title: myb-silenced CD34+ HPCs 5

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

institute: Centre for Regenerative Medicine

description: miEP of myb-silenced CD34+ HPCs at 24 hours post-Nucleofection, fifth donor

data_processing:
RT-qPCR data were analysed using the Exiqon GenEx software for the inter-plate calibration, the definition of a Ct=40 as detection cutoff, the labeling of not-amplified wells as missing data and the setting of a cutoff for miRNAs with a low call-rate (i.e. the deletion of the assays with a detection rate <30% of samples, therefore keeping the assays detected in at least 3 out of 10 analysed samples for further analyses). For RT-qPCR data normalization, SNORD49A was used as reference gene, as the best normalizer identified among the candidates by the NormFinder algorithm.   Statistical analysis on ΔCT values between MYBsiRNA and NegCTR samples was performed by a two-tail paired t-Student test using the GenEx software.    The normalization and all the data analysis were performed according to the manufacturers instructions using the software GenEx. miRNA expression relative quantification (RQ) was achieved using the comparative cycle threshold (CT) method using  SNORD49A as the housekeeping gene (HKG). To normalize the data,  for each of the 5 replicates ΔΔCT was calculated as the difference between siRNA Myb sample and NegCTR sample (set as calibrator). The average of the ΔΔCT for each target was used to calculate the Relative Quantity (RQ) value, which was expressed as 2^−ΔΔCT.
Fold Change (FC) worksheet reports the relative quantity (RQ) = 2^-ΔΔCt, where -ΔΔCt = -[ΔCt siRNA Myb -ΔCt NegCTR]. To make the RQ value symmetric for up- and down-regulated genes, FC was used in the Tables for ease of interpretation (for RQ > 1, FC = RQ; for RQ < 1 FC = −1/RQ).

label: SYBR Green

source_name: Myb siRNA 3N

label_protocol: miRCURY LNA Universal RT microRNA PCR system, Ready-to-use Human miRNome Panels I and II (Exiqon, Copenhagen, Denmark)

growth_protocol: Human CD34+ cells were purified from umbilical cord blood (CB) samples, collected after normal deliveries, according to the institutional guidelines for discarded material. Mononuclear cells were isolated by Ficoll-Hypaque (Lympholyte; Cederlane Labs) gradient separation, washed twice with phosphate-buffered saline, and then CD34+ cells were purified by immunomagnetic sorting (EasySep Human CD34 Positive Selection kit, StemCell Technologies Inc.). The purity of CD34+ cells, assessed by flow cytometry, was always >95%. After immunomagnetic separation, CD34+ cells were seeded in 24-well plates at 5 x 10^5/mL in Iscove modified Dulbecco medium (IMDM; Euroclone) containing 20% Human Serum (Bio-Whittaker), stem cell factor (SCF; 50 ng/mL), Fms-like tyrosine kinase 3 ligand (Flt3L; 50 ng/mL), thrombopoietin (TPO; 20 ng/mL), interleukin-6 (IL-6; 10 ng/mL), and interleukin-3 (IL-3; 10 ng/mL; all from Miltenyi).

extract_protocol: CD34+ cells were lysed in 700uL of QIAZOL Buffer (Qiagen, Valencia, CA, USA) after 24h from the last of 3 nucleofection cycles. Total RNA from CD34+ cells was extracted using miRNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.

treatment_protocol: Human CD34+ cells were transfected by using the 4D-Nucleofector™ System (Lonza) as previously reported (Norfo R et al., Blood, 2014). Briefly, starting from the day after CD34+ cell purification, each sample was electroporated three times, once every 24 hours, with a mix of three small interfering RNAs (siRNAs) targeting human MYB (Life Technologies). For each electroporation, 4×105 CD34+ cells were resuspended in 100 µL of P3 Primary Cell Solution (Lonza), containing 3 µg of siRNA mix, and pulsed with the program DS112. To exclude non-specific effects caused by interfering RNA (RNAi) nucleofection, one sample transfected with a non-targeting siRNA (NegCTR siRNA; Life Technologies) for each experiment was included.  After each Nucleofection cycle, cells were maintained in culture in 24-well plates at 5 x 10^5/mL in Iscove modified Dulbecco medium (IMDM; Euroclone) containing 20% Human Serum (Bio-Whittaker), stem cell factor (SCF; 50 ng/mL), Fms-like tyrosine kinase 3 ligand (Flt3L; 50 ng/mL), thrombopoietin (TPO; 20 ng/mL), interleukin-6 (IL-6; 10 ng/mL), and interleukin-3 (IL-3; 10 ng/mL; all from Miltenyi).

value: Cord Blood CD34+ cells

tag: sirna treatment

value: Myb siRNA

tag: nucleofection cycles

tag: donor


title: NegCTR CD34+ HPCs 5

status: Public on Aug 07 2015

type: RNA

country: Italy

description: miEP of NegCTR CD34+ HPCs at 24 hours post-Nucleofection, fifth donor

molecule: total RNA

organism: Homo sapiens

source_name: NegCTR 3N

tag: cell type

value: NegCTR


title: Sample DM12

type: genomic

city: San Francisco

first: Alan

middle: Hunter

last: Shain

state: CA

address: 555 MISSION BAY SOUTH BLVD RM 282 # 3118

department: Pathology and Dermatology

country: USA

institute: University of California San Francisco

hyb_protocol: Agilent Oligo aCGH hybridization kit. Manufacturer's instructions.

scan_protocol: Feature Extraction version 9.1 (Agilent Technologies)

data_processing: Agilent Feature Extraction Software (v 9.1) was used for background subtraction and LOWESS normalization.

molecule: genomic DNA

source_name: Sample DM12

label_protocol: Bioprome aCGH genomic labeling kit. Manufacturer's instructions.

extract_protocol: Qiagen Dneasy. Manufacturer's instructions.

tag: Stage

value: Primary Tumor

tag: tissue

value: FFPE

source_name: Pooled Normal male genomic DNA

tag: Sex

value: Male

value: Blood


title: EA normal 124 [Affymetrix]

city: Washington

first: Bi-Dar

last: Wang

state: DC

address: 2300 I street, NW

department: Pharmacology and Physiology

institute: The George Washington University Medical Center

description: needle biopsy specimen from prostate

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute. Transfer 200μl of hyb solution to each array, then tape holes and parafilm. Hybridize 16 hours at 45° at 60rpm. Fluidics washing is FS450_0001

scan_protocol: Affymetrix GeneChIP Scanner 3000

data_processing:
Data were processed using Partek Genomics Suite software. Quantile normalization and GC-RMA background correction were applied to probe intensities, gene level expression were summarized from the corrected/normalized intensities. Only core probe sets were used for data analysis.
HuEx-1_0-st-v2.r2.pgf

label: biotin

source_name: prostate biopsy from prostate cancer patient

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Samples were collected from patients, so there was no growth protocol.

extract_protocol: All RNA samples were purified by using Qiagen RNeasy micro kit (Qiagen). Samples were then treated with the RiobMinus, rRNA reduction kit (Invitrogen), cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

treatment_protocol: No treatment was performed on the collected tissue samples.

value: prostate


title: myb-silenced CD34+ HPCs 4

description: miEP of myb-silenced CD34+ HPCs at 24 hours post-Nucleofection, fourth donor


title: EA tumor 124 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: EA tumor 121 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: EA normal 105 [Affymetrix]

description: needle biopsy specimen from prostate


title: Sample DM2

source_name: Sample DM2


title: EA tumor 87 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: Sample DM98

source_name: Sample DM98


title: Sample DM11

source_name: Sample DM11


title: EA normal 87 [Affymetrix]

description: needle biopsy specimen from prostate


title: Sample DM1

source_name: Sample DM1


title: EA normal 121 [Affymetrix]

description: needle biopsy specimen from prostate


title: EA tumor 105 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: EA normal 60 [Affymetrix]

description: needle biopsy specimen from prostate


title: Sample DM99

source_name: Sample DM99


title: Sample DM94

source_name: Sample DM94


title: Sample DM95

source_name: Sample DM95


title: Sample DM96

source_name: Sample DM96


title: NegCTR CD34+ HPCs 4

description: miEP of NegCTR CD34+ HPCs at 24 hours post-Nucleofection, fourth donor


title: Sample DM93

source_name: Sample DM93


title: EA tumor 60 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: EA normal 58 [Affymetrix]

description: needle biopsy specimen from prostate


title: Sample DM14

source_name: Sample DM14


title: myb-silenced CD34+ HPCs 3

description: miEP of myb-silenced CD34+ HPCs at 24 hours post-Nucleofection, third donor


title: NegCTR CD34+ HPCs 3

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


title: myb-silenced CD34+ HPCs 2

description: miEP of myb-silenced CD34+ HPCs at 24 hours post-Nucleofection, second donor


title: NegCTR CD34+ HPCs 2

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


title: myb-silenced CD34+ HPCs 1

description: miEP of myb-silenced CD34+ HPCs at 24 hours post-Nucleofection, first donor


title: SH-SY5Y control rep2

city: Tallahassee

first: Cynthia

last: Vied

state: Florida

address: 1115 W. Call St

department: Translational Science Laboratory

institute: Florida State University

description: Mnase-chip of control SH-SY5Y cells

hyb_protocol: The labeled DNA was precipitated with 1 volume isopropanol, and hybridized according to manufacturer's protocols. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on a Nimblegen scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing:
Arrays were processed using Nimblegen's standard protocol for Nimblescan CGH arrays.
normalized log2 (mononucleosomally protected DNA/bare genomic DNA) ratio for Nucleosome Distribution experiments.

source_name: SH-SY5Y cells

label_protocol: 1 µg of mononucleosomally protected and genomic DNA was directly labeled by Klenow (Nimblegen) random priming with Cy3 and Cy5 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: We used undifferentiated SH-SY5Y cells (human neuroblastoma cell line; obtained directly from ATCC, Manassas, VA), maintained in culture according to protocols described by ATCC (1:1 F12:EMEM, 10% FBS, 50ug/mL gentamicin).  Cells were grown at 37°C until a 150-mm dish was 90% confluent (~2x107cells), at which time the medium was replaced with fresh medium containing nicotine or cocaine (each drug 10µM; Sigma, St. Louis, MO). The cultures were incubated for an additional 10, 60, and 90 min following addition of nicotine; or 5, 20, 40 and 60 min following addition of cocaine.  Biological replicates were two independently grown cultures treated on nonconsecutive days. At the designated time points, cells were fixed and crosslinked for 10 min in 1% PBS-buffered formaldehyde.  The reaction was stopped by incubation for 5 min with 125mM glycine.  Nuclei were isolated (0.3M sucrose, 2mM MgOAc2, 1mM CaCl2, 1% Nonidet P-40, 10mM HEPES, pH7.8) by centrifugation at 1000 X g for 5 min at 4°C.  Bare, unbound genomic DNA and mononucleosomally-protected DNA were isolated from each sample and purified as described previously (Sexton et al., 2014). A titration of micrococcal nuclease (MNase; 1-1.25U/mL; Worthington Biochemical Corp.) was used to digest bare, unbound DNA and mononucleosomally-protected DNA (Sexton et al., 2014) .

tag: cell line

tag: material

value: nucleosomally protected DNA

tag: treatment

value: Control

value: bare genomic DNA


title: EA tumor 57 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: SH-SY5Y control rep1

description: Mnase-chip of control SH-SY5Y cells

growth_protocol: We used undifferentiated SH-SY5Y cells (human neuroblastoma cell line; obtained directly from ATCC, Manassas, VA), maintained in culture according to protocols described by ATCC (1:1 F12:EMEM, 10% FBS, 50ug/mL gentamicin).  Cells were grown at 37°C until a 150-mm dish was 90% confluent (~2x107cells), at which time the medium was replaced with fresh medium containing nicotine or cocaine (each drug 10µM; Sigma, St. Louis, MO). The cultures were incubated for an additional 10, 60, and 90 min following addition of nicotine; or 5, 20, 40 and 60 min following addition of cocaine.

