title: Treatment 3 conditions 1 vs 2 replicate 1

city: Birmingham

first: John

middle: Kenneth

last: Colbourne

state: West Midlands

address: Edgbaston

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

hyb_protocol: Labeled products were pooled to serve as a Master Mix for Array set. The products were dried in a speedvac then resuspended in water prior to hybridization, which was performed with the NimbleGen hybridization kit. A single hybrization master for a given source and biological replicate was applied to each of 12 subarrays with the appropriate Sample Tracking Control (STC) following protocols described in Lopez, J.A. and J.K.  Colbourne. 2011. Dual-Labeled Expression Microarray Protocol for High-Throughput Genomic Investigations. CGB Technical Report 2011-02. doi:10.2506/cgbtr-201102.

scan_protocol: Axon GenePix 4200 Professional, 5 micron resolution

data_processing:
Raw signal intensity extract with NimbleScan 2.6 Software (Roche NimbleGen) in PAIR files. Quantile normalization to convert raw to processed data.
The Sample*.txt files are the normalized data values for the probes on the array.
GEO2_Matrix.txt is the final, processed data file reporting log2 ratios of the first condition over second condition, quantile normalized, four biological replicates averaged.

organism: Daphnia pulex

source_name: treatment 3, condition 2

label_protocol: DNA labeling using 1 O.D. CY-labeled random nonomer primer and 100U Klenow fragment (3>5 exo) per 1 μg double-stranded cDNA.

growth_protocol: The daphniids (50 adult animals per batch) were raised in 3-L glass beakers under a 16 h:8 h L:D photoperiod. Three-quarter of the culture medium (M4) was renewed once a week, and the animals were equally fed ad libitum with algae (Desmodesmus subspicatus; SAG 53.80, Göttingen, Germany).  Only adult female animals with a body length of 2−2.5 mm (between the base of the apical spine and the anterior part of the head) and carrying parthenogenetic eggs and embryos were used for experiments.

extract_protocol: Tissue was homogenized using Trizol reagent (Invitrogen) and extracted RNA was purified using the Qiagen RNeasy protocol with on-column DNase treatment from specific tissues. Total RNA amplified using MessageAmp II aRNA Kit (Ambion). aRNA converted to ds cDNA using SuperScript cDNA Synthesis Kit (Invitrogen).

treatment_protocol: Time-resolved experiments (acute heat stress) were carried out with long-term 20°C acclimated animals, which were exposed for three different time intervals (2, 4, and 8 h) to either 30 ± 0.2°C (test conditions) or 20 ± 0.3°C (control conditions). For this, 50 animals each were rapidly transferred with a sieve (mesh size: 1.2 mm) from 20°C-medium to a set of beakers containing 30°C-medium. As control, 50 animals each were transferred from 20°C-medium to another set of beakers with 20°C-medium. Only adult female animals with a body length of 2−2.5 mm (between the base of the apical spine and the anterior part of the head) and carrying parthenogenetic eggs and embryos were used for experiments. Animals were not fed during short-term exposures. During experiments, all animals were in good physical condition. After heat exposure, animals were transferred into 1.5-ml microcentrifuge tubes and shock-frozen in liquid nitrogen after removing adhering water with a tissue paper. Samples were short-term stored at -80°C.

tag: condition

value: heat shock to 30C

source_name: treatment 3, condition 1


title: Treatment 3 conditions 1 vs 2 replicate 4

status: Public on Sep 18 2017

type: RNA

molecule: total RNA

tag: treatment


title: IMCD3_rep2-1

city: Hannover

first: Oliver

last: Dittrich-Breiholz

address: Carl-Neuberg-Str. 1

department: Research Core Unit Genomics

country: Germany

institute: Medical School Hannover

hyb_protocol: cRNA fragmentation, hybridisation and washing steps were carried out as recommended in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent), except that 3000 ng of each labelled cRNA population were used for hybridisation.

scan_protocol: Slides were scanned using the Agilent Micro Array Scanner G2565BA at two different photomultiplier tube (PMT) settings (100 % and 5 %) to increase the dynamic range of the measurement (extended dynamic range mode).

data_processing: Data extraction and processing of raw fluorescence intensity values were performed with the ‘Feature Extraction software V9.5.3.1’ by using the extraction protocol file: GE2-v5_95_Feb07.xml.  Measurements of on-chip replicated features were averaged using the geometric mean of processed intensity values from both channels, ‘gProcessedSignal’ (gPS) and ‘rProcessedSignal’ (rPS), separately to retrieve one resulting value per unique non-control probe. Single features were excluded from averaging if they i) were manually flagged, ii) were identified as outliers by the Feature Extraction software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the PS distribution of the respective on-chip replicate population, or iv) showed a coefficient of variation of pixel intensities per feature that exceeded 0.5.  For inter-array normalisation, PS values were further transformed as follows: All PS values (gPS and rPS) of one particular microarray (‘Array i’ in the formula shown below) were multiplied with a microarray-specific scaling factor. This factor was calculated by dividing a ‘reference 75th percentile value’ (targeted at 1500 for the whole series) by the 75th percentile of the gPS values calculated by the Feature Extraction software for that microarray. Accordingly, normalised PS values (nPS) for all samples (microarray data sets) were calculated by the following formula:   normalised PSArray i = PSArray i x (1500 / 75th Percentile gPSArray i)  Finally, a lower intensity threshold was defined as 1% of the reference 75th percentile value (= 15). All nPS values below this intensity cutoff were substituted by the surrogate value of 15.

organism: Mus musculus

source_name: IMCD3_technical replicate of replicate2

label_protocol: Synthesis of Cy3- or Cy5-labelled cRNA was performed with the ‘Quick Amp Labeling kit, two color’ (#5190-0444, Agilent Technologies) according to the manufacturer’s recommendations using 500 ng of total RNA.

growth_protocol: IMCD3 cells (CRL-2123, ATCC) were grown in DMEM medium supplemented with 10% fetal calf serum (FCS; Biochrom), F12 (Invitrogen), 1x Glutamax (Gibco) and 1x Pen/Strep (Gibco) on 10 cm tissue culture dishes.

extract_protocol: Total RNA was extracted using the RNeasy Micro or Mini Kit (Qiagen) following the manufacturer’s instructions (including DNase digest). Total RNA was eluted in 40 µl H2O resulting in a concentration of 330 - 990 ng/µl.

treatment_protocol: Cells on two dishes were serum-starved in order to induce ciliogenesis by growing them for 48 h in medium lacking FCS before harvest (serum-starved IMCD3). Cells on two other dishes were split 1:10 the day before collection and did not reach confluency by the time of harvest (unstarved IMCD3).

tag: cell line


title: At_WOX5_2

city: Raleigh

first: Maria

middle: Angels

last: de Luis Balaguer

state: NC

address: 2115 Gardner Hall, Box 7612

department: Plant and Microbial Biology

country: USA

institute: North Carolina State University

description: Gene expression data from QC sorted cells under standard conditions for 5 days

hyb_protocol: Standard Operating Procedure performed at the Duke Microarray Facility

data_processing: Mas5; target intensity of 250

label: biotin

organism: Arabidopsis thaliana

source_name: WOX5::GFP sorted cells

label_protocol: Affy two-cycle labeling (raw 21-26) and one-cycle (everything else) labeling protocol

growth_protocol: Growth Media: Standard media for 5 days

extract_protocol: Affimetrix Kit

treatment_protocol: Seedling roots, 5 days after germination, either protoplasted cells or tissue

tag: ecotype

tag: cell type

value: WOX5::GFP sorted cells (xylem)


title: Treatment 3 conditions 1 vs 2 replicate 2


title: IMCD3_rep1


title: Treatment 3 conditions 1 vs 2 replicate 3


title: IMCD3_starved_rep1


title: IMCD3_rep2


title: ~E7.75 Noto GFP/GFP distal halves technical replicate1

hyb_protocol: cRNA fragmentation, hybridisation and washing steps were carried out as recommended in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent), except that 4000-5000 ng of each labelled cRNA population were used for hybridisation.

source_name: ventral node-containing distal halves of Noto GFP/GFP homozygotes at the early headfold stage (~E7.75)

label_protocol: Synthesis of Cy3- or Cy5-labelled cRNA was performed with the ‘Quick Amp Labeling kit, two color’ (#5190-0444, Agilent Technologies) according to the manufacturer’s recommendations using 500-1000 ng of total RNA.

extract_protocol: Total RNA was extracted using the RNeasy Micro or Mini Kit (Qiagen) following the manufacturer’s instructions (including DNase digest). Embryos were homogenised with a micro pestle in a 1.5 ml Eppendorf tube. Total RNA was eluted in 14-15 µl H2O resulting in an RNA concentration of around 400 ng/µl.

treatment_protocol: Noto GFP heterozygous and homozygous embryos were harvested at early headfold stage (~E7.75). The distal third of each embryo comprising the embryonic ventral node at the distal tip was sectioned and collected and pooled in RNA stabilisation solution (RNAlater, Ambion) at 4 °C in pools of 120 to 150 embryonic thirds.

tag: strain

value: NotoGFP, Sv129/CD-1 hybrid background


title: M3 MCF-7_GBK_48h

city: hohhot

first: xuemin

last: Cao

address: 内蒙古呼和浩特市玉泉区

country: China

institute: Inner Mongolia University

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: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Homo sapiens

label_protocol: standard Affymetrix protocol

growth_protocol: 37℃，5% CO2 cultured for 48h

extract_protocol: standard Affymetrix protocol

treatment_protocol: treat with GBK and cultured for 48h

value: GBK


title: Treatment 2 conditions 1 vs 2 replicate 2

source_name: treatment 2, condition 2

source_name: treatment 2, condition 1


title: Treatment 2 conditions 1 vs 2 replicate 3


title: Treatment 2 conditions 1 vs 2 replicate 1


title: Treatment 2 conditions 1 vs 2 replicate 4


title: Treatment 1 conditions 1 vs 2 replicate 2

source_name: treatment 1, condition 2

source_name: treatment 1, condition 1


title: Treatment 1 conditions 1 vs 2 replicate 3


title: ~E7.75 Noto GFP/+ distal halves technical replicate2

source_name: ventral node-containing distal halves of Noto GFP/+ heterozygotes at the early headfold stage (~E7.75)


title: Treatment 1 conditions 1 vs 2 replicate 4


title: E16.5 Foxj1 –/– lung lobes

hyb_protocol: cRNA fragmentation, hybridisation and washing steps were carried out as recommended in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent), except that 400 ng of each labelled cRNA population were used for hybridisation.

source_name: E16.5 homozygous Foxj1 –/– lung epithelium

label_protocol: 100 ng of total RNA of each condition were used to prepare aminoallyl-UTP-modified (aaUTP) cRNA (Amino Allyl MessageAmp™ II Kit; #AM1753; Life Technologies) as recommended by the company (applying one-round of amplification). The labelling of aaUTP-cRNA was performed by use of either Cy3 or Cy5 (25-8010-79, 25-8010-80; GE Healthcare).

extract_protocol: Total RNA was extracted using the RNeasy Micro or Mini Kit (Qiagen) following the manufacturer’s instructions (including DNase digest). Lung lobes were homogenised with a micro pestle in a 1.5 ml Eppendorf tube. Total RNA was eluted in 14-15 µl H2O resulting in an RNA concentration of around 180 ng/µl.

treatment_protocol: One lung for each genotype was dissected from male heterozygous and homozygous Foxj1lacZ litter mates at E16.5. Extralobular tissues were removed for better comparability with wildtype epithelium sections and the remaining lung lobes were frozen in liquid nitrogen and stored at –80 °C.

value: Foxj1lacZ, Sv129/CD-1 hybrid background


title: ~E7.75 Noto GFP/GFP distal halves technical replicate2


title: ~E7.75 Noto GFP/+ distal halves technical replicate1


title: E14.5 lung epithelium

source_name: E14.5 wildtype lung epithelium

extract_protocol: Total RNA was extracted using the RNeasy Micro or Mini Kit (Qiagen) following the manufacturer’s instructions (including DNase digest). Total RNA was eluted in 14-15 µl H2O resulting in an RNA concentration of around 20 ng/µl.

