title: Unpredictable chronic mild stress, fluoxetine treatment, biological replicate 1

description:
Gene expression data from unpredictable chronic mild stress, fluoxetine treatment, biological replicate 1
uCMS_FLX_1

value: Wistar

value: 2 months


title: MNC_4h_LPS+Ibuprofen_rep1

status: Public on Jul 02 2015

type: RNA

city: Borstel

first: Sebastian

last: Marwitz

address: Parkallee 3a

department: Histology

country: Germany

institute: Research Center Borstel - Leibniz Lung Center

hyb_protocol: 1650 ng of Cy3-labelled cRNA was fragmented according to Low Input Quick Amp Labelling Kit Protocol (Agilent) with 2xHI-RPM Hybridization Buffer for 30 min at 60°C. Hybridization on Agilent Human Whole Genome 4x44k V2 arrays was performed at 65°C for 17h under constant rotation in a hybidization oven. Washing was performed using the GE Wash buffer 1 (Agilent) at RT and Ge Wash Buffer 2 (Agilent) at 37°C for each 1 min. Washed slides were air-dried and immediately scanned.

scan_protocol: Slides were immediately scannend on an Agilent SureScan Scanner with Dye Channel =Green, 5 µm Resolution and scanning area=61 x 21.6 mm.

data_processing: Agilent Feature Extraction Software V 11.5 was used with default options (GE 1-color protocol) to extract raw data. Txt files were imported into GeneSpring software Version 13 under omission of compromised flags. Fags were accepted if at least 100 percent of samples in any 1 out of 7 conditions were detected.

molecule: total RNA

organism: Homo sapiens

source_name: Monocytes, 4h,LPS+Ibuprofen, replicate 1

label_protocol: Cy3-labelling of total RNA was conducted with the Low Input Quick Amp Labelling Kit (Agilent) according to manufacturer´s instructions. Dye incorporation rate and specific yield was calculated using an NanoDrop spectrophotometer.

extract_protocol: Total RNA was extracted directly after stimulation with the Qiagen Rneasy Mini Kit according to manufacturer´s instructions. RNA was stored at -80°C until further use.

treatment_protocol: cells were isolated from heparinized blood of 3 healthy donors by the Hypaque-Ficoll density gradient method.The cell number was equilibrated at 5 x 105 cells/ml RPMI 1640 containing 2 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin. For stimulation, 200 µl/well MNC were transferred into 96-well culture plates. The stimuli were serially diluted in RPMI 1640 and added to the cultures at 20 µl per well. Concentrations of 0.1 ng/ml LPS R60 from Salmonella enterica Minnesota rough mutants, 10 ng/ml Pep19-2.5 (Bachem, Lot. 1053821) and 1 µg/ml ibuprofen (Fluka 11892, Lot. BCBI499V) were applied in 0.9 % NaCl. The cultures were incubated for 4 h at 37°C under 5% CO2.

tag: cell type

value: Monocytes

tag: treatment

value: LPS + Ibuprofen


title: Unpredictable chronic mild stress, agomelatine treatment, biological replicate 3

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

description:
Gene expression data from unpredictable chronic mild stress, agomelatine treatment, biological replicate 3
uCMS_AGOM_3

hyb_protocol: According to the Affymetrix expression protocol (HWS kit)

data_processing: RMA probeset summary and quantile normalization (Expression console v.1.2, Affymetrix)

label: biotin

organism: Rattus norvegicus

source_name: Dentate gyrus, unpredictable chronic mild stress, agomelatine treatment

label_protocol: WT Expression Kit (Ambion) and WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Animals per housed under standard laboratory conditions

extract_protocol: RNeasy Mini Kit (Qiagen) including DNase treatment

treatment_protocol: As described in the paper. Briefly, male Wistar rats (200–250g, 2 month-old; Charles-River Laboratories) were maintained under standard laboratory conditions (12h light: 12h dark cycles, 22oC, relative humidity of 55%, ad libitum access to food and water). A validated unpredictable Chronic Mild Stress protocol (uCMS) was applied for 6 weeks, as previously described (Bessa et al, 2009b). During the last 2 weeks of the uCMS, animals were injected intraperitoneally daily with one of the four antidepressants (ADs): fluoxetine (10mg.kg-1 in ultra-pure water; Kemprotec); imipramine (10mg.kg-1 in 0.9% saline solution; Sigma-Aldrich); tianeptine (10mg.kg-1 in 0.9% saline solution; Kemprotec) and agomelatine (40mg.kg-1 in 0.5% hydroxyethylcellulose; Kemprotec). The doses were chosen based on previous studies (Banasr et al, 2006; Bessa et al, 2009b; McEwen et al, 2010; Morley-Fletcher et al, 2011; Rocher et al, 2004). Bodyweight gain was monitored weekly throughout the protocol (Supplementary Figure S1a). All procedures were carried out in accordance with EU Directive 2010/63/EU and NIH guidelines on animal care and experimentation.

tag: strain

tag: age

tag: gender

value: Male

tag: genotype

value: wild type

tag: stress

value: unpredictable chronic mild stress

tag: agent

value: agomelatine

tag: tissue

value: Dentate gyrus


title: CD24neg_T_off_rep3

description: Gene expression data from CD24neg_T_off_rep3

hyb_protocol: According to the Affymetrix expression protocol

data_processing: Expression console (v.1.3.0.187, Affymetrix) was used to obtain normalized RMA gene-level data (standard settings including sketch-quantile normalisation)

source_name: CD24negative population, HMLE-Twist1-ER, control

label_protocol: Ovation Pico WTA System V2 in combination with the Encore Biotin Module (Nugen)

growth_protocol: HMLE-Snail1-Er and HMLE-Twist1-ER cells were propagated in mammary epithelial cell growth medium (PromoCell) containing Pen/Strep (Invitrogen) according to standard protocols.

extract_protocol: RNeasy Mini Kit (Qiagen)

treatment_protocol: Treatment with 4-hydroxytamoxifen, mammosphere assay and FACS-sorting was performed as described in the paper

tag: cell line

value: HMLE

value: mammary epithelial cell line

value: female


title: Unpredictable chronic mild stress, fluoxetine treatment, biological replicate 3

description:
Gene expression data from unpredictable chronic mild stress, fluoxetine treatment, biological replicate 3
uCMS_FLX_3

scan_protocol: According to the Affymetrix expression protocol

source_name: Dentate gyrus, unpredictable chronic mild stress, fluoxetine treatment

value: fluoxetine


title: Unpredictable chronic mild stress, biological replicate 3

description:
Gene expression data from unpredictable chronic mild stress, biological replicate 3
uCMS_3

source_name: Dentate gyrus, unpredictable chronic mild stress

value: untreated


title: MNC_4h_Pep19-2.5_rep1

source_name: Monocytes, 4h,Pep19-2.5, replicate 1


title: CD24hi_T_onoff_rep1

description: Gene expression data from CD24hi_T_onoff_rep1

source_name: CD24high population, HMLE-Twist1-ER, treated with 4-hydroxytamoxifen for 15 days, then cultured for 9 days without 4-hydroxytam in 2D


title: CD24hi_T_onoff_3D_rep2

description: Gene expression data from CD24hi_T_onoff_3D_rep2

source_name: CD24high population, HMLE-Twist1-ER, treated with 4-hydroxytamoxifen for 15 days, then cultered 9 days in mammosphere assay without 4-hydroxytamoxifen


title: CD24hi_T_onoff_rep2

description: Gene expression data from CD24hi_T_onoff_rep2


title: CD24hi_T_on_rep2

description: Gene expression data from CD24hi_T_on_rep2

source_name: CD24high population, HMLE-Twist1-ER, treated with 4-hydroxytamoxifen for 15 days


title: CD24hi_T_on_rep3

description: Gene expression data from CD24hi_T_on_rep3


title: DT2008, dehydrated 10h, replicate 3

city: Lubbock

first: chien

middle: Van

last: ha

state: TX

address: 1006 Carton Avenue, Box 43135

department: IGCAST

country: USA

institute: texas tech university

hyb_protocol: Each sample was then hybridized to an Affymetrix soybean gene 1.0 ST array by standard procedures.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for array slides.

data_processing:
Raw data from. CEL files were initially analyzed by Affymetrix Expression Console with library files supplied by Affymetrix. Analysis were done using RMA method for gene levels without normalization. The log2 transformed data were exported individually for use in analysis in GeneSpring software. The data in text format were imported to GeneSping software and normalized using a 75 percentage threshhold. T-test were used to analyze for statistical significance of the same gene in different condition. To further increase the liability, multivarate test, FDR, was to used to calculate for the corrected p-values. All these tests were performed with Gene Spring GX11 software. Fold change data on the Series record represents drought/well-watered.
probe group file: SoyGene-1_0-st-v1.pgf
meta-probeset file: SoyGene-1_0-st-v1.mps

organism: Glycine max

source_name: DT2008_dehydrated 10h

label_protocol: Samples were then fragmented and end-labeled using Affymetrix GeneChip WT Terminal Labeling Kit according to the manufacturer's instructions.

growth_protocol: Williams 82 and DT2008 soybean plants were separately germinated in each 6-litre pot containing vermiculite soil (6 plants per pot) and grown under well-watered conditions in greenhouse conditions (30ºC, 12-h-light/12-h-dark, 150 μmol m-2 sec-1 photon flux density and 50% relative humidity).

extract_protocol: Soybean roots were collected and quickly frozen in liquid nitrogen, and stored at -80oC. Total RNA was extracted using triazol reagent, DNAse I treatment was perform prior to quality accessment by Agilent 2100 Bioanalyzer. All samples were prepared using the Ambion WT expression kit for cDNA synthesis, cRNA amplification, and conversion to sense strand cDNA according to the manufacturer's instructions

treatment_protocol: The 14-d-old plants were detached and exposed to dehydration on KimTowel papers for 0, 2 or 10h. All the roots were collected at the time of the treatment

tag: cultivar

tag: drought-responsive phenotype

value: enhanced tolerance

value: 14 day-old

tag: exposed to

value: dehydration for 10hr

value: roots


title: MNC_4h_Medium_rep1

source_name: Monocytes, 4h, Medium, replicate 1

value: Medium


title: Unpredictable chronic mild stress, imipramine treatment, biological replicate 1

description:
Gene expression data from unpredictable chronic mild stress, imipramine treatment, biological replicate 1
uCMS_IMIP_1

source_name: Dentate gyrus, unpredictable chronic mild stress, imipramine treatment

value: Wistar

value: 2 months

value: imipramine


title: Unpredictable chronic mild stress, agomelatine treatment, biological replicate 1

description:
Gene expression data from unpredictable chronic mild stress, agomelatine treatment, biological replicate 1
uCMS_AGOM_1

value: Male

value: wild type


title: DT2008, dehydrated 10h, replicate 2


title: MNC_4h_Ibuprofen_rep1

source_name: Monocytes, 4h, Ibuprofen, replicate 1

value: Monocytes

value: Ibuprofen


title: Unpredictable chronic mild stress, biological replicate 2

description:
Gene expression data from unpredictable chronic mild stress, biological replicate 2
uCMS_2

value: unpredictable chronic mild stress

value: Dentate gyrus


title: CD24hi_T_on_rep1

description: Gene expression data from CD24hi_T_on_rep1

value: HMLE

value: mammary epithelial cell line

value: female


title: Unpredictable chronic mild stress, biological replicate 1

description:
Gene expression data from unpredictable chronic mild stress, biological replicate 1
uCMS_1

value: untreated


title: CD24hi_T_off_rep3

description: Gene expression data from CD24hi_T_off_rep3

source_name: CD24high population, HMLE-Twist1-ER, control


title: DT2008, dehydrated 2h, replicate 2

source_name: DT2008_dehydrated 2h

value: enhanced tolerance

value: 14 day-old

value: dehydration for 2hr


title: NL61-NASH61L

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

hyb_protocol: A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix' PrimeView Human Gene Expression arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: Data were normalized using RMA as implemented in the Affy package (version 1.40.0) of Bioconductor. Expression values are represented on a log2-scale.

