title: Group 1

city: San Frnacisco

first: Chien-Chun

middle: Steven

last: Pai

address: 513 Parnassus Ave

department: Hematology Oncology

institute: UCSF

description: Mice were treated with anti-CTLA-4

scan_protocol: qRT-PCR was carried out with Qiagen RT-PCR array kit (Cat 330231) and the data was collected on Applied Biosystems Cycler (AB Step-One Plus)

data_processing:
Raw data were analyzed on Qiagen website under data analysis center for analysis. (http://www.qiagen.com/us/shop/genes-and-pathways/data-analysis-center-overview-page/)
The data analysis web portal calculates fold change/regulation using delta delta CT method, in which delta CT is calculated between gene of interest (GOI) and an average of reference genes (HKG), followed by delta-delta CT calculations (delta CT (Test Group)-delta CT (Control Group)). Fold Change is then calculated using 2^ (-delta delta CT) formula.
Fold changes of gene expression between treatment groups compared to control groups

label: SYBR Green

source_name: draining lymph node

label_protocol: RT-PCR array were performed using Qiagen apoptosis array kit (Cat 330231)

extract_protocol: RNA was extracted from sorted CD8+Spas-1 T cells using an Ambion micro RNA isolation kit  (AM1931) according to the manufacturer’s protocol, and genomic DNA was eliminated using DNase kit purchased from Qiagen. RNA quality was checked by the A260/A280 ratio using NanoDrop Lite (Thermal Scientific). 10ng RNA from each sample was used for subsequent cDNA synthesis. cDNA was synthesized and cDNA templates pre-amplified were using RT2 PreAMP cDNA synthesis kit (Qiagen Cat 330451) according the manufacturer’s protocol and ProFlex PCR machine (Applied Biosystems). cDNA samples derived were evaluated for apoptotic gene expression arrays using RT2 ProfilerTM PCR Array kits purchased from Qiagen (PAMM-012Zc-12, Cat 330231) with SYBR Green qPCR Mastermix (Qiagen Cat 330522). Quantitative real-time RT-PCR arrays was performed using Applied Biosystems Cycler (AB Step-ONE Plus).

treatment_protocol: Mice were treated with anti-CTLA-4 or anti-PD-1 or combo or isotype

tag: cell subsets

tag: time

value: Day 28


title: piglet_pig milk replacer with 0.6g/L lactoferrin_rep5

status: Public on Feb 28 2017

type: RNA

city: Beijing

first: yujie

last: shi

address: No.5 building No.5 Road Dijin

country: China

institute: Nestle research center- Beijing hub

description:
S3P06_H0059
Gene expression data from piglet hippocampus of control pig milk replacer with 0.6g/L lactoferrin

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45˚C on Affymetrix Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner G3000 7G system.

data_processing: The data were analyzed with Expression console software (1.1) using Robust Multichip Average(RMA) as normalization method.

label: Biotin

molecule: total RNA

organism: Sus scrofa

source_name: piglet hippocampus_pig milk replacer with 0.6g/L lactoferrin

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: Three-day-old male domestic piglets (Sus scrofa, Landrace×Large White cross) were purchased from a commercial piggery in Xiamen City, China and randomly placed in the 3 groups. All animals were kept in the temperature-controlled environment with a 12-h light (08:00~20:00) and a 12-h dark (20:00~08:00) cycle. The home pens contained a “nest” (a rubber tire covered with a clean towel), a heat lamp over the nest and an identical woody toy hang in the home pen. All facilities (including home pens and behavior room) were monitored for 24-h. The feeding time was fixed as 8:00, 13:00, 18:00, 22:30, with an extra 50mL milk/pig supplied at the last feeding.

extract_protocol: The extraction of total RNA was performed using Agencourt RNAdvance tissue kit according to the manufacturer's instructions.

treatment_protocol: Pig hippocampus samples were collected after sacrifice and immediately stored in liquid nitrogen tank until RNA extraction.