treatment_protocol: Lungs of CD-1 wildtype male E14.5 and E18.5 foetuses were dissected in PBS, embedded in Tissue Freezing Medium (Jung) on dry ice and stored at –80 °C. Embedded lungs were then cryo-sectioned at 10 µm, sections mounted on MembraneSlides 1.0 PEN (Zeiss), stained by dipping into Mayer’s hemalum solution (Merck) for better recognisability of histology, rinsed in water, air-dried at room temperature for 30 min and stored at –80 °C. Epithelia of intralobular airways were laser micro-dissected from these lung sections under a laser dissection microscope (Leica LMD6000). Epithelium sections of one whole E14.5 and E18.5 lung each were collected, transferred to Buffer RLT (RNeasy Micro kit, Qiagen), vortexed for 30 s and stored at –80 °C.


title: E18.5 lung epithelium

source_name: E18.5 wildtype lung epithelium


title: Conditions 2 vs 3 replicate 4

data_processing:
Raw signal intensity extract with NimbleScan 2.6 Software (Roche NimbleGen) in PAIR files. Quantile normalization to convert raw to processed data.
The Sample*.txt files are the normalized data values for the probes on the array.
GEO1_Matrix.txt is the final, processed data file reporting log2 ratios of the first condition over second condition, quantile normalized, four biological replicates averaged.

source_name: condition 3

treatment_protocol: Long-term-acclimated animals were kept at three different temperatures (i.e., 10 ± 0.5°C, 20 ± 0.3°C, and 24 ± 0.3°C) under normoxia (Po2 ≥ 20 kPa) for at least twelve weeks. During experiments, all animals were in good physical condition. After thermal acclimation, animals were transferred into 1.5-ml microcentrifuge tubes and shock-frozen in liquid nitrogen after removing adhering water with a tissue paper. Samples were short-term stored at -80°C.

tag: Sex

value: female

tag: developmental stage

value: adult

tag: tissue

value: whole body

value: Gräfenhain

source_name: condition 2


title: Treatment 1 conditions 1 vs 2 replicate 1


title: Conditions 2 vs 3 replicate 3


title: Conditions 2 vs 3 replicate 2


title: Conditions 2 vs 3 replicate 1


title: E16.5 Foxj1 +/– lung lobes

source_name: E16.5 heterozygous Foxj1 +/– lung epithelium


title: NA_rep 2

city: Aalborg East

first: Majken

last: Pagter

address: Fredrik Bajers Vej 7H

department: Chemistry and Bioscience

country: Denmark

institute: Aalborg University

hyb_protocol: For hybridization the Affymetrix Wash and Stain Kit was used with the Command Console V3.2

scan_protocol: For scanning the Arabidopsis Gene 1.0 ST FS450_0002 protocol was used

data_processing: The raw Arabidopsis Gene 1.0 ST intensities were imported into the RobiNA software to perform quality assessment and data normalization and to identify genes differentially regulated between cold acclimated plants and plants subjected to different durations of deacclimation. Data normalization was performed using the RMA method. Statistical analysis of differential gene expression between cold acclimated and deacclimated or non-acclimated plants was carried out using a linear model-based approach, applying a 0.05 cut-off for P-values after Benjamini-Hochberg correction for multiple testing and log2 fold ratio greater than 1 and lower than -1.

source_name: A. thaliana Col-0 non-acclimated replicate 2

label_protocol: For labeling and fragmentation the  NuGEN Encore Biotin Module was used according to the manusfacturer´s instructions

growth_protocol: Seeds from Arabidopsis thaliana Col-0 were sown in soil and grown in the greenhouse at 8-h day length with light supplementation to reach at least 200 µmol m-2 s-1 and a temperature of 20°C during the day, 18°C during the night. After three weeks of growth under these conditions plants were transferred to long days (16 h light/8 h dark), but otherwise similar growth conditions, for additionally one week of growth.

extract_protocol: Total RNA was isolated from a pool of rosettes from 10 different plants for each sample, using Trizol reagent (Invitrogen, Carlsbad, CA) and DNase treated with RapidOut DNA Removal Kit (Thermo Scientific, Waltham, MA). RNA quantity and quality were determined using a Nanodrop spectrophotomer (Nanodrop Technologies, Wilmington, DE), gel electrophoresis and a bioanalyzer (Agilent, Santa Clara, CA).

treatment_protocol: For cold acclimation, plants were transferred to a 4°C growth cabinet at 16-h day length with 90 µmol m-2 s-1. for three days. For deacclimation, cold acclimated plants were transferred back to the greenhouse at 20°C/18°C day/night temperature and at least 200 µmol m-2 s-1 light as described previously. Complete rosettes of non-acclimated and cold acclimated plants and plants deacclimated for 2 h, 4 h, 6 h, 12 h and 24 h were harvested from 10 individual replicate plants for RNA extraction and hybridization on Affymetrix Genechip Arabidopsis Gene 1.0 ST Arrays.

value: Rosettes

value: non-acclimated


title: Conditions 1 vs 3 replicate 4

source_name: condition 1


title: Conditions 1 vs 3 replicate 3


title: Conditions 1 vs 3 replicate 2


title: Conditions 1 vs 2 replicate 4


title: Conditions 1 vs 2 replicate 2


title: Conditions 1 vs 2 replicate 3


title: Conditions 1 vs 3 replicate 1


title: Eco_FCE_Liver_309

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

institute: FBN Dummerstorf

description:
Gene expression data from Liver sample of adults
Snowball arrays (Freeman et al. in BMC Biol 2012, 10:90), see the ArrayExpress database, accession no. A-AFFY-189

hyb_protocol: Labelled DNA was hybridized for 16 hr at 42°C on Snowball Arrays. Chips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500 and BioConductor.

organism: Sus scrofa

source_name: Liver

label_protocol: Each RNA sample was transcribed to DNA using the Ambion WT Expression Kit (Ambion, Austin, TX, USA). DNA preparations were fragmented and labelled with the WT Terminal Labeling Kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated using Qiazol reagent (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was column-purified using the RNeasy Kit (Qiagen, Hilden, Germany).

tag: classification according to the residual feed intake (rfi)

value: low

tag: gender

value: m

tag: sampling time point

value: day 140


title: Eco_FCE_Liver_318

value: high

value: w


title: Eco_FCE_Liver_310


title: Conditions 1 vs 2 replicate 1


title: Eco_FCE_Liver_324


title: Eco_FCE_Liver_301


title: Eco_FCE_Liver_303


title: Mast cells, peritoneum, treated [MC.P.treated1]

status: Public on Sep 15 2017

city: Hamburg

first: Christian

last: Schulze

address: Falkenried 94

institute: ZMNH

hyb_protocol: Following fragmentation, cRNA were hybridized on Mouse Gene 2.1 ST Arrays. GeneChips were washed and stained according to standard Affymetrix protocol

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

data_processing: Intensity data were processed with R and Bioconductor packages to obtain quantile-normalized (robust multi-array average, RMA) intensity values. Probe intensities were then combined into single expression values per transcriptcluster (Entrez Gene ID) using featureFilter function and Affymetrix mogene21 annotation data (resulting in 24,111 data rows).

label: Biotin

source_name: Mast cells_peritoneum_treated

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol

growth_protocol: Panc02 cells, C57BL/6J mice

extract_protocol: Mast cells from the peritoneum of tumor bearing mice were isolated by lavage. Mast cells  from cell suspensions of both compartments were purified by FACS-sorting staining for DAPI, CD45, CD11b, CD117, and FceRI. Total RNA was purified (Qiagen Rneasy Micro Columns)

treatment_protocol: Panc02 cells were injected subcutanously into the flanks of C57BL/6J mice. After reaching a tumor volume of 100 mm3, mice were randomized into treatment and control group. The treatment group received 40 mg/kg of the anti-angiogenic anti-VEGFR2 antibody DC101 whereas the other group received a placebo.

tag: injected with

value: Panc02 cells

tag: treated with

value: peritoneum

value: peritnoeal mast cells


title: Eco_FCE_Liver_323


title: Eco_FCE_Liver_317


title: Mast cells, peritoneum, treated [MC.P.treated2]

value: 40 mg/kg of the anti-angiogenic anti-VEGFR2 antibody DC101


title: Eco_FCE_Liver_307


title: Mast cells, peritoneum, ctrl [MC.P.ctrl1]

source_name: Mast cells_peritoneum_ctrl

value: placebo (control)


title: Eco_FCE_Liver_304


title: Mast cells, tumor, treated [MC.T.treated2]

source_name: Mast cells_tumor_treated

value: tumor

value: tumor-resident mast cells


title: Mast cells, tumor, treated [MC.T.treated1]


title: Mast cells, peritoneum, ctrl [MC.P.ctrl2]


title: Eco_FCE_Liver_308


title: 96hr siControl DIFF media 3

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description: Gene expression after 96 hours siControl transfection confluent in DIFF media, biological replicate 3

hyb_protocol: Microarray hybridization was performed at 65°C for 18 hours in Agilent's microarray hybridization chambers, followed by wash procedures according to the manufacturer’s recommended protocols

scan_protocol: Microarray was scanned in an Agilent scanner at 3μm resolution, and the array data was extracted with Agilent feature extraction software using the GE1_107_Sep09 protocol

data_processing: Agilent Feature Extraction Software (version 10.7.3.1) was used along with LOWESS normalization

source_name: Cell culture, LHCN-M2

label_protocol: 100ng of total RNA were labeled (Cy3) according to Agilent's labeling protocol

growth_protocol: LHCN-M2 cells were cultured in growth or differentiation media  at 37°C, 5% CO2, as described by zhu et al, Aging Cell (2007) 6, pp515-523.

extract_protocol: Total RNA was extracted using QIAGEN RNeasy Mini Kit following manufacturer's instructions

treatment_protocol: LHCN-M2 cells were treated with 20nM sicontrol or 20nM siZNF148 (dharmacon) for the indicated time in 6-well plates.

value: Muscle


title: 96hr siZNF148 DIFF media 2

description: Gene expression after 96 hours siZNF148 transfection confluent in DIFF media, biological replicate 2


title: 96hr siZNF148 DIFF media 3

description: Gene expression after 96 hours siZNF148 transfection confluent in DIFF media, biological replicate 3


title: Eco_FCE_Liver_302


title: Mast cells, tumor, ctrl [MC.T.ctrl1]

source_name: Mast cells_tumor_ctrl


title: 48hr siZNF148 DIFF media 2

description: Gene expression after 48 hours siZNF148 transfection confluent in DIFF media, biological replicate 2


title: 96hr siControl DIFF media 1

description: Gene expression after 96 hours siControl transfection confluent in DIFF media, biological replicate 1


title: 96hr siZNF148 DIFF media 1

description: Gene expression after 96 hours siZNF148 transfection confluent in DIFF media, biological replicate 1


title: Mast cells, tumor, ctrl [MC.T.ctrl2]


title: 48hr siZNF148 DIFF media 3

description: Gene expression after 48 hours siZNF148 transfection confluent in DIFF media, biological replicate 3


title: 48hr siZNF148 DIFF media 1

description: Gene expression after 48 hours siZNF148 transfection confluent in DIFF media, biological replicate 1


title: 96hr siZNF148 Growth media 2

description: Gene expression after 96 hours siZNF148 transfection confluent in growth media, biological replicate 2


title: 96hr siZNF148 Growth media 1

description: Gene expression after 96 hours siZNF148 transfection confluent in growth media, biological replicate 1


title: 96hr siZNF148 Growth media 3

description: Gene expression after 96 hours siZNF148 transfection confluent in growth media, biological replicate 3


title: 48hr siZNF148 Growth media 1

description: Gene expression after 48 hours siZNF148 transfection confluent in growth media, biological replicate 3


title: 96hr siControl Growth media 1

description: Gene expression after 96 hours siControl transfection confluent in growth media, biological replicate 1


title: 48hr siControl Growth media 2

description: Gene expression after 48 hours siControl transfection confluent in growth media, biological replicate 2


title: 48hr siControl Growth media 3

description: Gene expression after 48 hours siControl transfection confluent in growth media, biological replicate 3


title: 96hr siControl Growth media 2

description: Gene expression after 96 hours siControl transfection confluent in growth media, biological replicate 2


title: 48hr siControl DIFF media 2

description: Gene expression after 48 hours siControl transfection confluent in DIFF media, biological replicate 2


title: 48hr siControl DIFF media 1

description: Gene expression after 48 hours siControl transfection confluent in DIFF media, biological replicate 1


title: 48hr siControl DIFF media 3

description: Gene expression after 48 hours siControl transfection confluent in DIFF media, biological replicate 3


title: 48hr siControl Growth media 1

description: Gene expression after 48 hours siControl transfection confluent in growth media, biological replicate 1


title: 48hr siZNF148 Growth media 3

description: Gene expression after 48 hours siZNF148 transfection confluent in growth media, biological replicate 5


title: 96hr siControl DIFF media 2

description: Gene expression after 96 hours siControl transfection confluent in DIFF media, biological replicate 2


title: 24hr siControl Growth media 3

description: Gene expression after 24 hours siControl transfection subconfluent in growth media, biological replicate 3


title: 48hr siZNF148 Growth media 2

description: Gene expression after 48 hours siZNF148 transfection confluent in growth media, biological replicate 4


title: 24hr siZNF148 Growth media 3

description: Gene expression after 24 hours siZNF148 transfection subconfluent in growth media, biological replicate 3


title: siRNA CDK4/6, biological rep3

city: Barcelona

first: Míriam

last: Tarrado-Castellarnau

address: Av. Diagonal 643

country: Spain

institute: Universitat de Barcelona

description: Cells were transfected with a mix (siRNA CDK4/6) containing siRNA against CDK4 and siRNA against CDK6.

hyb_protocol: Biotinylated cRNA was hybridised to Affymetrix GeneChip® human genome U133 Plus 2.0 arrays following the manufacturer’s instructions (Affymetrix Inc., Santa Clara, CA, USA).

