title: Mouse colon epithelium DSS 1

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: colonic epithelial cells

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: Eight-week-old C57BL/6 mice were purchased from CLEA Japan.

extract_protocol: RNA extraction of  cells was performed according to the manufacturer’s instructions by ISOGEN2

treatment_protocol: 2.5% dextran sulfate sodium (DSS) was added to the drinking water for 5 days.

tag: agent

value: 2.5% dextran sulfate sodium (DSS)

tag: strain

value: 8 week old


title: liver_UK_T2_rep1

status: Public on Jan 23 2016

type: RNA

city: Dummerstorf

first: Constance

last: Nebendahl

address: Wilhelm-Stahl Allee 2

country: Germany

institute: Leibniz Institute for Farm Animal Biology

description: after 3-week feed restriction period, d 97

hyb_protocol: The Agilent Gene Expression Hybridization Kit was used to hybridize Cy3-labelled cRNA on oligonucleotide microarrays according to the manufacturer´s instructions and protocol (Agilent One-Color Microarray-Based Gene Expression Analysis)

scan_protocol: Arrays were scanned on an Agilent Microarray scanner with the use of software tools such as Agilent Feature Extraction version 10.5.1.1. and the scan software Agilent Scan control.

data_processing: The normalisation method selected for this experiment is quantile normalization. After performing normalization all gene expression values lower than 0% quantile were set to the value of this 0% quantile (2.438216375 for this experiment) to eliminate low level signals beeing too much scattered to be used in a reproducible analysis.

molecule: total RNA

organism: Sus scrofa

source_name: liver, low birth weight, control, T2

label_protocol: Cy3-labelled cRNA was prepared according to the manufacturer´s instructions (Agilent Quick Amp Labeling Kit, One Color Agilent, 5190-0442).

growth_protocol: Overall, piglets from one litter were selected for low (0.8-1.1 kg, U) or normal (1.4-1.6 kg, N) birth weight. From birth until weaning at day 28, U and N piglets were suckled by their dams with no creep feed. After weaning, piglets were housed individually and had free access to water and food. Feed intake was determined daily and body weights were monitored at weekly intervals. Different diets were administered during the study period to achieve or to exceed the nutrient intake recommendations for growing pigs (GfE (Gesellschaft für Ernährungsphysiologie, 2006). Thus, after weaning period, piglets were fed a diet containing a mixture of 50% (w/w) commercial pig feed, 30% rolled oats and 20% sucrose with a total energy and crude protein content of 16.3 MJ ME/kg.

extract_protocol: Total RNA was isolated with Triazol reagent (Qiazol, Qiagen, Germany) according to the manufacturer's instructions.

treatment_protocol: From day 76  until day 97 half of the U and N pigs were subjected to feed restriction (50% of ad libitum consumption) of a conventional pig diet (13.6 MJ ME/kg). Subsequently, both restricted (UR, NR) and control groups (UK, NK) were subjected to ad libitum feeding until day 131 (14.1 MJ ME/kg).

tag: gender

value: female

tag: development stage

value: adolescent

tag: group

value: UK

tag: time point


title: liver_NK_T3_rep1

description: after 5-week refeeding period, d 103

source_name: liver, normal birth weight, control, T3

value: NK

value: after 5-week refeeding period, d 103


title: liver_UK_T2_rep2

value: after 3-week feed restriction period, d 97


title: 2533.Scalp

type: genomic

city: Baltimore

first: Andrew

last: Jaffe

state: MD

address: 855 N Wolfe St, Ste 300

department: Clinical Sciences

country: USA

institute: Lieber Institute for Brain Development

description: Cultured human fibroblast sample on the Illumina 450k

hyb_protocol: Following manufacturer's protocol

scan_protocol: Following manufacturer's protocol

data_processing: idat files were read in using the minfi Bioconductor package and processed using the preprocessQuantile approach

molecule: genomic DNA

organism: Homo sapiens

source_name: Scalp fibroblast

label_protocol: Following manufacturer's protocol

growth_protocol: Scalp and Dura Tissue Cultures: The dura culture medium was prepared out of 1X DMEM (Ref#11960-044, GIBCO) with 10% by volume fetal bovine serum, 2% by volume 100X GlutaMAX (Cat#: 35050, GIBCO), 1% by volume Penicillin-Streptomycin/Amphotercin solution (Ref# 15140-122, GIBCO), and 1% by volume Gentamicin solution (Cat# 17105-041, Quality Biological). This culture medium was used in all subsequent steps of the dura culturing procedure. The scalp culture medium used for all subsequent steps of the scalp culturing procedure was made the same way except without the 1% Gentamycin. A rinsing solution was prepared out of 1X PBS (pH 7.2) (Ref# 21-040-CV, Corning Life Sciences), 1% by volume Penicillin-Streptomycin/Amphotericin solution (Ref# 15140-122, GIBCO), and 1% by volume Gentamicin (Cat# 17105-041, Quality Biological). The dissected scalp sample was washed with the rinsing solution three times, the fat tissues were cut away, and all hair was plucked out with forceps. The scalp sample was then placed epidermis side down on a dish and floated with Dispase II enzyme solution (2.4 units of the Dispase II enzyme per mL of PBS, Dispase II enzyme: Cat#17105-041, GIBCO). The dish was covered with parafilm and foil, and placed in a 37oC incubator for 24 hours. After the 24-hour period, the epidermis was peeled away from the dermis. The dermis was washed with the rinsing solution, dried, and cut into 2-3 mm2 pieces. The pieces were placed in a Falcon Easy Grip tissue culture 35×10 mm dish and one drop of scalp culture medium was added to each piece of scalp. The dish was placed in the incubator at 37oC and 5% CO2 for culturing. A similar procedure was followed for the dura samples. Dura samples were washed with the rinsing solution three times. Then, a few 2-3 mm2 pieces were cut from the dura mater and placed together in an Easy Grip cell culture 35×10 mm dish. One drop of dura culture medium was added to each dura piece. The culture dish was then placed in an incubator (at 37oC and 5% CO2) for culturing. The medium of each culture was changed to fresh medium 2-3 times per week to promote growth of the fibroblasts. On average, fibroblast cells started to proliferate at 7-14 days, however some samples took longer (up to 3 weeks).   Fibroblast Cell Cultures: The dura and scalp tissue cultures were monitored under a phase-contrast microscope. When the fibroblast growth reached 90-95% confluence, 1 mL of a 0.25% trypsin solution (Cat#T4049, Sigma) was added to each culture dish, and the cells were incubated for 5 to 8 min. Then, 1mL of media was added to each dish stop the enzymatic reaction. Next, the contents of each culture dish were transferred into separate 15 mL Falcon conical tubes and 8mL of media was added to each tube. The conical tubes were centrifuged for 5 min at 1100 rpm. The supernatant was discarded, 5mL of fresh media was added to each conical tube, and the contents of the tubes were transferred onto separate 25 cm3 cell culture Easy Flasks (Thermo Scientific, Cat# 156367), where they were kept in cultures for 3-5 days in an incubator (at 37oC and 5% CO2). When the cells reached 90-95% confluence, the cells from each 25 cm3 flask were transferred onto two 75 cm3 cell culture easy flasks (Thermo Scientific, Cat# 156499) and kept in cultures for continued growth. When the cells reached 90-95% confluence, they were incubated with 3 mL of 0.25% trypsin solution for 5 to 8 min, after which 3mL of fresh culture media was added to stop the enzymatic reaction. Then, the contents of the flasks were transferred into separate 15 mL Falcon conical tube and 4mL of media was added to each tube. The tubes were centrifuged (5 min, 1100 rpm), the supernatant was discarded and the pellets containing the fibroblasts were removed from the centrifuge tubes and transferred to cryoTube vials (Cat#375418, Thermo Scientific). 0.5 mL of recovery cell culture freezing medium (Cat#12648-010, GIBCO) was added to each vial, after which the vials were insulated with Styrofoam and placed into a -80oC freezer. Later, the tubes were transferred to a -152oC liquid nitrogen freezer. These frozen dura and scalp fibroblast cells were then used generate DNA methylation data.

extract_protocol: Genomic DNA was extracted from approximately 3 million cultured human fibroblast cells using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen)

treatment_protocol: Bisulfite conversion of 600 ng genomic DNA was performed with the EZ DNA methylation kit (Zymo Research)

tag: age

tag: Sex

value: M

tag: race

value: Cauc

tag: cell line

value: fibroblast


title: 2540.Dura

source_name: Dura mater fibroblast


title: 2385.Scalp

value: AA


title: 2435.Scalp


title: liver_NR_T2_rep3

source_name: liver, normal birth weight, restriction, T2

value: NR


title: 5008.Scalp


title: 5008.Dura


title: 2520.Dura


title: Huh7 KO#45

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: JMJD5 deficient Huh7 (#45) cells established by CRISPR/Cas9 system

hyb_protocol: Before hybridization, 600 ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 5µm resolution using a DNA microarray laser scanner (Agilent Technologies).

scan_protocol: The array was scanned using Agilent G2505C DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction, LOWESS normalization, and dye-normalization .

label_protocol: 200 ng of total RNA was labeled using Low Input Quick-Amp Labeling Kit (Agilent Technologies, Pato Alto, CA, USA). In brief, cDNA was reverse transcribed from 100 ng of total RNA with an oligo-dT-T7 promoter primer and AffinityScript MT -RT. Fluorescent antisense cRNA was synthesized with cyanine 3-CTP (Cy3-CTP), and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with miRNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent Technologies).

extract_protocol: Total RNAs were extracted using miRNeasy extraction kit (Qiagen) following manufacturer's instructions.

tag: cell type

value: JMJD5KOHuh7 #45 cells


title: 2540.Scalp


title: 2385.Dura


title: Mouse colon epithelium control

organism: Mus musculus

value: control


title: 5054.Dura

value: F


title: Huh7

description: Huh7 hepatoma cell line

source_name: Huh7 hepatoma cell line

value: Huh7 cells


title: liver_NR_T2_rep2


title: 2328.Dura


title: 2371.Scalp


title: 5054.Scalp


title: 2520.Scalp


title: 2468.Dura


title: 2371.Dura


title: OE19b

city: Rotterdam

first: Erik

last: Wiemer

address: Wytemaweg 80

department: Medical Oncology

country: Netherlands

institute: Erasmus University Medical Center

hyb_protocol: Fluorescently labeled RNA was hybridized to custom Exiqon LNA capture probes (based on miRBase version 10, annotation version 13), spotted in duplicate on Nexterion E glass slides, for 16 hours at 60°C in a Tecan HS4800 hybridization station. The capture probe set consists of 1344 probes of which 725 are capable of detecting human miRNAs.

scan_protocol: After hybridization, samples were washed and scanned using a Tecan LS Reloaded scanner. Image generation and feature extraction were performed using Imagene 6.0.

data_processing: The raw microRNA expression data, median signal minus median background, were normalized using quantile normalization. Obvious outliers were removed and human miRNAs were selected with an average expression above background. Duplicate spots on the array were averaged. Comparison between cell lines were assessed using Student's t test.

source_name: oesophageal cancer cell line OE19

label_protocol: 1 μg of total RNA of each separate cell line sample was labelled with CY3 using the ULS™ aRNA Labeling Kit (Kreatech Diagnostics, the Netherlands)

growth_protocol: OE19, OE21 and OE33 were cultured in RPMI 1640 medium, KYSE450 cells were cultured in a 1:1 mixture of RPMI 1640 and F12 HAMS medium. All culture media were supllemnetd with 10% fotal calf serum and 1% penicillin/Streptomycin. Cells were grown at 37°C, 5% CO2 in a humidified atmosphere.

extract_protocol: Total RNA was extracted from cell pellets using RNABee (BioConnect, the Netherlands) according to the manufacturer's instructions. All samples passed RNA quality control using Nanodrop 2000. MicroRNA profiling was performed as previously described (Pothof J. et al. 2009 / van Jaarsveld M.T.M. et al. 2013)

treatment_protocol: Cells were harvested by trypsinisation using standdard tissue culture procedures. Cell pellets were frozen at -80°C for storage.