source_name: Liver, Histology class 3

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).

growth_protocol: Clinical sample prior bariatric surgery

extract_protocol: Rneasy kit (Qiagen)

treatment_protocol: Samples collected during bariatric surgery

tag: patientid

value: 58 year

tag: bmi

value: liver


title: DT2008, dehydrated 2h, replicate 3

value: roots


title: CD24hi_S_onoff_3D_rep3

description: Gene expression data from CD24hi_S_onoff_3D_rep3

source_name: CD24high population, HMLE-Snail1-ER cells, treated with 4-hydroxytamoxifen for 15 days, then cultered 9 days in mammosphere assay without 4-hydroxytamoxifen


title: CD24hi_S_off_rep3

description: Gene expression data from CD24hi_S_off_rep3

source_name: CD24high population, HMLE-Snail1-ER cells, ctrl


title: DT2008, dehydrated 10h, replicate 1

value: dehydration for 10hr


title: NL79-NASH79L

source_name: Liver, Histology class 2

value: 47 year


title: DT2008, well-watered (0h), replicate 3

source_name: DT2008_well-watered (0h)

value: dehydration for 0hr (well-watered)


title: CD24hi_S_onoff_3D_rep1

description: Gene expression data from CD24hi_S_onoff_3D_rep1


title: CD24hi_T_off_rep1

description: Gene expression data from CD24hi_T_off_rep1


title: CD24hi_T_off_rep2

description: Gene expression data from CD24hi_T_off_rep2


title: NL70-NASHL70

value: 49 year


title: Williams 82, dehydrated 10h, replicate 2

source_name: Williams 82_dehydrated 10h

value: Williams 82


title: CD24hi_S_off_rep2

description: Gene expression data from CD24hi_S_off_rep2


title: NL64-NASHL64

value: 43 year

value: male


title: Williams 82, dehydrated 10h, replicate 3


title: NL53-NASH53L

value: 50 year


title: DT2008, dehydrated 2h, replicate 1


title: CD24hi_S_onoff_3D_rep2

description: Gene expression data from CD24hi_S_onoff_3D_rep2

value: HMLE

value: mammary epithelial cell line


title: Williams 82, dehydrated 2h, replicate 3

source_name: Williams 82_dehydrated 2h


title: BL57-NASH57L

value: 32 year

value: female


title: CD24hi_S_off_rep1

description: Gene expression data from CD24hi_S_off_rep1


title: NL73-NASH73L

value: 53 year


title: DT2008, well-watered (0h), replicate 1

value: enhanced tolerance

value: 14 day-old


title: NL65-NASH65L

value: 54 year

value: liver


title: DT2008, well-watered (0h), replicate 2

value: roots


title: NL56-NASHL56

value: 39 year


title: Streptomyces_48h_WD1

city: Hangzhou

first: Shui

middle: Ping

last: Liu

state: Zhejiang

address: 866, Yuhangtang road

department: Biohemistry and moleculer biology

country: China

institute: Zhejiang University

description: Gene expression after 48h

hyb_protocol: Each Slide was hybridized with 600ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Streptomyces chattanoogensis

source_name: Mycelium

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Grow in YEME for 48 hours, 200 r/min, 30℃

extract_protocol: Total RNA was isolated using the RNA extract kit (QIAGEN, Germany), according to the manufacturer’s instructions, and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Mycelium was collected from YEME culture by centrifugation, discard the supernatant, wash the mycelium twice by PBS buffer.

value: S.  chattanoogensis L10

value: wildtype

tag: developmental stage

value: exponential phase

tag: culture medium

value: YEME


title: Streptomyces_48h_WC2

description: Gene expression after 48h


title: Streptomyces_48h_WE1

description: Gene expression after 48h


title: Williams 82, dehydrated 10h, replicate 1

value: Williams 82

value: dehydration for 10hr


title: Williams 82, dehydrated 2h, replicate 2

value: dehydration for 2hr


title: Williams 82, well-watered (0h), replicate 3

source_name: Williams 82_well-watered (0h)

value: dehydration for 0hr (well-watered)


title: Streptomyces_48h_S36E1

description: Gene expression after 48h

value: WhiGch deletion


title: Streptomyces_48h_S36B2

description: Gene expression after 48h


title: NL76-NASH76L

source_name: Liver, Histology class 1

value: 44 year

value: female


title: Williams 82, dehydrated 2h, replicate 1


title: Williams 82, well-watered (0h), replicate 2


title: NL77-NASHL77

value: 48 year


title: NL69-NASH69L

value: 41 year


title: Streptomyces_48h_S36D1

description: Gene expression after 48h


title: Y69H_DMSO 3

status: Public on Jul 01 2015

city: Vancouver

first: Patrick

last: Plettner

state: BC

address: 100-570 West 7th Avenue

country: Canada

institute: BC Cancer Agency GSC

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

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the McGill University and Genome Quebec Innovation Centre

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Data were processed using the Affymetric Expression Console for background correction and normalization. Data analysis and statistical evaluations were performed with customized R codes (version 2.3.1, http://www.r-project.org/).

source_name: Y69H MEF2B-V5

label_protocol: Samples were labelled using the standard protocols of the McGill University and Genome Quebec Innovation Centre

growth_protocol: Cells were grown in 6 wells plates to 90% confluency

extract_protocol: RNA was isolated using the RNeasy Plus Kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: Cells were treated with 1.5uM ionomycin for 6 hours. DMSO treatment used a volume equivalent to the volume of DMSO in which the ionomycin was dissolved (1.07uL/mL) for 6 hours

tag: transfection

value: Y69H MEF2B-V5

value: DMSO


title: Y69H_DMSO 2

tag: treatment


title: D83V_DMSO 1

source_name: D83V MEF2B-V5

value: D83V MEF2B-V5


title: D83V_DMSO 2


title: Williams 82, well-watered (0h), replicate 1

value: 14 day-old

value: roots


title: D83V_DMSO 3


title: K4E_DMSO 3

source_name: K4E MEF2B-V5

value: K4E MEF2B-V5


title: K4E_DMSO 2


title: Y69H_DMSO 1


title: K4E_DMSO 1


title: NL55-NASH55L

value: liver


title: NL71-NASHL71

value: 58 year

value: male


title: untrans_iono 2

source_name: untransfected

value: ionomycin treated (1.5uM for 6hr)


title: untrans_iono 3


title: BL52-NASH52L

value: 49 year


title: untrans_DMSO 2


title: untrans_iono 1


title: untrans_DMSO 1


title: WT_iono 1

source_name: WT MEF2B-V5

value: WT MEF2B-V5


title: WT_DMSO 3


title: WT_DMSO 2


title: untrans_DMSO 3


title: WT_iono 3


title: WT_iono 2


title: NGPS iPSCs N-IIc13

city: Oviedo

first: Jose

last: Freije

state: Asturias

address: C/ Fernando Bongera s/n

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universidad de Oviedo

description: Gene expression data from NGPS iPSCs.

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix Human Exon 1.0 ST Array according to the protocols recommended by the manufacturer (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Washing and scanning were performed using Fluidics Station 400 and GeneChip Scanner (Affymetrix, Inc.).

data_processing:
After scanning, raw data (Affymetrix CEL files) were processed with RMAExpress (http://RMAExpress.bmbolstad.com), using default settings.
"Full" exons were included in the analysis. Transcript assignments are based on the hg18 genome.
Probe group file: HuEx-1_0-st-v2.r2.pgf
Meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.full.mps

source_name: NGPS iPSCs

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

growth_protocol: Fibroblasts and iPSCs were grown at 37 ºC, 5% CO2, under standard conditions for each cell type.

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

treatment_protocol: Not applicable.

tag: disease state

value: Nestor-Guillermo Progeria Syndrome (NGPS)

tag: cell type

value: induced pluripotent stem cells (iPSCs)


title: NGPS iPSCs N-Ic14

description: Gene expression data from NGPS iPSCs.


title: WT_DMSO 1


title: wild type mature, biological rep1

city: Roorkee

first: Harsh

last: Chauhan

state: Uttaranchal

address: Old Biotechnology Building

department: Department of Biotechnology

country: India

institute: Indian Institute of Technology Roorkee

description: Gene expression data from mature leaf of six weeks old plant.

hyb_protocol: Hybridization was done as described in the manual: biotin-labeled single-stranded aRNA targets were mixed in the 250ul of the Hybridization Mix (Affymetrix Inc., P/N 900720) containing a Hybridization Controls and Control Oligonucleotide B2 (Affymetrix Inc., P/N 900454). Samples were hybridized to GeneChip Barley Genome Array (Affymetrix Inc., P/N 900515) for 16h at 45°C.

scan_protocol: Affymetrix GeneChip Scanner 3000 (Affymetrix Inc.) was used to measure the fluorescent intensity emitted by the labeled target

data_processing: The data was analyzed by R software. The normalization of data was performed by the Gene Chip Robust Multiarray Analysis (GCRMA) algorithm

organism: Hordeum vulgare

source_name: mature plant leaf

label_protocol: biotin-labeled single-stranded cRNA targets were mixed in the 250ul of the Hybridization Mix (Affymetrix Inc., P/N 900720) containing a Hybridization Controls and Control Oligonucleotide B2 (Affymetrix Inc., P/N 900454).

growth_protocol: Barley plants were grown in potted soil under green house conditions with 20oC temperature and 16:8 nours day night regimn

extract_protocol: Promega SV Total RNA isolation kit, including on-column DNAse digestion

treatment_protocol: Second leaf from two weeks old seedling and mature leaf from six weeks old plants of wild type and two transgenic lines were sampled for RNA isolation.

value: Golden Promise

tag: genotype/variation

value: wild type

tag: age

value: six weeks old

value: mature leaf


title: Transgenic line BG9 seedling leaf, biological rep3

description: Gene expression data from second leaf of two weeks old plant.

source_name: seedling second leaf

value: Transgenic line BG9

value: two weeks old

value: second leaf


title: Control iPSCs c7

description: Gene expression data from control iPSCs.

source_name: Control iPSCs

value: control


title: Transgenic line BG8 mature leaf, biological rep2

value: Transgenic line BG8


title: Transgenic line BG9 mature leaf, biological rep2


title: Transgenic line BG9 mature leaf, biological rep3


title: Transgenic line BG8 mature leaf, biological rep3


title: NGPS iPSCs N-IIc3

description: Gene expression data from NGPS iPSCs.


