title: T4105 Cell treated

city: Nashville

first: Yan

last: Guo

state: TN

address: 639 Preston Research Bld

institute: Vanderbilt Cancer Center

description: Gene expression data

hyb_protocol: Following fragmentation, the RNA was loaded on to the Affymetrix HuGene-1_0-st-v1 GeneChip as directed (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 7G

data_processing: The primary microarray data was normalized using RMA method in Affymetrix Expression Console 1.1 and annotated using latest annotation file based on genome version hg19.  The analysis was done in R using LIMMA package.

label_protocol: The RNA was labeled with GeneChipR One-Cycle Target Labeling and Control Reagents.

growth_protocol: CD133+ cells were enriched from freshly dissociated subcutaneous xenograft tumors using a CD133+ Microbead kit from Miltenyi. Cells were cultured in neurobasal media supplemented with B-27 without vitamin A, 20 ng/ml EGF and bFGF.

extract_protocol: Total RNA was isolated from the cell lines using Qiagen RNeasy Mini kit as directed (Qiagen, Valencia, CA). The quality and quantity of the RNA was determined using the Agilent RNA 6000 NanoLabChip kit and Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Cells were treated with 100 micromolar tipifarnib and 100 micromolar RO4929097 for 24 hours before being harvested for RNA extraction.

tag: agent

value: tipifarnib and RO4929097


title: T4597 Cell Untreated

status: Public on Oct 11 2017

type: RNA

country: USA

description: Gene expression data

label: biotin

molecule: total RNA

organism: Homo sapiens

value: DMSO


title: normal donor cord blood 1

city: London

first: Prashant

last: Hiwarkar

address: 30 Guildford street

country: United Kingdom

institute: Institute of Child health, UCL

description: normal donor

hyb_protocol: Arrays were hybridized using Affymetrix GeneChip Fluidics Station 450 according to manufacturer's protocol

scan_protocol: Affymetrix Genechip 3000S scanner

data_processing:
Data were analyzed using the Bioconductor package affyPLM. Preprocessing followed the following procedures: (1) background correction; (2) normalization using the quantile method; (3) summarization of probe set values using the RMA method (Robust Multi-Array Average)
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps

source_name: cord blood donor

label_protocol: RNA was converted to cDNA and amplified (NuGEN WT-Ovation kit) and then fragmented (WT-Ovation kit) and labeled with biotin (FL-Ovation cDNA biotin module, NuGEN)

growth_protocol: not applicable

extract_protocol: Immediately after sorting cell pellets were lysed in RNA lysis buffer (Qiagen) and RNA was obtained using the RNAeasy mini-kit (Qiagen) in accordance with manufacturer’s protocol

treatment_protocol: Peripheral blood and cord blood mononuclear cells were isolated from normal donors and two months after bone marrow and cord blood transplant using Ficoll-Paque method.

tag: age

value: At birth

tag: tissue

value: cord blood

tag: genotype

value: wild-type


title: T4105 Cell Untreated

description: Gene expression data


title: T4302 Cell Untreated

description: Gene expression data


title: T4597 Cell treated

description: Gene expression data


title: IOSE80 lncRNA/mRNA 3

city: harbin

first: Gao

last: Ce

state: Heilongjiang

address: 哈尔滨市南岗区学府路246号

country: China

institute: The Second Affiliated Hospital of Harbin Medical University

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

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

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

source_name: IOSE80 lncRNA/mRNA

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

growth_protocol: SKOV3 /SKOV3-DDP /IOSE80

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

treatment_protocol: RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis or Agilent 2100 Bioanalyzer

tag: cell line

tag: molecule subtype

value: lncRNA and mRNA


title: SKOV3 lncRNA/mRNA 3

address: 哈尔滨市南岗区学府路246号

source_name: SKOV3 lncRNA/mRNA


title: SKOV3-DDP lncRNA/mRNA 3

address: 哈尔滨市南岗区学府路246号

source_name: SKOV3-DDP lncRNA/mRNA


title: SKOV3-DDP lncRNA/mRNA 2

address: 哈尔滨市南岗区学府路246号


title: prostate cancer (PCa) fine-needle aspiration (FNA) biopsy tissue4

city: Shanghai

first: qianllin

last: xia

address: 2901 Caolang Road, Jinshan District

institute: Shanghai Public Health Clinical Center, Fudan University

description:
PSA94.89
Gene expression data from proatate cancer lower than BPH.

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: The raw data were normalized by the MAS 5.0 algorithm (Affy packages in R) and were transformed by log2 for further analysis.

source_name: prostate cancer

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3' IVT PLUS Reagent Kit (Cat#902416, Affymetrix, Santa Clara, CA, US)followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: 8 prostate tissues came from fine-needle aspiration (FNA) biopsies .

extract_protocol: Total RNA was extracted using Takara RNAiso Plus Kit (Cat#9109, Takara, DaLian, LiaoNing, CN)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Directly after needle biopsy, the partial prostate tissues were injected with neutral-buffered formalin (4%) to allow for fast and equal fixation, and processed for routine pathologic diagnosis. The other parts of the prostate tissues were transported on ice to the RNAsafe Tissue Stabilizer (10604ES60, Yeason) and then stored at -80°C.

value: prostate

tag: tissue subtype

value: Prostate cancer (PCa)


title: SKOV3 lncRNA/mRNA 2

address: 哈尔滨市南岗区学府路246号


title: prostate cancer (PCa) fine-needle aspiration (FNA) biopsy tissue3

description:
PSA435.9
Gene expression data from proatate cancer lower than BPH.


title: prostate cancer (PCa) fine-needle aspiration (FNA) biopsy tissue1

description:
PSA17.23
Gene expression data from proatate cancer lower than BPH.


title: flox/flox γδ

city: Fukuoka

first: Yasunobu

last: Yoshikai

address: 3-1-1 Maidashi Higashi-ku

department: Division of Host Defense

country: Japan

institute: Medical Institute of Bioregulation, Kyushu University

hyb_protocol: cRNA was hybridized to Affymetrix Mouse Gene 2.0 ST array, washed and stained according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner

data_processing: The data were analyzed with median polish summarization and quantile normalization by Affymetrix® Power Tool version 1.15.0 software, and obtained normalized intensity values.

organism: Mus musculus

source_name: γδ T cells in the liver of 3-week-old CreRag1;Bcl11b flox/flox mice

label_protocol: The cRNA was amplified, labeled using GeneChip WT Pico Kit according to the manufacturer's instructions.

extract_protocol: 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: Single-cell suspensions were isolated from liver of 3-week-old WT and CreRag1;Bcl11b flox/flox mice. CD5+ NK1.1– γδ T cells and CD5– NK1.1+ γδ T cells from WT mice and γδ T cells from CreRag1;Bcl11b flox/flox mice were sorted using a FACSAria (BD Bioscience).

value: liver

tag: genotype/variation

value: CreRag1;Bcl11b flox/flox

tag: strain background


title: benign prostatic hyperplasia (BPH) fine-needle aspiration (FNA) biopsy tissue 1

description:
PSA10.4
Gene expression data from BPH lower than prostate cancer

source_name: benign prostatic hyperplasia

value: benign prostatic hyperplasia (BPH)


title: IOSE80 lncRNA/mRNA 2

address: 哈尔滨市南岗区学府路246号


title: SKOV3-DDP lncRNA/mRNA 1

address: 哈尔滨市南岗区学府路246号


title: prostate cancer (PCa) fine-needle aspiration (FNA) biopsy tissue2

description:
PSA41.74
Gene expression data from proatate cancer lower than BPH.


title: benign prostatic hyperplasia (BPH) fine-needle aspiration (FNA) biopsy tissue 4

description:
PSA8.9
Gene expression data from BPH lower than prostate cancer


title: benign prostatic hyperplasia (BPH) fine-needle aspiration (FNA) biopsy tissue 2

description:
PSA10.91
Gene expression data from BPH lower than prostate cancer


title: InVitro_24hr_K562_Ato-C

status: Public on Oct 12 2017

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

institute: Kinjo Gakuin University

description: Gene expression after 24hr in Ato-C-treated K562 cells

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes according to the manufacturers instructions. After the fragmentation reaction, equal amount of Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G2519F-026652) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent), for 1 minute with 37Â°C GE Wash buffer 2 (Agilent), and then dried for 1 minute at room temperature with acetonitrile.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 026652_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug 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-1000 Spectrophotometer.

extract_protocol: RNA was prepared using  NucleoSpin RNA kit (TaKaRa Bio Inc., Shiga, Japan) following the manufacturer's recommendations.  RNA concentration was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: The CML cell lines were incubated in a RPMI 1640 medium supplemented with 20% heat-inactivated fetal bovine serum. The cells were then treated with the indicated concentration of ATO and/or CDDP for 24 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: cell type

value: CML cell line

tag: gender

value: female


title: SKOV3 lncRNA/mRNA 1

address: 哈尔滨市南岗区学府路246号


title: IOSE80 lncRNA/mRNA 1

address: 哈尔滨市南岗区学府路246号


title: Ad-Zip8 infected primary mouse articular chondrocytes, rep 1

status: Public on Oct 10 2017

city: Gwangju

first: Yoonkyung

last: Won

address: 123 Cheomdangwagiro

country: South Korea

institute: Gwangju Institute of Science and Technology

description:
biological rep 1
Gene expression data from Ad-Zip8 infected primary mouse articular chondrocytes

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC). Probe signals in the raw data were normalized by the RMA (Robust Multi-array Average)

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: Cultured were maintained at 37 °C in an humidified atmosphere containing 5% CO2 as a monolayer in Dulbecco’s modified Eagle’s medium (DMEM; Gibco) supplemented with 10% fetal bovine serum and antibiotics (penicillin G and streptomycin). 37 °C, 5% CO2

extract_protocol: Total RNA was extracted from mouse articular chondrocytes using a Purelink RNA mini kit (Ambion). The concentration, purity, and integrity of the extracted RNA were determined by spectrophotometry.

treatment_protocol: Primary mouse articular chondrocytes were infected with null(control) or recombinant adenovirus expressing zinc transporter ZIP8. The cells were harvested for total RNA extraction at 24 h post infection.

value: articular chondrocytes

tag: strain

value: ICR

value: 5 days

value: WT

tag: treatment

value: Ad-Zip8 infected


title: Ad-Zip8 infected primary mouse articular chondrocytes, rep 4

description:
biological rep 4
Gene expression data from Ad-Zip8 infected primary mouse articular chondrocytes


title: Ad-null infected primary mouse articular chondrocytes, rep 2

description:
biological rep 2
Gene expression data from Ad-null control infected primary mouse articular chondrocytes

value: Ad-null infected


title: Ad-null infected primary mouse articular chondrocytes, rep 4

description:
biological rep 4
Gene expression data from Ad-null control infected primary mouse articular chondrocytes


title: Ad-null infected primary mouse articular chondrocytes, rep 3

description:
biological rep 3
Gene expression data from Ad-null control infected primary mouse articular chondrocytes


title: Ad-Zip8 infected primary mouse articular chondrocytes, rep 2

description:
biological rep 2
Gene expression data from Ad-Zip8 infected primary mouse articular chondrocytes


title: Ad-Epas1(HIF-2a) infected primary mouse articular chondrocytes, biological rep 2

description: Gene expression data from Ad-Epas1(HIF-2a) infected primary mouse articular chondrocytes

treatment_protocol: Primary mouse articular chondrocytes were infected with null(control) or recombinant adenovirus expressing Hypoxia inducible factor-2 alpha (HIF-2α). The cells were harvested for total RNA extraction at 24 h post infection.

