title: NBS3_1

description:
replicate 1
SAMPLE 3

source_name: fibroblasts from NBS patient 3

value: fibroblasts


title: differentiation-day7_rep2

status: Public on Aug 18 2017

type: RNA

city: London

first: Sylvane

last: Desrivieres

address: 16 De Crespigny Park

department: MRC-SGDP Centre

country: United Kingdom

institute: King's College London

description:
replicate 2
6303213048_H

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data were extracted by the Illumina BeadStudio software, mloess normalized and log2 transformed and further processed in R statistical environment using the lumi and limma Bioconductor packages.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: SPC04 human neural stem cell line

label_protocol: Samples were processed using the TargetAmp-Nano Labeling Kit (Cambio, Cambridge, UK) and hybridized to Illumina HumanHT-12 v4 Expression BeadChips according to the manufacturers’ instructions at the Biomedical Genomics microarray core facility of the University of California, San Diego, CA, USA

growth_protocol: Cells were plated on tissue culture flasks that had been freshly coated with laminin (20 μg ml−1 in Dulbecco’s modified Eagle’s medium:F12 for 3 h at 37 °C), at a density of 20 000 cells cm−2 and routinely grown into a reduced minimum media formulation consisting of Dulbecco’s modified Eagle’s medium:F12 with 0.03% human serum albumin, 100 μg ml−1 human Apo-transferrin, 16.2 μg ml−1 putrescine dihydrochloride, 5 μg ml−1 human insulin, 60 ng ml−1 progesterone, 2 mm L- glutamine and 40 ng ml−1 sodium selenite. This reduced minimum medium was also supplemented with growth factors (10 ng ml−1 basic fibroblast growth factor and 20 ng ml−1 epidermal growh factor) and 100 nm 4-hydroxy-tamoxifen. Cell differentiation was triggered when cells reached about 80% confluence by depleting the medium of growth factors and 4-hydroxy-tamoxifen. This was achieved in two steps. First, the growth factor- and 4-hydroxy-tamoxifen-depleted medium was supplemented with 10 μm of the γ-secretase inhibitor N-[N-(3,5-difluorophenacetyl)-L-alanyl]-S-phenylglycine t-butyl ester and 100 nm all-trans-retinoic acid for 48 h. We referred to this stage as ‘pre-differentiation’. Afterward, differentiation was achieved by maintaining the cells in reduced minimum media without any supplements for up to 7 days, with media change every 2 days.

extract_protocol: Total RNA was extracted from triplicate SPC04 differentiation experiments using the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

tag: cell line

tag: tissue

value: fetal spinal cord

tag: differentiation stage

value: differentiated for 7 days


title: pre-differentiated_rep3

description:
replicate 3
6303213048_J

value: pre-differentiated


title: NBS5_1

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

country: Germany

institute: Universitätsklinikum Düsseldorf

description:
replicate 1
SAMPLE 5

data_processing: The data were normalised using rank invariant normalisation with BeadStudio version 3 (Illumina)

source_name: fibroblasts from NBS patient 5

label_protocol: Illumina Gene Expression protocols contain a first- and second-strand  reverse transcription step, followed by a single in vitro transcription  (IVT) amplification that incorporates biotin-labeled nucleotides.  Subsequent steps include array hybridization, washing, blocking, and  streptavadin-Cy3 staining. Fluorescence emission by Cy3 is quantitatively  detected for downstream analysis.

growth_protocol: The fibroblasts were grown in DMEM containing 10 % FBS and 1x penicillin/streptomycin and kept at 37 °C with 5 % CO2 in a standard cell culture incubator.

extract_protocol: The RNA was isolated using Direct-zol™ RNA MiniPrep Kit (Zymo Research; #R2050).

treatment_protocol: No special treatment

tag: cell type

tag: disease state

value: Nijmegen-Breakage Syndrome


title: undifferentiated_rep2

description:
replicate 2
6303213048_E

value: undifferentiated


title: differentiation-day7_rep1

description:
replicate 1
6303213048_D


title: differentiation-day3_rep1

description:
replicate 1
6303213048_C

value: differentiated for 3 days


title: undifferentiated_rep1

description:
replicate 1
6303213048_A


title: NBS3_2

description:
replicate 2
SAMPLE 4


title: CCR6n [PAA031]

city: Montréal

first: Jean-Philippe

last: Goulet

state: Québec

address: C.P. 6128, succursale Centre-ville

country: Canada

institute: Université de Montréal

hyb_protocol: High quality RNA was reverse transcribed and hybridized on the Illumina HumanHT12 V4 Expression BeadChip

data_processing: quantile normalisation using Bioconductor

source_name: PBMC

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

extract_protocol: Total cellular RNA was extracted from matched memory CCR6+/CCR6- CD4+ T-cells isolated by FACS using RNeasy columns kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were collected by leukapheresis and cryopreserved until use.

tag: stimulation

value: neg

tag: donor

value: CD4+ T-Cells


title: NBS1_1

description:
replicate 1
SAMPLE 1

source_name: fibroblasts from NBS patient 1


title: differentiation-day3_rep2

description:
replicate 2
6303213048_G


title: NBS5_2

description:
replicate 2
SAMPLE 6


title: differentiation-day3_rep3

description:
replicate 3
6303213048_K


title: undifferentiated_rep3

description:
replicate 3
6303213048_I


title: LNCaP-Bic

city: Guangzhou

first: Xu

last: Chen

state: Guangdong

address: 107. W. Yanjiang Road

department: Department of Urology

country: China

institute: Sun Yat-sen Memorial Hospital

hyb_protocol: Hybridization was performed at 45℃ with rotation for 16 h (Agilent Hybridization Oven G2545A). The GeneChip arrays were washed on an CapitalBio Slide Washer8.

scan_protocol: GeneChips were scanned using Agilent G2565CA Microarray Scanner.

data_processing: The hybridization data were analyzed using Agilent Feature Extraction(v10.7). Intensity values were then processed with Agilent GeneSpring and normalized.

source_name: prostate cancer cell line LNCaP-Bic

label_protocol: An aliquot of 0.1 µg of total RNA was used to synthesize double-stranded cDNA,then cRNA was produced by T7 Enzyme Mix.Then cDNA was produced by reverse transcription using CbcScriptⅡ enzyme.The resulting cDNA were fragmented and labled with cy3/cy5 according to the protocols from Affymetrix.

growth_protocol: LNCaP cells were cultured in phenol red free RPMI-1640 containing 10% FBS (Shanghai ExCell Biology, China).LNCaP-AI cells were cultured in phenol red free RPMI-1640 containing 10% charcoal stripped FBS (Gibco, Shanghai, China), whereas LNCaP-Bic were cultured in the same medium as LNCaP-AI with a bicalutmide(Sigma, St. Louis, Missouri, USA) concentration of 20μM. All medium were suppemented with 1% penicillin/streptomycin.Cells were grown in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol: Total RNA was extracted using Trizol reagent and was further purified using Qiagen RNeasy Mini Kit according to the manufactures’ instructions. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantitated spectrophotometrically.

treatment_protocol: LNCaP-Bic and LNCaP-AI cells were constructed by continuously passaged in two different castration mediums for 12 months.

value: LNCaP-Bic

tag: tissue type

value: prostate cancer

tag: androgen response state


title: LNCaP-AI

source_name: prostate cancer cell line LNCaP-AI

value: LNCaP-AI


title: differentiation-day7_rep3

description:
replicate 3
6303213048_L


title: pre-differentiated_rep2

description:
replicate 2
6303213048_F


title: shMEF2A day7_Rep1

description:
replicate 1
SAMPLE 16

hyb_protocol: Samples were hybridized to Illumina HumanHT-12 v4 Expression BeadChips according to the manufacturers’ instructions at the High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics, Oxford, UK

scan_protocol: Arrays were scanned with the Illumina iscan and gene expression reports created using the Illumina GenomeStudio software.

data_processing: Raw expression data were pre-processed by variance stabilizing transformation and quantile normalization using the lumi package in R.

label_protocol: Total RNA samples were processed using the TargetAmp™-Nano Labeling Kit (Cambio Ltd.)

growth_protocol: Cells were grown and differentiated for 7 or 14 days as described in Jeffries, A. R., Perfect, L. W., Ledderose, J., Schalkwyk, L. C., Bray, N. J., Mill, J. and Price, J. (2012), Stochastic Choice of Allelic Expression in Human Neural Stem Cells. STEM CELLS, 30: 1938–1947. doi: 10.1002/stem.1155. Cells were treated with lentiviruses for 2 days before induction of differentiation, after which period virus was removed from cells and replaced with differentiation media.

extract_protocol: Cells were harvested using RLT buffer with B-Mercaptoethanol and homogenized using Qiashredder spin columns. RNA was extracted using Qiagen Rneasy mini kit with DNaseI digestion in accordance with the prescribed protocol provided with the kit. RNA quality control was performed with the Agilent Bioanalyser.

treatment_protocol: The lentiviral Gipz (thermo scientific) and lentiviral LegoG systems were used to produce the shRNAs against MYT1L and MEF2A, respectively

value: Differentiation day 7

tag: genetic modification


title: shMEF2A day7_Rep2

description:
replicate 2
SAMPLE 17


title: pre-differentiated_rep1

description:
replicate 1
6303213048_B


title: shMEF2A day7_Rep3

description:
replicate 3
SAMPLE 18


title: control_MYT1L day14_Rep2

description:
replicate 2
SAMPLE 14

value: Differentiation day 14

value: control for shMYT1L


title: control_MEF2A day7_Rep3

description:
replicate 3
SAMPLE 10

value: control for shMEF2A


title: shMYT1L day14_Rep1

description:
replicate 1
SAMPLE 11


title: shMYT1L day7_Rep2

description:
replicate 2
SAMPLE 2


title: control_MYT1L day7_Rep2

description:
replicate 2
SAMPLE 5


title: SKOV3.ip_RAD51-AS1 knockdown 1

status: Public on Aug 17 2017

city: Shanghai

first: Xiaodan

last: Zhang

address: Room 208, 413 Zhaozhou Road

department: Department of Gynecology

institute: Obstetrics and Gynecology Hospital of Fudan University

description:
YANGBEN1_(HTA-2_0)
Gene expression data from exprimental group (knockdown of RAD51-AS1 expression by transfection with ASO-targeting RAD51-AS1)

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Human Transcriptome Array 2.0 in GeneChip® Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G

data_processing:
The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method, with the assistance of the online analysis platform in GCBI website (https://www.gcbi.com.cn).
Details of methods for each analysis can be find in  http://college.gcbi.com.cn/fangfaxue/index.jhtml.

source_name: SKOV3.ip_RAD51-AS1 knockdown

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using GeneChip® WT PLUS Reagent Kit

growth_protocol: All cells were cultured in RPMI1640 (Gibco BRL, Gaithersburg, MD, USA) containing 10% fetal bovine serum (FBS; Gibco) with 100 units/ml penicillin and 100 mg/ml streptomycin and cultured in a humidified 5% CO2 incubator at 37°C.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit and RNase-Free Dnase Set.

treatment_protocol: Antisense oligonucleotides (ASO) targeting RAD51-AS1 and negative control (NC) were designed and synthesized by Ribobio (Guangzhou, China). Cells were transfected with 50 nM ASO-targeting RAD51-AS1, or 50 nM NC using Lipofectamine 3000 (Invitrogen). Twenty-four hours after transfected with 50 nM RAD51-AS1-ASOs or negative control siRNA, total RNA from skov3.ip cells was extracted using TRIzol reagent (Life Technologies).

value: epithelial ovarian cancer cells

tag: transfected with

value: 50nM RAD51-AS1-ASOs

tag: time point

value: 24h after transfection


title: control_MYT1L day7_Rep4

description:
replicate 4
SAMPLE 7

value: fetal spinal cord


title: control_MYT1L day14_Rep3

description:
replicate 3
SAMPLE 15


title: control_MYT1L day14_Rep1

description:
replicate 1
SAMPLE 13


title: control_MYT1L day7_Rep1

description:
replicate 1
SAMPLE 4


title: shMYT1L day7_Rep1

description:
replicate 1
SAMPLE 1


title: shMYT1L day14_Rep2

description:
replicate 2
SAMPLE 12


title: I12-2_A7063 [_8450989009_F]