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

data_processing: The data were analyzed with the R-Project Bioconductor statistical tools package and standardised using the Robust Multi-array Average (RMA) method. The simpleaffy package was used to compute the RMA expression values (signal intensities (SI) on the base 2 logarithm scale (log2SI) representing gene expression levels).

source_name: Human colorectal carcinoma HCT116 cells

label_protocol: Biotinylated cRNA were prepared according to the following the manufacturer’s instructions (Affymetrix Inc., Santa Clara, CA, USA)

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle medium (Gibco, Thermo Fisher Scientific Inc., Waltham, MA, USA) / Nutrient mixture HAM F12 (Biological Industries) (DMEM/F12, 1:1 mixture) with L-glutamine and 12.5 mM D-glucose. Media were supplemented with 10% heat-inactivated FBS, penicillin (50 U/mL) and streptomycin (50 µg/mL). Cells were incubated at 37 ºC in a humidified atmosphere with 5% CO2.

extract_protocol: Total RNA was isolated from frozen plates using Trizol reagent (Invitrogen) and the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocols. RNA integrity was tested using lab-on-a-chip technology on the BioAnalyzer 2100 (Agilent, Palo Alto, CA, USA).

treatment_protocol: Cells were transfected using Lipofectamine RNAiMAX (Invitrogen) transfection reagent following the manufacturer’s instructions. We tested different concentrations of lipid transfection reagent and siRNA, transfection periods and cell numbers plated for transfection. The optimised transfection conditions that delivered the best knockdown results were selected by quantitative reverse transcription-polymerase chain reaction (RT-qPCR) and Western blot, while cell population was maintained in a state of exponential growth during all the experiment. Briefly, 5×104 cells/well were seeded in antibiotic-free medium in 6-well flat-bottom tissue culture plates and transfected the next day with a mix (siRNA CDK4/6) containing 30 nM of ON-TARGETplus SMARTpool siRNA against CDK4 (L-003238-00, GE Healthcare Dharmacon Inc., Lafayette, CO, USA) and 30 nM of Silencer Select siRNA against CDK6 (s51, Ambion, Austin, TX, USA) or with a mix (siRNA Control) containing 30 nM of ON-TARGETplus Non-Targeting Control Pool siRNA (D-001810-10, GE Healthcare Dharmacon Inc.) and 30 nM of Silencer Select Negative Control siRNA (4390844, Ambion). After 24 h, culture medium was replaced with fresh medium with antibiotics. Cells were analysed 96 h after transfection.

tag: transfection

value: siRNA CDK4/6


title: siRNA CDK4/6, biological rep2


title: 24hr siControl Growth media 1

description: Gene expression after 24 hours siControl transfection subconfluent in growth media, biological replicate 1


title: siRNA CDK4/6, biological rep1


title: 24hr siControl Growth media 2

description: Gene expression after 24 hours siControl transfection subconfluent in growth media, biological replicate 2


title: siRNA Control, biological rep1

description: Cells transfected with a mix (siRNA Control) containing Non-Targeting Control Pool siRNA and Silencer Select Negative Control siRNA.

value: siRNA Control


title: 24hr siZNF148 Growth media 1

description: Gene expression after 24 hours siZNF148 transfection subconfluent in growth media, biological replicate 1


title: siRNA Control, biological rep2


title: Neuroblastoma MYCN/Ret M919T.Tum32288

city: Paris

first: Isabelle

last: Janoueix-Lerosey

address: 26 rue d'Ulm

country: France

institute: Institut Curie

hyb_protocol: Hybridization was performed by Institut Curie Affymetrix Microarray Core Facility according to the manufacturer's instructions. Samples were hybridized to Affymetrix MOE430.2 array

scan_protocol: Scanning was performed by Institut Curie Affymetrix Microarray Core Facility according to the manufacturer's instructions

data_processing: Arrays were normalized by the GCRMA procedure using Brainarray annotations (Brainarray V.16.0.0, ENTREZG)

source_name: MYCN/Ret M919T tumor

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

extract_protocol: RNA was collected from tumors using the miRNeasy kit (Qiagen) according to the manufacturer's instructions.

value: 129S2-C57BL6/J mixed background

value: Neuroblastoma


title: siRNA Control, biological rep3


title: SPT3_GCN5_Nascent_Replicate 2

city: Illkirch

first: Didier

last: Devys

address: 1 rue Laurent Fries / BP 10142

institute: Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)

hyb_protocol: Following fragmentation, 4μg of cRNAs were hybridized for 16 hours at 45°C, 60 rpm on GeneChip® Yeast Genome 2.0 arrays (Affymetrix).

scan_protocol: The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) using the FS450_0003 script and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 1.56µm.

data_processing: Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.1.2. CEL files were further processed with Affymetrix Expression Console software version 1.4.1 to calculate probeset signal intensities, using the Affymetrix statistics-based algorithms MAS-5.0 with default settings and global scaling as normalization method. The trimmed mean target intensity of each chip was arbitrarily set to 100. SPT20 arrays were analysed together with WT1 and WT2. SPT3_GCN5 arrays were analysed together with WT7 and WT8. All the other mutants were analysed together with WT3, WT4, WT5 and WT6.

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae deleted for SPT3 and GCN5

label_protocol: Biotinylated cRNA targets were prepared from 150ng of total RNA using the “MessageAmp™ Premier RNA Amplification Kit from Ambion, according to the Instruction Manual # 4386269 Revision B, 18 september 2007.

growth_protocol: For each yeast strain and condition, 100mL of S. cerevisiae cells were grown in YPD medium at 30°C to an OD600 ≈ 0.8.

extract_protocol: Total RNAs were extracted using RiboPure yeast kit (Ambion, Life Technologies) according to the description provided by the manufacturer. This first sample is the steady-state RNA fraction. 200μg of total RNA was biotinylated using 200μL of 1mg/mL EZ-link HPDP- Biotin (Pierce) in 100μL of biotinylation buffer (100mM Tris- HCl at pH 7.5, 10mM EDTA) and adjusted to a final volume of 1000μL with DEPC-treated RNase-free water (Sigma-Aldrich) for 3 h at room temperature, protected from light and gentle agitation. After chloroform extraction and isopropanol precipitation, newly-synthesized biotinylated RNAs were bound to 100μL of μMACS streptavidin microbeads. Purification of labeled RNA was then carried out using μMACS streptavidin starting kit (Miltenyi Biotec). Labeled RNAs were eluted twice with 200μL of 100mM DTT and precipitated overnight. This purified labeled RNA is the newly-synthesized RNA used for the array hybridization.

treatment_protocol: Newly-synthesized RNAs were labeled for 6 min by adding 4-thiouracil (Sigma-Aldrich) until a final concentration of 5mM. In parallel, wild-type S. pombe cells were similarly grown in YES medium, at 31°C, and labeled for 6 min to be used as a spike-in across all samples. Upon labeling, cells were immediately pelleted and flash-frozen in liquid N2 and stored at -80°C until further use. Immediately before freezing the cells, a small aliquot was collected for cell counting purposes. All experiments using deletion strains were performed using two independent biological replicates. Before total RNA extraction, S. cerevisiae and S. pombe cells were mixed in a ratio of 3:1.

tag: parental strain

tag: molecule type

value: newly-transcribed RNA

tag: genotype/variation

value: spt3[delta]gcn5[delta] strain


title: SPT3_GCN5_Total_Replicate 2

value: steady-state RNA


title: WT_Total_Replicate 8

source_name: S. cerevisiae wildtype strain

value: wild-type strain (control)


title: WT_Nascent_Replicate 8


title: Neuroblastoma MYCN/Ret M919T.Tum30499


title: WT_Nascent_Replicate 7


title: Neuroblastoma MYCN/Ret M919T.Tum31105


title: 24hr siZNF148 Growth media 2

description: Gene expression after 24 hours siZNF148 transfection subconfluent in growth media, biological replicate 2


title: Neuroblastoma MYCN/Ret M919T.Tum32297


title: Neuroblastoma MYCN/Ret M919T.Tum31003


title: UBP8_GCN5_Nascent_Replicate 3

source_name: S. cerevisiae deleted for UBP8 and GCN5

value: ubp8[delta]gcn5[delta] strain


title: UBP8_GCN5_Nascent_Replicate 2


title: WT_Total_Replicate 7


title: SPT3_GCN5_Total_Replicate 1


title: SPT3_GCN5_Nascent_Replicate 1


title: UBP8_GCN5_Nascent_Replicate 4


title: UBP8_GCN5_Nascent_Replicate 1


title: UBP8_GCN5_Total_Replicate 4


title: UBP8_GCN5_Total_Replicate 2


title: UBP8_GCN5_Total_Replicate 3


title: SPT8_Nascent_Replicate 2

source_name: S. cerevisiae deleted for SPT8

value: spt8[delta] strain


title: SPT8_Nascent_Replicate 1


title: UBP8_GCN5_Total_Replicate 1


title: SPT8_Total_Replicate 2


title: SPT8_Total_Replicate 1


title: SPT3_Total_Replicate 2

source_name: S. cerevisiae deleted for SPT3

value: spt3[delta] strain


title: SPT3_Nascent_Replicate 1


title: Sample 774 (Peak)

city: Boston

first: SAUMYA

last: Das

state: MA

address: 185 Cambridge Street

institute: MGH

hyb_protocol: not provided

scan_protocol: The samples were then scanned on an EMD Millipore Guava 6HT flow cytometer. Flow cytometry quantification data was analyzed with the Firefly™ Analysis Workbench software.

data_processing: To determine if a particular miRNA signal is detected, assay background is subtracted from the measured miRNA signal and the result is compared to a target-specific detection threshold. This detection threshold is based on comparison of fluorescence intensity of sample wells to negative (water only) wells. Samples with below-detection threshold fluorescence intensity were counted as missing for the analysis (to avoid bias). The normalization probes were chosen according to the geNorm algorithm and the data was normalized after subtracting the background from the raw data.

label: Fireplex

source_name: Plasma, after acute exercise

label_protocol: not provided

extract_protocol: In brief, plasma (40 μL) was mixed with 36 μL Digest Buffer and 4 μL Protease Mix and incubated at 60°C for 45 minutes with shaking. For each sample run, Firefly Particles (35 μL) were added to a well of a 96-well filter plate and filtered. Next, 25 μL of Hybe Buffer was added to each well followed by 25 μL of sample (or water in the case of no-sample controls). The plate was incubated at 37°C for 60 minutes with shaking.  After rinsing twice with 1X Rinse B and once with 1X Rinse A, 75 μL of 1X Labeling Buffer was added to each well. The plate was incubated at room temperature for 60 minutes with shaking. After two rinses with Rinse B followed by one rinse with 1X Rinse A, a catch plate was added to the vacuum manifold and the filter plate put under constant vacuum. 65 μL of 95°C RNAse-free water was added twice to each well to elute the ligated sample. 30 μL of this melt-off was added to a clean PCR plate and mixed with 20 μL PCR master mix. The mixture underwent 27 cycles of PCR amplification followed by 6 cycles of asymmetric amplification.  Next 60 μL of Hybe Buffer was added back to each well of the original particles followed by 20 μL of the PCR product, and the plate was incubated at 37°C for 30 minutes with shaking. After rinsing twice with 1X Rinse A, 75 μL of 1X Reporting Buffer was added to each well and the plate incubated at room temperature for 15 minutes with shaking.  After rinsing twice with 1X Rinse A, 175 μL of Run Buffer was added to each well.