value: Ad-Epas1(HIF-2a) infected


title: Ad-Epas1(HIF-2a) infected primary mouse articular chondrocytes, biological rep 1


title: Ad-Epas1(HIF-2a) infected primary mouse articular chondrocytes, biological rep 3


title: Ad-null infected primary mouse articular chondrocytes, rep 1

description:
biological rep 1
Gene expression data from Ad-null control infected primary mouse articular chondrocytes


title: Ad-Zip8 infected primary mouse articular chondrocytes, rep 3

description:
biological rep 3
Gene expression data from Ad-Zip8 infected primary mouse articular chondrocytes


title: Ad-Epas1(HIF-2a) infected primary mouse articular chondrocytes, biological rep 4


title: benign prostatic hyperplasia (BPH) fine-needle aspiration (FNA) biopsy tissue 3

description:
PSA6.17
Gene expression data from BPH lower than prostate cancer


title: IL-1b treated primary mouse articular chondrocytes, biological rep 3

description: Gene expression data from IL-1b treated primary mouse articular chondrocytes

treatment_protocol: Primary mouse articular chondrocytes were treated with Interleukin-1β. The cells were harvested for total RNA extraction at 24 h post treatment.

value: IL-1b treated


title: Ad-null infected primary mouse articular chondrocytes, biological rep 4

description: Gene expression data from Ad-null(control) infected primary mouse articular chondrocytes


title: IL-1b treated primary mouse articular chondrocytes, biological rep 2


title: Ad-null infected primary mouse articular chondrocytes, biological rep 1


title: Untreated primary mouse articular chondrocytes, biological rep 3

description: Gene expression data from untreated primary mouse articular chondrocytes

value: Untreated


title: genomic DNA from whole blood 1

type: genomic

first: Lei

last: Shi

address: No. 1665 Kongjiang Road

institute: Xinhua Hospital, Shanghai Jiao Tong University School of Medicine

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio software v3.2

label: Cy5 and Cy3

molecule: genomic DNA

source_name: genomic DNA from whole blood

label_protocol: Standard Illumina Protocol

growth_protocol: Not handled cell

extract_protocol: genomic DNA was extracted and purified from whole blood samples using Qiagen Dneasy Kit according to standard instructions

treatment_protocol: Not handled cell

value: Male

tag: age (y)


title: Ad-null infected primary mouse articular chondrocytes, biological rep 2


title: T4302 Cell treated

description: Gene expression data

value: tipifarnib and RO4929097


title: Ad-null infected primary mouse articular chondrocytes, biological rep 3


title: IL-1b treated primary mouse articular chondrocytes, biological rep 1


title: Untreated primary mouse articular chondrocytes, biological rep 1


title: Untreated primary mouse articular chondrocytes, biological rep 2


title: TR WT N

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description: Run-on labelling for WT BY4741

hyb_protocol: Hybridization Solution was: 0.5M Na-Phosphate buffer, 1mM EDTA and 7% SDS, pH 7.2. The hybridization protocol used was as follows. Macroarrays were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 3 ml of the same solution containing 1-5X10exp6 dpm/mL of radioactive sample and hybridized for 48h. Washing conditions were: 20 min at 65ºC in 1X SSC, 0.5% SDS, and twice at 65ºC for 10 min in 0.5X SSC, 0.1% SDS. After quantification, macroarrays were stripped by washing them once with 50 mM NaOH at 45ºC, once with 50 mM Tris-HCl, pH 7.5, 0.1x SSC, 0.1% SDS and once pouring with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the macroarrays were either checked with a Geiger counter.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) until quantification.

data_processing: Raw data was pre-processed in Excel 2007 and comes from image quantification and local background subtracted. Only data above 10% regard to local background was considered. Each GRO replicate were corrected by normalization with gDNA hybridization for corresponding macroarray used. Processed data is the average that results from Median Absolute Deviation normalization of each gDNA corrected replicate using ArrayStat software. For TR the average processed value for each gene was corrected by percentage of uridines present in each probe-coding strand as described in García-Martinez et al 2004.

organism: Saccharomyces cerevisiae

source_name: Wild type cells grown in YPD to exponential phase.

label_protocol: In vivo labeling by run-on (GRO) was done using 33P-UTP. Around 6 x 10exp8 yeast cells were used to perform in vivo transcription. After spinning down cells, the cells were washed and then were permeabilized with 20 mL of 0.5% sarkosyl. In vivo transcription was performed by resuspending cells in 115 µl of RNA water and adding 162 µL of Run On Mix (120 µl of 2.5x transcription buffer [50 mM Tris-HCl pH 7.7, 500 mM KCl, 80 mM MgCl2], 20 µl of AGC mix [10 mM each of CTP, ATP and GTP], 6 µl of DTT [0.1 M] and 13 µl of [α-33P]UTP [3000 Ci/mmol, 10 Ci/µL]). The mix was incubated for 5 minutes at 30ºC to allow transcription elongation. The reaction was stopped by adding 1 ml of cold distilled water to the mix.

growth_protocol: Experiments were initiated from exponential cultures growing in YPD

extract_protocol: Total RNA isolated from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automatic device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York.

value: BY4741 wild type


title: WT, biological replicate 4

city: Philadelphia

first: Wen

last: Lin

state: PA - Pennsylvania

address: 11-167, SCTR, 3400 Civic Center Blvd

institute: University of Pennsylvania

hyb_protocol: 5.5 ug labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99 degrees for 5 min and hybridized for 16 h at 45 degrees to Mouse Gene 2.0 ST GeneChips using the GeneChip Hybridization oven 645

scan_protocol: GeneChip 3000 7G scanner

data_processing: Affymetrix.cel files were normalized with RMA in Partek Genomics Suite (v6.6, Partek, Inc., St. Louis, MO)

label: Biotin

source_name: E12.5 mouse embryo heart

label_protocol: Biotinylated cDNA were prepared according to the standard protocol from 250ng total RNA (all protocols were conducted as described in the Ambion WT Expression Manual and the Affymetrix GeneChip Expression Analysis Technical Manual)

growth_protocol: Slc39a8+/- mice were mated and embryos were dissected from pregnant female mice at E12.5

extract_protocol: QIAGEN RNeasy

treatment_protocol: Hearts were dissected from the embryos, rinsed in PBS, and stored in -80 degree freezer until RNA extraction

value: E12.5 embryo

value: heart

value: wildtype


title: KO, biological replicate 4

value: Slc39a8 knockout (KO)


title: WT, biological replicate 3


title: KO, biological replicate 1


title: KO, biological replicate 2


title: WT, biological replicate 1


title: KO, biological replicate 3


title: WT, biological replicate 2


title: BeWo-DMSO48h-2

city: Graz

first: Andreas

last: Prokesch

state: Styria

address: Harrachgasse 21/7

department: Institute of Cell Biology, Histology, and Embryology

country: Austria

institute: Medical University Graz

hyb_protocol: cRNA was fragmented and hybridized to the Applied Biosystems Human Genome Survey Microarray V2.0 (29,098 genes) according to manufacturer's protocols.

scan_protocol: Imaging was done on an AB1700 chemilumiescent microarray analyzer (Applied Biosystems, Foster City, CA).

data_processing: Raw data was normalized using quantile-normalization according to manufucturer's protocols. Data was filtered to contain Ids with valid RefSeq annotation.

label: digoxigenin-UTP labeled cRNA

source_name: BeWo cells treated with DMSO for 48h

label_protocol: RNA was reverse-transcribed into ds-cDNA and then converted into labelled cRNA by in-vitro transcription (Nano-Amp RT-IVT Labeling Kit, Applied Biosystems) using digoxigenin-conjugated UTP nucleotides

growth_protocol: BeWo were cultured in DMEM/F12 (1:1, Gibco, life technologies; Paisley, UK) supplemented with 10% FCS, penicillin/streptomycin, amphotericin B and L-glutamine in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol: Total RNA was extracted with TriZol according to manufacturer's protocol.

treatment_protocol: BeWo cells were treated for 48 hours with 20µM Forskolin or with solvent (0.2% DMSO).

value: placenta

value: male

tag: disease state

value: choriocarcinoma

value: Trophoblast cell line BeWo

value: control


title: BeWo-Forsk48h-3

source_name: BeWo cells treated with Forskolin for 48h

value: Forskolin


title: BeWo-DMSO48h-3


title: BeWo-DMSO48h-1


title: BeWo-Forsk48h-2


title: BeWo-Forsk48h-1


title: Blood gDNA from M05_1

city: daejeon

first: Jonglyul

last: Park

address: 52, Eoeun-dong, Yuseong-gu

department: Medical genomics

institute: Korea Research Institute of Bioscience and Biotechnology

description:
Monozygotic Twin
SAMPLE 9

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iSCAN using standard recommended Illumina scanner setting

data_processing: GenomeStudio software v2010.3

extract_protocol: genomic DNA was extracted and purified from nine breast HMECs samples using Qiagen DNeasy Kit according to standard instructions


title: Blood gDNA from F06_1

description:
Monozygotic Twin
SAMPLE 23

value: Female


title: Blood gDNA from F04_1

description:
Monozygotic Twin
SAMPLE 19


title: Blood gDNA from M04_2

description:
Monozygotic Twin
SAMPLE 8


title: Blood gDNA from F06_2

description:
Monozygotic Twin
SAMPLE 24


title: Blood gDNA from F05_2

description:
Monozygotic Twin
SAMPLE 22


title: Blood gDNA from F01_1

description:
Monozygotic Twin
SAMPLE 13


title: Blood gDNA from F04_2

description:
Monozygotic Twin
SAMPLE 20


title: Blood gDNA from M02_1

description:
Monozygotic Twin
SAMPLE 3


title: Blood gDNA from M04_1

description:
Monozygotic Twin
SAMPLE 7


title: GM-CSF + IL-6,biological rep1

status: Public on Oct 09 2017

city: tianjin

first: Yunhuan

last: Gao

address: Wei Jin Road No. 94

department: School of Medicine

institute: Nankai University

description:
Gene expression data from GM-CSF + IL-6 induce MDSC
GM-CSF + IL-6.txt:gProcessedSignal(normalized)

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60℃ oe 30 min in a reaction volume of 22.5ul containing 1*Agilent fragmentation buffer and 2*Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction,22.5ul of 2*Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent mouse Gene Expression (8*60k)for 17 hours at 65℃in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with GE wash buffer1 and 1min with 37℃ GEwash buffer2,then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immeddiately after washing on the Agilent DNA Microarray Scanner(G2505C) using one-color scan setting for 4*180k array slides(Scan Area 61*21.6 mm, Scan resolution 3um,Dye channel is set to Green an Green PMT is set to 100%).

data_processing: The scanned image were analyed with Feature Extraction Sofeware 10.7.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw date. RAW date were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out 2 samples flagged as 'detected' were maintained.

source_name: Mouse myeloid-derived suppressor cells

label_protocol: Cyanine-3(Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification(QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Fresh mouse bone marrow cells were cultured in complete 1640 medium containing GM-CSF only or GM-CSF+IL6 for 4 days.