title: OE19a


title: OE19p


title: Huh7 KO#47

description: JMJD5 deficient Huh7 (#47) cells established by CRISPR/Cas9 system

value: JMJD5KOHuh7 #47 cells


title: KYSEp

source_name: oesophageal cancer cell line KYSE450


title: liver_U_T1_rep1

description: before feed restriction period, d 76

source_name: liver, low birth weight, T1

value: U

value: before feed restriction period, d 76


title: liver_NK_T2_rep2

source_name: liver, normal birth weight, control, T2

value: female

value: adolescent


title: liver_N_T1_rep1

description: before feed restriction period, d 76

source_name: liver, normal birth weight, T1

value: N


title: genetic line: Parent (winter type) - temperature: 20 C - rep3

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description: Barley Seedlings germinated on filter paper for 5 days at 20 degrees. (May still include original submitter created erros/discrepancies)

hyb_protocol: Affymetrix Basic Protocol

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization was performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org, Version: 2.12.1). The target value is 500 for all cases. The code was developed using R2.4.1 to 2.13.0, Bioconductor 1.9 to 2.12.1, and simpleaffy 2.8.0. to 2.28.0 The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html.

label: biotin

organism: Hordeum vulgare

source_name: whole plant (genetic line: Parent (winter type) - temperature: 20 C)

label_protocol: Affymetrix one-cycle target labeling

extract_protocol: Pine tree extraction method (Chang et al 1993)

tag: genetic line

value: Parent (winter type)

tag: treatment

tag: germplasm name

value: Dairokkaku

tag: tissue

value: whole plant ('PO:0000003')

value: 0 germination ('PO:0007057')

value: 5 days

tag: growth media

value: 3MM filter paper


title: liver_N_T1_rep3

description: before feed restriction period, d 76


title: liver_U_T1_rep2

description: before feed restriction period, d 76


title: genetic line: Parent (winter type) - temperature: 20 C - rep1


title: genetic line: +FT1/VRN3 - temperature: 4 C - rep3

description: Barley Seedlings germinated on filter paper for 5 days at 20 degrees then exposed to 4 degrees for one day (24 hours, starting and ending at noon) (May still include original submitter created erros/discrepancies)

source_name: whole plant (genetic line: +FT1/VRN3 - temperature: 4 C)

value: 4 C


title: liver_U_T1_rep3

description: before feed restriction period, d 76


title: KYSEb


title: liver_N_T1_rep2

description: before feed restriction period, d 76


title: genetic line: +FT1/VRN3 - temperature: 4 C - rep1


title: liver_NK_T2_rep1

value: NK

value: after 3-week feed restriction period, d 97


title: genetic line: Parent (winter type) - temperature: 4 C - rep1

source_name: whole plant (genetic line: Parent (winter type) - temperature: 4 C)


title: genetic line: +FT1/VRN3 - temperature: 4 C - rep2


title: genetic line: Parent (winter type) - temperature: 4 C - rep2


title: KYSEa


title: genetic line: Parent (winter type) - temperature: 4 C - rep3


title: OE21p

source_name: oesophageal cancer cell line OE21


title: OE21b


title: genetic line: +FT1/VRN3 - temperature: 20 C - rep3

source_name: whole plant (genetic line: +FT1/VRN3 - temperature: 20 C)


title: genetic line: +FT1/VRN3 - temperature: 20 C - rep2


title: OE33p

source_name: oesophageal cancer cell line OE33


title: liver_NK_T2_rep3


title: OE33b


title: genetic line: +FT1/VRN3 - temperature: 20 C - rep1


title: genetic line: +VRN1-8 - temperature: 4 C - rep2

source_name: whole plant (genetic line: +VRN1-8 - temperature: 4 C)


title: OE21a


title: OE33a


title: Genistein diet_Denervated treatment

city: Bunkyo-ku

first: Shinya

last: Aoyama

state: Tokyo

department: Applied Biological Chemistry

institute: University of Tokyo

hyb_protocol: Fragmentation and hybridization were performed using the GeneChip 3’ IVT express kit (Affymetrix, Santa Clara, CA, USA) according to the manifucture’s instructions.

scan_protocol: Fluorescence signals were scanned with the Affymetrix GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Array images were analyzed with the GeneChip Operating Software (GCOS version 1.1, Affymetrix) to obtain the gene expression ratios between the denervated control and the sham control, as well as those

organism: Rattus norvegicus

source_name: Denervation-treated soleus muscle fed genistein diet

label_protocol: Biotinylated aRNA were prepared using the GeneChip 3’ IVT express kit (Affymetrix, Santa Clara, CA, USA) according to the manifucture’s instructions.

growth_protocol: Rats and mice (as described below) were obtained from Charles River Japan (Tokyo) and housed individually in animal cages in a room maintained at 23±2°C and humidity (50±10%) on a 12-h light (0800–2000)/dark cycle. They were allowed free access to their diet and water.

extract_protocol: Ten days after the operation, the soleus muscle, gastrocnemius muscle and tibialis anterior muscle were collected, weighed, snap-frozen in liquid nitrogen and stored at −80°C until further analysis.

treatment_protocol: 10-week old male Wistar rats were divided into two groups (n=8 each) with equal mean body weights. The control group (CON) was fed a modified AIN-93G diet in which the soybean oil was replaced with corn oil. The genistein group (GEN) was fed an AIN-93G diet containing genistein (0.5 g/kg diet; LC Laboratories, Woburn, MA) for 24 days. On day 14, muscle atrophy was induced by excising the sciatic nerve in the left leg of the rat, and sham surgery was performed for the right leg of each rat during the same operation.

value: Wistar rat

value: male

value: 14 weeks old

tag: diet

value: diet containing 0.05% genistein

tag: treatment group

value: Denervated

value: soleus muslce


title: liver_NR_T2_rep1

value: female

value: adolescent

value: NR


title: genetic line: +VRN1-8 - temperature: 20 C - rep3

source_name: whole plant (genetic line: +VRN1-8 - temperature: 20 C)

value: Dairokkaku


title: P21 CP, rep 2

city: Sioux Falls

first: Haotian

last: Zhao

state: SD

address: 2301 E. 60th St. North

department: Children's Health Research Center

institute: Sanford Research

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: WT_P21 CP

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

extract_protocol: RNA was extracted with Trizol reagent , followed by clean-up and DNase I treatment with PureLink RNA Mini Kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: strain background

tag: genotype/variation

value: wild type

value: hindbrain choroid plexus (CP)


title: genetic line: +VRN1-8 - temperature: 4 C - rep3

value: whole plant ('PO:0000003')

tag: development stage

value: 0 germination ('PO:0007057')

value: 5 days


title: genetic line: -VRN2 - temperature: 4 C - rep3

description: Barley Seedlings germinated on filter paper for 5 days at 20 degrees then exposed to 4 degrees fro one day (24 hours, starting and ending at noon) (May still include original submitter created erros/discrepancies)

source_name: whole plant (genetic line: -VRN2 - temperature: 4 C)

value: 4 C

value: 3MM filter paper


title: genetic line: +VRN1-8 - temperature: 4 C - rep1


title: GBM BT TIMs

city: Houston

first: Amy

middle: B

last: Heimberger

state: TX

address: 1400 Holcombe Blvd., FC7.2000

department: Neurosurgery

institute: The University of Texas MD Anderson Cancer Center

description:
tissue myeloid cells
Each .gpr file represents a technical replicate of the same RNA hybridized onto an independent array.

hyb_protocol: Hybridization amount started from 2.5 μg total RNA and followed the Phalanx Human Whole Genome OneArray  v5.1 Pre-Hybridization/Hybridization protocol.

scan_protocol: The arrays were scanned with a GenePix 4000B (Molecular Devices) according to the manufacturer's instruction.   Signal in the 532/Cy3 channel in the raw data files is due to the scanner use of both channels during scanning despite the fact these arrays were hybridized solely with Cy5-labeled probes.

data_processing: Foreground values of target probes were imported from GPR files and the control probes were deleted. Intensities were normalized between arrays using the median scaling method in the LIMMA R package. The mean log2-transformed intensities of three technical replicates was calculated for each probe and this value was used in all further downstream analyses.

source_name: GBM BT TIMs

label_protocol: According the the manufacturer's protocol.

extract_protocol: Tumors were washed in RPMI medium and dissected to remove blood products and surrounding non-tumor brain tissue. The total tissue was broken down into smaller pieces and digested for 2 hours using a cancer cell isolation kit (Panomics). We have further refined our glioma-infiltrating macrophage isolation protocol by performing CD11b+ MACS positive selection after Percoll gradient centrifugation to achieve over 90% purity (Hussain SF et al. Neuro Oncol. 2006). The cells were suspended in RNAlater solution (Ambion, Austin, TX) in RNase-free tubes and stored at 4ºC overnight; after 24 hours, they were transferred to -20ºC until needed for total RNA extraction. Extraction was performed using the mirVana kit (Ambion), according to the manufacturer's instructions. Once extracted, RNA levels were analyzed for concentrations and purity using NanoDrop 2000 at 230, 260, and 280 nm.

value: tumor-infiltrating macrophages

tag: diagnosis

value: GBM


title: genetic line: +VRN1-8 - temperature: 20 C - rep1


title: GBM CD TIMs

source_name: GBM CD TIMs


title: genetic line: +VRN1-8 - temperature: 20 C - rep2


title: Control diet_Denervated treatment

source_name: Denervation-treated soleus muscle fed control diet

tag: strain

value: Wistar rat

tag: gender

value: male

value: 14 weeks old

value: control diet

value: sham-treated


title: genetic line: -VRN2 - temperature: 4 C - rep2

tag: age


title: P21 CP, rep 3


title: Genistein diet_Sham treatment

source_name: Sham-treated soleus muscle fed genistein diet

value: diet containing 0.05% genistein

value: Denervated

value: soleus muslce


title: P21 CP tumor, rep 3

source_name: Math1-cre;Rosa26-NICD1_P21 CP tumor

value: hindbrain choroid plexus (CP) tumors


title: genetic line: -VRN2 - temperature: 4 C - rep1

value: Dairokkaku


title: genetic line: -VRN2 - temperature: 20 C - rep3

source_name: whole plant (genetic line: -VRN2 - temperature: 20 C)

value: whole plant ('PO:0000003')


title: GBM PL TIMs

source_name: GBM PL TIMs


title: Control diet_Sham tretment

source_name: Sham-treated soleus muscle fed control diet


title: P21 CP, rep 1

value: wild type

value: hindbrain choroid plexus (CP)


title: P21 CP tumor, rep 1


title: GBM BT monocytes

description:
monocytes
Each .gpr file represents a technical replicate of the same RNA hybridized onto an independent array.

source_name: GBM BT monocytes

extract_protocol: The peripheral monocytes from GBM patients were purified based on the same Ficoll-Hypaque density gradient and anti-CD14 microbeads protocol as from the healthy donors. The purity and viability of cells were >90%. The cells were suspended in RNAlater solution (Ambion, Austin, TX) in RNase-free tubes and stored at 4ºC overnight; after 24 hours, they were transferred to -20ºC until needed for total RNA extraction. Extraction was performed using the mirVana kit (Ambion), according to the manufacturer's instructions. Once extracted, RNA levels were analyzed for concentrations and purity using NanoDrop 2000 at 230, 260, and 280 nm.