treatment_protocol: At the designated time points, cells were fixed and crosslinked for 10 min in 1% PBS-buffered formaldehyde.  The reaction was stopped by incubation for 5 min with 125mM glycine.


title: EA tumor 58 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: EA normal 57 [Affymetrix]

description: needle biopsy specimen from prostate


title: EA normal 28 [Affymetrix]

description: needle biopsy specimen from prostate


title: EA tumor 18 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: EA tumor 44 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: EA normal 18 [Affymetrix]

description: needle biopsy specimen from prostate


title: EA normal 16 [Affymetrix]

description: needle biopsy specimen from prostate


title: EA normal 30 [Affymetrix]

description: needle biopsy specimen from prostate


title: EA tumor 30 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: EA normal 139 [Affymetrix]

description: needle biopsy specimen from prostate


title: EA tumor 16 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: SH-SY5Y cocaine 60min rep1

description: Mnase-chip of 60 minute cocaine-treated SH-SY5Y cells

value: Cocaine 60 minutes


title: EA normal 15 [Affymetrix]

description: needle biopsy specimen from prostate


title: SH-SY5Y cocaine 60min rep2


title: SH-SY5Y cocaine 40min rep2

description: Mnase-chip of 40 minute cocaine-treated SH-SY5Y cells

value: Cocaine 40 minutes


title: AA_normal_120 [Affymetrix]

description: needle biopsy specimen from prostate


title: AA_tumor_155 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: AA_tumor_120 [Affymetrix]

description: needle biopsy specimen from prostate


title: EA tumor 9 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: SH-SY5Y cocaine 20min rep2

description: Mnase-chip of 20 minute cocaine-treated SH-SY5Y cells

value: Cocaine 20 minutes


title: EA normal 9 [Affymetrix]

description: needle biopsy specimen from prostate


title: 11053B-N3

city: Nanjing

first: rui

middle: hua

last: shi

state: jiangsu

address: guangzhou road 300#

department: gastroenterology

country: China

institute: the First Affiliated Hospital of Nanjing Medical University

description: gene expression of normal esophageal epithelial tissues

hyb_protocol: According to the Agilent miRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and post-hybridization washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.7.3.1 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by quantile normalization.

source_name: paired normal esophageal epithelial tissues NO3

label_protocol: Labeled RNAs were heat denatured and hybridized to Agilent miRNA microarray, according to manufacturer's protocol.

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

value: normal esophageal epithelial

tag: tissue type

value: frozen tissue

tag: gender

value: female

tag: age


title: SH-SY5Y cocaine 20min rep1


title: AA_normal_155 [Affymetrix]

description: needle biopsy specimen from prostate


title: SH-SY5Y cocaine 5min rep2

description: Mnase-chip of 5 minute cocaine-treated SH-SY5Y cells

value: Cocaine 5 minutes


title: EA normal 44 [Affymetrix]

description: needle biopsy specimen from prostate


title: SH-SY5Y cocaine 40min rep1


title: EA tumor 15 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: AA_normal_106 [Affymetrix]

description: needle biopsy specimen from prostate


title: SH-SY5Y cocaine 5min rep1


title: 11053B-N1

source_name: paired normal esophageal epithelial tissues NO1

value: male


title: AA_normal_84 [Affymetrix]

description: needle biopsy specimen from prostate


title: 11053B-N2

source_name: paired normal esophageal epithelial tissues NO2


title: AA_tumor_106 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: 11053B-T3

description: gene expression of ESCC

source_name: esophageal squamous cell carcinoma tissues NO3

value: esophageal squamous cell carcinoma


title: SH-SY5Y nicotine 90min rep2

description: Mnase-chip of 90 minute nicotine-treated SH-SY5Y cells

value: Nicotine 90 minutes


title: AA_normal_51 [Affymetrix]

description: needle biopsy specimen from prostate


title: AA_tumor_84 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: SH-SY5Y nicotine 90min rep1


title: 11053B-T2

description: gene expression of ESCC

source_name: esophageal squamous cell carcinoma tissues NO2


title: AA_normal_75 [Affymetrix]

description: needle biopsy specimen from prostate

source_name: prostate biopsy from prostate cancer patient


title: EA tumor 139 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: SH-SY5Y nicotine 60min rep2

description: Mnase-chip of 60 minute nicotine-treated SH-SY5Y cells

value: Nicotine 60 minutes


title: SH-SY5Y nicotine 60min rep1


title: AA_tumor_75 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: AA_tumor_51 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: AA_normal_49 [Affymetrix]

description: needle biopsy specimen from prostate


title: SH-SY5Y nicotine 10min rep2

description: Mnase-chip of 10 minute nicotine-treated SH-SY5Y cells

value: Nicotine 10 minutes


title: SH-SY5Y nicotine 10min rep1


title: 11053B-T1

description: gene expression of ESCC

source_name: esophageal squamous cell carcinoma tissues NO1


title: AA_tumor_49 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: AA_tumor_48 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: AA_normal_48 [Affymetrix]

description: needle biopsy specimen from prostate


title: AKC_10_4

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

country: Germany

institute: Institute for Biomedical Engineering

hyb_protocol: Samples were hybridized using Agilent standard hybridization protocol.

scan_protocol: Slides were scanned using a microarray scanner (Agilent Technologies).

data_processing: Raw data were pre-processed and quantile normalized using R/Bioconductor. The expression level of individual gene was then calculated by averaging the signal intensities of all corresponding probe sets.

organism: Mus musculus

source_name: pancreata, Atm-/- , 10 weeks old

label_protocol: 50 ng of each sample was labelled with the Low Input Quick Amp Kit (Agilent Technologies) according to the manufacturer’s instructions.

extract_protocol: RNA was extracted according to manufacturer’s instructions using the RNeasy Mini or Micro Kits (Qiagen) and eluted in 40 or 15 μl RNase-free H2O.

tag: genotype/variation

value: p48Cre/+;KrasG12D/+;Atm-/- (AKC)

value: pancreata

value: 10 weeks


title: AA_normal_35 [Affymetrix]

description: needle biopsy specimen from prostate

value: prostate


title: AKC_10_3


title: AA_tumor_43 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: myb-silenced CD34+ HPCs, 3 Nucleofections, donor 5

description: GEP of myb-silenced CD34+ HPCs at 24 hours after the third Nucleofection, fifth donor

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

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

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

source_name: siRNA Myb 3N

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

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

treatment_protocol: Human CD34+ cells were transfected by using the 4D-Nucleofector™ System (Lonza) as previously reported (Norfo R et al., Blood, 2014). Briefly, starting from the day after CD34+ cell purification, each sample was electroporated once, twice or three times, once every 24 hours, with a mix of three small interfering RNAs (siRNAs) targeting human MYB (Life Technologies). For each electroporation, 4×105 CD34+ cells were resuspended in 100 µL of P3 Primary Cell Solution (Lonza), containing 3 µg of siRNA mix, and pulsed with the program DS112. To exclude non-specific effects caused by interfering RNA (RNAi) nucleofection, one sample transfected with a non-targeting siRNA (NegCTR siRNA; Life Technologies) for each experiment was included.  After each Nucleofection cycle, cells were maintained in culture in 24-well plates at 5 x 10^5/mL in Iscove modified Dulbecco medium (IMDM; Euroclone) containing 20% Human Serum (Bio-Whittaker), stem cell factor (SCF; 50 ng/mL), Fms-like tyrosine kinase 3 ligand (Flt3L; 50 ng/mL), thrombopoietin (TPO; 20 ng/mL), interleukin-6 (IL-6; 10 ng/mL), and interleukin-3 (IL-3; 10 ng/mL; all from Miltenyi).

value: Cord Blood CD34+ cells

value: siRNA Myb


title: AKC_10_1


title: AA_tumor_34 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: NegCTR CD34+ HPCs, 3 Nucleofections, donor 5

description: GEP of NegCTR CD34+ HPCs at 24 hours after the third Nucleofection, fifth donor

source_name: Neg CTR 3N

value: Neg CTR


title: KC_10_2

source_name: pancreata, Atm+/+, 10 weeks old

value: p48Cre/+;KrasG12D/+;Atm+/+ (KC)


title: AA_tumor_32 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: myb-silenced CD34+ HPCs, 2 Nucleofections, donor 5

description: GEP of myb-silenced CD34+ HPCs at 24 hours after the second Nucleofection, fifth donor

source_name: siRNA Myb 2N


title: AA_normal_43 [Affymetrix]

description: needle biopsy specimen from prostate


title: KC_10_3


title: AKC_10_2


title: myb-silenced CD34+ HPCs, 1 Nucleofection, donor 5

description: GEP of myb-silenced CD34+ HPCs at 24 hours post-Nucleofection,  fifth donor

source_name: siRNA Myb 1N


title: AKC_5_3

source_name: pancreata, Atm-/- , 5 weeks old

value: 5 weeks


title: NegCTR CD34+ HPCs, 2 Nucleofections, donor 5

description: GEP of NegCTR CD34+ HPCs at 24 hours after the second Nucleofection, fifth donor

source_name: Neg CTR 2N


title: KC_10_1


title: AA_normal_34 [Affymetrix]

description: needle biopsy specimen from prostate


title: AA_tumor_29 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: AKC_5_2


title: AA_tumor_35 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: AA_normal_32 [Affymetrix]

description: needle biopsy specimen from prostate


title: AKC_5_1


title: AA_normal_29 [Affymetrix]

description: needle biopsy specimen from prostate


title: myb-silenced CD34+ HPCs, 3 Nucleofections, donor 4

description: GEP of myb-silenced CD34+ HPCs at 24 hours after the third Nucleofection, fourth donor


title: KC_5_2

source_name: pancreata, Atm+/+, 5 weeks old


title: KC_5_3


title: NegCTR CD34+ HPCs, 3 Nucleofections, donor 4

description: GEP of NegCTR CD34+ HPCs at 24 hours after the third Nucleofection, fourth donor


title: KC_5_1


title: NegCTR CD34+ HPCs, 1 Nucleofection, donor 5

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

source_name: Neg CTR 1N


title: AA_normal_17 [Affymetrix]

description: needle biopsy specimen from prostate


title: AA_tumor_19 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: AA_normal_21 [Affymetrix]

description: needle biopsy specimen from prostate


title: AA_tumor_21 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: NegCTR CD34+ HPCs, 2 Nucleofections, donor 4

description: GEP of NegCTR CD34+ HPCs at 24 hours after the second Nucleofection, fourth donor


title: myb-silenced CD34+ HPCs, 1 Nucleofection, donor 4

description: GEP of myb-silenced CD34+ HPCs at 24 hours post-Nucleofection, fourth donor


title: AA_normal_19 [Affymetrix]

description: needle biopsy specimen from prostate


title: GBM1 - High DOSE - DMSO versus MRK003  - REP 3

city: Baltimore

first: Luigi

last: Marchionni

state: MD

address: 1550 Orleans St., CRB2, Room 1M52

department: Oncology

institute: Johns Hopkins University

hyb_protocol: Fragmentation was carried out by the Sidney Kimmel Comprehensive Cancer Center Microarray Core Facility by incubating at 60 degrees Celsius for 30 minutes and stopped by adding equal volume of 2x hybridization buffer (Agilent Technologies). Fragmented targets were added on 22 human 1Av2 Microarrays (Agilent Technologies). The microarrays were assembled into a hybridization chamber (Agilent Technologies) and hybridized at 60 degrees Celsius for 17 hours in a hybridization oven with rotation. Hybridized microarrays were washed and dried according to the Agilent microarray processing protocol. For target fragmentation, hybridization, and scanning, the experiment was split evenly into three distinct batches.

