title: miR17_Linearity_Rep1_RNA_Conc2_R136

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R136


title: miR17_Linearity_Rep1_RNA_Conc2_R135

status: Public on Jan 31 2018

type: RNA

city: Utrecht

first: Michael

last: VanInsberghe

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R135

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: Raw CT values were normalized to the cut-off CT derived from the distribution of single-cDNA-molecule amplification events

label: FAM

molecule: total RNA

organism: Homo sapiens

source_name: K562 total RNA

label_protocol: not applicable

growth_protocol: K562 cells were cultured in DMEM (Gibco) supplemented with 10% FBS (Gibco) and 1× GlutaMAX (Gibco).

extract_protocol: Total RNA was isolated using the miRVana RNA isolation kit (Ambion) according to manufacturer directions, omitting the size-enrichment step

tag: cell line

tag: concentration

value: 2 pg


title: miR17_Linearity_Rep1_RNA_Conc2_R138

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R138


title: Blood Buffy_IT20 [9305651085_R06C02]

type: genomic

city: Leiden

first: Roderick

last: Slieker

address: PO Box 9600

department: Medical Oncology

institute: Leiden University Medical Center

hyb_protocol: According to Illumina protocol

scan_protocol: According to Illumina protocol

data_processing: DNA methylation data was functional normalized. Probes were discarded if they had a low bead count (< 3), high detection P value  (> 0.01), or  a low success rate (< 95%). R statistics

label: biotin

molecule: genomic DNA

source_name: Blood Buffy

label_protocol: According to Illumina protocol

extract_protocol: Chlorophorm/isoamylalcohol protocol

tag: internal tissue id

tag: age

tag: Sex

value: M


title: miR17_Linearity_Rep1_RNA_Conc2_R137

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R137


title: GAPDH_Linearity_Rep1_RNA_Conc200_R45

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R45


title: miR17_Linearity_Rep1_RNA_Conc2_R133

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R133


title: GAPDH_Linearity_Rep1_RNA_Conc200_R43

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R43


title: GAPDH_Linearity_Rep1_RNA_Conc200_R44

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R44


title: GAPDH_Linearity_Rep1_RNA_Conc200_R41

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R41


title: Blood Buffy_IT22 [9343114006_R02C02]

value: F


title: PASMC-healthy control 2

city: Kingston

first: Stephen

last: Archer

state: Ontario

address: 94 Stuart Street

department: Medicine

country: Canada

institute: Queen's University

hyb_protocol: Hybridization at 48ºC for 16-18 hours.

scan_protocol: Fluorescent signals were captured using the Affymetrix GeneChip Scanner 3000

data_processing: Subsequent signal normalization (rma) and analysis were performed using the Affymetrix Expression Console and Transcriptome Analysis Console software, respectively. A pre specified 2-fold change threshold and ANOVA P < 0.05 was used as selection criteria for significantly regulated human miRNAs.

source_name: PASMC-healthy control

label_protocol: RNA samples were prepared using the FlashTag Biotin HSR RNA Labeling Kit (Affymetrix) according to manufacterers recommendations.

growth_protocol: PAH PASMC were isolated from PAH patients. Normal PASMC were isolated from control subjects. PASMC lines were studied within 6 passages

extract_protocol: extracted using the mirVana miRNA isolation kit (Ambion/Life Technologies) according to manufacturer’s protocol. RNA quality was assessed by measurement of absorbance at 260nm and 280nm using a spectrophotometer (cutoff of 1.8-2.2) and by calculation of a RNA integrity number (RIN) in an Agilent Bioanalyzer (RIN > 6).

treatment_protocol: No treatment was performed

tag: disease state

value: healthy


title: PASMC-pulmonary arterial hypertension 6

source_name: PASMC-pulmonary arterial hypertension

value: pulmonary arterial hypertension patient


title: Brain_IT24 [9343114042_R02C02]

source_name: Brain


title: GAPDH_Linearity_Rep1_RNA_Conc200_R46

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R46


title: PASMC-healthy control 3


title: PASMC-pulmonary arterial hypertension 5


title: Blood Buffy_IT10 [9305651029_R05C02]


title: miR17_Linearity_Rep1_RNA_Conc2_R128

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R128


title: GAPDH_Linearity_Rep1_RNA_Conc200_R49

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R49


title: miR17_Linearity_Rep1_RNA_Conc2_R129

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R129


title: miR17_Linearity_Rep1_RNA_Conc2_R130

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R130


title: Blood Buffy_IT17 [9305651085_R01C01]


title: miR17_Linearity_Rep1_RNA_Conc2_R134

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R134


title: miR17_Linearity_Rep1_RNA_Conc2_R132

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R132


title: Blood Buffy_IT2 [9305651136_R03C02]


title: miR17_Linearity_Rep1_RNA_Conc2_R131

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R131


title: PASMC-healthy control 1


title: GAPDH_Linearity_Rep1_RNA_Conc200_R36

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R36


title: GAPDH_Linearity_Rep1_RNA_Conc200_R37

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R37


title: GAPDH_Linearity_Rep1_RNA_Conc200_R38

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R38


title: GAPDH_Linearity_Rep1_RNA_Conc200_R33

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R33


title: miR17_Linearity_Rep1_RNA_Conc2_R125

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R125


title: GAPDH_Linearity_Rep1_RNA_Conc200_R40

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R40


title: miR17_Linearity_Rep1_RNA_Conc2_R123

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R123


title: miR17_Linearity_Rep1_RNA_Conc2_R122

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R122


title: miR17_Linearity_Rep1_RNA_Conc2_R121

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R121


title: PASMC-pulmonary arterial hypertension 4


title: GAPDH_Linearity_Rep1_RNA_Conc200_R42

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R42


title: GAPDH_Linearity_Rep1_RNA_Conc200_R29

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R29


title: miR17_Linearity_Rep1_RNA_Conc2_R139

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R139


title: Blood Buffy_IT15 [9305651029_R03C02]


title: GAPDH_Linearity_Rep1_RNA_Conc200_R27

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R27


title: Blood Buffy_IT14 [9305651117_R04C01]


title: Blood Buffy_IT13 [9305651077_R04C01]


title: GAPDH_Linearity_Rep1_RNA_Conc200_R39

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R39


title: miR17_Linearity_Rep1_RNA_Conc2_R127

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R127


title: PASMC-pulmonary arterial hypertension 3


title: PASMC-pulmonary arterial hypertension 1


title: PASMC-pulmonary arterial hypertension 2


title: Blood Buffy_IT4 [9305651177_R01C02]


title: GAPDH_Linearity_Rep1_RNA_Conc200_R34

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R34


title: miR17_Linearity_Rep1_RNA_Conc2_R115

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R115


title: GAPDH_Linearity_Rep1_RNA_Conc200_R26

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R26


title: miR17_Linearity_Rep1_RNA_Conc2_R124

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R124


title: Adipose.14d.HFD.rep4

city: Camperdown, Sydney

first: Rima

last: Chaudhuri

state: NSW

address: D17 Johns Hopkins Drive

department: Charles Perkins Center

country: Australia

institute: University of Sydney

hyb_protocol: Fifteen micrograms of labeled cRNA was fragmented by incubating at 94°C for 30 min in 40 mM Tris-acetate pH 8.1, 100 mM potassium acetate and 30 mM magnesium acetate. Ten micrograms of fragmented cRNA was then hybridized to Mouse Genome 430 2.0 arrays at 45°C for 19 hours in a rotisserie oven set at 60 rpm.

