title: set35_Adipo_CTL_140425_(MoGene-2_0-st)

description: in-direct co-culture method

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Human 2.0 ST Array at 45°C for 16hour.

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

data_processing: Raw data were extracted automatically in Affymetrix data extraction protocol using the software provided by Affymetrix GeneChip® Command Console® Software (AGCC). After importing CEL files, the data were summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix® Expression Console™ Software (EC).

source_name: 3T3-L1_cocultured with_none (control)

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

tag: cell type

value: adipocyte cell line

value: none (control)


title: P229

status: Public on Mar 09 2017

type: genomic

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

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

department: PEBC

country: Spain

institute: IDIBELL

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

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Genome Studio V2011.2; the 'complete_data.txt' contains unmethylated and methylated signal intensities along with average beta and Pval.

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Prostate Tumor

label_protocol: Standard Illumina labelling protocol

extract_protocol: DNA extracted by Phenol:Chloroform:Isoamylalcohol (Sigma)

tag: disease state

value: Tumor sample

tag: tissue

value: Prostate Tumor

tag: sample type

value: fresh frozen tissue


title: P257


title: P236


title: PCa_A5

type: RNA

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

description: Prostate adenocarcinoma from Caucasian men.

hyb_protocol: Samples were hybridized to oligonucleotide glass arrays with sequences representing probes for 866 human and 89 human viral miRNAs from the Sanger miRBase (release 12.0) (Human miRNA Microarray V3, Agilent Technologies). After 20 hours, slides were washed and scanned.

scan_protocol: Slides were scanned with the dual-laser Agilent scanner G2505B.

data_processing: The LIMMA (LInear Models for Microarray Analysis) package was used to analyze miRNA expression profiles in normal prostates and prostate cancer tissues. Raw intensity values were background subtracted (method = subtract with an offset of 20) and normalized using the quantile method. Duplicated probes were averaged.

molecule: total RNA

source_name: Prostate cancer

label_protocol: MiRNA expression profiling was carried out using the one-colour labelling method. Labelling, hybridization, washing and slide scanning were performed following the manufacturer's protocol (Agilent Technologies). Briefly, 100 ng of total RNA were dephosphorylated and denaturated; then a ligation and labeling step with Cy3 was performed.

extract_protocol: Total RNA was isolated following standard TriReagent protocol (Sigma-Aldrich) and DNase treatment was performed (TURBO DNase-free, Life Technologies). Total RNA quality and quantity were checked by means of Bioanalyzer (Agilent Technologies) and NanoDrop ND-1000 Spectrophotometer (Thermo Scientific), respectively.

value: prostate adenocarcinoma

tag: gender

value: male

tag: population

value: Caucasian


title: PCa_AA65


title: PCa_A3


title: genomic DNA from Adjacent Normal 5

city: Kolkata

first: Raghunath

last: Chatterjee

state: WB

address: 203 BT Road, HGU, Indian Statistical Institute

department: Human Genetics Unit

country: India

institute: Indian Statistical institute

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450Beadchip using standard Illumina protocol

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

data_processing: IDAT files were processed using RnBeads for data processing. We used SWAN normailzation. After normalization and quality control checking, the signal intesities along with the detection P-values are calculated for each CpG probes. Normalized average beta values are calculated using RnBead software implemented in R software.

label: Cy5 and Cy3

source_name: Adjacent Normal

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from OSCC samples using Qiagen Tissue & Blood DNA Kit according to standard instructions

tag: subject status

value: oral squamous cell carcinoma (OSCC) patient

value: Female

tag: tissue type

value: Adjacent Normal

value: Normal

tag: hpv status


title: P251


title: PCa_A2


title: m_SET33_231_(MoGene-2_0-st)

city: Seoul

first: Hyeong-Gon

last: Moon

address: 101, Daehak-ro Jongno-gu

department: Surgery

country: South Korea

institute: Seoul National University Hospital

description: in-direct co-culture method

label: biotin

organism: Mus musculus

source_name: 3T3-L1_cocultured with_MDA-MB-231

growth_protocol: 3T3-L1 cells were cultured in DMEM supplemented with 10% bovine serum at 37°C in 5% CO2. 3T3-L1 cells were grown to confluency and induced with adipogenesis media (DMEM with 10% FBS, 10μg/ml insulin, 0.5mM IBMX and 1μM dexamethasone). After 2 days, the media was changed with DMEM with 10% FBS and 10μg/ml insulin and maintained for 4 days. After 8 days of differentiation with DMEM with 10% FBS, the cells were used for further experiments.

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

treatment_protocol: 3T3-L1 cells were cultured in a indirect co-culture wells with breast cancer cells

tag: cell line

tag: cocultured with


title: Normal_T114

description: Peripheral region of the prostate from Caucasian men without PCa.

source_name: Normal prostate

value: normal prostate


title: m_SET33_CTL_(MoGene-2_0-st)

description: in-direct co-culture method


title: Normal_T218


title: m_SET36_7_(MoGene-2_0-st)

description: in-direct co-culture method

source_name: 3T3-L1_cocultured with_MCF7


title: set35_Adipo_231_140425_(MoGene-2_0-st)

description: in-direct co-culture method


title: m_SET36_231_(MoGene-2_0-st)

description: in-direct co-culture method


title: genomic DNA from OSCC lesion4

source_name: Disease OSCC

value: Male

value: OSCC lesion

value: Disease


title: P223


title: P227


title: set35_Adipo_7_140425_(MoGene-2_0-st)

description: in-direct co-culture method


title: P238


title: Normal_T188


title: Normal_T319


title: Normal_T337


title: m_SET36_CTL_(MoGene-2_0-st)

description: in-direct co-culture method


title: m_SET33_7_(MoGene-2_0-st)

description: in-direct co-culture method


title: P228


title: P268


title: P270


title: P263


title: Normal_CG04mag05


title: P262


title: P266


title: Normal_T229


title: Normal_CM17mag05


title: Normal_RF128apr05


title: Normal_TL28apr05


title: P209


title: Normal_T190


title: Normal_T202


title: Normal_T189


title: Normal_T66


title: P245


title: P230


title: Normal_VG25mag05


title: P265


title: Normal_T323


title: Normal_T10


title: Normal_T63


title: Normal_FI01giu05


title: P249


title: Normal_BA27apr05


title: Normal_GA25mag05


title: PrEc_Ctrl_rep2

description: Prostate Epithelial Cells

hyb_protocol: Samples were hybridized to oligonucleotide glass arrays with sequences representing probes for 866 human and 89 human viral miRNAs from the Sanger miRBase (release 12.0) (Human miRNA Microarray V3, Agilent Technologies). After 20 hours slides were washed and scanned.

scan_protocol: Slides were scanned with the dual-laser Agilent scanner G2505B

data_processing: The LIMMA (LInear Models for Microarray Analysis) package was used to identify differentially expressed miRNAs in PrEc ESE3 knock-down cells versus control cells. Raw intensity values normalized using the quantile method. Duplicated probes were averaged.

source_name: Control PrEc cell lines

label_protocol: MiRNA expression profiling was carried out using the one-colour labelling method. Labelling, hybridization, washing and slide scanning were performed following the manufacturers protocol (Agilent Technologies). Briefly, 100 ng of totRNA were dephosphorylated and denaturated; then a ligation and labeling step with Cy3 was performed.

growth_protocol: PrEc with stable ESE3 knockdown (ESE3-KD) were maintained in PrEC growth medium (PrEGM;Cambrex, Lonza Group Ltd.) supplemented with G418 (200µg/ml).

extract_protocol: RNA was extracted with Trizol

value: PrEc

tag: modification

value: control


title: PrEc_ESE3-KD_rep2

description: Prostate Epithelial Cells

source_name: PrEc cell lines with ESE3 knock down

value: ESE3 knock down


title: P269

value: Tumor sample


title: P242

value: Prostate Tumor


title: P264

value: fresh frozen tissue


title: CP8

source_name: Normal Prostate

value: Morphologically normal tissue

value: Normal Prostate


title: P254


title: P241


title: CP5


title: CP7


title: CP1


title: PrEc_ESE3-KD_rep1

description: Prostate Epithelial Cells


title: PrEc_Ctrl_rep1

description: Prostate Epithelial Cells


title: CP6


title: TB190

source_name: Bladder Tumor

value: Bladder Tumor


title: P252


title: TB212


title: TB188


title: TB207


title: TB209


title: TB192


title: TB206


title: TB205


title: TB186


title: RWPE-1_Pre-miR-424_vs_Pre-Ctrl_N

description: RWPE-1 with pre-miR-424 vs. control, normal labelling.

hyb_protocol: Equal amounts of differentially labeled specimens from sample and reference were put together, fragmented and hybridized to oligonucleotide glass arrays with sequences representing 27,958 Entrez Gene RNAs and 7,419 lincRNAs (Agilent-028004 Human Gene Expression 8x60K Microarray, Agilent Technologies). All steps were performed using the In Situ Hybridization kit-plus (Agilent Technologies) and following the 60-mer oligo microarray processing protocol (Agilent Technologies). Then, slides were washed following the Agilent wash procedure. For each sample, a dye-swap replicate was performed.

scan_protocol: Slides were scanned with the dual-laser Agilent scanner G2505C.

data_processing: The LIMMA (LInear Models for Microarray Analysis) package was used to analyze gene expression profiles of RWPE-1 following pre-miR-424 transfection versus control. Raw intensity values were background subtracted (method = normexp, offset = 50) and normalized using the loess method, for the within array normalizaton, and Aquantile, for the between array normalization. Duplicated probes were averaged.

source_name: RWPE-1 transfected with pre-miR-424

label_protocol: RNA was amplified by means of the Amino Allyl MessageAmp II aRNA Kit (Life Technologies) to obtain amino allyl antisense RNA (aaRNA) following the method developed by Eberwine and coworkers. Briefly: mRNA was reverse transcribed in cDNA single strand; after the second strand synthesis, cDNA was in vitro transcribed in aaRNA including amino allyl modified nucleotides (aaUTP). Both dsDNA and aaRNA underwent a purification step using columns provided with the kit. mRNA amplification was checked by means of Bioanalyzer (Agilent Technologies) and NanoDrop ND-1000 Spectrophotometer (Thermo Scientific). Labeling was performed using NHS ester Cy3 or Cy5 dyes (Amersham Biosciences) able to react with the modified RNA. Labeling efficiency and labeled mRNA quantity were checked by means of NanoDrop ND-1000 Spectrophotometer (Thermo Scientific).

growth_protocol: RWPE-1 were maintained in keratinocyte serum-free growth medium (KSF; Lonza) with specific supplements.

extract_protocol: RNA was extracted by Direct-zol RNA Mini-prep kit (Zymo Research).

treatment_protocol: RWPE-1 were transfected with 30nM of Pre-miR-424 or Negative control #1.

value: noncancerous prostate epithelial cell line

tag: transfection

source_name: RWPE-1 transfected with pre-control

value: PRE-CTR


title: RWPE-1_Pre-miR-424_vs_Pre-Ctrl_DS

description: RWPE-1 with pre-miR-424 vs. control, dye-swap labelling.


title: TB196


title: TB211


title: TB197


title: TB204


title: TB189


title: DPN6

city: Ningbo

first: Jin

last: Xu

address: 818 Fenghua Road

country: China

institute: Ningbo University

hyb_protocol: 0.1 µg Cy5-labeled aRNA of the respective sample was fragmented and hybridized onto HlncOA 1.0 using Phalanx OneArray hybridization kit (Phalanx Biotech Group). Hybridization was performed for 17h, rotating at a speed of 10rpm at 65℃ in an Agilent hybridization oven (G2545A). After hybridization, microarrays were washed 1 minute at room temperature with Wash Buffer 1 and 1 minute with 37℃Wash buffer 2.