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

country: USA

institute: National Institute of Allergy and Infectious Diseases

scan_protocol: Standard Illumina scanning protocol with Illumina HiScan-SQ

data_processing: Signal data was extracted from the image files with the Gene Expression module (v. 1.9.0) of the GenomeStudio software (v. 2011.1) from Illumina, Inc. Signal intensities were converted to log 2 scale. Probes that did not have detection p-value < 0.1 in at least 2 arrays were removed from the dataset.  After filtering probes, quantile normalization was applied across all arrays.

organism: Mus musculus

source_name: bone-marrow derived macrophages

label_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion)

growth_protocol: BMDM were prepared from 6-8 week old C57BL/6 mice by the following procedure. Bone marrow was flushed out with complete DMEM, plated at a density of 0.3 million cells/ml in non-tissue culture treated flasks (BD bioscience, Chicago, IL), and cells were cultured in complete DMEM supplemented with 60 ng/ml of recombinant mouse M-CSF (R&D, Minneapolis, MN, cat# 416-ML-050) for 6 days.

extract_protocol: RNA was purified by Qiagen RNAeasy kit

treatment_protocol: BMDM were plated at a density of 0.22 x 106 cells/ml in a 24-well dish (BD Falcon) in a total volume of 0.9 ml. 24 hr after plating, the cells were treated with single or dual TLR ligands diluted in 0.1 ml of complete DMEM, for time periods as indicated.

tag: strain

tag: treatment

tag: treatment time

tag: experiment


title: IR12-2_A7065 [_8450989009_H]

value: poly(I:C) + R848


title: control_MYT1L day7_Rep3

description:
replicate 3
SAMPLE 6


title: shMYT1L day7_Rep3

description:
replicate 3
SAMPLE 3


title: SKOV3.ip_negative control 1

description:
DUIZHAO1_(HTA-2_0)
Gene expression data from control group (transfected with negative control siRNA)

value: 50nM negative control siRNA


title: R12-2_A7064 [_8450989009_G]


title: control_MEF2A day7_Rep2

description:
replicate 2
SAMPLE 9


title: SKOV3.ip_negative control 3

description:
DUIZHAO3_(HTA-2_0)
Gene expression data from control group (transfected with negative control siRNA)


title: NT12-2_A7062 [_8450989009_E]

value: untreated control


title: NBS1_2

description:
replicate 2
SAMPLE 2

value: fibroblasts

value: Nijmegen-Breakage Syndrome


title: SKOV3.ip_RAD51-AS1 knockdown 3

description:
YANGBEN3_(HTA-2_0)
Gene expression data from exprimental group (knockdown of RAD51-AS1 expression by transfection with ASO-targeting RAD51-AS1)


title: I8-2_A7059 [_8450989009_B]

value: 8 h


title: control_MEF2A day7_Rep1

description:
replicate 1
SAMPLE 8


title: SKOV3.ip_negative control 2

description:
DUIZHAO2_(HTA-2_0)
Gene expression data from control group (transfected with negative control siRNA)


title: R8-2_A7060 [_8450989009_C]


title: NT8-2_A7058 [_8450989009_A]


title: SKOV3.ip_RAD51-AS1 knockdown 2

description:
YANGBEN2_(HTA-2_0)
Gene expression data from exprimental group (knockdown of RAD51-AS1 expression by transfection with ASO-targeting RAD51-AS1)


title: IR4-2_A7057 [_8450989008_H]

value: 4 h


title: R4-2_A7056 [_8450989008_G]


title: I4-2_A7055 [_8450989008_F]


title: NT12-1_A7038 [_7604659039_E]


title: IR8-1_A7037 [_7604659039_D]


title: NT4-2_A7054 [_8450989008_E]


title: R12-1_A7040 [_7604659039_G]


title: R8-1_A7036 [_7604659039_C]


title: NT4-1_A7030 [_7604659034_E]


title: I12-1_A7039 [_7604659039_F]


title: IR4-1_A7033 [_7604659034_H]


title: NT8-1_A7034 [_7604659039_A]


title: NT2-2_A7050 [_8450989008_A]

value: 2 h


title: IR12-1_A7041 [_7604659039_H]


title: I8-1_A7035 [_7604659039_B]


title: R4-1_A7032 [_7604659034_G]


title: NT2-1_A7026 [_7604659034_A]


title: IR2-2_A7053 [_8450989008_D]


title: I1-2_A7047 [_7604659020_F]

value: 1 h


title: I2-1_A7027 [_7604659034_B]


title: R2-1_A7028 [_7604659034_C]


title: NT1-2_A7046 [_7604659020_E]


title: R2-2_A7052 [_8450989008_C]


title: I2-2_A7051 [_8450989008_B]


title: R1-2_A7048 [_7604659020_G]


title: IR1-2_A7049 [_7604659020_H]


title: I4-1_A7031 [_7604659034_F]


title: IR0.5-2_A7045 [_7604659020_D]


title: R0.5-2_A7044 [_7604659020_C]


title: I0.5-2_A7043 [_7604659020_B]


title: IR1-1_A7025 [_7604659010_H]


title: NT0.5-2_A7042 [_7604659020_A]


title: R0.5-1_A7020 [_7604659010_C]


title: I0.5-1_A7019 [_7604659010_B]


title: I1-1_A7023 [_7604659010_F]


title: IR0.5-1_A7021 [_7604659010_D]


title: NT0.5-1_A7018 [_7604659010_A]


title: NT1-1_A7022 [_7604659010_E]


title: IL_8 h_A7320 [_8803799029_F]

value: poly(I:C) + LPS


title: RI_8 h_A7316 [_8803799029_B]

value: R848 + poly(I:C)


title: PL_8 h_A7321 [_8803799029_G]

value: Pam3CSK4 + LPS


title: RL_8 h_A7318 [_8803799029_D]

value: R848 + LPS


title: R1-1_A7024 [_7604659010_G]


title: LPS_8 h_A7315 [_8803799029_A]

value: LPS


title: Pam_8 h_A7314 [_8803799024_H]


title: pIC_8 h_A7313 [_8803799024_G]


title: RP_8 h_A7317 [_8803799029_C]

value: R848 + Pam3CSK4


title: R848_8 h_A7312 [_8803799024_F]


title: _NT_8 h_A7311 [_8803799024_E]


title: RI_8 h_A7305 [_8803799014_F]


title: LPS_8 h_A7304 [_8803799014_E]


title: PL_8 h_A7310 [_8803799024_C]


title: RP_8 h_A7306 [_8803799014_G]


title: IL_8 h_A7309 [_8803799024_B]


title: Pam_8 h_A7303 [_8803799014_D]


title: IP_8 h_A7319 [_8803799029_E]

value: poly(I:C) + Pam3CSK4


title: IP_8 h_A7308 [_8803799024_A]


title: RL_8 h_A7307 [_8803799014_H]


title: R848_8 h_A7301 [_8803799014_B]


title: _NT_8 h_A7300 [_8803799014_A]


title: Pam_1 h_A7270 [_8778571010_H]


title: R848_1 h_A7268 [_8778571010_F]


title: pIC_8 h_A7302 [_8803799014_C]


title: _NT_1 h_A7256 [_8778571010_D]


title: pIC_1 h_A7269 [_8778571010_G]


title: RL_1 h_A7263 [_8778571009_H]


title: IP_1 h_A7264 [_8778571010_A]


title: IL_1 h_A7265 [_8778571010_B]


title: Pam_1 h_A7259 [_8778571009_D]


title: _NT_1 h_A7267 [_8778571010_E]

description: amplification replicate


title: RP_1 h_A7262 [_8778571009_G]


title: RI_1 h_A7261 [_8778571009_F]


title: PL_1 h_A7266 [_8778571010_C]


title: pIC_1 h_A7258 [_8778571009_C]


title: LPS_1 h_A7260 [_8778571009_E]


title: RL_4 h_A7296 [_8709381094_D]


title: _NT_1 h_A7256 [_8778571009_A]


title: IL_4 h_A7298 [_8709381094_F]


title: RP_4 h_A7295 [_8709381094_C]


title: RI_4 h_A7294 [_8709381094_B]


title: PL_4 h_A7299 [_8709381094_G]


title: R848_1 h_A7257 [_8778571009_B]


title: IP_4 h_A7297 [_8709381094_E]


title: LPS_4 h_A7293 [_8709381094_A]


title: Pam_4 h_A7292 [_8709381081_H]


title: pIC_4 h_A7291 [_8709381081_G]


title: IL_4 h_A7287 [_8709381081_B]


title: R848_4 h_A7290 [_8709381081_F]


title: PL_4 h_A7288 [_8709381081_C]


title: _NT_4 h_A7278 [_8709381081_D]

description: amplification replicate


title: IP_4 h_A7286 [_8709381081_A]


title: _NT_4 h_A7289 [_8709381094_H]

description: amplification replicate


title: _NT_4 h_A7289 [_8709381081_E]


title: RI_4 h_A7283 [_8709381080_F]


title: pIC_4 h_A7280 [_8709381080_C]


title: RP_4 h_A7284 [_8709381080_G]


title: IR8-2_A7061 [_8450989009_D]


title: RL_4 h_A7285 [_8709381080_H]


title: Pam_4 h_A7281 [_8709381080_D]


title: R848_4 h_A7279 [_8709381080_B]


title: PL_1 h_A7277 [_8709381076_G]


title: _NT_1 h_A7267 [_8709381076_H]


title: _NT_4 h_A7278 [_8709381080_A]


title: RP_1 h_A7273 [_8709381076_C]


title: RI_1 h_A7272 [_8709381076_B]


title: IP_1 h_A7275 [_8709381076_E]


title: LPS_1 h_A7271 [_8709381076_A]


title: IL_1 h_A7276 [_8709381076_F]


title: RL_1 h_A7274 [_8709381076_D]


title: IR2-1_A7029 [_7604659034_D]


title: Runx1t1 Knock-downed ECFC

city: Taipei

first: Ko-Hsun

last: Liao

state: Taipei

address: No. 155, Sec. 2, Linong St., Beitou District,

department: Institute of Microbiology and Immunology

country: Taiwan

institute: National Yang-Ming University

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing:
We calculated RMA log expression units from Affymetrix GeneChip array data using the 'affy' package of the Bioconductor suite of software for the R statistical programming language
The default RMA settings, from R statistical,  were used to background-correct, normalize and summarize all expression values. We identified significant differences between sample groups

source_name: Cord blood

label_protocol: Affymetrix

growth_protocol: ECFCs (late EPCs) emerged at 2–4 weeks after initial seeding and were cultivated using 2% FBS-containing EGM2. All the cells were trypsinized to prepare single-cell suspensions for further experiments.

extract_protocol: We used total RNA from treated ECFCs, and homogenized clinical samples and extracted the RNA using Trizol solution (Gibco/BRL) followed by RNeasy Mini kit (Qiagen) purification.

treatment_protocol: The Runx1t1 shRNA (TRCN0000271292, 5'-GCGATCTCTCACCGTACTAAG-3') and the control vector (pLKO_TRC005) were purchased from the RNAi Core Facility of the Academia Sinica, Taipei, Taiwan.  The shRNAs were transducted to ECFC by lentivirus  for 48 hours.

tag: cell

value: endothelial colony-forming cells

tag: age


title: Primary_Tumor 8186

city: Montpellier Cedex 5

first: Pierre

last: Martineau

address: 208 Rue des Apothicaires

department: IRCM

country: France

institute: Inserm

hyb_protocol: Following fragmentation, cRNA were hybridized on GeneChip Human Genome U133 Plus 2.0 array.

scan_protocol: GeneChips were scanned using a laser scanner.

data_processing: Processing and normalization was done using the Robust Multi-array Average (RMA)

source_name: Tissue samples taken from colorectal cancer patients

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol.