scan_protocol: Arrays were washed and stained in the Affymetrix Fluidics station and scanned on GeneChip scanner 3000.

data_processing: Data analysis files were generated using manufacturer’s GeneChip Command Console system (Affymterix).

organism: Mus musculus

source_name: adipose tissue

label_protocol: The methods for preparation of labeled cRNA and array hybridization were provided by Affymetrix (Santa Clara, CA). Briefly, 3 ug of total RNA was converted into double-stranded cDNA using a cDNA synthesis kit SuperScript Choice (Invitrogen, Carlsbad, CA) and a T7-(dT)24 oligomer primer (Integrated DNA Technologies, Coralville, IO). Double-stranded cDNA was purified using affinity resin Sample Cleanup Module Kit (Affymetrix). Labeled cRNA was generated using a T7 RNA polymerase and biotin-labeled nucleotides in an in vitro transcription reaction (Enzo Diagnostics, Farmingdale, NY). The labeled cRNA was purified using Sample Cleanup Module Kit (Affymetrix).

growth_protocol: C57Bl/6 mice were group housed on a 12-h light/dark cycle with free access to food and water.

extract_protocol: Total RNA was isolated using Qiagen Kit.

treatment_protocol: Mice were fed a standard chow (13% of calories from fat) diet until 6 weeks of age and then either continued on standard chow, or fed a high fat diet (HFD, 46% of calories from fat) for 5 days or 14 days.

tag: strain

tag: diet

value: 14 day high fat


title: GAPDH_Linearity_Rep1_RNA_Conc200_R24

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R24


title: GAPDH_Linearity_Rep1_RNA_Conc200_R31

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R31


title: GAPDH_Linearity_Rep1_RNA_Conc200_R32

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R32


title: GAPDH_Linearity_Rep1_RNA_Conc200_R35

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R35


title: miR17_Linearity_Rep1_RNA_Conc2_R126

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R126


title: miR17_Linearity_Rep1_RNA_Conc2_R114

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R114


title: GAPDH_Linearity_Rep1_RNA_Conc200_R30

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R30


title: miR17_Linearity_Rep1_RNA_Conc2_R120

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R120


title: miR17_Linearity_Rep1_RNA_Conc2_R111

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R111


title: GAPDH_Linearity_Rep1_RNA_Conc200_R28

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R28


title: GAPDH_Linearity_Rep1_RNA_Conc200_R21

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R21


title: miR17_Linearity_Rep1_RNA_Conc2_R109

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R109


title: miR17_Linearity_Rep1_RNA_Conc2_R116

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R116


title: miR17_Linearity_Rep1_RNA_Conc2_R119

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R119


title: siRNAm_vs_Contr_repl1

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

country: Spain

institute: Centro Nacinal de Biotecnologia-CSIC

hyb_protocol: 825 ng of Cy3 and Cy5 probes were mixed and hybridized for 17 hours at 65ºC in GEx Hybridization Buffer HI-RPM in a hybridization oven. Arrays were washed according to the manufacturer’s instructions and dried by centrifugation.

scan_protocol: Images were scanned at 5mm resolution on Agilent DNA Microarrays Scanner (G2565BA, Agilent Technologies) and they were analyzed with Feature Extraction software (Agilent Technologies).

data_processing: Raw intensities were background-substracted by NORMEXP method with a offset of 50. Signals (in log2 scale) were then normalized by LOWESS algorithm (intra-arrays normalization) followed by adjustment of their quantiles (inter-arrays normalization).

source_name: Control

label_protocol: 200 ng of total RNA were reverse transcribed using oligo dT-T7 primer, and cDNA converted into aRNA using T7 RNA polimerase, that simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP. All the step were carried put according to 'Two color Microarray-Based GeneExpression Analysis Protocol', Agilent Technologies )

growth_protocol: HEK293T cells were grown in DEMEM + 10% bovine serum

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen, 15596-026) according to manufacturer's instructions and purified with an RNeasy mini kit (Qiagen, 74104).

treatment_protocol: HEK293T cells were transfected with plasmids expressing a control siRNA or a siRNA especific for CHD6 protein. 48H post-transfection, total RNA was isolated and used for transcriptome analysis.

tag: sirna

value: control siRNA

source_name: siRNAm

value: siRNA especific for CHD6 protein


title: miR17_Linearity_Rep1_RNA_Conc2_R107

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R107


title: miR17_Linearity_Rep1_RNA_Conc2_R117

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R117


title: siRNAm_vs_Contr_repl3


title: siRNAm_vs_Contr_repl4


title: miR17_Linearity_Rep1_RNA_Conc2_R118

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R118


title: GAPDH_Linearity_Rep1_RNA_Conc200_R25

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R25


title: Adipose.5d.HFD.rep2

value: 5 day high fat


title: siRNAm_vs_Contr_repl2


title: GAPDH_Linearity_Rep1_RNA_Conc200_R18

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R18


title: miR17_Linearity_Rep1_RNA_Conc2_R113

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R113


title: miR17_Linearity_Rep1_RNA_Conc2_R112

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R112


title: Adipose.14d.HFD.rep1


title: Adipose.Chow.rep2

value: standard chow


title: miR17_Linearity_Rep1_RNA_Conc2_R105

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R105


title: Adipose.14d.HFD.rep2


title: Adipose.5d.HFD.rep4


title: GAPDH_Linearity_Rep1_RNA_Conc200_R22

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R22


title: GAPDH_Linearity_Rep1_RNA_Conc200_R20

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R20


title: miR17_Linearity_Rep1_RNA_Conc20_R103

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R103

value: 20 pg


title: Adipose.14d.HFD.rep3


title: miR17_Linearity_Rep1_RNA_Conc2_R108

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R108


title: miR17_Linearity_Rep1_RNA_Conc20_R102

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R102


title: Adipose.5d.HFD.rep3


title: miR17_Linearity_Rep1_RNA_Conc20_R101

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R101


title: GAPDH_Linearity_Rep1_RNA_Conc200_R23

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R23


title: miR17_Linearity_Rep1_RNA_Conc2_R110

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R110


title: Dex.rep2

source_name: Adipose Tissue

growth_protocol: 3T3-L1 preadipocytes were differentiated into adipocytes using established protocols (PMID: 10926832).

extract_protocol: The cells were harvested and total RNA was isolated using Qiagen Kit.

treatment_protocol: Hyperinsulinemia (CI) was mimicked by addition of 10 nM insulin to adipocytes at 1200, 1600, and 2000 hr on day 1 and 0800 hr on the following day. Glucocorticoid-induced insulin resistance (DEX) was created with 20 nM dexamethasone (0.01% ethanol carrier as control) changed every other day for 8 days. Chronic low-dose inflammation (TNF) was mimicked in 3T3-L1 adipocytes by incubation with 2 ng/ml TNFα for 4 days. Treatments were staggered so that cells were the same day post-differentiation when processed.

tag: tissue

value: adipose

tag: treatment


title: Dex.rep1

value: 20 nM dexamethasone (0.01% ethanol carrier as control) changed every other day for 8 days


title: miR17_Linearity_Rep1_RNA_Conc20_R99

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R99


title: GAPDH_Linearity_Rep1_RNA_Conc200_R17

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R17


title: GAPDH_Linearity_Rep1_RNA_Conc200_R19

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R19


title: TNF.rep3

value: 2 ng/ml TNF[alpha] for 4 days


title: Adipose.5d.HFD.rep1


title: GAPDH_Linearity_Rep1_RNA_Conc200_R12

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R12


title: Adipose.Chow.rep3


title: Adipose.Chow.rep4


title: VP16-SOX9∆TAD-1

city: Paris

first: Masaya

last: OSHIMA

address: 123 boulevard de Port Royal

country: France

institute: INSERM U1016

description: VP16-SOX9∆TAD-ires-GFP transfected EndoC-ßH1 cells

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® Human Gene 2.0 ST (Affymetrix) at 45°C for 17 hours. After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix).