title: Transgenic line BG8 mature leaf, biological rep1


title: Transgenic line BG9 mature leaf, biological rep1


title: Transgenic line BG8 seedling leaf, biological rep3


title: Control Fibs

description: Gene expression data from control fibroblasts.

source_name: Control fibroblasts

value: adult fibroblasts


title: Control iPSCs c10


title: Transgenic line BG9 seedling leaf, biological rep2


title: Transgenic line BG9 seedling leaf, biological rep1


title: wild type mature, biological rep2


title: wild type mature, biological rep3


title: Transgenic line BG8 seedling leaf, biological rep2


title: Transgenic line BG8 seedling leaf, biological rep1


title: wild type seedling, biological rep3


title: NGPS Fibs N-II

description: Gene expression data from NGPS fibroblasts.

source_name: NGPS fibroblasts


title: NGPS Fibs N-I


title: wild type seedling, biological rep2


title: wild type seedling, biological rep1


title: P0_Retina_4

city: Miami

first: Dmitry

last: Ivanov

state: FL

address: 1638 NW 10th Avenue

department: Ophthalmology

institute: University of Miami Miller School of Medicine

description:
Sample name: P0_19709346
We processed individual samples that each contained 200,000-500,000 cells.

hyb_protocol: Biotinylated complementary RNA samples were fragmented, diluted in a formamide-containing hybridization buffer, and loaded on to the Mouse Exonic Evidence Based Oligonucleotide (MEEBO) microarray slides enclosed in custom hybridization chambers (for more information on the MEEBO oligonucleotide set please refer to http://alizadehlab.stanford.edu/). The slides were hybridized for 16-18 hours in a Model 400 hybridization oven (Scigene, Sunnyvale, CA).

scan_protocol: After hybridization, the microarray slides were washed under stringent conditions, stained with Streptavidin-Alexa-647 (Invitrogen, Carlsbad, CA), and scanned using an Axon GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA).

data_processing: Spot intensities for each probe were calculated by subtracting median local background from median local foreground for each spot. The spot intensities were then normalized. After removing data for low quality spots, the mouse probes’ intensities were filtered to identify all probes with intensity above a normalized threshold. For statistical analysis, microarray data were examined for differences by One-way ANOVA or Student's t-test. Values of P < 0.05 were designated as statistically significant.

organism: Mus musculus

source_name: whole retinal cell populations

label_protocol: RNA samples were extracted from whole retina and Notch1+ cells using the Absolutely RNA® Nanoprep kit (Agilent Technologies, Santa Clara, CA). Biotin-labeled complementary RNA was made from total RNA according to Van Gelder’s protocol (Van Gelder RN, von Zastrow ME, Yool A, Dement WC, Barchas JD, et al. (1990) Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc Natl Acad Sci U S A 87: 1663-1667.)

extract_protocol: To isolate Notch1+ cells we employed an immunomagnetic cell separation approach using monoclonal biotin conjugated anti-Notch1 mouse antibodies and anti-biotin magnetic microbeads.

tag: strain

value: retina

value: Postnatal Day 0 (P0)

value: whole retinal cell populations


title: P0_Retina_3

description:
Sample name: P0_19709345
We processed individual samples that each contained 200,000-500,000 cells.


title: P0_Retina_2

description:
Sample name: P0_19709344
We processed individual samples that each contained 200,000-500,000 cells.


title: P0_Notch1_4

description:
Sample name: P0_19709335
We processed individual samples that each contained 200,000-500,000 cells.

source_name: Notch1 positive cells isolated from developing retinas

value: Notch1+ cells


title: E14_Retina_2

description:
Sample name: E14_19709352
We processed individual samples that each contained 200,000-500,000 cells.

value: Embryonic Day 14 (E14)


title: P0_Notch1_3

description:
Sample name: P0_19709334
We processed individual samples that each contained 200,000-500,000 cells.


title: P0_Notch1_2

description:
Sample name: P0_19709333
We processed individual samples that each contained 200,000-500,000 cells.


title: E14_Notch1_3

description:
Sample name: E14_19709349
We processed individual samples that each contained 200,000-500,000 cells.


title: E14_Retina_1

description:
Sample name: E14_19709350
We processed individual samples that each contained 200,000-500,000 cells.


title: P0_Notch1_1

description:
Sample name: P0_19709332
We processed individual samples that each contained 200,000-500,000 cells.


title: P0_Retina_1

description:
Sample name: P0_19709343
We processed individual samples that each contained 200,000-500,000 cells.


title: E14_Notch1_2

description:
Sample name: E14_19709348
We processed individual samples that each contained 200,000-500,000 cells.


title: Mock_Liver

city: Taichung

first: Chien-Yun

last: Hsiang

address: 91 Hsueh-Shih Road

country: Taiwan

institute: China Medical University

hyb_protocol: Cy5-labeled RNA targets were hybridized to the Mouse Whole Genome OneArrayTM (Phalanx Biotech Group, Hsinchu, Taiwan)

scan_protocol: The slides were scanned by an Axon 4000 scanner (Molecular Devices, Sunnyvale, CA).

data_processing: The Cy5 fluorescent intensity of each spot was analyzed by Genepix 4.1 software (Molecular Devices, Sunnyvale, CA). The signal intensity of each spot was corrected by subtracting background signals in the surrounding. We filtered out spots that signal-to-noise ratio was less than 0 or control probes. Spots that passed aforementioned criteria were normalized by the R program in the limma package using quantile normalization (Smyth, 2005).

label_protocol: Fluorescence-labeled RNA targets were prepared from 5 μg of total RNA using MessageAmpTM aRNA kit (Ambion, Austin, TX, USA) and cyanine (Cy5) dye (Amersham Pharmacia, Piscataway, NJ, USA).

extract_protocol: Total RNAs were extracted from muscle, adipose tissue, and liver using RNeasy Mini kit (Qiagen, Valencia, CA).

treatment_protocol: PBS

value: ob/ob mice (B6.V-Lepob/J)

value: liver


title: E14_Retina_3

description:
Sample name: E14_19709353
We processed individual samples that each contained 200,000-500,000 cells.


title: Mock_Muscle

value: muscle


title: E14_Notch1_1

description:
Sample name: E14_19709347
We processed individual samples that each contained 200,000-500,000 cells.


title: MCSE_Liver

treatment_protocol: aqueous extract of MC seeds


title: MCSE_Adipose tissue

source_name: MCSE_mice_adipose tissue

value: adipose tissue


title: MCSE_Muscle


title: Mock_Adipose tissue

source_name: Mice_adipose tissue


title: HEK-293T_194

city: Shanghai

first: Chunyang

last: Bao

state: Shanghai

address: Shanghai Medical College, Fudan University 1207 Rm., 2# Bldg., 270 Dong An Rd.

department: Fudan University Shanghai Cancer Center

institute: Fudan University

description: Gene expression data from HEK-293T cells transfected with miR-194 mimics

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

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0  (Agilent technologies, Santa Clara, CA, US).

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol, using the GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US).

growth_protocol: HEK-293T cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and antibiotics at 37°C and 5% CO2.

treatment_protocol: We used lipofectamine 2000 reagent (Invitrogen) to transfect cells with in vitro synthesized miRNA mimic (Genepharma) at a final concentration of 50 nM.

value: HEK-293T (human kidney epithelial cell line)

value: transfected with mir-194 mimics for 48 hrs


title: hMSC [mRNA]

city: Yufu

first: Masanori

last: Kawano

address: 1-1 Idaigaoka, Hasama-machi

country: Japan

institute: Oita University

description: Gene expression data from human mesenchymal stem cell line

hyb_protocol: The double-strand cDNA was used as a template for in vitro transcription to generate biotin-labeled cRNA. After fragmentation, 12.5 ug of cRNA was hybridized to the GeneChip array for 16 hr.

scan_protocol: The GeneChips were washed and stained using the GeneChip Fluidics Station 450 (Affymetrix) and then scanned with the GeneChip Scanner 3000 (Affymetrix).

data_processing: The microarray numerical values were analyzed using the GeneSpring GX 11.0 software, according to the RMA16 Algorithm: quantile normalization, filter by flags (detected), filter by expression on the normalized data (20.0–100.0th percentile).

source_name: Human Mesenchymal Stem Cell Line

label_protocol: Biotinylated cRNA was synthesized from total RNA using the Affymetrix 3` IVT Express Kit according to manufacturer’s protocols.

growth_protocol: Osteosarcoma cells were cultured in a high-glucose medium, DMEM supplemented with 10% FBS and 1% penicillin and streptomycin.

extract_protocol: Total RNA was extracted with the TRizol reagent and cDNA was synthesized according to the manufacturer's protocol.

treatment_protocol: Cultured Cells are removed by treatment with Trypsin-EDTA　when they reach to 70–80% confluence.

value: hMSC

value: mesenchymal stem cells


title: NY [mRNA]

description: Gene expression data from human osteosarcoma cell line

source_name: Human Osteosarcoma Cell Line

value: NY

value: osteosarcoma cells


title: Saos [mRNA]

value: Saos


title: Hu09 [mRNA]


title: HEK-293T_NC

description: Gene expression data from HEK-293T cells transfected with negative control mimics

value: transfected with negative control mimics for 48 hrs


title: Stromal tissue_replicate 3

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

institute: CRCHUL

hyb_protocol: Fifteen micrograms of fragmented cRNA were hybridized for 16 hrs at 45°C under constant rotation, using a human oligonucleotide array U133 Plus 2.0 (Genechip, Affymetrix). After hybridization, chips were processed using the Affymetrix GeneChip Fluidic Station 450 (protocol EukGE-WS2v5_450). Staining was made with streptavidin-conjugated phycoerythrin (SAPE, Molecular Probes), followed by amplification with a biotinylated anti17 streptavidin antibody (Vector Laboratories), and followed by a second round of SAPE.

scan_protocol: Chips were scanned with a GeneChip scanner 3000 G7 (Affymetrix)

data_processing: Background subtraction and normalization of probe set intensities were performed using the method of Robust Multiarray Analysis (RMA) described by Irizarry et al. (Irizarry et al, 2003).

label: Biotin

source_name: Laser Micro-dissection of the stromal compartment of PDACs

label_protocol: Fifteen micrograms of total RNA were reverse transcribed into cDNA using Superscripts reverse transcriptase (Invitrogen) and T7-oligo-d(T)24 (Geneset) as a primer. Second-strand synthesis was performed using T4 DNA polymerase and E.Coli DNA ligase, and then phosphorylated blunt ends were generated using T4 polynucleotide kinase. cDNA was purified by phenol-chloroform extraction using phase lock gels (Brinkmann). Then, cDNAs were in vitro transcribed for 16 hrs at 37°C by using the IVT Labelling Kit (Affymetrix) to produce biotinylated cRNAs. Labelled cRNA was purified using the RNeasy Mini Kit column (QIAGEN). Purified cRNA was fragmented to 200-30mers using a fragmentation buffer. The quality of total RNA, cDNA synthesis, cRNA amplification and fragmentation was monitored by capillary electrophoresis (Bioanalyzer 2100, Agilent Technologies).

extract_protocol: Total RNA extraction was done with the RNAeasy Mini kit (Qiagen). RNA quality has been measured with the bioanalyzer 2100 (Agilent).

treatment_protocol: Frozen sections (20µm) were obtained from selected tissue samples. After a brief staining with Hematoxylin and Eosin, sections were dehydrated. A surface of aproximatively 2.106 mm2 for epithelial compartment and 4.106 mm2 for stromal compartment has been microdissected, using the PALM system (P.A.L.M. Microlaser Technologies AG, Bernried, Germany). The microdissected material was immediately dissolute in a buffer containing β-mercaptoethanol and RNA carrier, and frozen before RNA extraction.

tag: sample type

value: Freshly frozen tissue sample

tag: tissue type

value: pancreatic ductal adenocarcinoma (PDACs)

tag: tissue subtype

value: stromal compartment


title: HOS [mRNA]

tag: cell line

value: HOS


title: Stromal tissue_replicate 1


title: Glandular tissue_replicate 1

source_name: Laser Micro-dissection of the epithelial compartment of PDACs

value: epithelial compartment


title: Stromal tissue_replicate 2


title: Benign prostate glands, PC2562

city: Aarhus N

first: Martin

middle: Mørck

last: Mortensen

address: Brendstrupgaardsvej 100

department: Dept. of Urology

country: Denmark

institute: Aarhus University Hospital

hyb_protocol: The labeled cDNA was loaded onto the Affymetrix U133 Plus 2.0 GeneChip according to the manufacturer's protocol.