tag: breed

value: Domestic pig (Landrace×Large White)

tag: gender

value: male

tag: age

value: postnatal day 38 (piglet)

tag: feeding group

tag: tissue

value: Hippocampus


title: piglet_pig milk replacer_rep3

description:
S2P11_H0052
Gene expression data from piglet hippocampus of control pig milk replacer

source_name: piglet hippocampus_contrl milk replacer

value: contrl milk replacer


title: Group 2

state: CA

country: USA

description: Mice were treated with anti-PD-1

organism: Mus musculus

tag: treatment

value: anti-PD-1 DANA


title: Group 3

description: Mice were treated with both anti-CTLA-4 and anti-PD-1

value: Combo DANA


title: piglet_pig milk replacer_rep1

description:
S1P03_H0003
Gene expression data from piglet hippocampus of control pig milk replacer


title: piglet_pig milk replacer with 0.6g/L lactoferrin_rep3

description:
S2P05_H0046
Gene expression data from piglet hippocampus of control pig milk replacer with 0.6g/L lactoferrin


title: piglet_pig milk replacer with 0.6g/L lactoferrin_rep2

description:
S2P04_H0045
Gene expression data from piglet hippocampus of control pig milk replacer with 0.6g/L lactoferrin


title: Group 4(Control Group)

description: Mice were treated with isotype control


title: piglet_pig milk replacer with 0.6g/L lactoferrin_rep1

description:
S2P03_H0044
Gene expression data from piglet hippocampus of control pig milk replacer with 0.6g/L lactoferrin


title: piglet_pig milk replacer with 1.2g/L lactoferrin_rep5

description:
S2P09_H0050
Gene expression data from piglet hippocampus of control pig milk replacer with 1.2g/L lactoferrin

source_name: piglet hippocampus_pig milk replacer with 1.2g/L lactoferrin


title: piglet_pig milk replacer with 1.2g/L lactoferrin_rep1

description:
S1P07_H0007
Gene expression data from piglet hippocampus of control pig milk replacer with 1.2g/L lactoferrin


title: Col-0 leaves

city: Berlin

first: Reinhard

last: Kunze

state: Berlin

address: Albrecht-Thaer-Weg 6

department: Institute of Biology

country: Germany

institute: Freie Universität Berlin

description: Gene expression after 6 weeks N starvation

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was fragmented in 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. Hybridization was performed in a Agilent hybridization oven at standard conditions as recommended by the manufacturer. Subsequently, microarrays were washed 1 minute with GE Wash Buffer 1 (Agilent) at 23°C and 1 minute with GE Wash buffer 2 (Agilent) at 37°C.

scan_protocol: Microarrays were scanned immediately after washing with an Agilent High-Resolution Scanner (G2505C) using default settings.

data_processing: The images were processed with the Agilent Feature Extraction software 10.1 using default settings  (protocol GE1_105_Dec08 (Read Only) and GridName US91803681_252963410002_S01_grid (from grid_file)). The resulting processed signals of all individual hybridizations were quantile-normalized using the ranked median quantiles according to Bolstad et al. (2003. Bioinformatics 19, 185-193).

organism: Arabidopsis thaliana

source_name: Col-0 leaves

label_protocol: Cy3-labeled cRNA was synthesized with the Agilent Quick Amp Labeling Kit one-cCy3-labeled cRNA was synthesized with the Quick Amp Labeling Kit, one-color (Agilent Technologies catalog number 5190-0442) according to the manufacturer's instructions.