value: monocytes


title: genetic line: -VRN2 - temperature: 20 C - rep2

value: 0 germination ('PO:0007057')

value: 5 days

value: 3MM filter paper


title: genetic line: -VRN2 - temperature: 20 C - rep1


title: GBM MW TIMs

source_name: GBM MW TIMs

value: tumor-infiltrating macrophages

value: GBM


title: P0 CP, rep 3

source_name: WT_P0 CP


title: P21 CP tumor, rep 2


title: GBM PL monocytes

source_name: GBM PL monocytes


title: GBM CD monocytes

source_name: GBM CD monocytes


title: genetic line: +VRN1-10 - temperature: 4 C - rep3

source_name: whole plant (genetic line: +VRN1-10 - temperature: 4 C)

value: 4 C


title: GBM MW monocytes

source_name: GBM MW monocytes


title: P0 CP tumor, rep 3

source_name: Math1-cre;Rosa26-NICD1_P0 CP tumor


title: P0 CP, rep 2


title: Healthy donor monocytes 3

source_name: Healthy donor monocytes 3

value: healthy


title: P0 CP tumor, rep 2


title: Healthy donor monocytes 2

source_name: Healthy donor monocytes 2


title: P0 CP tumor, rep 1


title: genetic line: +VRN1-10 - temperature: 20 C - rep1

source_name: whole plant (genetic line: +VRN1-10 - temperature: 20 C)


title: genetic line: +VRN1-10 - temperature: 20 C - rep3


title: Healthy donor monocytes 4

source_name: Healthy donor monocytes 4


title: genetic line: Parent (winter type) - temperature: 20 C - rep2

source_name: whole plant (genetic line: Parent (winter type) - temperature: 20 C)

value: Parent (winter type)


title: genetic line: +VRN1-10 - temperature: 20 C - rep2


title: Healthy donor monocytes 1

source_name: Healthy donor monocytes 1


title: P0 CP, rep 1


title: genetic line: +VRN1-10 - temperature: 4 C - rep1


title: genetic line: +VRN1-10 - temperature: 4 C - rep2


title: PK-9

status: Public on Jan 22 2016

city: Yufu

first: Naoki

last: Hijiya

state: Oita

address: 1-1, Idaigaoka Hasama-machi

department: Medicine

institute: Oita University

description: Genomic DNA was extracted from tissues of normal renal cortex obtained from 12 patients with ureteral or renal pelvic carcinoma, neither of which exhibited invasion or metastasis to the renal cortex. The same amount of genomic DNA extracted from 12 patients was mixed and used as the control DNA.

hyb_protocol: Dissolved in hybridization buffer (Agilent Oligo aCGH Hybridization Kit; Agilent Technologies), denatured and hybridized to the CGH array at 65℃ for 24 h

scan_protocol: A microarray was scanned using Microarray acanner (Agilrny Technologies) at a pixel resolution size of 5μm

data_processing: Microarray images were analyzed using FEATURE EXTRACTION v. 9.1 (Agilent Technologies) with linear normalization protocol CGH-v4_91 (Case 1-12) or CGH-v4_95_Feb07 (Case 14, 16-20, 22-31 and 40), and the resulting data were imported into DNA Analytics v. 3.4 (Agilent Technologies). After normalization of the raw data, the log2ratio of Cy5 (cancer) to Cy3 (control) was calculated. Next, aberrant regions were determined using the ADM-2 algorithm at a threshold of 8.0. To detect gains and losses, we set the values of parameters for the aberration filters as: minimum number of probes in region 2, minimum absolute average log2ratio for region 0.3, maximum number of aberrant regions 10,000, and percentage penetrance per feature 0. We set the value of the minimum absolute average log2 ratio at 0.3 to detect regions showing a change in the averaged copy number of more than 1.23-fold (log2(1.23) = 0.3).

source_name: Pancreatic cancer cell line

label_protocol: Agilent Genomic DNA Labeling Kit Plus(Agilent)

extract_protocol: Standard proteinase K-digestion method

source_name: mixed genomic DNA of normal renal cortex : FFPE sample

value: male


title: KP-1-NL


title: TCC-Pan2


title: PK-1


title: PANC-1


title: PK-45H


title: AsPC-1

description: Genomic DNA of human peripheral blood mononuclear cells from 8-healthy donors was prepared. The same amount of genomic DNA extracted from 8 donors was mixed and used as the control DNA.

source_name: mixed genomic DNA of human peripheral blood mononuclear cells


title: PK-59


title: KP4-1


title: MIA Paca2

value: MIA Paca2


title: BxPC-3


title: SUIT-2


title: PK-9 [expression]

description: Cultured in accordance with the supplier's instructions. Total RNA for expression analysis was extracted using an RNeasy Mini kit (Qiagen).

hyb_protocol: Gene Expression Hybridization kit was used for hybridization in accordance with the manufacture's instructions (Agilent Technologies).

scan_protocol: Microarray images were obtained by using a laser confocal scanner G2565BA (Agilent Technologies).

data_processing:
Feature Extraction software (Version 9.1, Agilent Technologies) with the manufacturer’s recommended settings was applied for the microarray image analysis. Analysis of the microarray images was performed with Genespring 7.3.1 Software (Agilent Technologies).
The signal intensities of probe set data were median-normalized per chip, followed by filtering based on signal intensity and flagged values.The genes downregulated due to loss at 8p11.22-ter were identified using following filters: locating at 8p11.22-ter, showing more than two-fold increasing normalized data in cell lines without loss at 8p11.22-ter compared with those with loss at 8p11.22-ter, and showing more than 1,000 of raw data in cell lines without loss at 8p11.22-ter.

label_protocol: Cy3-labeled cRNA targets were generated using Quick Amp Labeling Kit, one-color (Agilent Technologies).

growth_protocol: All cell lines were cultured in accordance with the supplier's instructions.

tag: 8p status

value: with 8p loss


title: PK-45H [expression]

extract_protocol: Total RNA for expression analysis was extracted using an RNeasy Mini kit (Qiagen).

value: without 8p loss

tag: cell line


title: Rice seedlings roots Cd Replicate 2

city: Tainan City

first: Chung-Yi

last: Lin

address: No.1, University Road

country: Taiwan

institute: National Cheng Kung University

description: Biological replicate 2 of 3. Rice seedling roots treated with 25 μM Cd

hyb_protocol: Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent Rice Oligo 4×44K Microarray (Agilent Technologies, USA) at 60°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3 and 625 nm for Cy5. Scanned images are analyzed by Feature extraction software 9.5.3 (Agilent Technologies, USA).

data_processing: An image analysis and normalization software is used to quantify signal and background intensity for each feature, substantially normalized the data by rank-consistency-filtering LOWESS method.

organism: Oryza sativa

source_name: Roots of rice seedlings were exposed to  25μM Cd

label_protocol: 0.5 μg of total RNA was amplified by a Fluorescent Linear Amplification Kit (Agilent Technologies, USA) and labeled with Cy3-CTP or Cy5-CTP (CyDye, PerkinElmer, USA) during the in vitro transcription process. Sample RNA was labeled by Cy5 and RNA from control RNA was labeled by Cy3. 0.825 μg of Cy-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer (Agilent Technologies, USA) at 60℃ for 30 minutes.

growth_protocol: 6-day-old seedlings

extract_protocol: Total RNA were extracted using QIAGEN RNeasy kit follwed by DNAse treatment. The RNA samples were further purified and concentrated by RNeasy MinElute Cleanup.

treatment_protocol: Rice roots exposed to  5μM Cu and 25μM Cd

value: cadmium

value: 6 day

tag: cultivar

value: root

source_name: Rice seedlings roots were exposed to water

value: water


title: PK-1 [expression]


title: Rice seedlings roots Cd Replicate 3

description: Biological replicate 3 of 3. Rice seedling roots treated with 25 μM Cd


title: AsPC-1 [expression]


title: KP-1-NL [expression]


title: TCC-Pan2 [expression]


title: PANC-1 [expression]


title: Rice seedlings roots Cu Replicate 1

description: Biological replicate 1 of 3. Rice seedling roots treated with 5 μM Cu

source_name: Roots of rice seedlings were exposed to 5μM Cu

value: copper


title: Rice seedlings roots Cd Replicate 1

description: Biological replicate 1 of 3. Rice seedling roots treated with 25 μM Cd


title: Rice seedlings roots Cu Replicate 3

description: Biological replicate 3 of 3. Rice seedling roots treated with 5 μM Cu


title: BxPC-3 [expression]


title: MIA Paca2 [expression]


title: KP4-1 [expression]


title: Rice seedlings roots Cu Replicate 2

description: Biological replicate 2 of 3. Rice seedling roots treated with 5 μM Cu


title: SUIT-2 [expression]


title: human embryoid body_BMP4 treated_6days_rep3

city: Seoul

first: Hyung-Min

last: Chung

address: 120 Neungdong-ro, Gwangjin-gu

department: Department of Medicine

country: South Korea

institute: Konkuk university school of medicine

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each mouse-6 expression bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA).   Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual.

scan_protocol: Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions.

data_processing: Raw data were extracted using the software provided by the manufacturer(Illumina BeadStudio (Gene Expression Module). Array data were filtered by detection p-value < 0.05 (similar to signal to noise) in at least 50% samples (we applied a filtering criterion for data analysis; higher signal value was required to obtain a detection p-value < 0.05). Selected probe signal value was transformed by logarithm and normalized by quantile method. The comparative analysis between test group and control group was carried out using one-way ANOVA test and fold-change. False discovery rate (FDR) was controlled by adjusting p value using Benjamini-Hochberg algorithm.

source_name: human embryonic stem cell

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions.

growth_protocol: The undifferentiated hESC cell line H9 was cultured according to protocols from WiCell Research Institute. As we have previously reported, hESCs cell line H9 was cultured on mouse embryonic fibroblasts (MEFs) feeder layers in DMEM/F-12 medium supplemented with 20% knockout serum replacement, 1 mM glutamine, 0.1 mM β-mercaptoethanol, 0.1 mM nonessential amino acids, and 4 ng/ml human recombinant bFGF (all supplements were purchased from Invitrogen Corporation, USA) at 37°C in 5% CO2 and 95% humidity. For EB formation, hESCs were detached from feeder cells by dispase (Invitrogen, Carlsbad, CA, USA), and were suspended in DMEM/F12 medium supplemented with 10% SR, 1 mM L-glutamine, 1% penicillin-streptomycin, 1% nonessential amino acids, 0.1 mM mercaptoethanol, and 40 nM Bone morphogenetic protein 4 (BMP4, R&D Systems, Minneapolis, MN, USA). On day 6, hEBs were dissociated with Tryp-LE (Invitrogen, USA), and were plated onto collagen coated plates at 1 x 105 cells/ ml in EGM2-MV (Lonza, San Diego, CA) for one day. The medium was changed the next day in order to discard non-adherent cells, and the adherent cells were passaged upon reaching confluency.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol.


title: human embryonic stem cell derived perivascular progenitor cell_experiment_rep2


title: human embryonic stem cell derived perivascular progenitor cell_experiment_rep1


title: human embryoid body_BMP4 treated_6days_rep2


title: PK-59 [expression]


title: human embryonic stem cell derived perivascular progenitor cell_experiment_rep3


title: human embryonic stem cell_control_rep1


title: HUVEC_1

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

description: Replicate 1

hyb_protocol: Samples were hybridized to Illumina Human HT-12 V4.0 arrays following the manufacturer's instructions.

scan_protocol: Illumina Human HT-12 V4.0 arrays were scanned using an Illumina iScan system following the manufacturer's instructions.

data_processing: Arrays were processed using the Bioconductor beadarray package. Data were background corrected using the negative control probes and then quantile normalized, using the neqc function in the Bioconductor limma package. Background corrected and normalized data were then log2 transformed.

source_name: Human umbilical vein endothelial cells

label_protocol: Samples were processed for hybridization to Illumina HumanHT-12 V4.0 arrays following the manufacturer's instructions.

growth_protocol: Human kidney microvascular cells were purified from either fetal kidneys between 100 and 135 days post conception or adult kidney biopsies with normal kidney function. The fetal kidneys at that stage exhibit established nephron microstructures, including glomeruli, tubules and interstitia and begin to produce urine. To purify these human kidney peritubular microvascular endothelial cells (hKMECs), we first used flow cytometric analysis to identify the cell population. Fetal and adult kidney tissues were processed mechanically, followed by enzymatic dissociation and sieving through a strainer to remove glomeruli and large vessels, to obtain a single cell suspension. The endothelial cell population was identified as CD31+CD45-, and accounted for 1.67 ± % of cells in fetal kidney tissues, and 0.77 ± % in adults.