scan_protocol: Microarrays were scanned by the Sidney Kimmel Comprehensive Cancer Center Microarray Core Facility with the Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies for expression microarrays with 100% PMT and 10 micometer resolutions. Data was extracted using Feature Extraction Software version 8.1 (Agilent Technologies). For target fragmentation, hybridization, and scanning, the experiment was split evenly into three distinct batches.

data_processing: Within-array normalization between the two channels was achieved using the loess method, while the quantile method was applied for normalizatoin between arrays. No background subtraction was performed prior to normalization. Data pre-processing was performed using the R/Bioconductor package limma.

label_protocol: Total RNA (1 microgram) was reverse transcribed into first- and second-strand cDNA by MMLV-RT using an oligo(dT) primer that incorporates a T7 promoter sequence. The cDNA was then used as a template for in vitro transcription in the presence of T7 RNA polymerase and cyanine-labeled CTPs. The labeled cRNA was purified using RNeasy mini kit (Qiagen) and followed by quantification on both concentrations of cRNA and dye labeled. RNA spike-in controls (Agilent Technologies) were added to the RNA samples before amplification and labeled according to manufacturer’s protocol. In total, 0.75 mircrogram of each sample labeled with Cy3 or Cy5 was mixed with control targets (Agilent Technologies). For target fragmentation, hybridization, and scanning, the experiment was split evenly into three distinct batches.

growth_protocol: Cells were treated immediately on plating with drugs as specified. Cell biomass was measured using CellTiter96 (Promega) at regular intervals after treatment. Neurosphere nucleofection assays were performed using the AMAXA NSC Nucleofector Kit (Lonza) according to manufacturer’s instructions, using program A-033 with 2,000,000 cells per condition. Cells were nucleofected with Hes1 (PMID:18550849) or a control plasmid and allowed to recover for 24 hours in normal media before treatment with MRK-003 or vehicle. Transfection efficiency was quan-tified by cotransfection with CAG-green fluorescent protein (GFP) and microscopic quantification of the percentage of GFP-expressing cells. Cells were harvested after 48 hours for analysis.

extract_protocol: RNA was extracted using an RNeasy kit (Qiagen) with on-column DNase treatment (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: All gliobalstoma cell lines (GBM1, GBM2, GBM10, and GBM14) were maintained as neurosphere cultures in serum-free neuro-sphere media as previously described (PMID:15466194). Cells were counted using GUAVA Viacount reagent according to the manufacturer’s instruc- tions (Millipore) and equal numbers of viable cells were used for all experiments.


title: EA tumor 28 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: AA_normal_13 [Affymetrix]

description: needle biopsy specimen from prostate


title: AA_normal_10 [Affymetrix]

description: needle biopsy specimen from prostate


title: GBM1 - High DOSE - MRK003 versus DMSO  - REP 1


title: NegCTR CD34+ HPCs 1

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

source_name: NegCTR 3N

value: NegCTR


title: GBM1 - Low DOSE - MRK003 versus DMSO  - REP 3


title: GBM2 - Low DOSE - MRK003 versus DMSO  - REP 2


title: GBM2 - Low DOSE - MRK003 versus DMSO  - REP 3


title: GBM1 - Low DOSE - MRK003 versus DMSO  - REP 2


title: NegCTR CD34+ HPCs, 1 Nucleofection, donor 4

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


title: GBM14 - High DOSE - DMSO versus MRK003  - REP 2


title: GBM2 - Low DOSE - MRK003 versus DMSO  - REP 1


title: AA_tumor_13 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: myb-silenced CD34+ HPCs, 2 Nucleofections, donor 3

description: GEP of myb-silenced CD34+ HPCs at 24 hours after the second Nucleofection, third donor


title: myb-silenced CD34+ HPCs, 3 Nucleofections, donor 3

description: GEP of myb-silenced CD34+ HPCs at 24 hours after the third Nucleofection, third donor


title: NegCTR CD34+ HPCs, 2 Nucleofections, donor 3

description: GEP of NegCTR CD34+ HPCs at 24 hours after the second Nucleofection, third donor


title: myb-silenced CD34+ HPCs, 1 Nucleofection, donor 3

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


title: GBM1 - High DOSE - MRK003 versus DMSO  - REP 2


title: NegCTR CD34+ HPCs, 1 Nucleofection, donor 3

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


title: NegCTR CD34+ HPCs, 3 Nucleofections, donor 3

description: GEP of NegCTR CD34+ HPCs at 24 hours after the third Nucleofection, third donor


title: AA_normal_6 [Affymetrix]

description: needle biopsy specimen from prostate


title: myb-silenced CD34+ HPCs, 3 Nucleofections, donor 2

description: GEP of myb-silenced CD34+ HPCs at 24 hours after the third Nucleofection, second donor


title: GBM14 - High DOSE - MRK003 versus DMSO  - REP 1


title: AA_normal_4 [Affymetrix]

description: needle biopsy specimen from prostate


title: GBM10 - High DOSE - DMSO versus MRK003  - REP 3


title: AA_tumor_17 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: myb-silenced CD34+ HPCs, 2 Nucleofections, donor 4

description: GEP of myb-silenced CD34+ HPCs at 24 hours after the second Nucleofection, fourth donor


title: AA_tumor_6 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: AA_tumor_4 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: AA_tumor_10 [reanalysis Affymetrix]

description: needle biopsy specimen from prostate


title: NegCTR CD34+ HPCs, 3 Nucleofections, donor 2

description: GEP of NegCTR CD34+ HPCs at 24 hours after the third Nucleofection, second donor


title: 10-OPEA - 3

city: La Jolla

first: Alisa

last: Huffaker

address: 9500 Gilman Drive #0116

department: Cell & Developmental Biology

institute: UC San Diego

description: 10-oxo-11-phytoenoic acid

hyb_protocol: Biotin labeled samples were hybridized to Affymetrix maize GeneChips at UF-ICBR using a GeneChip Hybridization Oven 640 with standard hybridization protocol

scan_protocol: Affymetrix maize GeneChips were scanned at UF ICBR with a GeneChip Scanner 3000 7G per standard procedure

data_processing: Data extraction was executed by the UF ICBR gene expression core and provided as CEL files. Data analysis was performed using ArrayStar 4 software (DNASTAR, Inc.). To minimize probe-specific affinity differences, all data were preprocessed using Robust MultiArray Analysis and quantile normalization.

organism: Zea mays

source_name: Emergent but non-fully-expanded 4th leaf_10-oxo-11-phytoenoic acid

label_protocol: For each sample, 1 μg of total RNA was provided to the University of Florida Interdisciplinary Center Biotechnology Research (UF-ICBR) Gene Expression Core for cDNA synthesis, reverse transcription, and biotin labeling using the Affymetrix GeneChip 3′ IVT express kit and protocol (Affymetrix).

growth_protocol: Zea mays (variety Golden Queen) seeds were germinated in MetroMix 200 (Sun Gro Horticulture Distribution, Inc.) supplemented with 14-14-14 Osmocote (Scotts Miracle-Gro) and grown in a greenhouse with a 12-h photoperiod, minimum of 300 μmol m−2 s−1 of photosynthetically active radiation supplied by supplemental lighting, 70% relative humidity, and temperature cycle of 24 °C/28 °C (night/day).

extract_protocol: Total RNA was isolated using the Nucleospin RNA Plant kit (Macherey-Nagel bmbH Inc., Duren, Germany) according to the manufacturers protocol and First Strand cDNA was synthesized using the Superscript III First Strand cDNA synthesis kit (Invitrogen, Carlsbad, CA, USA) with random decamer primers.

treatment_protocol: For gene expression analysis, spot application of 10-OPEA was carried out by applying four 10µl droplets of either the control solution [ (H20/DMSO/0.1% Tween 20) (95:5:0.1; v/v/v)] or the same containing 2mM 10-OPEA onto the middle portion of partially emerged leaf 4 of 14-day old plants approximately 15 cm from the distal tip with 2 droplets on each side of the midrib 2 cm apart. At 90 min post treatment, control and 10-OPEA treated tissues were collected in liquid N2.

tag: cultivar

value: Golden Queen

value: Leaf


title: GBM10 - High DOSE - MRK003 versus DMSO  - REP 2


title: 10-OPEA - 2

description: 10-oxo-11-phytoenoic acid


title: 5%DMSO/0.1%Tween 20 in H20 - 2

description: Dimethyl sulfoxide/Tween 20/H2O

source_name: Emergent but non-fully-expanded 4th leaf_Dimethyl sulfoxide/Tween 20/H2O


title: 5%DMSO/0.1%Tween 20 in H20 - 3

description: Dimethyl sulfoxide/Tween 20/H2O


title: NegCTR CD34+ HPCs, 3 Nucleofections, donor 1

description: GEP of NegCTR CD34+ HPCs at 24 hours after the third Nucleofection, first donor


title: 10-OPEA - 1

description: 10-oxo-11-phytoenoic acid


title: NegCTR CD34+ HPCs, 2 Nucleofections, donor 2

description: GEP of NegCTR CD34+ HPCs at 24 hours after the second Nucleofection, second donor


title: myb-silenced CD34+ HPCs, 2 Nucleofections, donor 2

description: GEP of myb-silenced CD34+ HPCs at 24 hours after the second Nucleofection, second donor


title: GBM1 - Low DOSE - MRK003 versus DMSO  - REP 1


title: myb-silenced CD34+ HPCs, 2 Nucleofections, donor 1

description: GEP of myb-silenced CD34+ HPCs at 24 hours after the second Nucleofection, first donor


title: myb-silenced CD34+ HPCs, 1 Nucleofection, donor 2

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


title: NegCTR CD34+ HPCs, 2 Nucleofections, donor 1

description: GEP of NegCTR CD34+ HPCs at 24 hours after the second Nucleofection, first donor


title: DCA versus SEMP 2

city: Vancouver

first: Hirofumi

last: Hara

state: BC

address: 2350 Health Science Mall

department: Microbilogy and Immunology

country: Canada

institute: University of British Columbia

hyb_protocol: DNA microarrays were incubated with SlideHyb Hybridization Buffer no. 1 (Ambion) in an automated hybridization machine, GeneTac HybStation (Genomic Solutions) at 42 degree C for 18 h.

scan_protocol: Scanned using a GenePix 4000B scanner (Axon Instruments)

data_processing: The spot intensities were quantified using Imagene 6.1 (BioDiscovery). LOWESS Normalization (VSN), background subtracted data obtained from log2 of processed Red signal/processed Green signal.

organism: Sphingobium sp. SYK-6

source_name: SYK-6 treated with DCA

label_protocol: Total RNA (6 ug) was labeled using an indirect method in which aminoallyl-dUTPs were incorporated by reverse transcription using a mixture of two kinds of random hexamers, normal-GC-content (Invitrogen) and high-GC-content (70%) (Sigma), 5-(3-aminoallyl)-dUTP (Ambion), and PrimeScript II reverse transcriptase (Takara Bio Inc.).

growth_protocol: Cells of SYK-6 were grown in Wx-SEMP until OD600 of the culture reached 0.5.

extract_protocol: Total RNA was isolated using ISOGEN II reagent (Nippon Gene) according to the manufacture's instructions.

treatment_protocol: Cultures were further incubated with 2 mM DCA for 6 h, with 2 mM vanillate for 2 h, or without any substrates for 2 h.

tag: strain

value: DCA for 6 hours

source_name: SYK-6 grown on SEMP

value: grown on SEMP


title: Vanillate versus SEMP 3

source_name: SYK-6 treated with vanillate

value: vanillate for 2 hours


title: DCA versus SEMP 1


title: Vanillate versus SEMP 1


title: NegCTR CD34+ HPCs, 1 Nucleofection, donor 1

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


title: myb-silenced CD34+ HPCs, 3 Nucleofections, donor 1

description: GEP of myb-silenced CD34+ HPCs at 24 hours after the third Nucleofection,first donor


title: myb-silenced CD34+ HPCs, 1 Nucleofection, donor 1

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


title: DCA 1

type: mixed

description: Sample 7

data_processing: The spot intensities were quantified using Imagene 6.1 (BioDiscovery). Variance Stabilization and Normalization (VSN), background subtracted data obtained from log2 of processed Red signal/processed Green signal.