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

data_processing: Data was RMA normalized and intensity measures generated using GeneSpring version 11 software.

source_name: Laser micro dissected benign prostate glands

label_protocol: A total of 5ng RNA was amplified and converted to cDNA using Nugen Pico-RNA system. After amplification, the cDNA was fragmented and labeled using NuGen FL-Ovation kit.

extract_protocol: RNA extraction was performed using RNeasy Micro kit from Qiagen (Germany).

tag: tissue

value: benign prostate glands

tag: t-stage

tag: bcr


title: Glandular tissue_replicate 3


title: MG63 [mRNA]


title: Benign prostate glands, PC2560


title: Benign prostate glands, PC2584


title: Benign prostate glands, PC2581


title: Glandular tissue_replicate 2


title: Benign prostate glands, PC2611


title: Benign prostate glands, PC2543


title: Benign prostate glands, PC2546


title: Benign prostate glands, PC2554


title: Benign prostate glands, PC2580


title: Benign prostate glands, PC1744


title: Prostate cancer cells, PC0948

source_name: Laser micro dissected prostate tumor tissue

value: prostate tumor

value: Positive

value: YES


title: Prostate cancer cells, PC0930

value: Negative

value: NO


title: Prostate cancer cells, PC0751


title: Prostate cancer cells, PC0717


title: Prostate cancer cells, PC0845


title: Prostate cancer cells, PC0711


title: Prostate cancer cells, PC0825


title: Prostate cancer cells, PC0888


title: Prostate cancer cells, PC0828


title: Prostate cancer cells, PC0904


title: Prostate cancer cells, PC0933


title: Benign prostate glands adjacent to cancer, PC0832


title: Prostate cancer cells, PC0750


title: Prostate cancer cells, PC0866


title: Prostate cancer cells, PC0836


title: NGPS iPSCs N-IIc5

description: Gene expression data from NGPS iPSCs.

value: Nestor-Guillermo Progeria Syndrome (NGPS)

value: induced pluripotent stem cells (iPSCs)


title: Benign prostate glands adjacent to cancer, PC0269


title: Prostate cancer cells, PC0646


title: Prostate cancer cells, PC0254


title: Prostate cancer cells, PC0266


title: Benign prostate glands adjacent to cancer, PC0818


title: Prostate cancer cells, PC0255


title: Prostate cancer cells, PC0539


title: Prostate cancer cells, PC0279


title: Prostate cancer cells, PC0746


title: Prostate cancer cells, PC0713


title: Prostate cancer cells, PC0251


title: Benign prostate glands adjacent to cancer, PC0275


title: Prostate cancer cells, PC0913


title: Prostate cancer cells, PC0486


title: Prostate cancer cells, PC0296


title: Prostate cancer cells, PC0265


title: Mac_MCF7-patient1-sample2

city: Goettingen

first: Annalen

last: Bleckmann

address: Robert-Koch-Straße 40

department: Hematology/Oncology

institute: University Medical Center Goettingen

description: Macrophage from patient 1 after co-culture with MCF-7, second sample

hyb_protocol: 1.65µg of each labeled cDNA sample were fragmented and applied. Hybridizations were performed for 17 hours at 10 rpm and 65°C in a hybridization oven (Agilent). Labeled RNA samples were hybridized to Human miRNA 8x15K V3 microarrays (#G4470C, Agilent). Hybridizations were performed for 20 hours at 10 rpm and 65°C in a hybridization oven (Agilent).

scan_protocol: Cy3 intensities were detected by one-color scanning using the G2505B Agilent DNA microarray scanner at 5µm or 3µm resolution.

data_processing: Raw Median signal intensities were log2-transformed and quantile normalized.

source_name: Macrophage

label_protocol: Global gene expression analyses utilized the “Human GE 4x44K v2 Microarray Kit” (Agilent, Böblingen, Germany) and the QuickAmp Labeling Kit Cy3 One-Color (Agilent) as well as the RNA Spike-In Kit (Agilent). 500ng of total RNA were used as starting material for the synthesis of cDNA. Following in-vitro transcription, the quality and quantity of labeled RNA was determined using the NanoDrop D-1000 UV-VIS Spectrophotometer (Peqlab, Erlangen, Germany). For human miRNA microarray analyses, 200ng of total RNA were labeled using the miRNA Complete Labeling and Hyb Kit (Agilent).

extract_protocol: Total RNA for array experiments was isolated using TRIZOL reagent according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA). RNA integrity for each sample was confirmed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). Samples used for microarray experiments exhibited a RIN number greater than 7.5. Each RNA sample was then split into two aliquots that were either processed for the miRNA or the mRNA microarray.

treatment_protocol: The ER+ and PR+ human breast cancer cell line MCF-7 was purchased from DSMZ and maintained in RPMI-1640 medium (PAA Laboratories Inc., Cölbe, Germany) supplemented with 10% fetal calf serum (FCS, Invitrogen, Karlsruhe, Germany). Human macrophages were derived from mononuclear peripheral blood cells. Briefly, monocytes were obtained from buffy coats of healthy donors through double-density-gradient isolation. Macrophages were differentiated by culturing monocytes in fluorinated ethylene propylene-coated cell culture bags (CellGenix, Freiburg, Germany) in the presence of M-CSF (Immunotools, Friesoythe, Germany) for 7 days. For indirect co-culture experiments, macrophages were seeded in hanging cell culture inserts (0.4µm pore size, PET; Millipore, Billerica, MA, USA) and co-cultured with MCF-7 cells at a ratio of 2:1 under normoxia for 24 hours.

tag: coculture

value: coculture with MCF-7

tag: patient


title: Prostate cancer cells, PC0247


title: Prostate cancer cells, PC0230


title: Prostate cancer cells, PC0188


title: Prostate cancer cells, PC0173


title: Mac-patient3-sample2

description: Untreated macrophage from patient 3, second sample

value: control


title: Prostate cancer cells, PC0187


title: Mac_MCF7-patient2-sample2

description: Macrophage from patient 2 after co-culture with MCF-7, second sample


title: Prostate cancer cells, PC0244


title: Mac_MCF7-patient3-sample1

description: Macrophage from patient 3 after co-culture with MCF-7, first sample


title: Prostate cancer cells, PC0168


title: Prostate cancer cells, PC0171


title: Reference_Sample

city: Incheon

first: Eui-jin

last: Lee

address: 665-8 Bupyong 6 Dong, Bupyong-Gu

department: Institute of Catholic Integrative Medicine

country: South Korea

institute: Incheon St. Mary's hospital

description: PromoCell; Heidelberg, Germany

hyb_protocol: The hybridization was incubated in Agilent SureHyb chambers for 17 hr in a Rotisserie Hybridization Oven set to 65℃ and rotating at 10 rpm.

scan_protocol: Arrays were scanned using an Agilent Technologies Scanner G2505C US92903705 (Agilent Technologies, Inc).

data_processing: Extracted data analyzed with R-programming (Variance Stabilization and Normalization, the VSN package)

source_name: Human bone marrow mesenchymal stem cells

label_protocol: Total RNA (10-200ng) was reverse transcribed into cDNA by incorporating a T7 promoter primer prior to the generation of ?uorescent cRNA using an Agilent Quick Amp Labeling KIT (Agilent Technologies).

growth_protocol: The cultures were incubated in alpha-MEM medium supplemented with 10% heat-inactivated fetal bovine serum and bFGF at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted from the cultured cells by QiagenRNeasy Mini KIT (Qiagen, Crawley, UK) according to the manufacturer’s instructions.

tag: gender

value: male

value: reference


title: Mac-patient4-sample1

description: Untreated macrophage from patient 4, first sample


title: Mac-patient2-sample1

description: Untreated macrophage from patient 2, first sample


title: SFSC_osteoarthritis female

description: OCT4 low expression

source_name: Human synovial fluid derived stem cells

value: femal

value: osteoarthiritis


title: Su(H) Kc rep3

type: genomic

city: Cambridge

first: Sarah

last: Bray

address: Downing Street

department: PDN

country: United Kingdom

institute: University  of Cambridge

hyb_protocol: Samples were prepared and hybridized to GeneChip Drosophila Tiling 2.0R Array according to Affymetrix specifications.