extract_protocol: Total RNA was extracted from endothelial, stromal and epithelial cells cultured in 12-well dishes using RNasy kit (Qiagen).

treatment_protocol: After sorting, the purified cells were immediately cultured in conditions favoring endothelial cell growth for up to three passages. Isolated hKMECs from both fetal and adult tissue formed sheets in 2D culture with consistent expression of CD31 and VE Cadherin at cell-cell contacts.

value: umbilical cord

tag: cell type

value: umbilical vein endothelial cells


title: human embryonic stem cell_control_rep3


title: FHK8_Endo_1

description: Replicate 1

source_name: Human kidney microvascular cells

value: kidney

value: kidney microvascular cells


title: HUVEC_2

description: Replicate 2


title: FHK8_Endo_2

description: Replicate 2


title: HUVEC_3

description: Replicate 3


title: FHK8_Endo_3

description: Replicate 3


title: Rat prostate_intraperitoneal injection of STZ_rep 3

city: guangzhou

first: li

last: jun

state: guangdong

address: Tianhe District Tianhe Road, No. 600

country: China

institute: The third affiliated hospital of sun YAT-SEN University

hyb_protocol: 12.5 ul of Hy3-labelled sample mixed with 2×Hybridization buffer and Nuclease-free Buffer in a reaction volume of 180 ul was Prepare the hybridization mix in a PCR tube.Load the 180ul target hybridization mix into the hybridization assembly through the sample loading opening .Place the hybridization assembly into a 56℃ oven and set it on a rotator at 2 rotations per minute (RPM) for overnight.After hybridization, disassembled the hybridization assembly, and wash the slides at 56℃ for 2min. using Wash buffer A.Wash for 2min. at room temperature in Wash buffer B and C.Wash briefly in water.Dry the slides by centrifugation for 5 min. at 200* g(1000rpm).

scan_protocol: Slides were scanned immediately after washing on  the Axon GenePix 4000B microarray scanner.

data_processing: GenePix pro V6.0 is used to read the raw intensity of the image.The intensity of green signal is calculated after background subtraction and four Replicated spots of each probe on the same slide have been averaged. Median Normalization Method was used to obtain 'Normalized Data', Normalized Data= (Foreground-Background)/median, the median is 50 percent quantile of microRNA intensity which is larger than 50 in all samples after background correction.After normalization, the statistical significance of differentially expressed miRNA was analyzed by T-test.Unsupervised hierarchical clustering and Correlation analysis was performed on miRNA data.

label_protocol: Hy3™ labeled cRNA was prepared from 1 ug RNA using the miRCURYTM Array Power Labeling kit (Cat #208032-A, Exiqon) according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer

growth_protocol: The rats were housed in polycarbonate cages in a controlled environment, with an illumination schedule of 12 h light/12 h dark.

extract_protocol: RNA was prepared using the trizol® Reagent (Invitrogen life technologies) following the manufacturer's recommendations.  The protocol includes differential lysis of C33A、CASKI、HELA and SIHA cells, and RNasey Mini Kit(Qiagen p/n 74104). RNA quantification and quality control used a NanoDrop-1000 spectrophotometer .

treatment_protocol: Diabetic condition was induced by a single intraperitoneal injection of STZ (60 mg/kg (Sigma), dissolved in an ice-cold 0.1M citrate buffer). STZ is a widely used N-nitroso derivative of D-glucosamine, which functions as a toxin that selectively destroys the insulin-producing cells of the pancreas, rendering the rat diabetic within 24 h of injection. Blood glucose levels were monitored to confirm the presence of diabetes (blood glucose＞300 mg/dl). Control rats were injected with citrate buffers only. After 4 weeks, rats in both groups were killed by pentobarbital (60 mg, intraperitoneal). The ventral lobe of the prostate from each rat was dissected immediately.Each tissue block was cut into two parts, with one-half used for pathological examination (morphological and immunohistochemical analysis) and the other half for molecular analysis (microarray and real-time PCR detection),which were kept frozen at -80℃ until they were microdissected.

value: Sprague Dawley

tag: weight

tag: injected with

value: STZ (60 mg/kg)

tag: sample group

value: Hyperglycaemic

value: prostate


title: Rat prostate_intraperitoneal injection of citrate buffers_rep 3

value: male

value: citrate buffer

value: control

tag: tissue


title: Rat prostate_intraperitoneal injection of STZ_rep 1


title: GP07034-ND-C

city: New York

first: Yongzhong

state: New York

address: 1470 Madison Avenue btw. 101st and 102nd Streets

department: Genetics

institute: Mount Sinai Medical Center

description: subcutaneous adipose tissue

data_processing: Raw expression intensity was background subtracted and normalized by the average normalization algorithm as implemented in GenomeStudio Gene Expression Module v1.0 application software (Illumina). Normalized data were used for further analysis. Data for 17,434 probes annotated as an Entrez gene and with a detection p-value of ≤0.01 in 90% of the samples were used for final analysis.

source_name: subcutaneous adipose tissue

extract_protocol: Total RNA was isolated from whole adipose tissue using the RNAeasy Lipid Tissue Mini kit (QIAGEN Inc-USA, Valencia, CA). The quantity and quality of the isolated total RNA samples were determined by ultraviolet spectrophotometry (Nanodrop, Thermo Scientific, Pittsburgh, PA) and electrophoresis (Experion nucleic acid analyzer, BioRad Laboratories, Inc., Hercules, CA), respectively. High-quality RNA with RIN (RNA integrity number) >8 was used for genome-wide transcriptome analysis.

value: subcutaneous adipose tissue

tag: ethnicity

value: Caucasian

value: Female


title: GP07053-ND-C

description: subcutaneous adipose tissue


title: GP08074-ND-C

description: subcutaneous adipose tissue

value: Male


title: Rat prostate_intraperitoneal injection of STZ_rep 2


title: GP07019-ND-C

description: subcutaneous adipose tissue


title: GP09007-ND-C

description: subcutaneous adipose tissue


title: GP03127-ND-C

description: subcutaneous adipose tissue


title: Rat prostate_intraperitoneal injection of citrate buffers_rep 2


title: GP08084-ND-C

description: subcutaneous adipose tissue


title: GP03211-ND-C

description: subcutaneous adipose tissue


title: Rat prostate_intraperitoneal injection of citrate buffers_rep 1


title: human embryoid body_BMP4 treated_6days_rep1


title: GP08086-ND-A

description: subcutaneous adipose tissue

value: African


title: GP09024-ND-A

description: subcutaneous adipose tissue


title: GP06075-ND-C

description: subcutaneous adipose tissue


title: GP06024-ND-C

description: subcutaneous adipose tissue


title: GP08043-ND-C

description: subcutaneous adipose tissue


title: GP07048-ND-A

description: subcutaneous adipose tissue


title: human embryonic stem cell_control_rep2


title: GP06015-ND-C

description: subcutaneous adipose tissue


title: GP09012-ND-A

description: subcutaneous adipose tissue


title: GP06063-ND-A

description: subcutaneous adipose tissue


title: Primary human hepatocytes (cryopreserved), biological rep1

city: Cambridge

first: Derek

last: Peters

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

hyb_protocol: Hybridization to Affymetrix U219 gene expression arrays was perfrormed according to manufacturer's instructions

scan_protocol: Arrays were scanned and converted into GeneChip probe result files (CEL) using Affymetrix Expression Console software.

data_processing: Data were processed using Affymetrix Transcriptome Analysis Console software and using Bioconductor in R

label_protocol: Biotinylated complementary DNA was prepared according to manufacturer's instructions (Affymetrix)

extract_protocol: Total RNA from each human cell type was extracted with Trizol (Invitrogen) and purified using the Clean & Concentrator-5 kit (Zymo Research).


title: GP08079-ND-C

description: subcutaneous adipose tissue


title: GP09014-ND-C

description: subcutaneous adipose tissue


title: GP08089-ND-A

description: subcutaneous adipose tissue


title: GP06032-ND-C

description: subcutaneous adipose tissue


title: GP07036-ND-C

description: subcutaneous adipose tissue


title: Primary human hepatocytes (cryopreserved), biological rep2


title: GP06004-ND-A

description: subcutaneous adipose tissue


title: iPS ASGR1+ cells, biological rep1

source_name: FACS-isolated ASGR1+ HLCs differentiated from hiPSCs

value: iPS ASGR1+ cells


title: GP06094-ND-C

description: subcutaneous adipose tissue


title: iPS ASGR1+ cells, biological rep2


title: HUES9 HLCs, biological rep1

source_name: HLCs differentiated from HUES9 hESCs

value: HUES9 HLCs


title: GP08023-ND-C

description: subcutaneous adipose tissue


title: GP07011-ND-C

description: subcutaneous adipose tissue


title: iPS HLCs, biological rep2

source_name: HLCs differentiated from hiPSCs

value: iPS HLCs


title: GP08020-ND-C

description: subcutaneous adipose tissue


title: HUES9 HLCs, biological rep2


title: iPS HLCs, biological rep1


title: HUES9 ASGR1+ cells, biological rep2

source_name: FACS-isolated ASGR1+ HLCs differentiated from HUES9 hESCs

value: HUES9 ASGR1+ cells


title: GP08009-ND-A

description: subcutaneous adipose tissue


title: HepG2 hepatoma cells, biological rep1

source_name: HepG2 hepatoma cells

value: HepG2 hepatoma cells


title: HepG2 hepatoma cells, biological rep2


title: T-42_E_4_S

city: Barcelona

first: Maria Rosa

last: Faner

state: Barcelona

address: C/Casanova 143, planta 2A,

department: Cellex

country: Spain

institute: Fundació Privada Clinic

description: former smoker

hyb_protocol: Hybridization was performed with GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc) according to manufactures instructions

scan_protocol: GeneChips were scanned using the GeneChip®Scanner 3000 7G (Affymetrix Inc).

data_processing: Raw expression measures were summarized after background correction and normalization steps using the rma methodology in the affy package from the Bioconductor project.

source_name: Lung tissue from COPD patient

label_protocol:
cRNA amplification and biotin labeling was synthesized from 150 ng total RNA by means of cDNA synthesis followed by an in vitro transcription reaction in the presence of T7 RNA Polymerase and biotinylated nucleotide analog/ribonucleotide mix  (3'IVT Express Kit, Affymetrix Inc, Santa Clara, CA)
Biotin-labeled cRNA was cleanup and quantified with magnetic beads and subsequently fragmented.