growth_protocol: Arabidopsis seeds were germinated and pre-cultured on rockwool moistened with tap water for one week. Subsequently, plants were grown hydroponically under non-sterile conditions in a growth cabinet under the following conditions: 10 h/14 h light/dark; light intensity 280 μmol m−2 sec−1; day/night temperature 22°C/18°C and 60 % relative humidity. Tap water was substituted in the second week by half-strength nutrient solution containing 0.5 mM KH2PO4, 0.5 mM MgSO4, 125 μM K2SO4, 125 μM CaCl2, 50 μM Na–Fe–EDTA, 50 μM KCl, 30 μM H3BO3, 5 μM MnSO4, 1 μM ZnSO4, 1 μM CuSO4, and 0.7 μM NaMoO4, pH 5.8 with KOH. Nitrogen was supplied as 0.5 mM KNO3. In the third week, the plants were supplied with full-strength hydroponic growth medium (1 mM KH2PO4, 1 mM MgSO4, 250 μM K2SO4, 250 μM CaCl2, 100 μM Na–Fe–EDTA, 50 μM KCl, 30 μM H3BO3, 5 μM MnSO4, 1 μM ZnSO4, 1 μM CuSO4, and 0.7 μM NaMoO4, pH 5.8 with KOH), containing 1 mM KNO3. From week four until harvest (week nine), the plants were further cultivated in the full-strength growth medium, but nitrogen was supplied as 0.1 mM NH4NO3. The nutrient solution was renewed once a week during the first 3 weeks, twice in the fourth week and every 3 days for the following weeks.

extract_protocol: Total RNA was extracted from frozen and ground tissue according to Verwoerd et al. (1989. Nucleic Acids Res. 17, 2362) and purified with the RNeasy Mini Kit (Qiagen, Hilden, Germany). RNA was photometrically quantified with a NanoPhotometer (Implen, München, Germany) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cultivar

value: leaves

value: N starvation


title: piglet_pig milk replacer with 0.6g/L lactoferrin_rep4

description:
S2P06_H0047
Gene expression data from piglet hippocampus of control pig milk replacer with 0.6g/L lactoferrin


title: nrt1.5 roots

source_name: nrt1.5 roots

value: roots


title: Col-0 roots

source_name: Col-0 roots


title: piglet_pig milk replacer_rep2

description:
S1P04_H0004
Gene expression data from piglet hippocampus of control pig milk replacer


title: nrt1.5 leaves

source_name: nrt1.5 leaves


title: piglet_pig milk replacer with 1.2g/L lactoferrin_rep2

description:
S1P08_H0008
Gene expression data from piglet hippocampus of control pig milk replacer with 1.2g/L lactoferrin


title: Hippocampal T2

first: changwei

last: wei

address: 8 Gongren Tiyuchang Nanlu, Chaoyang District

department: Department of Anesthesiology

institute: Beijing Chao-Yang Hospital, Capital Medical University

description: Bilateral hippocampal tissue

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: POCD hippocampal tissue 2

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

growth_protocol: The animals used in this study were C57BL/6 mice purchased from Beijing Vital River Laboratory Animal Technology Co., Ltd. (Beijing, China). The mice were male, aged 12–14 months, and weighed 25–35 g. The room temperature and humidity were controlled at 25°C and 55%, respectively. All mice were acclimated to the environment for 1 week prior to the initiation of the study.

extract_protocol: Total RNA was extracted from the POCD and control group hippocampal tissues using TRIzol (Invitrogen, Carlsbad, CA, USA) according to manufacturer’s instructions. Subsequently, total RNA was assessed by electrophoresis on a denaturing agarose gel and quantified by NanoDrop spectrophotometer (NanoDrop, USA).

treatment_protocol: Mice from the POCD group were experienced tibia fracture surgery, mice from the control group did not receive any prior treatment or surgery.