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

data_processing:
The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls. The observations of some of these metrics and the study of the distribution of raw data show no outlier experiment.
The data were analyzed with R Bioconductor packages using using RMA as normalization method

label_protocol: Total RNA is reverse transcribed following the GeneChip™ WT PLUS Reagent Kit (applied biosystems). Briefly, the resulting double strand cDNA is used for amplification based on SPIA technology. After purification according to Nugen protocol, 3.6 ug of Sens Target DNA are fragmented and biotin labelled using Encore Biotin Module kit (Nugen).

extract_protocol: RNeasy Micro kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: EndoC-ßH1 cells were transfected and sorted 48h post-transfection prior to RNA extraction

tag: cell type

value: VP16-SOX9∆TAD-ires-GFP transfected


title: VP16-SOX9∆TAD-2

source_name: VP16-SOX9∆TAD-ires-GFP transfected EndoC-ßH1 cells


title: TNF.rep1


title: VP16-2

description: VP16-ires-GFP transfected EndoC-ßH1 cells

value: VP16-ires-GFP transfected


title: miR17_Linearity_Rep1_RNA_Conc2_R106

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R106


title: CI.rep1

value: 10 nM insulin to adipocytes at 1200, 1600, and 2000 hr on day 1 and 0800 hr on the following day


title: miR17_Linearity_Rep1_RNA_Conc20_R97

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R97


title: GAPDH_Linearity_Rep1_RNA_Conc200_R16

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R16


title: GAPDH_Linearity_Rep1_RNA_Conc200_R7

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R7


title: Dex.rep3


title: GAPDH_Linearity_Rep1_RNA_Conc200_R14

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R14


title: GAPDH_Linearity_Rep1_RNA_Conc200_R15

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R15


title: GAPDH_Linearity_Rep1_RNA_Conc200_R5

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R5


title: GAPDH_Linearity_Rep1_RNA_Conc200_R11

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R11


title: miR17_Linearity_Rep1_RNA_Conc20_R104

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R104


title: GAPDH_Linearity_Rep1_RNA_Conc200_R13

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R13


title: miR17_Linearity_Rep1_RNA_Conc20_R93

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R93


title: miR17_Linearity_Rep1_RNA_Conc20_R98

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R98


title: miR17_Linearity_Rep1_RNA_Conc20_R100

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R100


title: SOX9WT-1

description: SOX9WT-ires-GFP transfected EndoC-ßH1 cells

value: SOX9WT-ires-GFP transfected


title: GAPDH_Linearity_Rep1_RNA_Conc200_R10

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R10


title: MCS-2

description: MCS-ires-GFP transfected EndoC-ßH1 cells

value: MCS-ires-GFP transfected


title: 3t3-L1.rep3


title: CI.rep2


title: Adipose.Chow.rep1


title: miR17_Linearity_Rep1_RNA_Conc20_R96

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R96


title: miR17_Linearity_Rep1_RNA_Conc20_R91

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R91


title: GAPDH_Linearity_Rep1_RNA_Conc200_R8

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R8


title: SM_RNA_Conc0.008_R206

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R206

source_name: K562 total RNA at limiting dilution

tag: dilution

value: 0.008× relative to highest concentration


title: miR17_Linearity_Rep1_RNA_Conc20_R89

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R89


title: GAPDH_Linearity_Rep1_RNA_Conc200_R9

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R9


title: GAPDH_Linearity_Rep1_RNA_Conc200_R6

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R6


title: miR17_Linearity_Rep1_RNA_Conc20_R95

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R95


title: 3t3-L1.rep2


title: GAPDH_Linearity_Rep1_RNA_Conc200_R4

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R4


title: SOX9WT-2

source_name: SOX9WT-ires-GFP transfected EndoC-ßH1 cells


title: SM_RNA_Conc0.008_R185

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R185


title: Sample _E

type: SRA

city: Nantes

first: Victor

last: GOURAIN

address: 30 Bd Jean Monnet

institute: Centre de recherche en transplantation et immunologie

library_source: transcriptomic

data_processing:
Base-calling with bcl2fastq
alignment with tophat 2
raw expression with HTSeq in union mode
normalization with the R packages DESeq2
differential expression analysis with the R packages DESeq2
Genome_build: GRCm38_75
Supplementary_files_format_and_content: raw count at gene level, output of HTSeq

source_name: Bone marrow

growth_protocol: Bone marrow derived mast cells were obtained by culturing  cells from the femur and tibia of  male C57BL/6 mice aged 8-10 weeks  for 4 weeks in mast cell medium (IMDM supplemented with 10% FBS, 2 mML-glutamine, I mM pyruvate, 100 ng stem cell factor/kit ligand, 5 ng/ml IL3, 50 µM β-mecaptoethanol, 1% penicillin/streptomycin 10000 U/ml) in T-75 flask  at 37°C, 5% CO2 and 95% humidity in an incubator. BMMC medium was changed every three days. To do this, cells in suspension (BMMCs) were centrifuged at 1300 rpm for 7 min, to pellet the BMMCs after which they are recultured.

extract_protocol:
Total RNA was extracted from 3 × 10^6 cells for PEP+/+ and PEP-/- BMMCs using innuPREP RNA Mini Kit (Analytik Jena AG, Jena, Germany)
TruSeq stranded mRNA kit v2 (Illumina)

treatment_protocol: Samples 1 & A  are replicates for PEP+/+  BMMCs treated with IgE (0.05 µg/ml)  for  3 h. Samples 2 & B  are replicates for PEP+/+  BMMCs treated with Dex (10^-7 M) for 8 h and IgE (0.05 µg/ml) for 3 h. Samples 3 & C  are replicates for PEP+/+  BMMCs treated with IgE (0.05 µg/ml)  for  3 h and DNP (200 ng/ml) for 1 h. Samples 4 & D  are replicates for PEP+/+  BMMCs treated with  Dex (10^-7 M) for 8 h, IgE (0.05 µg/ml)  for  3 h, and DNP (200 ng/ml) for 1 h. Samples 5 & E  are replicates for PEP-/-  BMMCs treated with IgE (0.05 µg/ml)  for  3 h. Samples 6 & F  are replicates for PEP-/-  BMMCs treated Dex (10^-7 M) for  8 h and IgE (0.05 µg/ml) for  3 h. Samples 7 & G  are replicates for PEP-/-  BMMCs treated with IgE (0.05 µg/ml)  for  3 h and DNP (200 ng/ml) for 1 h. Samples 8 & H  are replicates for PEP-/-  BMMCs treated with Dex for 8 h, IgE (0.05 µg/ml)  for 3 h and DNP (200 ng/ml) for 1 h.

tag: genotype

value: PEP-/-

value: IgE (0.05 µg/ml) for 3 h.