extract_protocol: Rneasy kit (Qiagen) for total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Samples were collected before chemotherapy

tag: center

value: Montpellier

tag: Sex

value: Male

tag: who performance status

tag: tumor location

value: Right colon

tag: synchronous metastase

value: Yes

tag: pn

value: pNX

tag: pt

value: pTX

tag: regimen

value: FOLFIRINOX

tag: response category

value: PR

tag: response status

value: R

tag: pfs censored

tag: pfs

tag: os censored

tag: os


title: Primary_Tumor 8067

value: Rectum-sigmoid junction

value: FOLFIRI

value: CR


title: SHRNA ECFC


title: Primary_Tumor 8088

value: Female

value: Left colon

value: FOLFIRI+BEVACIZUMAB


title: hADSC Normoxia rep2

city: Daegue

first: Jieon

last: Lee

address: 333. Techno Jungang-daero Hyeongpung-myeon, Dalseong-gun

department: Chemical Engineering

country: South Korea

institute: POSTECH

description: Normal

data_processing: The data were normalised using quantile normalisation with MATLAB

source_name: adipocyte-derived stem cells (hADSCs)

growth_protocol: Human Adipose-Derived Stem Cells were purchased from Invitrogen (Carlsbad, CA), which are isolated from human adipose tissue collected during liposuction procedures.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: For hypoxia samples, the cells were incuabated in hypoxic condition (<0.5%) for 48 hours.

tag: o2 concentration


title: Primary_Tumor 8170

value: FOLFIRINOX+BEVACIZUMAB


title: Primary_Tumor 8055


title: Primary_Tumor 8133


title: Primary_Tumor 8135

value: SD

value: NR


title: Primary_Tumor 6169

value: Toulouse

value: Male


title: Primary_Tumor 8141

value: Montpellier

value: Transverse colon

value: Yes


title: hADSC Hypooxia rep2

description: Treated for 48 hrs


title: Primary_Tumor 6184

value: pNX

value: pTX

value: PD


title: Primary_Tumor 8065

value: PR

value: R


title: Primary_Tumor 8082

value: Rectum

value: No

value: XELIRI+BEVACIZUMAB


title: Primary_Tumor 6156

value: Left colon

value: FOLFIRINOX


title: Primary_Tumor 8024

value: Right colon

value: FOLFOX


title: hADSC Normoxia rep1

description: Normal


title: Primary_Tumor 8017

value: SD

value: NR


title: Primary_Tumor 6148

value: Toulouse

value: Male

value: Rectum-sigmoid junction

value: FOLFIRI+BEVACIZUMAB


title: Primary_Tumor 6157

value: Female


title: Primary_Tumor 8025

value: Montpellier

value: Yes


title: Primary_Tumor 6101

value: PR

value: R


title: Primary_Tumor 6096

value: No


title: Primary_Tumor 6069


title: Primary_Tumor 6058


title: Primary_Tumor 6059


title: Primary_Tumor 6057

value: Rectum

value: FOLFIRI+ERBITUX


title: Primary_Tumor 5146

value: Nimes

value: Left colon


title: Day 14 Itolizumab

city: Bangalore

first: Pradip

last: Nair

state: Karnataka

address: SEZ unit, Plot no 2 & 3, Phase IV B.I.A, Bommasandra-Jigani Link Road,

country: India

institute: Biocon Research Ltd

description: D14_Stim pol+Ito

hyb_protocol: 600ng of labeled cRNA were hybridized on the array using the Hi-RPM large Hybridization Kit (Part No: 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression Wash Buffers Set (Part No: 5188-5327).  The hybridized, washed microarray slides were then scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D) at 5 micron resolution.

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX: 75th percentile shift  method

source_name: Blood

label_protocol: The samples were labeled using Agilent Low Input Quick Amp Labeling Kit one color (Part number: 5190-02305).30ng of total RNA was reverse transcribed using oligodT primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using  RNeasy Mini Kit(Qiagen, Cat No: 74106). Concentration and amount of dye incorporated was determined using Nanodrop. Samples that pass the QC for specific activity were taken for hybridization.

growth_protocol: PBMCs were left unstimulated or stimulated with anti-CD3/ anti- CD28 beads in presence of control or Itolizumab, in Th17 polarizing conditions. Samples were collected for microarray analysis on days 3, 6, 8, 10 and 14.

extract_protocol: RNA was extracted using the Qiagen RNeasy mini kit following the manufacturer's recommendations.

treatment_protocol: Itolizumab or control antibody were added at the beginning of the experiment on day 0 at 40 μg/ml

tag: subject status

value: normal healthy volunteer

tag: tissue

value: blood

tag: cell type

value: PBMCs

tag: stimulated with

value: anti-CD3/anti-CD28 beads in presence of Itolizumab

tag: time point

value: day 14


title: Primary_Tumor 6056

tag: center

value: Toulouse

tag: Sex

value: Male

tag: age

tag: who performance status

tag: tumor location


title: Primary_Tumor 6120

value: Female

value: Right colon

tag: synchronous metastase

tag: pn

tag: pt

tag: regimen

value: FOLFIRI+BEVACIZUMAB

tag: response category

value: SD

value: NR


title: Primary_Tumor 6049

value: No

value: pNX

value: pTX

tag: response status

tag: pfs censored

tag: pfs

tag: os censored

tag: os


title: Primary_Tumor 6050

value: Rectum-sigmoid junction

value: Yes

value: FOLFIRI


title: Primary_Tumor 6068

value: Rectum


title: Primary_Tumor 6045

value: PR

value: R


title: Primary_Tumor 5077

value: Nimes


title: Day 8 Itolizumab

description: D8_Stim pol+Ito

scan_protocol: scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D)

tag: subject status

value: normal healthy volunteer

tag: tissue

value: blood

tag: cell type

value: PBMCs

tag: stimulated with

value: anti-CD3/anti-CD28 beads in presence of Itolizumab

value: day 8


title: Day 14 Control

description: D14_stim pol+hR3

value: anti-CD3/anti-CD28 beads in presence of control

tag: time point

value: day 14


title: Primary_Tumor 6028

tag: center

value: Toulouse

tag: Sex

value: Male

tag: age

tag: who performance status

value: FOLFIRI+BEVACIZUMAB

value: SD

value: NR


title: Day 6 Control

description: D6_stim pol+hR3

value: day 6


title: Day 6 Itolizumab

description: D6_Stim pol+Ito


title: Day 8 Control

description: D8_stim pol+hR3


title: Primary_Tumor 5036

tag: tumor location

value: Rectum-sigmoid junction

tag: synchronous metastase

value: Yes

tag: pn

tag: pt

value: FOLFOX+BEVACIZUMAB

value: PD


title: Day 10 Itolizumab

description: D10_Stim pol+Ito

value: normal healthy volunteer

value: day 10


title: Day3 Control

description: D3_stim pol+hR3

value: blood

value: PBMCs


title: Day3 Itolizumab

description: D3_Stim pol+Ito

value: anti-CD3/anti-CD28 beads in presence of Itolizumab


title: Day 1 unstimulated PBMCs/ Normal healthy Volunteer

value: none (unstimulated control)

value: day 1


title: Primary_Tumor 4098

value: Bordeaux â€“ Haut-Leveque

value: Female

value: Right colon

value: pNX

value: pTX

tag: regimen

tag: response category

value: PR

tag: response status

value: R

tag: pfs censored


title: Day 10 Control

description: D10_stim pol+hR3

tag: subject status

value: anti-CD3/anti-CD28 beads in presence of control


title: Primary_Tumor 4070

value: Male

value: Yes

value: FOLFIRI+BEVACIZUMAB

value: SD

value: NR

tag: pfs

tag: os censored

tag: os


title: Primary_Tumor 3030

value: Bordeaux - CRLC


title: LPS_4 h_A7282 [_8709381080_E]

tag: strain

tag: treatment

value: LPS

tag: treatment time

value: 4 h


title: Primary_Tumor 3021

tag: center

tag: Sex

tag: age

value: FOLFIRI


title: Primary_Tumor 2073

value: Bordeaux CHU

tag: who performance status

tag: tumor location

value: Rectum

tag: synchronous metastase

value: FOLFOX+BEVACIZUMAB

value: PD


title: Primary_Tumor 2048

value: No

tag: pn

tag: pt

tag: regimen

value: FOLFOX


title: Primary_Tumor 1172

value: Limoges

value: Right colon

value: pNX

value: pTX

tag: response category

tag: response status

tag: pfs censored


title: Primary_Tumor 1158

value: Male

value: Yes

tag: pfs

tag: os censored


title: Primary_Tumor 1051

value: Left colon

value: PR

value: R

tag: os


title: Primary_Tumor 1043

value: Female

value: Rectum-sigmoid junction

value: NR


title: Primary_Tumor 2016

value: Bordeaux CHU

value: FOLFIRI


title: Primary_Tumor 1074

value: SD


title: Primary_Tumor 1085

value: No


title: Primary_Tumor 1038

value: PD


title: Primary_Tumor 1005

value: Limoges


title: Primary_Tumor 1033

value: Rectum

value: FOLFOX


title: Primary_Tumor 1001

value: Right colon


title: Primary_Tumor 1015

value: Male


title: Primary_Tumor 1029

value: FOLFIRI+BEVACIZUMAB


title: Primary_Tumor 12_009

value: Paris


title: Primary_Tumor 1008


title: Primary_Tumor 12_008


title: Primary_Tumor 12_015

value: Yes

value: PR


title: Primary_Tumor 12_011

value: Left colon


title: Primary_Tumor 1032

value: Female

value: R


title: Primary_Tumor 1003


title: Primary_Tumor 12_012

value: CR


title: Primary_Tumor 12_001


title: Primary_Tumor 12_016

value: FOLFIRI

value: NR


title: Primary_Tumor 10_014

value: SD


title: Primary_Tumor 11_005

value: Lilles


title: hADSC Hypooxia rep1

description: Treated for 48 hrs

tag: o2 concentration


title: Primary_Tumor 12_007

value: No


title: Primary_Tumor 12_003


title: Primary_Tumor 12_005


title: Primary_Tumor 11_001

value: PD


title: Primary_Tumor 06_005

value: Nancy


title: Primary_Tumor 06_006

value: Right colon

value: FOLFOX


title: Primary_Tumor 10_005

value: Limoges

value: Male

value: Caecum


title: Primary_Tumor 10_007

value: Yes


title: Primary_Tumor 05_007

value: Toulouse


title: Primary_Tumor 06_001

value: Female

value: PR


title: Primary_Tumor 05_001

value: Left colon

value: R


title: Primary_Tumor 05_005

value: FOLFIRI


title: Primary_Tumor 10_012

value: Rectum

value: SD

value: NR


title: Primary_Tumor 04_042

value: Bordeaux

value: PD


title: Primary_Tumor 05_006


title: Primary_Tumor 10_009


title: Primary_Tumor 04_045


title: Primary_Tumor 04_039

value: Right colon

value: pNX

value: pTX


title: Primary_Tumor 04_035

value: FOLFOX


title: Primary_Tumor 04_037

value: Male


title: Primary_Tumor 04_044

value: Yes


title: Primary_Tumor 04_038


title: Primary_Tumor 04_032

value: Rectum-sigmoid junction


title: Primary_Tumor 04_040


title: Primary_Tumor 04_036

value: Female


title: Primary_Tumor 04_030


title: Primary_Tumor 04_026

value: PR


title: Primary_Tumor 04_016


title: Primary_Tumor 04_028


title: Primary_Tumor 04_034


title: Primary_Tumor 04_031

value: Left colon


title: Primary_Tumor 04_029


title: Primary_Tumor 04_020

value: R


title: Primary_Tumor 04_022

value: FOLFIRI


title: Primary_Tumor 04_027


title: Primary_Tumor 04_011

value: Rectum


title: Non-metastases, biological rep3

first: Jia-kuan

last: Li

address: Fengyang Road

department: Urology

institute: Changzheng Hospital

description: Gene expression data from non-metastatic ccRCC tissue.

hyb_protocol: Following fragmentation, ~20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Glue Grant Human Transcriptome Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: The data were analyzed with log scale robust multi-array analysis (RMA) using Affymetrix Power Tools as normalization method.

source_name: non-metastatic ccRCC tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip® Eukaryotic Double  Strand Whole Transcript   Protocol, Affymetrix).