tag: strain


title: Hippocampal T5

description: Bilateral hippocampal tissue

source_name: POCD hippocampal tissue 5


title: Hippocampal T3

description: Bilateral hippocampal tissue

source_name: POCD hippocampal tissue 3


title: Hippocampal T6

description: Bilateral hippocampal tissue

source_name: POCD hippocampal tissue 6


title: Hippocampal T1

description: Bilateral hippocampal tissue

source_name: POCD hippocampal tissue 1


title: Hippocampal T4

description: Bilateral hippocampal tissue

source_name: POCD hippocampal tissue 4


title: PLX_2511_PRE

status: Public on Feb 27 2017

city: San Francisco

first: David

last: Quigley

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

description: Gene expression data from untreated mouse skin

hyb_protocol: 90 microliters of hybridization sample were incubated in the Affymetrix GeneTitan Hybridization Oven instrument for 16 hours at 48C

scan_protocol: Arrays were processed with the Affymetrix GeneTitan Fluidics Station instrument, using the MoGene-1_1-st-v1-96 fluidics script and GeneTitan Hybridization, Wash, and Stain Kit for WT Array Plates.  Arrays were scanned in the Affymetrix GeneTitan Multi-Channel (MC) instrument with the AGCC GeneTitan Instrument Control.

data_processing: CEL files were background corrected and normalized with RMA using oligo in R and a custom probe database which avoids SNPs in FVB and Spretus genomes. Tail and backskin were separately batch-corrected for plate and Log2 transformed

label: biotin

source_name: dorsal skin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

growth_protocol: Mice were housed in standard conditions with standard chow and water ad libitum