scan_protocol: HlncOA 1.0arrays were scanned by Agilent Microarray Scanner( G2505C ) HD_1X color protocol （Dye channel: R ; Scan resolution : 2 um; Tiff: 20-bit; Red PMT gain: 100%; XDR: No）and quantify the fluoresence intensity.

data_processing: Data processing was performed and calculated by R language (v3.3.0). The probes will filter out control probes and normalized by median scaling method between all samples. Pair-wise comparisons between samples were calculated by Bioconductor limma package and presented by log2 fold change and p-value.

source_name: Diabetic peripheral neuropathy

label_protocol: 0.5 µg of total RNA was reverse-transcribed and amplified using Onearray Amino Allyl aRNA Amplification Kit  (Phalanx Biotech Group).  Indirect labeled the aa-UTP by NHS-Cy5 (AAT Bioquest ). Dye incorporation and aRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using Trizol Reagent (Thermo Fisher Scientific) following the manufacture`s instructions. RNA quality was assessed by spectrophotometry(NanoDrop, ND1000) and gel electrophoresis. To be considered as high-quality, the RNA had to have the result of A260/A280≧1.8, A260/A230≧1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

value: Diabetic peripheral neuropathy


title: TB200


title: TB203


title: TB194


title: DPN5


title: TB199


title: RT132

source_name: Renal Tumor

value: Renal Tumor


title: NB5

source_name: Normal Bladder

value: Normal Bladder


title: TB202


title: TB208


title: TB198


title: RT151


title: NB4


title: TB193


title: DPN2


title: TB191


title: NB8


title: NB9


title: DPN4


title: TB201


title: RT144


title: TB195


title: RT155


title: DPN3


title: RT160


title: CN5

source_name: healthy

value: healthy


title: CN6


title: NB6


title: RT133


title: RT150


title: CN3


title: DM6

source_name: diabetes mellitus

value: diabetes mellitus


title: CN1


title: DPN1


title: RT143


title: CN4


title: RT128


title: DM4


title: RT157


title: DM5


title: RT161


title: PDGFRb-TK late pericyte ablation control

city: Houston

first: Valerie

last: LeBleu

state: TX

address: 1881 East Road

country: USA

institute: MDACC

description:
WT Late
GCV injected

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: GenomeStudio

source_name: 4T1 breast tumor

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

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

tag: treatment

value: late pericyte ablation control

tag: pdgfrb tk

value: Positive

value: 4T1 breast tumor

tag: genotype

value: PDGFRb-TK


title: RT152

value: Tumor sample


title: DM3


title: DM2


title: RM-HNSCC_40

status: Public on Mar 08 2017

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Agilent hybridization protocol

scan_protocol: StandardAgilent scanning protocol; raw data were generated using the Feature Extraction Software v10.7.3.1 (Agilent Technologies)

data_processing: The data were processed and quantile normalized using AgMicroRNA R package (Lopez-Romero, BMC Genomics 2011; 12:64). A filtering step was applied and the final matrix contains 614 out of 3799 features. Based on gIsGeneDetected information provided by the Agilent's Feature Extraction software, miRNAs detected in at least 25% of samples were selected.

source_name: tumor

label_protocol: RNA from each sample was labeled according to the manufacturer's recommendations.

extract_protocol: RNA was extracted with QIAGEN FFPE RNeasy mini kit in accordance with manufacturer's protocol.

value: recurrent/metastatic (RM) HNSCC

tag: pfs following cetuximab-ct treatment


title: PDGFRb-TK early pericyte ablation

description:
PDGFRB-TK Early
GCV injected

value: early pericyte ablation


title: PDGFRb-TK early pericyte ablation control

description:
WT Early
GCV injected

value: early pericyte ablation control


title: PDGFRb-TK late pericyte ablation

description:
PDGFRB-TK Late
GCV injected

value: late pericyte ablation


title: RM-HNSCC_37


title: RT137

value: fresh frozen tissue


title: RT164


title: RM-HNSCC_36


title: RM-HNSCC_33


title: RM-HNSCC_30


title: RM-HNSCC_29


title: RM-HNSCC_28


title: NK5

source_name: Normal Kidney

value: Morphologically normal tissue

value: Normal Kidney


title: RM-HNSCC_32


title: RM-HNSCC_27


title: RM-HNSCC_26


title: RM-HNSCC_38


title: RM-HNSCC_25


title: RM-HNSCC_24


title: RT159


title: CN2


title: RT163


title: RT154


title: RM-HNSCC_31


title: RM-HNSCC_22


title: RM-HNSCC_21


title: RM-HNSCC_19


title: NK7


title: NK2


title: RM-HNSCC_20


title: NK8


title: RM-HNSCC_16


title: NK1


title: RM-HNSCC_15


title: RM-HNSCC_14


title: RM-HNSCC_39


title: RM-HNSCC_13


title: RM-HNSCC_12


title: RM-HNSCC_11


title: RM-HNSCC_09


title: RM-HNSCC_10


title: RM-HNSCC_17


title: RM-HNSCC_07


title: RM-HNSCC_08


title: RM-HNSCC_05


title: RM-HNSCC_06


title: DM1


title: RM-HNSCC_03


title: RM-HNSCC_02


title: RM-HNSCC_04


title: RM-HNSCC_01


title: middle_ripening-control-day14-3

city: Potsdam

first: Christian

last: Kappel

address: Karl-Liebknecht-Str. 24-25, Haus 26

department: Institut für Biochemie und Biologie

country: Germany

institute: Universität Potsdam

hyb_protocol: Labelling, hybridization and scanning were done by Genotoul Biopuces plateform (Toulouse, France).

data_processing: Data were RMA normalized using R/Bioconductor.

organism: Vitis vinifera

source_name: berry

growth_protocol: Fruiting cuttings of Vitis vinifera L. Cv Cabernet Sauvignon (Ollat and Gaudillère, 1998) were grown in a greenhouse, in pots of 0.5 L containing a mixture of perlite, sand and vermiculite (1:1:1). A drip irrigation system supplied water and a complete nutrient solution to the roots about five times a day all along the experiment, avoiding any water or nutrient shortage. All fruiting cuttings bore only one single cluster and lateral shoots were removed as soon as they appeared during growth. Before the experiment, the tip of each shoot was removed as soon as 16 leaves per plant were produced to maintain about the same leaf area in all plants and a high leaf to fruit ratio (Ollat and Gaudillère, 1998). Therefore, all bunches were assumed to experience neither water nor assimilate limitation. In addition, the fruit cuttings were selected on the basis of similar vegetative growth and vigour as well as size and compactness of bunches.

extract_protocol: Berries collected from Cabernet Sauvignon fruit cuttings were quickly frozen in liquid nitrogen, ground to a fine powder with a Dangoumau blender, and stored at –80°C prior to use. Total RNA from deseeded berries was extracted according to Lecourieux et al., 2010. RNA isolation was followed by Dnase I treatment. The purity and quantity of the RNA were determined using a Nanodrop 1000 spectrophotometer (Thermo Scientific). RNA integrity was determined using a Bioanalyzer 2100 (Agilent) with RNA 6000 Nano Kit I (Agilent).  For each sample, reverse transcription was performed from 2 µg of purified RNA using the Moloney murine leukemia virus reverse transcriptase (Promega) according to the manufacturer’s instructions. The cDNA obtained was diluted (1:10) in distilled water.

treatment_protocol: Both control and heat stress treatments were applied for 14 d periods, at 3 phenological stages, namely middle-green (30 days after fruit set), veraison (50% of berries turning to a visible red color) and middle-ripening (80 days after fruit set). Total soluble solids (TSS) content in berries was determined before, during and after each treatment using a digital refractometer (Atago, Tokyo). Before treatments, middle-green, veraison and middle-ripening berries displayed a TSS of 3.9 +/- 0.3, 8.9 +/- 1.4 and 14.1 +/- 1.1 °Bx, respectively (mean of replicates +/- SD). Three sets of 25 fruiting cuttings were used as controls (GC (Green Control), VC (Véraison Control) and RC (Ripening Control)); the temperature of their bunch closely followed greenhouse ambient air temperature. Three sets of 25 bunches from other fruiting cuttings were submitted to heat stress : GHS (Green Heat Stress), VHS (Véraison Heat Stress) and RHS (Ripening Heat Stress). The clusters were submitted to an elevated temperature airflow produced by fan heaters (common domestic models, used at 1000 W). Only bunches were heated since shoots, leaves and roots were all protected from the heated airflow by extruded polystyrene foam deflectors. Air heating was applied repeatedly during 14 d, from 7:00 a.m. To 7:00 p.m. Every day to mimic usual diurnal temperature course of exposed berries. To avoid any differential effect linked to airflow and possible mechanical stress, simple fan blowers were used to create a continuous airflow around the control clusters during 14 d, from 7:00 a.m. To 7:00 p.m. Every day. The temperatures in control and heated berries (ten replicates for each treatment) were monitored continuously by copper-constantan thermocouples inserted into the berries, connected to a Campbell datalogger (Campbell Scientific). After treatments, each set of fruiting cuttings was replaced in control conditions until harvest. In order to analyse short- and long-term responses for each treatment, 3 control and 3 heat-stressed berries per cluster (25 clusters per condition) were sampled in the evening (7:00 p.m.) at 3 different time points after treatment (1 d, 7 d, and 14 d), immediately frozen in liquid nitrogen and stored at -80°C. To obtain 3 experimental replicates, each of the 3 berries collected per cluster were used to constitute 3 groups of 25 berries for each condition.

tag: cultivar

value: Cabernet Sauvignon

value: berry

tag: developmental stage

value: middle-ripening

value: control

tag: treatment duration

value: 14 days


title: middle_ripening-HS-day14-3

scan_protocol: Labelling, hybridization and scanning were done by Genotoul Biopuces plateform (Toulouse, France).

tag: tissue

value: heat stress


title: middle_ripening-control-day14-2

label_protocol: Labelling, hybridization and scanning were done by Genotoul Biopuces plateform (Toulouse, France).


title: middle_ripening-HS-day14-1


title: veraison-HS-day14-3

value: veraison


title: middle_ripening-control-day14-1


title: veraison-HS-day14-2


title: middle_ripening-HS-day14-2


title: NK3

tag: disease state

tag: sample type


title: RM-HNSCC_35


title: veraison-control-day14-1


title: middle_ripening-HS-day7-1

value: 7 days


title: middle_ripening-HS-day7-2


title: green-HS-day14-3

value: middle-green


title: veraison-control-day14-3


title: green-HS-day14-2


title: green-control-day14-2


title: veraison-control-day14-2


title: veraison-HS-day14-1


title: green-HS-day14-1


title: middle_ripening-HS-day7-3


title: RM-HNSCC_18


title: green-control-day14-3


title: middle_ripening-control-day7-2


title: middle_ripening-control-day7-1


title: middle_ripening-HS-day1-3

value: 1 day


title: middle_ripening-HS-day1-1


title: middle_ripening-HS-day1-2


title: RM-HNSCC_34

value: recurrent/metastatic (RM) HNSCC


title: middle_ripening-control-day1-3


title: middle_ripening-control-day1-1


title: veraison-HS-day7-3


title: veraison-HS-day7-1


title: veraison-HS-day7-2


title: veraison-control-day7-3


title: middle_ripening-control-day7-3


title: RM-HNSCC_23


title: middle_ripening-control-day1-2


title: green-HS-day7-2


title: veraison-HS-day1-3


title: veraison-control-day7-1


title: green-control-day7-3


title: green-HS-day7-3


title: veraison-control-day7-2


title: green-HS-day7-1


title: veraison-HS-day1-2


title: green-control-day7-2


title: veraison-control-day1-2


title: veraison-control-day1-3


title: green-control-day14-1


title: veraison-HS-day1-1


title: veraison-control-day1-1


title: green-HS-day1-3


title: green-control-day7-1


title: green-HS-day1-2


title: green-control-day1-2


title: Normal_GB08giu05_DS

description: Peripheral region of the prostate from Caucasian men without PCa vs Prostate Commercial Reference (dye-swap labelling)

hyb_protocol: Equal amounts of differentially labeled specimens from sample and reference were put together, fragmented and hybridized to oligonucleotide glass arrays with sequences representing 27,958 Entrez Gene RNAs and 7,419 lincRNAs (Human Gene Expression 8x60K Microarray, Agilent Technologies). All steps were performed using the In Situ Hybridization kit-plus (Agilent Technologies) and following the 60-mer oligo microarray processing protocol (Agilent Technologies). Then, slides were washed following the Agilent wash procedure. For each sample, a dye-swap replicate was performed.