tag: age

tag: bmi

tag: diabetes

tag: hypertension

tag: hyperlipidemia

tag: smoking

tag: diuretic

value: No

tag: statin

tag: race

value: Caucasian


title: Sample 795 (Peak)


title: GCN5_Nascent_Replicate 4

source_name: S. cerevisiae deleted for GCN5

value: gcn5[delta] strain


title: Sample 759 (Peak)

value: Yes


title: Sample 758 (Peak)


title: SPT3_Total_Replicate 1


title: Sample 629 (Peak)

value: Never


title: Sample 574 (Peak)

value: Former


title: Sample 608 (Peak)


title: Sample 683 (Peak)


title: Sample 617 (Peak)


title: DN012

city: Leuven

first: Tim

last: Dierckx

state: Vlaams Brabant

address: Herestraat 49 - 1040

department: Microbiology and Immunology

country: Belgium

institute: KU Leuven

description:
unique sample, no replicates
18578

hyb_protocol: Affymetrix GeneChip Human Gene 1.0 ST arrays were hybridized with biotin-labeled cDNA, washed, stained, and scanned according to the protocol described in WT Sense Target Labeling Assay Manual (Version 4; FS450_0007).

scan_protocol: Affymetrix GeneChip Human Gene 1.0 ST arrays were scanned according to the protocol described in WT Sense Target Labeling Assay Manual (Version 4; FS450_0007).

data_processing: Data were analysed using the Affymetrix GeneChip software based on the Robust Multichip Average (RMA) expression values as obtained with the xps package version 1.8.0.

source_name: healthy_PBMCs ex vivo

label_protocol: Whole Human Genome microarray analysis was performed by the VIB MicroArray Facility (Leuven, Belgium). Labeling of RNA (100ng each) with Ambion kit was performed using manufacturer's instructions.

growth_protocol: PBMCs from LCL patients and healthy controls were processed in parallel and immediately frozen in Trizol lysis buffer to preserve RNA integrity.

extract_protocol: Following Trizol extraction, total RNA was further purified using RNeasy kit, according to the manufacturer’s protocol (QIAGEN, Venlo, the Netherlands).

treatment_protocol: Untreated, ex vivo PBMCs

tag: subject status

value: healthy control

tag: tissue

value: PBMCs ex vivo


title: DN005

description:
unique sample, no replicates
18576


title: Sample 565 (Peak)

value: Current


title: Sample 561 (Peak)


title: GCN5_Nascent_Replicate 3


title: Sample 526 (Peak)


title: SPT3_Nascent_Replicate 2


title: GCN5_Nascent_Replicate 1


title: Sample 536 (Peak)


title: DN006

description:
unique sample, no replicates
18575


title: GCN5_Nascent_Replicate 2


title: GCN5_Total_Replicate 4


title: DN011

description:
unique sample, no replicates
18574


title: DN010

description:
unique sample, no replicates
18573


title: DN007

description:
unique sample, no replicates
18572


title: Neuroblastoma MYCN/Ret M919T.Tum31577

tag: strain

value: 129S2-C57BL6/J mixed background

value: Neuroblastoma


title: Sample 387 (Peak)


title: Sample 385 (Peak)


title: GCN5_Total_Replicate 1


title: GCN5_Total_Replicate 2


title: UBP8_Nascent_Replicate 4

source_name: S. cerevisiae deleted for UBP8

value: newly-transcribed RNA

value: ubp8[delta] strain


title: UBP8_Nascent_Replicate 3


title: porcine heartR-1-H

city: wuhan

first: kang

last: chao

state: hubei

address: shizhishan

department: College of Veterinary Medicine

institute: huazhong Agricultural university

description:
Gene expression after 4 days in heart from pig infected with PBS
heart, control, replicate2

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit ( 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)

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US)

data_processing:
Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) was applied to read the data . Raw data were normalized by Expression Console.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0

source_name: heart, control

label_protocol: Total RNA were amplified, labeled and purified by using Affymetrix WT Amplication Kit ( Affymetrix, Santa Clara, CA, US) and GeneChip WT Terminal Labeling Kit (Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cDNA

growth_protocol: A total of 9 piglets of high-heathy status were purchased from a commercial herd of free E. rhusiopathiaeand raised in isolated facilities. All pigs were determined to be negative for E. rhusiopathiae

extract_protocol: Total RNA was extracted and purified using RNeasy mini kit (QIAGEN, GmBH, Germany) following 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).

treatment_protocol: Pigs from each group were sacrificed to collect Heart tissues, which were immediately preserved in liquid nitrogen and subsequently stored in a -80℃ freezer.

value: heart

tag: infection

value: control


title: UBP8_Nascent_Replicate 1


title: LCL 03/040

description:
unique sample, no replicates
18566

source_name: LCL_PBMCs ex vivo

value: localized cutaneous leishmaniasis (LCL) patient


title: UBP8_Nascent_Replicate 2


title: porcine heart50H

description:
Gene expression after 4 days in heart from pig infected withE. rhusiopathiae (attenuated strain)
heart, E. rhusiopathiae (attenuated strain), replicate2

value: E. rhusiopathiae (attenuated strain)


title: LCL 03/076

description:
unique sample, no replicates
18567


title: porcine heart98H

description:
Gene expression after 4 days in heart from pig infected with PBS
heart, control, replicate1


title: porcine heart96H

description:
Gene expression after 4 days in heart from pig infected with E. rhusiopathiae (attenuated strain)
heart, E. rhusiopathiae (attenuated strain), replicate3


title: LCL 03/043

description:
unique sample, no replicates
18565


title: porcine heart95H

description:
Gene expression after 4 days in heart from pig infected with E. rhusiopathiae (attenuated strain)
heart, E. rhusiopathiae (attenuated strain), replicate1


title: Sample 508 (Peak)


title: GCN5_Total_Replicate 3

value: steady-state RNA


title: UBP8_Total_Replicate 4


title: Sample 493 (Peak)

value: No

value: Caucasian


title: Sample 461 (Peak)


title: Sample 459 (Peak)

value: Yes


title: Sample 383 (Peak)


title: DN002

description:
unique sample, no replicates
18570


title: LCL 03/072

description:
unique sample, no replicates
18569


title: UBP8_Total_Replicate 3


title: DN004

description:
unique sample, no replicates
18577


title: DN003

description:
unique sample, no replicates
18571


title: LCL 03/085

description:
unique sample, no replicates
18564


title: porcine heartR-2-H

description:
Gene expression after 4 days in heart from pig infected with PBS
heart, control, replicate3


title: LCL 03/073

description:
unique sample, no replicates
18568


title: porcine heart32H-2

description:
Gene expression after 4 days in heart from pig infected with E. rhusiopathiae (high virulence)
heart, E. rhusiopathiae (high virulence), replicate3

value: E. rhusiopathiae (high virulence)


title: LCL 038

description:
unique sample, no replicates
18563


title: Sample 368 (Peak)

value: Never


title: Sample 356 (Peak)

value: Former


title: Sample 442 (Peak)


title: Sample 378 (Peak)


title: LCL 135

description:
unique sample, no replicates
18562

value: PBMCs ex vivo


title: UBP8_Total_Replicate 1


title: SPT7_Nascent_Replicate 2

source_name: S. cerevisiae deleted for SPT7

value: spt7[delta] strain


title: Sample 366 (Peak)


title: porcine heart32H

description:
Gene expression after 4 days in heart from pig infected with E. rhusiopathiae (high virulence)
heart, E. rhusiopathiae (high virulence), replicate1


title: UBP8_Total_Replicate 2


title: LCL 096

description:
unique sample, no replicates
18559


title: SPT7_Nascent_Replicate 4


title: porcine heart71H

description:
Gene expression after 4 days in heart from pig infected with E. rhusiopathiae (high virulence)
heart, E. rhusiopathiae (high virulence), replicate2


title: SPT7_Nascent_Replicate 1


title: Sample 331 (Peak)


title: Sample 322 (Peak)


title: SPT7_Nascent_Replicate 3


title: LCL 122

description:
unique sample, no replicates
18560


title: LCL 082

description:
unique sample, no replicates
18558


title: LCL 080

description:
unique sample, no replicates
18557


title: LCL 112

description:
unique sample, no replicates
18561


title: Sample 348 (Peak)


title: SPT7_Total_Replicate 4


title: LCL 081

description:
unique sample, no replicates
18555


title: LCL 099

description:
unique sample, no replicates
18556


title: Sample 278 (Peak)


title: Sample 267 (Peak)


title: Sample 257 (Peak)

value: African American


title: SPT7_Total_Replicate 3


title: Sample 231 (Peak)


title: SPT7_Total_Replicate 2


title: Sample 259 (Peak)

value: Current


title: Sample 429 (Peak)


title: WT_Nascent_Replicate 6

value: newly-transcribed RNA

value: wild-type strain (control)


title: WT_Nascent_Replicate 5


title: Sample 215 (Peak)


title: Sample 212 (Peak)


title: LCL 097

description:
unique sample, no replicates
18552


title: SPT7_Total_Replicate 1


title: WT_Nascent_Replicate 4


title: bc19

description:
unique sample, no replicates
18551

value: healthy control


title: LCL 066

description:
unique sample, no replicates
18554


title: Sample 175 (Peak)


title: Sample 163 (Peak)


title: Sample 166 (Peak)


title: Sample 167 (Peak)


title: LCL 064

description:
unique sample, no replicates
18553


title: WT_Nascent_Replicate 3


title: Sample 157 (Peak)


title: Sample 139 (Peak)


title: bc15

description:
unique sample, no replicates
18550


title: bc12

description:
unique sample, no replicates
18549


title: WT_Total_Replicate 5


title: WT_Total_Replicate 6


title: WT_Total_Replicate 4


title: Sample 127 (Peak)


title: WT_Total_Replicate 3


title: SPT20_Nascent_Replicate 2

source_name: S. cerevisiae deleted for SPT20

value: spt20[delta] strain


title: Sample 120 (Peak)


title: Sample 115 (Peak)


title: SPT20_Nascent_Replicate 1


title: SPT20_Nascent_Replicate 3


title: SPT20_Total_Replicate 4


title: Sample 109 (Peak)


title: Sample 92 (Peak)


title: Sample 89 (Peak)


title: SPT20_Total_Replicate 2


title: SPT20_Total_Replicate 3


title: SPT20_Total_Replicate 1


title: WT_Nascent_Replicate 2


title: Sample 81 (Peak)


title: Healthy Tissue from GBM 9

city: IStanbul

first: Sukru

last: Gulluoglu

address: Acibadem Mah. IStek vakfi binasi

country: Turkey

institute: Yeditepe University

description: miRNA expression data from fresh frozen healthy brain tissue sample

hyb_protocol: 943 ng of ss-cDNA were hybridized for 20 hr at 48C on Human Gene 2.1 ST Array. Array strpis were washed and stained in the GeneAtlas Fluidics station (Affymetrix)

scan_protocol: GeneChips were scanned using the GeneAtlas Array scanner

data_processing: The resulting data were analyzed with Transcriptome Analysis Console 3 software and DAVID online tool

source_name: Fresh frozen healthy brain tissue sample

label_protocol: Fragmented and Labeled ss-cDNA were prepared according to WT PLUS Reagent Kit from 500 ng total RNA

growth_protocol: Normal Human Astrocytes were obtained from Lonza ( NJ, USA) and grown with AGM BulletKit (Lonza, NJ, USA). Human Fetal Astrocytes were obtained from ABM (Richmond, Canada), grown in collagen coated plates according to manufacturer’s protocol