source_name: SYK-6 genomic DNA


title: DCA versus SEMP 3


title: Vanillate versus SEMP 2


title: miR486-3p mimic 2

description: GEP of miR-486-3p mimic CD34+ HPCs at 24 hours post-Nucleofection, second donor

source_name: miR-486-3p mimic

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

treatment_protocol: Human CD34+ cells were transfected by using the 4D-Nucleofector™ System (Lonza) as previously reported (Norfo R et al., Blood, 2014). Briefly, starting from the day after CD34+ cell purification, each sample was electroporated twice, once every 24 hours, with mirVana miR-486-3p mimic or mirVana miRNA mimic Negative Control #1 (Neg-mimic). For each electroporation, 4×10^5 CD34+ cells were resuspended in 100 µL of P3 Primary Cell Solution (Lonza), containing 3 µg of miRNA, and pulsed with the program DS112. After each Nucleofection cycle, cells were maintained in culture in 24-well plates at 5 x 10^5/mL in Iscove modified Dulbecco medium (IMDM; Euroclone) containing 20% Human Serum (Bio-Whittaker), stem cell factor (SCF; 50 ng/mL), Fms-like tyrosine kinase 3 ligand (Flt3L; 50 ng/mL), thrombopoietin (TPO; 20 ng/mL), interleukin-6 (IL-6; 10 ng/mL), and interleukin-3 (IL-3; 10 ng/mL; all from Miltenyi).


title: miR486-3p mimic 3

description: GEP of miR-486-3p mimic CD34+ HPCs at 24 hours post-Nucleofection, third donor


title: Vanillate 1

description: Sample 4


title: 5%DMSO/0.1%Tween 20 in H20 - 1

description: Dimethyl sulfoxide/Tween 20/H2O


title: DCA 3

description: Sample 9


title: NegCTR mimic 3

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

source_name: NegCTR mimic


title: SEMP 3

description: Sample 3

value: SEMP


title: Vanillate 2

description: Sample 5


title: SEMP 1

description: Sample 1


title: miR486-3p mimic 1

description: GEP of miR-486-3p mimic CD34+ HPCs at 24 hours post-Nucleofection, first donor


title: NegCTR mimic 1

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


title: GBM10 - High DOSE - MRK003 versus DMSO  - REP 1


title: DCA 2

description: Sample 8


title: SEMP 2

description: Sample 2


title: Vanillate 3

description: Sample 6


title: NegCTR CD34+ HPCs, 1 Nucleofection, donor 2

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


title: NahG-Désirée_0dpi_mock_bottomLeaf_rep1

status: Public on Aug 06 2015

city: Ljubljana

first: Ziva

last: Ramsak

address: Večna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

hyb_protocol: Hybridization mixture was set up using Gene Expression Hybridization Kit (Agilent Technologies) and applied to the microarray. The hybridization at 65°C for 17 h was followed by washing with increasing stringency using Gene Expression Wash Buffers (Agilent) and drying with acetonitrile (SIGMA). All these steps were performed at IMGM Laboratories GmbH, Germany

scan_protocol: Fluorescent signal intensities were detected with Scan Control A8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.7.3.1 Software (Agilent Technologies). All these steps were performed at IMGM Laboratories GmbH, Germany.

data_processing: Data was analyzed in R environment with limma and Agi4x44PreProcess packages. Robust spline normalization was used (rsn), background was not subtracted.

label: Cy 3

organism: Solanum tuberosum

source_name: NahG-Désirée_whole mock-inoculated bottom leaf_0dpi

label_protocol: 100 ng total RNA per sample were introduced into an RT-IVT reaction. Prior to RT-IVT, the total RNA samples were spiked with in-vitro synthesized polyadenylated transcripts (One-Color RNA Spike-In Mix, Agilent Technologies).  The spiked total RNA was reverse transcribed into cDNA and then converted into labeled cRNA by in-vitro transcription (Low Input Quick-Amp Labeling Kit One-Color, Agilent Technologies) incorporating Cyanine-3-CTP.

growth_protocol: Two weeks after node segmentation, they were transferred to soil in a growth chamber, and kept at 21 ±2 °C in the light and 18 ±1 °C in the dark, at a relative humidity of 75% ±2%, with 70-90 μmol/m2/s2 radiation (L36W/77 lamp, Osram, Germany) and a 16-h photoperiod

extract_protocol: Total RNA from the inoculated leaves was extracted, treated, purified, and quality controlled as described previously  (Baebler ret al., MPP, 2009)

treatment_protocol: After 4 weeks of growth in soil, the potato plants were inoculated with PVYNTN (isolate NIB-NTN, AJ585342) as described in [Plant Pathol 2010, 59:1121-1132]. For the mock-inoculated plants, the same procedures were performed with sap from healthy potato plants.