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

treatment_protocol: The MDSCs were collected for further total RNA extraction.

value: bone marrow cells

tag: treated with

value: GM-CSF + IL-6

tag: induced cell type

value: Myeloid-derived suppressor cells (MDSCs)


title: Blood gDNA from M06_2

description:
Monozygotic Twin
SAMPLE 12

value: Male


title: Blood gDNA from M06_1

description:
Monozygotic Twin
SAMPLE 11


title: Blood gDNA from F01_2

description:
Monozygotic Twin
SAMPLE 14


title: cHL-Treg, biological rep4

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

description:
Gene expression data from cHL LN CD4+ T reg cells
cHL-Treg 4

hyb_protocol: Hybridization of Affymetrix HuGeneST 1.0 arrays was performed as recommenden by the manufacturer

scan_protocol: The microarrays were washed and stained in an Affymetrix Fluidics station and scanned in a GC3000 scanner with G7 update, as recommended by Affymetrix

data_processing: Signal summarization was done in Partek Genomics Suite using the RMA algorithm

source_name: Human cHL LN Treg 4

label_protocol: Total RNA samples (60 pg) were amplified and labelled using the  Ovation One-Direct System Kit from NuGEN Technologies Inc.

growth_protocol: Cells were immediately frozen after isolation

extract_protocol: Lymphocytes were extracted from human lymph nodes or tonsils by scalpel and mesh filters. Whole extract was subsequently treated with CD4, CD25 and CD127 AB and sorted via flow cytometry. The dry cell pellets were then frozen.

treatment_protocol: Tissue samples were kept cold at all time points of isolation

value: Classical Hodgkin lymphoma (cHL) lymph node

value: Hodgkin lymphoma

value: Treg cells

tag: surface marker

value: CD4+CD25highCD127- 4


title: cHL-Treg, biological rep3

description:
Gene expression data from cHL LN CD4+ T reg cells
cHL-Treg 3

source_name: Human cHL LN Treg 3

value: CD4+CD25highCD127- 3


title: Blood gDNA from M02_2

description:
Monozygotic Twin
SAMPLE 4


title: cHL-Treg, biological rep1

description:
Gene expression data from cHL LN CD4+ T reg cells
cHL-Treg 1

source_name: Human cHL LN Treg 1

value: CD4+CD25highCD127- 1


title: GM-CSF ONLY,biological rep1

description:
Gene expression data from GM-CSF ONLY induce MDSC
GM-CSF ONLY.txt:gProcessedSignal(normalized)

value: GM-CSF ONLY


title: Blood gDNA from M01_1

description:
Monozygotic Twin
SAMPLE 1


title: Blood gDNA from M05_2

description:
Monozygotic Twin
SAMPLE 10


title: Blood gDNA from F05_1

description:
Monozygotic Twin
SAMPLE 21


title: Blood gDNA from F02_1

description:
Monozygotic Twin
SAMPLE 15


title: Blood gDNA from M01_2

description:
Monozygotic Twin
SAMPLE 2


title: cHL-Treg, biological rep5

description:
Gene expression data from cHL LN CD4+ T reg cells
cHL-Treg 5

source_name: Human cHL LN Treg 5

value: CD4+CD25highCD127- 5


title: Blood gDNA from M03_2

description:
Monozygotic Twin
SAMPLE 6


title: Blood gDNA from F02_2

description:
Monozygotic Twin
SAMPLE 16


title: Blood gDNA from M03_1

description:
Monozygotic Twin
SAMPLE 5


title: cHL-Th, biological rep1

description:
Gene expression data from cHL LN CD4+ T helper cells
cHL-Th 1

source_name: Human cHL LN Th 1

value: CD4+ T helper cells

value: CD4+CD25-CD127high 1


title: cHL-Th, biological rep4

description:
Gene expression data from cHL LN CD4+ T helper cells
cHL-Th 4

source_name: Human cHL LN Th 4

value: CD4+CD25-CD127high 4


title: Blood gDNA from F03_1

description:
Monozygotic Twin
SAMPLE 17


title: cHL-Th, biological rep2

description:
Gene expression data from cHL LN CD4+ T helper cells
cHL-Th 2

source_name: Human cHL LN Th 2

value: CD4+CD25-CD127high 2


title: ton-Treg, biological rep5

description:
Gene expression data from tonsil CD4+ T reg cells
ton-Treg 5

source_name: Human tonsil Treg 5

value: tonsil


title: cHL-Th, biological rep3

description:
Gene expression data from cHL LN CD4+ T helper cells
cHL-Th 3

source_name: Human cHL LN Th 3

value: CD4+CD25-CD127high 3


title: cHL-Treg, biological rep2

description:
Gene expression data from cHL LN CD4+ T reg cells
cHL-Treg 2

source_name: Human cHL LN Treg 2

value: CD4+CD25highCD127- 2


title: ton-Treg, biological rep3

description:
Gene expression data from tonsil CD4+ T reg cells
ton-Treg 3

source_name: Human tonsil Treg 3


title: Blood gDNA from F03_2

description:
Monozygotic Twin
SAMPLE 18

value: Female


title: ton-Treg, biological rep2

description:
Gene expression data from tonsil CD4+ T reg cells
ton-Treg 2

source_name: Human tonsil Treg 2


title: ton-Treg, biological rep1

description:
Gene expression data from tonsil CD4+ T reg cells
ton-Treg 1

source_name: Human tonsil Treg 1


title: ton-Th, biological rep5

description:
Gene expression data from tonsil CD4+ T helper cells
ton-Th 5

source_name: Human tonsil Th 5

value: CD4+CD25-CD127high 5


title: ton-Th, biological rep3

description:
Gene expression data from tonsil CD4+ T helper cells
ton-Th 3

source_name: Human tonsil Th 3


title: ton-Th, biological rep2

description:
Gene expression data from tonsil CD4+ T helper cells
ton-Th 2

source_name: Human tonsil Th 2


title: ton-Th, biological rep1

description:
Gene expression data from tonsil CD4+ T helper cells
ton-Th 1

source_name: Human tonsil Th 1


title: IN54_98 BERKO  MN

city: Huddinge

first: Ivan

last: Nalvarte

address: Hälsovägen 7

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

description: SST-RMA expression values dervied from Affymetrix Expression Console software (v. 1.4)

hyb_protocol: Fragmented cDNA was hybridized to mouse Clariom D (MTA 1.0) arrays for 16 hr at 45°C in a GeneChip Hybridization Oven 645, and the arrays were subsequently washed and stained in an Affymetrix Fluidics Station 450.

scan_protocol: Scanning of arrays was performed in an Affymetrix GeneChip scanner 3000 7G

data_processing: CEL files were analyzed in Affymetrix Expression Console (v. 1.4) using the SST-RMA method, and all samples passed the quality control. The CEL files were transformed to CHP (signal intensity) files and further analyzed using Affymetrix Transcriptome Analysis Console (TAC)

source_name: MN BERKO

label_protocol: 150ng of total RNA was used to prepare biotinylated cDNA according to the GeneChip WT Plus Reagent Kit labeling protocol.

growth_protocol: All cultures were maintined in feeder-free conditions. mESCs were cultured in LIF+di knockout-DMEM medium. Neural induction was performedin insulin-transferrin-selenium-Fibronectin knockout-DMEM/F12 medium. NPC expansion was performed in N2+FGFb+Laminin knockout DMEM/F12 medium. mDPCs were maintined in N2+FGFb+FGF8b+Shh+Ascorbic acid DMEM/F12 medium. MNs were maintained in N2+Ascorbic acid DMEM/F12 medium.

extract_protocol: Total RNA was extracted useing AllPrep DNA/RNA/Protein extraction kit (Qiagen)

treatment_protocol: NPCs and mDPCs were treated for 4 days with vehicle (DMSO) or 0.5 nM LY3201 (ERb selective agonist)

value: ERb knockout

tag: devlopmental stage cells

value: MN


title: IN59_10 BERKO+LY3201  MN

source_name: MN BERKO+LY3201


title: IN60_104 BERKO+LY3201  MN


title: ton-Th, biological rep4

description:
Gene expression data from tonsil CD4+ T helper cells
ton-Th 4

source_name: Human tonsil Th 4

tag: tissue


title: IN52_96 BERKO  MN


title: ton-Treg, biological rep4

description:
Gene expression data from tonsil CD4+ T reg cells
ton-Treg 4

source_name: Human tonsil Treg 4

value: Treg cells


title: IN53_97 BERKO  MN


title: IN48_92 BERKO+LY3201 mDPC

source_name: mDPC BERKO+LY3201

value: mDPC


title: IN57_101 WT+LY3201  MN

source_name: MN WT+LY3201

value: wild type


title: IN56_10 WT+LY3201  MN


title: IN50_94 WT  MN

source_name: MN WT


title: IN49_93 WT MN


title: IN44_88 BERKO mDPC

source_name: mDPC BERKO


title: IN38_82 WT mDPC

source_name: mDPC WT


title: IN43_87 BERKO mDPC


title: IN41_85 WT+LY3201 mDPC

source_name: mDPC WT+LY3201


title: IN39_83 WT mDPC


title: IN46_90 BERKO+LY3201 mDPC


title: IN35_69 BERKO+LY3201 NPC

source_name: NPC BERKO+LY3201

value: NPC


title: IN36_70 BERKO+LY3201 NPC


title: GM-CSF ONLY, biological rep1 [miRNA]

description:
Gene expression data from GM-CSF ONLY induce MDSC
GM-CSF ONLY.txt:gTotalProbeSignal(normalized)

source_name: Mouse myeloid-derived suppressor cells

value: bone marrow cells

value: GM-CSF ONLY

value: Myeloid-derived suppressor cells (MDSCs)


title: GM-CSF + IL-6 ,biological rep1 [miRNA]

description:
Gene expression data from GM-CSF + IL-6 induce MDSC
GM-CSF+IL-6.txt:gTotalProbeSignal(normalized)

value: GM-CSF + IL-6


title: IN42_86 WT+LY3201 mDPC


title: IN16_54.1 WT+LY3201 NPC

source_name: NPC WT+LY3201


title: IN19_56.1 BERKO mESC

source_name: mESC BERKO

value: mESC


title: IN32_67 BERKO NPC

source_name: NPC BERKO


title: IN03_42 WT mESC

source_name: mESC WT


title: IN17_54 WT+LY3201 NPC


title: IN02_41 WT mESC


title: IN14_52 WT NPC

source_name: NPC WT


title: IN33_68 BERKO NPC


title: IN20_56 BERKO mESC


title: orc4-Y232C (RM-rDNA)

status: Public on Oct 06 2017

city: Seattle

first: Joseph

last: Sanchez

state: Washington

address: Foege Building S-250, 3720 15th Ave NE

department: Molecular and Cellular Biology

institute: University of Washington

hyb_protocol: Microarray hybridization was performed as described on http://www.fenglab-genomestabilityresearch.org/p/protocols.html (Part III.  Agilent microarray hybridization and scanning)

scan_protocol: Microarray scanning was performed as described on http://www.fenglab-genomestabilityresearch.org/p/protocols.html (Part III.  Agilent microarray hybridization and scanning)

data_processing:
(Extraction Software: Agilent Feature Extractor)  (Extraction Software Version: 10.5.1.1)  (Datafile type: Agilent result file)
Background subtracted median values from the two channels were used to calculate the ratio of Cy3:Cy5 as the raw ratio of ssDNA (S/G1). The raw normalized ratios of ssDNA for all genomic locations were then smoothed over a 22 kb window by loess smoothing.

source_name: orc4-Y232C (RM-rDNA) G1 phase

label_protocol: ssDNA labeling was performed as described on http://www.fenglab-genomestabilityresearch.org/p/protocols.html (Part II.  Random-primed in-gel labeling of ssDNA by Klenow)

growth_protocol: Early log phase (OD660 ~0.25) cells were arrested in G1 by the addition of alpha-factor at a final concentration 3 μM.

extract_protocol: Genomic DNA was extracted as described on http://www.fenglab-genomestabilityresearch.org/p/protocols.html (Part I.  Sample collection and Preparation of Yeast DNA Embedded in Agarose Plugs)

treatment_protocol: Alpha factor arrested cells were synchronously released into S phase by addition of pronase (0.3 mg/ml) into media containing 200 mM Hydroxyurea.  Cells were collected at 30 min post release.

value: ssDNA in orc4-Y232C (RM-rDNA)

tag: phase

value: G1 phase

source_name: ssDNA in orc4-Y232C (RM-rDNA) +HU 30 min

value: orc4-Y232C (BY-rDNA)

value: S phase


title: ORC4 (BY-rDNA)

source_name: ssDNA in ORC4 (BY-rDNA) G1 phase

value: ORC4 (BY-rDNA)

source_name: ssDNA in ORC4 (BY-rDNA) +HU 30 min


title: Malignant lymphoma 8

first: Shinya

last: Toyokuni

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

institute: Nagoya University

hyb_protocol: The labeled DNA was hybridized with Agilent SurePrint G3 Mouse CGH 4x180k microarray at 65°C for 24 hours according to the manufacturer's protocol (Version 7.1).

scan_protocol: The slides were scanned in an Agilent DNA microarray scanner with SureScan High-Resolution Technology (G2565CA).