value: Bone marrow derived mast cells (BMMCs)

tag: age of tissue in culture

value: 4 weeks

tag: gender

value: male


title: Sample _F

value: Dex (10^-7 M) for 8 h and IgE (0.05 µg/ml) for 3 h.


title: TNF.rep2


title: SM_RNA_Conc0.008_R183

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R183


title: miR17_Linearity_Rep1_RNA_Conc20_R92

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R92


title: Sample _C

value: PEP+/+

value: IgE (0.05 µg/ml) for 3 h and DNP (200 ng/ml) for 1 h.


title: GAPDH_Linearity_Rep1_RNA_Conc200_R3

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R3


title: miR17_Linearity_Rep1_RNA_Conc20_R94

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R94

value: 20 pg


title: VP16-1

description: VP16-ires-GFP transfected EndoC-ßH1 cells


title: Sample _H

value: Dex (10^-7 M) for 8 h, IgE (0.05 µg/ml) for 3 h and DNP (200 ng/ml) for 1 h.


title: 3t3-L1.rep1

value: adipose


title: Sample _B


title: GAPDH_Linearity_Rep1_RNA_Conc200_R2

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R2


title: GAPDH_Linearity_Rep1_RNA_Conc200_R1

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against GAPDH. Chip cell processing unit R1


title: MCS-1

description: MCS-ires-GFP transfected EndoC-ßH1 cells


title: Sample _G


title: Sample _D

value: Dex (10^-7 M) for 8 h, IgE (0.05 µg/ml) for 3 h, and DNP (200 ng/ml) for 1 h.


title: miR17_Linearity_Rep1_RNA_Conc20_R90

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R90


title: miR17_Linearity_Rep1_RNA_Conc20_R84

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R84


title: miR17_Linearity_Rep1_RNA_Conc20_R87

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R87


title: Sample _7


title: Sample _8


title: miR17_Linearity_Rep1_RNA_Conc20_R85

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R85


title: miR17_Linearity_Rep1_RNA_Conc20_R82

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R82


title: miR17_Linearity_Rep1_RNA_Conc20_R81

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R81


title: SM_RNA_Conc0.008_R175

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R175


title: Sample _4


title: SM_RNA_Conc0.008_R176

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R176


title: miR17_Linearity_Rep1_RNA_Conc20_R86

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R86


title: SM_RNA_Conc0.04_R139

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R139

value: 0.04× relative to highest concentration


title: Sample _6


title: miR17_Linearity_Rep1_RNA_Conc20_R83

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R83


title: miR17_Linearity_Rep1_RNA_Conc20_R88

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R88


title: SM_RNA_Conc0.008_R161

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R161


title: donor_6_rep_3

city: Nizhny Novgorod

first: Dmitry

last: Knyazev

address: Malaya Yamskaya, 71

country: Russia

institute: I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology

hyb_protocol: Fragmented labeled RNA (2 ug) was hybridized at 40oC for 18-20 hours in Hyb-solution (6xSSPE, 20mM EDTA, 0,05% Tween-20, salmon sperm DNA 10 mg/ml, 0,04% SDS,  formamide 25%vol). Arrays were sequentially washed  by 3хSSPE, 0,05% Tween-20 → 0,5хSSPE, 0,05% ТTween20 → 2xPBS 0,1% Tween-20. Subsequent blocking, labeling, label wash, substrate solution treatment were fulfilled using ElectraSense Detection Kit (CustomArray Inc., WA, USA)

scan_protocol: Amperometric signal measurements were performed using ElectraSense Reader device and ElectraSense application software (CustomArray Inc., WA, USA)

data_processing: Feature data from .ecd-files was exported to csv.-files using ElectraSense Analysis 3.4.2. All calculations were performed in Python and R. Background correction was made using rma.background.correct  function from preprocessCore package [Bolstad B (2017). preprocessCore: A collection of pre-processing functions. R package version 1.40.0, https://github.com/bmbolstad/preprocessCore.] . MM-probes were excluded from processed data. Samples of same type were organized in matrix 1042xN, where 1042 – number of probes and N – number of repeating measures of sample. Two matrix of samples to compare were normalized using normalize.quantiles.robust function from preprocessCore package [Bolstad B (2017). preprocessCore: A collection of pre-processing functions. R package version 1.40.0, https://github.com/bmbolstad/preprocessCore.] . To calculate fold-change and its significance, stats.ttest function from scipy.stats package [Jones E, Oliphant E, Peterson P, et al. SciPy: Open Source Scientific Tools for Python, 2001-, http://www.scipy.org/ [Online; accessed 2017-11-13] was used. subColSummarizeMedianpolish [Bolstad B (2017). preprocessCore: A collection of pre-processing functions. R package version 1.40.0, https://github.com/bmbolstad/preprocessCore.] was used to calculate overall gene expression, using all the probes aimed to isoforms of a gene. P=0.05 was selected as threshold value. Fold-changes ≥ 1,1 and ≤ -1,1 were taken into consideration.

source_name: peripheral blood leukocytes

label_protocol: 1. Total RNA (1,5-2 ug) was converted to T7promoter-containing cDNA by Mint cDNA synthesis kit (Evrogen, Russia, http://evrogen.ru/technologies/Mint-cDNA-synthesis.shtml), kit' 3'-oligo-T-primer was replaced by T7promoter-containing-oligo-T-primer (DNA-synthesis, Russia); 2. cDNA was complemented to ds-cDNA by 15-cycles PCR amplification; 3. ds-cDNA (2 ug) was transcribed by T7 RNA-polimerase (Thermo Scientific, EU). Biotin-labeled RNA was obtained using biotinylated UTP (DNA-synthesis, Russia) by substitution of a half of its unlabeled counterpart in reaction mix.

extract_protocol: Total RNA was isolated by magnetic beads-containg kit (Magnosorb kit, Russia) followed by phenol-chloroform purification