value: NahG-Désirée

value: no-inoculation

tag: time point

value: 0 dpi

tag: leaf location

value: bottom


title: Désirée_0dpi_mock_upperLeaf_rep3

source_name: cv. Désirée_whole mock-inoculated upper leaf_0dpi

value: Désirée

value: upper


title: NahG-Désirée_0dpi_mock_bottomLeaf_rep2


title: Désirée_0dpi_mock_bottomLeaf_rep2

source_name: cv. Désirée_whole mock-inoculated bottom leaf_0dpi


title: Désirée_0dpi_mock_upperLeaf_rep2


title: NahG-Désirée_0dpi_mock_bottomLeaf_rep3


title: NahG-Désirée_5dpi_PVY_bottomLeaf_rep2

source_name: NahG-Désirée_whole PVY-inoculated bottom leaf_5dpi

value: PVY-inoculation

value: 5 dpi


title: NahG-Désirée_5dpi_PVY_bottomLeaf_rep1


title: Désirée_0dpi_mock_upperLeaf_rep1


title: NahG-Désirée_7dpi_PVY_bottomLeaf_rep3

source_name: NahG-Désirée_whole PVY-inoculated bottom leaf_7dpi

value: 7 dpi


title: NahG-Désirée_7dpi_PVY_bottomLeaf_rep1


title: NahG-Désirée_5dpi_PVY_bottomLeaf_rep3


title: NahG-Désirée_7dpi_PVY_bottomLeaf_rep2


title: Désirée_0dpi_mock_bottomLeaf_rep3


title: Désirée_0dpi_mock_bottomLeaf_rep1


title: NahG-Désirée_3dpi_PVY_bottomLeaf_rep2

source_name: NahG-Désirée_whole PVY-inoculated bottom leaf_3dpi

value: 3 dpi


title: NegCTR mimic 2

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

value: Cord Blood CD34+ cells


title: NahG-Désirée_4dpi_PVY_bottomLeaf_rep2

source_name: NahG-Désirée_whole PVY-inoculated bottom leaf_4dpi

value: 4 dpi


title: NahG-Désirée_4dpi_PVY_bottomLeaf_rep1


title: NahG-Désirée_3dpi_PVY_bottomLeaf_rep1


title: NahG-Désirée_4dpi_PVY_bottomLeaf_rep3


title: NahG-Désirée_1dpi_PVY_bottomLeaf_rep3

source_name: NahG-Désirée_whole PVY-inoculated bottom leaf_1dpi

value: 1 dpi


title: NahG-Désirée_3dpi_PVY_bottomLeaf_rep3


title: NahG-Désirée_7dpi_mock_bottomLeaf_rep3

source_name: NahG-Désirée_whole mock-inoculated bottom leaf_7dpi

value: mock-inoculation


title: NahG-Désirée_1dpi_PVY_bottomLeaf_rep2


title: NahG-Désirée_7dpi_mock_bottomLeaf_rep2


title: NahG-Désirée_5dpi_mock_bottomLeaf_rep3

source_name: NahG-Désirée_whole mock-inoculated bottom leaf_5dpi


title: NahG-Désirée_4dpi_mock_bottomLeaf_rep1

source_name: NahG-Désirée_whole mock-inoculated bottom leaf_4dpi


title: NahG-Désirée_5dpi_mock_bottomLeaf_rep2


title: NahG-Désirée_3dpi_mock_bottomLeaf_rep3

source_name: NahG-Désirée_whole mock-inoculated bottom leaf_3dpi


title: NahG-Désirée_4dpi_mock_bottomLeaf_rep2


title: NahG-Désirée_7dpi_mock_bottomLeaf_rep1


title: NahG-Désirée_5dpi_mock_bottomLeaf_rep1


title: NahG-Désirée_4dpi_mock_bottomLeaf_rep3


title: NahG-Désirée_3dpi_mock_bottomLeaf_rep2


title: NahG-Désirée_1dpi_mock_bottomLeaf_rep2

source_name: NahG-Désirée_whole mock-inoculated bottom leaf_1dpi


title: NahG-Désirée_1dpi_mock_bottomLeaf_rep3


title: Désirée_7dpi_PVY_upperLeaf_rep3

source_name: cv. Désirée_whole PVY-inoculated upper leaf_7dpi


title: NahG-Désirée_3dpi_mock_bottomLeaf_rep1


title: Désirée_9dpi_PVY_upperLeaf_rep1

source_name: cv. Désirée_whole PVY-inoculated upper leaf_9dpi

value: 9 dpi


title: NahG-Désirée_5dpi_PVY_bottomLeaf_rep4


title: Désirée_11dpi_PVY_upperLeaf_rep1

source_name: cv. Désirée_whole PVY-inoculated upper leaf_11dpi

value: 11 dpi


title: Désirée_11dpi_PVY_upperLeaf_rep3


title: Désirée_8dpi_PVY_upperLeaf_rep1

source_name: cv. Désirée_whole PVY-inoculated upper leaf_8dpi

value: 8 dpi


title: Désirée_5dpi_PVY_upperLeaf_rep3

source_name: cv. Désirée_whole PVY-inoculated upper leaf_5dpi


title: Désirée_7dpi_PVY_upperLeaf_rep2


title: Désirée_9dpi_PVY_upperLeaf_rep2


title: Désirée_11dpi_PVY_upperLeaf_rep2


title: Désirée_9dpi_PVY_upperLeaf_rep3


title: NahG-Désirée_1dpi_mock_bottomLeaf_rep1

value: NahG-Désirée


title: Désirée_8dpi_PVY_upperLeaf_rep3


title: Désirée_8dpi_PVY_upperLeaf_rep2


title: Désirée_7dpi_PVY_upperLeaf_rep1


title: Désirée_5dpi_PVY_upperLeaf_rep2


title: Désirée_4dpi_PVY_upperLeaf_rep2

source_name: cv. Désirée_whole PVY-inoculated upper leaf_4dpi


title: Désirée_4dpi_PVY_upperLeaf_rep3


title: Désirée_4dpi_PVY_upperLeaf_rep1


title: Désirée_3dpi_PVY_upperLeaf_rep1

source_name: cv. Désirée_whole PVY-inoculated upper leaf_3dpi


title: Désirée_3dpi_PVY_upperLeaf_rep3


title: Désirée_1dpi_PVY_upperLeaf_rep1

source_name: cv. Désirée_whole PVY-inoculated upper leaf_1dpi


title: Désirée_7dpi_PVY_bottomLeaf_rep2

source_name: cv. Désirée_whole PVY-inoculated bottom leaf_7dpi


title: Désirée_7dpi_PVY_bottomLeaf_rep3


title: Désirée_1dpi_PVY_upperLeaf_rep2


title: Désirée_7dpi_PVY_bottomLeaf_rep1


title: Désirée_3dpi_PVY_upperLeaf_rep2


title: Désirée_4dpi_PVY_bottomLeaf_rep2

source_name: cv. Désirée_whole PVY-inoculated bottom leaf_4dpi


title: Désirée_5dpi_PVY_upperLeaf_rep1


title: Désirée_1dpi_PVY_upperLeaf_rep3


title: Désirée_5dpi_PVY_bottomLeaf_rep3

source_name: cv. Désirée_whole PVY-inoculated bottom leaf_5dpi


title: Désirée_3dpi_PVY_bottomLeaf_rep2

source_name: cv. Désirée_whole PVY-inoculated bottom leaf_3dpi


title: Désirée_11dpi_mock_upperLeaf_rep3

source_name: cv. Désirée_whole mock-inoculated upper leaf_11dpi


title: Désirée_1dpi_PVY_bottomLeaf_rep1

source_name: cv. Désirée_whole PVY-inoculated bottom leaf_1dpi


title: Désirée_4dpi_PVY_bottomLeaf_rep1


title: Désirée_11dpi_mock_upperLeaf_rep2


title: Désirée_5dpi_PVY_bottomLeaf_rep2


title: Désirée_4dpi_PVY_bottomLeaf_rep3


title: Désirée_1dpi_PVY_bottomLeaf_rep2


title: Désirée_3dpi_PVY_bottomLeaf_rep3


title: Désirée_3dpi_PVY_bottomLeaf_rep1


title: Désirée_5dpi_PVY_bottomLeaf_rep1


title: Désirée_11dpi_mock_upperLeaf_rep1


title: Désirée_9dpi_mock_upperLeaf_rep3

source_name: cv. Désirée_whole mock-inoculated upper leaf_9dpi


title: Désirée_8dpi_mock_upperLeaf_rep3

source_name: cv. Désirée_whole mock-inoculated upper leaf_8dpi


title: Désirée_9dpi_mock_upperLeaf_rep1


title: Désirée_9dpi_mock_upperLeaf_rep2


title: Désirée_7dpi_mock_upperLeaf_rep2

source_name: cv. Désirée_whole mock-inoculated upper leaf_7dpi


title: Désirée_8dpi_mock_upperLeaf_rep2


title: Désirée_7dpi_mock_upperLeaf_rep3


title: Désirée_5dpi_mock_upperLeaf_rep1

source_name: cv. Désirée_whole mock-inoculated upper leaf_5dpi


title: NahG-Désirée_1dpi_PVY_bottomLeaf_rep1

source_name: NahG-Désirée_whole PVY-inoculated bottom leaf_1dpi


title: Désirée_5dpi_mock_upperLeaf_rep2


title: Désirée_1dpi_PVY_bottomLeaf_rep3


title: Désirée_8dpi_mock_upperLeaf_rep1


title: Désirée_5dpi_mock_upperLeaf_rep3


title: Désirée_4dpi_mock_upperLeaf_rep3

source_name: cv. Désirée_whole mock-inoculated upper leaf_4dpi


title: Désirée_3dpi_mock_upperLeaf_rep1

source_name: cv. Désirée_whole mock-inoculated upper leaf_3dpi


title: Désirée_3dpi_mock_upperLeaf_rep2


title: Désirée_3dpi_mock_upperLeaf_rep3


title: Désirée_1dpi_mock_upperLeaf_rep3

source_name: cv. Désirée_whole mock-inoculated upper leaf_1dpi


title: Désirée_4dpi_mock_upperLeaf_rep1


title: Désirée_4dpi_mock_upperLeaf_rep2


title: Désirée_7dpi_mock_bottomLeaf_rep2

source_name: cv. Désirée_whole mock-inoculated bottom leaf_7dpi


title: Désirée_7dpi_mock_bottomLeaf_rep1


title: Désirée_1dpi_mock_upperLeaf_rep1


title: Désirée_5dpi_mock_bottomLeaf_rep1

source_name: cv. Désirée_whole mock-inoculated bottom leaf_5dpi


title: Désirée_5dpi_mock_bottomLeaf_rep2


title: Désirée_3dpi_mock_bottomLeaf_rep3

source_name: cv. Désirée_whole mock-inoculated bottom leaf_3dpi


title: Désirée_1dpi_mock_upperLeaf_rep2


title: Désirée_4dpi_mock_bottomLeaf_rep2

source_name: cv. Désirée_whole mock-inoculated bottom leaf_4dpi


title: Désirée_4dpi_mock_bottomLeaf_rep3


title: Désirée_1dpi_mock_bottomLeaf_rep3

source_name: cv. Désirée_whole mock-inoculated bottom leaf_1dpi


title: Désirée_7dpi_mock_bottomLeaf_rep3


title: Désirée_3dpi_mock_bottomLeaf_rep2


title: Désirée_1dpi_mock_bottomLeaf_rep2


title: Désirée_4dpi_mock_bottomLeaf_rep1


title: Désirée_1dpi_mock_bottomLeaf_rep1


title: IL-7Ra high EM CD8+ T cells #2

city: LA

first: Sungyong

last: You

address: Beverly Blvd 8400

department: Surgery

institute: Cedars-Sinai Medical Center

description: normal EM CD8+ T cells

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: genomic DNA from IL-7Ra high EM CD8+ T cells

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from IL-7Ra high and low EM CD8+ T cells using Qiagen DNeasy Kit according to standard instructions

tag: disease state

value: normal

tag: cell population

value: IL-7Ra high EM CD8+ T cells

tag: sample number


title: IL-7Ra low EM CD8+ T cells #2

description: normal EM CD8+ T cells

source_name: genomic DNA from IL-7Ra low EM CD8+ T cells

value: IL-7Ra low EM CD8+ T cells


title: Désirée_3dpi_mock_bottomLeaf_rep1

value: Désirée

value: bottom


title: 025C-B

city: Gothenburg

first: Claes

middle: M

last: Gustafsson

address: Medcinaregatan 9A

department: Department of Medical biochemistry and cell biology

country: Sweden

institute: Gothenburg University

hyb_protocol: According to the GeneChip expression analysis technical manual that is available for download at www.affymetrix.com.

data_processing: Raw data (CEL files) was imported into ArrayStar 4, per-gene normalized to median and filtered on flags.

label: Biotin

organism: Saccharomyces cerevisiae

source_name: yeast cells

label_protocol: Labeling was performed according to the GeneChip expression analysis technical manual that is available for download at www.affymetrix.com.

growth_protocol: Yeast cells were grown SC-ura plus galactose medium

extract_protocol: RNA was isolated from yeast cells according to Xue et al. 2004 (Yeast 21(1):25-39).

tag: overexpression


title: 025C-A

scan_protocol: According to the GeneChip expression analysis technical manual that is available for download at www.affymetrix.com.


title: Désirée_7dpi_mock_upperLeaf_rep1

value: upper


title: IL-7Ra low EM CD8+ T cells #1

description: normal EM CD8+ T cells


title: 4741-B

value: GST


title: 4741-C


title: 4741-A


title: IL-7Ra high EM CD8+ T cells #1

description: normal EM CD8+ T cells


title: 025C-C


title: 0.1 Se Mouse Lung 1

city: Salt Lake City

first: Michael

middle: T

last: Howard

state: UT

department: Human Genetics

institute: University of Utah

description: Biological replicate 1 of 3.

hyb_protocol: Following fragmentation, 10 micrograms of cRNA were hybridized to Mouse Genome 430 2.0 Array for 16 hours at 45C. Arrays were washed and stained in the Affymetrix Fluidics Station 430.

scan_protocol: The Affymetrix GeneChip scanner 3000 was used to scan the microarrays

data_processing: Affy probe level analysis: bMAS5. Using R version 2.15.2 (2012-10-26) and BioConductor package affy version 1.36.0. Excluded if Signal < 100

source_name: 0.1 Se_FVB/N_lung

label_protocol: RNA (100 ng) was reverse transcribed and labeled with biotin using Affymetrix 3’ IVTexpress Labeling kit following manufacturer’s protocol.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) following manufacturer's instructions. RNA quality was checked on Agilent Bioanalyzer.  All samples used for microarray analysis have high quality score (RIN >9).

treatment_protocol: Mice were fed diets supplemented with 0 or 0.1 ppm Se for 6 weeks

value: FVB/N

tag: diet

value: 0.1 ppm Selenium

value: male

tag: tissue

value: lung


title: 0 Se Mouse Lung 1

description: Biological replicate 1 of 3.

source_name: 0 Se_FVB/N_lung

value: 0 Selenium

tag: Sex


title: 0.1 Se Mouse Liver 2

description: Biological replicate 2 of 3.

source_name: 0.1 Se_FVB/N_liver

value: liver


title: 0.1 Se Mouse Lung 2

description: Biological replicate 2 of 3.


title: 0 Se Mouse Lung 2

description: Biological replicate 2 of 3.


title: 0.1 Se Mouse Liver 1

description: Biological replicate 1 of 3.


title: 0 Se Mouse Liver 3

description: Biological replicate 3 of 3.

source_name: 0 Se_FVB/N_liver


title: 0 Se Mouse Liver 1

description: Biological replicate 1 of 3.


title: 0 Se Mouse Lung 3

description: Biological replicate 3 of 3.


title: 0 Se Mouse Liver 2

description: Biological replicate 2 of 3.


title: 0.1 Se Mouse Liver 3

description: Biological replicate 3 of 3.


title: 0.1 Se Mouse Lung 3

description: Biological replicate 3 of 3.


title: Rec8_ChIP_3h_rep2

city: New York

first: Andreas

last: Hochwagen

state: NY

address: 1009 Silver Center 100 Washington Square East

institute: New York University

hyb_protocol: Samples were co-hybridized to custom Agilent arrays in 1X Agilent hybridization buffer at 65 degrees for 16 hours. Samples were washed according to manufacturer's instructions.

scan_protocol: Agilent scanner using the AgilentHD_CGH protocol (5μM resolution, 100% PMT for each laser). Images were quantified using Agilent Feature Extraction Software (version 10.1.1.1).

data_processing: Cy3 and Cy5 levels and background were calculated using Agilent Feature Extractor software. Background normalization, log2 ratios for each experiment and scale normalizations across each set of duplicated experiments were calculated using the marrray package in R (Yang, et al., 2001), a computer language and environment for statistical computing (v2.1.0, http://www.r-project.org).

source_name: meiotic time point 3h INPUT

label_protocol: Half of the immunoprecipitated DNA or one tenth of the input DNA was labeled with Cy3- or Cy5-dUTP (GE Healthcare) by random priming using 4 µg random nonamer oligo (Integrated DNA Technologies) and 10 units of Klenow (New England Biolabs). Unincorporated dye was removed using microcon columns (30-kDa MW cutoff, Millipore).

growth_protocol: Cells were pre-grown in presporulation medium (BYTA) and transferred into sporulation medium (SPO) at 0 hours. Samples were isolated at the indicated timepoints.

extract_protocol: 25 ml of cells were harvested after 3 hours in sporulation media. Chromatin immunoprecipitation was performed as described (Aparicio et al., 1997). One tenth of the lysate was removed as an input sample. Proteins were immunoprecipitated with the indicated antibodies in combination with 20 µl GammaBind-Sepharose (GE Healthcare) for 16 hours at 4°C.

tag: genotype

source_name: meiotic time point 3h ChIP

tag: antibody

value: Anti-3HA (Cat#:11867431001, Roche Applied Science)


title: rec8delta-pREC8-SCC1_SCC1_ChIP_3h_rep2

value: rec8 delta; pREC8-SCC1::3HA


title: dmc1_ssDNA_5h_rep1

description:
wt_rep1
GSM744402
ssDNA enrichment

source_name: meiotic time point 0h ssDNA enrichment

label_protocol: 1.5 μg of ssDNA was labeled with Cy3-dUTP or Cy5-dUTP (GE Healthcare) by random priming without denaturation using 4 µg random nonamer oligo (Integrated DNA Technologies) and 10 units of Klenow (New England Biolabs). Unincorporated dye was removed using microcon columns (30-kDa MW cutoff, Millipore).