extract_protocol: Trizol followed by Qiagen RNEasy clean-up

treatment_protocol: Mice were aged to 7 weeks, untreated

value: dorsal skin

tag: Sex

value: F

value: telogen

tag: batch


title: PLX_2497_PRE


title: PLX-vehicle_2465_PRE

value: M


title: PLX_2383_PRE


title: PLX_2468_PRE


title: PLX_2529_PRE

value: anagen


title: PLX_2403_PRE


title: PLX_2483_PRE


title: PLX_2473_PRE


title: PLX_2498_PRE


title: PLX_2489_PRE


title: LGX_2358_PRE


title: PLX_2406_PRE


title: PLX_2522_PRE


title: LGX_2342_PRE


title: Hippocampal C5

description: Bilateral hippocampal tissue

source_name: Control hippocampal tissue 5


title: Hippocampal C2

description: Bilateral hippocampal tissue

source_name: Control hippocampal tissue 2


title: Hippocampal C3

description: Bilateral hippocampal tissue

source_name: Control hippocampal tissue 3


title: Hippocampal C1

description: Bilateral hippocampal tissue

source_name: Control hippocampal tissue 1


title: LGX_2263_PRE


title: LGX_2272_PRE


title: LGX_2268_PRE


title: LGX_2245_PRE


title: LGX_2244_PRE


title: Hippocampal C4

description: Bilateral hippocampal tissue

source_name: Control hippocampal tissue 4


title: Hippocampal C6

description: Bilateral hippocampal tissue

source_name: Control hippocampal tissue 6


title: PLX-vehicle_2460_PRE


title: LGX_2340_PRE


title: LGX_2336_PRE


title: PLX_2407_PRE


title: LGX_2239_PRE


title: LGX_2220_PRE


title: LGX_2288_PRE


title: PLX_2488_PRE


title: PLX_2509_PRE


title: PLX_2521_PRE


title: PLX_2530_PRE


title: LGX_2228_PRE


title: PLX_2477_PRE


title: PLX_2517_PRE


title: LGX_2193_PRE


title: PLX_2449_PRE


title: PLX_2470_PRE


title: PLX_2475_PRE


title: PLX_2434_PRE


title: PLX_2512_PRE


title: LGX_2196_PRE


title: LGX_2187_PRE


title: PLX_2528_PRE


title: PLX_2412_PRE


title: PLX_2391_PRE


title: LGX_2362_PRE


title: PLX_2385_PRE


title: LGX_2354_PRE


title: LGX_2333_PRE


title: LGX_2310_PRE


title: LGX_2316_PRE


title: PLX_2414_PRE


title: LGX_2305_PRE


title: PLX_2409_PRE


title: LGX_2294_PRE


title: LGX_2215_PRE


title: LGX_2225_PRE


title: LGX_2254_PRE


title: LGX_2277_PRE


title: LGX_2216_PRE


title: PLX_2531_PRE


title: PLX_2525_PRE


title: LGX_2274_PRE


title: LGX_2258_PRE


title: LGX_2186_PRE


title: PLX_2516_PRE


title: PLX_2496_PRE


title: PLX_2524_PRE


title: PLX_2432_PRE


title: PLX_2499_PRE


title: PLX_2513_PRE


title: PLX-vehicle_2400_PRE


title: PLX_2402_PRE


title: NOVA-vehicle_2280_PRE


title: PLX_2507_PRE


title: PLX_2518_PRE


title: PLX-vehicle_2463_PRE


title: LGX_2349_PRE


title: LGX_2353_PRE


title: LGX_2356_PRE


title: NOVA-vehicle_2201_PRE


title: LGX_2313_PRE


title: PLX_2534_PRE


title: PLX_2474_PRE


title: PLX-vehicle_2466_PRE


title: LGX_2241_PRE


title: LGX_2260_PRE


title: LGX_2298_PRE


title: LGX_2275_PRE


title: LGX_2296_PRE


title: LGX_2311_PRE


title: LGX_2184_PRE


title: LGX_2185_PRE


title: LGX_2238_PRE


title: PLX_2491_PRE


title: LGX_2240_PRE


title: PLX_2500_PRE


title: PLX_2480_PRE


title: PLX_2438_PRE


title: LGX_2194_PRE


title: PLX_2485_PRE


title: PLX_2454_PRE


title: PLX_2495_PRE


title: PLX_2487_PRE


title: PLX_2439_PRE


title: PLX_2437_PRE


title: PLX_2430_PRE


title: PLX_2481_PRE


title: PLX_2447_PRE


title: PLX_2471_PRE


title: PLX_2510_PRE


title: PLX_2523_PRE


title: PLX_2440_PRE


title: PLX_2411_PRE


title: PLX_2519_PRE


title: LGX_2350_PRE


title: LGX_2346_PRE


title: PLX_2381_PRE


title: NOVA-vehicle_2234_PRE


title: NOVA-vehicle_2207_PRE


title: LGX_2315_PRE


title: LGX_2303_PRE


title: LGX_2337_PRE


title: LGX_2192_PRE


title: LGX_2213_PRE


title: LGX_2335_PRE


title: C306 control, biological rep2

city: Mohali

first: Jitendra

last: Kumar

state: Punjab

address: National Agri-Food Biotechnology Institute (Department of Biotechnology, Government of India) C-127, Industrial Area S.A.S. Nagar, Phase 8 Mohali-160071, Punjab, India

country: India

description: Gene expression data from control C306 plant leaf.

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr on GeneChip Wheat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner (Affymetrix).

data_processing: The data were analyzed with GeneSpring GX v12 (Agilent Technologies) and RMA-normalized.

organism: Triticum aestivum

source_name: C306 plants with regular watering

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Wheat plants were grown with regular watering or watering withheld.

extract_protocol: Spectrum Plant Total RNA Kit (Sigma-Aldrich) was used for the extraction of total RNA follwing the manufacturer's instructions.

treatment_protocol: The control plants received continued watering; however, the watering was withheld in drought treated plants, starting at 27 days of plant age.

value: leaf

value: 48 day old wheat plants


title: Mutant 2

city: Sioux Falls

first: Kameswaran

last: Surendran

state: SD

address: 2310 East 60th Street North

department: Children's Research Center

institute: Sandord Research

description: whole kidney from mutant mouse 1

hyb_protocol: Standard Illumina hybridization protocol: The labeled cRNA (1500ng for Mouse) was hybridized overnight at 58°C onto the Expression BeadChip mouse GW-6 (>46,000 gene transcripts; Illumina, San Diego, CA, USA) according to the manufacturer's instructions

scan_protocol: Standard Illumina scanning protocol:. BeadChips were subsequently washed and developed with fluorolink streptavidin- Cy3 (GE Healthcare). BeadChips were scanned with an Illumina BeadArray Reader. Data was generated from Imagedata using Illumina software, GenomeStudio.