scan_protocol: Slides were scanned with the dual-laser Agilent scanner G2505C

data_processing: The LIMMA (LInear Models for Microarray Analysis) package was used to analyze gene expression profiles of normal prostates and prostate cancer tissues. Raw intensity values were background subtracted (method = normexp, offset = 50) and normalized using the loess method, for the within array normalizaton, and Aquantile, for the between array normalization. Duplicated probes were averaged. Then, Cy3 and Cy5 channels were separated using the separate channel analysis of two-color data, available within the Limma package.

source_name: Prostate Commercial Reference

label_protocol: RNA isolated from tissues and from a commercial pool of RNA from organ donor healthy prostates (Becton Dickinson) was amplified by means of the Amino Allyl MessageAmp aRNA Kit (Life Technologies) to obtain amino allyl antisense RNA (aaRNA) following the method developed by Eberwine and coworkers. Briefly: mRNA was reverse transcribed in cDNA single strand; after the second strand synthesis, cDNA was in vitro transcribed in aaRNA including amino allyl modified nucleotides (aaUTP). Both dsDNA and aaRNA underwent a purification step using columns provided with the kit. Labeling was performed using NHS ester Cy3 or Cy5 dyes (Amersham Biosciences) able to react with the modified RNA. Labeling efficiency and mRNA quantity were checked by means of NanoDrop ND-1000 Spectrophotometer (Thermo Scientific).

extract_protocol: Tissue and biopsy samples were homogenized (Ultra – TurraxT8, Ika – Werke) and totRNA was isolated following TriReagent (Sigma Aldrich) protocol. TotRNA quality and quantity were checked by means of Agilent 2100 bioanalyzer (Agilent Technologies) and NanoDrop ND-1000 Spectrophotometer (Thermo Scientific) respectively.

tag: reference

tag: sample id

value: Normal Prostate


title: Normal_PS26mag05_N

description: Peripheral region of the prostate from Caucasian men without PCa vs Prostate Commercial Reference (normal labelling)

value: a commercial pool of RNA from organ donor healthy prostates (Becton Dickinson)


title: Normal_DG08giu05_DS


title: green-HS-day1-1


title: Normal_CD15giu05_N


title: Normal_T218_N


title: Normal_T114_N


title: green-control-day1-1


title: Normal_MG16giu05_DS


title: green-control-day1-3


title: Normal_GB08giu05_N


title: Normal_CD15giu05_DS


title: Normal_T114_DS


title: Normal_MG16giu05_N


title: Normal_DG08giu05_N


title: Normal_T218_DS


title: Normal_T138_DS


title: Normal_T63_DS


title: Normal_PS26mag05_DS


title: Normal_T191_DS


title: Normal_T188_N


title: Normal_T188_DS


title: Normal_T191_N


title: Normal_T63_N


title: Normal_T190_N


title: Normal_T229_N


title: Normal_T66_DS


title: Normal_T229_DS


title: Normal_T190_DS


title: Normal_T66_N


title: Normal_T138_N


title: PCa_D40_DS

description: Prostate adenocarcinoma from Caucasian men vs Prostate Commercial Reference (dye-swap labelling)

source_name: Prostate Cancer

value: Prostate adenocarcinoma


title: PCa_A9_DS


title: PCa_F51_N

description: Prostate adenocarcinoma from Caucasian men vs Prostate Commercial Reference (normal labelling)


title: PCa_D40_N


title: PCa_L16_DS


title: PCa_CC8_DS


title: PCa_F51_DS


title: PCa_CC8_N


title: PCa_CC35_N


title: PCa_CC91_DS


title: PCa_A2_DS


title: PCa_CC91_N


title: PCa_CC87_DS


title: PCa_L16_N


title: PCa_A2_N


title: PCa_CC35_DS


title: PCa_A9_N


title: PCa_D37_DS


title: PCa_D37_N


title: PCa_CC83_DS


title: PCa_I81_DS


title: PCa_CC75_N


title: PCa_CC75_DS


title: PCa_CC62_DS


title: PCa_I81_N


title: PCa_CC41_DS


title: PCa_CC87_N


title: PCa_CC62_N


title: PCa_CC83_N


title: PCa_CC17_N


title: PCa_Q70_N


title: PCa_Q70_DS


title: PCa_CC41_N


title: PCa_CC17_DS


title: PCa_P57_DS


title: PCa_Z55_N


title: PCa_CC3_DS


title: PCa_CC3_N


title: PCa_Z55_DS


title: PCa_P57_N


title: PCa_C25_N


title: PCa_A3_N


title: PCa_C25_DS


title: Inorganic arsenic-transformed (iAs-T) Replicate 1 [splice level]

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

description: Inorganic arsenic-transformed (iAs-T)

hyb_protocol: Samples were hybridized with GeneChip Human Transcriptome 2.0 Arrays (Affymetrix).

scan_protocol: Array scanning was performed at the University of Kentucky Microarray Core Facility according to the manufacturer's instructions (Affymetrix).

data_processing: CEL files were RMA summarized and processed using the Affymetrix Expression Console software version 1.4.1.46. Probes were RMA normalized for analysis at the alternative splice level.

source_name: iAs-transformed BEAS-2B cells

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Cell cultures were incubated at 37 degrees with humidified air and 5% CO2. Cells were harvested after each treatment. Cells were grown ensuring that 95% of the cells were viable. Harvested cells were centrifuged for five minutes at 200 X g.

extract_protocol: RNA was extracted using Qiagen RNeasy kit according to manufacturer's instructions.

treatment_protocol: Cells were treated with 0.5 uM Sodium Arsenite for 56 days until transformation.

tag: cell type

value: lung epithelial cell line

value: inorganic sodium arsenite


title: PCa_H75_N


title: PCa_W28_DS


title: PCa_W28_N


title: PCa_P60_DS


title: PCa_P60_N


title: Inorganic arsenic-transformed (iAs-T) Replicate 2 [splice level]

description: Inorganic arsenic-transformed (iAs-T)

tag: cell line


title: Normal (NT) Replicate 2 [splice level]

description: Normal (NT)

source_name: Normal BEAS-2B cells


title: Normal (NT) Replicate 1 [splice level]

description: Normal (NT)


title: PCa_CRYO_N

value: CRYO


title: PCa_AA79_N


title: PCa_L12_N


title: PCa_AA88_N


title: PCa_G65_DS


title: PCa_CRYO_DS


title: PCa_AA88_DS


title: PCa_Z56_DS


title: PCa_K6_N


title: PCa_G65_N


title: PCa_Z59_DS


title: PCa_BB36_N


title: PCa_I88_DS


title: PCa_I88_N


title: PCa_H75_DS


title: PCa_BB36_DS


title: PCa_AA79_DS


title: PCa_Z59_N


title: PCa_Z56_N


title: PCa_Y48_N


title: PCa_Y48_DS


title: PCa_K6_DS


title: PCa_V18_DS


title: PCa_M26_N


title: PCa_W25_DS


title: PCa_V18_N


title: PCa_W25_N


title: PCa_G70_DS


title: PCa_C27_DS


title: PCa_G70_N


title: PCa_BB5_DS


title: PCa_M26_DS


title: PCa_BB5_N


title: PCa_AA65_N


title: PCa_B12_DS


title: PCa_AA69_N


title: PCa_C27_N


title: PCa_B17_N


title: PCa_B17_DS


title: PCa_AA65_DS


title: PCa_A3_DS


title: PCa_X40_N


title: PCa_X40_DS


title: PCa_P55_N


title: PCa_Y44_DS


title: PCa_AA69_DS


title: PCa_P55_DS


title: PCa_Y44_N


title: PCa_B12_N


title: PR-3

city: Tokyo

first: zhu

last: yun

address: takanawa 4-21-12

country: Japan

institute: scinet company

hyb_protocol: The arrays were hybridized at 65℃ overnight

scan_protocol: The arrays were scaned using FLA-8000 (FUJIFILM).

data_processing: The signal intensities were quantified using ArrayGauge software (FUJIFILM). The ratio of the signal intensity for E2- or each lignan-treated sample to that for the control sample was caculated for each gene, and then normalized using control genes .

source_name: breast cancer cells

label_protocol: Five mg of total RNA was reverse-transcribed and labeled with cy3 (GE Healthcare) using SuperScript Indirect cDNA labeling system (Invitrogen).

extract_protocol: Total RNA was extracted using RNeasy plus mini kit (QIAGEN).

value: breast cancer cells

tag: lignan

value: pinoresinol


title: PR-2

value: breast cancer


title: PR-1


title: MR-2

value: matairesinol


title: EL-3

value: enterolactone


title: EL-2


title: MR-3


title: PCa_Y50_DS


title: PCa_B11_DS


title: PCa_B11_N


title: PCa_A5_N


title: MR-1


title: PCa_A5_DS


title: EL-1


title: PCa_AA97_N


title: PCa_AA90_DS


title: PCa_Y50_N


title: ED-1

value: enterodiol


title: SE-3

value: sesamin


title: PCa_AA97_DS


title: PCa_AA90_N


title: SE-2


title: PCa_L12_DS


title: Cont-3

data_processing: The signal intensities were quantified using ArrayGauge software (FUJIFILM). The ratio of the signal intensity for E2- or each capsainoid-treated sample to that for the control sample was caculated for each gene, and then normalized using control genes. The log2 values of the normalized ratios data: GSE64155_CAP_array_ratio.txt

tag: agent

value: control


title: ED-2


title: Cont-1


title: ED-3


title: Cont-2


title: FB, biological rep1

city: Taipei

first: pei-shan

last: Hou

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

country: Taiwan

institute: Institute of Anatomy and Cell Biology, School of Medicine, National Yang-Ming Chiao-Tung University.

hyb_protocol: following the standard procedure with GeneChip® Hybridization Oven 640

scan_protocol: following the standard procedure

data_processing:
following the standard procedure with Affymetrix GeneChip® Scanner 3000
Raw data were normalized independently for each experiment using Robust Multichip Average. Comparisons were performed with GeneSpring software.

source_name: FB

label_protocol: following the standard procedure

growth_protocol: cells were cultured in NPC medium

extract_protocol: RNA were extracted following standard procedure in QIAquick kit.

treatment_protocol: no specific treatment

value: fibroblast


title: Reanalysis_H484

city: Aalborg

first: Julie

middle: Støve

last: Bødker

address: Sdr. Skovvej 15

department: Department of Heamatology

country: Denmark

institute: Aalborg University Hospital

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1358993

hyb_protocol: Included in the label protocol, see above.