extract_protocol: RNA later presserved tissue, RNA extracted with miRNeasy Mini Kit, Quigen

tag: emphysema

value: YES

tag: gold stage

value: Lung


title: T-30_E_4_S

description: former smoker


title: GP08087-ND-C

description: subcutaneous adipose tissue


title: GP08065-ND-C

description: subcutaneous adipose tissue


title: GP04103-ND-C

description: subcutaneous adipose tissue


title: T-32_E_3_S

description: former smoker


title: GP06005-ND-C

description: subcutaneous adipose tissue


title: GP08008-ND-A

description: subcutaneous adipose tissue


title: HUES9 ASGR1+ cells, biological rep1


title: GP07046-ND-A

description: subcutaneous adipose tissue


title: GP06055-ND-C

description: subcutaneous adipose tissue


title: T-31_E_4_S

description: former smoker


title: GP06049-ND-C

description: subcutaneous adipose tissue


title: GP06011-ND-C

description: subcutaneous adipose tissue


title: 81_NE_2_S

description: former smoker

value: NO


title: GP08083-ND-A

description: subcutaneous adipose tissue


title: 87_NE_3_L

description: former smoker


title: GP09031-ND-A

description: subcutaneous adipose tissue


title: 85D_E_2_S

description: former smoker


title: 83_NE_2_L

description: former smoker


title: GP06076-ND-C

description: subcutaneous adipose tissue


title: 80_NE_2_N

description: former smoker


title: 8_NE_2_L

description: former smoker


title: GP07033-ND-C

description: subcutaneous adipose tissue


title: GP06023-ND-A

description: subcutaneous adipose tissue


title: 79_NE_2_S

description: former smoker


title: GP07041-ND-A

description: subcutaneous adipose tissue


title: GP06018-ND-A

description: subcutaneous adipose tissue


title: 75_NE_2_L

description: former smoker


title: 73_E_2_L

description: former smoker


title: 68_E_2_L

description: former smoker


title: GP01162-ND-C

description: subcutaneous adipose tissue


title: GP06008-ND-A

description: subcutaneous adipose tissue


title: 74_NE_2_L

description: former smoker


title: GP02254-ND-C

description: subcutaneous adipose tissue


title: 67_NE_1_N

description: former smoker


title: 71_NE_2_L

description: former smoker


title: GP08000-ND-C

description: subcutaneous adipose tissue


title: GP06082-ND-A

description: subcutaneous adipose tissue


title: GP06090-ND-C

description: subcutaneous adipose tissue


title: 64_NE_2_L

description: former smoker


title: 65_NE_2_L

description: former smoker


title: GP09004-ND-C

description: subcutaneous adipose tissue


title: 61_E_1_L

description: former smoker


title: GP08021-ND-C

description: subcutaneous adipose tissue


title: GP06096-ND-A

description: subcutaneous adipose tissue


title: 62_NE_2_N

description: former smoker


title: GP07016-ND-C

description: subcutaneous adipose tissue


title: GP08011-ND-C

description: subcutaneous adipose tissue


title: 55_E_2_S

description: former smoker


title: 60_E_2_L

description: former smoker


title: 58_E_2_L

description: former smoker


title: 59_NE_2_N

description: former smoker


title: 56_E_2_L

description: former smoker


title: GP05089-ND-C

description: subcutaneous adipose tissue


title: GP07003-ND-C

description: subcutaneous adipose tissue


title: 51_NE_2_L

description: former smoker


title: GP08003-ND-A

description: subcutaneous adipose tissue


title: 66_NE_1_N

description: former smoker


title: GP06069-ND-C

description: subcutaneous adipose tissue


title: 54_E_1_L

description: former smoker


title: 53_E_2_L

description: former smoker


title: 52_E_2_L

description: former smoker


title: 57_E_1_L

description: former smoker


title: Diffuse Large B Cell Lymphoma normal sample 84

city: Salamanca

first: Elena

last: Sebastián

address: Paseo de San Vicente

department: Hematology

institute: Hospital Universitario de Salamnca

hyb_protocol: Affymetrix Genome-Wide Human SNP 6.0 Array

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

data_processing: Gains and losses were evaluated with visual inspection by 2 different observers using Nexus Biodiscovery software (Biodiscovery, El Segundo, CA, USA). The CNAs with a minimum size of 100kb were considered real. Loss of heterozigosity regions where considered when size was >5Mb. CNAs were considered germinal CNAs by analyzing the corresponding constitutional DNA of each sample. In cases in which normal DNA was not available, alterations were cross checked in copy number variation database (http://dgv.tcag.ca/dgv/app/). Physiological deletions of the immunoglobulin heavy and light chain loci (IGH@14q32, IGK@2p11, and IGL@22q11.22) were excluded from the analysis. Results on both arrays were integrated in a unique database.

label: Biotin

source_name: NORMAL, Diffuse Large B Cell Lymphoma sample

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Tumor DNA was extracted from diagnostic samples. High-molecular weight (HMW) DNA from fresh samples was isolated using the DNAzol reagent (MRC, Cincinnati, OH, USA). DNA extraction on formalin-fixed paraffin-embedded (FFPE) tissue was done with the RecoverAll™ Total Nucleic Acid Isolation Kit (AmbionInc-Applied Biosystems, Foster City, CA, USA) or QuickExtract™ FFPE DNA Extraction Kit (Epicenter Biotechnologies, Madison, WI, USA). DNA from non-tumoral matched samples was isolated using DNAzolor theMagNA Pure LC system (Roche Diagnostics GmbH, Mannheim, Germany).

value: Diffuse large B cell lymphoma de novo

tag: type of sample

value: Normal sample


title: GP09027-ND-C

description: subcutaneous adipose tissue


title: GP07030-ND-A

description: subcutaneous adipose tissue


title: GP07026-ND-C

description: subcutaneous adipose tissue


title: Diffuse Large B Cell Lymphoma normal sample 78


title: Diffuse Large B Cell Lymphoma normal sample 83


title: GP07029-ND-C

description: subcutaneous adipose tissue


title: GP08101-ND-C

description: subcutaneous adipose tissue


title: Diffuse Large B Cell Lymphoma normal sample 64


title: Diffuse Large B Cell Lymphoma normal sample 61


title: GP06003-ND-C

description: subcutaneous adipose tissue


title: 50_E_2_S

description: former smoker


title: 5_NE_2_N

description: former smoker


title: Diffuse Large B Cell Lymphoma normal sample 51


title: GP06041-ND-A

description: subcutaneous adipose tissue


title: Diffuse Large B Cell Lymphoma normal sample 58


title: GP06001-ND-A

description: subcutaneous adipose tissue


title: 49_NE_2_N

description: former smoker


title: Diffuse Large B Cell Lymphoma normal sample 52


title: Diffuse Large B Cell Lymphoma normal sample 69


title: Diffuse Large B Cell Lymphoma normal sample 48


title: Diffuse Large B Cell Lymphoma normal sample 49


title: Diffuse Large B Cell Lymphoma normal sample 47


title: Diffuse Large B Cell Lymphoma normal sample 42


title: 44_E_2_S

description: former smoker


title: Diffuse Large B Cell Lymphoma normal sample 57


title: 45_E_1_L

description: former smoker


title: 42_NE_1_N

description: former smoker


title: GP07050-ND-C

description: subcutaneous adipose tissue


title: Diffuse Large B Cell Lymphoma normal sample 41


title: GP06050-ND-C

description: subcutaneous adipose tissue


title: GP09028-ND-C

description: subcutaneous adipose tissue


title: Diffuse Large B Cell Lymphoma normal sample 56


title: 47_E_2_L

description: former smoker


title: Diffuse Large B Cell Lymphoma normal sample 40


title: Diffuse Large B Cell Lymphoma normal sample 38


title: 43_E_3_L

description: former smoker


title: Diffuse Large B Cell Lymphoma normal sample 39


title: GP06002-ND-A

description: subcutaneous adipose tissue


title: Diffuse Large B Cell Lymphoma normal sample 37


title: Diffuse Large B Cell Lymphoma normal sample 45


title: Diffuse Large B Cell Lymphoma normal sample 36


title: Diffuse Large B Cell Lymphoma normal sample 35


title: Diffuse Large B Cell Lymphoma normal sample 34


title: Diffuse Large B Cell Lymphoma normal sample 31


title: GP06064-ND-C

description: subcutaneous adipose tissue


title: Diffuse Large B Cell Lymphoma normal sample 26


title: 4_NE_2_N

description: former smoker


title: GP07018-ND-C

description: subcutaneous adipose tissue


title: GP07047-ND-C

description: subcutaneous adipose tissue


title: 32_NE_2_N

description: former smoker


title: GP08073-ND-C

description: subcutaneous adipose tissue


title: Diffuse Large B Cell Lymphoma normal sample 25


title: Diffuse Large B Cell Lymphoma normal sample 24


title: 35_NE_2_L

description: former smoker


title: Diffuse Large B Cell Lymphoma normal sample 22


title: Diffuse Large B Cell Lymphoma normal sample 23


title: 38_E_1_L

description: former smoker


title: Diffuse Large B Cell Lymphoma normal sample 21


title: Diffuse Large B Cell Lymphoma normal sample 27


title: Diffuse Large B Cell Lymphoma normal sample 30


title: GP08080-ND-C

description: subcutaneous adipose tissue


title: Diffuse Large B Cell Lymphoma normal sample 20


title: Diffuse Large B Cell Lymphoma normal sample 19


title: 31_E_2_S

description: former smoker


title: Diffuse Large B Cell Lymphoma normal sample 11


title: Diffuse Large B Cell Lymphoma normal sample 14


title: 30_E_2_S

description: former smoker


title: GP07044-ND-C

description: subcutaneous adipose tissue


title: Diffuse Large B Cell Lymphoma normal sample 7


title: Diffuse Large B Cell Lymphoma normal sample 4


title: 2_NE_2_L

description: former smoker


title: Diffuse Large B Cell Lymphoma normal sample 2


title: GP09026-ND-C

description: subcutaneous adipose tissue


title: GP08104-ND-C

description: subcutaneous adipose tissue


title: 20_E_3_S

description: former smoker


title: Diffuse Large B Cell Lymphoma tumor sample 84

source_name: TUMOR, Diffuse Large B Cell Lymphoma sample

value: Tumoral sample


title: GP07054-ND-C

description: subcutaneous adipose tissue


title: 48_E_3_L

description: former smoker


title: Diffuse Large B Cell Lymphoma tumor sample 83


title: GP02274-ND-C

description: subcutaneous adipose tissue


title: GP03120-ND-C

description: subcutaneous adipose tissue


title: 17_NE_1_N

description: former smoker


title: GP08099-ND-C

description: subcutaneous adipose tissue


title: Diffuse Large B Cell Lymphoma tumor sample 81


title: Diffuse Large B Cell Lymphoma tumor sample 80


title: GP07049-ND-C

description: subcutaneous adipose tissue


title: 16_NE_2_N

description: former smoker


title: GP06056-ND-C

description: subcutaneous adipose tissue


title: Diffuse Large B Cell Lymphoma tumor sample 79


title: GP09011-ND-A

description: subcutaneous adipose tissue


title: Diffuse Large B Cell Lymphoma tumor sample 78


title: 29_E_3_L

description: former smoker


title: 122_NE_2_L

description: former smoker


title: 120_NE_3_L

description: former smoker


title: GP08090-ND-C

description: subcutaneous adipose tissue


title: Diffuse Large B Cell Lymphoma tumor sample 71


title: Diffuse Large B Cell Lymphoma tumor sample 69


title: 15_NE_2_S

description: former smoker


title: GP06006-ND-C

description: subcutaneous adipose tissue


title: GP09032-ND-C

description: subcutaneous adipose tissue


title: GP03062-ND-C

description: subcutaneous adipose tissue


title: 119_NE_2_L

description: former smoker


title: GP08106-ND-C

description: subcutaneous adipose tissue


title: 12_NE_1_N

description: former smoker


title: Diffuse Large B Cell Lymphoma tumor sample 68


title: Diffuse Large B Cell Lymphoma tumor sample 66


title: Diffuse Large B Cell Lymphoma tumor sample 67


title: 118_E_2_S

description: former smoker


title: 117_E_2_S

description: former smoker


title: Diffuse Large B Cell Lymphoma tumor sample 64


title: GP06097-ND-A

description: subcutaneous adipose tissue


title: Diffuse Large B Cell Lymphoma tumor sample 63


title: GP06073-ND-A

description: subcutaneous adipose tissue


title: GP08081-ND-A

description: subcutaneous adipose tissue


title: Diffuse Large B Cell Lymphoma tumor sample 62


title: IDC (Case 22)

hyb_protocol: Dissolved in hybridization buffer (Agilent Oligo aCGH Hybridization Kit; Agilent Technologies), denatured and hybridized to the CGH array at 65℃ for 40 h

source_name: IDC : FFPE sample

value: male

source_name: mixed genomic DNA of normal renal cortex : FFPE sample


title: GP07056-ND-C

description: subcutaneous adipose tissue

value: subcutaneous adipose tissue


title: GP07000-ND-C

description: subcutaneous adipose tissue

value: Caucasian


title: 113_E_4_S

description: former smoker


title: GP07023-ND-C

description: subcutaneous adipose tissue


title: IDC (Case 18)