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software 10.7 using default parameters (CGH_107_Sep09 protocol).

source_name: C57BL/6 mouse normal kidney

label_protocol: The extracted genomic DNA was labeled using Aagilent Sure tag DNA labeling kit according to the manufacturer's protocol (Version 7.1).

extract_protocol: Genomic DNA was extracted using DNeasy Blood & Tissue Kit (QIAGEN).

treatment_protocol: The treated groups initially consisted of 20 male mice for each. Ferric nitrilotriacetate was injected intraperitoneally 5 times a week for 12 weeks. The administration was started at a dose of 3 mg iron/mouse kg weight for the first week. And the dose was increased to 5 mg iron/mouse kg weight for the next 11 weeks. The mice were euthanized at ~120 weeks.

value: normal kidney

value: Malignant lymphoma

tag: genotype

value: Mutyh wild type

value: untreated


title: Renal cell carcinoma 1

value: Renal cell carcinoma

value: Mutyh kockout

value: Fe-NTA 3 mo


title: IN15_53 WT NPC

value: wild type

value: NPC


title: Renal cell carcinoma 2


title: Malignant lymphoma 2


title: ORC4 (RM-rDNA)

source_name: ssDNA in ORC4 (RM-rDNA) G1 phase

value: ORC4 (RM-rDNA)

source_name: ssDNA in ORC4 (RM-rDNA) +HU 30 min


title: orc4-Y232C (BY-rDNA)

source_name: orc4-Y232C (BY-rDNA) G1 phase

value: ssDNA in orc4-Y232C (BY-rDNA)

source_name: ssDNA in orc4-Y232C (BY-rDNA) +HU 30 min


title: Malignant lymphoma 1


title: Malignant lymphoma 3


title: ARPE-19_24h_2ADR_rep1

city: Hangzhou

first: Yuchen

address: 866 Yuhangtang Road

institute: Zhejiang University School of Medicine

hyb_protocol: 0.6 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 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028004 SurePrint G3 Human GE 8x60K array(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 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 12.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: ARPE-19 cell, 24hr, 2ADR, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: ARPE-19 cells were cultured in DMEM/F12 medium (Hyclone, Logan, UT, USA), containing 10% fetal bovine serum and 0.1% antibiotics in a humidified 5% CO2 atmosphere at 37°C.

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's instructions

treatment_protocol: ARPE-19 cells were sham washed or treated with 1 μM, 2 μM, 4 μM adriamycin for 24 h

tag: cell line


title: Malignant lymphoma 7


title: Imiquimod_4h_Card14-/-_rep1

city: Ibaraki

first: Yayoi

last: Natsume-Kitatani

state: Osaka

address: 7-6-8 Asagi Saito

institute: National Institutes of Biomedical Innovation, Health and Nutrition

description:
Gene expression in ear skin at 4h after imiquimod cream treatment in Card14-/- mice
Ear skin, 4h, Imiquimod cream-treat, Card14-/-, replicate 1

hyb_protocol: Before hybridization, 600 ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations to Agilent-014850 arrays were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual.

scan_protocol: Scanning of microarrays was performed with 5µm resolution using a DNA microarray laser scanner (Agilent Technologies). The array was scanned using Agilent G2505C DNA microarray scanner.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1). Expression intensities (gProcessedSignal) were replaced with 0 if  glsWellAboveBG is 0 before normalization.
Quartile normalization was performed with the limma package in R

label_protocol: 200 ng of total RNAs were independently reverse-transcribed using oligo-dT primers containing the T7 RNA polymerase promoter sequence to generate cDNAs and AffinityScript, RTase, which were then subjected to in vitro transcription using T7 RNA polymerase to label the cRNAs with Cy3-CTP (Amersham Pharmacia Biotech, Piscataway, NJ) using a Low input Quick-Amp Labeling Kit (Agilent Technologies).

extract_protocol: The tissue was homogenized by adding a 5 mm diameter Zirconium bead (Funakoshi, Japan) and shaking with a MixerMill 300 (Qiagen GmbH., Germany) at a speed of 20 Hz for 5 min. Total RNA was isolated using TRIzol reagent (InVitrogen) and  purified using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. Samples were treated with DNase with the RNase-Free DNase Set (Qiagen). RNA quality and quantity were determined. with a Bioanalyzer 2100 (Agilent Technologies)

treatment_protocol: To induce psoriasiform dermatitis, both mouse ears were treated once with a topical dose of 62.5 mg of Beselna cream (outside Japan, IMQ is sold as Aldara™; 3M Pharmaceuticals, St Paul, MI, USA) containing 5% IMQ (purchased from Mochida Pharmaceutical Co., Ltd)

value: Ear skin

value: Imiquimod-cream


title: Renal cell carcinoma 3


title: Imiquimod_4h_Tlr7-/-Tlr9-/-_rep2

description:
Gene expression in ear skin at 4h after imiquimod cream treatment in Tlr7-/-Tlr9-/- mice
Ear skin, 4h, Imiquimod cream-treat, Tlr7-/-Tlr9-/-, replicate 2


title: Imiquimod_4h_Tlr7-/-Tlr9-/-_rep1

description:
Gene expression in ear skin at 4h after imiquimod cream treatment in Tlr7-/-Tlr9-/- mice
Ear skin, 4h, Imiquimod cream-treat, Tlr7-/-Tlr9-/-, replicate 1


title: Malignant lymphoma 5


title: Malignant lymphoma 6


title: Imiquimod_4h_Tlr7-/-_rep1

description:
Gene expression in ear skin at 4h after imiquimod cream treatment in Tlr7-/- mice
Ear skin, 4h, Imiquimod cream-treat, Tlr7-/-, replicate 1


title: Malignant lymphoma 4


title: ARPE-19_24h_4ADR_rep1

source_name: ARPE-19 cell, 24hr, 4ADR, replicate 1


title: Renal cell carcinoma 4


title: Imiquimod_4h_Tlr9-/-_rep1

description:
Gene expression in ear skin at 4h after imiquimod cream treatment in Tlr9-/- mice
Ear skin, 4h, Imiquimod cream-treat, Tlr9-/-, replicate 1


title: Imiquimod_4h_Card14-/-_rep2

description:
Gene expression in ear skin at 4h after imiquimod cream treatment in Card14-/- mice
Ear skin, 4h, Imiquimod cream-treat, Card14-/-, replicate 2


title: Control_0hr_Card14-/-_rep1

description:
Gene expression of control from ear skin in Card14-/- mice
Ear skin, 0h, Non-treat, Card14-/-, replicate 1

source_name: Ear skin, 0h, Non-treat, Card14-/-


title: Imiquimod_4h_WT_rep1

description:
Gene expression in ear skin at 4h after imiquimod cream treatment in WT mice
Ear skin, 4h, Imiquimod cream-treat, WT, replicate 1

source_name: Ear skin, 4h, Imiquimod cream-treat, WT

value: WT


title: Control_0hr_Tlr9-/-_rep1

description:
Gene expression of control from ear skin in Tlr9-/- mice
Ear skin, 0h, Non-treat, Tlr9-/-, replicate 1

source_name: Ear skin, 0h, Non-treat, Tlr9-/-


title: ARPE-19_24h_1ADR_rep1

source_name: ARPE-19 cell, 24hr, 1ADR, replicate 1


title: Control_0hr_Tlr7-/-Tlr9-/-_rep1

description:
Gene expression of control from ear skin in Tlr7-/-Tlr9-/- mice
Ear skin, 0h, Non-treat, Tlr7-/-Tlr9-/-, replicate 1

source_name: Ear skin, 0h, Non-treat, Tlr7-/-Tlr9-/-


title: Control_0hr_Tlr7-/-_rep1

description:
Gene expression of control from ear skin in Tlr7-/- mice
Ear skin, 0h, Non-treat, Tlr7-/-, replicate 1

source_name: Ear skin, 0h, Non-treat, Tlr7-/-


title: Control_0hr_WT_rep1

description:
Gene expression of control from ear skin in WT mice
Ear skin, 0h, Non-treat, WT, replicate 1

source_name: Ear skin, 0h, Non-treat, WT


title: 1100110pre-treatment

status: Public on Oct 05 2017

city: Aurora

first: Matthew

middle: Alan

last: Burchill

state: Colorado

department: Department of Medicine

institute: University of Colorado - Anschutz Medical Campus

description:
preDAA_Subject9
Gene expression from patient with chronic HCV infection prior to treatment

hyb_protocol: 16 hours at 45 degrees C in a genechip hybridization oven 640

scan_protocol: Gene chip scanner 7G

data_processing: Partek Genomics Suite (PGS) v6.6 (Partek, St Louis, MO) was used to quantitate gene expression to log2 values using RMA background correction with quantile normalization and medial polish for probeset summarization. A paired t-test was used to generate p-values for all genes (53,617 transcripts) comparing pre- vs post- DAA treatment

source_name: patient PBMCs with chronic HCV infection prior to treatment

label_protocol: 100ng of mRNA was labeled using the WT Plus Reagent

extract_protocol: RNA was extracted using the Qiagen Rneasy isolation protocol following manufactor directions

value: Peripheral Blood Mononuclear cells (PBMC)

value: Preatment

tag: diagnosis

value: chronic HCV infection

tag: subject number


title: 1100110post-treatment

description:
postDAA_Subject9
Gene expression from patient 12-weeks after treatment start

source_name: patient PBMCs 12-weeks after treatment start

value: Post-treatment


title: 0800117pre-treatment

description:
preDAA_Subject8
Gene expression from patient with chronic HCV infection prior to treatment


title: 0800117post-treatment

description:
postDAA_Subject8
Gene expression from patient 12-weeks after treatment start


title: 0100143post-treatment

description:
postDAA_Subject6
Gene expression from patient 12-weeks after treatment start


title: 0600099pre-treatment

description:
preDAA_Subject7
Gene expression from patient with chronic HCV infection prior to treatment


title: 1000139pre-treatment

description:
preDAA_Subject4
Gene expression from patient with chronic HCV infection prior to treatment


title: 300129post-treatment

description:
postDAA_Subject2
Gene expression from patient 12-weeks after treatment start


title: 0100121pre-treatment

description:
preDAA_Subject5
Gene expression from patient with chronic HCV infection prior to treatment


title: 1000139post-treatment

description:
postDAA_Subject4
Gene expression from patient 12-weeks after treatment start


title: TPEN_untreated_rep1

city: Pohang

first: Bhin

last: Jin-hyuk

address: Ji-gok research center, hyoja-dong, Nam-gu

department: Department of Chemical engineering

institute: POSTECH

hyb_protocol: Standard Agilent hybridization protocols

scan_protocol: Agilent Technologies Scanner G2505C

data_processing: Control probes were excluded before data processing. Scanned signal intensity (gMedianSignal) was log2-transformed. The data processing including quantile normalization was done using MATLAB 7.13.0 (R2011b).