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

data_processing:
The CEL files were processed with Biconductor Starr package, signal values were quantile normaised between all samples and the normalised log2 rations of sample/input reported for each replicate experiment as *.sgr files (chromosome, start, ratio).
Sg290rep123_quant-all_Ringo_hw350v10.sgr, Sg290rep123_quant-all_Ringo_normalNullzero_hw350v10g200FDR1_filtered.bed
The Sg290rep123_quant-all_Ringo_hw350v10.sgr file contain the median of replicate ratios smoothed into window scores using a sliding window of 700bp and 10 minimum Probes in window with the Bioconductor Ringo package. The bed file was created assuming a normalNull distribution centred around zero and the resulting p-values were adjusted for multiple testing using the fdr method.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Su(H) Kc replicate 3

label_protocol: Library was generated using GenomePlex® Complete Whole Genome Amplification (WGA) Kit #WGA2-50RXN. The amplification reaction was complemented by adding 0.75ul of 10mM dUTP. The amplification was performed for 14 cycles. Samples were then fragmented and hybridized to GeneChip Drosophila Tiling 2.0R Array according to Affymetrix specifications.

growth_protocol: Kc167 cells where growth on Schneider’s media complemented with 5% Fetal bovine serum and 100U of penicillin streptomycin  at 25˚C.

extract_protocol: Chromatin extraction was performed from one 10cm of confluent Kc167 cell per conditions, cell were washed twice with PBS and crosslinked with 1%FA for 10 minutes at 25˚C. The cross liking reaction was stopped by adding glycine to a final concentration of 150mM. Crossliked cells were washed three times with ice-cold PBS and were collected in 600µl of extraction buffer (50 mM Tris-HCl pH 8; 10 mM EDTA; 1% SDS; 1x complete proteinase inhibitor Roche). Sonication was performed using Bioruptor UCD-200 (Diagenode) for 7 minutes on setting ‘high’ at 4˚C (30’’ on 30’’ off). 150ul chromatin was diluted 1 in 10 on dilution buffer (20mM Tris-HCl pH 8.1; 150 mM NaCl; 2mM EDTA; 1% Triton X-100; 1x Roche complete inhibitor). Chromatin was pre-cleared by incubating the diluted chromatin with 50µl of protein A/G agarose (Santa Cruz) plus 0.5ug of rabbit IgG for 2-3 hours. Pre-cleared chromatin was incubated overnight with 40µl of protein A/G agarose beads plus 1ul of rabbit anti-GFP (ab290). Beads were washed twice in dilution buffer, twice in wash buffer I (20 mM Tris-HCl pH 8; 50 mM NaCl; 2 mM EDTA; 1% Triton X-100; 0.01% SDS), twice in wash buffer II (10 mM Tris-HCL pH 8; 250 mM LiCl; 1 mM EDTA; 1% NP-40; 0.25% deoxycholic acid) and once with TE buffer (10 mM Tris-HCL pH 8; 1 mM EDTA). Chromatin was eluted from the beads using elution buffer (100 mM NaHC03, 1% SDS) for 10 min at 65˚C with agitation. Chromatin was decrosslinked by adding NaCl to a final concentration of 300mM and incubated overnight at 65˚C. DNA was treated with 10ng/ul RNAse A for 30 min at 37˚C and 2 hous with 20ng/µl proteinase K before cleaning with Qiagen PCR cleaning columns.

treatment_protocol: Kc167 were transfected with GFP-Su(H) plasmid containing  ~7kb of  Su(H) locus (~1.8kb of the upstream to ~2kb of downstream sequence from genomic region) using Fugene. Cells were then grown under permanent selection with 2μg/ml puromycin.

value: Kc167 (with GFP-Su(H) stable transfection)

tag: antibody

value: anti-GFP (abcam, ab290)


title: Su(H) Kc Input rep3

source_name: Su(H) Kc Input replicate 3


title: Prostate cancer cells, PC0172


title: Su(H) Kc Input rep1

source_name: Su(H) Kc Input replicate 1


title: SHR_E16.0_kidney3 [exon-level]

city: Berlin

first: Reinhold

last: Kreutz

address: Charitéplatz 1

institute: Charité

description: LEO-MWF-19-Leo_302-220212-RatGe-St1-0.CEL

hyb_protocol: Arrays were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: Affymetrix GeneChip® Scanner 3000 7G using GeneChip® Operating Software (GCOS) for image processing

data_processing:
After normalization the arrays have been checked for outliers by principal component analysis (PCA), using a correlation dispersion matrix and normalized Eigenvector scaling. The analysis of differential expression of summarized gene level expression has been performed with Partek Genomic Suite version 6.5
RaGene-1_0-st-v1.r4.pgf
RaGene-1_0-st-v1.r4.mps

source_name: SHR-E16.0 kidney

label_protocol: Terminal labeling kits (Ambion, New-York, USA)

growth_protocol: Rat embryonic kidney dissected at day E15.5/E16.0 respectively

extract_protocol: embryonic kidneys were harvested, snap-frozen in liquid nitrogen and stored at -80°C. Total RNA preparations of male kidney tissues were performed for MWF rats at developmental stage E15.5 and SHRs at E16.0 (n=4) using the RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. The quality and concentration of the purified total RNA were confirmed by spectroscopy.

treatment_protocol: not applicable

value: SHR

value: kidney


title: SFSC_degenerated_cartilage

description: OCT4 high expression

value: degenerated cartilage


title: Su(H) Kc rep1

source_name: Su(H) Kc replicate 1


title: Mac_MCF7-patient1-sample1

description: Macrophage from patient 1 after co-culture with MCF-7, first sample

hyb_protocol: 1.65µg of each labeled cDNA sample were fragmented and applied. Hybridizations were performed for 17 hours at 10 rpm and 65°C in a hybridization oven (Agilent). Labeled RNA samples were hybridized to Human miRNA 8x15K V2 microarrays (#G4470B, Agilent). Hybridizations were performed for 20 hours at 10 rpm and 65°C in a hybridization oven (Agilent).


title: SFSC_osteoarthritis male

description: OCT4 low expression


title: Mac_MCF7-patient4-sample2

description: Macrophage from patient 4 after co-culture with MCF-7, second sample


title: Mac-patient1-sample1

description: Untreated macrophage from patient 1, first sample


title: KP H3K56ac

data_processing:
The CEL files were processed with Biconductor Starr package, signal values were quantile normaised between all samples and the normalised log2 rations of sample/input reported for each replicate experiment as *.sgr files (chromosome, start, ratio).
KcLz12_r12.sm_quant-all_Ringo_hw300v8.bedgraph, KcLz12_r12.sm_quant-all_normalNullmode_hw300v8g200FDR1.bed
The *bedgraph files contain the median of replicate ratios smoothed into window scores using a sliding window of 600bp and 8 minimum Probes in window with the Bioconductor Ringo package (Bioconductor 3.0). The bed files were created assuming a normalNull distribution centred around zero and the resulting p-values were adjusted for multiple testing using the fdr method.

source_name: H3K56ac ChIP in Kc cells with pMT transfection

extract_protocol: Chromatin extraction was performed from one 10cm of confluent Kc167 cell per conditions, cell were washed twice with PBS and crosslinked with 1%FA for 10 minutes at 25˚C. The cross liking reaction was stopped by adding glycine to a final concentration of 150mM. Crossliked cells were washed three times with ice-cold PBS and were collected in 500µl of extraction buffer (50 mM Tris-HCl pH 8; 10 mM EDTA; 1% SDS; 1x complete proteinase inhibitor Roche). Sonication was performed using Bioruptor UCD-200 (Diagenode) for 10 minutes on setting ‘high’ at 4˚C (30’’ on 30’’ off). 100ul chromatin was diluted 1 in 10 on dilution buffer (20mM Tris-HCl pH 8.1; 150 mM NaCl; 2mM EDTA; 1% Triton X-100; 1x Roche complete inhibitor). Chromatin was pre-cleared by incubating the diluted chromatin with 50µl of protein A agarose (Santa Cruz) plus 0.5ug of rabbit IgG for 2-3 hours. Pre-cleared chromatin was incubated overnight with 4ul of rabbit anti-H3K56ac (39281). 50µl of protein A agarose beads were then added to the chromatin and incubated for another 3 hours. Beads were washed twice in dilution buffer, twice in wash buffer I (20 mM Tris-HCl pH 8; 50 mM NaCl; 2 mM EDTA; 1% Triton X-100; 0.01% SDS), twice in wash buffer II (10 mM Tris-HCL pH 8; 250 mM LiCl; 1 mM EDTA; 1% NP-40; 0.25% deoxycholic acid) and once with TE buffer (10 mM Tris-HCL pH 8; 1 mM EDTA). Chromatin was eluted from the beads using elution buffer (100 mM NaHC03, 1% SDS) for 10 min at 65˚C with agitation. Chromatin was decrosslinked by adding NaCl to a final concentration of 300mM and incubated overnight at 65˚C. DNA was treated with 10ng/ul RNAse A for 30 min at 37˚C and 4 hous with 20ng/µl proteinase K before cleaning with Qiagen PCR cleaning columns.

treatment_protocol: Kc167 were transfected with pMT-puro plasmid or pMT-puro-Lz, which contains the coding sequence of Lz using Fugene. Cells were then grown under permanent selection with 2μg/ml puromycin.

value: Kc167 (with pMT-puro stable transfection)

value: anti-H3K56ac (Active Motif, 39281)


title: SHR_E16.0_kidney2 [exon-level]

description: LEO-MWF-18-Leo_301-220212-RatGe-St1-0.CEL


title: Mac-patient1-sample2

description: Untreated macrophage from patient 1, second sample


title: SHR_E16.0_kidney4 [exon-level]

description: LEO-MWF-20-SHR_E16_022-220212-RatGe-St1-0.CEL


title: SHR_E16.0_kidney1 [exon-level]

description: LEO-MWF-17-Leo_264-220212-RatGe-St1-0.CEL


title: DMSO treated EB, replicate 2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Gene expression microarray data was normalized using RMA method followed by median to all the samples.

source_name: DMSO treated EB

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The embryoid body formation was initiated with an ES cell count of 1million cells per ml. The ES cells were resuspended in conditioned medium (Globalstem) containing 1% PVA (Sigma). This suspension was added to low attachment petri plates (Tarsons) and incubated at 37°C for 48 hours without disturbing the plates. The EBs were allowed to grow in size and were visualized at regular intervals under the light microscope. Once the clumping of cells was clearly evident, the EBs were transferred to DMEM medium (Invitrogen) supplemented with 20% KSR (Invitrogen) and 10% FBS (Biological Industries) onto 0.1% gelatin pre-coated dishes.

treatment_protocol: Media changes were given every 5-7 days with the differentiation media. Compound treatment was generally given between the day 2 and day 4 of EB formation for 48 hours time point.

tag: source cell line

tag: source cell type

value: Human ES cell line (hESC)

value: hESC-derived embryoid body (EB)

tag: treated with

value: DMSO (control)


title: KL H3K56ac rep2

source_name: H3K56ac ChIP in Kc cells with Lz transfection, replicate 2

value: Kc167 (with pMT-puro-Lz stable transfection)


title: KL H3K56ac rep1

source_name: H3K56ac ChIP in Kc cells with Lz transfection, replicate 1


title: KP H3K56ac rep2

data_processing:
The CEL files were processed with Biconductor Starr package, signal values were quantile normaised between all samples and the normalised log2 rations of sample/input reported for each replicate experiment as *.sgr files (chromosome, start, ratio).
KN56ac_r12.sm_quant-all_Ringo_hw300v8.bedgraph, KP56ac_r12.sm_quant-all_Ringo_hw300v8.bedgraph, KP56ac_r12.sm_quant-all_normalNullmode_hw300v8g200FDR1.bed, KN56ac_r12.sm_quant-all_normalNullmode_hw300v8g200FDR1.bed, Kc_nicd12-quantNorm.wig, Kc_nicd12-2kb-peaks-FDR1.bed
The *bedgraph files contain the median of replicate ratios smoothed into window scores using a sliding window of 600bp and 8 minimum Probes in window with the Bioconductor Ringo package (Bioconductor 3.0). The bed files were created assuming a normalNull distribution centred around zero and the resulting p-values were adjusted for multiple testing using the fdr method. The difference between wildtype and N-activation H3K56ac signal was calculated as the subtraction of quantile normalised ChIP signal files (*quantNorm.wig). The *-2kb-peaks-FDR1.bed files were calculated as follows. All ChIP signal files were averaged over a 2kb window (in 200bp increments), and the noise distribution based on two replicates estimated. This noise distribution is used to call differentially enriched 2kb regions at 1% FDR, with overlapping 2kb regions merged together.

