanghai

address: No.639, Zhizaoju road

institute: Shanghai Jiaotong University

description: lncRNA expression

hyb_protocol: 1.5 ug of Cy3-labelled cDNA 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 Human Gene Expression Microarray 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 (G2505B).

data_processing: Feature Extraction software (version 10.7.1.1, Agilent Technologies) was used to analyze array images to obtain raw data. GeneSpring software (version 12.5, Agilent Technologies) was employed to finish the basic analysis of the raw data. Initially, the raw data were normalized using the quantile algorithm. The probes with at least 100 percent of samples in any 1 condition out of 2 conditions having flags that indicate “Detected” were chosen for further data analysis. Differentially expressed lncRNAs were then identified through fold change, and p values were calculated using t-tests. The thresholds set for up- and down-regulated genes were a fold change ≥ 2.0 and a p value ≤ 0.05.

source_name: Tumor sample obtained from patient 4

label_protocol: The RNA samples were first reverse transcribed into cDNA, and these cDNA samples were then labeled using a Low Input Quick-Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA).

growth_protocol: All cancer samples and paired normal samples obtained from GC patients with primary GC from Zhongshan hospital, Fudan University.

extract_protocol: Total RNA was extracted from cancer cells using TRIzol Reagent (Invitrogen, Shanghai, China), and cDNA was synthesized using a PrimeScript RT reagent kit (Takara, Kusatsu, Shiga, Japan).

treatment_protocol: All clinical samples were quickly stored in liquid nitrogen after surgical resection.

tag: cancer status

value: tumor sample

tag: tissue

value: stomach

tag: gender

value: male


title: Tumor sample obtained from patient 5

description: lncRNA expression

source_name: Tumor sample obtained from patient 5


title: Tumor sample obtained from patient 10

description: lncRNA expression

source_name: Tumor sample obtained from patient 10


title: Tumor sample obtained from patient 9

description: lncRNA expression

source_name: Tumor sample obtained from patient 9


title: 253949423924_1_2

value: Pass


title: Tumor sample obtained from patient 2

description: lncRNA expression

source_name: Tumor sample obtained from patient 2


title: Tumor sample obtained from patient 8

description: lncRNA expression

source_name: Tumor sample obtained from patient 8

value: female


title: DFX3

status: Public on May 13 2016

city: Ube

first: Hirofumi

last: Harima

state: Yamaguchi

address: Minami Kogushi 1-1-1

department: Department of Gastroenterology and Hepatology

institute: Yamaguchi University Graduate School of Medicine

description: Gene expression after administration of Deferasirox

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v2; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: removed tumor, Deferasirox 200 mg/kg

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

treatment_protocol: Pancreatic cancer cells (BxPC-3) in culture were harvested and viable cells (5 × 106 cells) were injected subcutaneously into the backs of the mice. When tumor volumes reached 150 mm3, treatment began. The treatment group of mice received Deferasirox suspended in saline, which was administered by oral gavage every second day, with three treatments per week, over 21 days at concentrations of 200 mg/kg. The control mice were treated with the vehicle alone. At the end of the experiment, the mice were sacrificed and the tumors were excised and processed for genetic analyses.

tag: cell line

value: pancreatic cancer cell line BxPC-3

value: DFX

value: removed tumor


title: Tumor sample obtained from patient 7

description: lncRNA expression

source_name: Tumor sample obtained from patient 7


title: DFX2


title: DFX1


title: Control2

description: Gene expression after administration of Vehicle alone

source_name: removed tumor, vehicle alone

value: Control


title: Control3


title: Tumor sample obtained from patient 3

description: lncRNA expression

source_name: Tumor sample obtained from patient 3


title: Control1


title: Tumor sample obtained from patient 6

description: lncRNA expression

source_name: Tumor sample obtained from patient 6


title: khES-3

status: Public on Jun 22 2016

city: Seattle

first: Takafumi

last: Hiramoto

address: 1959 NE Pacific Street, HSB K-260

department: Division of Hematology

institute: University of Washington

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were normalized by the quantile algorithm with the Bioconductor.

source_name: ES cells

growth_protocol: All cells were cultured on irradiated mouse embryonic fibroblasts in standard human pluripotent stem cell media with basic fibroblast growth factor.

extract_protocol: Total RNA was isolated from semi-confluent cells using  RNeasy mini kit (Quiagen).

treatment_protocol: The cells were collected by picking up clumps manually.

value: embryonic stem cells


title: TKZP4

source_name: fibroblast-derived iPS cells

value: induced pluripotent stem cells


title: wilms tissue 25

status: Public on May 11 2016

city: Homburg

first: Nicole

last: Ludwig

address: Kirrberger Strasse

department: Human Genetics

country: Germany

institute: Saarland University

hyb_protocol: The mRNA expression profile was determined using Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray according to the manufacturers recommendations

scan_protocol: Array´s were scanned with the Agilent Scanner with default settings.

data_processing: Raw expression values were extracted using the Feature Extraction Software and GeneSpring Software of Agilent. Data was quantil normalized.

source_name: wilms tissue 30

extract_protocol: Total RNA including miRNAs was isolated using theQiagen miRNeasy Kit according to manufacturers recommendations.  RNA concentration was measured using NanoDrop2000 (ThermoScientific). RNA integrity was measured using the PicoRNA kit (Agilent) on a Bioanalyzer2100.