label: Cyanine 3-CTP

source_name: TPEN(-) human keratinocytes

label_protocol: Refer to the Agilent Gene Expression System Manual

growth_protocol: Normal human keratinocytes (Cascade Biologies, Portland, OR, USA) were maintained in keratinocytes growth (KGM) GOLD medium (Lonza, Based, Switzerland)

extract_protocol: Total RNA was isolated from tissues using Qiazol (QIAGEN) following the manufacturers’ protocols.

treatment_protocol: siRNA transfection was performed with ON-TARGETplus SMARTpool siRNA (Life Technologies) using Lipofectamine RNAimax (Life Technologies).

value: Human keratinocytes


title: TPEN_untreated_rep2


title: ARPE-19_control_rep1 (#2)

source_name: ARPE-19 cell, control


title: 0600099post-treatment

description:
postDAA_Subject7
Gene expression from patient 12-weeks after treatment start


title: TPEN_treated_rep1

source_name: TPEN(+) human keratinocytes


title: 300074post-treatment

description:
postDAA_Subject1
Gene expression from patient 12-weeks after treatment start


title: 600043pre-treatment

description:
preDAA_Subject3
Gene expression from patient with chronic HCV infection prior to treatment


title: 0100143pre-treatment

description:
preDAA_Subject6
Gene expression from patient with chronic HCV infection prior to treatment


title: 300074pre-treatment

description:
preDAA_Subject1
Gene expression from patient with chronic HCV infection prior to treatment


title: 0100121post-treatment

description:
postDAA_Subject5
Gene expression from patient 12-weeks after treatment start


title: 300129pre-treatment

description:
preDAA_Subject2
Gene expression from patient with chronic HCV infection prior to treatment


title: TPEN_treated_rep2


title: Sample 4_OKF6/Tert2 E6E7 Cy3

city: Santiago

first: Ulises

last: Urzua

address: Independencia 1027

department: Basic and Clinical Oncology

country: Chile

institute: University of Chile

hyb_protocol: The labeled cDNA was purified by Minelute columns (QIAGEN). Absorbance readings at 260, 550 and 650 nm were measured to estimate labeling efficiency using a Nanodrop1000 spectrophotometer (Thermo Scientific). 39 uL the labeled cDNA were combined with 45 ul of formamide solution 2X (0.2% SDS, 0.2 ug/mL fish sperm DNA, 10X SSC buffer) and denatured at 95° C for 3 min. The total 90 uL of this mixture were deposited on the microarray, covered with a LifterSlip and incubated in a ArrayIt hybridization cassette for 22 h at 42° C.

scan_protocol: The slides were washed sequentially in 4 buffer solutions (SSC+SDS), 2 -min each, dried by low-speed centrigugation and then scanned in a Perkin Elmer Scan Array Lite instrument at 10um resolution and 75%PMT.

data_processing: The scanned images were analyzed with GenePix pro 6.0. GPR data files were uploaded to mAdb (https://madb.nci.nih.gov/) and normalized by print-tip loess.

source_name: OKF6/tert2 V

label_protocol: RNA quality was verified by 0.9% agarose gel electrophoresis. 15 μg of RNA  were labeled by reverse transcription in a 35 uL reaction containing 3 ug of random primers, 3 ug oligo-dT, 10 nmoles of dATP, dGTP and dTCP, 4 nmoles of dTTP, 2.5 nmol of either Cy3 or Cy5-dUTP, 40 U of RNAsin and 800 U of M-MLV Reverse Transcriptase (Promega). After incubation at 37ºC for 2 h, 300 additional U of enzyme and further incubated for 2 h.

growth_protocol: Cells were grown in RPMI-1640 basal medium supplemented with 10% FBS and antibiotics (gentamicin, penicillin and streptomicin) at 37ºC with 5% CO2 atmosphere. For subculture, cells were trypsinized 3-5 min and treated with fresh medium containing FBS. Stably transfected OKF6/Tert2 cells were selected and grown in a culture medium containing 0.1 μg/mL G418.

extract_protocol: Total RNA was obtained using Trizol reagent (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: Cells were cultured to 80% confluence and serum depleted for 24 h.

value: oral human cells

tag: transfected with

value: empty pLXSN  vector

source_name: OKF6/Tert2 E6E7

value: E6E7 HPV-16 genes using pLXSN vector


title: Sample 2_OKF6/Tert2 E6E7 Cy3

tag: cell type


title: Sample 1_OKF6/Tert2 E6E7 Cy5


title: Sample 3_OKF6/Tert2 E6E7 Cy5


title: 600043post-treatment

description:
postDAA_Subject3
Gene expression from patient 12-weeks after treatment start


title: UMSCC-17B cisplatin resistant

status: Public on Oct 04 2017

city: BETHESDA

first: PING

last: JIN

state: MD

address: 9000 ROCKVILLE PIKE

department: DTM

institute: CC/DTM/NIH

description: Cisplatin-resistance comparison

hyb_protocol: RNA was amplified and labeled using an Agilent LowInput QuickAmp Labeling Kit and subsequently mixed with Universal Human Reference RNA (Stratagene, Santa Clara, CA, USA) and cohybridized to Agilent Chip Whole Human genome, 4x44k slides according to the protocol provided by Agilent.

scan_protocol: The slides were incubated for 17h at 65°C and then the scanned using the Agilent B Scanner.

data_processing: Raw images were obtained by scanning the slides with an Agilent Scan G2505B and Agilent Scan Control software (version 9.5). The images were extracted using the Feature Extraction Software (Agilent Technologies). Partek Genomic Suite 6.6 (Partek Inc., St. Louis, MO, USA) was used for data visualization, identification of differentially expressed transcripts and hierarchical cluster analysis. We transformed the fluorescence intensity data to log2 ratios of each sample versus the universal human RNA reference (Stratagene, Santa Clara, CA, USA).

growth_protocol: UMSCC cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 2mM L-glutamine, 1mM sodium pyruvate, 1% nonessential amino acids (Life Technologies, Inc.), 1% Penicillin-Streptomycin (Invitrogen, CA). Adherent monolayer cultures were maintained on plastic plates and incubated at 37°C in 5% CO2 condition.

extract_protocol: Total RNA was extracted from each cell line using miRNA Easy Kit (Qiagen, Germantown, MD) and RNA was evaluated using NanoDrop 2000 (Thermo Scientific, Wilmington, DE).

value: cell line

tag: phenotype

value: cisplatin resistant

source_name: universal human reference RNA

tag: sample type

value: pooled whole human RNA


title: UMSCC-74B cisplatin sensitive

description: 7 pairs comparision

label_protocol: RNA was amplified and labeled using an Agilent LowInput QuickAmp Labeling Kit and subsequently mixed with Universal Human Reference RNA (Stratagene, Santa Clara, CA, USA)

value: cisplatin sensitive


title: UMSCC-17A cisplatin resistant

description: Cisplatin-resistance comparison


title: UMSCC-22A cisplatin sensitive

description: 7 pairs comparision


title: UMSCC-14B cisplatin sensitive

description: 7 pairs comparision


title: UMSCC-14A cisplatin resistant

description: Cisplatin-resistance comparison


title: UMSCC-17B cisplatin sensitive

description: 7 pairs comparision


title: UMSCC-17A cisplatin sensitive

description: 7 pairs comparision


title: UMSCC-14B cisplatin resistant

description: Cisplatin-resistance comparison


title: UMSCC-10A cisplatin sensitive

description: 7 pairs comparision


title: UMSCC-14A cisplatin sensitive

description: 7 pairs comparision


title: UMSCC-74A cisplatin sensitive

description: 7 pairs comparision


title: UMSCC-22B cisplatin sensitive

description: 7 pairs comparision


title: Glioblastoma_patient_36

city: Odense

first: Bjarne

middle: Winther

last: Kristensen

address: Winsloewsparken 15

department: Dept. of Pathology

country: Denmark

institute: Odense University Hospital

description: Patient ID 36

hyb_protocol: The hybridization, washing and staining processes were performed using Affymetrix GeneChip Hybridization, Wash and Stain Kit on the Affymetrix Hybridization Oven 645 and Affymetrix Fluidics Station 450X. Samples were hybridized to the Affymetrix GeneChip miRNA 2.0 Array.

scan_protocol: GeneChips were  scanned on an Affymetrix 3000 G7 scanner according to manufacturer’s instructions.

data_processing: Data was generated using the Affymetrix GeneChipTM command ConsoleTM software. Data was processed in R using the Methods for Affymetrix Oligonucleotide Arrays R package (Bioconductor). Expression data was normalized using the robust multi-array average (justRMA) method where the raw intensity values are background-corrected, log2-transformed and then quartile-normalized.  A linear model was fit to the normalized data to obtain an expression measure for each probe set on each array.  Please note that only the probesets that pertain to human, defined by containing the letters hsa were analyzed, resulting in the reduced data set of  2226 ID_REFs out of a possible 20715 presented in the platform records.

source_name: Brain tumor tissue

label_protocol: RNA was biotin-labeled using the FlashTagTM Biotin HSR RNA Labeling Kit (Affymetrix). An input of 400 ng total RNA was used for each reaction.

extract_protocol: Total RNA was extracted using the RecoverAllTMTotal Nucleic Acid Isolation Kit from Ambion (AM1975)

treatment_protocol: Fresh tissue biopsies were fixed in 4% neutral buffered formaldehyde and subsequently paraffin embedded. For 20 µm sections were cut from each specimen, placed in RNAse-free cryotubes, andstored at -20 °C until extraction.

tag: subject id

tag: gender

value: Female

tag: age

tag: overall survival (months)

tag: survival status

value: Deceased

tag: resection

value: Unknown

tag: postsurgical-treatment

value: Radiation

tag: isocitrate dehydrogenase 1 status

value: Wildtype

value: primary glioblastoma tissue

tag: tissue type

value: Formalin-fixed and paraffin-embedded tissue


title: Glioblastoma_patient_35

description: Patient ID 35

value: Male

value: Complete

value: Radiation, TMZ (at tumor relapse)

tag: tissue


title: Glioblastoma_patient_37

description: Patient ID 37

value: Partial


title: UMSCC-11B cisplatin sensitive

description: 7 pairs comparision


title: UMSCC-11A cisplatin sensitive

description: 7 pairs comparision


title: UMSCC-10B cisplatin sensitive

description: 7 pairs comparision


title: Glioblastoma_patient_40

description: Patient ID 40


title: Glioblastoma_patient_39

description: Patient ID 39


title: UMSCC-83A cisplatin sensitive

description: 7 pairs comparision


title: UMSCC-83B cisplatin sensitive

description: 7 pairs comparision


title: iPS 5 day 2

city: beijing

first: liang

middle: sheng

last: xian

address: shuangqing road

institute: chinese academy of science

description: 25 [9372538043_E]

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Gene expression data were imported and analyzed using the BRB-ArrayTools.
The reduced 700 data set (fold_change_data.txt) represents significantly up- or down-regulated genes with fold change > 2 and P-value < 0.05, by student t-test, between Day 0 and Day 5 samples.