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

treatment_protocol: Not Applicable

tag: location

value: not available

tag: gender

tag: sample type

value: fresh frozen healthy brain tissue


title: Human Fetal Astrocyte

description: miRNA expression data from fetal human astrocyte cell line

source_name: Fetal  Human Astrocytesgrown under standard methods

value: fetal human astrocyte cell line


title: WT_Nascent_Replicate 1

tag: parental strain

tag: molecule type

tag: genotype/variation


title: Sample 39 (Peak)

tag: age

tag: bmi

tag: diabetes

value: No


title: Sample 46 (Peak)

tag: hypertension

tag: hyperlipidemia

tag: smoking

value: Caucasian


title: Sample 52 (Peak)

value: Yes

tag: diuretic

tag: statin

tag: race


title: Sample 55 (Peak)


title: Sample 82 (Peak)


title: Sample 30 (Peak)


title: Sample 16 (Peak)


title: Healthy Tissue from GBM 4


title: Sample 8 (Peak)


title: WT_Total_Replicate 2

value: steady-state RNA


title: Taf5 anchor away, plus rapamycin, steady-state RNA, replicate 2

description: Gene expression steady-state RNA in a Taf5 anchor-away strain after exposure to rapamycin

data_processing: Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.1.2. CEL files were further processed with Affymetrix Expression Console software version 1.4.1 to calculate probeset signal intensities, using the Affymetrix statistics-based algorithms MAS-5.0 with default settings and global scaling as normalization method. The trimmed mean target intensity of each chip was arbitrarily set to 100.

source_name: S. cerevisiae culture in exponential growth

growth_protocol: For each yeast strain and condition, 200mL of S. cerevisiae cells were grown in YPD medium at 30°C to an OD600 ≈ 0.8.

treatment_protocol: The culture was divided into two equal volumes of 100mL each and to one of those cultures rapamycin was added (+RAPA) until a final concentration of 1μg/mL, for 30 min, to allow nuclear depletion of either Taf4 or Taf5. To the other half of the culture, the control samples (-RAPA/minus rapamycin), only the vehicle (DMSO) was added. Newly synthesized RNAs were labeled for 6 min by adding 4-thiouracil (Sigma-Aldrich) until a final concentration of 5mM. In parallel, wild-type S. pombe cells were similarly grown in YES medium, at 31°C, and labeled for 6 min to be used as a spike-in across all samples. Cells were immediately pelleted and flash-frozen in liquid N2 and stored at -80°C until further use. Immediately before freezing the cells, a small aliquot was collected for cell counting purposes. S. cerevisiae and S. pombe cells were mixed in a ratio of 3:1.

tag: genotype

value: S. cerevisiae:MATalpha tor1-1; fpr1::NAT; RPL13A-2xFKB12::TRP1; TAF4-FRB::HYGRO

tag: molecule

value: Total RNA

tag: treatment

value: after exposure to rapamycin


title: Healthy Tissue 2

tag: location

tag: gender


title: WT_Total_Replicate 1

tag: parental strain


title: Taf5 anchor away, plus rapamycin, steady-state RNA, replicate 1


title: Taf5 anchor away, plus rapamycin, newly-synthesized RNA, replicate 1

description: Gene expression nascent RNA in a Taf5 anchor-away strain after exposure to rapamycin

value: Newly-synthesized RNA


title: Healthy Tissue from GBM 5

tag: sample type


title: Human Fetal Astrocyte

description: Gene expression data from fetal human astrocyte cell line


title: Healthy Tissue from GBM 9

description: Gene expression data from fresh frozen healthy brain tissue sample


title: Taf5 anchor away, plus rapamycin, newly-synthesized RNA, replicate 2


title: Healthy Tissue 3


title: Normal Human Astrocytes

description: Gene expression data from normal human astrocyte cell line

source_name: Normal Human Astrocytesgrown under standard methods

value: normal human astrocyte cell line


title: Sample 6 (Peak)

value: Current


title: Healthy Tissue from GBM 5


title: SPT20_Nascent_Replicate 4

tag: molecule type

value: newly-transcribed RNA

tag: genotype/variation


title: Taf5 anchor away, minus rapamycin, newly-synthesized RNA, replicate 2

description: Gene expression nascent RNA in a Taf5 anchor-away strain without exposure to rapamycin (control)

value: no exposure to rapamycin (control)


title: Healthy Tissue from GBM 1


title: Healthy Tissue 1


title: Healthy Tissue 2


title: Glioblastoma Multiforme 16

description: miRNA expression data from fresh frozen GBM tumor sample

source_name: Fresh frozen glioblastoma multiforme tumor sample

value: Cingulate Gyrus

value: F

value: fresh frozen GBM tumor


title: Sample 1 (Peak)

tag: age

tag: bmi

value: Never


title: Normal Human Astrocytes

description: miRNA expression data from normal human astrocyte cell line

value: not available


title: Taf5 anchor away, minus rapamycin, newly-synthesized RNA, replicate 1


title: Healthy Tissue 3

value: fresh frozen healthy brain tissue


title: Healthy Tissue from GBM 1


title: Healthy Tissue from GBM 4


title: Healthy Tissue 1


title: Glioblastoma Multiforme 15

value: Corpus Callosum (Splenium)

value: M


title: Glioblastoma Multiforme 16

description: Gene expression data from fresh frozen GBM tumor sample


title: Sample 795 (Baseline)

source_name: Plasma, before exercise

tag: diabetes

tag: hypertension

value: No

value: Caucasian


title: Glioblastoma Multiforme 14

value: Temporal neocortex


title: Taf5 anchor away, minus rapamycin, steady-state RNA, replicate 2

description: Gene expression steady-state RNA in a Taf5 anchor-away strain without exposure to rapamycin (control)

value: S. cerevisiae:MATalpha tor1-1; fpr1::NAT; RPL13A-2xFKB12::TRP1; TAF4-FRB::HYGRO

value: Total RNA


title: Glioblastoma Multiforme 15


title: Glioblastoma Multiforme 14


title: Glioblastoma Multiforme 13

value: Hipokampus (Limbik)


title: Sample 629 (Baseline)

value: Yes

tag: hyperlipidemia

tag: smoking


title: Glioblastoma Multiforme 9


title: Taf4 anchor away, plus rapamycin, newly-synthesized RNA, replicate 1

description: Gene expression nascent RNA in a Taf4 anchor-away strain after exposure to rapamycin

value: Newly-synthesized RNA

value: after exposure to rapamycin


title: Taf4 anchor away, plus rapamycin, steady-state RNA, replicate 2

description: Gene expression steady-state RNA in a Taf4 anchor-away strain after exposure to rapamycin


title: Taf4 anchor away, minus rapamycin, newly-synthesized RNA, replicate 2

description: Gene expression nascent RNA in a Taf4 anchor-away strain without exposure to rapamycin (control)

value: no exposure to rapamycin (control)


title: Taf4 anchor away, plus rapamycin, steady-state RNA, replicate 1


title: Glioblastoma Multiforme 11

value: Parietal Neocortex


title: Glioblastoma Multiforme 10

value: Frontal neocortex

value: fresh frozen GBM tumor


title: Sample 758 (Baseline)

tag: diuretic

tag: statin


title: Glioblastoma Multiforme 12

value: Occipital Neocortex

value: F


title: Sample 683 (Baseline)

value: Never

tag: race


title: Glioblastoma Multiforme 10

value: M


title: Glioblastoma Multiforme 11


title: Taf4 anchor away, minus rapamycin, newly-synthesized RNA, replicate 1

tag: genotype

tag: molecule


title: Sample 574 (Baseline)

value: No

value: Former


title: Glioblastoma Multiforme 12

tag: location


title: Sample 565 (Baseline)

value: Current

value: Caucasian


title: Taf4 anchor away, minus rapamycin, steady-state RNA, replicate 2

description: Gene expression steady-state RNA in a Taf4 anchor-away strain without exposure to rapamycin (control)

value: S. cerevisiae:MATalpha tor1-1; fpr1::NAT; RPL13A-2xFKB12::TRP1; TAF4-FRB::HYGRO

value: Total RNA

tag: treatment


title: Glioblastoma Multiforme 6

tag: gender


title: Glioblastoma Multiforme 8

value: İnsular (Limbik)

tag: sample type


title: Sample 774 (Baseline)


title: Taf4 anchor away, minus rapamycin, steady-state RNA, replicate 1

tag: parental strain


title: Glioblastoma Multiforme 7

value: Corpus Callosum (Splenium)


title: Glioblastoma Multiforme 13

value: Hipokampus (Limbik)


title: Sample 759 (Baseline)

value: Yes


title: Sample 561 (Baseline)


title: Sample 608 (Baseline)


title: Glioblastoma Multiforme 5

value: Temporal neocortex


title: Sample 536 (Baseline)


title: Glioblastoma Multiforme 4

value: Frontal neocortex


title: Taf5 anchor away, minus rapamycin, steady-state RNA, replicate 1

value: no exposure to rapamycin (control)


title: Taf4 anchor away, plus rapamycin, newly-synthesized RNA, replicate 2

value: Newly-synthesized RNA

value: after exposure to rapamycin


title: Glioblastoma Multiforme 9

value: fresh frozen GBM tumor


title: Glioblastoma Multiforme 7

value: M


title: Glioblastoma Multiforme 5

value: F


title: Glioblastoma Multiforme 3

value: Nucleus (Talamus)


title: Sample 526 (Baseline)

value: No

value: Former


title: Glioblastoma Multiforme 8


title: Glioblastoma Multiforme 6


title: Glioblastoma Multiforme 3


title: Sample 508 (Baseline)


title: Glioblastoma Multiforme 2


title: Glioblastoma Multiforme 1


title: Sample 461 (Baseline)

value: Never

value: Caucasian


title: Sample 459 (Baseline)


title: Sample 442 (Baseline)


title: Glioblastoma Multiforme 4


title: 03-2013_ISM vs IDAM-2weeks_rep2

city: Newark

first: G

middle: Marcela

last: Rodriguez

state: NJ

address: 225 Warren St

department: Public Health Research Institute

institute: Rutgers University

description: Experiment 3 Biological replicate 2 of 3

hyb_protocol: Prehybridization  1. Prepare Prehybridization Solution (Fresh Each Time) **this volume is based on a glass dish with a base measurement of 11x8cm. This dish allows for a pre-hyb of 1-4 slides. Adjust volume accordingly based on size of dish and/or number of slides. 106.0ml dH2O 3.0g BSA 1.2ml 10%SDS  2. Add Prehybridization solution to a glass slide-staining dish and place post-processed slides array side up into solution. Make sure there are no bubbles on the surfaces of the slides.  3. Place the staining jar containing the Prehybridization solution and slides into a waterbath and hybridize for 1 hour at 42oC.  4. Take the prehybridized slides out of the Prehybridization solution and place into a slide holder submerged in a slide-washing tray containing nuclease-free water. Wash slides for 2 minutes with constant shaking up and down.  5. Transfer slide rack to a slide washing tray containing isopropanol and wash for 2 minutes with constant shaking up and down.  6. Take the slides in the isopropanol bath to the centrifuge to keep the slides wet until you can dry them rapidly. Spin at 600 RPM in a 50ml conical for 3 minutes to dry. **Complete this step within one hour of hybridization  III. Hybridization  1. Add the following to the 5µl labeled sample. 0.5µl 10 mg/ml tRNA 1.0µl 20X SSC 2.5ul Formamide 1.0µl 1% SDS  2. Heat to 98 oC for 2 minutes. Spin in centrifuge for 1 min at 12,000 Xg. Let cool for 5 min.  3. Pipette cooled 10µl hybridization solution on microarray. Apply 22 x 22 coverslip to cover array (if bubbles appear under the cover slip, they will slowly migrate to the edges provided that the volume is accurate).  4. OPTIONAL: Apply thin wall of rubber cement around the 4 corners of the coverslip to avoid movement. This step is recommended if your waterbath is not perfectly level. 5. Hybridize in standard hyb. chambers with ~40µl water under each slide (20ul under both ends of each slide) overnight in 50oC water bath **Bubbles (esp. large ones) can be troublesome for your arrays since they can cause areas of non-hybridization. To avoid bubbles, do not use the blowout feature of the pipette when adding the probe to the slide. Also, clean your coverslips with alcohol and lint-free wipes before placing over probe.  IV. Post Hyb washes (next day)  1. Remove cover slip while array is submerged in first wash solution (2XSSC + 0.1% SDS), transfer to submerged microscope slide staining racks and rinse for 1 min in 1X SSC+0.05% SDS with agitation/shaking.  2. Rinse in 0.06X SSC with shaking. Transfer to another submerged staining rack and wash 2 min in fresh 0.06X SSC with shaking.  3. Centrifuge 3 min at 1000 rpm in a 50ml conical (array edge up) to dry. Scan immediately.