value: female


title: 112_E_4_S

description: former smoker


title: IDC (Case 24)


title: IDC (Case 12)


title: 111_E_4_S

description: former smoker


title: 115_E_2_S

description: former smoker


title: 107_E_3_S

description: former smoker


title: GP09019-ND-C

description: subcutaneous adipose tissue

value: Male


title: 103_E_3_S

description: former smoker


title: GP08004-ND-C

description: subcutaneous adipose tissue

value: Female


title: 104_E_4_S

description: former smoker


title: Diffuse Large B Cell Lymphoma tumor sample 61


title: IDC (Case 23)


title: Diffuse Large B Cell Lymphoma tumor sample 58


title: 102_E_4_S

description: former smoker


title: Diffuse Large B Cell Lymphoma tumor sample 57


title: IDC (Case 16)


title: Diffuse Large B Cell Lymphoma tumor sample 52


title: IDC (Case 9)


title: IDC (Case 11)


title: IDC (Case 10)


title: GP08085-ND-A

description: subcutaneous adipose tissue

value: African


title: Diffuse Large B Cell Lymphoma tumor sample 56


title: Diffuse Large B Cell Lymphoma tumor sample 51


title: IDC (Case 19)


title: 101_E_4_S

description: former smoker


title: IDC (Case 17)


title: IDC (Case 8)


title: GP06086-ND-C

description: subcutaneous adipose tissue


title: GP01175-ND-C

description: subcutaneous adipose tissue


title: Diffuse Large B Cell Lymphoma tumor sample 49


title: 1_NE_1_N

description: former smoker


title: GP07025-ND-C

description: subcutaneous adipose tissue


title: IDC (Case 7)


title: Diffuse Large B Cell Lymphoma tumor sample 48


title: GP06042-ND-A

description: subcutaneous adipose tissue


title: 10_NE_2_N

description: former smoker


title: GP09005-ND-A

description: subcutaneous adipose tissue


title: IDC (Case 5)


title: GP06062-ND-A

description: subcutaneous adipose tissue


title: IDC (Case 4)


title: IDC (Case 6)


title: IDC (Case 2)


title: IDC (Case 3)


title: IDC (Case 1)


title: GP07040-ND-A

description: subcutaneous adipose tissue


title: GP07017-ND-A

description: subcutaneous adipose tissue


title: GP06031-ND-C

description: subcutaneous adipose tissue


title: mother 1 egg 3

city: Amsterdam

first: Han

last: Rauwerda

state: Nederland

address: Sciencepark 904

department: SILS

institute: University of Amsterdam

description:
mother 1 egg 3 (mothers are siblings)
252823310117_1

hyb_protocol: Samples were labeled by incubating 5 µg of amino-allyl labeled amplified RNA in 50 mM carbonate buffer (pH 8.5) with Cy3 or Cy5 mono-reactive dyes (GE Healthcare) for 1 hour at room temperature. Reactions were quenched with hydroxylamine (Sigma-Aldrich), purified with the E.Z.N.A. MicroElute RNA Clean Up Kit and the yield and CyDye incorporation were measured on a NanoDrop ND-2000. Finally, 4.4 ug test and 2.2 ug reference labeled amplified RNA was combined and hybridized to custom-designed D. rerio 4x180k SurePrint G3 microarrays (Agilent Technologies, GEO accession GPL15180) for 17 hours at 65°C.

scan_protocol: Scanned on an Agilent  G2565CA scanner

data_processing: Images were quantified using Agilent Feature Extraction Software, version 10.7.3.1.

organism: Danio rerio

source_name: wt ABTL egg of mother 1

label_protocol: Polyadenylated ribo-depleted RNA was amplified and labeled using amino-allyl-CTP (TriLink Biotechnologies) in a modified version of a standard T7 RNA polymerase-based in vitro transcription protocol (Van Gelder et al., 1990). Amplified RNA was purified using the E.Z.N.A. MicroElute RNA Clean Up Kit (Omega Bio-Tek), quantified using a NanoDrop ND-2000 and its quality was checked on RNA ScreenTapes (Agilent Technologies). Reference samples were compiled from a pool of eggs.

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org).

extract_protocol: RNA was isolated from single oocytes as described previously (de Jong et al., 2010). RNA concentrations were measured on a NanoDrop ND-2000 (Thermo Scientific), and RNA integrity was assessed on a 2200 TapeStation system using RNA ScreenTapes (Agilent Technologies).  Total RNA was polyadenylated using the Poly(A) Polymerase Tailing Kit (Epicentre). Prior to amplification and labeling, polyadenylated total RNA was depleted for ribosomal RNA (rRNA) using a set of biotinylated single-stranded DNA oligonucleotides designed to hybridize to Danio rerio 18S and 28S rRNA

treatment_protocol: Eggs were obtained by squeezing according to http://zfin.org/zf_info/zfbook/chapt2/2.8.html#4

tag: clutch/mother id

value: mother 1

value: wt ABTL egg of mother

tag: molecule type

value: ribodepleted total RNA


title: Invasive region of IPMN-inv (Case 40)

source_name: IPMN : FFPE sample


title: GP07052-ND-C

description: subcutaneous adipose tissue


title: GP06085-ND-C

description: subcutaneous adipose tissue


title: mother 2 egg 2

description:
mother 2 egg 2 (mothers are siblings)
252823310117_4

source_name: wt ABTL egg of mother 2

value: mother 2


title: mother 5 egg 3

description:
mother 5 egg 3 (mothers are siblings)
252823310116_4

source_name: wt ABTL egg of mother 5

value: mother 5


title: mother 3 egg 4

description:
mother 3 egg 4 (mothers are siblings)
252823310117_3

source_name: wt ABTL egg of mother 3

value: mother 3


title: GP08001-ND-C

description: subcutaneous adipose tissue


title: GP06014-ND-C

description: subcutaneous adipose tissue


title: CIS region of IPMN-inv (Case 40)


title: Invasive region of IPMN-inv (Case 31)


title: Invasive region of IPMN-inv (Case 30)


title: Control A08_10

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

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

department: PEBC

institute: IDIBELL

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

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

data_processing: Genome Studio V2011.2

label: Cy3, Cy5

source_name: Brain

label_protocol: Standard Illumina labelling protocol

growth_protocol: N/A. Primary patient samples.

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

treatment_protocol: Untreated.

tag: condition

value: Control

tag: health state

value: Healthy

value: BA9 Grey matter


title: CIS region of IPMN-inv (Case 31)

tag: gender


title: Control A08_86

tag: age


title: GP09034-ND-C

description: subcutaneous adipose tissue

source_name: subcutaneous adipose tissue


title: mother 2 egg 5

description:
mother 2 egg 5 (mothers are siblings)
252823310116_2


title: mother 3 egg 1

description:
mother 3 egg 1 (mothers are siblings)
252823310116_1


title: Invasive region of IPMN-inv (Case 29)


title: Parkinson's disease BK-1182

value: Parkinson's disease

value: Diseased donor


title: mother 4 egg 4

description:
mother 4 egg 4 (mothers are siblings)
252823310116_3

source_name: wt ABTL egg of mother 4

value: mother 4


title: Parkinson's disease BK-680


title: GP06070-ND-C

description: subcutaneous adipose tissue

value: subcutaneous adipose tissue

value: Caucasian


title: Invasive region of IPMN-inv (Case 28)

value: male


title: Control 29_09

value: Male


title: mother 3 egg 2

description:
mother 3 egg 2 (mothers are siblings)
252823310074_4


title: GP06074-ND-C

description: subcutaneous adipose tissue


title: Parkinson's disease BK-476


title: CIS region of IPMN-inv (Case 29)

description: Genomic DNA was extracted from tissues of normal renal cortex obtained from 12 patients with ureteral or renal pelvic carcinoma, neither of which exhibited invasion or metastasis to the renal cortex. The same amount of genomic DNA extracted from 12 patients was mixed and used as the control DNA.


title: Parkinson's disease BK-574


title: Control A10_98


title: CIS region of IPMN-inv (Case 28)


title: Invasive region of IPMN-inv (Case 27)


title: Parkinson's disease BK_1027


title: GP07057-ND-A

description: subcutaneous adipose tissue

value: African


title: Control G07_145


title: CIS region of IPMN-inv (Case 30)

value: female


title: mother 4 egg 1

description:
mother 4 egg 1 (mothers are siblings)
252823310074_2

value: wt ABTL egg of mother


title: GP08105-ND-C

description: subcutaneous adipose tissue


title: mother 2 egg 3

description:
mother 2 egg 3 (mothers are siblings)
252823310074_1

value: ribodepleted total RNA


title: Lewy Body disease BK-1066

value: Lewy Body disease


title: mother 5 egg 4

description:
mother 5 egg 4 (mothers are siblings)
252823310117_2

value: mother 5


title: Lewy Body disease BK-424

value: Female


title: CIS region of IPMN-inv (Case 27)


title: GP07043-ND-C

description: subcutaneous adipose tissue


title: GP06053-ND-C

description: subcutaneous adipose tissue


title: mother 3 egg 5

description:
mother 3 egg 5 (mothers are siblings)
252823310073_4

value: mother 3


title: Lewy Body disease BK-1159


title: mother 4 egg 5

description:
mother 4 egg 5 (mothers are siblings)
252823310073_3


title: Lewy Body disease BK-458


title: GP02320-ND-C

description: subcutaneous adipose tissue


title: CIS region of IPMN-inv (Case 26)


title: Invasive region of IPMN-inv (Case 26)


title: GP08002-ND-C

description: subcutaneous adipose tissue


title: Invasive region of IPMN-inv (Case 25)


title: CIS region of IPMN-inv (Case 25)


title: Invasive region of IPMN-inv (Case 20)


title: GP08082-ND-C

description: subcutaneous adipose tissue


title: mother 1 egg 2

description:
mother 1 egg 2 (mothers are siblings)
252823310074_3

value: mother 1


title: mother 1 egg 4

description:
mother 1 egg 4 (mothers are siblings)
252823310072_4


title: Diffuse Large B Cell Lymphoma tumor sample 47

description:
Hybridized to Affymetrix OncoScan FFPE Express
47T

hyb_protocol: Affymetrix OncoScan™ FFPE Express

scan_protocol: Affymetrix® GeneChip® Scanner 3000G to detect target bound to 360k format GeneChip® Arrays after staining with a fluorescent detection stain.

source_name: Diffuse large B cell lymphoma tumor sample

label_protocol: As per manufacturer (Affymetrix) for OncoScan v2

extract_protocol: DNA extraction on formalin-fixed paraffin-embedded (FFPE) tissue was done with the RecoverAll™ Total Nucleic Acid Isolation Kit (AmbionInc-Applied Biosystems, Foster City, CA, USA) or QuickExtract™ FFPE DNA Extraction Kit (Epicenter Biotechnologies, Madison, WI, USA). DNA from non-tumoral matched samples was isolated using DNAzolor theMagNA Pure LC system (Roche Diagnostics GmbH, Mannheim, Germany).