source_name: iPSC

label_protocol: Use high-density silica bead-based microarray technology

extract_protocol: RNAs were extracted with QIAGEN Rneasy mini plus kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: iPSC line

tag: clone

value: Nac1 null iPS clone #5

tag: time point

value: line 5 day 2


title: iPS 7 day 2

description: 27 [9372538043_A]

value: Nac1 null iPS clone #7

value: line 7 day 2


title: iPS 5 day 5

description: 55 [9372538043_D]

value: line 5 day 5


title: iPS 5 day 0

description: 05 [9372538043_C]

value: line 5 day 0


title: iPS 7 day 0

description: 07 [9372538043_B]

value: line 7 day 0


title: Glioblastoma_patient_34

description: Patient ID 34

value: Female

value: Deceased


title: Glioblastoma_patient_33

description: Patient ID 33

value: Radiation

value: Wildtype


title: Glioblastoma_patient_32

description: Patient ID 32

value: primary glioblastoma tissue

value: Formalin-fixed and paraffin-embedded tissue


title: Glioblastoma_patient_30

description: Patient ID 30

value: Male


title: Glioblastoma_patient_31

description: Patient ID 31


title: Glioblastoma_patient_27

description: Patient ID 27


title: Glioblastoma_patient_29

description: Patient ID 29


title: Glioblastoma_patient_38

description: Patient ID 38

value: Complete


title: Glioblastoma_patient_25

description: Patient ID 25

value: Unknown


title: Glioblastoma_patient_22

description: Patient ID 22

value: Partial


title: Glioblastoma_patient_23

description: Patient ID 23


title: B600_20

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: Natl. Inst. Public Health & Environment

hyb_protocol: RNA was amplified, biotin-labelled and hybridized to Affymetrix GeneChip HT RG-230 PM Array Plates according to the provided protocols by Affymetrix (Santa Clara, CA).

scan_protocol: After staining, the HT Array plate was read by the Affymetrix GeneChip® HT Scanner and analyzed by the Affymetrix GeneChip® Operating Software.

data_processing: The Affymetrix CEL files were  normalized by using the Robust Multichip Average (RMA) algorithm and the Brainarray custom CDF version 19 probe set annotation (http://brainarray.mbni.med.umich.edu/Brainarray/)

organism: Rattus norvegicus

source_name: B600, replicate 4

growth_protocol: After acclimating for 2 weeks, virgin female rats were housed with male rats for a 3-hour mating period (9:00-12:00, described as GD 0). Mated dams were afterwards individually housed. Rats were daily monitored for their general health condition during the period of the present study.

extract_protocol: For transcriptomics, cultured embryos were isolated from the yolk sac and ectoplacental cone, placed in 200μL RNAlater (Ambion, Austin, Texas), stored for one week at 4oC, and then stored for further processing at -80oC.  After the embryos were thawed on ice, they were separately homogenized by passing them 10 times though a 1mL syringe with a 26G needle. RNA was further isolated by using the RNeasy Micro Plus RNA isolation kit and manufacturer’s protocol. RNA was eluted with 14μM RNase-free H2O and stored at -80oC. Quantity and quality of the isolated RNA were measured with Nanodrop (Nanodrop Technologies Inc., Wilmington, Delaware) and 2100 BioAnalyzer (Agilent Technologies, Palo Alto, California). Samples with absorbance value between 1.9 and 2.2 (ratio 260mm/280mm) and RNA integrity number (RIN) higher than 8 were further used for performing the microarray analysis.

treatment_protocol: On GD 10, between 9:00 and 12:00 a.m., dams were euthanized by intracardiac injection of T61R (Intervet, The Netherlands). Rat embryos were immediately separated from the uterus. The peripheral trophoblastic cell zone and parietal yolk sac membrane were removed under the microscope leaving both the visceral yolk sac and ectoplacental cone intact. Embryos with 2-4 somites were separately cultured in flasks with 2 mL culture medium, containing 90% pregnant bovine serum and 10% rat serum, diluted with 14% Hank’s solution and supplemented with 1.6 mg/mL D-glucose and 75 ug/mL L-methionine. The culture flasks were placed in rotating incubators, completely protected from light exposure and with stable internal temperature of 37.7oC. Rat WEC were exposed for 4 hours (0-4h) to the tested compounds at their ID10 values, dissolved in 0.1 DMSO.

value: whole embryo

tag: batch

value: B

tag: exposure


title: B600_17

source_name: B600, replicate 1

label_protocol: RNA was amplified, biotin-labelled and hybridized to Affymetrix GeneChip HT RG-230 PM Array Plates according to the provided protocols by Affymetrix (Santa Clara, CA).


title: iPS 7 day 5

description: 57 [9372538043_F]

tag: cell type

value: iPSC line

value: Nac1 null iPS clone #7

value: line 7 day 5


title: Glioblastoma_patient_24

description: Patient ID 24


title: B600_24

source_name: B600, replicate 8


title: Glioblastoma_patient_28

description: Patient ID 28


title: B599_15

source_name: B599, replicate 6


title: Glioblastoma_patient_17

description: Patient ID 17


title: Glioblastoma_patient_18

description: Patient ID 18


title: B600_19

source_name: B600, replicate 3


title: Glioblastoma_patient_26

description: Patient ID 26


title: B599_14

source_name: B599, replicate 5


title: B600_23

source_name: B600, replicate 7


title: B600_21

source_name: B600, replicate 5


title: B600_18

source_name: B600, replicate 2


title: B599_16

source_name: B599, replicate 7


title: Glioblastoma_patient_15

description: Patient ID 15

value: None/unknown


title: B599_12

source_name: B599, replicate 3


title: Glioblastoma_patient_13

description: Patient ID 13


title: B599_9

source_name: B599, replicate 8


title: B600_22

source_name: B600, replicate 6


title: Glioblastoma_patient_19

description: Patient ID 19


title: Glioblastoma_patient_11

description: Patient ID 11


title: Glioblastoma_patient_20

description: Patient ID 20


title: B595_5

source_name: B595, replicate 5


title: B599_13

source_name: B599, replicate 4


title: B599_10

source_name: B599, replicate 1


title: Glioblastoma_patient_16

description: Patient ID 16

source_name: Brain tumor tissue


title: B595_3

source_name: B595, replicate 3


title: B595_8

source_name: B595, replicate 8


title: Glioblastoma_patient_9

description: Patient ID 9

value: Radiation, TMZ (at tumor relapse)


title: Glioblastoma_patient_14

description: Patient ID 14


title: B595_6

source_name: B595, replicate 6


title: Glioblastoma_patient_1

description: Patient ID 1


title: B595_1

source_name: B595, replicate 1


title: Glioblastoma_patient_8

description: Patient ID 8


title: Glioblastoma_patient_5

description: Patient ID 5


title: Glioblastoma_patient_4

description: Patient ID 4


title: TEB_56

source_name: tebuconazole, replicate 8

value: 115µM tebuconazole


title: Glioblastoma_patient_3

description: Patient ID 3

value: Deceased


title: B599_11

source_name: B599, replicate 2


title: Glioblastoma_patient_7

description: Patient ID 7

value: Female

value: Radiation


title: TEB_53

source_name: tebuconazole, replicate 5


title: TEB_55

source_name: tebuconazole, replicate 7


title: B595_7

source_name: B595, replicate 7


title: Glioblastoma_patient_12

description: Patient ID 12

value: Wildtype

value: primary glioblastoma tissue


title: B595_4

source_name: B595, replicate 4


title: Glioblastoma_patient_2

description: Patient ID 2

value: Male

value: Formalin-fixed and paraffin-embedded tissue


title: Glioblastoma_patient_6

description: Patient ID 6

value: Radiation, TMZ/CCNU/PCV (at tumor relapse)


title: TEB_54

source_name: tebuconazole, replicate 6


title: TEB_51

source_name: tebuconazole, replicate 3


title: TEB_52

source_name: tebuconazole, replicate 4


title: TEB_50

source_name: tebuconazole, replicate 2


title: PRO_48

source_name: propiconazole, replicate 8

value: 220µM propiconazole


title: PRO_46

source_name: propiconazole, replicate 6

value: whole embryo


title: B595_2

source_name: B595, replicate 2

value: B


title: PRO_44

source_name: propiconazole, replicate 4


title: PRO_41

source_name: propiconazole, replicate 1


title: PRO_42

source_name: propiconazole, replicate 2


title: PRO_47

source_name: propiconazole, replicate 7


title: PRO_45

source_name: propiconazole, replicate 5


title: TEB_49

source_name: tebuconazole, replicate 1


title: PRO_43

source_name: propiconazole, replicate 3


title: FEN_39

source_name: fenarimol, replicate 7

value: 140µM fenarimol


title: BAVdil_8

city: Reus

first: Neus

last: Martínez-Micaelo

address: Avda. de la Universitat, 1

institute: Pere Virgili Health Research Institute

description: circulating miRNA expression

hyb_protocol: The samples were hybridized on the arrays with the inclusion of a hybridization spike-in solution (Agilent Technologies) to monitor hybridization efficiency.

scan_protocol: The arrays were scanned with a G2565CA Microarray Scanner System with SureScan High-Resolution Technology (Agilent Technologies) using Scan Control software.

data_processing: The Feature Extraction 11.5.11 (Agilent Technologies) and GeneSpring 12.6.1. software packages were used for data processing.

source_name: BAVdil

label_protocol: miRNAs were dephosphorylated and labelled with cyanine 3-cytidine biphosphate including a labelling spike-in solution (Agilent Technologies) to assess labelling efficiency.

extract_protocol: Total RNA was extracted from 250 μl of plasma using TRIzol reagent according to the manufacturer’s instructions (Invitrogen) and purified using an RNeasy minikit (Qiagen). To increase RNA recovery, 1 μg of MS2 carrier RNA was added to each plasma sample. The quality of total isolated RNA was determined using the Agilent 2100 Bioanalyzer.