scan_protocol: After washing, the arrays were scanned with a GenePix4000B scanner (Molecular Devices, Sunnyvale, CA). The images were processed using GenePix Pro and the resulting text files were exported to Microsoft Excel.

data_processing: The chips were normalized using the global normalization option within Genepix Pro. The data were filtered by removing all spots that were below the background noise or flagged as ‘bad’. Spots were considered to be below the background noise if the sum of the median intensities of the two channels was less than twice the highest average background of the chip.

organism: Mycobacterium tuberculosis

source_name: Rv (Wild type Mycobacterium tuberculosis)

label_protocol: Synthesis and Labeling of cDNA  1. Bring 1.5µg of RNA to a volume of 11µl (in a PCR tube) with nucleotide-free water and add 2.2µl (2mg/ml) random primers (pulse spin to collect contents).  2. Heat 2 min at 98oC, snap cool on ice.  3. (Keep on ice) and add 11.1µl of the following reaction mix: 5.0µl 5X First-Strand buffer 2.5µl 100 mM DTT 2.3µl low dTdNTP mix (5mM A,G,C and 0.2mM T stock) 1.5ul Cy3 or Cy5 Then add 1.2ul Superscript, vortex to mix and spin to collect contents  4. Incubate 10 min at 25oC followed by 90 min at 42oC in PCR machine. **Can freeze or leave at 4oC overnight if necessary  5. Prime an Amicon Ultra 10K column with 400µl of 25% TE and spin for 5 min at 14,000 Xg.  Empty flow-through from collection tube and return primed column.  Add another 400ul of 25% TE followed by both reactions (cy3 and cy5) to column and centrifuge at 14,000 Xg for 7 min.  Empty flow-through, and add yet another 400ul of 25% TE, centrifuge at 14,000 Xg for 7 min.  Empty flow-through once more, add 400ul of 25% TE and centrifuge at 14,000 Xg for 12 min.  Empty the flow-through.  6. Recover cDNA by inverting Amicon filter into the same collection tube and centrifuge at 1,000 Xg for 2 min.  7. Using a speedvac, concentrate sample to 5ul.  The detailed labeling and hybridization protocol can be obtained at http://www.cag.icph.org/downloads_page.htm#LabelingProtocols.

growth_protocol: Mycobacterium tuberculosis was cultured in iron (Fe) depleted minimal medium (MM) for two passages and one passage in MM containing 50 micromolar deferoxamine (DFO). After  passage in MM-DFO cells were maintatined in the same medium or in medium withou DFO and supplemented with 50 micromolar Ferric Chloride.

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

treatment_protocol: Mycobacterium tuberculosis was treated with DFO or supplemented with Ferric chloride after two passages in MM and one in DFO.

tag: culture condition

value: Iron sufficiency

value: Iron depletion

tag: time

value: 2 weeks


title: 03-2013_ISM vs IDAM-2weeks_rep3

description: Experiment 3 Biological replicate 3 of 3


title: Glioblastoma Multiforme 2


title: 03-2013_ISM vs  IDAM-2weeks_rep1

description: Experiment 3 Biological replicate 1 of 3


title: 03-15-13_ISM vs IDAM-1week_rep3

value: 1 week


title: Sample 429 (Baseline)

tag: age

tag: bmi


title: Sample 387 (Baseline)

tag: diabetes

tag: hypertension

value: Yes


title: Sample 383 (Baseline)

tag: hyperlipidemia

tag: smoking


title: 03-15-13_ISM vs IDAM-1week_rep2


title: Glioblastoma Multiforme 1

value: Frontal neocortex


title: Sample 368 (Baseline)

tag: diuretic

tag: statin


title: Sample 378 (Baseline)

tag: race


title: Sample 493 (Baseline)


title: 03-15-13_ISM vs IDAM-1week_rep1


title: 03-15-13_ISM vs IDAM 1day_rep3

value: 1 day


title: Sample 617 (Baseline)


title: Sample 366 (Baseline)


title: 03-15-13_ISM vs IDAM 1day_rep1


title: 01-18-13_ISM vs IDAM1week_rep3

description: Experiment 2 Biological replicate 3 of 3


title: Sample 385 (Baseline)


title: Sample 356 (Baseline)


title: 01-18-13_ISM vs IDAM1week_rep2

description: Experiment 2 Biological replicate 2 of 3


title: Sample 348 (Baseline)


title: Sample 331 (Baseline)


title: Sample 322 (Baseline)


title: Sample 278 (Baseline)


title: 09-21-12_IDAM 1day vs IDAM1week_rep1

description: Experiment 1 Biological replicate 1 of 3


title: 03-15-13_ISM vs IDAM 1day_rep2


title: 01-18-13_ISM vs IDAM1week_rep1

description: Experiment 2 Biological replicate 1 of 3


title: 09-21-12_IDAM 1day vs IDAM1week_rep3

description: Experiment 1 Biological replicate 3 of 3


title: 09-21-12_IDAM 1day vs IDAM1week_rep2

description: Experiment 1 Biological replicate 2 of 3


title: 01-18-13_ISM vs IDAM 1day_rep2


title: Sample 267 (Baseline)


title: Sample 231 (Baseline)


title: Sample 257 (Baseline)

value: African American


title: 01-18-13_ISM vs IDAM 1day_rep3


title: 01-18-13_ISM vs IDAM 1day_rep1


title: 09-21-12_ISM vs IDAM2weeks_rep2


title: Sample 175 (Baseline)


title: Sample 167 (Baseline)


title: Sample 215 (Baseline)


title: Sample 212 (Baseline)


title: 09-19-12_ISM vs IDAM1week_rep1


title: 09-21-12_ISM vs IDAM2weeks_rep1


title: Sample 166 (Baseline)


title: 09-19-12_ISM vs IDAM1week_rep2


title: Sample 163 (Baseline)


title: Sample 259 (Baseline)

value: Current


title: Sample 157 (Baseline)


title: 09-19-12_IDAM 1  day vs ISM_rep3


title: 09-19-12_IDAM 1 day vs ISM_rep2


title: Sample 139 (Baseline)


title: 09-19-12_IDAM 1day vs ISM_rep1


title: 09-21-12_ISM vs IDAM2weeks_rep3


title: 09-19-12_ISM vs IDAM1week_rep3


title: Sample 127 (Baseline)


title: Sample 115 (Baseline)


title: Sample 82 (Baseline)


title: Sample 89 (Baseline)


title: Sample 92 (Baseline)


title: Sample 55 (Baseline)


title: Sample 81 (Baseline)


title: Col-0, biological rep3

city: Ames

first: Stephanie

middle: C

last: Morriss

state: Iowa

department: Biochemistry, Biophysics and Molecular Biology

institute: Iowa State University

description:
Col_3
Gene expression data from 10-day-old Col-0 seedlings.

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 hr at 45°C on Arabidopsis GeneChip ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Affymetrix® GeneChip® Command Console™ and Affymetrix® Expression Console™ Software using Robust Multichip Analysis.

source_name: 10-day-old Arabidopsis seedlings Col-0

label_protocol: Biotinylated amplified RNA (aRNA) was prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip® 3' IVT Express Kit, Affymetrix, part number 901229).

growth_protocol: Seedlings were grown on MS-agar for 10 days under light intensity of 120µmol/m2/s and a 16 hour light regime at 21°C.

extract_protocol: RNA was extracted from 50-100 µg of ground tissue using the Qiagen RNeasy plant mini kit according to the manufacturer's instructions. RNA was then treated with TURBO DNase (Life Technologies) to remove contaminating genomic DNA.

tag: ecotype/background

tag: genotype/variation

value: wild type

tag: tissue

value: seedling

value: 10 days


title: rns2-2, biological rep1

description:
rns2-2_1
Gene expression data from 10-day-old rns2-2 seedlings.

source_name: 10-day-old Arabidopsis seedlings rns2-2


title: Col-0, biological rep2

description:
Col_2
Gene expression data from 10-day-old Col-0 seedlings.


title: rns2-2, biological rep2

description:
rns2-2_2
Gene expression data from 10-day-old rns2-2 seedlings.


title: Col-0, biological rep1

description:
Col_1
Gene expression data from 10-day-old Col-0 seedlings.


title: Sample 39 (Baseline)


title: Sample 30 (Baseline)


title: rns2-2, biological rep3

description:
rns2-2_3
Gene expression data from 10-day-old rns2-2 seedlings.


title: Paced-induced HF Replicate 4

city: Singapore

first: Lee Lee

last: Wong

address: 14 Medical Drive, 08-01

department: Medicine

country: Singapore

institute: National University of Singapore

description: Biological replicate 4 of 4. HF, heart tissue harvested after 14 days of pacing at 225 bpm

hyb_protocol: The labeled samples were hybridized to the miRCURY LNATM microRNA array 7th Gen (Exiqon, Denmark), which contains probes targeting all microRNAs. The hybridisation was performef according to the miRCURY LNATM microRNA array instruction manual using a Tecan HS4800TM hybridization (Tecan, Austria).

scan_protocol: Scanned using Agilent G2565BA microarray scanner system (Agilent Technologies, Inc., USA) Images were quantified usingImaGene® 9 (miRCURY LNATM microRNA array analysis software, Exiqon, Denmark).

data_processing: Data were analyzed using ImaGene® 9 (miRCURY LNA™ microRNA Array Analysis Software, Exiqon, Denmark). Following background correction and Lowess (LOcally WEighted Scatterplot Smoothing) global normalization, the threshold for detected miRNA was 1.2 times above 25th percentile of the overall signal intensity (analysis performed using R/Bioconductor). To investigate miRNA regulation in HF and HF-R, miRNA intensity was log2 transformed. Those miRNAs which exhibited absolute fold changes ≥1.2 or ≤-1.2 with a p-value <0.05 (Student’s t-test) underwent further analysis using GeneSpring GX.

organism: Ovis aries

source_name: Left ventricular heart tissue

label_protocol: 500 ng RNA from sampleswere labeled with Hy3™ and Hy5™ fluorescent respectively (the miRCURY LNA™ miRNA Hi-Power Labeling Kit, Hy3™/Hy5™, Exiqon, Denmark) following the manufacturer’s protocol.

tag: strain

value: Coopworth ewes

tag: treatment

value: subjected to rapid LV pacing at ~220bpm for 13 days

source_name: Reference RNA sample

value: reference


title: HF Recovery Replicate 1

description: Biological replicate 1 of 3. HF-R, heart tissue harvasted after additional 14 days of dicontinuation of pacing

value: sampled 26 days following cessation of pacing

tag: sample type


title: HF Recovery Replicate 2

description: Biological replicate 2 of 3. HF-R, heart tissue harvasted after additional 14 days of dicontinuation of pacing


title: Sample 8 (Baseline)

value: No

value: Former

value: Caucasian


title: Paced-induced HF Replicate 3

description: Biological replicate 3 of 4. HF, heart tissue harvested after 14 days of pacing at 225 bpm


title: Sample 120 (Baseline)

value: Never


title: Sample 16 (Baseline)


title: Sample 109 (Baseline)


title: Paced-induced HF Replicate 1

description: Biological replicate 1 of 4. HF, heart tissue harvested after 14 days of pacing at 225 bpm


title: Paced-induced HF Replicate 2

description: Biological replicate 2 of 4. HF, heart tissue harvested after 14 days of pacing at 225 bpm


title: Normal Control Replicate 2

description: Biological replicate 2 of 2. Control sham, heart tissue harvested

value: No treatment


title: HF Recovery Replicate 3

description: Biological replicate 3 of 3. HF-R, heart tissue harvasted after additional 14 days of dicontinuation of pacing


title: Sample 6 (Baseline)


title: Sample 52 (Baseline)

value: Yes


title: Sample 46 (Baseline)


title: Normal Control Replicate 1

description: Biological replicate 1 of 2. Control sham, heart tissue harvested


title: Sample 1 (Baseline)


title: shRNA-H2A.Z.2 rep 1

status: Public on Sep 14 2017

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description:
251487920212-3
Gene expression from neurons treated with shRNA-H2A.Z.2 shRNA.