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

treatment_protocol: ccRCC tissues were collected from patients. These tissues were flash frozen in liquid nitrogen immediately after surgery and subsequently stored at -80℃. All the resected nodules or metastatic masses were identified as renal tumor by pathologic examination. No patients received anticancer treatments before surgery in this study.

tag: tissue

value: kidney

tag: cell type

value: non-metastatic clear cell renal cell carcinoma (ccRCC)


title: Primary_Tumor 04_014

tag: center

value: Bordeaux

tag: Sex

value: CR


title: Primary_Tumor 04_023

tag: age

tag: who performance status

value: SD

value: NR


title: Primary_Tumor 04_021

tag: tumor location

tag: synchronous metastase

value: pNX

value: pTX


title: Primary_Tumor 04_019

value: Male

tag: pn

tag: pt

value: FOLFOX


title: Primary_Tumor 04_015

value: Yes

tag: regimen

tag: response category


title: Primary_Tumor 04_008

value: Female

tag: response status

tag: pfs censored


title: Non-metastases, biological rep2


title: Primary_Tumor 04_012

value: PR

tag: pfs

tag: os censored


title: Metastases, biological rep2

description: Gene expression data from metastatic ccRCC tissue.

source_name: metastatic ccRCC tissue

value: metastatic clear cell renal cell carcinoma (ccRCC)


title: Primary_Tumor 04_009

value: R

tag: os


title: Primary_Tumor 04_025

value: Left colon


title: Primary_Tumor 04_007

value: Transverse colon

value: FOLFIRI


title: Primary_Tumor 04_006


title: Metastases, biological rep1

tag: tissue

value: kidney


title: Primary_Tumor 04_003

value: Bordeaux

value: Rectum


title: Non-metastases, biological rep1

tag: cell type

value: non-metastatic clear cell renal cell carcinoma (ccRCC)


title: Metastases, biological rep3


title: Primary_Tumor 04_005

tag: center

value: SD

value: NR


title: control /BaP 100µg/L [S98]

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

hyb_protocol: 43°C, 16/20 h, hybridization buffer Northern Max (Ambion). Pre-hybridization for 1h in same conditions.

scan_protocol: Scanned on Chip Reader (Applied biosystems Laboratories) at 5 µm resolution

data_processing: Offset background subtracted, global mean normalisation across microarray surfaces and local mean normalisation across element signal intensity. Data obtained from log2 of processed Ch2 signal / processed Ch1 signal.

organism: Mytilus galloprovincialis

source_name: Gills tissue, individual samples non exposed to BaP considered as control

label_protocol: 5 µg of total RNA were primed with 0.5 µg oligodT(19)VN primer at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 400 U ReverseAid MuLV H minus  RTase (Fermentas), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labeled dCTP or Cy5-label dCTP

extract_protocol: Total RNA extracted from the digestive gland of a single individual mussel using Trizol following manufacturer's instructions

tag: gender

value: female

source_name: Gills tissue, individual samples exposed to BaP 100µgL during 3 days.


title: Primary_Tumor 04_002

tag: Sex

value: Male

tag: age


title: Primary_Tumor 02_007

value: Montpellier

tag: who performance status

tag: tumor location

value: Right colon

value: FOLFOX


title: Primary_Tumor 02_011

tag: synchronous metastase

value: No

tag: pn

value: CR


title: Primary_Tumor 02_010

value: Caecum

value: Yes

tag: pt

tag: regimen


title: control /BaP 100µg/L [S97]


title: Primary_Tumor 02_009

value: Female

value: Rectum-sigmoid junction

tag: response category

value: PR

tag: response status

value: R


title: control /BaP 50µg/L [S67]

source_name: Gills tissue, individual samples exposed to BaP 50µgL during 3 days.


title: control /BaP 100µg/L [S96]


title: control /BaP 50µg/L [S66]


title: control /BaP 50µg/L [S65]


title: control /BaP 5µg/L [S62]

source_name: Gills tissue, individual samples exposed to BaP 5µgL during 3 days.


title: control /BaP 5µg/L [S64]


title: control /BaP 5µg/L [S63]


title: control /BaP 100µg/L [S95]


title: control /BaP 50µg/L [S68]


title: control /BaP 100µg/L [S93]

source_name: Digestive gland tissue, individual samples non exposed to BaP considered as control

source_name: Digestive gland tissue, individual samples exposed to BaP 100µgL during 3 days.


title: Primary_Tumor 02_008

value: Left colon

value: FOLFIRI

tag: pfs censored

tag: pfs


title: control /BaP 100µg/L [S94]


title: Primary_Tumor 04_001

value: Bordeaux

value: SD

tag: os censored

tag: os


title: Primary_Tumor 02_006

value: PD

value: NR


title: Primary_Tumor 02_005

value: Montpellier

value: Male


title: Primary_Tumor 01_010

value: Tours

value: FOLFOX


title: control /BaP 100µg/L [S92]

value: female


title: control /BaP 50µg/L [S108]

source_name: Digestive gland tissue, individual samples exposed to BaP 50µgL during 3 days.


title: control /BaP 5µg/L [S103]

source_name: Digestive gland tissue, individual samples exposed to BaP 5µgL during 3 days.


title: control /BaP 50µg/L [S107]


title: control /BaP 5µg/L [S104]


title: control /BaP 5µg/L [S61]


title: control /BaP 5µg/L [S102]


title: control /BaP 100µg/L [S91]


title: control /BaP 50µg/L [S106]


title: control /BaP 5µg/L [S101]


title: Placenta from ICSI-ET_1

status: Public on Aug 16 2017

city: Sendai

first: Hitoshi

last: Hiura

address: 2-1 Seiryo-cho, Aoba-ku

department: Obstetrics and Gynecology

country: Japan

institute: Tohoku University Graduate School of Medicine

description: miRNA expression in placenta from ICSI-ET #127

hyb_protocol: Each labeled Samples were prepared for hybridization by adding nuclease-free water, Hyb Spike-In solution, 10X GE Blocking Agent and 2X Hi-RPM Hybridization Buffer. 45μl of hybridization solutions were dispensed into the gasket slide and assembled to the Agilent SurePrint G3 Human miRNA 8 x 60K Microarrays v21.0, and then rotated at 20 rpm for 20 h at 55°C.

scan_protocol: The microarray slides were scanned immediately after washing on the Agilent G4900DA SureScan Microarray Scanner System using 3 µm resolution.

data_processing: The scanned images were analyzed using Feature Extraction Software 11.0.1.1 (Agilent Technologies). Subsequent analysis was carried out in R software (http://www.r-project.org) using functions and packages collected in the Bioconductor project. Raw microarray data were filtered by detection in all samples. Selected miRNA values were transformed by logarithm and normalized by the quantile method.

source_name: Placenta from ICSI-ET #127

label_protocol: 100 ng of total RNA was dephosphorylated at 37°C for 30 min with calf intestinal phosphatase and denatured by using 100% DMSO at 100°C for 7 min. Samples were labeled with pCp-Cy3 using T4 ligase by incubation at 16°C for 2 hour. The labeled RNA samples were purified in a Vacuum Concentrator for one hour. Once samples are completely dried.

extract_protocol: Total RNA was isolated using a miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol and followed by DNase I (Qiagen) treatment. RNA concentrations were measured by means of a NanoDrop ND-1000 spectrophotometer (Thermo Scientific). RNA quality and integrity were assessed by using automated gel electrophoresis on an Agilent 2100 Bioanalyzer system (Agilent Technologies). Samples were stored at -80ºC until RNA labeling.

tag: tissue

value: placenta

tag: maternal age


title: Placenta from ICSI-FET_2

description: miRNA expression in placenta from ICSI-FET #108

source_name: Placenta from ICSI-FET #108

tag: gender

value: male


title: Placenta from ICSI-ET_4

description: miRNA expression in placenta from ICSI-ET #141

source_name: Placenta from ICSI-ET #141


title: Placenta from ICSI-ET_3

description: miRNA expression in placenta from ICSI-ET #139

source_name: Placenta from ICSI-ET #139


title: RKO_control_rep2

city: Chuo-ku

first: Naoto

last: Tsuchiya

state: Tokyo

address: 5-1-1 Tsukiji

institute: National Cancer Center Research Institute

hyb_protocol: Hybridization was performed using an Gene Expression Hybridization Kit (Agilent technologies) according to manufacturer's instruction. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Array was scanned with an Agilent Microarray Scanner.

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

source_name: RKO cells transfected with miRNA negative control,replicate 2

label_protocol: Cy3-labeled cRNA was prepared from 175 ng RNA using low Input Quick Amp Labeling Kit, one color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen).

growth_protocol: HCT116 and RKO cells were cultured in DMEM medium supplemented with 10% heat-inactivated fetal calf serum. The cultures were incubated at 37 ºC in a humidified air with 5% CO2.

extract_protocol: Total RNAs from the transfected HCT116 or RKO cells were extracted using miRNeasy mini kit (QIAGEN) according to the manufacturer’s protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: HCT116 and RKO cells were transfected with either 5 nM of a Pre-miR-101 miRNA Precursor Molecule (Ambion) or a Pre-miR miRNA Molecule Negative Control #2 (Ambion) for 3 days using HiPerFect (Qiagen) according to the manufacturer’s instructions, and then total RNAs were prepared as described below.

tag: cell line

value: RKO

tag: transfection

value: negative control


title: HCT116_control_rep1

source_name: HCT116 cells transfected with miRNA negative control,replicate 1


title: RKO_miR-101_rep2

source_name: RKO cells transfected with miR-101, replicate 2


title: RKO_miR-101_rep3

source_name: RKO cells transfected with miR-101, replicate 3


title: RKO_control_rep3

source_name: RKO cells transfected with miRNA negative control,replicate 3


title: RKO_control_rep1

source_name: RKO cells transfected with miRNA negative control,replicate 1


title: Placenta from ICSI-ET_2

description: miRNA expression in placenta from ICSI-ET #135

source_name: Placenta from ICSI-ET #135


title: Placenta from ICSI-FET_4

description: miRNA expression in placenta from ICSI-FET #192

source_name: Placenta from ICSI-FET #192


title: HCT116_miR-101_rep3

source_name: HCT116 cells transfected with miR-101, replicate 3


title: HCT116_miR-101_rep1

source_name: HCT116 cells transfected with miR-101, replicate 1


title: RKO_miR-101_rep1

source_name: RKO cells transfected with miR-101, replicate 1


title: HCT116_miR-101_rep2

source_name: HCT116 cells transfected with miR-101, replicate 2


title: MK_T4 TPO-ANA Biological Rep 2

city: Cardiff

first: Lee

middle: Ryan

last: Butcher

address: Llandaff, Campus, Western Avenue, Llandaff

institute: Cardiff Metropolitan University

description: Gene expression data from megakaryocytes differentiated in culture in the presence of TPO & Anagrelide

hyb_protocol: Purified cRNA was fragmented and hybridised to Affymetrix Human Genome U133 Plus 2.0 oligonucleotide chips according to Affymetrix standard protocols (www.affymetrix.com)

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)

data_processing: The data were analyzed using GeneSpring (Agilent Technologies).  Arrays were normalised using Affymetrix Microarray Suite version 5  (MAS 5.0).

label: Biotin

source_name: Hematopoietic progenitor cells differentiated for 4 days with TPO and anagrelide

label_protocol: Biotinylated cRNA were prepared according to standard Affymetrix protocols (www.affymetrix.com)

growth_protocol: Umbilical cord blood-derived CD34+ cells were expanded for 4 days in StemspanTM medium supplemented with 2% human umbilical cord blood plasma and a mixture of heamatopoietic growth factors (TPO, SCF, Flt3 ligand and IL-3). To promote terminal megakaryocytic differentiation cells were subcultured for 4 days in fresh medium supplemented with 2% cord blood plasma and 40 ng/ml TPO

extract_protocol: Total RNA was extracted using RNeasy reagen  (Qyagen). On-column DNAse digestion was performed to eliminate genomic DNA contamination.