data_processing: The data were normalised using quantile normalisation

source_name: Mouse Kidney RNA

label_protocol: Biotinylated cRNA were prepared using 500ng of RNA and with Illumina® RNA Amplification Kit from Ambion (Austin, TX, USA)

growth_protocol: mice were housed in cages with a 12 hour night and 12 hour day cycle and fed regular rodent chow

extract_protocol: RNA was extracted using Rneasy Mini kits from Qiagen, treated with DNAse. Quality of RNA was verified using BioAnalyzer (Agilent Tech.)

treatment_protocol: HoxB7Cre was used to inactivate RBPJ floxed alleles and hence Notch signlaing in the collecting ducts

value: mixed background

value: embryonic day 18.5

tag: genotype

value: kidney


title: SH-SY5Y_60min BDNF treated_rep3

city: Naples

first: Aldo

last: Donizetti

state: Naples

address: via Cinthia

department: Biology

country: Italy

institute: Federico II University

description: gene expression after 60 min of BDNF treatment (cells treated with BDNF, replicate 3)

hyb_protocol: Hybridization was conducted in a rotating oven for 17 hours at 65°C on the Agilent SurePrint G3 8x60K custom lncRNA expression array (Agilent Technologies). This array contains 22,001 lncRNA probes targeting the Gencode v15 human lncRNA annotation, together with 17,535 catalogue probes targeting protein-coding genes. The slide was washed according to Agilent protocol: separation of the sandwich, wash for one minute in Wash Buffer 1 at room temperature, wash for one minute in Wash Buffer 2 at 37° C.

scan_protocol: The slide was scanned using the High-Resolution Microarray C Scanner (Agilent Technologies) using the G3-GX scanning protocol.

data_processing: The image file was processed using the Agilent Feature Extraction software (v10.7.3 - GE1-107_Sep09 protocol): the microarray grid was correctly placed and outlier pixels (which were rejected) and inlier pixels were identified. Normalization was performed according to the Quantile method (baseline: median of samples).

organism: Homo sapiens

source_name: SH-SY5Y_60min BDNF treated_replicate3

label_protocol: Fluorescently-labeled cRNA was produced following the Low Input Quick Amp Labeling (LIQA) protocol v6.5 (Agilent Technologies), with a sample input of 50 ng of total RNA. One-color Spike-Ins were added to the samples for quality control.

growth_protocol: SH-SY5Y cells (ATCCｮ) were grown and propagated in Dulbecco's modified Eagle's medium (DMEM, Microtechｮ), supplemented with 2 mM L-glutamine (Lonza BioWhittakerTM), and a solution of 1% penicillin/streptomycin (Lonza BioWhittakerTM) and 15% Fetal Bovine Serum (FBS, Gibcoｮ). For BDNF treatment on a more homogeneous neuronal cell population, we performed an enrichment procedure based on the different substrate adherence between the two cell phenotypes: neuroblastic (N-type) and epithelial-like (S-type). The obtained N-enriched population of SHSY-5Y was differentiated  by decreasing FBS concentration from 15% to 1.5% and adding 10 μM of RA (retinoic acid-RA, Sigma-Aldrichｮ) for 6 days (the medium was refreshed every 2 days).

extract_protocol: Total cellular RNA was isolated using an RNeasyｮ Mini Kit (Qiagen) according to the RNeasyｮ Mini Handbook (Qiagen). DNA contamination was efficiently removed by on-column DNAse digestion (Qiagen). The concentration and the purity of the RNA sample were assessed using NanoDropｮ 1000 (Thermo Scientific). Total RNA quality was assessed by an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: After 6 days of differentiation, the medium containing 1.5% FBS and RA was removed and substituted with a medium without FBS for two groups of cells. One of these groups was treated with 10 ng/mL of BDNF (PeproTechｮ) for 1 h, whereas the second group was not treated and used as a control for the gene expression analysis.