extract_protocol: To isolate ssDNA, ~109 cells were fixed in 70% ethanol at –20°C. Cells were spheroplasted in sorbitol buffer (1M sorbitol, 1% beta-mercaptoethanol, 0.2 mg/ml zymolyase 100T, 0.1M EDTA, pH 7.4), lysed in NDS (0.6% SDS, 300mM EDTA, 10mM Tris.HCl, pH 9.5). DNA deproteinated with proteinase K (0.25mg/ml; Roche) at 50°C, twice phenol extracted, treated with RNase A, and stored in TE (1mM EDTA, 10mM Tris.HCl, pH 7.5) at 4°C. 25 μg DNA were digested to completion with EcoRI (New England Biolabs). ssDNA was enriched by batch absorption to BND cellulose. Briefly, a 50% slurry of BND-cellulose was equilibrated in NET (1M NaCl, 10mM Tris, pH 7.6, 1mM EDTA). Digested DNA was adjusted to 1M NaCl and ssDNA was incubated with a 500 μl bed volume of BND-cellulose for 5 minutes. Resin was washed with five bed volumes of NET. ssDNA was eluted five times with 600 μl NET + 1.8% caffeine. DNA was precipitated and concentrated for microarray analysis.

value: dmc1 delta

source_name: meiotic time point 5h ssDNA enrichment


title: A2780/SRSF3si2 Dox rep1

city: Rockford

first: Xiaolong

last: He

state: IL

address: 1601 Parkview Ave.

department: Biopharmaceutical Sciences

institute: University of Illinois at Chicago

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Labeled sense DNA fragments were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) according to Affymetrix's protocol. The experiments were carried out at Asuragen.

scan_protocol: Arrays were scanned according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Partek Genomics Suite Version 6.6 was employed yo analyze the data.

source_name: ovarian cancer cell line_SRSF3 knockdown

label_protocol: Single-stranded sense DNA was synthesized with the WT cDNA Synthesis and Amplification Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix) (Carried out by Asuragen)

growth_protocol: A2780/SRSF3si2 cells were grown in DMEM supplemented with 10% FBS and 2 mM L-glutamine at 37 °C, 5% CO2.

extract_protocol: Total RNAs were extracted from cells using TRIzol reagent (Invirogen) and then processed with Turbo DNA-free kit (Ambion) to remove any contaminated genomic DNAs.

treatment_protocol: The cells were treated with or without doxycycline at the concentration of 0.1ug/ml for three days

tag: cell line

tag: cell type

value: ovarian cancer

tag: treatment

value: SRSF3 knockdown


title: cont_vs_H2_3days_rep3

city: Kawasaki-city

first: Shigeo

last: Ohta

state: Kanagawa

address: 1-394, Kosugi-machi, Nakahara-ku

department: Department of Biochemistry and Cell Biology

country: Japan

institute: Institute of Development and Aging Sciences, Graduate School of Medicine, Nippon Medical School

description: Gene expression after exposure to H2

hyb_protocol: Hybridization were performed using Gene Expression Hybridization Kit  (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer's instructions. 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes and the fragmentation mixture were hybridized to Agilent SurePrint G3 Human GE 8x60K v2 Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven (10r.p.m.).  Wash were performed using Gene Expression Wash Buffers Pack  (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer's instructions.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1. (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Control, 3days, replicate 3

label_protocol: Cyanine-3 (Cy3) or Cyanine-5 (Cy5) labeled cRNA was prepared from 0.1 ug RNA using the Low-Input QuickAmp Labeling Kit, Two-Color (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer's instructions.

growth_protocol: Mice were fed ad libitum and housed in a temperature-controlled room (22–24 °C) under a 12-hour light/dark cycle.

extract_protocol: Total RNA was extracted using an RNeasy Mini Kit according to the manufacturers’ protocol (Qiagen, Valencia, CA, USA).  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: For 14-days administration of H2, mice were given H2-water (water with dissolved molecular hydrogen at saturated level: 0.8mM) as drinking water. For 1-, 3-, and 7-days administration of H2, MgH2, which reacts with H2O and produces H2, was used. Mice were received MgH2 orally by stomach gavage at 0.9 mg/kg once a day.

value: db/db

tag: gender

tag: age

value: 8 weeks-old

source_name: H2, 3days, replicate 3


title: Rec8_ChIP_3h_rep1

tag: strain


title: A2780/SRSF3si2 No Dox rep2

source_name: ovarian cancer cell line_no knockdown

value: No SRSF3 knockdown


title: dmc1_ssDNA_5h_rep2

description:
wt_rep2
GSM744403
ssDNA enrichment


title: rec8delta-pREC8-SCC1_SCC1_ChIP_3h_rep1


title: cont_vs_H2_7days_rep2

description: Gene expression after exposure to H2

source_name: Control, 7days, replicate 2

source_name: H2, 7days, replicate 2


title: cont_vs_H2_7days_rep1

description: Gene expression after exposure to H2

source_name: Control, 7days, replicate 1

source_name: H2, 7days, replicate 1


title: VEGF--up4

city: Kuopio

first: Mikko

middle: Petri

last: Turunen

address: Neulaniementie 2

department: AIVI

country: Finland

institute: University of Eastern Finland

description: >99% of cells expressing GFP and VEGF-A upregulated

hyb_protocol: Following fragmentation, 12,5 ug of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip scanner.

data_processing: Data were background adjusted with GC-RMA, quantile normalized, and median polish summarized using Matlab R2012b.

source_name: C166 cells transduced with lentiviral vector (MOI10) encoding GFP + shRNA that upregulates VEGF-A

label_protocol: Gene chip 3´IVT express kit standard protocol

growth_protocol: C166 cells (ATCC:CRL-2583) were cultured in DMEM containing 10% FBS, 100 units/ml penicillin and 100 ug/ml streptomycin. Cells were grown in a humidified 95% air/5% CO2 incubator at 37C.

extract_protocol: Standard TRI-reagent total-RNA isolation protocol

treatment_protocol: Cells were at 20% confluency when transduced with lentiviral vector enconding GFP or additionally shRNA that either up- or downregulates VEGF-A expression. The fresh medium was changed 72h after transduction. Cells were collected for analysis at day 7.

value: endothelial cell


title: A2780/SRSF3si2 Dox rep2


title: VEGF-down3

description: >99% of cells expressing GFP and VEGF-A downregulated

source_name: C166 cells transduced with lentiviral vector (MOI10) encoding GFP + shRNA that downregulates VEGF-A


title: VEGF-down4


title: VEGF--up3


title: VEGF--up1


title: dmc1-rec8delta_pREC8-SCC1_ssDNA_5h_rep2

description:
rec8delta_pREC8-SCC1_rep2
ssDNA enrichment

value: dmc1 delta; pREC8-SCC1; rec8 delta


title: dmc1-rec8delta_pREC8-SCC1_ssDNA_5h_rep1

description:
rec8delta_pREC8-SCC1_rep1
ssDNA enrichment


title: cont_vs_H2_1day_rep2

description: Gene expression after exposure to H2

source_name: Control, 1day, replicate 2

source_name: H2, 1day, replicate 2


title: VEGF--up2


title: A2780/SRSF3si2 No Dox rep1


title: cont_vs_H2_3days_rep2

description: Gene expression after exposure to H2

source_name: Control, 3days, replicate 2

source_name: H2, 3days, replicate 2


title: cont_vs_H2_3days_rep1

description: Gene expression after exposure to H2

source_name: Control, 3days, replicate 1

source_name: H2, 3days, replicate 1


title: cont_vs_H2_1day_rep3

description: Gene expression after exposure to H2

source_name: Control, 1day, replicate 3

source_name: H2, 1day, replicate 3


title: cont_vs_H2_1day_rep1

description: Gene expression after exposure to H2

source_name: Control, 1day, replicate 1

source_name: H2, 1day, replicate 1


title: VEGF-down2


title: VEGF-down1


title: cont_vs_H2_2weeks_rep3

description: Gene expression after exposure to H2

source_name: Control, 2weeks, replicate 3

source_name: H2, 2weeks, replicate 3


title: cont_vs_H2_7days_rep3

description: Gene expression after exposure to H2

source_name: Control, 7days, replicate 3

source_name: H2, 7days, replicate 3


title: GFP1

description: >99% of cells expressing GFP

source_name: C166 cells transduced with lentiviral vector (MOI10) encoding GFP


title: GFP2

description: >99% of cells expressing GFP


title: TM4_DOS_4

city: Montreal

first: Thomas

middle: Constantine

last: Nardelli

state: Quebec

address: 3655 Prom. Sir-William-Osler

department: Pharmacology and Therapeutics

institute: McGill University

hyb_protocol: All steps were done according to the manufacturer's protocol.

scan_protocol: Microarray chips were scanned using an Agilent SureScan G2600D Microarray Scanner. Probe intensities were converted to numerical values using Feature Extraction ver. 11.5.1.1  software with protocol GE1_1105_Oct12 and grid 028005_D_F_20110614.

data_processing: Probe values were imported into GeneSpring 12.6.1 and normalized using percentile shift normalization to the 75th percentile with a baseline transformation to the median of all samples.

label_protocol: RNA was converted to cRNA and labeled with Cy3 using the Agilent Low Input Quick Amp Labeling Kit

growth_protocol: TM4 cells were seeded in six well plates containing 250,000 cells in each well and allowed to adhere for 24 hours.

extract_protocol: Qiagen RNeasy Plus Mini Kit was used for RNA extraction. Supernatant was aspirated and 600μL Buffer RLT supplemented with 6μL β-mercaptoethanol was added to each well. Samples were pipetted several times to mechanically disrupt the cells and stored at -80°C for future extraction. On the day of extraction, lysates were further homogenized using QIAShredder columns. RNA was extracted from the flow-through as per the manufacturer's instructions.

treatment_protocol: 10-4M treatment (DOS, BDB, MEHP, DOM, and DINCH) or vehicle (1.0% DMSO) were added for 48 hours prior to RNA extraction.

value: TM4 Immortalized Sertoli Cell Line

tag: agent

value: DOS

tag: time

value: 48 hours


title: Désirée_5dpi_mock_bottomLeaf_rep3

source_name: cv. Désirée_whole mock-inoculated bottom leaf_5dpi

tag: genotype/variation

value: Désirée

value: mock-inoculation

tag: time point

value: 5 dpi

tag: leaf location

value: bottom


title: GFP4

description: >99% of cells expressing GFP


title: TM4_DMSO_4

value: DMSO


title: TM4_DINCH_3

value: DINCH


title: 250ng 16S rRNA gene amplicon of mouse caecal sample C_SR10

type: other

city: Clermont-Ferrand

first: william

last: tottey

address: 28 place Henry Dunant

country: France

institute: EA-CIDAM 4678

description: 16S rRNA gene amplified from gDNA extracted from medium from a bioreactor.

hyb_protocol: For microarray hybridization, 250ng of each labelled faecal sample were used. Hybridization was performed following the Agilent OligoaCGH hybridization protocol (Agilent Technologies, Palo Alto, CA) at 65°C for 24h.

scan_protocol: slides were scanned at a 3-µm resolution using a Surescan microarray scanner (Agilent Technologies, Palo Alto, CA).

data_processing: Pixel intensities were extracted using the “Feature Extraction” software (Agilent Technologies, Palo Alto, CA). No normalization step was performed and the retained intensity value for each probe was the ratio between the spot’s median intensity signals and the median of background signals.

organism: uncultured bacterium

label_protocol: For each sample, the purified 16S rRNA gene PCR products (1 µg) were labelled with either Cy3 or Cy5 using the Genomic DNA ULS labelling Kit (Agilent Technologies, Palo Alto, CA) following the manufacturer’s instructions.