treatment_protocol: Anagrelide (300 nM) or equivalent amount of vehicle (DMSO) was added at the beginning of the differentiation step

value: Hematopoeitic progenitor cells


title: HCT116_control_rep2

source_name: HCT116 cells transfected with miRNA negative control,replicate 2


title: HCT116_control_rep3

source_name: HCT116 cells transfected with miRNA negative control,replicate 3


title: Placenta from ICSI-FET_3

description: miRNA expression in placenta from ICSI-FET #153

source_name: Placenta from ICSI-FET #153


title: MK_T4 TPO-ANA Biological Rep 3


title: MK_T4 TPO-ANA Biological Rep 1


title: MK_T4 TPO-DMSO Biological Rep 3

description: Gene expression data from megakaryocytes differentiated in culture in the presence of TPO

source_name: Hematopoietic progenitor cells differentiated for 4 days with TPO and drug vehicle (DMSO)


title: MK_T4 TPO-DMSO Biological Rep 1


title: MK_T4 TPO-DMSO Biological Rep 2


title: Placenta from spontaneous pregnancy_3

description: miRNA expression in placenta from spontaneous pregnancy #60

source_name: Placenta from spontaneous pregnancy #60


title: Placenta from spontaneous pregnancy_4

description: miRNA expression in placenta from spontaneous pregnancy #63

source_name: Placenta from spontaneous pregnancy #63


title: Placenta from spontaneous pregnancy_2

description: miRNA expression in placenta from spontaneous pregnancy #56

source_name: Placenta from spontaneous pregnancy #56


title: Placenta from spontaneous pregnancy_1

description: miRNA expression in placenta from spontaneous pregnancy #44

source_name: Placenta from spontaneous pregnancy #44


title: Control, 3

city: Cologne

first: Olivier

middle: R.

last: Baris

state: NRW

address: Robert-Koch Str. 39

department: Center for Physiology and Pathophysiology

institute: University of Cologne

description: Gene expression data from newborn mouse epidermis

hyb_protocol: Hybridization was performed according to standard protocols for Affymetrix Mouse Gene 2.0 arrays. Fluidics washing was done using the Affymetrix Wash and Stain Kit (#900720), protocol FS450_0002

scan_protocol: Arrays were scanned with Affymetrix Gene ChIP Scanner 3000 7G and images were processed using the Expression Console.

data_processing: Genespring 14.5, Quantile normalization

source_name: epidermis, P0

label_protocol: Applause WT-Amp Plus ST (NuGen)

extract_protocol: Maxwell® 16 LEV simplyRNA Tissue Kit

tag: strain

tag: genotype/variation


title: paired-control-5

city: Jinan

first: Jun

last: Jiao

address: Wenhuaxi Road

institute: Shandong University

description:
circular RNA microarray
control5

hyb_protocol: Five microliter 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer were used to fragment 1μg of each labeled cRNA, followed by heat at 60 °C for 30 min. Finally, 25μl 2 × Hybridization buffer was added to dilute the labeled cRNA and 50μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide, incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After incubation, the hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing:
Scanned images were imported into Agilent Feature Extraction software (version 11.0.1.1) for raw data extraction. Quantile normalization and subsequent data processing were performed using the R software package.
Please note that GPL19978 contains all of 5490 circular RNAs (circRNAs) that can be detected in all of the human tissues and organisms. In the current study of human cervical carcinoma, only  3008 circRNAs were detected as expressed in human cervical carcinoma(SCC) and normal cervical cells(control). Therefore both normalized and raw data matrix contains 3008 data rows.

source_name: normal cervical cells from SCC-paired-control 5

label_protocol: The enriched circRNAs were amplified and transcribed into fluorescent complementary RNA (cRNA) utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

extract_protocol: Total RNA was isolated from 10 samples using TRIzol reagent according to the manufacturer's protocol, and then treated with Rnase R to remove linear RNAs and enrich circRNAs.

tag: tissue type

value: paracancerous cervical tissue

tag: tumor stage

tag: differentiation of tumor

tag: molecule subtype

value: non-linear RNA


title: paired-control-4

description:
circular RNA microarray
control4

source_name: normal cervical cells from SCC-paired-control 4


title: SCC-4

description:
circular RNA microarray
SCC4

source_name: SCC tissue cells from SCC 4

value: cervical cancer tissue

value: loe


title: K320E, 4


title: K320E, 3


title: K320E, 2


title: paired-control-3

description:
circular RNA microarray
control3

source_name: normal cervical cells from SCC-paired-control 3


title: K320E, 1


title: 10wk-old dOB-Pot1a

city: Fukuoka

first: Kentaro

last: Hosokawa

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

department: Department of Stem Cell Biology and Medicine

institute: Graduate School of Medical Sciences, Kyushu University

description: Gene expression data from 10wk-old HSCs after 3days culture cultured with MTM-dOB-Pot1a

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.

source_name: 10wk-old female mice, bone marrow, dOB-Pot1a

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

growth_protocol: 10wk-old and 60wk-old LT-HSCs were cultured in SFO3 medium contained stem cell factor(100ng/mL), Thrombopoietin(100ng/mL) and  with control-MTM, MTM-Pot1a or MTM-dOB-Pot1a at 37C for 3days.

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: After culture, LT-HSCs were sorted into the Buffer RLT by using FACS ARIAIII.

tag: age

value: Bone marrow

tag: cell type


title: Pot1a

description: Gene expression data from 10wk-old HSCs after Pot1a gene transduction and 3days culture.

source_name: 10wk-old male mice, bone marrow, Pot1a

growth_protocol: 10wk-old LT-HSCs were cultured in SFO3 medium contained stem cell factor(100ng/mL), Thrombopoietin(100ng/mL) at 37C for 1day (pre-culture) or 3days (after transfection culture).

treatment_protocol: After pre-culture, genes were transduced into cells by using retro viral solutions (mock control, full length WT-Pot1a) .

value: Pot1a overexpression


title: Control

description: Gene expression data from 10wk-old HSCs after control gene transduction and 3days culture.

source_name: 10wk-old male mice, bone marrow, control

value: control


title: Human Tig3 LaminB1

type: genomic

city: Parkville

first: Carolyn

middle: A

last: de Graaf

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

hyb_protocol: The labeled MePCR DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, 50 μg per sample was combined into 33.6 μl water, and mixed with 2.4 μl Alignment oligo, 24 μl hybridization component A, and 60 μl 2x Hybridization Buffer. The entire 120 μl was used for hybridization in Tecan hybridization stations for 16-18 h at 42C. Arrays were then washed in 42 °C Nimblegen washbuffer1, and room temperature Nimblegen washbuffer 2 and 3. All buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Microarrays were scanned in a Agilent Scanner (Model G2505C, Serial number US22502518), which uses Scan Control software (Version A.8.1.3). Slides were first placed in a slide holder before putting it in the Scanner Carousel, which was installed in the scanner. Slides were double-pass scanned at maximum PMT for each channel, at a 2 um per pixel resolution.

data_processing: Arrays were quantified with NimbleScan 2.5. Raw .pair files were read with the Ringo package for R and the loess normalized. The score was calculated as the log2 Dam-LaminB1: Dam ratio of the normalized data.

molecule: genomic DNA

source_name: Dam-LaminB1 DamID DNA

label_protocol: 1.5 µg MePCR DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3/Cy5 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html). Labeling time was extended to 12 hours to increase yield.

growth_protocol: Cells were propagated in DMEM (GIBCO) supplemented with 9% fetal bovine serum.

extract_protocol: 1-2x10e5 cells were infected with lenti-virus expressing Dam or Dam-Lamin B1. After 48 hours gDNA was isolated with the Qiagen Blood and Tissue kit per the manufacturers protocol. 2.5 μg of gDNA was digested with DpnI (New England Biolabs), adapters were ligated with T4 ligase (New England Biolabs), and the ligation reaction was subsequently digested with DpnII (New England Biolabs). 500 ng of the DpnII digested material was used as input for a PCR amplification of methylated fragments (MePCR), see Vogel et al., 2008, Nature Protocols for details. MePCR fragments were purified by Qiaquick Spin columns (Qiagen).

treatment_protocol: Cells were maintained for 48 hours after infection with the lentivirus

tag: infection

value: Dam-LaminB1 lenti virus

source_name: Dam-only DamID DNA

value: Dam-Only lenti virus


title: paired-control-1

description:
circular RNA microarray
control1

source_name: normal cervical cells from SCC-paired-control 1


title: SCC-5

description:
circular RNA microarray
SCC5

source_name: SCC tissue cells from SCC 5

value: high


title: paired-control-2

description:
circular RNA microarray
control2

source_name: normal cervical cells from SCC-paired-control 2


title: Control, 2


title: 10wk-old M-Pot1a

description: Gene expression data from 10wk-old HSCs after 3days culture cultured with MTM-Pot1a

source_name: 10wk-old female mice, bone marrow, MTM-Pot1a


title: SCC-1

description:
circular RNA microarray
SCC1

source_name: SCC tissue cells from SCC 1

value: moderate


title: SCC-2

description:
circular RNA microarray
SCC2

source_name: SCC tissue cells from SCC 2

value: low


title: SCC-3

description:
circular RNA microarray
SCC3

source_name: SCC tissue cells from SCC 3


title: 60wk-old control

description: Gene expression data from 60wk-old HSCs after 3days culture cultured with control MTM

source_name: 60wk-old female mice, bone marrow, control

value: female


title: 60wk-old M-Pot1a

description: Gene expression data from 60wk-old HSCs after 3days culture cultured with MTM-Pot1a

source_name: 60wk-old female mice, bone marrow, MTM-Pot1a


title: 10wk-old control

description: Gene expression data from 10wk-old HSCs after 3days culture cultured with control MTM

source_name: 10wk-old female mice, bone marrow, control


title: sir1-1 roots, biological replicate 3

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

description: Gene expression data from roots of 7-week-old sir1-1 Arabidopsis plants.

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of Arabidopsis thaliana AraGene-1_0-st-type from Affymetrix. A Custom CDF Version 16 with Tair based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

organism: Arabidopsis thaliana

source_name: Arabidopsis roots,sir1-1 mutant

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

growth_protocol: Plants were grown hydroponically for total 7 weeks under short-day conditions (8h light / 16 h dark)

extract_protocol: RNA was extracted from roots using the peqGOLD Total RNA Kit according to the manufacturer´s instruction

tag: genotype


title: sir1-1 roots, biological replicate 2


title: serat tko roots, biological replicate 3

description: Gene expression data from roots of 7-week-old serat tko Arabidopsis plants.

source_name: Arabidopsis roots, serat tko mutant

value: serat tko


title: serat tko roots, biological replicate 2


title: serat tko roots, biological replicate 1


title: Wild type roots, biological rep1

description: Gene expression data from roots of 7-week-old wild type Arabidopsis plants.

source_name: Arabidopsis roots, wild type

value: wild type


title: sir1-1 roots, biological replicate 1


title: Wild type roots, biological rep3


title: control /BaP 50µg/L [S105]

source_name: Digestive gland tissue, individual samples non exposed to BaP considered as control

source_name: Digestive gland tissue, individual samples exposed to BaP 50µgL during 3 days.


title: Wild type roots, biological rep2


title: Placenta from ICSI-FET_1

description: miRNA expression in placenta from ICSI-FET #106

source_name: Placenta from ICSI-FET #106

value: placenta


title: MM455_shBRN2_DOX_96h

city: Brisbane

first: Glen

middle: M

last: Boyle

state: Queensland

address: 300 Herston Road Herston

department: Department of Cell and Molecular Biology, Cancer Program

institute: QIMR Berghofer Medical Research Insitute

hyb_protocol: Labelled cRNA was hybridized to HumanHT-12 v4 BeadChip Arrays (Illumina Inc, San Diego, CA, USA), and then washed and scanned according to standard Illumina protocols.

data_processing: Data were extracted in GenomeStudio (Illumina) using default analysis settings and no normalization method.  Resulting data were imported into GeneSpring GX v12.5 (Agilent Technologies, Santa Clara, CA, USA).  Expression values were normalized using quantile normalization with default settings.

source_name: MM455 melanoma cells expressing shRNA targeting BRN2 treated with doxycycline, 96h

label_protocol: Biotinylated cRNA was prepared with the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX, USA).

growth_protocol: Cells were cultured in 10% heat-inactivated fetal calf serum (Invitrogen, Melbourne, Australia) in RPMI-1640 medium supplemented with 100 U/ml penicillin, 100 µg/ml streptomycin, 3 mM HEPES at 5% CO2, 99% humidity at 37oC.

extract_protocol: RNA was extracted using Qiagen RNeasy mini kit as per manufacturer’s instructions, then DNase treated and purified.  RNA concentration was determined using the NanoDrop 2000 (Thermo Scientific, Wilmington, DE, USA).

treatment_protocol: Cells were treated with 50 ng/ml doxycycline for 96 hours, then harvested for RNA extraction.

tag: shRNA

tag: treatment

value: Doxycycline


title: MM649_shMITF_DOX_96h

scan_protocol: Labelled cRNA was hybridized to HumanHT-12 v4 BeadChip Arrays (Illumina Inc, San Diego, CA, USA), and then washed and scanned according to standard Illumina protocols.

source_name: MM649 melanoma cells expressing shRNA targeting MITF treated with doxycycline, 96h

value: shMITF


title: MM455_shBRN2_veh_96h

source_name: MM455 melanoma cells expressing shRNA targeting BRN2 treated with vehicle, 96h

value: Vehicle


title: A02_shMITF_veh_96h

source_name: A02 melanoma cells expressing shRNA targeting MITF treated with vehicle, 96h


title: S limited shoot, biological rep4

description: Gene expression data from shoots of 7-week-old Arabidopsis plants grown under S limitation.