scan_protocol: Gene Chips were scanned using the Affymetrix GeneChip scanner 3000 7G

data_processing: Data were analyzed using R version 3.3.1  and several R and Bioconductor packages. The .CEL-files were pre-processed using the Robust Multichip Average procedure (RMA) as implemented in the just.rma function from the Bioconductor package affy. All RMA-normalised arrays passed the statistical quality control provided by the function arrayQualityMetrics in the R-package arrayQualityMetrics.

source_name: Diffuse Large B-Cell Lymphoma

label_protocol: Biotinylated cRNA were prepared using the GeneChip 3' IVT Express Kit (#P/N901229, Affymetrix) from 100 ng total RNA using manual P/N702646 Rev.4.

growth_protocol: Not applicable

extract_protocol: Total RNA was purified from frozen diagnostic DLBCLs by homogenizing the sample in Trizol and incubating for 5 minutes at RT. 200µl chloroform was added and incubated 2 minutes at RT, the mixture was centrifuged at 12,000 g for 10 minutes at 4°C. The aqueous phase was transferred to a new tube and 100 % ethanol added in 1.25X the volume. Mix well and transfer to mirVANA columns (#1561, Ambion) and follow the manufacturer’s instruction from this point.

treatment_protocol: Diagnostic samples of diffuse large B-cell lymphoma (DLBCL), of Follicular Lymphoma (FL) and of one transformed Follicular Lymphoma (tFL) (from our case patient). A relapse sample from the tFL patient.

value: Diffuse Large B-Cell Lymphoma


title: Reanalysis_H452

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1359024


title: Reanalysis_H479

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1358991


title: Reanalysis_H454

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1359025


title: SOX1+NP

value: neural progenitor


title: FB, biological rep2


title: Reanalysis_H457

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1359027


title: Reanalysis_H450

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1359022


title: Reanalysis_H473

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1358990


title: Reanalysis_H451

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1359023


title: Reanalysis_H449

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1359021


title: Reanalysis_H456

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1359026


title: Reanalysis_H446

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1359018


title: Reanalysis_H45

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1358987


title: Reanalysis_H438

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1359011


title: Reanalysis_H440

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1359013


title: Reanalysis_H441

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1359014


title: Reanalysis_H437

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1359010


title: Reanalysis_H442

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1359015


title: Reanalysis_H443

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1359016


title: Reanalysis_H447

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1359019


title: Reanalysis_H448

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1359020


title: Reanalysis_H380

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1358981


title: Reanalysis_H444

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1359017


title: Reanalysis_H378

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1358979


title: HPC90

city: London

first: Timothy

last: Powell

address: 16 De Crespigny Park

department: Social, Genetic & Developmental Psychiatry

country: United Kingdom

institute: King's College London

data_processing: Data were backgroundcorrected, transformed (log2) and normalised (quantile) in Lumi (R package)

label_protocol: Standard Illumina TotalPrep kit amplification and labeling protocol

growth_protocol: The multipotent, human hippocampal progenitor cell line HPC0A07/03C (provided by ReNeuron, Surrey, UK) was used for all experiments, as described previously (Anacker et al., 2011). ReNeuron’s HPC0A07/03C cells were obtained from a 12-week old foetus and immortalised with c-mycER technology. In the presence of growth factors (FGF2 and EGF) and 4-OHT, progenitors cells proliferate indefinitely, on removal of growth factors cells differentiate into neurons and astrocytes. Cells were grown in Dulbecco’s Modified Eagle’s Media/F12 (DMEM:F12, Invitrogen, Paisley, UK) supplemented with 0.03% human albumin (Baxter Healthcare, Compton, UK), 100 μg/mL human apo-transferrin (Sigma, St Louis, MO, USA), 16.2 μg/mL human putrescine DiHCl (Sigma), 5 μg/mL human insulin (Sigma), 60 ng/mL progesterone (Sigma), 2 mM l-glutamine (Sigma) and 40 ng/mL sodium selenite (Sigma), 10 ng/mL human bFGF (Pepro Tech EC Ltd, London, UK), 20 ng/mL human EGF (Pepro Tech EC Ltd) and 100 nM 4-OHT (Sigma). The cell line underwent routine checking for mycoplasma contamination every 6 weeks. All cells were grown at 37°C, 5% CO2, and in a humidified atmosphere. Within these sets of experiments each ‘biological replicate’ represents a subculture of cells obtained from a different passage.

extract_protocol: Trireagent (Sigma) following the standard protocol, with an additional ethanol precipitation step

treatment_protocol: Stage 1: Cells were seeded on 6-well plates for 24 hours. Stage 2: Proliferating media containing antidepressant drug doses were given to cells for 48 hours. Stage 3: Media was aspirated and RNA was isolated (proliferating conditions); Media was aspirated and replaced with differentiating media containing corresponding doses of antidepressants and left to inclubate for 7 days (Differentiating conditions). Stage 4: After 7-day treatment, media was aspirated and RNA isolated (Differentiating conditions only).

tag: drug

value: Escitalopram

tag: dose

tag: Stage

value: differentiating


title: HPC88


title: HPC92

value: proliferating


title: Reanalysis_H345

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1358974


title: HPC95


title: Reanalysis_H439

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1359012


title: HPC91


title: Reanalysis_H344

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1358973


title: Reanalysis_H333

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1358971


title: HPC93


title: Reanalysis_H371

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1358978


title: HPC89


title: HPC87

value: Nortriptyline


title: HPC82


title: Reanalysis_H297

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1358961


title: Reanalysis_H330

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1358970


title: HPC86


title: HPC83


title: HPC85


title: HPC79


title: HPC94


title: HPC81


title: HPC77


title: Reanalysis_H300

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1358964


title: HPC84


title: Reanalysis_H321

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1358968


title: Reanalysis_H318

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1358967


title: HPC80


title: HPC78


title: HPC76


title: Reanalysis_H296

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1358960


title: HPC75


title: Reanalysis_H295

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1358959


title: SE-1


title: HPC73


title: HPC74


title: Reanalysis_H285

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1358957


title: HPC69


title: HPC72


title: HPC70


title: HPC61


title: HPC71


title: HPC67


title: Reanalysis_H22

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1358951


title: HPC65


title: HPC64


title: Reanalysis_H12

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1358942


title: Reanalysis_H302

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1358965

source_name: Primary Transformed Follicular Lymphoma of case patient


title: HPC60


title: HPC59


title: Reanalysis_H14

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1358944


title: Reanalysis_H2

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1358948


title: HPC62


title: Reanalysis_H284

description:
Gene expression data from diagnostic samples of diffuse large B-cell lymphoma
GSM1358956


title: HPC66


title: HPC58


title: H385

description: Gene expression data from diagnostic samples of diffuse large B-cell lymphoma

source_name: Relapse Transformed Follicular Lymphoma of case patient


title: HPC57


title: HPC68


title: HPC63


title: H317

source_name: Follicular Lymphoma

value: Follicular Lymphoma


title: HPC53


title: HPC55


title: H316


title: H328


title: HPC51


title: HPC52


title: H312


title: H292


title: H310


title: HPC46


title: HPC44


title: HPC50


title: HPC48


title: HPC49


title: HPC42


title: HPC41


title: HPC45


title: HPC40


title: HPC47


title: HPC39


title: H281


title: iENP-13F, biological rep2

hyb_protocol: Standard Affymetrix protocol with GeneChip® Hybridization Oven 640

scan_protocol: Standard Affymetrix protocol with Affymetrix GeneChip® Scanner 3000

data_processing: Raw data were normalized independently for each experiment using Robust Multichip Average. Comparisons were performed with GeneSpring software.

label_protocol: Standard Affymetrix protocol

value: iENP

tag: protocol


title: HPC43


title: iENP-7F, biological rep2


title: HPC37


title: iENP-13F, biological rep1


title: HPC38


title: HPC54


title: iENP-15F, biological rep2


title: HPC35


title: HPC28


title: iENP-6F, biological rep1


title: iENP-15F, biological rep1


title: HPC36


title: Inorganic arsenic-transformed (iAs-T) Replicate 1 [gene level]

description: Inorganic arsenic-transformed (iAs-T)

data_processing: CEL files were RMA summarized and processed using the Affymetrix Expression Console software version 1.4.1.46. Probes were RMA normalized for analysis at the gene level.

value: lung epithelial cell line

tag: treatment

value: inorganic sodium arsenite


title: HPC32


title: HPC27


title: HPC34


title: iENP-6F, biological rep2


title: HPC33


title: iENP-7F, biological rep1


title: HPC31


title: HPC30


title: HPC22


title: HPC20


title: HPC21


title: HPC29


title: HPC25


title: hESC-derived NP, biological rep1

source_name: hESC-NP

value: hESC-NP


title: Ca9-22 cells expresess with PTHLH vecotr

first: Wei-Min

last: Chang

state: Not Applicable

address: 128 Academia Road, Section 2, Nankang,

institute: Academia Sinica

description: Gene expression data from CX-1 cells expressing RAB3C

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 PLUS 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The raw data were normalized by GeneSpring GX software and upload with raw values.

source_name: JCRB

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

growth_protocol: Cells were cultured in 5% CO2 incubator at 37℃.

extract_protocol: Qiagene RNeasy mini kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cell were selected with blasticidin for two weeks.  Stably transduced cells were use for this experiment.

value: Ca9-22 cells

tag: expression

value: PTHLH vector


title: HPC26


title: HPC23


title: HPC24


title: Normal (NT) Replicate 2 [gene level]

description: Normal (NT)


title: HPC19


title: Normal (NT) Replicate 1 [gene level]

description: Normal (NT)


title: Ca9-22 cells expresess with empty vector

description: Gene expression data from CX-1 cells expressing control vector

value: empty vector


title: hESC-derived NP, biological rep2


title: Inorganic arsenic-transformed (iAs-T) Replicate 2 [gene level]

description: Inorganic arsenic-transformed (iAs-T)


title: HPC56


title: HPC15


title: HPC17


title: NES NC2

city: hangzhou

first: Xiao

last: Chen

state: zhejiang

address: yu hang tang road 866#

department: School of Medicine

institute: Zhejiang University

description: Gene expression data from normal TSPC

hyb_protocol: The fragmented cRNA was hybridized to Human Genome U133 Plus 2.0 Array containing 47,000 transcripts. Hybridization was performed at 45oC with rotation for 16 h (AffymetrixGeneChip Hybridization Oven 640). The GeneChip arrays were washed and then stained (streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.

scan_protocol: The GeneChip arrays were scanned using the GeneChip Scanner 3000

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

source_name: tendon stem/progenitor cells isolated from tendon

label_protocol: An aliquot of 100ng of total RNA was used to synthesize double-stranded cDNA, and then produce biotin-tagged cRNA using the MessageAmpTM II aRNA Amplification Kit. The resulting bio-tagged cRNA were fragmented to strands of 35-200 bases in length according to the protocols from Affymetrix.

growth_protocol: Cells were cultured in low glucose DMEM supplemented with 10% (v/v) fetal bovine serum  and 1% penicillin-streptomycin

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

treatment_protocol: Cells were placed on ice in the Trizol solution

value: tendon stem/progenitor cells

tag: genotype

value: normal


title: HPC16


title: HPC18


title: HPC14


title: NES SH2

description: Gene expression data from NES knockdown TSPCs

value: NES knockdown


title: HPC7


title: HPC12


title: NES NC1

description: Gene expression data from normal TSPC


title: HPC9


title: HPC8


title: HPC10


title: HPC3


title: HPC13


title: NES SH1

description: Gene expression data from NES knockdown TSPC


title: HPC4


title: HPC1


title: HPC6


title: HPC11


title: BX95

description:
Cells transfected with CCAR2 siRNA
Sample name: 9240300005_F.AVG

data_processing: The data were processed and normalised using quantile normalisation with BeadStudio software v3.8

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Illumina MicroRNA Expression Profiling Assay Guide).