source_name: H3K56ac ChIP in Kc cells with pMT transfection, replicate 2

treatment_protocol: Kc167 were transfected with pMT-puro plasmid or pMT-puro-NICD, which contains the introcellular domain of Notch receptor using Fugene. Cells were then grown under permanent selection with 2μg/ml puromycin.


title: TBBD treated EB, replicate 2

source_name: TBBD treated EB

tag: cell type

value: 10uM TBBD for 48 h


title: MWF_E15.5_kidney4 [exon-level]

description: LEO-MWF-04-Leo_363-220212-RatGe-St1-0.CEL

source_name: MWF-E15.5 kidney

value: MWF

tag: age


title: Su(H) Kc Input rep2

source_name: Su(H) Kc Input replicate 2


title: MWF_E15.5_kidney3 [exon-level]

description: LEO-MWF-03-Leo_242-220212-RatGe-St1-0.CEL

tag: strain


title: KP input

source_name: Kc cells with PMT transfection, input


title: MWF_E15.5_kidney2 [exon-level]

description: LEO-MWF-02-Leo_160-220212-RatGe-St1-0.CEL


title: KP H3K56ac rep1

source_name: H3K56ac ChIP in Kc cells with pMT transfection, replicate 1


title: KN H3K56ac rep2

source_name: H3K56ac ChIP in Kc cells with NICD transfection, replicate 2

value: Kc167 (with pMT-puro-NICD stable transfection)


title: MWF_E15.5_kidney1 [exon-level]

description: LEO-MWF-01-Leo_58-220212-RatGe-St1-0.CEL


title: KN input

source_name: Kc cells with NICD transfection, input


title: TBBD treated EB, replicate 1


title: Su(H) Kc rep2

source_name: Su(H) Kc repplicate 2


title: KN H3K56ac rep1

source_name: H3K56ac ChIP in Kc cells with NICD transfection, replicate 1


title: PC 73 TNE (6)

city: Pittsburgh

first: John

middle: Michael

last: Krill-Burger

state: PA

address: Rm. WG21.3 Shadyside Hospital

institute: University of Pittsburgh Medical Center

hyb_protocol: Refer to miRCURY LNA (TM) microRNA Array microarray kit instruction manual v9.2 (manual procedure)

scan_protocol: Scanner=GenePix 4000B [92209] PixelSize=10 BackgroundSubtraction=LocalFeature PMTGain=650 Genepix software package was used to generate an intensity value for each probe by taking the median spot intensity and subtracting the median local background. Bad spots or areas of the array with obvious defects were manually flagged. Flagged spots were not included in subsequent analyses.

data_processing: The hsa_negative probes were averaged for each array and used as a threshold value. The array's threshold was subtracted from all of the array's averaged discovery probes. PC73 TNE was the overlapping standard run in each of the six batches. Comparison of the overlapping sample was used to carry out an inter-batch normalization.

source_name: Prostate Biopsy

label_protocol: Refer to miRCURY LNA (TM) microRNA Array Power Labeling Kit

extract_protocol: Qiagen miRNeasy (miR+mRNA)

tag: Tumor Normal Epithelial

tag: Batch 6


title: PC 97 S

tag: Tumor Stromal


title: PC 102 S


title: PC 100 S


title: PD 15 NS

tag: Donor Normal Stem Cells


title: PD 15 DNE

tag: Donor Normal Epithelial


title: PD 14 S

tag: Donor Normal Stromal


title: PD 15 S


title: PD 14 NS


title: PD 14 DNE


title: PC 96 S

tag: Batch 5


title: PC 94 S


title: PD 10 S

tag: Donor Stromal


title: PD 13 S


title: PD 12 S


title: PC 73 TNE (5)


title: PC 73 TNE (4)

tag: Batch 4


title: PC 75 S


title: PC 102 TE

tag: Tumor Epithelial

tag: Batch 3


title: PC 73 S


title: PD 11 S


title: PC 89 S


title: PC 81 S


title: PD 10 NS

tag: Normal Stem Cells


title: PC 74 S


title: PD 102 TNE


title: PD 11 DNE


title: PD 13 DNE


title: PD 11 NS


title: PC 102 TNE HS


title: DMSO treated EB, replicate 1

tag: source cell line

tag: source cell type


title: PC 75 TNE


title: PD 12 DNE


title: PC 75 TE


title: PC 94 TNE

tag: Batch 2


title: PC 81 TNE


title: PC 99 TNE


title: PC 94 TE


title: PC 99 TE


title: PC 81 TE


title: PD 10 DNE


title: PC 81 TS

tag: Tumor Stem Cells


title: PC 73 TNE (2)


title: PC 60 TS


title: PC 73 TNE (3)


title: PC 73 TS


title: PC 100 TE

tag: Batch 1


title: PC 100 TNE

tag: Tumor Normal Epithelial


title: PC 79 TE


title: PD 13 NS


title: PC 96 TE


title: PC 73 TE


title: PC 96 TNE


title: PC 97 TNE


title: HL60, 72h control, sucrose density gradient Fraction 9

city: Rome

first: Giulia

last: Fontemaggi

address: Via Elio Chianesi, 53

country: Italy

institute: Italian National Cancer Institute Regina Elena

description: microRNA expression in control proliferating HL60 cells

hyb_protocol: Labeled RNA was hybridized to slides for 20h at 55°C

scan_protocol: Scanning and image analysis were performed using the Agilent DNA Microarray Scanner (P/N G2565BA). Feature Extraction Software (Version 10.5) was used for data extraction from raw microarray image files using the miRNA_105_Dec08 FE protocol.

data_processing:
miRNAs were called present if at least 2 of the fractions in one of the two experimental conditions presented values over the cut-off (set at 5). Data were normalized over the median and standardized.
Expression values were standardized, so that the expression of each miRNA has mean 0 and standard deviation 1

source_name: Fraction 9 from ribo/polysomal fractionation of proliferating cells

label_protocol: Total RNA (100 ng) was labeled and hybridized to Human miRNA microarray V3 (Agilent)

growth_protocol: HL-60 cell line was maintained in RPMI 1640 medium supplemented with 1 x penicillin/streptomycin solution, 1 x L-glutamine and 10% Fetal Bovine Serum.

extract_protocol: Total RNA for microarray analyses was extracted using Trizol (Invitrogen, Carlsbad, CA, USA) from fractions obtained by sucrose density gradient centrifugation. Genomic DNA contamination was eliminated through a DNase I (Qiagen, Chatsworth, CA) digestion step. RNA was further purified on Qiagen RNeasy columns for gene expression profiling (Qiagen, Chatsworth, CA). The concentration and purity of total RNA were assessed using a Nanodrop TM 1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

treatment_protocol: Not applicable

tag: cell type

value: HL60 cells, promyeloblasts

tag: treatment

value: control

tag: sucrose density gradient fraction


title: HL60, 72h control, sucrose density gradient Fraction 8

source_name: Fraction 8 from ribo/polysomal fractionation of proliferating cells


title: HL60, 72h control, sucrose density gradient Fraction 7

source_name: Fraction 7 from ribo/polysomal fractionation of proliferating cells


title: HL60, 72h control, sucrose density gradient Fraction 4

source_name: Fraction 4 from ribo/polysomal fractionation of proliferating cells


title: HL60, 72h control, sucrose density gradient Fraction 6

source_name: Fraction 6 from ribo/polysomal fractionation of proliferating cells


title: HL60, 72h control, sucrose density gradient Fraction 5

source_name: Fraction 5 from ribo/polysomal fractionation of proliferating cells


title: HL60, 72h control, sucrose density gradient Fraction 3

source_name: Fraction 3 from ribo/polysomal fractionation of proliferating cells


title: PC 89 TNE


title: HL60, 72h VitD3, sucrose density gradient Fraction 11

description: microRNA expression in VitD3-treated HL60 cells

source_name: Fraction 11 from ribo/polysomal fractionation of differentiated cells


title: PC 74 TS


title: PC73 TNE (1)


title: PC 89 TE


title: HL60, 72h VitD3, sucrose density gradient Fraction 10

source_name: Fraction 10 from ribo/polysomal fractionation of differentiated cells


title: PC 74 TNE


title: PC 74 TE


title: HL60, 72h VitD3, sucrose density gradient Fraction 9

source_name: Fraction 9 from ribo/polysomal fractionation of differentiated cells


title: HL60, 72h VitD3, sucrose density gradient Fraction 4

source_name: Fraction 4 from ribo/polysomal fractionation of differentiated cells


title: HL60, 72h VitD3, sucrose density gradient Fraction 6

source_name: Fraction 6 from ribo/polysomal fractionation of differentiated cells


title: HL60, 72h VitD3, sucrose density gradient Fraction 3

source_name: Fraction 3 from ribo/polysomal fractionation of differentiated cells


title: HL60, 72h control, sucrose density gradient Fraction 10

source_name: Fraction 10 from ribo/polysomal fractionation of proliferating cells


title: HL60, 72h VitD3, sucrose density gradient Fraction 8

source_name: Fraction 8 from ribo/polysomal fractionation of differentiated cells


title: HL60, 72h VitD3, sucrose density gradient Fraction 5

source_name: Fraction 5 from ribo/polysomal fractionation of differentiated cells


title: HL60, 72h VitD3, sucrose density gradient Fraction 7

source_name: Fraction 7 from ribo/polysomal fractionation of differentiated cells


title: HL60, 72h control, sucrose density gradient Fraction 11

source_name: Fraction 11 from ribo/polysomal fractionation of proliferating cells


title: PC 99 S

source_name: Prostate Biopsy

tag: Tumor Stromal

tag: Batch 6


title: XinWX 0 dpa vs. XinFLM 0 dpa rep2

city: Nanjing

first: Wang

middle: Li

last: Man

address: Weigang N0.1

institute: Nanjing Agricultural University

description: Comparative analysis of transcriptome profiles of lintless-fuzzless mutant (XinWX) and linted-fuzzless mutant (XinFLM) at 0 dpa, replicate 2

hyb_protocol: Cy3 and Cy5-labeled cDNA resolved in 80 µL hybridization solution (3×SSC, 0.2% SDS, 5 × Denhart’s, 25% formamide). DNA in hybridization solution was denatured at 95°C for 3 min prior to loading onto a microarray. Slides were hybridized at 42°C overnight and transferred to fresh containers with Wash Solution 1 (0.2% SDS, 2 × SSC) at 42°C for 5 min and then immersed in Wash Solution 2 (0.2 × SSC) at room temperature for 5 min.

scan_protocol: All microarrays were scanned with a LuxScan scanner using the LuxScan 3.0 software (Captalbio Corp).

data_processing: Data were filtered and corrected for bias using the following steps: (1) Low quality spots (dust particles, scratches, high background, or irregularly shaped spots) were manually flagged and excluded. (2) Faint spots with intensity < 400 units after subtraction of the background were removed. (3) Statistical analyses were carried out using the LIMMA package (version 3.4.5) in R (version2.12.2). All operations were performed according to those described in the user’s guide of LIMMA. The data were normalized within arrays using the “LOWESS” method (Yang et al., 2002) and across arrays by the “Aquantile” method (Yang et al., 2003). Normalized data were fitted to linear models in LIMMA to analyze DEGs using a moderated t-statistic (eBays) method (Symth et al., 2004). The p-values were corrected by applying the false discovery rate (FDR) correction (Benjamini and Hochberg, 2000).