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of AraGene-1_0-st-type from Affymetrix. A Custom CDF Version 19 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: Arabidopsis shoot, S limitation

extract_protocol: RNA was extracted using the peqGOLD Total RNA Kit according to the manufacturer´s instruction

treatment_protocol: For sulfur limitation condition, Arabidopsis plants were grown in full nutrient supply for 2 weeks and then exposed to sulfur limitation for the following 5 weeks.

value: sulfur


title: MM455_shNEG_veh_96h

source_name: MM455 melanoma cells expressing shRNA targeting lacZ treated with vehicle, 96h

value: shNEG


title: HT144_shBRN2_DOX_96h

source_name: HT144 melanoma cells expressing shRNA targeting BRN2 treated with doxycycline, 96h


title: HT144_shBRN2_veh_96h

source_name: HT144 melanoma cells expressing shRNA targeting BRN2 treated with vehicle, 96h


title: MM649_shNEG_DOX_96h

source_name: MM649 melanoma cells expressing shRNA targeting lacZ treated with doxycycline, 96h


title: A02_shBRN2_DOX_96h

source_name: A02 melanoma cells expressing shRNA targeting BRN2 treated with doxycycline, 96h


title: HT144_shMITF_DOX_96h

source_name: HT144 melanoma cells expressing shRNA targeting MITF treated with doxycycline, 96h


title: MM649_shBRN2_DOX_96h

source_name: MM649 melanoma cells expressing shRNA targeting BRN2 treated with doxycycline, 96h


title: MM649_shNEG_veh_96h

source_name: MM649 melanoma cells expressing shRNA targeting lacZ treated with vehicle, 96h


title: A02_shNEG_veh_96h

source_name: A02 melanoma cells expressing shRNA targeting lacZ treated with vehicle, 96h


title: A02_shMITF_DOX_96h

source_name: A02 melanoma cells expressing shRNA targeting MITF treated with doxycycline, 96h


title: MM455_shMITF_veh_96h

source_name: MM455 melanoma cells expressing shRNA targeting MITF treated with vehicle, 96h


title: HT144_shNEG_DOX_96h

source_name: HT144 melanoma cells expressing shRNA targeting lacZ treated with doxycycline, 96h


title: MM649_shMITF_veh_96h

source_name: MM649 melanoma cells expressing shRNA targeting MITF treated with vehicle, 96h


title: HT144_shNEG_veh_96h

source_name: HT144 melanoma cells expressing shRNA targeting lacZ treated with vehicle, 96h


title: A02_shBRN2_veh_96h

source_name: A02 melanoma cells expressing shRNA targeting BRN2 treated with vehicle, 96h


title: MM455_shMITF_DOX_96h

source_name: MM455 melanoma cells expressing shRNA targeting MITF treated with doxycycline, 96h


title: MM455_shNEG_DOX_96h

source_name: MM455 melanoma cells expressing shRNA targeting lacZ treated with doxycycline, 96h


title: HT144_shMITF_veh_96h

source_name: HT144 melanoma cells expressing shRNA targeting MITF treated with vehicle, 96h


title: A02_shNEG_DOX_96h

source_name: A02 melanoma cells expressing shRNA targeting lacZ treated with doxycycline, 96h


title: MM649_shBRN2_veh_96h

source_name: MM649 melanoma cells expressing shRNA targeting BRN2 treated with vehicle, 96h


title: Control, 1

source_name: epidermis, P0


title: sir1-1 shoot, biological replicate 3

description: Gene expression data from shoots of 7-week-old sir1-1 Arabidopsis plants.

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of ATH1-121501-type from Affymetrix. A Custom CDF Version 19 with TAIR based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: Arabidopsis shoot,sir1-1 mutant

growth_protocol: Plants were grownon soil for total 7 weeks under short-day conditions (8h light / 16 h dark)

value: 7 weeks

value: mut

tag: volume

value: small


title: sir1-1 shoot, biological replicate 1


title: Control shoot, biological rep3

description: Gene expression data from shoots of 7-week-old Arabidopsis plants grown in full nutrient media.

source_name: Arabidopsis shoot, control condition

value: control


title: S limited shoot, biological rep3

source_name: Arabidopsis shoot, S limitation


title: S limited shoot, biological rep1


title: S limited shoot, biological rep2


title: sir1-1 shoot, biological replicate 2


title: Control shoot, biological rep4


title: Wild type shoot, biological rep3

description: Gene expression data from shoots of 7-week-old wild type Arabidopsis plants.

source_name: Arabidopsis shoot, wild type

value: wt

value: big


title: CD44lowCD24high Rep2

city: KOLKATA

first: Sangeeta

last: Ghuwalewala

state: West Bengal

address: 4, Raja S. C. Mullick Road

department: Cancer Biology and Inflammatory Disorder Division

institute: CSIR-Indian Institute of Chemical Biology

description: Replicate 2

hyb_protocol: Purified biotin labelled cRNAs were hybridised to the BeadChip using Direct hybridisation Whole-Gene Expression assay, according to the manufacturer's protocol (Illumina Inc., San Diego, CA). Subsequent steps include washing, blocking, and streptavidin-Cy3 staining followed by serial nonstringent washing steps to remove unbound conjugate.

scan_protocol: The Illumina bioarrays were read in an Illumina iScan Reader and the primary intensity data were obtained in standard file format, using Genome  Studio Software

data_processing: Avg Signal Intensity from raw data was background substracted using Genome Studio and imported to bioconductor Lumi Package for data transformation (Log2 transformed)and Robust Spline method is used for normalisation. Differential expression was performed using bioconductor package Limma. Genes with Adjusted Pvalue< 0.05, and fold change ≥ 1.5 were considered significant.

source_name: CD44 low CD24 high

label_protocol: From the isolated RNA the mRNA was converted to cDNA followed by labelled cRNA preparation using Illumina® TotalPrep™ RNA Amplification Kit

growth_protocol: Oral cancer cell line SCC25 was procured from ATCC and cultured in DMEM-F12 medium (Life Technologies, Thermo Fisher Scientific Inc., MA USA) supplemented with 10% fetal calf serum

extract_protocol: Total RNA was extracted from the different fractions of SCC25 using Qiagen RNeasy Mini Kit (Qiagen, Hilden, Germany) using manufacturer’s protocol. Briefly, the cells were lysed with RLT lysis buffer and mixed with equal volume of 70% ethanol. The mix was then passed through RNeasy Spin column and flow-through was discarded. This is followed by on column DNase treatment. The RNA-bound column was subsequently washed with wash buffer and the RNA were eluted in RNase free water.The integrity of RNA was ascertained using Agilent Bioanalyser (Santa Clara).

treatment_protocol: SCC25 was subjected to Magnetic Bead based Sorting of three subpopulations; CD44highCD24low,  CD44lowCD24low and CD44lowCD24high. The unsorted SCC25 cell populations was also used in this study.

value: Male

tag: age (yrs)

tag: tissue

value: Tongue

value: Biopsy of Squamous Cell Carcinoma


title: Wild type shoot, biological rep2


title: Control, 4


title: Wild type shoot, biological rep1


title: CD44lowCD24high Rep1

description: Replicate 1

tag: cell line

tag: gender


title: CD44lowCD24low Rep2

description: Replicate 2

source_name: CD44 low CD24 low


title: CD44lowCD24low Rep1

description: Replicate 1


title: Unsorted SCC25 Rep1

description: Replicate 1

source_name: Unsorted SCC25


title: CD44highCD24low Rep2

description: Replicate 2

source_name: CD44 high CD24 low


title: Control shoot, biological rep2


title: ESCC Tissue - Donor 5

status: Public on Aug 15 2017

first: Kory

middle: R

last: Johnson

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

description: ESCC Tissue - Donor 5

hyb_protocol: Labeled cRNA were hybridized to Affymetrix HG-U133 Plus 2 GeneChip (Affymetrix, Inc) in blinded interleaved fashion according to manufacturer’s guidelines.

scan_protocol: The Affymetrix Gene Chip Scanner 3000 was used to scan each Affymetrix HG-U133 Plus 2 GeneChip (Affymetrix, Inc) according to manufacturer’s guidelines and generate one CEL file per hybridized cRNA.

data_processing: The Affymetrix Expression Console (Affymetrix, Inc) was used to generate both RMA normalized gene expression and RNA normalized transcript expression per CEL file.

source_name: Donor 5

label_protocol: RNA labeling performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix HG-U133 Plus 2 GeneChip (Affymetrix, Inc).

extract_protocol: Total RNA was isolated using Trizol reagent (Ambion) and the RNeasy plus mini kit (Qiagen) according to the manufacturer’s instructions. RNA was treated with RNAse (Turbo DNA Free, Invitrogen) and was eluted from the column in nuclease-free water and quantified on a Nanodrop 8000 (Thermo Scientific).  RNA quality and quantity was ensured using the Bioanalyzer (Agilent, Inc) and NanoDrop (Thermo Scientific, Inc) respectively

tag: escc

value: positive

tag: race

value: African American


title: CD44highCD24low Rep1

description: Replicate 1


title: Healthy Tissue - Donor 6

description: Healthy Tissue - Donor 6

source_name: Donor 6

value: negative


title: ESCC Tissue - Donor 7

description: ESCC Tissue - Donor 7

source_name: Donor 7


title: ESCC Tissue - Donor 6

description: ESCC Tissue - Donor 6


title: Healthy Tissue - Donor 7

description: Healthy Tissue - Donor 7


title: Unsorted SCC25 Rep2

description: Replicate 2


title: Healthy Tissue - Donor 3

description: Healthy Tissue - Donor 3

source_name: Donor 3


title: POVA [251911910877_S01_2_3]

city: Madrid

first: Fatima

last: Sanchez-Cabo

address: Melchor Fernandez Almagro

country: Spain

institute: CNIC

description: Expression of miRNAs from CD4 T cells sorter from coculture with cDCs + OVA

hyb_protocol: 100 ng of Cy3 labelled RNA were hybridized for 20 hours at 55ºC in a hybridization oven  (G2545A, Agilent) set to 15 rpm in a final concentration of 1X GE Blocking Agent and 1X Hi-RPM Hybridization Buffer, according to manufacturer's instructions (miRNA Microarray System Protocol, Agilent Technologies).

scan_protocol: Arrays were scanned at 5mm resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for miRNA Microarray v2.0 (miRNA Microarray System Protocol, Agilent Technologies).

data_processing: Images provided by the scanner were analyzed using Agilent´s software Feature Extraction version 10.7.3.1 and protocol miRNA_105_Jan09

source_name: CD4 T cells (cDCs+OVA)

label_protocol: miRNA Labeling Kit (Agilent Technologies) was used to label RNA. Basically, 100 ng of total RNA were dephosphorylated and Cyanine 3-pCp molecule was ligated to the 3´ end of each RNA molecule by using T4 RNA ligase.

growth_protocol: Mouse naive CD4+ T cells were isolated from cell suspensions of lymph nodes or spleen. Cell suspensions were incubated with biotinylated antibodies (BD Biosciences) against CD8, CD19, CD25, CD11b, CD11c, CD45R, MHC-II (I-Ab), DX5, IgM, Gr-1 and F4/80 and subsequently with streptavidin microbeads (MACS; Miltenyi Biotec). CD4+ T cells were negatively selected in auto-MACS Pro Separator (Miltenyi Biotec) according to the manufacturer's instructions. At this point DC preparations were characterized as CD11c+ MHCII+ Ly6G-. To obtain both pDCs and cDCs, bone marrow cell suspensions were cultured with 100 ng ml-1 Flt3-ligand for 8 d and maturation was subsecuently induced by 6 µg ml-1 of CpG. pDCs and cDCs were isolated using MACS system B220-labeled beads and auto-MACS Pro Separator (Miltenyi Biotec) being pDCs B220+ fraction and cDCs B220- fraction.