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

organism: Rattus norvegicus

source_name: Resting cortical dissociated neurons, shRNA-H2A.Z.2 shRNA

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer's protocol.

growth_protocol: Cells were grown in Neurobasal media supplemented with B27.

extract_protocol: RNA was extracted with the Qiagen RNeasy kit and columns and was DNase digested in column.

treatment_protocol: Cells were treated with lentiviruses for seven days and RNA was extracted.

tag: cell type

value: Cortical neurons

tag: shRNA

tag: time point

value: 7 days


title: ShRNA-H2A.Z.1 rep 2

description:
251487920213-1
Gene expression from neurons treated with ShRNA-H2A.Z.1 shRNA.

source_name: Resting cortical dissociated neurons, ShRNA-H2A.Z.1 shRNA


title: Sc_rep 4

description:
251487920538-2
Gene expression from neurons treated with Scrambled shRNA.

source_name: Resting cortical dissociated neurons, Scrambled shRNA

value: Scrambled


title: shRNA-H2A.Z.2 rep 2

description:
251487920213-2
Gene expression from neurons treated with shRNA-H2A.Z.2 shRNA.


title: ShRNA-H2A.Z.1 rep 4

description:
251487920538-3
Gene expression from neurons treated with ShRNA-H2A.Z.1 shRNA.


title: shRNA-H2A.Z.2 rep 4

description:
251487920538-4
Gene expression from neurons treated with shRNA-H2A.Z.2 shRNA.


title: BM-MSC PV 10950

city: Salamanca

first: Beatriz

middle: Roson

last: Burgo

address: Campus Miguel de Unamuno

department: Cancer Research Centre

institute: Consejo Superior de Investigaciones Científicas & Universidad de Salamanca

hyb_protocol: Affymetrix manufacture's protocol for Human Gene Chip Array 1.0 ST

data_processing:
Data was processed within R/Bioconductor, using affy package tools. justRMA normalization function was applied. Probeset sumarization into ENSEMBL genes (v57) was performed with the CDF genemapperhumangene1.0cdf_3.0 from GATExplorer (http://bioinfow.dep.usal.es/xgate/mapping/mapping.php?content=rprogram)
RMA signal estimates at gene level were calculated applying the unambiguous mapping of probes from GATExplorer (CDF probe to gene mappings tab-delimited-file: probes2genes-Human_Gene_1.0.txt available at http://bioinfow.dep.usal.es/xgate/mapping/mapping.php?content=downloads). Intensity values were processed within R – version 3.1.0 (CDF package genemapperhumangene1.0cdf_3.0)

source_name: BM-MSC PV

growth_protocol: Bone marrow mononuclear cells (BM-MNC) were isolated by density gradient centrifugation Ficoll-Paque (density: 1.077k GE Healthcare BioSciences) and were cultured in standard DMEM culture medium. Adherent cells were selected through three culture passages. Isolated BM-MSC were characterized fulfilling the minimal criteria established by the International Society for Cellular Therapy (ISCT).

extract_protocol: Total RNA from cultured populations was extracted using TRIzol reagent according to the manufactures’s instructions (Invitrogen).

treatment_protocol: No drug treatment applied

tag: subject status

value: myeloproliferative neoplasms (MPN) patient with JAK2V617F mutation; Polycythemia Vera (PV)

tag: subject id

tag: mutation

value: Bone marrow mononuclear cells (BM-MNC)


title: Sc_rep 2

description:
251487920212-4
Gene expression from neurons treated with Scrambled shRNA.


title: BM-MSC PV 10707

scan_protocol: Affymetrix manufacture's protocol for Human Gene Chip Array 1.0 ST


title: Sc_rep 3

description:
251487920213-3
Gene expression from neurons treated with Scrambled shRNA.


title: BM-MSC ET 10777

source_name: BM-MSC ET

label_protocol: Affymetrix manufacture's protocol for Human Gene Chip Array 1.0 ST

value: myeloproliferative neoplasms (MPN) patient with JAK2V617F mutation; Essential Thrombocythemia (ET)


title: BM-MSC PV 10714


title: BM-MSC CML 10833

source_name: BM-MSC CML

value: Chronic Myeloid Leukemia (CML) patients

value: Philadelphia Positive


title: BM-MSC CML 10500


title: BM-MSC Healthy Donor 10518

source_name: BM-MSC Healthy Donor

value: BM-MSC Healthy Donor; control

value: Healthy Donor 10518

value: Control


title: BM-MSC CML 10819


title: BM-MSC CML 10891


title: BM-MSC PV 10930


title: ShRNA-H2A.Z.1 rep 3

description:
251487920213-4
Gene expression from neurons treated with ShRNA-H2A.Z.1 shRNA.


title: BM-MSC ET 11023


title: BM-MSC ET 10901


title: BM-MSC CML 10720


title: BM-MSC CML 10969


title: BM-MSC Healthy Donor 10461

value: Healthy Donor 10461


title: ShRNA-H2A.Z.1 rep 1

description:
251487920212-2
Gene expression from neurons treated with ShRNA-H2A.Z.1 shRNA.


title: BM-MSC ET 10739


title: Sc_rep 1

description:
251487920212-1
Gene expression from neurons treated with Scrambled shRNA.


title: shRNA-H2A.Z.2 rep 3

description:
251487920538-1
Gene expression from neurons treated with shRNA-H2A.Z.2 shRNA.


title: BM-MSC Healthy Donor 10441

value: Healthy Donor 10441


title: BM-MSC Healthy Donor 10354

value: Healthy Donor 10354


title: BM-MSC Healthy Donor 10356

value: Healthy Donor 10356


title: BM-MSC Healthy Donor 10341

value: Healthy Donor 10341


title: BM-MSC Healthy Donor 10363

value: Healthy Donor 10363


title: BM-MSC Healthy Donor 10283

value: Healthy Donor 10283


title: mammary epithelial cells from lactating sow, 3 h post challenge with heat-inactivated E. coli [918_Pool_3 hpc]

first: Siriluck

last: Ponsuksili

address: Wilhelm-stahl-allee 2

institute: FBN

description:
918_Pool_3 hpc
miRNA expression data from mammary epithelial cells of lactating sow 3 hpc with E. coli

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42°C on Affymetrix GeneChip miRNA arrays. GeneChips were washed and processed to detect biotin-containing transcripts by Streptavidin-PE (Phycoerythrin) conjugate.

data_processing: Data were analysed with Expression Console and quantified by med polish

label_protocol: Biotinylated cRNA were prepared from miRNA according to FlashTag Biotin RNA Labeling Kit for Affymetrix GeneChip miRNA arrays (Genisphere, Hatfield, PA, USA) according to the manufacturer’s recommendations Affymetrix GeneChip miRNA Array protocols (Affymetrix, Santa Clara, CA, USA)

growth_protocol: Approximately 4.4 x 10^5 cells from each individual were seeded and cultured in collagen-coated 6-well plates. Cells were grown to a confluency of about 90% and then experiment started.

extract_protocol: Total RNA was isolated using Qiagen miReasy Mini kit TRI Reagent (Qiagen, Hilden, Germany) according to the manufacturer’s protocol for small-RNA. Then small RNA was cleaned up using the Rneasy MinElute Clean up kit  (Qiagen, Hilden, Germany).

treatment_protocol: Mammary epithelial cells from lactating sows were challenged for 3 h and for 24 h with heat-inactivated E. coli isolate from milk of PDS-positive sows. Unchallenged cells were carried as controls.

tag: developemental stage

value: lactating sow

value: porcine mammary epithelial cells

tag: challenged with

value: heat-inactivated E. coli

value: 3 h post challenge


title: BM-MSC Healthy Donor 10320

value: Healthy Donor 10320

value: Bone marrow mononuclear cells (BM-MNC)


title: mammary epithelial cells from lactating sow, 24 h post challenge with heat-inactivated E. coli [918_Pool_24 hpc]

description:
918_Pool_24 hpc
miRNA expression data from mammary epithelial cells of lactating sow 24 hpc with E. coli

value: 24 h post challenge


title: unchallenged mammary epithelial cells from lactating sow [378_Pool_0 hpc]

description:
378_Pool_0 hpc
miRNA expression data from mammary epithelial cells of lactating sow

value: none (control)


title: unchallenged mammary epithelial cells from lactating sow [918_Pool_0 hpc]

description:
918_Pool_0 hpc
miRNA expression data from mammary epithelial cells of lactating sow


title: unchallenged mammary epithelial cells from lactating sow [K_Pool_0 hpc]

description:
K_Pool_0 hpc
miRNA expression data from mammary epithelial cells of lactating sow


title: BM-MSC Healthy Donor 10265

value: BM-MSC Healthy Donor; control

value: Healthy Donor 10265


title: mammary epithelial cells from lactating sow, 24 h post challenge with heat-inactivated E. coli [K_Pool_24 hpc]

description:
K_Pool_24 hpc
miRNA expression data from mammary epithelial cells of lactating sow 24 hpc with E. coli


title: mammary epithelial cells from lactating sow, 3 h post challenge with heat-inactivated E. coli [378_Pool_3 hpc]

description:
378_Pool_3 hpc
miRNA expression data from mammary epithelial cells of lactating sow 3 hpc with E. coli


title: mammary epithelial cells from lactating sow, 24 h post challenge with heat-inactivated E. coli [378_Pool_24 hpc]

description:
378_Pool_24 hpc
miRNA expression data from mammary epithelial cells of lactating sow 24 hpc with E. coli


title: Heatstress_T1_38_S14

city: Riyadh

first: Musa

last: Gabere

address: Kashmalaan

department: Bioinformatics

country: Saudi Arabia

institute: King Abdullah International Medical Research Center,  NGHA

hyb_protocol: GeneChip Hybridization Wash and Stain Kit (cat # 900720) was procured from Affymetrix and used according to the manufacturer's protocol. The arrays were then washed using Affymetrix fluidics stations.

scan_protocol: The arrays were scanned.

data_processing:
Data processing using Expression Console Software. The default recommended settings by Expression Console were used to analyze the data.
Probe group file: hgu133plus.db

source_name: PBMCs, heat stress, 15 min after exposure

label_protocol: GeneChip® 3' IVT PLUS Reagent Kit (cat # 902416) was procured from Affymetrix and used according to the manufacturer's protocol.

extract_protocol: RNA was isolated from PBMC samples using the SV Total RNA Isolation System (Promega, USA) KiT according to manufacturer's protocol.

treatment_protocol: Heat stress.

value: Peripheral blood mononuclear cells (PBMCs)

value: Heat stress

value: 15 minutes after the exposure

tag: gender

value: Male

tag: age

tag: subject identifier


title: mammary epithelial cells from lactating sow, 3 h post challenge with heat-inactivated E. coli [K_Pool_3 hpc]

description:
K_Pool_3 hpc
miRNA expression data from mammary epithelial cells of lactating sow 3 hpc with E. coli


title: Heatstress_T0_98_S13

source_name: PBMCs, before heat stress exposure

value: Before exposed to heat stress

value: Female


title: Heatstress_T0_37_S14


title: Heatstress_T0_40_S15


title: Heatstress_T1_99_S13


title: Heatstress_T1_97_S12


title: Heatstress_T1_41_S15


title: Heatstress_T1_44_S11


title: Heatstress_T0_96_S12


title: Heatstress_T2_46_S12

source_name: PBMCs, heat stress, 1 hr after exposure

value: One hour after the exposure


title: Heatstress_T2_30_S13


title: Heatstress_T2_39_S14


title: Heatstress_T1_35_S10


title: Heatstress_T0_91_S11


title: Heatstress_T2_36_S10


title: Heatstress_T2_45_S11


title: Heatstress_T2_42_S15


title: Heatstress_T0_87_S9


title: Heatstress_T0_85_S8


title: Heatstress_T0_34_S10


title: Heatstress_T2_29_S9


title: Heatstress_T2_28_S7


title: Heatstress_T2_43_S8


title: Heatstress_T1_86_S8


title: Heatstress_T1_84_S7


title: Heatstress_T2_33_S6


title: Heatstress_T0_83_S7


title: Heatstress_T2_27_S5


title: Heatstress_T1_32_S6


title: Heatstress_T0_31_S6


title: Heatstress_T0_79_S5


title: Heatstress_T2_26_S4


title: sample.19.SP_post-S

city: Bedford Park

first: Damian

middle: James

last: Hussey

address: Flinders Drive

country: Australia

institute: Flinders University

data_processing:
Raw fluorescence data was processed using OpenArray® Real-Time qPCR Analysis Software (BioTrove™, version 1.0.4). Raw fluorescence data was exported in .csv file format for subsequent processing in R software.
The CSV files were imported into R software (3.1.0) and the fractional cycle (Ct) at which the second derivative maximum of a logistic curve fit to the raw fluorescence data was determined.  Any microRNA that had no Ct value for a particular sample was assigned the value of 40.
Mann Whitney U tests were used to generate lists of differentially expressed microRNAs in the comparison of control squamous tissues vs post-ablation neosquamous tissues, and for the comparison of post-ablation squamous tissues vs. post-ablation neosquamous tissues.  Significance was set at p<0.05.
False Discovery rates were estimated using the Benjamini-Hochberg procedure (Benjamini, Yoav; Hochberg, Yosef (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing (PDF). Journal of the Royal Statistical Society, Series B. 57 (1): 289–300.)
Fold Change worksheet reports the the ratios of normalized relative expression levels.