organism: Gossypium hirsutum

source_name: XinFLM 0 dpa

label_protocol: The cRNA amplification and labeling Kit (CapitalBio,Beijing, China) was used to amplify and label RNA following the manufacturer’s protocol.The transcription products were purified with the Nucleospin® Extract II Kit (MACHEREY-NAGEL), and then labeled with Cy5 and Cy3-dCTP, respectively by the Klenow enzyme.

extract_protocol: Total RNA of ovule and fiber mixture from -1 - 1 DPA of XinWX and XinFLM were extracted using a CTAB-acidic phenolic method.

tag: tissue

value: ovule and fiber mixtures

tag: developmental stage (days post anthesis; dpa)

value: 0 dpa

tag: genotype

value: fuzzless-linted mutant (XinFLM)

source_name: XinWX 0 dpa

value: lintless-fuzzless mutant (XinWX)


title: XinWX 1 dpa vs. XinFLM 1 dpa rep3

description: Comparative analysis of transcriptome profiles of lintless-fuzzless mutant (XinWX) and linted-fuzzless mutant (XinFLM) at 1 dpa, replicate 3

source_name: XinWX 1 dpa

value: 1 dpa

source_name: XinFLM 1 dpa


title: XinWX 1 dpa vs. XinFLM 1 dpa rep2

description: Comparative analysis of transcriptome profiles of lintless-fuzzless mutant (XinWX) and linted-fuzzless mutant (XinFLM) at 1 dpa, replicate 2


title: HMCL_12h_DMSO_replicate 1

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

description: U266 human multiple myeloma cell line, harbouring K601N BRAF mutation, was treated with PLX4032 drug, a BRAF inhibitor that has recently demonstrated promising anti-myeloma results in vitro (Lohr et al., 2014) and in clinical settings (Andrulis et al., 2013).

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on GeneChip Gene 1.0 ST array, according to the standard Affymetrix protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning  of the arrays was performed using the GeneChip Scanner 7G.

data_processing: The raw intensity expression values were processed by Robust Multi-array Average procedure (RMA), with the re-annotated Chip Deﬁnition Files from BrainArray libraries version 18.0.0, available at http://brainarray.mbni.med.umich.edu.

source_name: U266 human multiple myeloma cell line treated with DMSO for 12 hours

label_protocol: Biotinylated single stranded cDNA samples were prepared starting from 100 nanograms of purified total RNA, according to the standard Affymetrix protocol (GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Gibco BRL). RNA was purified using the Rneasy Mini Kit according to the manufacturer's instruction (Qiagen).

treatment_protocol: U266 cells were treated with PLX4032 (30 µM) or DMSO for 12 hours

tag: cell line

value: Human multiple myeloma cell line, established from peripheral blood


title: XinWX 0 dpa vs. XinFLM 0 dpa rep1

description: Comparative analysis of transcriptome profiles of lintless-fuzzless mutant (XinWX) and linted-fuzzless mutant (XinFLM) at 0 dpa, replicate 1


title: pPCL at diagnosis, MUT>20% sample 63

description: KRAS MUT>20%

source_name: Highly purified PCs from human pPCL patient, BRAF, NRAS or KRAS MUT>20%

treatment_protocol: Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases.

value: Bone marrow plasma cells

tag: pc dyscrasia

value: pPCL


title: HMCL_12h_30uM_PLX4032_replicate 1

source_name: U266 human multiple myeloma cell line treated with PLX4032 (30uM)  for 12 hours


title: XinWX -1 dpa vs. XinFLM -1 dpa rep2

description: Comparative analysis of transcriptome profiles of lintless-fuzzless mutant (XinWX) and linted-fuzzless mutant (XinFLM) at -1 dpa, replicate 2

source_name: XinFLM -1 dpa

value: -1 dpa

source_name: XinWX -1 dpa


title: XinWX 0 dpa vs. XinFLM 0 dpa rep3

description: Comparative analysis of transcriptome profiles of lintless-fuzzless mutant (XinWX) and linted-fuzzless mutant (XinFLM) at 0 dpa, replicate 3


title: HMCL_12h_DMSO_replicate 2


title: XinWX 1 dpa vs. XinFLM 1 dpa rep1

description: Comparative analysis of transcriptome profiles of lintless-fuzzless mutant (XinWX) and linted-fuzzless mutant (XinFLM) at 1 dpa, replicate 1


title: HMCL_12h_30uM_PLX4032_replicate 2


title: sPCL, MUT>20% sample 68

description: BRAF MUT>20%

source_name: Highly purified PCs from human sPCL patient, BRAF, NRAS or KRAS MUT>20%

value: sPCL


title: sPCL, MUT>20% sample 66

description: NRAS MUT>20%


title: pPCL at diagnosis, MUT>20% sample 62

description: NRAS MUT>20%


title: pPCL at diagnosis, MUT>20% sample 64

description: BRAF MUT>20%


title: sPCL, MUT>20% sample 67

description: NRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 55

description: KRAS MUT>20%

source_name: Highly purified PCs from human MM patient, BRAF, NRAS or KRAS MUT>20%

value: MM


title: XinWX -1 dpa vs. XinFLM -1 dpa rep3

description: Comparative analysis of transcriptome profiles of lintless-fuzzless mutant (XinWX) and linted-fuzzless mutant (XinFLM) at -1 dpa, replicate 3


title: XinWX -1 dpa vs. XinFLM -1 dpa rep1

description: Comparative analysis of transcriptome profiles of lintless-fuzzless mutant (XinWX) and linted-fuzzless mutant (XinFLM) at -1 dpa, replicate 1


title: pPCL at diagnosis, MUT>20% sample 58

description: BRAF MUT>20%


title: sPCL, MUT>20% sample 65

description: NRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 54

description: BRAF MUT>20%, NRAS MUT>20%


title: pPCL at diagnosis, MUT>20% sample 59

description: KRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 56

description: NRAS MUT>20%


title: pPCL at diagnosis, MUT>20% sample 61

description: BRAF MUT>20%


title: MM at diagnosis, MUT>20% sample 53

description: NRAS MUT>20%


title: pPCL at diagnosis, MUT>20% sample 60

description: BRAF MUT>20%


title: MM at diagnosis, MUT>20% sample 57

description: NRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 50

description: KRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 49

description: NRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 51

description: KRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 52

description: KRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 35

description: NRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 42

description: NRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 38

description: NRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 44

description: NRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 32

description: KRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 37

description: NRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 47

description: KRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 26

description: NRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 25

description: NRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 41

description: KRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 45

description: KRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 27

description: BRAF MUT>20%


title: MM at diagnosis, MUT>20% sample 31

description: KRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 46

description: BRAF MUT<20%, NRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 40

description: NRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 30

description: NRAS MUT<20%, BRAF MUT>20%


title: MM at diagnosis, MUT>20% sample 34

description: NRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 43

description: KRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 48

description: NRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 28

description: NRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 39

description: KRAS MUT<20%, BRAF MUT>20%


title: MM at diagnosis, MUT>20% sample 24

description: KRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 36

description: NRAS MUT<20%, KRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 29

description: KRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 33

description: BRAF MUT>20%


title: MM at diagnosis, MUT>20% sample 21

description: KRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 23

description: BRAF MUT>20%


title: MM at diagnosis, MUT>20% sample 14

description: KRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 22

description: NRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 17

description: KRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 13

description: NRAS MUT<20%, KRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 15

description: KRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 18

description: KRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 6

description: NRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 12

description: KRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 8

description: NRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 19

description: BRAF MUT>20%


title: MM at diagnosis, MUT>20% sample 11

description: KRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 16

description: KRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 5

description: BRAF, KRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 20

description: KRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 2

description: KRAS MUT>20%


title: MM at diagnosis, MUT<20% sample 11

description: NRAS MUT<20%

source_name: Highly purified PCs from human MM patient, BRAF, NRAS or KRAS MUT<20%


title: sPCL, MUT<20% sample 14

description: KRAS MUT<20%

source_name: Highly purified PCs from human sPCL patient, BRAF, NRAS or KRAS MUT<20%


title: MM at diagnosis, MUT>20% sample 1

description: KRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 10

description: NRAS MUT>20%


title: pPCL at diagnosis, MUT<20% sample 13

description: KRAS MUT<20%

source_name: Highly purified PCs from human pPCL patient, BRAF, NRAS or KRAS MUT<20%


title: MM at diagnosis, MUT>20% sample 7

description: KRAS MUT>20%


title: MM at diagnosis, MUT<20% sample 9

description: NRAS MUT<20%


title: MM at diagnosis, MUT<20% sample 10

description: NRAS MUT<20%


title: MM at diagnosis, MUT>20% sample 4

description: KRAS MUT>20%


title: MM at diagnosis, MUT>20% sample 9

description: KRAS MUT>20%


title: MM at diagnosis, MUT<20% sample 8

description: KRAS MUT<20%


title: MM at diagnosis, MUT>20% sample 3

description: NRAS MUT>20%


title: pPCL at diagnosis, MUT<20% sample 12

description: BRAF MUT<20%


title: MM at diagnosis, MUT<20% sample 7

description: KRAS MUT<20%


title: sPCL, WT sample 59

description: BRAF, NRAS, KRAS WT

source_name: Highly purified PCs from human sPCL patient, BRAF, NRAS and KRAS WT


title: MM at diagnosis, MUT<20% sample 3

description: BRAF, KRAS MUT<20%


title: MM at diagnosis, MUT<20% sample 1

description: KRAS MUT<20%


title: pPCL at diagnosis, WT sample 54

description: BRAF, NRAS, KRAS WT

source_name: Highly purified PCs from human pPCL patient, BRAF, NRAS and KRAS WT


title: MM at diagnosis, MUT<20% sample 2

description: BRAF MUT<20%


title: pPCL at diagnosis, WT sample 55

description: BRAF, NRAS, KRAS WT


title: pPCL at diagnosis, WT sample 47

description: BRAF, NRAS, KRAS WT


title: pPCL at diagnosis, WT sample 56

description: BRAF, NRAS, KRAS WT


title: pPCL at diagnosis, WT sample 48

description: BRAF, NRAS, KRAS WT


title: pPCL at diagnosis, WT sample 57

description: BRAF, NRAS, KRAS WT


title: sPCL, WT sample 60

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 45

description: BRAF, NRAS, KRAS WT

source_name: Highly purified PCs from human MM patient, BRAF, NRAS and KRAS WT


title: MM at diagnosis, MUT<20% sample 6

description: NRAS, KRAS MUT<20%


title: pPCL at diagnosis, WT sample 52

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 40

description: BRAF, NRAS, KRAS WT


title: pPCL at diagnosis, WT sample 53

description: BRAF, NRAS, KRAS WT


title: pPCL at diagnosis, WT sample 50

description: BRAF, NRAS, KRAS WT


title: pPCL at diagnosis, WT sample 49

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, MUT<20% sample 4

description: KRAS MUT<20%


title: MM at diagnosis, WT sample 42

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 38

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, MUT<20% sample 5

description: BRAF, KRAS MUT<20%


title: MM at diagnosis, WT sample 46

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 41

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 43

description: BRAF, NRAS, KRAS WT


title: pPCL at diagnosis, WT sample 58

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 39

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 44

description: BRAF, NRAS, KRAS WT


title: pPCL at diagnosis, WT sample 51

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 29

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 21

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 36

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 37

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 23

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 33

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 26

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 17

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 16

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 19

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 31

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 22

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 35

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 32

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 24

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 30

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 15

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 25

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 27

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 28

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 20

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 18

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 10

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 14

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 11

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 34

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 13

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 8

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 9

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 12

description: BRAF, NRAS, KRAS WT


title: NBR2

city: Hong Kong

first: Margaret

last: Ip

address: Main clinic building, Prince of Whales Hospital, City one, Shatin

department: Department of Microbiology

institute: The Chinese University of Hong Kong

description: Test

data_processing:
The cycle threshold (Ct) raw data was analyzed by two manufacturer’s softwares; SDS 2.4 and RQ Manager 1.2.1.
The expression level of each miRNA was calculated by the relative quantity (RQ value) (2-∆∆Ct) method. The internal control, Mammal U6, was selected for normalization across all experiments. The Ct raw data were determined by using an automatic baseline and a threshold of 0.2(RQ Manager, ABI, Life Technologies).