title: donor_6_rep_1


title: donor_5_rep_3

value: female


title: SM_RNA_Conc0.008_R165

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R165


title: SM_RNA_Conc0.008_R174

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R174


title: Sample _A


title: miR17_Linearity_Rep1_RNA_Conc20_R77

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R77


title: donor_6_rep_2


title: Sample _1


title: Sample _5


title: miR17_Linearity_Rep1_RNA_Conc20_R80

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R80


title: SM_RNA_Conc0.04_R140

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R140


title: donor_5_rep_1


title: Sample _2


title: miR17_Linearity_Rep1_RNA_Conc20_R79

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R79


title: SM_RNA_Conc0.2_R94

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R94

value: 0.2× relative to highest concentration


title: Sample _3


title: donor_4_rep_2


title: donor_5_rep_2


title: SM_RNA_Conc0.2_R103

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R103


title: SM_RNA_Conc0.04_R152

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R152


title: SM_RNA_Conc0.04_R114

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R114


title: miR17_Linearity_Rep1_RNA_Conc20_R74

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R74


title: donor_3_rep_3


title: donor_4_rep_3


title: miR17_Linearity_Rep1_RNA_Conc20_R78

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R78


title: miR17_Linearity_Rep1_RNA_Conc20_R72

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R72


title: SM_RNA_Conc0.2_R87

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R87


title: SM_RNA_Conc0.2_R77

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R77


title: miR17_Linearity_Rep1_RNA_Conc20_R76

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R76


title: SM_RNA_Conc0.2_R88

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R88


title: SM_RNA_Conc0.2_R76

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R76


title: SM_RNA_Conc0.2_R75

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R75


title: miR17_Linearity_Rep1_RNA_Conc20_R68

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R68


title: miR17_Linearity_Rep1_RNA_Conc20_R75

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R75


title: SM_RNA_Conc0.2_R93

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R93


title: donor_2_rep_2


title: SM_RNA_Conc0.2_R74

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R74


title: donor_4_rep_1


title: miR17_Linearity_Rep1_RNA_Conc20_R66

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R66


title: miR17_Linearity_Rep1_RNA_Conc20_R67

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R67


title: miR17_Linearity_Rep1_RNA_Conc20_R65

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R65


title: donor_1_rep_3


title: SM_RNA_Conc0.2_R80

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R80


title: donor_3_rep_2


title: miR17_Linearity_Rep1_RNA_Conc20_R63

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R63


title: donor_2_rep_3


title: miR17_Linearity_Rep1_RNA_Conc20_R69

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R69


title: SM_RNA_Conc0.2_R68

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R68


title: miR17_Linearity_Rep1_RNA_Conc20_R71

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R71


title: miR17_Linearity_Rep1_RNA_Conc20_R61

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R61


title: miR17_Linearity_Rep1_RNA_Conc20_R73

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R73


title: donor_2_rep_1


title: SM_RNA_Conc0.2_R73

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R73


title: patient_5_recovery_rep1 CMV

tag: Stage

value: after recovery


title: SM_RNA_Conc0.2_R65

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R65

tag: cell line


title: donor_3_rep_1


title: SM_RNA_Conc0.2_R61

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R61


title: SM_RNA_Conc0.2_R60

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R60


title: miR17_Linearity_Rep1_RNA_Conc20_R57

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R57

tag: concentration


title: miR17_Linearity_Rep1_RNA_Conc20_R58

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R58


title: SM_RNA_Conc0.2_R86

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R86


title: patient_5_recovery_rep3 CMV


title: miR17_Linearity_Rep1_RNA_Conc20_R70

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R70


title: donor_1_rep_1


title: SM_RNA_Conc0.2_R71

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R71


title: SM_RNA_Conc0.2_R56

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R56


title: miR17_Linearity_Rep1_RNA_Conc20_R62

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R62


title: SM_RNA_Conc0.2_R67

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R67


title: donor_1_rep_2


title: SM_RNA_Conc0.2_R66

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R66


title: SM_RNA_Conc0.2_R69

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R69


title: miR17_Linearity_Rep1_RNA_Conc20_R64

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R64


title: patient_5_acute_rep3 CMV

value: acute mononucleosis


title: patient_5_recovery_rep2 CMV


title: miR17_Linearity_Rep1_RNA_Conc20_R54

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R54


title: miR17_Linearity_Rep1_RNA_Conc20_R60

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R60


title: miR17_Linearity_Rep1_RNA_Conc20_R55

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R55


title: SM_RNA_Conc0.2_R54

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R54


title: patient_5_acute_rep1 CMV


title: miR17_Linearity_Rep1_RNA_Conc200_R52

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R52


title: patient_4_recovery_rep2 CMV


title: patient_4_acute_rep2 CMV


title: SM_RNA_Conc1_R51

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R51

value: 1× relative to highest concentration


title: patient_4_recovery_rep1 CMV


title: patient_4_recovery_rep3 CMV


title: patient_4_acute_rep1 CMV


title: miR17_Linearity_Rep1_RNA_Conc20_R53

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R53


title: patient_3_recovery_rep2 CMV


title: patient_4_acute_rep3 CMV


title: miR17_Linearity_Rep1_RNA_Conc20_R56

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R56


title: miR17_Linearity_Rep1_RNA_Conc200_R51

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R51


title: patient_5_acute_rep2 CMV


title: miR17_Linearity_Rep1_RNA_Conc200_R50

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R50


title: SM_RNA_Conc1_R50

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R50


title: miR17_Linearity_Rep1_RNA_Conc20_R59

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R59


title: SM_RNA_Conc0.2_R53

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R53


title: SM_RNA_Conc1_R46

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R46


title: SM_RNA_Conc1_R44

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R44


title: SM_RNA_Conc1_R48

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R48


title: patient_3_recovery_rep3 CMV


title: miR17_Linearity_Rep1_RNA_Conc200_R44

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R44


title: miR17_Linearity_Rep1_RNA_Conc200_R48

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R48


title: SM_RNA_Conc1_R47

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R47


title: SM_RNA_Conc1_R43

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R43


title: miR17_Linearity_Rep1_RNA_Conc200_R49

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R49


title: patient_2_recovery_rep3 CMV


title: patient_3_acute_rep1 CMV


title: patient_3_acute_rep2 CMV


title: patient_2_recovery_rep1 CMV


title: patient_2_recovery_rep2 CMV


title: patient_2_acute_rep3 CMV


title: SM_RNA_Conc1_R40

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R40


title: patient_3_acute_rep3 CMV


title: 35S::SUP-GR Mock_rep3

city: Singapore

first: Yifeng

last: XU

address: 1 Research Link

country: Singapore

institute: Temasek Life Sciences Laboratory

hyb_protocol: Hybridization was performed  following NimbleGen standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed  following NimbleGen standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Arabidopsis thaliana

source_name: 35S::SUP-GR in Ler wild-type

label_protocol: Labeling was performed following NimbleGen standard operating protocol. See www.nimblegen.com.

growth_protocol: The seeds of the indicated genotype were planted on soil, and grown at 22°C under continuous light conditions. The inflorescence with flower buds earlier than stage 10 was sampled from Mock and DEX-treated plants.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).

treatment_protocol: 10 µm dexamethasone diluted from a 30 mM stock in ethanol were used for the DEX treatment, while the Mock treatment was conducted with the same amount of ethanol, by inverting the plants and submerging the inflorescence for 1 min in solution containing either 10 µm DEX  or ethanol, together with 0.015% Silwet L-77.