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

tag: knockdown


title: HPC2


title: HPC5


title: BX93

description:
Cells transfected with CCAR2 siRNA
Sample name: 9240300005_D.AVG


title: DGM-00083_u

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: upper or lower lobe ene expression in the small airway epithelium of an active smoker

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: smoker id

tag: tissue

value: upper lobe of small airway epithelium


title: BX91

description:
Cells transfected with control siRNA
Sample name: 9240300005_B.AVG

value: siCTRL


title: BX94

description:
Cells transfected with CCAR2 siRNA
Sample name: 9240300005_E.AVG


title: DGM-02164_l

value: lower lobe of small airway epithelium


title: DGM-00083_l


title: DGM-00153_l


title: DGM-00139_u


title: DGM-02164_u


title: BX90

description:
Cells transfected with control siRNA
Sample name: 9240300005_A.AVG


title: EG77

description:
Parental cells
Sample name: 3999350054_L.AVG

source_name: BJ-hTERT

value: BJ-hTERT

value: wildtype


title: DGM-00139_l


title: DGM-00196_l


title: EG75

description:
Parental cells
Sample name: 3999350054_J.AVG


title: 177Lu GOT1-Control xenograft, 168 h, 0 MBq #2

city: Boston

first: Johan

last: Spetz

state: MA

address: HSPH2, Room 229, 655 Huntington Ave.

department: JBL Center for Radiation Sciences

institute: Harvard School of Public Health

scan_protocol: Standard Illumina iScan N240 scanning protocol Direct Hyb

data_processing: The data were normalized using quantile normalization with BASE

label_protocol: Illumina®Totalprep-96RNA Amplification kit 4397949 RevC, (Modification of Amplification kit v 2.2)

extract_protocol: Total RNA was extracted with RNeasy Lipid Tissue Mini Kit according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyzer.

tag: host strain

value: Balb/c nude mouse

tag: xenograft tissue

tag: time point

tag: amount administered

value: 0 MBq

tag: nuclide


title: EG70

description:
Cells transfected with CRISPR/Cas9
Sample name: 3999350054_E.AVG

tag: cell line

value: CCAR2 KO


title: EG76

description:
Parental cells
Sample name: 3999350054_K.AVG


title: DGM-00738_l


title: 177Lu GOT1-Control xenograft, 72 h, 0 MBq #2


title: EG69

description:
Cells transfected with CRISPR/Cas9
Sample name: 3999350054_D.AVG


title: 177Lu GOT1-Control xenograft, 168 h, 0 MBq #1


title: DGM-00196_u


title: 177Lu GOT1-Control xenograft, 72 h, 0 MBq #1


title: DGM-00808_l


title: DGM-00808_u


title: 177Lu GOT1-Lu-oct, 1 d, 15 MBq #5

source_name: 177Lu GOT1-Lu-oct, 1 d, 15 MBq

value: 15 MBq


title: 177Lu GOT1-Control xenograft, 24 h, 0 MBq #1


title: DGM-00738_u


title: DGM-00332_u


title: 177Lu GOT1-Control xenograft, 24 h, 0 MBq #2


title: DGM-00153_u


title: 177Lu GOT1-Lu-oct, 1 d, 5+10 MBq #3

source_name: 177Lu GOT1-Lu-oct, 1 d, 5+10 MBq

value: 5 MBq at t=0, 10 MBq at t=1d


title: DGM-00332_l


title: 177Lu GOT1-Lu-oct, 1 d, 15 MBq #4


title: 177Lu GOT1-Lu-oct, 1 d, 5+10 MBq #2


title: 177Lu GOT1-Lu-oct, 7 d, 15 MBq #6

source_name: 177Lu GOT1-Lu-oct, 7 d, 15 MBq


title: 177Lu GOT1-Lu-oct, 1 d, 5+10 MBq #1


title: 177Lu GOT1-Lu-oct, 7 d, 15 MBq #4


title: EG71

description:
Cells transfected with CRISPR/Cas9
Sample name: 3999350054_F.AVG


title: DGM-00993_l


title: 177Lu GOT1-Lu-oct, 1 d, 15 MBq #6


title: 177Lu GOT1-Lu-oct, 7 d, 15 MBq #5


title: DGM-01009_l


title: DGM-00993_u


title: 177Lu GOT1-Lu-oct, 3 d, 15 MBq #1

source_name: 177Lu GOT1-Lu-oct, 3 d, 15 MBq


title: 177Lu GOT1-Lu-oct, 7 d, 5+10 MBq #5

source_name: 177Lu GOT1-Lu-oct, 7 d, 5+10 MBq


title: 177Lu GOT1-Lu-oct, 3 d, 15 MBq #2


title: DGM-01009_u


title: 177Lu GOT1-Lu-oct, 7 d, 5+10 MBq #6


title: 177Lu GOT1-Lu-oct, 7 d, 5+10 MBq #4


title: FA_N4_MBD

city: Chuoshi

first: Kunio

last: Miyake

state: Yamanashi

address: 1110 Shimokato

institute: Yamanashi University

hyb_protocol: Samples were prepared and hybridized to GeneChip Mouse Promoter 1.0R Array according to Affymetrix specifications.

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

data_processing: The signal intensity data was analyzed with the Partek Genomic suite 6.6

source_name: PR diet with supplemental folic acid (FA), restriction digestion, anti-MBD2

extract_protocol: Genomic DNA was fragmentated using restriction digestion with methylation-insensitive restriction enzymes (MseІ, BfaІ and CSP6І). The enrichment of methylated DNA was performed by MethylMiner Methylated DNA Enrichment kit (Thermo Fisher)

treatment_protocol: DNA were extracted simultaneously using AllPrep DNA/RNA Mini Kit (Qiagen).

value: restriction digestion, anti-MBD2

tag: strain

value: Brain

source_name: PR diet with supplemental folic acid (FA), restriction digestion, none

value: restriction digestion, none


title: 177Lu GOT1-Lu-oct, 3 d, 5+10 MBq #1

source_name: 177Lu GOT1-Lu-oct, 3 d, 5+10 MBq


title: 177Lu GOT1-Lu-oct, 3 d, 5+10 MBq #2


title: FA_N3_MBD

label_protocol: Samples were prepared and hybridized to GeneChip Mouse Promoter 1.0R Array according to Affymetrix specifications.


title: DGM-01088_l


title: FA_N1_MBD


title: DGM-01088_u


title: PR_N4_MBD

source_name: Protein-restricted diet (PR), restriction digestion, anti-MBD2

source_name: Protein-restricted diet (PR), restriction digestion, none


title: 177Lu GOT1-Lu-oct, 3 d, 5+10 MBq #3


title: PR_N3_MBD


title: FA_N2_MBD


title: 177Lu GOT1-Control xenograft, 41 d, 0 MBq #1C


title: Mouse apoE KO fed with n-3 PUFA depleted-diet, supplemented with prebiotics

city: Brussels

first: Jean-Baptiste

last: Demoulin

address: av Hippocrate 75, B1.74.05

department: de Duve Institute

country: Belgium

institute: Université catholique de Louvain

description: Gene expression data from KO DEF PRE mice cecal tissue

hyb_protocol: Affymetrix hybridization control and hybridization wash and stain kit.

scan_protocol: The wash and stain protocols were runned on an Affy 450 station. The chips were scanned according to the Affymetrix standard procedure.

data_processing: Affymetrix Gene Expression Console and APT suite tool. Normalization: RMA-sketch procedure; signal detection p-values: DABG procedure.

source_name: cecum, apoE KO fed with n-3 PUFA depleted-diet, supplemented with prebiotics

label_protocol: Biotinylated cRNAs were prepared from 100 ng of total RNA according to Affymetrix kits.

growth_protocol: two groups of mice:  WT and KO were recruited for this experiment

extract_protocol: For the cecal tissue of each mice, RNA extraction was done using Tripure (Roche). After extraction RNAs from 6 mice per group were pooled, mice were selected based on their RNA quality.

treatment_protocol: each group of mice were fed with n-3 PUFA depleted-diet (D08041806, Research Diets) supplemented or not with prebiotics for the last fifteen days (250mg/d/mouse, Orafti®P95, Tienen, Belgium)

value: cecal tissue

value: apoE knock-out

tag: age

value: 21 weeks


title: 177Lu GOT1-Control xenograft, 41 d, 0 MBq #1B1


title: 177Lu GOT1-Lu-oct, 41 d, 15 MBq 2 #3

source_name: 177Lu GOT1-Lu-oct, 41 d, 30 MBq


title: 177Lu GOT1-Lu-oct, 41 d, 10+5 MBq 2 #3

source_name: 177Lu GOT1-Lu-oct, 41 d, 10+5 MBq

value: 10 MBq at t=0, 5 MBq at t=1d


title: 177Lu GOT1-Lu-oct, 41 d, 10+5 MBq 2 #1


title: 177Lu GOT1-Lu-oct, 41 d, 15 MBq 2 #1


title: PR_N2_MBD


title: Mouse wild-type fed with n-3 PUFA depleted-diet, supplemented with prebiotics

description: Gene expression data from WT DEF mice cecal tissue

source_name: cecum, wild-type fed with n-3 PUFA depleted-diet, supplemented with prebiotics