tag: disease state

value: Bicuspid aortic valve patient with aortic dilation

value: Plasma

value: male


title: BAVdil_9

description: circulating miRNA expression


title: FEN_38

source_name: fenarimol, replicate 6


title: BAVdil_6

description: circulating miRNA expression


title: FEN_35

source_name: fenarimol, replicate 3


title: BAVdil_2

description: circulating miRNA expression


title: BAVdil_5

description: circulating miRNA expression


title: FEN_40

source_name: fenarimol, replicate 8


title: FEN_36

source_name: fenarimol, replicate 4


title: BAVdil_1

description: circulating miRNA expression


title: BAVdil_7

description: circulating miRNA expression


title: FEN_37

source_name: fenarimol, replicate 5


title: BAVdil_3

description: circulating miRNA expression


title: FEN_34

source_name: fenarimol, replicate 2


title: BAV_8

description: circulating miRNA expression

source_name: BAV

value: Bicuspid aortic valve patient


title: DMSOb_31

source_name: DMSO vehicle batch B, replicate 7

value: DMSO 0.1%


title: BAV_7

description: circulating miRNA expression


title: BAVdil_4

description: circulating miRNA expression


title: BAV_6

description: circulating miRNA expression


title: DMSOb_28

source_name: DMSO vehicle batch B, replicate 4


title: DMSOb_29

source_name: DMSO vehicle batch B, replicate 5


title: FEN_33

source_name: fenarimol, replicate 1


title: DMSOb_25

source_name: DMSO vehicle batch B, replicate 1


title: DMSOb_32

source_name: DMSO vehicle batch B, replicate 8


title: BAV_4

description: circulating miRNA expression


title: DMSOb_26

source_name: DMSO vehicle batch B, replicate 2


title: DMSOb_27

source_name: DMSO vehicle batch B, replicate 3


title: TDF_068

source_name: triadimefon, replicate 7

value: A

value: 150 µM triadimefon


title: BAV_2

description: circulating miRNA expression


title: TAV_6

description: circulating miRNA expression

source_name: TAV

value: Healthy tricuspid aortic valve control


title: BAV_5

description: circulating miRNA expression


title: TDF_064

source_name: triadimefon, replicate 3


title: BAV_3

description: circulating miRNA expression


title: TDF_066

source_name: triadimefon, replicate 5


title: BAV_9

description: circulating miRNA expression


title: TDF_033

source_name: triadimefon, replicate 1


title: DMSOb_30

source_name: DMSO vehicle batch B, replicate 6


title: TAV_1

description: circulating miRNA expression


title: PTZ_079

source_name: prothioconazole, replicate 4

value: 250 µM prothioconazole


title: PTZ_043

source_name: prothioconazole, replicate 3


title: TAV_5

description: circulating miRNA expression


title: TDF_065

source_name: triadimefon, replicate 4


title: MCZ_052

source_name: miconazole, replicate 5

value: 25 µM miconazole


title: MCZ_007

source_name: miconazole, replicate 4


title: TAV_3

description: circulating miRNA expression


title: TAV_2

description: circulating miRNA expression


title: MCZ_004

source_name: miconazole, replicate 1


title: TDF_034

source_name: triadimefon, replicate 2


title: KTZ_054

source_name: ketoconazole, replicate 6

value: 40 µM ketoconazole


title: KTZ_050

source_name: ketoconazole, replicate 3


title: TDF_067

source_name: triadimefon, replicate 6


title: PTZ_027

source_name: prothioconazole, replicate 1


title: TAV_4

description: circulating miRNA expression


title: PTZ_081

source_name: prothioconazole, replicate 6


title: KTZ_022

source_name: ketoconazole, replicate 2


title: DFZ_061

source_name: difenoconazole, replicate 8

value: 110 µM difenoconazole


title: PTZ_080

source_name: prothioconazole, replicate 5


title: BAV_1

description: circulating miRNA expression

source_name: BAV


title: PTZ_028

source_name: prothioconazole, replicate 2


title: KTZ_070

source_name: ketoconazole, replicate 8


title: MCZ_057

source_name: miconazole, replicate 8


title: MCZ_056

source_name: miconazole, replicate 7


title: DFZ_058

source_name: difenoconazole, replicate 5


title: MCZ_006

source_name: miconazole, replicate 3


title: MCZ_055

source_name: miconazole, replicate 6


title: KTZ_069

source_name: ketoconazole, replicate 7


title: KTZ_021

source_name: ketoconazole, replicate 1


title: DFZ_059

source_name: difenoconazole, replicate 6


title: DFZ_048

source_name: difenoconazole, replicate 4


title: DFZ_032

source_name: difenoconazole, replicate 3


title: KTZ_053

source_name: ketoconazole, replicate 5


title: DFZ_030

source_name: difenoconazole, replicate 1


title: MCZ_005

source_name: miconazole, replicate 2


title: KTZ_051

source_name: ketoconazole, replicate 4


title: DFZ_031

source_name: difenoconazole, replicate 2


title: FLU_093

source_name: flusilazole, replicate 7

value: 25 µM flusilazole


title: FLU_098

source_name: flusilazole, replicate 8


title: DFZ_060

source_name: difenoconazole, replicate 7


title: FLU_090

source_name: flusilazole, replicate 6


title: FLU_087

source_name: flusilazole, replicate 5


title: FLU_083

source_name: flusilazole, replicate 4


title: FLU_082

source_name: flusilazole, replicate 3


title: FLU_037

source_name: flusilazole, replicate 1


title: siTRAP150-1

city: Dayton

first: Michael

last: Markey

state: OH

address: 3640 Colonel Glenn Hwy.

department: Biochemistry and Molecular Biology

institute: Wright State Unviersity

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the WSU Center for Genomics Research Core Facility.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 according to the manufacturer's instruction (Affymetrix).

data_processing:
The array CEL files were acquired using Affymetrix Command Console (AGCC version 4.1). CHP files were generated using Affymetrix Expression Console v1.4.1
affymetrix-algorithm-name = rma-exon-core : dabg
affymetrix-algorithm-version = 1.0
affymetrix-array-type = HuEx-1_0-st-v2
program-name = Expression Console
program-version = 1.4.1.46

label_protocol: As per manufacturer (Afftmetrix)

growth_protocol: HeLa grown in DMEM 10% FBS, 1% pen/strep for 24 hours prior to transfection.

extract_protocol: RNA extraction was performed by using Qiagen RNAeasy mini prep kit according to the manufacturer's instructions.  RNA was treated with TURBO DNA-free (Ambion).

treatment_protocol: Oligofectamine with siRNA against Btf, TRAP150, or luciferase (control).

tag: cell line

value: HeLa

tag: treated with


title: FLU_038

source_name: flusilazole, replicate 2

value: whole embryo


title: DMSOa_150

source_name: DMSO vehicle batch A, replicate 8

value: 0.1% DMSO


title: siBtf siRNA1-1


title: DMSOa_143

source_name: DMSO vehicle batch A, replicate 6


title: siBtf siRNA1-2


title: siCon-3

source_name: HeLa_Control siRNA

value: Control siRNA


title: siTRAP150-3


title: DMSOa_149

source_name: DMSO vehicle batch A, replicate 7


title: DMSOa_139

source_name: DMSO vehicle batch A, replicate 5


title: MDSC transfection overexpression control lentivirus,biological rep1

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

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

source_name: Mouse myeloid-derived suppressor cells

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

growth_protocol: Fresh mouse bone marrow cells were transfected with lentivirus and cultured in complete 1640 medium containing GM-CSF and IL6 for 4 days.

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

tag: strain

tag: transfection

value: overexpression control lentivirus


title: MDSC transfection silncMDSC,biological rep1

growth_protocol: Fresh mouse bone marrow cells were transfected with siRNA and cultured in complete 1640 medium containing GM-CSF and IL6 for 4 days.

value: silncMDSC


title: siCon-4


title: MDSC transfection shlncMDSC lentivirus,biological rep1

value: shlncMDSC lentivirus


title: MDSC transfection lncMDSC overexpression lentivirus,biological rep1

value: lncMDSC overexpression lentivirus


title: siBtf siRNA2-2


title: siCon-2


title: siBtf siRNA2-3


title: siTRAP150-2


title: DMSOa_047

source_name: DMSO vehicle batch A, replicate 2


title: siCon-1


title: siTRAP150-4


title: DMSOa_029

source_name: DMSO vehicle batch A, replicate 1


title: siBtf siRNA1-3


title: MDSC transfection control shRNA lentivirus,biological rep1

value: control shRNA lentivirus


title: siBtf siRNA2-1


title: DMSOa_099

source_name: DMSO vehicle batch A, replicate 3

value: A


title: DMSOa_137

source_name: DMSO vehicle batch A, replicate 4


title: siBtf siRNA1-4


title: siBtf siRNA2-4


title: Chemostat_PcDS17690-Ara1

status: Public on Oct 03 2017

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

institute: Delft University of Technology

description: P. chrysogenum DS17690 aerobic arabinose-limited chemostat with a dilution rate of 0.03h-1.

hyb_protocol: Hybridization, washing and scanning of Affymetrix chips was performed following the manufacturer’s instructions.

scan_protocol: Scanning of the Affymetrix Genechip® microarrays was performed with The Affymetrix scanner 3000 following Affymetrix instructions

data_processing: Data were processed with the GeneChip® Operating Software version 1.2 (GCOS 1.2) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 300.

label: Biotin-Streptavidin

organism: Penicillium chrysogenum

source_name: aerobic arabinose-limited chemostat pH5.0, 25°, P. chrysogenum (IS18)

growth_protocol: Penicillium chrysogenum DS17690) was kindly provided by DSM Bio-based Products & Services B.V. (Delft, The Netherlands)) and grown in mineral medium (pH 5.5), containing 3.5 g (NH4)2SO4, 0.8 g KH2PO4, 0.5 g MgSO4·7H2O and 10 ml of trace element solution (15 g L−1 Na2EDTA·2H2O, 0.5 g L−1 Cu2SO4·5H2O, 2 g L−1 ZnSO4·7H2O, 2 g L−1 MnSO4·H2O, 4 g L−1 FeSO4·7H2O, and 0.5 g L−1 CaCl2·2H2O) per litre of demineralised water.  The mineral medium was supplemented with 7.5 g L−1 arabinose. Aerobic carbon-limited chemostat cultures of P. chrysogenum were grown at 25 °C in 3-L turbine-stirred bioreactors (Applikon, Schiedam, The Netherlands) with a working volume of 1.8 L and a dilution rate of 0.03 h-1 as described previously (Veiga et al., Metab Eng. 2012;14(4):437-48. doi: 10.1016/j.ymben.2012.02.004)

extract_protocol: For each array, total RNA was extracted from a single tube using the hot-phenol method (Schmitt et al., 1990, Nucleic Acids Res., 18: 3091–3092).  mRNA extraction, cDNA synthesis, cRNA synthesis and labeling, as well as array hybridization were performed as described in the Affymetrix GeneChip Expression Analysis Technical Manual, 2000, Affymetrix, Santa Clara, CA

treatment_protocol: Sampling for transcriptome analysis from aerobic chemostat cultures at steady-state, was performed as previously described, using liquid nitrogen for rapid quenching of metabolism (Veiga et al., Metab Eng. 2012;14(4):437-48. doi: 10.1016/j.ymben.2012.02.004). Samples were stored at -80°C in a mixture of phenol/chloroform and TEA buffer until further processing for total RNA extraction.

tag: carbon source

value: Arabinose


title: MDSC transfection control siRNA,biological rep1

first: Yunhuan

institute: Nankai University

value: control siRNA


title: Wild Type EGFR rep1

city: Suita

first: Izumi

last: Nagatomo

address: 2-2 Yamada-oka

department: Respiratory Medicine and Clinical Immunology

institute: Osaka University Graduate School of Medicine

description: Gene expression at steady state

hyb_protocol: The Cy3-cRNA was hybridized to microarrays (SurePrint G3 Mouse Gene Expression 8x60K, Agilent Single-Color 28005). First, Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction solution containing 1x Agilent Fragmentation Buffer and 2x Agilent Gene Expression Blocking Agent. To stop the fragmentation reaction, 2x Hi-RPM Hybridization Buffer was added to the reaction mixtures. The mixtures were hybridized to the arrays at 65°C for 17 hours with rotation at 10 rpm. After hybridization, microarrays were washed at room temperature for 1 minute with Gene Expression Wash Buffer 1 (Agilent) followed by a second wash at 37°C for 1 minute with Wash Buffer 2 (Agilent), and then dried immediately by brief centrifugation.

scan_protocol: Fluorescent signals were read on an Agilent microarray scanner. The selected protocol was AgilentG3_GX_1color for G3 format. Scan settings were verified for one-color scans.

data_processing: Raw data were imported into GeneSpring, and expression values were normalized by scale to median.

source_name: Cell Line, NIH3T3, Wild Type EGFR

label_protocol: RNA was reverse-transcribed into T7-cDNA, and Cy3-cRNA was obtained from an in vitro transcription reaction. Labeling was performed using the Low Input Quick Amp Labeling Kit, One-Color, followed by column purification with the RNeasy Mini Kit (Qiagen). cRNA yield was checked on a NanoDrop Spectrophotometer.