extract_protocol: Total DNA was extracted from either cecal or faecal mouse samples using Qiagen’s DNA Stool Kit (Qiagen, West Sussex, UK). 10ng of sample was then used for PCR amplification. 16S rRNA genes were amplified using universal primers 27F (AGAGTTTGATCMTGGCTCAG) and 1492R (TACGGYTACCTTGTTACGACT). PCR reactions were performed in a 50µl volume, using DreamTaq DNA polymerase (Fermentas, St. Leon-Rot, Germany). The PCR reaction consisted of an initial denaturation step at 95°C for 5min followed by 35 cycles of denaturation at 95°C for 30 s, annealing at 58°C for 40 s and elongation at 72°C for 2 min. A final extension step was performed at 72°C for 5 min. PCR product size was verified by electrophoresis with 1% (w/v) agarose gel and were purified using the MinElute PCR Purification Kit (Qiagen Ltd., UK) following manufacturer’s instructions and stored at -20°C.

treatment_protocol: Two experimental diets were prepared in this study. Twenty-four male Wistar rats (Charles River Laboratories, l’Arbresle, France, baseline body weight 75-100 g) were fed a standard diet (A04, SAFE Diets, France). The animals were first acclimatized one week before being randomly distributed into two groups (n=12/group). The rats were then fed either the refined rye (RR) or the whole rye (WR) diet for 12 weeks. The first was obtained by mixing the standard diet flour (A03, SAFE Diets, France) with 50% RR. The second was prepared by mixing the same standard diet A03 flour with 50% WR.

value: 12 weeks of treatment

value: refined rye

tag: sample type

value: mouse gut microbiota


title: 250ng 16S rRNA gene amplicon of mouse faecal sample t12_SC12

value: whole rye


title: Wenmai6-21 d Replicate 2

city: Beijing

first: Xiuliang

last: Zhu

address: Zhongguancun street 12#

institute: The Chinese Academy of Agricultural Sciences

description:
Gene expression after Rhizoctonia cerealis infection for 21 d
S2-21

hyb_protocol: 0.8 ug of Cy3/Cy5-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a   reaction  volume  of  55ul  containing  1x  Agilent  fragmentation  buffer  and  2x  Agilent  blocking  agent  following  the   manufacturers'  instructions.  On  completion  of  the  fragmentation  reaction,  55ul  of  2x  Agilent  hybridization  buffer  was   added to the fragmentation mixture and hybridized to Agilent-022297 Wheat Gene Expression Microarray (Agilent) for 17   hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room   temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately   by brief centrifugation

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan   setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT   is set to 100%).

data_processing: The  scanned  images  were  analyzed  with  Feature  Extraction  Software  10.7.1.1  (Agilent)  using  default  parameters  to   obtain  background  subtracted  and  spatially  detrended  Processed  Signal  intensities  as  the  raw  data.  Raw  data  were   normalized  in  quantile  algorithm  with  Genespring  12.0(Agilent).  Probe  that  at  least  1  out  of  2  samples  flagged  as   Detected were maintained.

organism: Triticum aestivum

source_name: Wenmai6 leaf sheath_21days

label_protocol: Cyanine-3/5  (Cy3/Cy5)  labeled  cRNA  was  prepared  from  0.2  ug  RNA  using  the  Two-Color  Low  RNA  Input  Linear   Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification   (QIAGEN,  Valencia,  CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000   Spectrophotometer.

growth_protocol: All wheat plants were grown in a glasshouse at 22°C-14 h light (intensity of 300 μmol m-2 s-1) and 12°C-10 h dark conditions.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Wheat were inoculated with small toothpicks harboring the well-developed mycelia of Rhizoctonia cerealis for 4 d,21d.

tag: cultivar

value: Wenmai 6

tag: phenotype

value: susceptible

value: Leaf sheath

value: day 30


title: Shanhongmai-4 d Replicate 1

description:
raw data file: 10187_1_4.txt available on sample GSM1696067
Gene expression after Rhizoctonia cerealis infection for 4 d
R2-4

source_name: Shanhongmai leaf sheath_4days

value: Shanhongmai

value: resistant

tag: tissue


title: CI12633-21 d Replicate 1

description:
raw data file: 10187_1_3.txt available on sample GSM1696066
Gene expression after Rhizoctonia cerealis infection for 21 d
R1-21

source_name: CI12633 leaf sheath_21days


title: Wenmai6-4 d Replicate 2

description:
Gene expression after Rhizoctonia cerealis infection for 4 d
S2-4

source_name: Wenmai6 leaf sheath_4days


title: cont_vs_H2_2weeks_rep1

description: Gene expression after exposure to H2

source_name: Control, 2weeks, replicate 1

value: db/db

value: liver

value: male

value: 8 weeks-old

source_name: H2, 2weeks, replicate 1


title: Wenmai6-21 d Replicate 1

description:
Gene expression after Rhizoctonia cerealis infection for 21 d
S1-21


title: CI12633-4 d Replicate 1

description:
raw data file: 10187_1_1.txt available on sample GSM1696065
Gene expression after Rhizoctonia cerealis infection for 4 d
R1-4

source_name: CI12633 leaf sheath_4days


title: TM4_DMSO_3

value: TM4 Immortalized Sertoli Cell Line

value: 48 hours


title: TM4_DINCH_4

value: DINCH


title: TM4_DINCH_2


title: TM4_BDB_4

value: BDB


title: Shanhongmai-21 d Replicate 1

description:
raw data file: 10188_1_2.txt available on sample GSM1696068
Gene expression after Rhizoctonia cerealis infection for 21 d
R2-21

source_name: Shanhongmai leaf sheath_21days


title: TM4_DOM_3

value: DOM


title: TM4_MEHP_4

value: MEHP


title: TM4_BDB_3


title: TM4_MEHP_3


title: TM4_DOS_3

value: DOS


title: Wenmai6-4 d Replicate 1

description:
Gene expression after Rhizoctonia cerealis infection for 4 d
S1-4

value: Wenmai 6


title: cont_vs_H2_2weeks_rep2

description: Gene expression after exposure to H2

source_name: Control, 2weeks, replicate 2

source_name: H2, 2weeks, replicate 2


title: TM4_DOM_4


title: 250ng 16S rRNA gene amplicon of mouse caecal sample C_SR5

description: 16S rRNA gene amplified from gDNA extracted from a batch sample

value: 12 weeks of treatment

value: refined rye

value: mouse gut microbiota


title: 250ng 16S rRNA gene amplicon of mouse faecal sample t12_SC9

description: 16S rRNA gene amplified from gDNA extracted from a faecal sample

value: whole rye


title: TM4_DMSO_2

value: DMSO


title: 250ng 16S rRNA gene amplicon of mouse caecal sample C_SR4


title: 250ng 16S rRNA gene amplicon of mouse faecal sample t12_SC8


title: 250ng 16S rRNA gene amplicon of mouse caecal sample C_SR3


title: TM4_BDB_2


title: 250ng 16S rRNA gene amplicon of mouse faecal sample t12_SC5


title: TM4_DOS_1


title: TM4_MEHP_2


title: TM4_DOM_2


title: 250ng 16S rRNA gene amplicon of mouse caecal sample C_SR1


title: TM4_DINCH_1


title: 250ng 16S rRNA gene amplicon of mouse faecal sample t12_SR10


title: TM4_BDB_1


title: 250ng 16S rRNA gene amplicon of mouse faecal sample t12_SC7


title: 250ng 16S rRNA gene amplicon of mouse faecal sample t0_SR5

value: start of experiment


title: TM4_DOM_1


title: 250ng 16S rRNA gene amplicon of mouse caecal sample C_SC9


title: 250ng 16S rRNA gene amplicon of mouse faecal sample t0_SR4


title: TM4_MEHP_1


title: 250ng 16S rRNA gene amplicon of mouse faecal sample t0_SR10


title: 250ng 16S rRNA gene amplicon of mouse caecal sample C_SC8


title: GFP3

description: >99% of cells expressing GFP

value: endothelial cell


title: U2OS_miR-634_rep1

city: Tokyo

first: Jun

last: Inoue

address: Yushima 1-5-45, Bunkyo-ku

department: Molecular Cytogenetics

institute: Tokyo Medical & dental univ.

description: Gene expression in miR-634 transfected cells

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K (G4851A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-107) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were maintained with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA fractions were prepared using TRIsure (BIOLINE,London, UK) following the manufacturer's recommendations. The protocol includes clean up step after TURBO DNA-free™ Kit (Ambion, Austin, TX) digestion. RNAs were quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Mir-NC or miR-634 were transfected into cells using RNAiMax

value: Osteosarcoma

tag: transfection


title: U2OS_miR-NC_rep1

description: Gene expression in miR-NC transfected cells

value: miR-NC


title: 250ng 16S rRNA gene amplicon of mouse faecal sample t0_SR3


title: 250ng 16S rRNA gene amplicon of mouse caecal sample C_SC7


title: U2OS_miR-634_rep2


title: TM4_DMSO_1

value: TM4 Immortalized Sertoli Cell Line


title: 250ng 16S rRNA gene amplicon of mouse caecal sample C_SC5


title: U2OS_miR-NC_rep2


title: KYSE850_miR-634_rep2

value: Esophageal cancer


title: 250ng 16S rRNA gene amplicon of mouse faecal sample t0_SR1


title: KYSE850_miR-634_rep1


title: 250ng 16S rRNA gene amplicon of mouse faecal sample t12_SR5


title: 250ng 16S rRNA gene amplicon of mouse faecal sample t0_SC12


title: KYSE850_miR-NC_rep1


title: 250ng 16S rRNA gene amplicon of mouse faecal sample t12_SR3


title: 250ng 16S rRNA gene amplicon of mouse faecal sample t12_SR4


title: 250ng 16S rRNA gene amplicon of mouse faecal sample t0_SC9


title: HeLa_miR-634_rep2

value: HeLa

value: Cervical caner


title: HeLa_miR-634_rep1


title: HT875-Con3

city: Bethesda

first: WeiPing

last: Chen

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

hyb_protocol: E. Coli whole genome expression array chips were washed and stained in the Affymetrix Fluidics Station 400s

scan_protocol: Chips were scanned with an Affymetrix Scanner with standard settings

data_processing: Data was analyzed with RMA using the program Partek 6.6

organism: Escherichia coli

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA

extract_protocol: RNA were isolated from wild type and mutants. Trizol extraction of total RNA was performed according to standard affymetrix labeling protocols.

treatment_protocol: E. coli strains HT874, HT873, HT875, HT873 treated with or no polyamines by Trizol protocol.


title: 250ng 16S rRNA gene amplicon of mouse faecal sample t0_SC8


title: HeLa_miR-NC_rep1


title: 250ng 16S rRNA gene amplicon of mouse caecal sample C_SC12


title: HT875-Con2


title: 250ng 16S rRNA gene amplicon of mouse faecal sample t12_SR1


title: 250ng 16S rRNA gene amplicon of mouse faecal sample t0_SC7


title: HT873-Con3


title: HT873-PA2


title: HT875-Con1


title: 250ng 16S rRNA gene amplicon of mouse faecal sample t0_SC5


title: HT873-PA3


title: HT873-PA1


title: HT873-Con2


title: KYSE850_miR-NC_rep2


title: HT875-PA3


title: HT875-PA2


title: 9-HT874-PA3


title: 8-HT874-PA2


title: 7-HT874-PA1


title: HeLa_miR-NC_rep2


title: HT873-Con1


title: HT875-PA1


title: 6-HT873-PS-60min3


title: 5-HT873-PS-60min2


title: 4-HT873-PS-60min1


title: 2-HT873-PA2


title: 3-HT873-PA3


title: fc1 at T2, biological rep1

first: Jesse

middle: Daniel

last: Woodson

address: 10010 N. Torrey Pines Rd.

department: Plant Biology

institute: The Salk Institute

description: Gene expression data during (120 min) de-etiolation

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized on Affymetrix GeneChip Arabidopsis ATH1 Genome Array using the GeneChip Hybridization, Wash, and Stain Kit according to the manufacturer’s instructions.

scan_protocol: Arrays were scanned using a GeneChip scanner 3000 7G (Affymetrix)

data_processing: Data was RMA pre-processed using the Chipster 2.0 open source platform (pre-set Affymetrix normalization) to generate normalized expression values and to identify genes that show a reliable level of RNA.