value: wild-type


title: 177Lu GOT1-Lu-oct, 41 d, 15 MBq 2 #4


title: 177Lu GOT1-Control xenograft, 41 d, 0 MBq #1B2


title: PR_N1_MBD


title: BX92

description:
Cells transfected with control siRNA
Sample name: 9240300005_C.AVG

value: siCTRL


title: 177Lu GOT1-Lu-oct, 41 d, 5+10 MBq 2 #2


title: 177Lu GOT1-Lu-oct, 41 d, 5+10 MBq 2 #3


title: CD_N2_MBD

source_name: Control diet (CD, AIN93G), restriction digestion, anti-MBD2

source_name: Control diet (CD, AIN93G), restriction digestion, none


title: Mouse wild-type fed with n-3 PUFA depleted-diet

description: Gene expression data from WT DEF PRE mice cecal tissue

source_name: cecum, wild-type fed with n-3 PUFA depleted-diet

value: n-3 PUFA depleted-diet


title: Mouse apoE KO fed with n-3 PUFA depleted-diet

description: Gene expression data from KO DEF mice cecal tissue

source_name: cecum, apoE KO fed with n-3 PUFA depleted-diet


title: CD_N1_MBD


title: CD_N4_MBD


title: 177Lu GOT1-Lu-oct, 41 d, 10+5 MBq #5


title: 177Lu GOT1-Control xenograft, 41 d, 0 MBq #2


title: 177Lu GOT1-Lu-oct, 41 d, 5+10 MBq 2 #4


title: 177Lu GOT1-Sonidegib, 41 d, 0 MBq Lu, Sonidegib #5

value: 0 MBq, 80 mg/kg

value: Lutetium-177-octreotate, Sonidegib


title: 177Lu GOT1-Lu-oct, 41 d, 5+10 MBq #2

source_name: 177Lu GOT1-Lu-oct, 41 d, 5+10 MBq

value: Balb/c nude mouse


title: 177Lu GOT1-Lu-oct, 41 d, 5+10 MBq #3P


title: 177Lu GOT1-Combination, 41 d, 30 MBq Lu, Sonidegib #3P

value: 30 MBq, 80 mg/kg


title: 177Lu GOT1-Lu-oct, 41 d, 30 MBq #5

value: 30 MBq


title: 177Lu GOT1-Lu-oct, 41 d, 10+5 MBq 2 #2


title: 177Lu GOT1-Combination, 41 d, 30 MBq Lu, Sonidegib #5


title: 177Lu GOT1-Lu-oct, 41 d, 30 MBq #4


title: 177Lu GOT1-Lu-oct, 41 d, 30 MBq #3


title: 177Lu GOT1-Lu-oct, 41 d, 5+10 MBq #4


title: brain_naive_D2_rep5

city: Portland

first: Nicole

last: Walter

state: OR

address: 3181 SW Sam Jackson Park Road

department: Behavioral Neuroscience

institute: Oregon Health & Science University

data_processing: Lumi, quantile normalized

source_name: whole brain, naïve

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

extract_protocol: Trizol

treatment_protocol: naïve

value: whole brain

tag: gender

value: male

tag: developmental stage

value: adult


title: brain_naive_R8_rep8


title: brain_naive_R2_rep6


title: brain_naive_R8_rep9


title: brain_naive_B6_rep10


title: brain_naive_R8_rep7


title: 177Lu GOT1-Lu-oct, 41 d, 10+5 MBq #3P


title: brain_naive_R8_rep10


title: brain_naive_R8_rep5


title: 177Lu GOT1-Sonidegib, 41 d, 0 MBq Lu, Sonidegib #2


title: 177Lu GOT1-Combination, 41 d, 30 MBq Lu, Sonidegib #4


title: brain_naive_D2_rep6


title: 177Lu GOT1-Sonidegib 41 d, 0 MBq Lu, Sonidegib #2P

source_name: 177Lu GOT1-Sonidegib, 41 d, 0 MBq Lu, Sonidegib


title: brain_naive_R8_rep6


title: uterus_E2,rat-3 [miRNA]

city: Rensselaer

first: Sridar

middle: V

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

hyb_protocol: Following labeling, 12.5uL of biotin-labeled samples were hybridized for 16 hr at 48C on GeneChip miRNA3.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix Scanner 3000 7G with AGCC software.

data_processing:
CEL files were analyzed for quality using Affymetrix Expression Console software, and the RMA-DBAG was used for normalization
affymetrix-algorithm-name = rma : dabg
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

organism: Rattus norvegicus

source_name: rat uterus, 72 h treatment, E2

label_protocol: Biotinylated miRNA were prepared according to the standard Affymetrix FlashTag HSR protocol from 100 ng total RNA

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

treatment_protocol: Rats were treated with vehicle control (DMSO) or 4µg/kg/d 17β-Estradiol (E2) for three consecutive days. Uteri were obtained 24 h after the last treatment. Biological samples from three rats were analyzed for each treatment group.

value: Lewis

value: female

tag: treated with

value: 4µg/kg/d 17β-Estradiol (E2)

value: uterus


title: 177Lu GOT1-Sonidegib, 41 d, 0 MBq Lu, Sonidegib #3


title: uterus_E2,rat-2 [miRNA]


title: uterus_E2,rat-1 [miRNA]


title: uterus_DMSO,rat-2 [miRNA]

source_name: rat uterus, 72 h treatment, VEHICLE

value: vehicle control (DMSO)


title: 177Lu GOT1-Control xenograft, 41 d, 0 MBq #1

value: 0 MBq


title: 177Lu GOT1-Lu-oct, 41 d, 10+5 MBq #1

value: 10 MBq at t=0, 5 MBq at t=1d


title: brain_naive_D2_rep4


title: uterus_DMSO,rat-3 [miRNA]


title: 177Lu GOT1-Combination, 41 d, 30 MBq Lu, Sonidegib #3


title: 177Lu GOT1-Control xenograft, 41 d, 0 MBq #3


title: 177Lu_GOT2-Control_xenograft_0_MBq_#2


title: brain_naive_R2_rep5


title: brain_naive_B6_rep9


title: brain_naive_B6_rep7


title: 177Lu GOT1-Lu-oct, 41 d, 5+10 MBq #3

value: 5 MBq at t=0, 10 MBq at t=1d


title: 177Lu GOT1-Lu-oct, 41 d, 30 MBq #3P


title: 177Lu_GOT2-Control_xenograft_0_MBq_#1


title: 177Lu GOT1-Lu-oct, 41 d, 5+10 MBq #2P


title: 177Lu GOT1-Lu-oct, 41 d, 10+5 MBq #3


title: brain_naive_R8_rep4


title: brain_naive_R2_rep3


title: 177Lu_GOT2-70h_xenograft_10_MBq_#3

value: 10 MBq


title: brain_naive_B6_rep3


title: brain_naive_R8_rep3


title: 177Lu_GOT2-70h_xenograft_10_MBq_#2


title: brain_naive_B6_rep6


title: 177Lu_GOT2-23h_xenograft_10_MBq_#3


title: brain_naive_B6_rep4


title: brain_naive_B6_rep8


description: Hybridized to SNP6.0

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: The .CEL files, generated through AGCC after scanning the arrays, were imported to Partek Genomics Suite Software v. 6.6 (6.14.0828) using interrogating probes only with a pre-background adjustment for GC content and probe sequence. Probe sets wire summarized using allele specific summarization, and normalized against the human Hapmap genome (default in the Partek software).

label: Biotin

source_name: Malignant lymphnode from case patient - primary diagnose: transformed follicular lymphoma

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: The tumor sample was after removal snap frozen and stored in OCT at - 80 oC. From each OCT block, 3x20 µm cuts were obtained using a microtome; the slices were washed twice in PBS and homogenized using the TissueLyser II (Qiagen). DNA extraction was performed using the DNeasy Blood & Tissue kit (Qiagen). From one of the patients (H380) a peripheral blood sample was included as a normal control sample (BB39). Mononuclear cells were isolated from the blood sample by Ficoll-Paque Plus (GE Health Care, Uppsala, Sweden) and stored in 10 % DMSO and 20 % serum at – 80 oC. For DNA extraction, the cells were thawed, washed twice in PBS and genomic DNA extracted using the DNeasy Blood & Tissue kit (Qiagen). The DNA was eluted in water and the concentration measured using a Nanodrop (Thermo Scientific). The saliva sample was collected using the Oragene DNA Self-Collection Kit (OG-500) and the DNA purified from non-involved mucosa cells using the Oragene DNA purifier (OG-L2P) following manufactures instructions in protocol PD-PR-006 Issue 3.2 (DNA Genotek Inc, Ottawa, Ontario, Canada).

value: Malignant lymphnode from case patient - primary diagnose:transformed follicular lymphoma


title: brain_naive_B6_rep5

scan_protocol: Standard Illumina scanning protocol


title: 177Lu_GOT2-70h_xenograft_10_MBq_#1


title: uterus_DMSO,rat-1 [miRNA]


title: brain_naive_R2_rep4


title: brain_naive_R2_rep2


title: 177Lu_GOT2-23h_xenograft_10_MBq_#2


title: brain_naive_R8_rep2


title: 177Lu_GOT2-23h_xenograft_10_MBq_#1


title: brain_naive_D2_rep3


title: 177Lu_GOT2-0.5h_xenograft_10_MBq_#1


title: brain_naive_B6_rep2


title: 177Lu GOT1-Control xenograft, 0 MBq #2

source_name: 177Lu GOT1-Control xenograft, 0 MBq


title: brain_naive_B6_rep1


description: Hybridized to SNP6.0

source_name: Malignant lymphnode from case patient - relapse diagnose: transformed follicular lymphoma

value: Malignant lymphnode from case patient - relapse diagnose:transformed follicular lymphoma


title: 177Lu GOT1-Control xenograft, 0 MBq #1

value: Balb/c nude mouse


title: brain_naive_R8_rep1


title: brain_naive_D2_rep2


title: brain_naive_R2_rep1


title: 177Lu_GOT2-0.5h_xenograft_10_MBq_#2


title: 177Lu GOT1-24h xenograft, 7 MBq #1

source_name: 177Lu GOT1-24h xenograft, 7 MBq

value: 7 MBq


title: 177Lu GOT1-24h xenograft, 7 MBq #2


title: brain_naive_D2_rep1


title: PC3 siYAP WSS 3hrs rep3

first: Pamela

middle: L

last: Wenzel

address: 6431 Fannin St, MSB 4.130

department: Integrative Biology & Pharmacology

institute: University of Texas Health Science Center at Houston

data_processing: Raw signals of all the build-in controls were checked as quality control for the performance of the arrays. Sample-independent controls were used to check: a. Hybridization (control molecules at low, medium and high concentrations); b. Signal generation (background, noise, biotin labeling and hybridization at high and low stringency). Housekeeping genes were used as sample-dependent controls.  Background was subtracted and arrays were quantile normalized.

source_name: PC3 siYAP WSS 3hrs rep3

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

growth_protocol: PC3 cells were maintained in F-12K (ATCC) supplemented with 10% fetal bovine serum, 1% penicillin and streptomycin antibiotics at 37C in 5% CO2 (v/v). Cells were passaged by treatment with 0.25% Trypsin-EDTA (Gibco).

extract_protocol: Cells were directly lysed on PDMS channels with RLT lysis buffer. Total RNA was immediately extracted with the QIAGEN Rneasy kit.

treatment_protocol: Poly(dimethylsiloxane) (PDMS, Sylgard 184 silicone elastomer kit, mixed with a ratio of 10 wt% cross-linker; Dow Corning) was poured over a master mold, and incubated overnight at 60C. The cylindrical channels were 35 mm in length and 1.8 mm in diameter. This channel was connected to a single Harvard Apparatus PHD ULTRA 4400 with Remote syringe pump. After 24 hours of incubation, cells were cultured for 3 hours in static or in the presence of WSS (0.05 dyne/cm^2).

tag: organ

value: prostate

tag: cancer stage

value: malignant tumor

tag: duration

value: 3 hours

tag: force

tag: drug

value: YAP1 siRNA


title: N2_OA(+)_rep.1

city: Kyoto

first: Masaharu

last: Uno

address: Sakyo-ku

department: Graduate School of Biostudies

institute: Kyoto University

description: Gene expression data from WT worms with Oa administration.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip C. elegans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: GeneSpring GX

organism: Caenorhabditis elegans

label_protocol: 3' IVT

growth_protocol: Animals from synchronized eggs were grown under normal condition for three days. Then, young adult animals were transferred to NGM plates with or without 20 mg/mL of octopamine.

extract_protocol: Total RNA was extracted with TRIzol reagent (Invitrogen, Carlsbad, CA, USA) from frozen 5-day-old N2, daf-16, and ser-3; ser-6 mutants treated with or without 20 mg/mL OA.

treatment_protocol: Animals were treated with or without octopamine for 2 days.

tag: strain/background

tag: genotype/variation

value: wild-type

value: day 4 adult

tag: tissue

value: whole body

tag: octopamine administration


title: ser-3;ser-6_OA(+)_rep.1

description: Gene expression data from ser-3;ser-6 worms with Oa administration.


title: daf-16_OA(-)_rep.1

description: Gene expression data from daf-16 worms without Oa administration.


title: PC3 siCTL WSS 3hrs rep2

hyb_protocol: Standard Illumina hybridization protocol

source_name: PC3 siCTL WSS 3hrs rep2

value: CTL siRNA


title: PC3 siYAP WSS 3hrs rep2

source_name: PC3 siYAP WSS 3hrs rep2


title: daf-16_OA(+)_rep.1

description: Gene expression data from daf-16 worms with Oa administration.