label: FAM

source_name: THP-1 cells

label_protocol: The TaqMan®MicroRNA Reverse Transcription Kit (Applied Biosystems, Foster City, CA, USA) was used for preparation of cDNA.

growth_protocol: THP-1 Cells were incubated with phorbolmyristate acetate (5ng/ml PMA) for 48hours to induce differentiation into a macrophage phenotype. MTB isolates were cultured in Middlebrook7H9 (BD Biosciences) at 370C, 5% CO2 until the cultures reached McFarland 1 (about 107 CFU/mL).

extract_protocol: RNA was isolated from macrophages with the mirVanaTM miRNA Isolation Kit (Ambion, Austin, TX, USA) in accordance with the manufacturer’s instructions.

treatment_protocol: The MTB cells were harvested by centrifugation and the pellet was resuspended in RPMI medium and added to the macrophages. Macrophages were infected at a multiplicity of infection (MOI) of 3 bacilli/cell for 2 hours, and the excess free-floating bacilli were removed by washing the culture with fresh RPMI containing 10µg/ml gentamicin. The culture was incubated in a fresh RPMI medium without antibiotics at 37°C, 5% CO2for 72-hours.

value: Monocyte-derived macrophage

tag: infected strain

value: Non-Beijing resistant MTB strain 2


title: NBS2

description: Test

value: Non-Beijing sensitive MTB strain 2


title: BR3

description: Test

value: Beijing resistant MTB strain 3


title: BS2

description: Test

value: Beijing sensitive MTB strain 2


title: BR2

description: Test

value: Beijing resistant MTB strain 2


title: BR1

description: Test

value: Beijing resistant MTB strain 1


title: NBR3

description: Test

value: Non-Beijing resistant MTB strain 3


title: NBS3

description: Test

value: Non-Beijing sensitive MTB strain 3


title: NBR1

description: Test

value: Non-Beijing resistant MTB strain 1


title: no-infected con 2

description: control

value: no infection


title: BS3

description: Test

value: Beijing sensitive MTB strain 3


title: no-infected con 1

description: control


title: Active3

description: Test

source_name: whole blood

growth_protocol: PBMCs were freshly harvested from the patients’ whole blood by using the Ficoll-Hypaque column (GE healthcare).The PBMC was resuspended in ice-cold monocyte adhesion medium (RPMI1640 + 7.5% autologous plasma, 1% penicillin-streptomycin) and incubated in a petri dish for 90minutes at 370C. The adherent monocytes were washed with warm RPMI medium several times to remove loosely attached cells. The monocytes were detached by incubation with PBS containing 5 mM EDTA for 10–20 minutes at room temperature and were collected by centrifugation. The monocytes were refed by fresh medium every 2 days and allowed to differentiate into macrophages for 10 days in vitro.

tag: age

tag: gender

value: Male

tag: infection status

value: Active TB patient


title: Active2

description: Test


title: Active1

description: Test


title: Latent4

description: Test

value: Latent TB patient


title: Latent2

description: Test

value: Female


title: Latent3

description: Test


title: MM at diagnosis, WT sample 6

description: BRAF, NRAS, KRAS WT

value: Bone marrow plasma cells

value: MM


title: Latent1

description: Test

value: Monocyte-derived macrophage


title: NBS1

description: Test

value: Non-Beijing sensitive MTB strain 1


title: MM at diagnosis, WT sample 4

description: BRAF, NRAS, KRAS WT


title: Control2

description: control

value: Healthy control


title: BS1

description: Test

value: Beijing sensitive MTB strain 1


title: Control3

description: control


title: MM at diagnosis, WT sample 7

description: BRAF, NRAS, KRAS WT


title: Control1

description: control


title: MM at diagnosis, WT sample 1

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 3

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 5

description: BRAF, NRAS, KRAS WT


title: MM at diagnosis, WT sample 2

description: BRAF, NRAS, KRAS WT


title: WIGMOR-self-cured-sample4

city: Montpellier

first: Anne

last: Geiger

address: Laboratoire de Recherches et de Coordination sur les Trypanosomoses TA,A-17 / G Campus international de Baillarguet

country: France

institute: UMR 177 IRD-CIRAD

description: Total RNA, 10 days, control sample with contact, sample 4

hyb_protocol: 800 ng of Cy3-labelled cRNA (specific activity > 15 pmol Cy3/ug cRNA) hybridized to Agilent Wigglesworthia_v1 custom Oligo Microarrays (earray Design ID = 050087; earray Slide Layout =  IS-15744-8-V1) 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).

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner using one color scan setting for 8x15k array slides.

data_processing: The scanned images were analyzed with Feature Feature Extraction 11.0.1 (Agilent technologies) using protocol GE1_1100_Jul11 and Grid 050087_D_F_20130611 to obtain background subtracted and spatially detrended Processed Signal intensities. All data were normalized by quantile normalization and by median of all samples for each probe.

organism: Wigglesworthia glossinidia endosymbiont of Glossina morsitans

source_name: WIGMOR-self-cured

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared using the Low Input Quick Amp WT Labeling Kit (One color) according to the manufacturer's instructions

extract_protocol: trizol to extract the RNA

tag: status

value: Control self-cured

tag: timepoint

value: 10 days

value: control with parasite contact


title: cross-fraction normalized NanoString counts for the 4-to-7 ribosomes pooled polysome fraction_DU145_24 hrs normoxia

city: Toronto

first: Kenneth

middle: Chung-kan

last: Chu

state: Ontario

address: 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

hyb_protocol: Hybridization was carried out according to the NanoString protocol.

scan_protocol: according to the NanoString protocol

data_processing: Assay bias was removed in a within cell-line fashion by globally scaling counts from each assay so that the geometric means of post-scaling positive control code counts are constant. Background noise was removed in a with-assay fashion by subtracting the sum of the mean and two times the standard deviation of the negative control code counts. Precipitation bias removal was performed only on the pooled polysome assays in a within-cell-line within-treatment fashion by globally scaling counts from each assay so that the geometric means of the post-scaling spike-in code counts are constant.

source_name: human prostate cancer cell line

label_protocol: RNA was not labelled.

growth_protocol: Both cell lines, GM05757 and DU145, were cultured in alpha-modified Eagles Medium. DU145 was supplemented with 10% fetal calf serum and 1% L-Glutamine. GM05757 was supplemented with 15% of calf serum.

extract_protocol: Total RNA was extracted from GM05757 and DU145 with TRIZOL, according to the manufacturer's protocol. Polysome mRNAs from GM05757 and DU145 cytoplasmic lysates were isolated by sedimentation through a sucrose gradient and subsequent fractionation. Fractions containing the different numbers of polysomes were collected in 0.55 M final concentration of guanidinium–HCl, phenol-chloroform extracted and subjected to precipitation with ethanol. Spike-in control RNAs were added at this stage.  Glycogen was used as carrier.

treatment_protocol: GM05757 cells were exposed to anoxia (0% oxygen) and normoxia for 24 hours. DU145 cells were exposed to hypoxia (0.2% oxygen) and normoxia for 72 hours.

value: human prostate cancer cells

value: 72 hours of normoxia

tag: pooled polysome fraction

value: 4 to 7 ribosomes

tag: molecule subtype

value: mRNA with 4 to 7 attached ribosomes


title: cross-fraction normalized NanoString counts for the 0-to-3 ribosomes pooled polysome fraction_DU145_24 hrs normoxia

tag: cell type

tag: treatment

value: 0 to 3 ribosomes

value: mRNA with 0 to 3 attached ribosomes


title: positive-control, negative-control normalized total RNA code counts_DU145_24 hrs normoxia

value: total RNA (nuclear + cytoplasmic)


title: cross-fraction normalized NanoString counts for the 8-or-more ribosomes pooled polysome fraction_GM05757_24 hrs normoxia

source_name: normal human fibroblast cell line

value: normal human fibroblast

value: 24 hours of normoxia

value: 8 or more ribosomes

value: mRNA with 8 or more attached ribosomes


title: cross-fraction normalized NanoString counts for the 8-or-more ribosomes pooled polysome fraction_DU145_24 hrs normoxia


title: cross-fraction normalized NanoString counts for the 8-or-more ribosomes pooled polysome fraction_DU145_24 hrs anoxia

value: 72 hours of hypoxia


title: positive-control, negative-control normalized total RNA code counts_DU145_24 hrs anoxia


title: cross-fraction normalized NanoString counts for the 4-to-7 ribosomes pooled polysome fraction_GM05757_24 hrs normoxia


title: cross-fraction normalized NanoString counts for the 0-to-3 ribosomes pooled polysome fraction_GM05757_24 hrs normoxia


title: positive-control, negative-control normalized total RNA code counts_GM05757_24 hrs normoxia


title: cross-fraction normalized NanoString counts for the 4-to-7 ribosomes pooled polysome fraction_DU145_24 hrs anoxia


title: cross-fraction normalized NanoString counts for the 0-to-3 ribosomes pooled polysome fraction_DU145_24 hrs anoxia


title: WIGMOR-Control-sample3

description: Total RNA, 10 days, control sample without contact, sample 3

source_name: WIGMOR-Control

value: Control

value: Control without parasite contact


title: WIGMOR-self-cured-sample2

description: Total RNA, 10 days, control sample with contact, sample 2

value: Control self-cured


title: WIGMOR-self-cured-sample3

description: Total RNA, 10 days, control sample with contact, sample 3

value: 10 days


title: WIGMOR-Control-sample4

description: Total RNA, 10 days, control sample without contact, sample 4


title: WIGMOR-self-cured-sample1

description: Total RNA, 10 days, control sample with contact, sample 1

value: control with parasite contact


title: positive-control, negative-control normalized total RNA code counts_GM05757_24 hrs anoxia

value: 24 hours of anoxia


title: cross-fraction normalized NanoString counts for the 8-or-more ribosomes pooled polysome fraction_GM05757_24 hrs anoxia


title: WIGMOR-Control-sample2

description: Total RNA, 10 days, control sample without contact, sample 2


title: WIGMOR-Control-sample1

description: Total RNA, 10 days, control sample without contact, sample 1