tag: diagnosis

value: Diffuse large B cell lymphoma de novo

value: Tumor sample

value: FFPE

tag: type

value: non-GC

tag: status

value: alive


title: Diffuse Large B Cell Lymphoma tumor sample 45

description:
Hybridized to Affymetrix OncoScan FFPE Express
45T

value: GC

value: exitus


title: GP07027-ND-C

description: subcutaneous adipose tissue

value: subcutaneous adipose tissue

value: Caucasian

value: Male


title: mother 3 egg 3

description:
mother 3 egg 3 (mothers are siblings)
252823310072_3

value: wt ABTL egg of mother


title: GP07009-ND-C

description: subcutaneous adipose tissue


title: mother 5 egg 1

description:
mother 5 egg 1 (mothers are siblings)
252823310073_2

value: ribodepleted total RNA


title: GP09033-ND-C

description: subcutaneous adipose tissue


title: Invasive region of IPMN-inv (Case 14)

value: female

value: male


title: mother 2 egg 1

description:
mother 2 egg 1 (mothers are siblings)
252823310072_2

value: mother 2


title: mother 1 egg 5

description:
mother 1 egg 5 (mothers are siblings)
252823310073_1


title: Lewy Body disease DLB2

value: Lewy Body disease

value: Female

value: Diseased donor

value: BA9 Grey matter


title: GP06030-ND-C

description: subcutaneous adipose tissue


title: CIS region of IPMN-inv (Case 14)


title: Diffuse Large B Cell Lymphoma tumor sample 41

description:
Hybridized to Affymetrix OncoScan FFPE Express
41T

value: Diffuse large B cell lymphoma de novo

value: Tumor sample

value: FFPE


title: Diffuse Large B Cell Lymphoma tumor sample 42

description:
Hybridized to Affymetrix OncoScan FFPE Express
42T

value: GC

value: alive


title: mother 4 egg 3

description:
mother 4 egg 3 (mothers are siblings)
252823310072_1

value: mother 4


title: Down Syndrome with Alzheimer's disease 38_08

value: Down Syndrome with Alzheimer's disease


title: Down Syndrome with Alzheimer's disease 31_07

value: Male


title: mother 4 egg 2

description:
mother 4 egg 2 (mothers are siblings)
252823310053_4

value: wt ABTL egg of mother


title: Diffuse Large B Cell Lymphoma tumor sample 39

description:
Hybridized to Affymetrix OncoScan FFPE Express
39T

value: exitus


title: Down Syndrome with Alzheimer's disease 31_08


title: mother 2 egg 4

description:
mother 2 egg 4 (mothers are siblings)
252823310053_3

value: ribodepleted total RNA


title: PIE cells+L.plantarumTL2766_ETEC PAMPs challenge_12h

city: San Miguel de Tucumán

first: Julio

last: Villena

state: Tucumán

address: Chacabuco 145

country: Argentina

institute: CERELA-CONICET

description: Gene expression after 48h L.plantarumTL2766 stimulation and 12h ETEC PAMPs challenge

hyb_protocol: Hybridisation with Porcine (V2) Gene Expression Microarray (Agilent Technologies) was performed at Hokkaido System Science Co.

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing:
Data normalization and expression analysis were performed with GeneSpring software version 6.1 (Agilent Technologies).
Expression data were considered significant when they differed at least 2 fold between treated and untreated PIE cells, and results are expressed as log2 scale (log2 ratio). Genes whose expressions were increased more than 2-fold (log2 > 1) after treatment with ETEC PAMPs were selected

source_name: PIE cells, L.plantarumTL2766, 48h, ETEC PAMPs, 12h, replicate 1

label_protocol: Labelling was done as recommended by Agilent Technologies using 200 ng of RNA

growth_protocol: PIE cells, which are non-transformed intestinal cultured cells originally derived from intestinal epithelia isolated from an unsuckled neonatal swine, were maintained in Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen Corporation, Carlsbad, CA) supplemented with 10% fetal calf serum (FCS), 100 mg/ml penicillin, and 100 U/ml streptomycin at 37°C in an atmosphere of 5% CO2. PIE cells were seeded at 3 x 104 cells/12-well plate on type I collagen-coated plates (Sumitomo Bakelite Co., Tokyo, Japan) and cultured for 3 days. Control medium or lactobacilli (5 x 107 cells/ml) were added and 48 h later, cells were stimulated with ETEC PAMPs (5 x 107 cells/ml). 12 h after ETEC stimulation total RNA was extracted for microarray studies.

extract_protocol: Total RNA was isolated from PIE cells samples using PureLink RNA Mini Kit (life technologies inc. gaithersburg md) with DNase. RNA integrity of all samples were evaluated by Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), using the RNA 6000 Nano Kit.

tag: cell line

value: Porcine intestinal epitheliocytes-derived cell line

value: 3 days


title: Diffuse Large B Cell Lymphoma tumor sample 37

description:
Hybridized to Affymetrix OncoScan FFPE Express
37T

value: non-GC

value: female


title: Down Syndrome 35_06

value: Down Syndrome

value: Diseased donor


title: GP06019-ND-C

description: subcutaneous adipose tissue

value: subcutaneous adipose tissue

value: Caucasian


title: Diffuse Large B Cell Lymphoma tumor sample 38

description:
Hybridized to Affymetrix OncoScan FFPE Express
38T

value: Diffuse large B cell lymphoma de novo

value: Tumor sample

value: FFPE


title: GP08006-ND-A

description: subcutaneous adipose tissue

value: African


title: mother 1 egg 1

description:
mother 1 egg 1 (mothers are siblings)
252823310053_2

value: mother 1


title: GP07010-ND-C

description: subcutaneous adipose tissue

value: Male


title: PIE cells+L.jenseniiTL2937_ETEC PAMPs challenge_12h

description: Gene expression after 48h L.jenseniiTL2937 stimulation and 12h ETEC PAMPs challenge

source_name: PIE cells, L.jenseniiTL2937, 48h, ETEC PAMPs, 12h, replicate 1


title: GP07032-ND-A

description: subcutaneous adipose tissue


title: N2_IF_AD14

city: Shanghai

first: Jing-Dong

middle: Jackie

last: Han

address: Yueyang Road 320

department: CAS-MPG Partner Institute for Computational Biology

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description: Gene expression data for N2 worms under IF condition, on adult day 14

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

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

data_processing: processed by RMA in affy package in R

organism: Caenorhabditis elegans

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

growth_protocol: N2 worms were grown under 20 ℃, FUDR added from AD0.

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

treatment_protocol: Before AD2, all N2 worms are fed with live OP50 bacteria at 1x10^10 bacteria/ml. From AD2, Worms are fed with UV-kiled OP50 bacteria with concentrations according to different regimens: AL,1x10^10 bacteria/ml; CR, 1x10^8 bacteria/ml; IF, fasting and AL provided in turn every two days.

tag: strain

tag: diet

value: intermittent fasting

value: whole body

value: adult day 14


title: Diffuse Large B Cell Lymphoma tumor sample 36

description:
Hybridized to Affymetrix OncoScan FFPE Express
36T

tag: tissue

value: GC

value: alive


title: PIE cells_ETEC PAMPs challenge_12h

description: Gene expression after 12h ETEC PAMPs challenge

source_name: PIE cells, ETEC PAMPs, 12h, replicate 1

value: Porcine intestinal epitheliocytes-derived cell line

value: 3 days


title: GP07031-ND-A

description: subcutaneous adipose tissue

hyb_protocol: Standard Illumina hybridization protocol

tag: ethnicity


title: Down Syndrome  32_08

value: Down Syndrome

value: BA9 Grey matter


title: Diffuse Large B Cell Lymphoma tumor sample 35

description:
Hybridized to Affymetrix OncoScan FFPE Express
35T

value: non-GC


title: CIS region of IPMN-inv (Case 20)

description: Genomic DNA was extracted from tissues of normal renal cortex obtained from 12 patients with ureteral or renal pelvic carcinoma, neither of which exhibited invasion or metastasis to the renal cortex. The same amount of genomic DNA extracted from 12 patients was mixed and used as the control DNA.

value: male


title: GP02338-ND-C

description: subcutaneous adipose tissue

value: subcutaneous adipose tissue

value: Caucasian

value: Female


title: mother 5 egg 2

description:
mother 5 egg 2 (mothers are siblings)
252823310053_1

value: mother 5

value: wt ABTL egg of mother

value: ribodepleted total RNA


title: Alzheimer's disease 31_05

value: Alzheimer's disease

value: Male

value: Diseased donor


title: Alzheimer's disease 17_08


title: GP07055-ND-C

description: subcutaneous adipose tissue


title: N2_IF_AD10

description: Gene expression data for N2 worms under IF condition, on adult day 10

value: intermittent fasting

value: whole body

value: adult day 10


title: Diffuse Large B Cell Lymphoma tumor sample 31

description:
Hybridized to Affymetrix OncoScan FFPE Express
31T

value: Diffuse large B cell lymphoma de novo

value: Tumor sample

value: FFPE

value: GC

value: alive


title: Diffuse Large B Cell Lymphoma tumor sample 34

description:
Hybridized to Affymetrix OncoScan FFPE Express
34T

value: non-GC

value: female


title: Alzheimer's disease A09_26

value: BA9 Grey matter


title: Alzheimer's disease A10_51


title: Diffuse Large B Cell Lymphoma tumor sample 29

description:
Hybridized to Affymetrix OncoScan FFPE Express
29T


title: Diffuse Large B Cell Lymphoma tumor sample 27

description:
Hybridized to Affymetrix OncoScan FFPE Express
27T


title: Diffuse Large B Cell Lymphoma tumor sample 25

description:
Hybridized to Affymetrix OncoScan FFPE Express
25T


title: GP09025-ND-C

description: subcutaneous adipose tissue

value: subcutaneous adipose tissue

value: Caucasian

value: Female


title: Diffuse Large B Cell Lymphoma tumor sample 24

description:
Hybridized to Affymetrix OncoScan FFPE Express
24T


title: N2_CR_AD8

description: Gene expression data for N2 worms under CR condition, on adult day 8

value: calorie restriction

value: adult day 8


title: N2_AL_AD10

description: Gene expression data for N2 worms under AL condition, on adult day 10

value: ad libitum


title: GP07006-ND-C

description: subcutaneous adipose tissue

value: Male


title: N2_IF_AD8

description: Gene expression data for N2 worms under IF condition, on adult day 8

value: intermittent fasting

value: whole body


title: N2_AL_AD8

description: Gene expression data for N2 worms under AL condition, on adult day 8


title: N2_IF_AD12

description: Gene expression data for N2 worms under IF condition, on adult day 12

value: adult day 12


title: Alzheimer's disease A09_151

value: Alzheimer's disease

value: Diseased donor


title: Diffuse Large B Cell Lymphoma tumor sample 30

description:
Hybridized to Affymetrix OncoScan FFPE Express
30T

value: Diffuse large B cell lymphoma de novo

value: Tumor sample

value: FFPE


title: N2_CR_AD10

description: Gene expression data for N2 worms under CR condition, on adult day 10

value: adult day 10


title: Diffuse Large B Cell Lymphoma tumor sample 26

description:
Hybridized to Affymetrix OncoScan FFPE Express
26T

value: non-GC

value: alive


title: Diffuse Large B Cell Lymphoma tumor sample 23

description:
Hybridized to Affymetrix OncoScan FFPE Express
23T


title: Alzheimer's disease A08_127

value: BA9 Grey matter


title: Diffuse Large B Cell Lymphoma tumor sample 22

description:
Hybridized to Affymetrix OncoScan FFPE Express
22T

value: GC


title: Diffuse Large B Cell Lymphoma tumor sample 21

description:
Hybridized to Affymetrix OncoScan FFPE Express
21T

value: female


title: Diffuse Large B Cell Lymphoma tumor sample 20

description:
Hybridized to Affymetrix OncoScan FFPE Express
20T


title: Diffuse Large B Cell Lymphoma tumor sample 19

description:
Hybridized to Affymetrix OncoScan FFPE Express
19T

value: exitus


title: N2_CR_AD6

description: Gene expression data for N2 worms under CR condition, on adult day 6

value: calorie restriction

value: adult day 6


title: N2_AL_AD6

description: Gene expression data for N2 worms under AL condition, on adult day 6

value: ad libitum


title: Lewy Body disease 11_052

value: Lewy Body disease

value: Male


title: Diffuse Large B Cell Lymphoma tumor sample 40

description:
Hybridized to Affymetrix OncoScan FFPE Express
40T


title: Diffuse Large B Cell Lymphoma tumor sample 18

description:
Hybridized to Affymetrix OncoScan FFPE Express
18T


title: N2_IF_AD6

description: Gene expression data for N2 worms under IF condition, on adult day 6

value: intermittent fasting

value: whole body


title: Diffuse Large B Cell Lymphoma tumor sample 17

description:
Hybridized to Affymetrix OncoScan FFPE Express
17T

value: Diffuse large B cell lymphoma de novo


title: N2_IF_AD4

description: Gene expression data for N2 worms under IF condition, on adult day 4

value: adult day 4


title: N2_AL_AD2

description: Gene expression data for N2 worms under AL condition, on adult day 2

value: adult day 2


title: N2_CR_AD4

description: Gene expression data for N2 worms under CR condition, on adult day 4


title: Diffuse Large B Cell Lymphoma tumor sample 16

description:
Hybridized to Affymetrix OncoScan FFPE Express
16T

value: Tumor sample

value: FFPE


title: N2_AL_AD4

description: Gene expression data for N2 worms under AL condition, on adult day 4


title: Diffuse Large B Cell Lymphoma tumor sample 14

description:
Hybridized to Affymetrix OncoScan FFPE Express
14T

value: non-GC

value: alive


title: Diffuse Large B Cell Lymphoma tumor sample 13

description:
Hybridized to Affymetrix OncoScan FFPE Express
13T

value: GC


title: R1_T6_rep2

description: Gene expression data for worms under AL condition, on adult day 4

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

source_name: rsks-1(ok1255) fed with tax-6 RNAi vector containing HT1115 bacteria

growth_protocol: N2 worms grew under 20 ℃, FUDR added since AD0.