title: PC3 WSS 3hrs rep1

source_name: PC3 WSS 3hrs rep1

value: vehicle


title: ser-3;ser-6_OA(-)_rep.1

description: Gene expression data from ser-3;ser-6 worms without Oa administration.


title: PC3 siCTL WSS 3hrs rep1

source_name: PC3 siCTL WSS 3hrs rep1


title: PC3 WSS 3hrs rep3

source_name: PC3 WSS 3hrs rep3


title: PC3 static 3hrs rep3

source_name: PC3 static 3hrs rep3

value: 0 dyne/cm^2


title: PC3 siYAP WSS 3hrs rep1

source_name: PC3 siYAP WSS 3hrs rep1


title: PC3 WSS 3hrs rep2

source_name: PC3 WSS 3hrs rep2


title: PC3 static 3hrs rep2

source_name: PC3 static 3hrs rep2


title: PC3 static 3hrs rep1

source_name: PC3 static 3hrs rep1


title: LNCaP - overexpressing Notch1 - replicate 2

city: Biella

first: Paola

last: Ostano

address: via Malta 3

institute: Fondazione Edo ed Elvo Tempia

hyb_protocol: Biotin-labeled cRNA was hybridized on Human Affymetrix U95 Av2 array according to the manufacturer’s recommendation

data_processing: Raw Affymetrix CEL files were loaded into R and analyzed with RMA (Robust Multichip Average). The LIMMA (LInear Models for Microarray Analysis) package was then used to identify differentially expressed genes.

source_name: LNCaP

label_protocol: The resulting cDNAs were used for preparation of biotin-labeled cRNA probes preparation and hybridization to the Affymetrix U95 Av2 gene expression platform

extract_protocol: Total RNA (5-8 ug) was used as template for double stranded cDNA preparations with T7-(dT)24 oligonucleotide primers for the first strand reaction.

value: LNCaP

tag: variation

value: overexpressing Notch1


title: LNCaP - overexpressing Notch1 - replicate 1


title: PC3 siCTL WSS 3hrs rep3

city: Houston

source_name: PC3 siCTL WSS 3hrs rep3


title: cells were treated with TGF-β1 (5ng/ml) and NCB-0846 (3µM)

first: Teppei

last: Sugano

address: Sendagi, Bunkyo-ku

institute: Graduate School of Medicine,

hyb_protocol: The dyied Cy3-labelled miRNA was Resuspended in 18 μL of nuclease-free water, 4.5 μL of the 10X GE Blocking Agent and 22.5 μL of 2x Hi-RPM Hybridization Buffer was added following the manufacturer’s instructions. After the sample was incubated at 100°C for 5 minutes, and immediately transfer to an ice water bath for 5 minutes, and hybridized to Human miRNA Microarray kit 8x60K rel.21.0 (Agilent) for 20 hours at 55°C in a rotating Agilent hybridization oven.  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), then dried immediately

scan_protocol: Microarrays were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green PMT is set to XDR Hi 100% and XDR Lo 5%).

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

source_name: Cell line

label_protocol: Cyanine-3 (Cy3) labeled miRNA was prepared from 100ng total RNA using the miRNA Complete Labeling and hyb kit (Agilent) according to the manufacturer's instructions.

extract_protocol: Total RNA were prepared with RNeasy Mini Kit  (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: After serum starvation for 24 h, cells were treated with DMSO (control), TGF-β1 (5ng/ml) or co-treated with TGF-β1 and NCB-0846 (3µM) or NCB-970 (3µM) for 48 h.

tag: cell type

value: non-small cell lung cancer cells

value: TGF-β1 (5ng/ml) and NCB-0846 (3µM)


title: LNCaP - GFP control - replicate 1

tag: cell line

value: GFP control


title: cells were treated with DMSO (control)

description: DMSO

value: DMSO (control)


title: LNCaP - GFP control - replicate 2


title: PKm2KI ES (undifferentiated)

city: Suita

first: Masamitsu

last: Konno

state: Osaka

address: Yamadaoka 2-2

institute: Osaka Univ.

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse GE 8x60K Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: M2KI ES

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions.

growth_protocol: Thiree kinds of ES cells were cultured the medium containing LIF. EB were cultured the medium without LIF for 3 or 7 days in floating culture.

extract_protocol: RNAeasy column purification (QIAGEN, Valencia, CA).

tag: genotype

value: PKm2 knock-in

value: ES (undifferentiated)


title: PKm2KI ES (EB day7)

source_name: M2KI EB day7

value: ES (EB day7)


title: PC3 - GFP control - replicate 2


title: PKm2KI ES (EB day3)

source_name: M2KI EB day3

value: ES (EB day3)


title: PC3 - overexpressing Notch1 - replicate 1


title: PC3 - GFP control - replicate 1


title: PC3 - overexpressing Notch1 - replicate 2


title: cells were treated with TGF-β1 (5ng/ml)

value: TGF-β1 (5ng/ml)


title: PKm1KI ES (EB day3)

source_name: M1KI EB day3

value: PKm1 knock-in


title: PKm1KI ES (undifferentiated)

source_name: M1KI ES


title: PKm1KI ES (EB day7)

source_name: M1KI EB day7


title: wild type ES (EB day3)

source_name: wild type EB day3

value: wild type


title: AorticSMC_Wildtype_AdMyocd_rep2

city: Augusta

first: Xiaochun

last: Long

state: GA

address: 1460 Laney Walker Blvd, CL-3004

department: Vascular Biology Center

institute: Augusta University

hyb_protocol: 50 ul of hybridization solution containing the labeled cRNA was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed and fixed.

scan_protocol: Agilent DNA Microarray Scanner (part number G2505C) was used to scan the arrays.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 4 out of 8 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, each sample was transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/ug cRNA) were measured by NanoDrop ND-1000. 1 ug of each labeled cRNA was fragmented by adding 5 ul 10 × Blocking Agent and 1 ul of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 ul 2 × GE Hybridization buffer was added to dilute the labeled cRNA.

growth_protocol: DMEM/F12 with 20%FBS for maintaining, DMEM/F12 with 10% for experiment

extract_protocol: miR-easy kit extracted RNA (0.5 ug) was submitted for microarray.

treatment_protocol: Adenovirus transduction with MOI=100 for 3 days before harvest.

tag: tissue type

value: Cultured mouse aortic smooth muscle cell

tag: passage


title: AorticSMC_SRFknockout_AdEmpty_rep2


title: Aorta_Wildtype_rep1

source_name: Freshly isolated aorta tissue

value: Freshly isolated aorta tissue


title: wild type ES (EB day7)

source_name: wild type EB day7


title: Liver_Wildtype_rep1

source_name: Freshly isolated liiver tissue

value: Freshly isolated liiver tissue


title: AorticSMC_SRFknockout_AdEmpty_rep1


title: cpm2 leaves treated with 1 mM CuCl2 treatment for 24 h replicate 3

city: Utsunomiya

first: Koji

last: Miyamoto

state: Tochigi

address: 1-1 Toyosatodai

department: Department of Biosciences

institute: Teikyo University

description: Biological replicate 3 of 3.

hyb_protocol: Agilent protocol G4140-90040

scan_protocol: Agilent Technologies Scanner G2505C US22502560

data_processing: After data was analyzed by Fearure Extraction software (Agilent), data normalization was performed using Subio Platform with Basic Plug-in (Subio Inc).

organism: Oryza sativa

label_protocol: Low RNA input Linear Amplification/Labeling Kit (Agilent)

growth_protocol: Wild-type rice plants (Oryza sativa L., cv. Nihonmasari) and cpm2 mutants were grown in a glass house under natural daylight.

extract_protocol: RNeasy Plant Mini Kit (Qiagen)

treatment_protocol: The leaf disks (6 mmϕ) were excised from the uppermost rice leaf blades of 1.5 month-old plants. Then the leaf disks were floated on water or 1 mM CuCl2.

tag: cultivar

value: Nihonmasari

value: leaves

tag: agent

value: 1 mM CuCl2

tag: time point


title: wild type ES (undifferentiated)

source_name: wild type ES


title: cpm2 leaves treated with 1 mM CuCl2 treatment for 2 h replicate 3

description: Biological replicate 3 of 3.

value: 2 h


title: AorticSMC_Wildtype_AdMyocd_rep1


title: AorticSMC_Wildtype_AdEmpty_rep2


title: pool3_D27_CD4

city: Utrecht

first: Jules

last: Meijerink

address: Uppsalalaan 8

country: Netherlands

institute: Princess Máxima Center for Pediatric Oncology

hyb_protocol: Per sample, 7.5μg cRNA of the obtained biotinylated cRNA samples was fragmented and hybridized in a final concentration of 0.0375 μg/μl on the Affymetrix HT HG U133+ PM (Affymetrix).

scan_protocol: After an automated process of washing and staining by the GeneTitan machine using the Affymetrix HWS Kit for GeneTitan, absolute values of expression were calculated from the scanned array using the Affymetrix Command Console v3.2 software.

data_processing: Affymetrix gene expression CEL files were processed using Partek® Genomics Suite® 6.6. Robust Multi-array Average (RMA). In brief, the intensity levels were quantile normalized after background correction.

source_name: CD4+ cells sorted at day 27 of co-culture

label_protocol: Biotinylated cRNA was prepared using the Affymetrix 3’ IVT Express Kit (Affymetrix) according to the manufacturer’s specifications with an input of 100ng total RNA

growth_protocol: OP9-DL1 co-cultures were performed according to the original protocol. Briefly, CD34+ human HSC isolated from umbilical cord blood were plated into culture dishes, which were seeded with a monolayer of OP9-DL1 cells beforehand. The α-MEM used for culture was supplemented with 20% FBS plus PSF. Recombinant human SCF, FLT3L, and IL7 were added at the initiation of coculture and every 2-3 days during transfer of HSC-derived cells onto new OP9-DL1 plated cells.

extract_protocol: RNA was isolated using RNeasy Micro Kit according to the manufacturer’s protocol (Qiagen).

treatment_protocol: Cell sorting was performed at 5 time points (days 0, 7, 12, 18, and 27) based on the expression of cell surface markers including CD45, CD34, CD7, CD5, CD1a, CD4 and CD8 using the FACSAria II. Sorted populations were collected, washed twice in PBS, lysed in buffer RLT (Qiagen) plus 1/100 β-mercaptoethanol and stored at -80oC

tag: developmental stage

value: early T-cell development

tag: sorting markers


title: pool3_D27_CD4CD8

source_name: CD4+CD8+(DP) cells sorted at day 27 of co-culture


title: pool3_D18_CD5

source_name: CD5+ cells sorted at day 18 of co-culture


title: pool3_D12_CD5

source_name: CD5+ cells sorted at day 12 of co-culture


title: Control (0 h) of cpm2 leaves replicate 3

description: Biological replicate 3 of 3.

source_name: Control (0 h) of cpm2 leaves

value: Control (0 h)


title: cpm2 leaves treated with warter for 24 h replicate 3

description: Biological replicate 3 of 3.

value: warter


title: cpm2 leaves treated with warter for 2 h replicate 3

description: Biological replicate 3 of 3.

source_name: cpm2 leaves treated with warter for 2 h


title: pool3_D27_CD8

source_name: CD8+ cells sorted at day 27 of co-culture


title: cpm2 leaves treated with warter for 6 h replicate 3

description: Biological replicate 3 of 3.

source_name: cpm2 leaves treated with warter for 6 h

value: 6 h


title: cpm2 leaves treated with 1 mM CuCl2 treatment for 6 h replicate 3

description: Biological replicate 3 of 3.