value: 35S::SUP-GR in Ler wild-type

value: mock

tag: phenotype

value: control

value: inflorescences with flower buds earlier than stage 10


title: 35S::SUP-GR Mock_rep2


title: 35S::SUP-GR Mock_rep1


title: miR17_Linearity_Rep1_RNA_Conc200_R38

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R38


title: miR17_Linearity_Rep1_RNA_Conc200_R47

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R47


title: SM_RNA_Conc1_R45

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R45


title: miR17_Linearity_Rep1_RNA_Conc200_R45

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R45


title: miR17_Linearity_Rep1_RNA_Conc200_R43

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R43


title: SM_RNA_Conc1_R42

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R42


title: SM_RNA_Conc1_R41

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R41


title: miR17_Linearity_Rep1_RNA_Conc200_R46

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R46


title: SM_RNA_Conc1_R49

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R49


title: miR17_Linearity_Rep1_RNA_Conc200_R37

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R37


title: SM_RNA_Conc0.2_R59

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R59


title: 35S::SUP-GR DEX_rep2

value: DEX

value: DEX treatment will lead to reduced size in organs


title: SM_RNA_Conc1_R35

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R35


title: patient_1_recovery_rep2 CMV

value: male

tag: age


title: miR17_Linearity_Rep1_RNA_Conc200_R36

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R36


title: patient_1_acute_rep3 CMV


title: 35S::SUP-GR DEX_rep1


title: patient_1_acute_rep2 CMV


title: miR17_Linearity_Rep1_RNA_Conc200_R42

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R42


title: 35S::SUP-GR DEX_rep3


title: miR17_Linearity_Rep1_RNA_Conc200_R40

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R40


title: miR17_Linearity_Rep1_RNA_Conc200_R34

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R34


title: miR17_Linearity_Rep1_RNA_Conc200_R39

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R39


title: SM_RNA_Conc1_R37

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R37


title: patient_1_acute_rep1 CMV


title: SM_RNA_Conc1_R39

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R39


title: patient_2_acute_rep2 CMV


title: miR17_Linearity_Rep1_RNA_Conc200_R32

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R32


title: patient_4_recovery_rep3 EBV


title: miR17_Linearity_Rep1_RNA_Conc200_R41

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R41


title: SM_RNA_Conc1_R31

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R31


title: SM_RNA_Conc1_R38

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R38


title: patient_1_recovery_rep3 CMV


title: SM_RNA_Conc1_R34

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R34


title: miR17_Linearity_Rep1_RNA_Conc200_R31

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R31


title: patient_1_recovery_rep1 CMV


title: patient_2_acute_rep1 CMV


title: miR17_Linearity_Rep1_RNA_Conc200_R35

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R35


title: miR17_Linearity_Rep1_RNA_Conc200_R30

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R30


title: SM_RNA_Conc1_R32

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R32


title: patient_3_recovery_rep1 CMV


title: miR17_Linearity_Rep1_RNA_Conc200_R29

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R29


title: miR17_Linearity_Rep1_RNA_Conc200_R33

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R33


title: miR17_Linearity_Rep1_RNA_Conc200_R28

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R28


title: patient_4_recovery_rep2 EBV


title: SM_RNA_Conc1_R29

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R29


title: patient_4_acute_rep2 EBV


title: SM_RNA_Conc1_R30

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R30


title: patient_4_acute_rep1 EBV


title: patient_3_recovery_rep2 EBV


title: miR17_Linearity_Rep1_RNA_Conc200_R26

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R26


title: patient_4_acute_rep3 EBV


title: SM_RNA_Conc1_R25

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R25


title: miR17_Linearity_Rep1_RNA_Conc200_R25

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R25


title: patient_3_acute_rep3 EBV


title: SM_RNA_Conc1_R33

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R33


title: SM_RNA_Conc1_R23

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R23


title: miR17_Linearity_Rep1_RNA_Conc200_R27

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R27


title: SM_RNA_Conc1_R27

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R27


title: SM_RNA_Conc1_R28

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R28


title: patient_4_recovery_rep1 EBV


title: patient_3_recovery_rep3 EBV


title: patient_3_recovery_rep1 EBV


title: SM_RNA_Conc1_R21

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R21


title: SM_RNA_Conc1_R36

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R36


title: patient_3_acute_rep1 EBV


title: patient_3_acute_rep2 EBV


title: SM_RNA_Conc1_R24

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R24


title: SM_RNA_Conc1_R22

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R22


title: miR17_Linearity_Rep1_RNA_Conc200_R22

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R22


title: SM_RNA_Conc1_R18

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R18


title: miR17_Linearity_Rep1_RNA_Conc200_R23

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R23


title: patient_2_recovery_rep2 EBV


title: SM_RNA_Conc1_R26

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R26


title: patient_2_acute_rep3 EBV


title: miR17_Linearity_Rep1_RNA_Conc200_R24

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R24


title: miR17_Linearity_Rep1_RNA_Conc200_R18

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R18


title: SM_RNA_Conc1_R17

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R17


title: SM_RNA_Conc1_R16

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R16


title: SM_RNA_Conc1_R19

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R19


title: patient_2_recovery_rep3 EBV


title: SM_RNA_Conc1_R20

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R20


title: patient_2_recovery_rep1 EBV


title: SM_RNA_Conc1_R14

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R14


title: miR17_Linearity_Rep1_RNA_Conc200_R19

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R19


title: miR17_Linearity_Rep1_RNA_Conc200_R20

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R20


title: miR17_Linearity_Rep1_RNA_Conc200_R21

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R21


title: SM_RNA_Conc1_R15

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R15


title: miR17_Linearity_Rep1_RNA_Conc200_R16

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R16


title: patient_2_acute_rep2 EBV


title: miR17_Linearity_Rep1_RNA_Conc200_R17

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R17


title: patient_2_acute_rep1 EBV


title: SM_RNA_Conc1_R13

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R13


title: SM_RNA_Conc1_R12

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R12


title: miR17_Linearity_Rep1_RNA_Conc200_R14

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R14


title: miR17_Linearity_Rep1_RNA_Conc200_R15

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R15


title: patient_1_acute_rep1 EBV


title: patient_1_acute_rep3 EBV


title: miR17_Linearity_Rep1_RNA_Conc200_R13

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R13


title: thoracic aorta 2

first: Marja

last: Steenman

address: 8 quai Moncousu

institute: L'institut du thorax

description:
H215_5
primary SMCs from thoracic aorta rep2

hyb_protocol: 600 ng of Cy3-labeled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent Hi-RPM hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression microarrays (G4851B) 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). Next, microarrays were washed 30 seconds in acetonitrile and 30 seconds in Stabilization and Drying Solution.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data were normalized using R statistical software. Raw values of all probes on all arrays were normalized against a virtual median chip (median raw intensity per row) using a locally weighted scattered plot smoother analysis (LOWESS). Values for replicate probes were averaged. The data were filtered to remove probes with low intensity values.

source_name: primary SMCs from thoracic aorta

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from100 ng RNA using the Low Input QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using Macherey Nagel NucleoSpin columns. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was assessed using an Agilent 2200 TapeStation system.

treatment_protocol: Non atheromatous, healthy arteries were harvested from allografts obtained from deceased donors. Fresh tissue was washed with cold PBS and dissociated with an enzymatic mix including collagenase, elastase and DNase in High glucose DMEM. A first short digestion step permitted endothelial cell isolation. Then mechanical dissociation followed by a longer incubation with the digestion mix allowed SMC isolation. Occlusive debris was removed using a 70 µm mesh strainer. Additional centrifugation removed smaller debris. Cells were plated in gelatin-coated 12 wells plates in complete SMCBM2.

value: thoracic aorta

value: primary Smooth Muscle Cells (SMCs)


title: miR17_Linearity_Rep1_RNA_Conc200_R12

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R12


title: RE9

city: Beijing

first: Qian

last: Jiang

state: Beijing

address: No.56 Nanlishi Road Xicheng District Beijing

department: Hematology Oncology Centre

country: China

institute: Beijing Childrens' Hospital Capital Medical University

data_processing:
（SDS2.4）RQ Manager. The original ct values of the plasma miRNAs were normalized using the control miRNA: U6.
The Ct value is the number of PCR cycles when the fluorescence value reaches the threshold, which is a parameter without unit. The Ct value has a linear relationship with the logarithm of the original template copy number, and the more the initial copy number, the smaller the Ct value.

label: TaqMan®

source_name: plasma from child who was suffered relapse after chemotherapy

label_protocol: The reverse of RNA was performed using the TaqMan MicroRNA Reverse Transcription Kit following the Manufacturer’s instructions. Quantitative real-time PCR were performed (7900HT, ABI) with 12 cycles at 95℃ for 15 seconds and 60℃ for 4minutes. And hold at 99.9℃ for 10 minutes.

growth_protocol: The plasma that was seperated from the blood in 8 hours from the blood drawing,

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

treatment_protocol: The blood samples were stored in 4℃. Centifuge at the speed of 1500rpm/min for 10 minutes at 4℃ and repeat the procedure once. The plasma was stored at -80℃.