extract_protocol: Total RNA was isolated and purified from WT-EGFR– and Mut-EGFR– expressing NIH3T3 cells using the AllPrep DNA/RNA Mini kit (Qiagen). RNA was quantified on a NanoDrop spectrophotometer, and quality was monitored on an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: N/A.

tag: genotype/variation

value: Wild Type EGFR


title: Ctrl preTs 1

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

hyb_protocol: 5.5 μg of biotinylated cDNA were fragmented and placed in a hybridization cocktail containing four biotinylated hybridization controls (BioB, BioC, BioD, and Cre) as recommended by the manufacturer. Samples were hybridized to an identical lot of Affymetrix Clariom™ (MTA-1_0) for 17 hours at 45°C. Steps for washing and staining were processed on the fluidics station 450 using the GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix; Santa Clara, CA).

scan_protocol: Image Analysis was performed on GCOS3000 Scanner and GCOS1.2 Software Suite (Affymetrix; Santa Clara, CA).

data_processing: Signal intensities (raw data) were log2 transformed and normalized using RMA summarization method.

molecule: polyA RNA

source_name: splenocytes, T cell

label_protocol: 2-10 ng of total RNA were used for biotin labelling according GeneChip® Pico Kit (Affymetrix).

growth_protocol: Tom+ cells were sorted from in vitro culture on day 20 or from harvested splenocytes on day 28 after transplantation.

extract_protocol: RNAeasy (Qiagen). Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany).

value: spleen

value: T cell

tag: genotype/variation = control


title: Ctrl T cells_2


title: Ctrl T cells_3


title: CAR preTs 3

tag: genotype/variation = CAR


title: CAR cells_2


title: Keratinocytes treated with tofacitinib+IL-22 rep1

city: Stockholm

first: Ankit

last: Srivastava

state: - Select a State -

address: CMM L8:02

institute: Karolinska Institutet

description: Gene expression data from keratinocytes trated with tofacitinib and  IL-22

hyb_protocol: cRNA were hybridized  to the standard Affymetrix protocol  (GeneTitan® Instrument User Guide for Expression  Array Plates Affymetrix).

scan_protocol: Array plate was scanned using Affymetrix GeneTitan Scanner.

data_processing: The data were analyzed with Expression Console using  global scaling as normalization method.

source_name: Keratinocytes treated with tofacitinib+IL-22 at 6 hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from  total RNA (GeneTitan® Instrument User Guide for Expression  Array Plates Affymetrix).

growth_protocol: Normal human keratinocytes were cultured in EpiLife serum-free medium including HKGS Growth Supplement and 100 U/ml penicillin/streptomycin at 37°C in 5% CO2.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: Cells were pretreated with tofacitinib (0.6μM) for the first hour, followed by IL-22 (20 ng/ml) treatment for 6 hours.

value: Skin

tag: age

value: Third passage


title: CAR preTs 2


title: Ctrl preTs 2


title: CAR cells_3


title: Keratinocytes treated with IL-22 rep3

description: Gene expression data from keratinocytes trated with IL-22

source_name: Keratinocytes treated with IL-22 at 6 hours


title: CAR preTs 1


title: Deletion Mutant EGFR rep1

description: Gene expression at steady state

source_name: Cell Line, NIH3T3, Deletion Mutant EGFR

value: Deletion Mutant EGFR


title: Deletion Mutant EGFR rep2

description: Gene expression at steady state


title: Keratinocytes treated with IL-22 rep2


title: Chemostat_PcDS17690-Ara2

source_name: aerobic arabinose-limited chemostat pH5.0, 25°, P. chrysogenum (IS20)

label_protocol: Hybridization, washing and scanning of Affymetrix chips was performed following the manufacturer’s instructions.


title: PH_17

city: Cologne

first: Bent

last: Brachvogel

address: Joseph-Stelzmann Street 52

institute: University of Cologne

hyb_protocol: Agilent miRNA labeling and hybridization Kit.

scan_protocol: Agilent G2505C scanner.

data_processing: GeneSpring 12, Normalization: Shift to 75 percentile.

source_name: femoral growth plate, prehypertrophic zone

extract_protocol: Trizol for RNA isolation.

tag: strain/background

value: 12 days

value: femoral growth plate

tag: growth plate zone

value: prehypertrophic zone


title: P_13

source_name: femoral growth plate, proliferative zone

label_protocol: Agilent miRNA labeling and hybridization Kit.

tag: tissue

value: proliferative zone


title: H_18

source_name: femoral growth plate, hypertrophic zone

value: hypertrophic zone


title: H_15


title: Keratinocytes treated with tofacitinib+IL-22 rep3


title: Ctrl T cells_1


title: PH_14


title: Untreated Keratinocytes rep1

description: Gene expression data from untreated keratinocytes

source_name: Untreated Keratinocytes at 6 hours


title: Untreated Keratinocytes rep2


title: Untreated Keratinocytes rep3


title: Keratinocytes treated with tofacitinib+IL-22 rep2


title: P_16


title: Wild Type EGFR rep2

description: Gene expression at steady state


title: Keratinocytes treated with IL-22 rep1


title: Ctrl preTs 3


title: CAR cells_1


title: Organoid5_tubule_73day_rep5

status: Public on Oct 02 2017

city: Toronto

first: York

middle: PC

last: Pei

state: Ontario

address: 8N838, 585 University Avenue

country: Canada

institute: University of Toronto

hyb_protocol: Fragmented and biotin-labelled ss-cDNAs were then hybridized to GeneChip Human Gene 2.0 ST Arrays for 16 hours at 45ºC. Hybridized arrays were then stained and washed in the Affymetrix Fluidics Station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: The (.DAT) image files were preprocessed using the Affymetrix GeneChip Command Console (AGCC) software v.4.3 to generate cell intensity (.CEL) files. The (.CEL) files were uploaded to the Affymetrix Expression Console software v1.4.1 for further processing and quality control. The probe set's signal intensities were then extracted and normalized using the robust multi-array average (RMA) algorithm embedded in the Expression Console software. The downstream paired sample t-test was carried out via Partek Genomics Suite 6.6 (Partek Inc.) to determine differentially expressed genes between cysts and tubules. Gene set enrichment analysis (GSEA) was used as the primary tool to identify potential gene pathways or gene sets that may modulate kidney organoid cyst growth.

source_name: Remnant tubule  from PKD1 mutant kidney organoid derived from human pluripotent stem cells at 73 days of culture

label_protocol: Biotin-labelled ss-cDNAs were prepared by using the GeneChip WT Pico Reagent Kit according to the standard Affymetrix protocol for 10 ng of total RNA.

growth_protocol: Kidney organoids with biallelic PKD mutations were cultured under conditions promoting cyst formation, without stimulation of cyclic AMP signaling. The cyst-like structures were microdissected from organoids after being cultured for 71-87 days. Seven paired samples (cyst-like structures and remnant tubular organoids) were used for the microarray study.

extract_protocol: The total RNA was extracted using RNeasy Micro Kit (Qiagen) following the manufacturer’s protocol with an on-column DNA digestion step to minimize genomic DNA contamination. The integrity of the RNA sample was assessed using the RNA 6000 Nano Assay on 2100 Bioanalyzer (Agilent Technologies) to ensure that the RNA integrity number (RIN) was greater than 7.

treatment_protocol: All tissues were washed in cold phosphate-buffered saline, snapped frozen in liquid nitrogen, and stored in a -80°C freezer.

tag: organoid

value: kidney organoid with CRISPR-induced PKD1 mutation

tag: organoid id

value: Tubule from PKD1 mutant kidney organoid


title: Organoid6_tubule_71day_rep6

source_name: Remnant tubule  from PKD1 mutant kidney organoid derived from human pluripotent stem cells at 71 days of culture


title: B2-3_SFTPC-pos-P3_Amiodarone_rep3

city: Kyoto

first: Shimpei

last: Gotoh

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Center for iPS cell Research and Application

institute: Kyoto University

description: P3 SFTPC+ cells treated with 10µM of amiodarone for 10 days.

hyb_protocol: 0.6 μg of labeled-cRNA was fragmented at 60°C for 30 minutes in 1x Agilent fragmentation buffer and 2x Agilent blocking agent. Fragmented samples were then hybridized to SurePrint G3 Human Gene Expression 8x60K v2 microarrays (Agilent Technologies) for 17 hours at 65°C.

scan_protocol: The array slides were scanned using a microarray scanner (Agilent Technologies, G2600D) with one color scan setting for 8x60k array slides.

data_processing:
To obtain expression level, the scanned images were processed with Feature Extraction Software (Agilent Technologies).
Normalized signal intensity with baseline correction to mean of the control samples using GeneSpring software GX13.0.

source_name: SFTPC-positive cells derived from B2-3 hiPSCs, P3, amiodarone

label_protocol: Cy3-labeled cRNA were generated from 0.1 µg of total RNA using the Low Input Quick Amp Labeling Kit (Agilent technologies) and purified by RNeasy column (Qiagen) according to the manufacturer's protocol.

growth_protocol: CPMhigh progenitor cells were induced from iPSCs via ventralized anterior foregut andodermal (VAFE) cells with the four-step treatment; Step 1: Activin, sodium butyrate, and CHIR99021 for 6 days; Step 2: SB431542 and Noggin for 4 days; Step 3: CHIR99021, BMP4 and ATRA; and Step 4: CHIR99021, FGF10, KGF and DAPT for 7 days. P0 SFTPC+ cells were induced from CPMhigh progenitor cells by forming AO in three-dimensional coculture with human fetal lung fibroblasts. P3 SFTPC+ cells were obtained from three-times passaged AO.

extract_protocol: Total RNA was extracted by using the PureLink RNA Mini Kit (Life Technologies) according to manufacturer's protocol. To digest genomic DNA, extracts were cleaned up by using the NucleoSpin RNA Clean-up XS kit (Macherey-Nagel).

treatment_protocol: After passaged three times every two weeks, AO were treated with 5 µM of GNE7915, 10 µM of amiodarone, or vehicle control (DMSO) for 10 days.

tag: originating cell line

value: B2-3 hiPSCs

value: SFTPC-positive cells

tag: drug

value: Amiodarone


title: Organoid7_tubule_71day_rep7


title: Organoid3_tubule_87day_rep3

source_name: Remnant tubule  from PKD1 mutant kidney organoid derived from human pluripotent stem cells at 87 days of culture


title: Organoid2_tubule_80day_rep2

source_name: Remnant tubule  from PKD1 mutant kidney organoid derived from human pluripotent stem cells at 80 days of culture


title: Organoid1_cyst_80day_rep1

source_name: Cyst from PKD1 mutant kidney organoid derived from human pluripotent stem cells at 80 days of culture

value: Cyst from PKD1 mutant kidney organoid


title: Organoid7_cyst_71day_rep7

source_name: Cyst from PKD1 mutant kidney organoid derived from human pluripotent stem cells at 71 days of culture


title: Organoid4_tubule_73day_rep4


title: Organoid2_cyst_80day_rep2


title: Organoid5_cyst_73day_rep5

source_name: Cyst from PKD1 mutant kidney organoid derived from human pluripotent stem cells at 73 days of culture


title: Organoid1_tubule_80day_rep1

source_name: Remnant tubule from PKD1 mutant kidney organoid derived from human pluripotent stem cells at 80 days of culture


title: B2-3_SFTPC-pos-P3_GNE7915_rep2

description: P3 SFTPC+ cells treated with 5µM of GNE7915 for 10 days.

source_name: SFTPC-positive cells derived from B2-3 hiPSCs, P3, GNE7915

tag: cell type