title: pool3_D12_CD7

source_name: CD7+ cells sorted at day 12 of co-culture


title: pool3_D18_CD1

source_name: CD1+ cells sorted at day 18 of co-culture


title: pool3_D7_CD7

source_name: CD7+ cells sorted at day 7 of co-culture


title: cpm2 leaves treated with 1 mM CuCl2 treatment for 24 h replicate 2

description: Biological replicate 2 of 3.


title: pool3_D7_CD5

source_name: CD5+ cells sorted at day 7 of co-culture


title: cpm2 leaves treated with 1 mM CuCl2 treatment for 2 h replicate 2

description: Biological replicate 2 of 3.


title: cpm2 leaves treated with warter for 24 h replicate 2

description: Biological replicate 2 of 3.


title: AorticSMC_Wildtype_AdEmpty_rep1


title: cpm2 leaves treated with 1 mM CuCl2 treatment for 6 h replicate 2

description: Biological replicate 2 of 3.


title: cpm2 leaves treated with warter for 6 h replicate 2

description: Biological replicate 2 of 3.


title: pool3_D0_CD34

source_name: UCB-derived HSCs (CD34+)

value: Hematopoietic progenitor


title: pool2_D27_CD8


title: pool2_D27_CD4CD8


title: pool2_D27_CD4


title: Retina_Covered_VioletLight

city: Tokyo

first: Mayumi

last: Oda

address: 35 Shinanomachi, Shinjuku

institute: Keio University

description: retina, covered under violet light.

hyb_protocol: 1650 ng of Cy3-labelled cRNA (specific activity >8.6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-026441 Gallus gallus Microarray (G2519F#26441) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by slowly removing the slide.

scan_protocol: Slides were scanned immediately after washing on an Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green at 20 bit).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 026441_D_F_20140626) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Gallus gallus

source_name: retina, covered under violet light.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with a NanoDrop 2000c Spectrophotometer.

growth_protocol: Myopia was induced in chicks by covering the right eye with glass goggles six days after hatching (covered). The left eye was uncovered and served as the control. Chicks wore goggles for 7 days in a 12-hour light and dark cycle. Violet light (VL) was illuminated for 7 days in 12-hour on and off cycles.

extract_protocol: Total RNA was extracted from tissue buttons using 1 ml of TRIzol ® Reagent (Invitrogen) according to the manufacturer’s recommendations. RNA quantity and quality was monitored by 260nm absorption and electrophoresis (Bioanalyzer 2000, Agilent).

treatment_protocol: The eyes of chicks were enucleated after euthanasia with CO2 on day 13. After extra ocular tissue was cleaned, tissue buttons 6 mm in diameter were excised with a surgical trephine from the part of the posterior hemisphere located temporal to the exit site of the optic nerve. Chorioretinal buttons were dissected from the tissue buttons.

tag: glass google

value: covered

tag: light color

value: violet light


title: Saliva from case patient

city: Aalborg

first: Julie

last: Bødker

address: Sdr. Skovvej 15

institute: Aalborg University Hospital

description: Hybridized to SNP6.0

source_name: Saliva from case patient with transformed follicular lymphoma

tag: gender

value: female


title: cpm2 leaves treated with warter for 2 h replicate 2

description: Biological replicate 2 of 3.


title: cpm2 leaves treated with 1 mM CuCl2 treatment for 6 h replicate 1

description: Biological replicate 1 of 3.


title: pool2_D18_CD1


title: Control (0 h) of cpm2 leaves replicate 2

description: Biological replicate 2 of 3.


title: Retina_Control_VioletLight

description: retina, control under violet light.

source_name: retina, control under violet light.

value: control


title: Retina_Covered_NormalLIght

description: retina, covered under normal light.

source_name: retina, covered under normal light.

value: normal light


title: pool2_D12_CD1

source_name: CD1+ cells sorted at day 12 of co-culture


title: cpm2 leaves treated with 1 mM CuCl2 treatment for 24 h replicate 1

description: Biological replicate 1 of 3.


title: Retina_Control_NormalLIght

description: retina, control under normal light.

source_name: retina, control under normal light.


title: cpm2 leaves treated with 1 mM CuCl2 treatment for 2 h replicate 1

description: Biological replicate 1 of 3.


title: N2_OA(-)_rep.1

description: Gene expression data from WT worms without Oa administration.

tag: strain/background

tag: genotype/variation

value: wild-type

tag: age

value: day 4 adult

value: whole body


title: cells were treated with TGF-β1 (5ng/ml) and NCB-970 (3µM)

source_name: Cell line

value: non-small cell lung cancer cells

tag: treated with

value: TGF-β1 (5ng/ml) and NCB-970 (3µM)


title: CD34+ NegCTR mimic donor 3

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

institute: Centre for Regenerative Medicine

description: GEP of NegCTR mimic CD34+ HPCs at 24 hours post-Nucleofection, third donor

hyb_protocol: Fragmented cRNA was hybridized for 16h at 45C on Affymetrix HG-U219 array strips in GeneAtlas Hybridization Station. GeneChips were washed and stained using GeneAtlas Hybridization, Wash, and Stain Kit for 3’IVT Arrays, according to the standard protocol supplied by Affymetrix (GeneAtlas 3’ IVT Express Kit, P/N 702833 Rev. 4).

scan_protocol: Affymetrix HG-U219 array strips were scanned by using GeneAtlas Scanner.

data_processing: Gene expression data were imported into Partek Genomics Suite 6.6 (Partek, St Louis, Mo) as CEL files using default parameters. Raw data were preprocessed, including background correction, normalization, and summarization using robust multiarray average (RMA) analysis.

source_name: CD34+ NegCTR mimic replicate 3

label_protocol: Gene expression profile (GEP) was performed on total RNA derived from 3 independent experiments.  Briefly, biotinylated aRNA were prepared according to the standard GeneAtlas 3’IVT Express Kit protocol from 100ng of  total RNA (P/N 702833 Rev. 4, Affymetrix). Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the aRNA concentration/quality as well as to optimize the aRNA fragmentation. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the aRNA sample concentration.

growth_protocol: Human CD34+ cells were purified from umbilical cord blood (CB) samples, collected after normal deliveries, according to the institutional guidelines for discarded material. Mononuclear cells were isolated by Ficoll-Hypaque (Lympholyte; Cederlane Labs) gradient separation, washed twice with phosphate-buffered saline, and then CD34+ cells were purified by immunomagnetic sorting (EasySep Human CD34 Positive Selection kit, StemCell Technologies Inc.). The purity of CD34+ cells, assessed by flow cytometry, was always >95%. After immunomagnetic separation, CD34+ cells were seeded in serum-free medium SYN-H (ABCell-Bio, Paris, France) supplemented with SCF (50 ng/ml), Flt3-ligand (Flt3L) (50 ng/ml), TPO (20ng/ml), IL-6 (10 ng/ml) and IL-3 (10 ng/ml) (all from Miltenyi Biotec).

extract_protocol: CD34+ cells were lysed in 700uL of QIAZOL Buffer (Qiagen, Valencia, CA, USA) after 24h from the last nucleofection. Total RNA from CD34+ cells was extracted using miRNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.

treatment_protocol: Human CD34+ cells were transfected by using the 4D-Nucleofector™ System (Lonza) as previously reported (Norfo R et al., Blood, 2014). Briefly, starting from the day after CD34+ cell purification, each sample was electroporated twice, once every 24 hours, with mirVana miR-34a-5p mimic or mirVana miRNA mimic Negative Control #1 (Neg-mimic). For each electroporation, 4×10^5 CD34+ cells were resuspended in 100 µL of P3 Primary Cell Solution (Lonza), containing 3 µg of miRNA, and pulsed with the program DS112. After each Nucleofection cycle, cells were maintained in culture in 24-well plates at 5 x 10^5/mL in serum-free medium SYN-H (ABCell-Bio, Paris, France) supplemented with SCF (50 ng/ml), Flt3-ligand (Flt3L) (50 ng/ml), TPO (20ng/ml), IL-6 (10 ng/ml) and IL-3 (10 ng/ml) (all from Miltenyi Biotec).

tag: cell type

tag: treatment

value: NegCTR mimic

tag: donor


title: cpm2 leaves treated with warter for 24 h replicate 1

description: Biological replicate 1 of 3.

value: Nihonmasari

tag: genotype

tag: tissue

value: leaves


title: cpm2 leaves treated with warter for 6 h replicate 1

description: Biological replicate 1 of 3.

tag: cultivar


title: CD34+ NegCTR mimic donor 2

description: GEP of NegCTR mimic CD34+ HPCs at 24 hours post-Nucleofection, second donor

source_name: CD34+ NegCTR mimic replicate 2


title: cpm2 leaves treated with warter for 2 h replicate 1

description: Biological replicate 1 of 3.

source_name: cpm2 leaves treated with warter for 2 h

tag: agent

value: 2 h


title: pool2_D12_CD5

source_name: CD5+ cells sorted at day 12 of co-culture

value: early T-cell development


title: pool2_D18_CD5

source_name: CD5+ cells sorted at day 18 of co-culture


title: pool2_D12_CD7

source_name: CD7+ cells sorted at day 12 of co-culture


title: CD34+ miR34a mimic donor 3

description: GEP of miR-34a-5p mimic CD34+ HPCs at 24 hours post-Nucleofection, third donor

source_name: CD34+ miR34a mimic replicate 3

value: miR-34a-5p mimic


title: CD34+ NegCTR mimic donor 1

description: GEP of NegCTR mimic CD34+ HPCs at 24 hours post-Nucleofection, first donor

source_name: CD34+ NegCTR mimic replicate 1


title: Wild-type rice leaves treated with 1 mM CuCl2 for 24 h replicate 3

description: Biological replicate 3 of 3.

value: Wild-type

value: 1 mM CuCl2

tag: time point


title: pool1_D27_CD4CD8

source_name: CD4+CD8+(DP) cells sorted at day 27 of co-culture

tag: developmental stage


title: pool2_D7_CD5

source_name: CD5+ cells sorted at day 7 of co-culture

tag: sorting markers


title: Control (0 h) of cpm2 leaves replicate 1

description: Biological replicate 1 of 3.

source_name: Control (0 h) of cpm2 leaves

value: Control (0 h)


title: Wild-type rice leaves treated with warter for 6 h replicate 3

description: Biological replicate 3 of 3.

value: warter

value: 6 h


title: pool2_D7_CD7

source_name: CD7+ cells sorted at day 7 of co-culture


title: Wild-type rice leaves treated with warter for 2 h replicate 3

description: Biological replicate 3 of 3.


title: pool1_D27_CD8

source_name: CD8+ cells sorted at day 27 of co-culture


title: Control (0 h) of wild-type rice leaves replicate 3

description: Biological replicate 3 of 3.

source_name: Control (0 h) of wild-type rice leaves


title: pool2_D0_CD34

source_name: CD34+ HSCs sorted from UCB material

value: Hematopoietic progenitor


title: pool1_D7_CD5


title: CD34+ miR34a mimic donor 2

description: GEP of miR-34a-5p mimic CD34+ HPCs at 24 hours post-Nucleofection, second donor

source_name: CD34+ miR34a mimic replicate 2


title: pool1_D18_CD5


title: pool1_D7_CD7


title: Wild-type rice leaves treated with 1 mM CuCl2 for 6 h replicate 3

description: Biological replicate 3 of 3.


title: Wild-type rice leaves treated with 1 mM CuCl2 for 24 h replicate 2

description: Biological replicate 2 of 3.