title: carotid artery 2

description:
H216_4
primary SMCs from carotid artery rep2

source_name: primary SMCs from carotid artery

value: carotid artery


title: carotid artery 1

description:
H206_16
primary SMCs from carotid artery rep1


title: thoracic aorta 1

description:
H205_8
primary SMCs from thoracic aorta rep1


title: miR17_Linearity_Rep1_RNA_Conc200_R11

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R11

source_name: K562 total RNA


title: RE7

value: plasma from child who was suffered relapse after chemotherapy


title: SM_RNA_Conc1_R10

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R10


title: infrapopliteal artery 2

description:
H204_6
primary SMCs from infrapopliteal artery rep2

source_name: primary SMCs from infrapopliteal artery

value: infrapopliteal artery


title: patient_1_acute_rep2 EBV


title: SM_RNA_Conc1_R9

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R9


title: abdominal aorta 2

description:
H212_10
primary SMCs from abdominal aorta rep2

source_name: primary SMCs from abdominal aorta

value: abdominal aorta


title: CR6

source_name: plasma from child who was reached bone marrow complete remission after chemotherapy


title: SM_RNA_Conc1_R8

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R8


title: RE8


title: CR5

value: plasma from child who was reached bone marrow complete remission after chemotherapy


title: SM_RNA_Conc1_R7

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R7


title: infrapopliteal artery 1

description:
H201_18
primary SMCs from infrapopliteal artery rep1


title: miR17_Linearity_Rep1_RNA_Conc200_R9

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R9


title: CR4


title: miR17_Linearity_Rep1_RNA_Conc200_R10

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R10


title: ND6

source_name: plasma from child who was new diagnosed with acute lymphoblastic leukemia


title: femoral artery 1

description:
H197_15
primary SMCs from femoral artery rep1

source_name: primary SMCs from femoral artery

value: femoral artery


title: SM_RNA_Conc1_R6

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R6


title: abdominal aorta 1

description:
H198_7
primary SMCs from abdominal aorta rep1


title: SM_RNA_Conc1_R5

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R5


title: miR17_Linearity_Rep1_RNA_Conc200_R8

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R8


title: miR17_Linearity_Rep1_RNA_Conc200_R7

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R7


title: SM_RNA_Conc1_R4

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R4


title: SM_RNA_Conc1_R3

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R3


title: ND4

value: plasma from child who was new diagnosed with acute lymphoblastic leukemia


title: K1_Kan, biological rep 1

city: Montpellier cedex1

first: Jean-Luc

last: Legras

address: 2, place Viala

department: UMR1083, Science pour l'Oenologie

institute: INRA

description: Gene expression in sample from K1_Kan strain, biological rep 1

hyb_protocol: Agilent gene expression microarrays 8x15k was used for the micro array hybridization, with one-color method. Array design is based on ID 016322 (Agilent Technologies, Santa Clara, CA, USA). A quantity of 600ng of labeled cRNA were hybridized for 17h in 65°C in a rotative hybridization oven (Corning) using the Expression Hybridization kit (Agilent Technologies, 5188-5242). Plate were washed with expression wash buffer kit (Agilent Technologies, 5188-5325 5188-5326).

scan_protocol: The array pictures were analyzed on a GenePix 4000B laser Scanner (Axon Instruments) and with the GenePix software Pro7

data_processing: Data normalization and statistical analysis were performed using R 2.14.2 software and the limma package. Normalization was done by the quantile method considering all arrays

organism: Saccharomyces cerevisiae

label_protocol: Cy3-labeled cRNA was synthesized with the One color RNA Spike-In kit (Agilent Technologies) and purified with RNeasy kit (Qiagen). Quality and quantity of RNA were controlled at each step by spectrometry (NanoDrop 1000, Thermo Scientific)

growth_protocol: Haploid (mat alpha) flor yeast strain  P3-D5 (indicated after P3_Kan as it carries a KanMx cassette) and  haploid wine yeast K1-280-2B (mat a)  were grown  in a shaken liquid culture performed at 28°C, on a synthetic media mimicking wine. Cells were harvested at 1 O.D at 600nm. As the cells are shaken flor yeast  do not produce a velum, nor wine strain that cannot produce any, so that in the end they grow in a similar maner.

extract_protocol: Total RNA extraction were perform with Trizol reagent (Gibco BRL, Life Technologies), purified by isopropanol precipitation then with RNeasy kit (Qiagen).

tag: yeast type

value: wine

tag: array

tag: block


title: miR17_Linearity_Rep1_RNA_Conc200_R5

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R5


title: P3_Kan, biological rep 1

description: Gene expression in sample from P3_Kan strain, biological rep 1

tag: strain

value: flor


title: miR17_Linearity_Rep1_RNA_Conc200_R6

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R6


title: miR17_Linearity_Rep1_RNA_Conc200_R3

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R3


title: femoral artery 2

description:
H203_17
primary SMCs from femoral artery rep2


title: ND5


title: miR17_Linearity_Rep1_RNA_Conc200_R2

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R2


title: miR17_Linearity_Rep1_RNA_Conc200_R1

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R1


title: H2

source_name: plasma from healthy children

value: plasma from healthy children


title: H1


title: 4 sample-Lentigo

status: Public on Jan 30 2018

city: swon

first: Tea jun

last: Park

address: 206, World cup-ro, Yeongtong-gu

department: Biochemistry and Molecular Biology

country: South Korea

institute: Ajou University School of Medicine

hyb_protocol: not provided

scan_protocol: not provided

data_processing: normaliztion and R stats package and clustering and ontology.

source_name: Skin

label_protocol: not provided

extract_protocol: RNA extract from the tissue using MN kit

value: skin


title: H3


title: 4 sample-perilesional normal


title: 3 sample-perilesional normal


title: 3 sample-Lentigo


title: SM_RNA_Conc1_R1

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R1

value: 1× relative to highest concentration


title: K1_Kan, biological rep 2, technical rep 2

description: Gene expression in sample from K1_Kan strain, biological rep 2, technical rep 2


title: miR17_Linearity_Rep1_RNA_Conc200_R4

description: This is a sample of purified K562 RNA diluted the specified concentration per cell processing unit, and assayed against hsa-miR-17-5p. Chip cell processing unit R4


title: P3_Kan, biological rep 2, technical rep 2

description: Gene expression in sample from P3_Kan strain, biological rep 2, technical rep 2


title: P3_Kan, biological rep 3

description: Gene expression in sample from P3_Kan strain, biological rep 3


title: K1_Kan, biological rep 3

description: Gene expression in sample from K1_Kan strain, biological rep 3


title: 4T1 spheroid rep3

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

description:
4T1P2247F
cell grown in DMEM/Nutrient Mixture F-12 Ham

data_processing:
Quality control with FastQC v 0.11.6
Mappping was done using STAR v 2.5.0 and RSEM v 1.3.0.
Genome_build: mm10 and hg19 UCSC annotation
Supplementary_files_format_and_content: tab delimited, including transcript counts, FPKM and TPM

growth_protocol: Cells grown in RPMI-1640 supplemented with 10% fetal bovine serum (FBS, Sigma-Aldrich) and Penicillin/Streptomycin solution at 1x dilution (Sigma-Aldrich) (bulk)

extract_protocol:
Total RNA was isolated from 2 x 10^6 cells ausing the TriZol reagent (Thermo-Fisher Scientific) and following manufacturer’s instructions.
Libraries for RNA sequencing were generated using TruSeq RNA sample preparation kit v2 (Illumina Inc., San Diego, CA, USA) following manufacturer’s instructions, using 1 µg of total RNA as input material and 15 PCR cycles for DNA amplification. Libraries were quantified by Qubit 2.0 Fluorometer using ds DNA High Sensitivity Qubit Assay (Thermo-Fisher Scientific) and pooled together in equimolar amounts.