organism: Arabidopsis thaliana

source_name: fc1 seedlings with 120 min light exposure

label_protocol: Biotinylated cRNA were prepared using the GeneChip 3’ IVT Express Kit from 450 ng total RNA (Affymetrix).

growth_protocol: Seeds were plated onto Linsmaier and Skoog medium pH 5.7 with 0.6% micropropagation type-1 agar powder. After a 4 day stratification in the dark at 4°C, plates were exposed to 120 μmol m-2 sec-1 at 22°C for 2 hours to initiate germination. Plates were then wrapped in aluminum foil and seedlings were grown in the dark for 4 days at 22°C.

extract_protocol: Total RNA was extracted using the RNeasy® Plant Mini Kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: For 30 and 120 minute light treatments, plates were unwrapped and exposed to 120 μmol m-2 sec-1 at 22°C for the indicated amount of time.

tag: ecotype

value: whole 4 day old seedlings

tag: genotype


title: fc1 at T2, biological rep2


title: 1-HT873-PA1


title: 12-HT874-PS-60min3


title: fc2 at T2, biological rep2

source_name: fc2 seedlings with 120 min light exposure


title: fc1 at T1, biological rep2

description: Gene expression data during (30 min) de-etiolation

source_name: fc1 seedlings with 30 min light exposure


title: wt at T2, biological rep1

source_name: wt seedlings with 120 min light exposure

value: wt


title: fc2 at T2, biological rep1


title: Bone marrow 4 from HCC patient 28

city: Beppu

first: Shotaro

last: Sakimura

address: 4546 Tsurumihara Tsurumi

department: Department of surgeryy

institute: Kyushu University Beppu Hospital

description: microRNA

hyb_protocol: Labeled RNAs were hybridized onto 3D-Gene Human microRNA Oligo chips containing 837 anti-sense probes printed in duplicate spots (Toray, Kamakura, Japan).

scan_protocol: After stringent washes, fluorescent signals were scanned with the 3D-Gene Scanner (Toray).

data_processing:
The scanned images were analyzed using GenePix Pro version 5.0 (Molecular Devices, Sunnyvale, CA, USA).
We filtered out star-miR and miR that are not annotated as hsa-miR. Raw data were quantile-normalized after log2 scaling. If the Agilent Probe Names are not unique, we chose the most variable probe.

source_name: Macrophage fraction of BM cells (CD14+ cell fraction)

label_protocol: Extracted total RNA was labeled with Cy3 using the miRCURY LNA Array miR labelling kit (Exiqon, Vedbaek, Denmark).

extract_protocol: Aspiration of BM was conducted under general anesthesia immediately before surgery. BM cells were separated into 3 fractions using a 3-step automagnetic-activated cell separation system (MACS) by MACS Cell Separators (Miltenyi Biotec, Bergisch Gladbach, Germany). CD45+, CD14+, and CD45−/EpCAM+ cell fractions were collected using CD45, CD14, and EpCAM (CD326) microbeads according to the manufacturer's instructions (Miltenyi Biotec). RNA was extracted from each BM fraction separated by the Auto MACS system using the miRNeasy Mini Kit (Qiagen, Venlo, Netherlands) according to the manufacturer’s protocol.

tag: cell type

tag: Sex

value: male

tag: Stage

value: stage 3

tag: recurrence

value: yes

tag: number of tumors

value: multiple


title: fc1 at T1, biological rep1


title: fc2 at T1, biological rep1

source_name: fc2 seedlings with 30 min light exposure


title: Bone marrow 3 from HCC patient 28

description: microRNA

source_name: Epithelial cell fraction of BM cells (CD45-/EpCAM+ cell fraction)

tag: age


title: wt at T1, biological rep2

source_name: wt seedlings with 30 min light exposure


title: wt at T1, biological rep1


title: fc2 at T1, biological rep2


title: fc1 at T0, biological rep1

description: Gene expression data before de-etiolation

source_name: fc1 mutant seedlings before light exposure


title: fc1 at T0, biological rep2


title: Bone marrow 2 from HCC patient 28

description: microRNA

source_name: Lymphocyte fraction of BM cells (CD45+ cell fraction)


title: flu at T0, biological rep2

source_name: flu mutant seedlings before light exposure

value: flu


title: 11-HT874-PS-60min2

tag: strain

tag: treatment


title: flu at T2, biological rep1

source_name: flu seedlings with 120 min light exposure


title: flu at T0, biological rep1


title: flu at T2, biological rep2


title: wt at T2, biological rep2


title: 10-HT874-PS-60min1


title: Bone marrow 1 from HCC patient 28

description: microRNA

source_name: whole BM fraction

value: whole BM fraction


title: flu at T1, biological rep2

source_name: flu seedlings with 30 min light exposure


title: flu at T1, biological rep1


title: Bone marrow 3 from HCC patient 21

description: microRNA

value: Epithelial cell fraction of BM cells (CD45-/EpCAM+ cell fraction)

value: stage 1

value: no

value: single


title: wt at T0, biological rep2

source_name: wt seedlings before light exposure


title: wt at T0, biological rep1


title: Bone marrow 2 from HCC patient 21

description: microRNA

value: Lymphocyte fraction of BM cells (CD45+ cell fraction)


title: Bone marrow 4 from HCC patient 21

description: microRNA

value: Macrophage fraction of BM cells (CD14+ cell fraction)


title: fc2 at T0, biological rep2

source_name: fc2 mutant seedlings before light exposure


title: fc2 at T0, biological rep1


title: NEW 059A

city: London

first: Alice

last: Gao

state: London

address: 237 Fulham Road

department: Breast Cancer Now

country: United Kingdom

institute: The Institute of Cancer Research

description: pre-treatment

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were transformed and normalized using variance-stabilizing transformation and robust spline normalization method in the Lumi package in R

source_name: breast tumour

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

extract_protocol: mRNA from treated cells was extracted with RNeasy Mini Kit (Qiagen), as per the manufacturer's instructions, and quantification performed using the Agilent 2100 Bioanalyzer (Expert Software version B.02.03) with RNA Nano LabChip Kits (Agilent Technologies).

tag: rmh lab code

value: NEW 059

value: female

tag: trtlong

value: Faslodex 500mg

value: pre-treatment

value: breast tumour


title: Bone marrow 2 from HCC patient 20

description: microRNA

value: male


title: Bone marrow 1 from HCC patient 20

description: microRNA

value: stage 3


title: Bone marrow 4 from HCC patient 20

description: microRNA


title: Bone marrow 3 from HCC patient 20

description: microRNA


title: Bone marrow 3 from HCC patient 13

description: microRNA

value: stage 2

value: yes


title: Bone marrow 1 from HCC patient 21

description: microRNA


title: Bone marrow 1 from HCC patient 13

description: microRNA


title: Bone marrow 2 from HCC patient 13

description: microRNA


title: Bone marrow 4 from HCC patient 13

description: microRNA


title: NEW 006A

description: pre-treatment

value: NEW 006


title: NEW 003A

description: pre-treatment

value: NEW 003


title: NEW 036A

description: pre-treatment

value: NEW 036


title: Bone marrow 3 from HCC patient 12

description: microRNA

value: Epithelial cell fraction of BM cells (CD45-/EpCAM+ cell fraction)

value: multiple


title: NEW 036B

description: on-treatment

value: on-treatment


title: NEW 031B

description: on-treatment

value: NEW 031


title: Squamous carcinoma (TE10) cell line Replicate 2

city: Baltimore

first: James

last: Donahue

address: 10 North Greene

institute: University of Maryland

description:
Biological replicate 2 of 2. Esophageal squamous cancer cells, harvested at passage 5.
PP6

hyb_protocol: The Hy3 labeled samples and a Hy5-labeled reference RNA samples were  mixed pair-wise and hybridized to the miRCURY LNA microRNA Array (7th Gen) , which contains capture probes targeting all microRNAs for human registered in the miRBASE 18.0.  The hybridization was performed according to the miRCURY LNA microRNA Array Instruction manual using a Tecan HS4800 hybridization station (Tecan, Austria).  http://www.exiqon.com/ls/documents/scientific/mircury-lna-microrna-array-7th-gen-hsa-mmu-rno-manual.pdf

scan_protocol: miRCURY LNA microRNA Array slides were scanned using the Agilent G2565BA Microarray scanner system Agilent Technologies Inc.,USA). The Image analysis was carried out using the Exiqon-tailored ImaGene9 data analysis software (www.exiqon.com/mirna-array-software)

data_processing: The quantified signals were background corrected (Noemexp with offset value 10) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.n the norm.xlxs a 'G' sheet contains the signals from the samples (Hy3) and a 'R' sheet which is the signals from the common reference (Hy5).

source_name: squamous cancer cell line

label_protocol: 750 ng total RNA from both sample and reference was labeled  with Hy3 and Hy5 fluorescent label, respectively, using the EXIQON miRCURY LNA microRNA Hi-Power Labeling Kit, HY3/Hy5 (Exiqon,Denmark) following the procedure described by the manufacture.  http://www.exiqon.com/ls/documents/scientific/mircury-lna-microrna-array-7th-gen-hsa-mmu-rno-manual.pdf

growth_protocol: Cells were cultured in RPMI medium supplemented with 10% heat inactivated Fetal Bovine Serum.

extract_protocol: Total RNA including miRNA was extracted using QIAGEN miRNeasy kit,  following manufacturer's instructions. The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile.

tag: cell line

value: TE10:Human esophageal squamous cells

tag: passage

value: Human cells derived from an esophageal squamous cell carcinoma


title: NEW 012A

description: pre-treatment

value: NEW 012

value: female


title: Squamous carcinoma (TE10) cell line Replicate 1

description:
Biological replicate 1 of 1. Esophageal squamous cancer cells, harvested at passage 5.
PP5


title: Squamous carcinoma (TE7) cell line Replicate 2

description:
Biological replicate 2 of 2. Esophageal squamous cancer cells, harvested at passage 5.
PP4

value: TE7:Human esophageal squamous cells


title: Normal epithelial (hESO) cell line Replicate 1

description:
Biological replicate 1 of 2. Esophageal epithelial cells, harvested at passage 5.
PP1

source_name: Normal epithelial cell line

growth_protocol: Cells were cultured in BEBM medium supplemented with 20% heat inactivated Fetal Bovine Serum and the BEGM bullet kit.

value: hESO:Normal human esophageal epithelial cells

value: Human esophageal epithelial cells derived from esophageal specimens harvested at the time of donor lung procurement


title: Normal epithelial (hESO) cell line Replicate 2

description:
Biological replicate 2 of 2. Esophageal epithelial cells, harvested at passage 5.
PP2


title: Bone marrow 2 from HCC patient 12

description: microRNA

value: Lymphocyte fraction of BM cells (CD45+ cell fraction)

value: male


title: Bone marrow 3 from HCC patient 10

description: microRNA

value: stage 1

value: no

value: single


title: Bone marrow 1 from HCC patient 12

description: microRNA

value: whole BM fraction

value: stage 2

value: yes


title: Bone marrow 4 from HCC patient 10

description: microRNA

value: Macrophage fraction of BM cells (CD14+ cell fraction)


title: Bone marrow 1 from HCC patient 10

description: microRNA


title: Bone marrow 2 from HCC patient 10

description: microRNA


title: NEW 003B

description: on-treatment

value: NEW 003

value: Faslodex 500mg

value: on-treatment

value: breast tumour


title: NEW 020B

description: on-treatment

value: NEW 020

value: female


title: Bone marrow 1 from HCC patient 6

description: microRNA


title: Bone marrow 3 from HCC patient 6

description: microRNA

value: Epithelial cell fraction of BM cells (CD45-/EpCAM+ cell fraction)


title: Bone marrow 2 from HCC patient 6

description: microRNA


title: NEW 012B

description: on-treatment

value: NEW 012