value: blastemal WT


title: wilms tissue 23

source_name: wilms tissue 27

label_protocol: The mRNA expression profile was determined using Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray according to the manufacturers recommendations

value: regressive WT


title: wilms tissue 21

source_name: wilms tissue 8


title: wilms tissue 22

source_name: wilms tissue 4


title: wilms tissue 28

source_name: wilms tissue 19


title: wilms tissue 26

source_name: wilms tissue 32


title: wilms tissue 27

source_name: wilms tissue 18

value: WT, diffuse anaplasia


title: wilms tissue 20

source_name: wilms tissue 17

value: mixed WT


title: Tumor sample obtained from patient 1

description: lncRNA expression

source_name: Tumor sample obtained from patient 1


title: wilms tissue 19

source_name: wilms tissue 24

value: WT, focal anaplasia


title: B_10188_40

source_name: benign

value: African-American


title: wilms tissue 17

source_name: wilms tissue 38


title: wilms tissue 24

source_name: wilms tissue 13


title: wilms tissue 16

source_name: wilms tissue 36


title: wilms tissue 14

source_name: wilms tissue 29


title: wilms tissue 18

source_name: wilms tissue 10


title: wilms tissue 7

source_name: wilms tissue 6

value: epithelial WT


title: wilms tissue 12

source_name: wilms tissue 12


title: wilms tissue 10

source_name: wilms tissue 23

value: stromal WT


title: wilms tissue 9

source_name: wilms tissue 37


title: wilms tissue 5

source_name: wilms tissue 5


title: wilms tissue 3

source_name: wilms tissue 2


title: wilms tissue 2

source_name: wilms tissue 61


title: wilms tissue 11

source_name: wilms tissue 3


title: wilms tissue 13

source_name: wilms tissue 34


title: wilms tissue 15

source_name: wilms tissue 35


title: wilms tissue 6

source_name: wilms tissue 9


title: wilms tissue 8

source_name: wilms tissue 7


title: DD.R7_trabecular structures_expression

status: Public on Apr 29 2016

city: Tomsk

first: Aleksei

middle: A

last: Sleptcov

state: Tomskaya oblasty

address: 10 Naberejnaya Ushaiki

country: Russia

institute: Research Institute of Medical Genetics

description:
gene expression of laser-microdissected breast tumor cells composing trabecular structures
Agilent DNA Microarray Scanner G2600D

hyb_protocol: 3.5 μg of the labeled cDNA were hybridized to SurePrint G3 Human GE v2, 8x60K microarrays (G4851B) for 24 h at 65°C in a rotating Agilent hybridization oven. The cDNA was not fragmented before hybridization. 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 G2600D using one color scan setting for 8x60k array slides. Images were quantified using Agilent Feature Extraction Software (version v. 10.7.3.1). Slides were scanned immediately after washing on the GenePix 4100A Scanner using one color scan setting for 8x60k array slides. Images were quantified using GenePix Pro 5.0 software.

data_processing: Agilent Feature Extraction Software (v. 10.7.3.1) was used for background subtraction and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: breast tumor from the patient DD

label_protocol: 2 μg of cDNA samples was Cy3-labeled using the SureTag DNA labeling kit (Agilent Technologies, Inc., USA), followed by RNAeasy MinElute column purification (Qiagen, USA). Dye incorporation and cDNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol:
laser microdissection protocol: Different morphological structures were isolated from 5 um hematoxylin&eosin stained sections of three different frozen breast tumor samples using PALM MicroBeam laser capture microdissection (Carl Zeiss, Germany). Each breast tumor was used for obtaining 90-120 samples (~900-1200 cells) of tubular, alveolar, and trabecular structures, 50-60 samples (up to 5000 cells) of solid structures, and 300-350 samples (~400-600 cells) of discrete groups of tumor cells. In addition, histologically normal ducts were microdissected from samples of tumor-adjacent normal breast tissue.
WTA protocol: RNA samples (a total of 18 samples) were amplified using the Ovation PicoSL WTA System V2 kit (NuGEN Technologies, Inc., USA). Amplified products (cDNA) were purified using QIAquick PCR Purification Kit (Qiagen, USA), had concentration ranging from 60 to 130 ng/ul, and stored at -80°C until gene expression microarray analysis.
Total RNA was extracted by RNeasy Plus Micro Kit (Qiagen, USA). Ribolock RNase inhibitor (Fermentas, Lithuania) was added to the isolated RNA. RNA quality was assessed by RIN using 2200 TapeStation Instrument and High Sensitivity R6K ScreenTape (Agilent Technologies, Inc., Santa Clara, USA). RIN varied from 4 to 8.

value: breast tumor

tag: tumor structure

value: trabecular structures

tag: patient id

value: DD

tag: histological type

value: invasive carcinoma of no special type

tag: molecular subtype

value: luminal B

tag: tnm stage

tag: therapy

value: without preoperative therapy


title: wilms tissue 1

source_name: wilms tissue 60


title: DD.R5_solid structures_expression

description:
gene expression of laser-microdissected breast tumor cells composing solid  structures
Agilent DNA Microarray Scanner G2600D

value: solid structures

value: female


title: DD.R1_tubular structures_expression

description:
gene expression of laser-microdissected breast tumor cells composing tubular structures
Agilent DNA Microarray Scanner G2600D

value: tubular structures


title: DD.R9_discrete groups of tumor cells_expression

description:
gene expression of laser-microdissected breast tumor cells composing discrete groups
Agilent DNA Microarray Scanner G2600D

value: discrete groups of tumor cells