label: FAMTM

source_name: post-S

label_protocol: PCR assays were performed by following the protocol for TaqMan@OpenArray Human MicroRNA Panel (4461104, Life technologies). 45 ng of RNA was used in the reverse transciption reaction for each sample. Megaplex Primer pools, Human Pools set v3.0 was used in the assay.

extract_protocol: After the biopsies were thawed and extra RNAlater@ solution removed,  the samples were homogenized in 500 ul TRIzol@ Reagent (Invitrogen, Carlsbad, CA, USA) and the manufacturer's protocol was followed to extract RNA. The RNA concentration was determined using the Biophotometer.

treatment_protocol: Musocal biopsy samples were collected from patients with Barrett's oesophagus or healthy controls. After collection, they were immediately stored in RNAlater® solution (Ambion, Austin, Texas, USA) as  the manufacturer’s protocol indicated

value: patients with Barrett's oesophagus who underwent APC ablation of their Barrett's mucosa

value: post-ablation Proximal squamous mucosa

tag: percentage of barrett's at 3-5 years

tag: molecule subtype

value: microRNA


title: Heatstress_T1_88_S9


title: Heatstress_T1_80_S5


title: sample.20.SP_post-S

tag: tissue


title: sample.20.B_pre-BE

source_name: pre-BE

value: pre-ablation Barrett's mucosa


title: sample.20.NS_post-NS

source_name: post-NS

value: Neo squamous oesophageal mucosa taken at 4-6 weeks post Argon plasma coagulation ablation of Barrett's oesophagus

value: Neo squamous > 5% Barrett's at 3-5 years


title: sample.19.NS_post-NS

value: Neo squamous < 5% Barrett's at 3-5 years


title: Heatstress_T0_75_S4


title: sample.15.NS_post-NS


title: sample.15.B_pre-BE


title: sample.14.SP_post-S


title: Heatstress_T1_74_S3


title: Heatstress_T2_25_S3


title: Heatstress_T1_76_S4


title: Heatstress_T2_72_S2


title: Heatstress_T0_73_S3


title: Heatstress_T1_48_S2


title: sample.14.NS_post-NS


title: sample.14.B_pre-BE


title: sample.13.NS_post-NS

value: Neo squamous oesophageal mucosa at 4-6 weeks post Argon plasma coagulation ablation of Barrett's oesophagus


title: sample.13.SP_post-S


title: sample.19.B_pre-BE


title: sample.13.B_pre-BE


title: sample.12.NS_post-NS


title: sample.12.SP_post-S


title: sample.12.B_pre-BE


title: Heatstress_T0_47_S2


title: sample.11.NS_post-NS


title: sample.11.SP_post-S


title: Heatstress_T2_71_S1


title: Heatstress_T0_77_S1


title: sample.11.B_pre-BE


title: sample.10.SP_post-S


title: sample.10.B_pre-BE


title: sample.10.NS_post-NS


title: sample.8.SP_post-S


title: sample.9.B_pre-BE


title: sample.9.NS_post-NS


title: sample.9.SP_post-S


title: Heatstress_T1_78_S1


title: sample.8.NS_post-NS


title: sample.8.B_pre-BE


title: sample34,non-canceroustissue,male

city: Shanghai

first: Zhuoan

last: Cheng

address: No.25/Ln2200 Xie-Tu Road

institute: Shanghai Cancer Insitute

description: Gene expression data from the corresponding non-cancerous  tissue

hyb_protocol: Following fragmentation, 10 ug of cRNA werewere prehybridized to U133A arrays at 45C for 60 minutes and then hybridized for 16 to 18 hours in a rotisserie oven at 60g.

scan_protocol: The arrays were scanned using the GeneArray scanner (Affymetrix).

data_processing: Data analysis was done using Affymetrix GeneChip 5.0 software.

source_name: The corresponding non-cancerous tissues

label_protocol: Labeled cRNA was generated from the cDNA sample by an in vitro transcription reaction that was supplemented with biotin-11-CTP and biotin-16-UTP (Enzo, Farmingdale, NY, via Affymetrix Enzo BioArray High-Yield Transcript Labeling kits) for 6 hours at 37jC in a PCR machine with no shaking. All of the labeled cRNA were purified using Affymetrix GeneChip Sample Cleanup module.

value: liver

tag: hbsag

value: positive

tag: tumor size


title: sample36,non-canceroustissue,male


title: sample32,non-canceroustissue,male


title: sample29,cancertissue,female

description: Gene expression data from the hepatocellular carcinoma  tissue

source_name: The hepatocellular carcinoma tissues


title: sample33,cancertissue,male


title: sample30,non-canceroustissue,female


title: sample.7.B_pre-BE


title: sample31,cancertissue,male


title: sample35,cancertissue,male


title: sample.7.NS_post-NS


title: sample.5.B_pre-BE


title: sample.6.SP_post-S


title: sample.6.B_pre-BE


title: sample.4.B_pre-BE


title: sample.4.SP_post-S


title: sample.4.NS_post-NS

value: Neo squamous oesophageal mucosa


title: sample.3.SP_post-S


title: sample.3.B_pre-BE


title: sample28,non-canceroustissue,female

value: negative


title: sample.2.NS_post-NS


title: sample.2.B_pre-BE

value: pre-ablation Barrett's oesophagus mucosa


title: sample.2.SP_post-S


title: sample.5.NS_post-NS


title: sample27,cancertissue,female


title: sample25,cancertissue,female


title: sample.3.NS_post-NS


title: sample.1.SP_post-S


title: sample23,cancertissue,female

value: 10*12 at left lateral lobe and 3*2 at right lobe


title: sample.1.NS_post-NS

value: Neo squamous oesophageal mucosa taken at 4-6 weeks post argon plasma coagulation ablation of Barrett's oesophagus


title: sample.34_control-S

source_name: control-S

value: healthy donor

value: Oesophageal squamous mucosa


title: sample.32_control-S


title: sample21,cancertissue,female

value: Female


title: sample24,non-canceroustissue,female


title: sample.29.repeat_control-S


title: sample.28_control-S


title: sample26,non-canceroustissue,female


title: sample.27_control-S


title: sample.26_control-S


title: sample.25_control-S


title: sample.23_control-S


title: sample.33_control-S


title: sample22,non-canceroustissue,female


title: sample4,non-canceroustissue,male

value: Male


title: sample2,non-canceroustissue,male


title: sample18,non-canceroustissue,male


title: sample16,non-canceroustissue,male


title: sample15,cancertissue,male


title: sample12,non-canceroustissue,male


title: sample5,cancertissue,male


title: sample1,cancertissue,male


title: sample6,non-canceroustissue,male


title: sample3,cancertissue,male


title: sample17,cancertissue,male


title: sample11,cancertissue,male


title: controle_ileum_92

first: Ingrid

last: Arijs

address: Herestraat 49

department: Clinical and Experimental Medicine

institute: KULeuven

description: Biopsy from normal ileal mucosa of control individual

hyb_protocol: After fragmentation of DNA, labeled DNA was hybridized for 16h at 45°C on Affymetrix Human Gene 1.0 ST arrays.

scan_protocol: The arrays were washed and stained in a fluidics station using the GeneChip hybridization, Wash end Stain kit (Affymetrix) and scanned using the Affymetrix 3000 GeneScanner.

data_processing: Probe level analysis was performed on the Affymetrix raw data (.cel files) with the robust multichip average (RMA) method implemented in the Bioconductor package 'aroma.affymetrix' to obtain a log2 expression value for each gene probe set

label_protocol: Biotin-labeled single-stranded DNA was synthesized using the Affymetrix GeneChip WT terminal Labeling kit (Affymetrix), according to manufacturer's instructions.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Benelux B.V.), according to the manufacturer’s instructions.

value: ileum

tag: disease

value: control

tag: disease activity

value: normal


title: controle_ileum_91

source_name: Biopsy from normal ileal mucosa of control individual


title: Hu761

city: La Jolla

first: Sunil

last: Kurian

state: CA

address: 10550 N Torrey Pines Road

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

description: SAMPLE 59

hyb_protocol: Standard Affymetrix 49 Format Hybridization with 15mg of fragmented cRNA

scan_protocol: Affymetrix EukGE-WS2v4

data_processing: RMAExpress

label: SAPE

source_name: Human Islet Cells

label_protocol: Ambion MessageAmp Biotin II Enhanced

growth_protocol: Islets frozen in RNA Later

extract_protocol: RNA was extracted using Trizol and purified on RNeasy Columns

tag: diabetes reversal status

value: Yes

value: pancreas

tag: cell type

value: islet cells


title: controle_ileum_95


title: Hu751

description: SAMPLE 56

value: No


title: controle_ileum_97


title: Hu749

description: SAMPLE 55


title: controle_ileum_89


title: Hu752

description: SAMPLE 57


title: controle_ileum_93


title: controle_ileum_96


title: controle_ileum_94


title: sample.24_control-S

tag: subject status

value: microRNA


title: controle_ileum_90


title: controle_ileum_87


title: CD_ileum_inactive_75

description: Biopsy from uninflamed ileal mucosa of inactive CD patient

value: CD

value: inactive


title: Hu748

description: SAMPLE 54


title: CD_ileum_inactive_74

source_name: Biopsy from uninflamed ileal mucosa of inactive CD patient


title: CD_ileum_inactive_70


title: controle_ileum_88


title: Hu747

description: SAMPLE 53


title: CD_ileum_inactive_68


title: Hu743

description: SAMPLE 51


title: CD_ileum_inactive_66


title: CD_ileum_inactive_72


title: CD_ileum_inactive_71


title: CD_ileum_inactive_69


title: CD_ileum_inactive_73


title: CD_ileum_active_59

description: Biopsy from inflamed ileal mucosa of active CD patient

value: active


title: Hu759

description: SAMPLE 58


title: Hu742

description: SAMPLE 50


title: CD_ileum_inactive_64


title: CD_ileum_inactive_65


title: Hu746

description: SAMPLE 52


title: CD_ileum_inactive_67


title: CD_ileum_inactive_63


title: CD_ileum_inactive_62


title: Hu741

description: SAMPLE 49


title: Hu739

description: SAMPLE 48


title: CD_ileum_active_58

source_name: Biopsy from inflamed ileal mucosa of active CD patient


title: Hu733

description: SAMPLE 47


title: CD_ileum_inactive_61


title: CD_ileum_active_54


title: CD_ileum_inactive_60


title: CD_ileum_active_56


title: sample.7.SP_post-S

value: patients with Barrett's oesophagus who underwent APC ablation of their Barrett's mucosa

value: post-ablation Proximal squamous mucosa


title: Hu731

description: SAMPLE 46


title: CD_ileum_active_57


title: CD_ileum_active_55


title: Hu719

description: SAMPLE 45


title: Hu718

description: SAMPLE 44


title: CD_ileum_active_51


title: CD_ileum_active_50


title: CD_ileum_active_52


title: Hu703

description: SAMPLE 43


title: Hu700

description: SAMPLE 42


title: CD_ileum_active_53


title: Hu694

description: SAMPLE 41


title: CD_ileum_active_49


title: Hu690

description: SAMPLE 39


title: CD_ileum_active_47


title: CD_ileum_active_45


title: CD_ileum_active_40


title: CD_ileum_active_41


title: CD_ileum_active_38


title: Hu691

description: SAMPLE 40


title: CD_ileum_active_37


title: CD_ileum_active_39


title: CD_ileum_active_42


title: Hu684

description: SAMPLE 36


title: Hu688

description: SAMPLE 38


title: Hu682

description: SAMPLE 35


title: CD_ileum_active_34


title: Hu687

description: SAMPLE 37


title: CD_ileum_active_43


title: CD_ileum_active_36