extract_protocol: Total RNA was extracted with Quiazol reagent and the miRNeasy® mini kit (Quiagen),

treatment_protocol: T cells were cocultured with the corresponding subset of DCs (8:1 T cell/DC ratio) in the presence or absence of chicken ovalbumin (OVA) 323-339 peptide for 18 h. CD4+ T cells from the coculture  were sorted on a flow cytometer.

tag: origin

value: CD4 T cells after coculture with cDCs in the presence of OVA

value: Primary CD4 T cells


title: Control shoot, biological rep1


title: Healthy Tissue - Donor 5

city: Bethesda

description: Healthy Tissue - Donor 5


title: ESCC Tissue - Donor 1

description: ESCC Tissue - Donor 1

source_name: Donor 1


title: COVA [251911910877_S01_2_2]

description: Expression of miRNAs from CD4 T cells sorter from coculture with pDCs +OVA

source_name: CD4 T cells (pDCs+OVA)

value: CD4 T cells after coculture with pDCs in the presence of OVA


title: Healthy Tissue - Donor 1

description: Healthy Tissue - Donor 1


title: Healthy Tissue - Donor 2

description: Healthy Tissue - Donor 2

source_name: Donor 2


title: C [251911910877_S01_1_3]

description: Expression of miRNAs from CD4 T cells sorter from coculture with cDCs

source_name: CD4 T cells (cDCs)

value: CD4 T cells after coculture with cDCs in the absence of OVA


title: ESCC Tissue - Donor 3

description: ESCC Tissue - Donor 3


title: COVA [251911910877_S01_2_1]

description: Expression of miRNAs from CD4 T cells sorter from coculture with pDCs + OVA


title: ESCC Tissue - Donor 2

description: ESCC Tissue - Donor 2


title: C [251911910877_S01_1_4]


title: POVA [251911910877_S01_2_4]

description: Expression of miRNAs from CD4 T cells sorter from coculture with cDCs +OVA


title: P [251911910877_S01_1_2]

description: Expression of miRNAs from CD4 T cells sorter from coculture with pDCs

source_name: CD4 T cells (pDCs)

value: CD4 T cells after coculture with pDCs in the absence of OVA


title: H1423 AD10_83.AVG_Signal

city: Oslo

first: Biljana

last: Stangeland

address: Sognsvannsveien 20

department: Institute of Surgical Research

country: Norway

institute: Oslo University Hospital

description: biological replicate AD10-4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were imported to gene expression analysis software “JExpress” (Molmine, Bergen, Norway) http://jexpress.bioinfo.no) and  normalised using quantile normalisation

source_name: patient cells growing as adherent cells in 10% serum

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

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: culture

value: Grown as adherent cells 10% serum

tag: cell or tissue type

value: GBM adherent cultures

value: GBM adherent cultures grown in 10% serum isolated from ultrasonic aspirate (UA-AD10)


title: P [251911910877_S01_1_1]


title: H1401 AD10_75.AVG_Signal

description: biological replicate AD10-3


title: H1404 AD1_81.AVG_Signal

description: biological replicate AD1-3

source_name: patient cells growing as adherent cells in 1% serum

value: Grown as adherent cells 1% serum

value: GBM adherent cultures grown in 1% serum isolated from ultrasonic aspirate (UA-AD1)


title: H1411 AD1_79.AVG_Signal

description: biological replicate AD1-2


title: H1339 AD10_73.AVG_Signal

description: biological replicate AD10-2


title: Liver_CON_48h_rep.4

city: Jena

first: S.

last: Lambeck

address: Erlanger Allee 101

institute: JUH

description:
in vivo
SAMPLE 16

hyb_protocol: Hybridization was in agreement with the Whole-Genome Gene Expression Direct Hybridization Assay protocol from Illumina. Biotinylated probes were prepared from total RNA, using the TargetAmp™-Nano Labeling Kit for Illumina® Expression BeadChip®. Amplification of RNA was in agreement to the protocol of the Illumina® for the BeadArray Reader 500 X

scan_protocol: Arrays were readout with the detection system iScan from Illumina.

data_processing: Raw data were obtained using GenomeStudio (v 1.9.0)  and annotation by MouseRef-8_V2_0_R3_11278551_A.bgx.xml. Robust spline normalization (rsn) and detection filtering were performed via lumi package within Bioconductor and R.

source_name: liver 48 h sepsis (CLP)

label_protocol: Amplification and biotinylation of RNA were carried out using the TargetAmp™-Nano Labeling Kit for Illumina® Expression BeadChip® (Epicentre).

extract_protocol:
RNA was isolated from whole livers using QIAcubeTM and RNeasy® Mini Kit from Qiagen in accordance to the Purification of Total RNA from Animal Tissues protocol. RNA concentration and purity were determined with the NanoDrop® ND-2000c spectrophotometer.
RNA was isolated from whole livers  using QIAcubeTM and RNeasy® Mini Kit from Qiagen in accordance to the Purification of Total RNA from Animal Cells Using Spin Technology protocol and the Purification of Total RNA from Animal Tissues protocol, respectively. RNA concentration and purity were determined with the NanoDrop® ND-2000c spectrophotometer.

treatment_protocol:
Cecal ligation and puncture (CLP) was performed as described (Rittirsch et al., 2009) consisting of 20-30% cecum ligation and double puncture with a 23 Gauge (G) needle. All animals received 0.9% saline (40 mL/kg) and Imipenem/Cilastatin (25 mg/kg, starting 2h after CLP and every 12 h ).
Animal experiments were carried out after approval of the local ethics committee. Cecal ligation and puncture (CLP) was performed as described (Rittirsch et al., 2009) consisting of 20-30% cecum ligation and double puncture with a 23 Gauge (G) needle. All animals received 0.9% saline (40 mL/kg) and Imipenem/Cilastatin (25 mg/kg, starting 2h after CLP and every 12 h).

value: liver

value: Fthlox/lox

tag: strain


title: Liver_del_48h_rep.4

description:
in vivo
SAMPLE 12

growth_protocol: Animal experiments were carried out after approval of the local ethics committee.

value: MxCreFthD/D


title: Liver_CON_48h_rep.3

description:
in vivo
SAMPLE 15


title: Liver_CON_48h_rep.2

description:
in vivo
SAMPLE 14


title: Liver_CON_0h_rep.3

description:
in vivo
SAMPLE 7

source_name: liver, untreated

treatment_protocol:
untreated control mice
Animal experiments were carried out after approval of the local ethics committee. Cecal ligation and puncture (CLP) was performed as described (Rittirsch et al., 2009) consisting of 20-30% cecum ligation and double puncture with a 23 Gauge (G) needle. All animals received 0.9% saline (40 mL/kg) and Imipenem/Cilastatin (25 mg/kg, starting 2h after CLP and every 12 h).


title: Liver_del_48h_rep.3

description:
in vivo
SAMPLE 11


title: Liver_CON_48h_rep.1

description:
in vivo
SAMPLE 13


title: H1404 Fr Tissue_80T.AVG_Signal

description: biological replicate Fr-3

source_name: Fresh ultrasonic aspirates tripsinized /from glioblastoma patient

value: GBM ultrasound aspirate

value: Fresh GBM ultrasonic aspirate (UA-FR)


title: H1339 Fr UA_74.AVG_Signal

description: biological replicate Fr-4


title: H1411 Fr Tissue_86.AVG_Signal

description: biological replicate Fr-2


title: H1446 Sp UA_71.AVG_Signal

description: biological replicate Sp-1

source_name: patient cells growing as spheres

value: Grown as spheres

value: GBM sphere cultures

value: GBM sphere cultures isolated from ultrasonic aspirate (Sp-UA)


title: lung tissues_KO2

city: Nanjing

first: wujian

last: xu

state: Jiangshu

address: 305 Esat Zhongshan Road

department: The department of respiratory disease

institute: Jinling Hospital

hyb_protocol: The labeled cRNAs were hybridized onto the microarray (Agilent SurePrint G3 Mouse GE (8*60K)) using the Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242).

scan_protocol: After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies, U.S.A.).

data_processing:
Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to obtain raw data. Genespring was employed to finish the basic analysis with the raw data. The raw data was normalized with the quantile algorithm. The probes where at least 75 % of the values in any one out of all conditions have flags in Detected were chosen for further data analysis. Differentially expressed genes were then identified through fold change and P value calculated with t-test.Afterwards, GO analysis and KEGG analysis were applied to determine the roles of these differentially expressed mRNAs. Finally, Hierarchical Clustering was performed to display the distinguishable genes' expression pattern among samples.
The threshold set for up- and down-regulated genes was a fold change > 2.0 and a P value < 0.05.

source_name: lung tissue, GGPPS1 knockout mice, treated with LPS for 12h

label_protocol: total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-2305).

extract_protocol: Total RNA was extracted from whole lung tissue and quantified using the NanoDrop ND-2000 (Thermo Scientific, U.S.A.). RNA integrity was assessed using a Agilent Bioanalyzer 2100 (Agilent Technologies).

tag: genotype/variation

value: GGPPS1 knockout

tag: agent

value: LPS

value: lung


title: lung tissues_KO4


title: Liver_del_48h_rep.2

description:
in vivo
SAMPLE 10


title: H1411 AD10_77.AVG_Signal

description: biological replicate AD10-1


title: Liver_del_48h_rep.1

description:
in vivo
SAMPLE 9

treatment_protocol:
Cecal ligation and puncture (CLP) was performed as described (Rittirsch et al., 2009) consisting of 20-30% cecum ligation and double puncture with a 23 Gauge (G) needle. All animals received 0.9% saline (40 mL/kg) and Imipenem/Cilastatin (25 mg/kg, starting 2h after CLP and every 12 h).
Animal experiments were carried out after approval of the local ethics committee. Cecal ligation and puncture (CLP) was performed as described (Rittirsch et al., 2009) consisting of 20-30% cecum ligation and double puncture with a 23 Gauge (G) needle. All animals received 0.9% saline (40 mL/kg) and Imipenem/Cilastatin (25 mg/kg, starting 2h after CLP and every 12 h).


title: H1339 AD1_72.AVG_Signal

description: biological replicate AD1-1


title: lung tissues_KO3


title: H1446 Fr UA_70.AVG_Signal

description: biological replicate Fr-1


title: ESCC Tissue - Donor 4

description: ESCC Tissue - Donor 4

source_name: Donor 4

value: positive

value: African American


title: Liver_CON_0h_rep.4

description:
in vivo
SAMPLE 8


title: lung tissues_KO1


title: Liver_CON_0h_rep.2

description:
in vivo
SAMPLE 6


title: lung tissues_CTL4

source_name: lung tissue, wildtype mice, treated with LPS for 12h

value: wildtype


title: Liver_CON_0h_rep.1

description:
in vivo
SAMPLE 5


title: Liver_del_0h_rep.1

description:
in vivo
SAMPLE 1


title: Bel-7402_Baicalein_80uM_rep3

city: Xi'an

first: Zongfang

last: Li

state: Shaanxi

address: 157 W 5th Road

department: the second affiliated hospital

institute: Xi’ an Jiaotong University

hyb_protocol: Labeled miRNA was hybridized to the array for 16 hours at 48 “C and 60 rpm and were then washed and stained using the GeneChip ® Hybridization Wash and Stain Kit in the 450 Fluidics Station according to the manufacturer's instructions.