treatment_protocol: Cells grown in DMEM/Nutrient Mixture F-12 Ham (Sigma-Aldrich) supplemented with 0.4% bovine serum albumin (BSA, Sigma-Aldrich), 20 ng/mL bFGF (PeproTech EC Ltd., London, UK), 20 ng/mL EGF (Sigma-Aldrich) and 5 µg/mL insulin (Sigma-Aldrich).  (spheroids)

value: Triple-negative breast cancer (TNBC)


title: 4T1  bulk rep1

description:
4T1E274
cell grown in RPMI-1640


title: 4T1  bulk rep2

description:
4T1E266
cell grown in RPMI-1640


title: 4T1 spheroid rep1

description:
4T1P2247A
cell grown in DMEM/Nutrient Mixture F-12 Ham


title: 4T1 spheroid rep2

description:
4T1P2247G
cell grown in DMEM/Nutrient Mixture F-12 Ham


title: 4T1  bulk rep3

description:
4T1E247D
cell grown in RPMI-1640


title: LJ root hair

city: Yongin-si

first: Moon

last: Sunok

state: Gyeonggi-do

address: 1732, Deogyeong-daero

department: genetic engineering

institute: kyung hee university

description: Gene expression in root hairs

hyb_protocol: Finally labeled cRNA with cyanine-3-CTP was hybridized onto the Rice Gene Expression Microarray, 4x44K containing 43,803 probes (Agilent, G2519F-015241).  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer, then dried immediately by brief centrifugation.

scan_protocol: After washing, the arrays were scanned using an Agilent Surescan microarray scanner (Agilent Technologies). Feature Extraction software (version 11.5.1.1; Agilent Technologies) was used to analyze the array images and obtain raw data. Technologies) was used to analyze the array images and obtain raw data.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Oryza sativa

source_name: root hairs

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low input quick amp labeling kit, one-color, (Agilent, 5190-2305) according to the manufacturer's instructions.

growth_protocol: After sterilizing, seeds of rice were placed on an MSO medium during 3 day.

extract_protocol: Total RNA was extracted with TRIzol and then purified using RNeasy plant mini Kit (Qiagen, 74903)

treatment_protocol: The seminal roots were detached and submerged in liquid nitrogen and then gently were rubbed to purify root hairs

value: Root hairs

tag: cultivar

value: Lon-gin


title: WT3H

city: Melbourne

first: Ashley

middle: P

last: Ng

state: Victoria

address: 1G Royal Parade, Parkville

department: Cancer and Haematology

institute: The Walter and Eliza Hall Institute of Medical Research

description:
sample name:
4_C3RJFACXX_TGACCA_L008

data_processing:
Reads mapped to mm10 using Subjunc aligner in the Subread package
Read counts were summarised by featureCounts using NZCBI RefSeq gene annotation
Genes were filtered as not expressed if failed to achieve at least 0.5 counts per million reads in at least half the samples
Library sizes were normalised using the TMM method in voom software package converting read counts to log2 counts per million with associated precision weights
Differential expression was assessed using empirical Bayes moderated t-statistics that utilised the edgeR and limma software packages including batch in the linear model.
Genome_build: mm10
Supplementary_files_format_and_content: csv file with normalised counts

source_name: LSK cells_MIG-Hhex

growth_protocol: LSK cells (~100-200k/mouse) were extracted from tibia, femur and humuros bones from C57BL/6 mice (via FACS sorting), the transduced with either MIG or MIG-Hhex retrovirus (bound to retronectin coated plates) and cultured for two days (in StemPro-34 (Gibco) media with Nutrient Suppliment, P/S, L-Glutamine, 10ng/mL mL-3, 10ng/mL mIL-6, 50ng/mL mSCF and 50ng/mL mFlt-3).

extract_protocol:
Total RNA was extracted using RNAeasy Kit from Qiagen from GFP+ sorted LSK cells 2 days post-infection
Illumina - Library Prep mRNA. HiSeq HT chemistry- Single Read (50/100)  or xHiSeq HT chemistry- Paired Read (50/100)

tag: vector

value: MIG-Hhex

value: Hhex

tag: tissue

value: bone marrow

value: LSK


title: WT691H

description:
sample name:
WT691H_C5LWPANXX_TCCGCGAA_L001

tag: cell type


title: WT3M

description:
sample name:
3_C3RJFACXX_TTAGGC_L008

source_name: LSK cells_MIG

value: MIG

value: wild-type


title: WT703H

description:
sample name:
WT703H_C5LWPANXX_AGCGATAG_L001


title: WT691M

description:
sample name:
WT691M_C5LWPANXX_CGGCTATG_L001


title: E18.5 WT mouse ear

city: Halifax

first: Boris

last: Kablar

state: Nova Scotia

address: 5850 College Street

department: Medical Neuroscience

institute: Dalhousie University

description: Gene expression data from wild-type fetal ear.

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse 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: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: E18.5 mouse ear

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

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

value: fetal ear

value: BALB/c


title: E18.5 Myf5-/-:MyoD-/- mouse ear

description: Gene expression data from double knock-out (MyoD-/-:Myf5-/-) fetal ear.

value: BALB/c Myf5:Myod null


title: E18.5 WT mouse mandible

description: Gene expression data from wild-type fetal mandible.

source_name: E18.5 mouse mandible

value: fetal mandible


title: E18.5 Myf5-/-:MyoD-/- mouse mandible

description: Gene expression data from double knock-out (MyoD-/-:Myf5-/-) fetal mandible.


title: DJ root hair2

description: Gene expression in root hairs

value: Don-gin


title: DJ root hair3

description: Gene expression in root hairs


title: Patient #2

city: New York

first: Daniela

last: Sia

address: 1425 Madison Avenue

department: Liver Diseases

country: USA

institute: Icahn school of Medicine at Mount Sinai

description: Gene expression data derived from the  paraffin-embedded tumoral tissue of patient#2 collected any time before treatment.

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: The data were analyzed with GenePattern (Broad Institute) using Expression file creator module and the RMA algorithm. Subsequently, the dataset was collapsed using the relative CHIP platform and  choosing the maximum expression value for the set.

source_name: Patient#2 before nivolumab

label_protocol: Standard Affymetrix protocol

extract_protocol: Total RNA was extracted from 3 five-uM thick FFPE sections using the QIAGEN RNeasy FFPE Kit  and quantified using Nanodrop. Tisseu sectiosn were macrodissected prior to RNa extraction to educe contamination of non-cancrous liver tissue. 50 ng of total RNA was submitted for whole-genome expression profiling using the Affymetrix Human Genome U219 Array Plate

treatment_protocol: Not applicable. Archived tissue was obtained at our Insitution upon patient's consent

tag: disease state

value: HCC

value: tumor (liver)


title: Patient #1

description: Gene expression data derived from the paraffin-embedded tumoral tissue of patient#1 collected any time before treatment.

source_name: Patient#1 before nivolumab


title: DJ root hair1

description: Gene expression in root hairs