treatment_protocol: Worms are fed with empty vector or tax-6 RNAi vector containing HT1115 bacteria since hatching.


title: Diffuse Large B Cell Lymphoma tumor sample 12

description:
Hybridized to Affymetrix OncoScan FFPE Express
12T


title: R1_EV_rep1

source_name: rsks-1(ok1255) fed with empty vector containing HT1115 bacteria

value: empty vector containing HT1115 bacteria


title: Diffuse Large B Cell Lymphoma tumor sample 10

description:
Hybridized to Affymetrix OncoScan FFPE Express
10T

value: exitus


title: Diffuse Large B Cell Lymphoma tumor sample 11

description:
Hybridized to Affymetrix OncoScan FFPE Express
11T


title: R1_EV_rep2


title: N2_T6_rep1

source_name: N2 fed with tax-6 RNAi vector containing HT1115 bacteria


title: Diffuse Large B Cell Lymphoma tumor sample 04

description:
Hybridized to Affymetrix OncoScan FFPE Express
04T


title: N2_T6_rep2

value: tax-6 RNAi vector containing HT1115 bacteria


title: IR12hB

city: Sao Paulo

first: Paulo

last: Lee Ho

state: SP

address: 1500 Vital Brazil

department: Centro de Biotecnologia

country: Brazil

institute: Instituto Butantan

hyb_protocol: Samples were hybridized to custom Agilent gene expression slides containing eight arrays of 15k spots, for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Images were captured by Agilent DNA Microarray Scanner Bundle with settings for one color scan

data_processing: Intensity values were extracted from scanned images with Agilent Feature Extraction software version 9.5.3, with default parameters.

organism: Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130

source_name: Culture 12h after UV-C dose of 4.5J/m²

label_protocol: Labeling with Cy3 was performed in 5ug RNA using Fairplay III kit from agilent, following manufacturer instructions.

growth_protocol: Bacteria were cultivated in enriched EMJH medium with no agitation until exponential phase. The cultures used were all from the third in vitro passage after recovery from kidneys of experimentally infected hamsters.

extract_protocol: RNA was isolated using RNA protect and the RNEasy kit from Qiagen, using the protocol 4 from manufacturer's manual

treatment_protocol: Bacterial cultures were poured in thin layers over petri dishes and then were exposed (or not) to 4.5 J/m² of UV-C. They were incubated 12h in the dark until harvest.

tag: treatment

value: Yes


title: Diffuse Large B Cell Lymphoma tumor sample 03

description:
Hybridized to Affymetrix OncoScan FFPE Express
03T

value: non available


title: DR_T6_rep1

source_name: daf-2 rsks-1 fed with tax-6 RNAi vector containing HT1115 bacteria

value: daf-2 rsks-1


title: DR_T6_rep2


title: IR12hC


title: N2_EV_rep1

source_name: N2 fed with empty vector containing HT1115 bacteria


title: R1_T6_rep1

treatment_protocol: Worms are fed with empty vector or tax-6 RNAi vector containing HT1115 bacteria from hatching.


title: Diffuse Large B Cell Lymphoma tumor sample 05

description:
Hybridized to Affymetrix OncoScan FFPE Express
05T

value: female


title: DR_EV_rep2

source_name: daf-2 rsks-1 fed with empty vector containing HT1115 bacteria


title: Diffuse Large B Cell Lymphoma tumor sample 08

description:
Hybridized to Affymetrix OncoScan FFPE Express
08T

value: Male


title: NIA_4

source_name: No treatment culture

value: No


title: Diffuse Large B Cell Lymphoma tumor sample 02

description:
Hybridized to Affymetrix OncoScan FFPE Express
02T

value: Diffuse large B cell lymphoma de novo


title: Diffuse Large B Cell Lymphoma tumor sample 07

description:
Hybridized to Affymetrix OncoScan FFPE Express
07T


title: N2_EV_rep2

value: whole body

value: adult day 4


title: NIA_3


title: D2_T6_rep1

source_name: daf-2(e1370) fed with tax-6 RNAi vector containing HT1115 bacteria


title: DR_EV_rep1


title: IR12hA


title: IR12hD


title: Diffuse Large B Cell Lymphoma tumor sample 01

description:
Hybridized to Affymetrix OncoScan FFPE Express
01T

value: Tumor sample


title: NIA_2


title: D2_T6_rep2


title: CPN_P14_KO3

city: Wako

first: Noriyuki

last: Kishi

state: Saitama

address: 2-1 Hirosawa

department: Lab for Marmoset Models for Brain Diseases

institute: RIKEN Center for Brain Science

description: Postnatal Day 14 callosal projection neurons purified by fluorescence-activated cell sorting from Mecp2 -/y cortex. RNA extracted using StrataPrep Total RNA Micro Kit (Stratagene). RNA amplified according to Affymetrix small sample protocol, using two consecutive rounds of linear in vitro transcription.

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on M430 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: P14 FACS-purified Mecp2 -/y callosal projection neurons

label_protocol: Biotinylated cRNA were prepared according to the Affymetric small sample target labeling protocol from approximately 50 ng total RNA.

extract_protocol: RNA was extracted from FACS-purified CPN using the StrataPrep Total RNA Micro Kit.

treatment_protocol: Retrogradely labelled P14 cortex was enzymatically digested in papain (20 U/ml) for 45 min with constant stirring. DNase was added for the last 5 min of enzymatic digestion and to the media during trituration at 10 U/ml. CPN were dissociated to a single cell suspension,and immediately preserved in RNAlater (Ambion).

tag: tissue type

value: neuronal

tag: cell type

value: callosal projection neurons

value: Postnatal Day 14


title: CPN_P14_WT3

description: Postnatal Day 14 wild-type callosal projection neurons purified by fluorescence-activated cell sorting from murine (C57BL/6) cortex. RNA extracted using StrataPrep Total RNA Micro Kit (Stratagene). RNA amplified according to Affymetrix small sample protocol, using two consecutive rounds of linear in vitro transcription.

source_name: P14 FACS-purified wild-type callosal projection neurons


title: CPN_P14_KO2


title: D2_EV_rep2

source_name: daf-2(e1370) fed with empty vector containing HT1115 bacteria


title: TR_N: M11012801

status: Public on Jan 21 2016

city: Kanagawa

first: Satoko

last: Takizawa

state: Kamakura

institute: Toray Industries, Inc.

description: miRNA

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).

data_processing:
Mean and standard deviation (SD) of the 5% trimmed signals of the negative controls were calculated. Signals of miRNAs over mean+2SD of the negative controls were subtracted with the mean of the negative controls. The undetected signal was replaced with the value that was the least signal intensity on each DNA chip minus 0.1 in log2 scale followed by quantile normalization.
R 3.0.2 was used for analysis.

source_name: serum

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

value: non-cancer

value: serum


title: TS_N: M11012703

description: miRNA


title: TS_N: M11012702

description: miRNA


title: TR_N: M11012501

description: miRNA


title: TS_N: M11012403

description: miRNA


title: TR_N: M11012701

description: miRNA


title: TR_N: M11012601

description: miRNA


title: TR_N: M11012602

description: miRNA


title: TR_N: M11012401

description: miRNA


title: D2_EV_rep1

value: empty vector containing HT1115 bacteria


title: TR_N: M11012502

description: miRNA


title: TR_N: M11012402

description: miRNA


title: AOE_EV_rep2

source_name: aak2(o/e) fed with empty vector containing HT1115 bacteria


title: NIA_1


title: TR_N: M11012503

description: miRNA


title: ADR_EV_rep2

source_name: aak2(o/e); daf-2 rsks-1 fed with empty vector containing HT1115 bacteria

value: aak2(o/e); daf-2 rsks-1


title: CPN_P14_WT2


title: TS_N: M11012103

description: miRNA


title: TR_N: M11012104

description: miRNA


title: ADR_EV_rep1


title: TR_N: M11012001

description: miRNA


title: TR_N: M11012101

description: miRNA


title: TR_N: M11012102

description: miRNA


title: TS_N: M11011904

description: miRNA


title: TR_N: M11011903

description: miRNA


title: CPN_P14_WT1

description: Postnatal Day 14 callosal projection neurons purified by fluorescence-activated cell sorting from wild-type murine (C57BL/6) cortex. RNA extracted using StrataPrep Total RNA Micro Kit (Stratagene). RNA amplified according to Affymetrix small sample protocol, using two consecutive rounds of linear in vitro transcription.


title: AOE_EV_rep1


title: TS_N: M11011902

description: miRNA


title: TS_N: M11011901

description: miRNA


title: TS_N: M11011801

description: miRNA


title: TS_N: M11011409

description: miRNA


title: TS_N: M11011702

description: miRNA


title: TR_N: M11011406

description: miRNA


title: TR_N: M11011408

description: miRNA


title: TR_N: M11011405

description: miRNA


title: TR_N: M11011802

description: miRNA


title: TS_N: M11011404

description: miRNA


title: TR_N: M11011301

description: miRNA


title: TR_N: M11011403

description: miRNA


title: TS_N: M11011402

description: miRNA


title: TS_N: M11011202

description: miRNA


title: TS_N: M11011204

description: miRNA


title: TS_N: M11011203

description: miRNA


title: TR_N: M11011102

description: miRNA


title: TR_N: M11011104

description: miRNA


title: TR_N: M11011201

description: miRNA


title: TS_N: M11010702

description: miRNA


title: TR_N: M11010703

description: miRNA


title: TR_N: M11011401

description: miRNA


title: TR_N: M11011101

description: miRNA


title: TR_N: M11010704

description: miRNA


title: TR_N: M11010701

description: miRNA


title: TR_N: M11011407

description: miRNA


title: TS_N: M11011103

description: miRNA


title: TS_N: M11010603

description: miRNA


title: TS_N: M11010705

description: miRNA


title: TS_N: M11010501

description: miRNA


title: TR_N: M11010505

description: miRNA


title: TR_N: M11010506

description: miRNA


title: TR_N: M11010403

description: miRNA


title: TR_N: M11010601

description: miRNA


title: TR_N: M11010402

description: miRNA


title: TR_N: M11010502

description: miRNA


title: TR_N: M10122806

description: miRNA


title: TR_N: M11010401

description: miRNA


title: TR_N: M10122805

description: miRNA


title: TS_N: M10122804

description: miRNA


title: TS_N: M10122803

description: miRNA


title: TR_N: M11010507

description: miRNA


title: TR_N: M11010503

description: miRNA


title: TR_N: M10122801

description: miRNA