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

data_processing: The raw data (CEL files) were extracted from the scanned images using the Affymetrix GeneChip Command Console. Expression data were generated by Affymetrix Expression Console software and normalized by the MAS5 method

source_name: Bel-7402 cell line treated with 80 uM  baicalein for 24h

label_protocol: Per RNA sample, 1 μg of total RNA was labeled with biotin using FlashTag® Biotin HSR RNA Labeling Kit (Genisphere, USA) according to the manufacturer's instructions.

growth_protocol: Human hepatocellular carcinoma cell lines Bel-7402 was cultured in Dulbecco’s modified Eagle’s medium (Hyclone, USA) supplemented with 10% fetal bovine serum (Gibco, USA), 1% penicillin-streptomycin (100 U/ml penicillin and 100 μg/ml streptomycin; Hyclone, USA) at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol: After a 24h incubation, the cell were harvested and the total RNA including miRNAs was extracted using TRIzol reagent (Invitrogen, USA) according to the manufacturers’ instructions.

treatment_protocol: The cell lines Bel-7402 was seeded in 6-well plate at a concentration of 2×10^5 per well and incubated overnight. Then the cells was treated with various concentration (0,40 and 80μM) of baicalein dissolved in DMSO (final DMSO concentration in growth media, 0.1%) for 24h.

tag: tumor type

value: Hepatocellular carcinoma


title: Bel-7402_Baicalein_80uM_rep1


title: Liver_del_0h_rep.2

description:
in vivo
SAMPLE 2

tag: genotype


title: Liver_del_0h_rep.3

description:
in vivo
SAMPLE 3


title: Bel-7402_Baicalein_40uM_rep2

source_name: Bel-7402 cell line treated with 40 uM  baicalein for 24h


title: lung tissues_CTL2


title: Liver_del_0h_rep.4

description:
in vivo
SAMPLE 4


title: lung tissues_CTL3


title: lung tissues_CTL1


title: KO_rep3

city: Pohang

first: Bhin

last: Jin-hyuk

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

department: Department of Chemical engineering

institute: POSTECH

description: RNAs isolated from iWAT of ZIP13-KO mice

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: iWAT of ZIP13-KO mice

label_protocol: Refer to the Agilent Gene Expression System Manual

growth_protocol: All mice were housed in specific pathogen-free barrier facilities, maintained under 12 hr light/dark cycle, and fed a standard rodent food (Oriental Yeast, Tokyo, Japan) or rodent food containing 60% fat (Research Diet, NJ, USA) from 8 to 14 week of age and provided with water ad libitum. Since Zip13-KO mice show hypodontia (15), all mice used experiments were fed powdered food. All mice were backcrossed onto C57BL/6J mice for at least 7 generations to minimize the contributions of genetic variation due to chimerism in the knock-in mice.

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

treatment_protocol: A bacterial artificial chromosome (BAC) clone containing the mouse ZIP13 was screened from an embryonic stem (ES) cell–BAC library. A targeting vector was created to eliminate the genomic region encompassing exons 6–8 by inserting a Neo-cassette into a region between exons 5 and 9 of ZIP13 and deleting the intervening exons. This vector was introduced into R1 ES cells and cloned homologous recombinants were selected with antibiotics and the genotypes verified.

tag: strain background

value: inguinal white adipose tissue


title: KO_rep1


title: Bel-7402_Baicalein_40uM_rep1


title: Bel-7402_Baicalein_80uM_rep2


title: WT_rep2

description: RNAs isolated from iWAT of WT mice

source_name: iWAT of WT mice

value: wild type


title: Bel-7402_Baicalein_40uM_rep3


title: Sig-M5_Vehicle_1

city: Watertown

first: Eric

last: Olson

state: MA

address: 480 Arsenal Street

institute: Syros Pharmaceuticals

description: Gene expression of cells treated with DMSO for 24hr.

hyb_protocol: Protocol of Dana Farber Cancer Institute Molecular Biology Core Facilities.

data_processing: Data were processed using the Bioconductor package affy using RMA normalization with default settings.

extract_protocol: Cell suspensions were centrifuged for 3 minutes at 300 x g and re-suspended TRIzol reagent.

treatment_protocol: Cells were treated with either SY-1425 (tamibarotene, 100nM for final concentration of 50nM) or DMSO for 24 hours

value: Acute myeloid leukemia

value: DMSO


title: Sig-M5_Treated_3

description: Gene expression of cells treated with SY-1425 (tamibarotene) for 24hr.

scan_protocol: Protocol of Dana Farber Cancer Institute Molecular Biology Core Facilities.

value: SY-1425 (tamibarotene)


title: Sig-M5_Vehicle_2

label_protocol: Protocol of Dana Farber Cancer Institute Molecular Biology Core Facilities.


title: WT_rep1

description: RNAs isolated from iWAT of WT mice


title: KO_rep2


title: NHBEC

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

description: SAMPLE 4

hyb_protocol: was carried out by Life & Brain GmbH, Bonn

data_processing:
Data extraction was done using GenomeStudio v2011.1
Unmethylated and methylated signal intensities in Series supplementary file

label: Cy5 and Cy3

source_name: NHBEC cells

growth_protocol: A549, H322 and A427 human cell lines were maintained in Dulbecco's modified Eagle's (DMEM) F12 medium (Invitrogen, Carlsbad, CA, USA) supplemented with 10% heat-inactivated fetal bovine serum (PAA Laboratories GmbH, Pasching, Austria). 100 units/ml penicillin, 0.1 mg/ml streptomycin, and 2 mM L-glutamine at 37°C in a 5% CO2, 95% O2 atmosphere. NHBEC were obtained from Clonetics (Brussels, Belgium) and grown in BEGM (Clonetic, Brussels, Belgium).

extract_protocol: DNA was isolated by phenol-chloroform extraction

value: NHBEC


title: OCI-M1_Treated_2


title: OCI-M1_Vehicle_2


title: Bel-7402_DMSO_rep2

source_name: Bel-7402 cell line treated with 0.1%  DMSO for 24h


title: Bel-7402_DMSO_rep1


title: Healthy Tissue - Donor 4

description: Healthy Tissue - Donor 4

value: negative


title: OCI-AML3_Vehicle_3


title: Bel-7402_DMSO_rep3


title: Sig-M5_Treated_2


title: H322

description: SAMPLE 3

scan_protocol: was carried out by Life & Brain GmbH, Bonn

source_name: H322 cells


title: A427

description: SAMPLE 2

source_name: A427 cells

label_protocol: was carried out by Life & Brain GmbH, Bonn


title: OCI-M1_Vehicle_3


title: A549

description: SAMPLE 1

source_name: A549 cells


title: OCI-M1_Treated_1


title: OCI-M1_Treated_3


title: OCI-AML3_Vehicle_2


title: KG-1a_Treated_2


title: NOMO-1_Treated_3


title: OCI-AML3_Vehicle_1


title: KG-1a_Treated_3


title: OCI-AML3_Treated_2


title: OCI-AML3_Treated_3


title: NOMO-1_Vehicle_3


title: KG-1a_Vehicle_2


title: MV-4-11_Vehicle_2


title: MV-4-11_Vehicle_3


title: NOMO-1_Vehicle_2


title: Sig-M5_Treated_1


title: KG-1a_Vehicle_1


title: KG-1a_Treated_1


title: OCI-AML3_Treated_1


title: MV-4-11_Treated_1


title: NOMO-1_Treated_1


title: NOMO-1_Vehicle_1


title: MV-4-11_Vehicle_1


title: Kasumi-1_Vehicle_2


title: NOMO-1_Treated_2


title: Kasumi-1_Vehicle_3


title: MV-4-11_Treated_3


title: WT_rep3

description: RNAs isolated from iWAT of WT mice


title: 1 Non-metastatic Colorectal Cancer

city: Shanghai

first: Yihua

last: Bei

address: 133 Nanchen Road

department: School of Life Science

institute: Shanghai University

description: Paraffin-embedded human non-metastatic colorectal cancer tissues

hyb_protocol: The labeled RNA were hybridized for 20 hr at 55°C on Agilent-038166 Array. After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: After washing, the arrays were scanned with the Agilent Scanner G2505C (Agilent Technologies).

data_processing:
Feature Extraction software (version10.7, Agilent Technologies) was used to analyze array images to get raw data. Next, Genespring software (version 10.0; Agilent Technologies) was employed to finish the basic analysis with the raw data according to scale to mean of all samples.
Differentially expressed miRNAs were identified through fold change as well as P value calculated using t-test.

source_name: Paraffin-embedded non-metastatic colorectal cancer tissues

label_protocol: Total RNA were dephosphorylated, denaturated, and then labeled with Cyanine3-pCp.

extract_protocol: Total RNA were isolated from paraffin-embedded human colorectal cancer tissues using mirVanaTM RNA Isolation Kit (AM1561) according to the manufacturer's instructions.

tag: developmental stage

value: non-metastatic


title: 3 Non-metastatic Colorectal Cancer


title: MV-4-11_Treated_2


title: 2 Non-metastatic Colorectal Cancer


title: 3 Metastatic Colorectal Cancer

description: Paraffin-embedded human metastatic colorectal cancer tissues

source_name: Paraffin-embedded metastatic colorectal cancer tissues

value: metastatic


title: 2 Metastatic Colorectal Cancer


title: 1 Metastatic Colorectal Cancer


title: Kasumi-1_Treated_2


title: Kasumi-1_Treated_1


title: GM-CSF DCs treated with soluble poly I:C  for 8h (with gentamycin) rep2

city: Marseille

first: Philippe

last: Pierre

address: Campus Luminy - case 906

institute: CIML - CNRS - INSERM

description: Gene expression data from GM-CSF DCs treated with soluble poly I:C  for 8h (with gentamycin)

hyb_protocol: Hybridization to chips (Affymetrix GeneChip Mouse Gene 1.0ST arrays) was performed according to the Affymetrix Expression Analysis Technical Manual.

scan_protocol: Image scanning was performed according to the Affymetrix Expression Analysis Technical Manual ?

data_processing: Gene Expression microarray raw data were normalized using limmaGUI software (R/Bioconductor, Boston, MA, USA). The sample table contains the log2 expression level of the samples, after summarization and median normalization (RMA).

source_name: Bone marrow derived GM-CSF DCs

label_protocol: For each sample, 200 ng of total RNA (except for PPE_AD3 for which 130 ng were used) was biotinylated using the Ambion WT Expression Kit (Cat # 4411974) and the Affymetrix GeneChip® WT Terminal Labeling Kit (Cat # 900671) according to Affymetrix recommendations.

growth_protocol: Mouse bone marrow derived GM-CSF DCs were cultured in RPMI supplemented with 5 % heat-inactivated fetal bovine serum, 50µM beta-mercaptoethanol and GM-CSF (for details see 1: Lelouard H, Gatti E, Cappello F, Gresser O, Camosseto V, Pierre P., Nature, 2002 May 9;417(6885):177-82). Cells were differentiated for 6 days before the experiment. When specified, chloramphenicol was added in the medium at 10µg/mL.

extract_protocol: commercial kit

treatment_protocol: Cells were treated during 8h and harvested before lysis. Control and Proteus mirabilis treated DCs were incubated with the bacteriostatic Chloramphenicol to avoid bacterial overgrowth. Guanbenz was used at 50 µM.

tag: genetic background

value: bone marrow

tag: cell type

value: GM-CSF DC

tag: Sex

value: male

tag: age

value: 7 weeks


title: Kasumi-1_Treated_3

tag: tissue

tag: cell line


title: GM-CSF DCs treated with soluble poly I:C  for 8h (with gentamycin) rep3


title: GM-CSF DCs treated with soluble poly I:C  for 8h + guanabenz (with gentamycin) rep1

description: Gene expression data from GM-CSF DCs treated with soluble poly I:C  for 8h + guanabenz (with gentamycin)


title: GM-CSF DCs treated with soluble poly I:C  for 8h + guanabenz (with gentamycin) rep2


title: GM-CSF DCs treated with lipofected poly I:C  for 8h (with gentamycin) rep3

description: Gene expression data from GM-CSF DCs treated with lipofected poly I:C  for 8h (with gentamycin)


title: GM-CSF DCs treated with lipofected poly I:C  for 8h (with gentamycin) rep1


title: GM-CSF DCs treated with lipofected poly I:C  for 8h + guanabenz (with gentamycin) rep2

description: Gene expression data from GM-CSF DCs treated with lipofected poly I:C  for 8h + guanabenz (with gentamycin)


title: GM-CSF DCs treated with soluble poly I:C  for 8h (with gentamycin) rep1


title: GM-CSF DCs treated with soluble poly I:C  for 8h + guanabenz (with gentamycin) rep3


title: GM-CSF DCs treated with lipofected poly I:C  for 8h + guanabenz (with gentamycin) rep1


title: GM-CSF DCs treated with lipofected poly I:C  for 8h + guanabenz (with gentamycin) rep3