tag: cell line

value: female

tag: cell type

value: neuroblastoma


title: Mutant 3

description: whole kidney from mutant mouse 1


title: PLX-vehicle_2368_PRE


title: Wild type 3

description: whole kidney from wild type mouse 3

value: RBPJ f/f;Rosa +/Eyfp


title: SH-SY5Y_60min BDNF treated_rep1

description: gene expression after 60 min of BDNF treatment (cells treated with BDNF, replicate 1)

source_name: SH-SY5Y_60min BDNF treated_replicate1


title: LGX_2269_PRE


title: SH-SY5Y_60min BDNF treated_rep2

description: gene expression after 60 min of BDNF treatment (cells treated with BDNF, replicate 2)

source_name: SH-SY5Y_60min BDNF treated_replicate2


title: LGX_2291_PRE


title: Wild type 1

description: whole kidney from wild type mouse 1


title: C306 drought, biological rep2

institute: National Agri-Food Biotechnology Institute

description: Gene expression data from drought treated C306 plant leaf.

source_name: C306 plants with no watering


title: LGX_2243_PRE


title: Wild type 2

description: whole kidney from wild type mouse 2


title: C306 control, biological rep1


title: C306 drought, biological rep1


title: SH-SY5Y_60min_control rep2

description: gene expression after 60 min of BDNF treatment (control cells not treated with BDNF, replicate 2)

source_name: SH-SY5Y_60min_control replicate2


title: Mutant 1

description: whole kidney from mutant mouse 1


title: SH-SY5Y_60min_control rep1

description: gene expression after 60 min of BDNF treatment (control cells not treated with BDNF, replicate 1)

source_name: SH-SY5Y_60min_control replicate1


title: WL711 control, biological rep2

description: Gene expression data from control WL711 plant leaf.

source_name: WL711 plants with regular watering


title: SH-SY5Y_60min_control rep3

description: gene expression after 60 min of BDNF treatment (control cells not treated with BDNF, replicate 3)

source_name: SH-SY5Y_60min_control replicate3


title: WL711 drought, biological rep1

description: Gene expression data from drought treated WL711 plant leaf.

source_name: WL711 plants with no watering


title: WL711 drought, biological rep2


title: WL711 control, biological rep1


title: S.mutans 48h biofilm, replicate 2

city: Guangzhou

first: Jia

last: Liu

state: Guangzhou

address: 74 Zhong Shan Er Road,

institute: Sun Yat Sen University

description:
Gene expression of 48h biofilm
[48h-2, 48h]

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Median normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies).

organism: Streptococcus mutans

source_name: S.mutans 48h biofilm

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

growth_protocol: Streptococcus mutans UA159 were grown at 37°C under anaerobic conditions (90% N2, 5% CO2, 5% H2) in BHI broth (Difco, Sparks, MD, USA). For biofilm formation, 1% sucrose was included in BHI medium.

extract_protocol: Biofilms at different dispersal stages were collected, suspended in lysis buffer (30 mM Tris-HCl, 1 mM EDTA, 20 mg/ml lysozyme, [pH8.0]) and incubated at 37oC with gentle agitation for 40min. Total RNA was extracted using RNeasy Mini kits (Qiagen). The obtained RNA from each sample was quantified using the NanoDrop ND-2000 and the RNA integrity was assessed using standard denaturing agarose gel electrophoresis.

tag: sample type

value: biofilm

tag: dispersal stage


title: S.mutans 96h biofilm, replicate 2

description:
Gene expression of 96h biofilm
[96h-2, 96h]

source_name: S.mutans 96h biofilm


title: S.mutans 96h biofilm, replicate 1

description:
Gene expression of 96h biofilm
[96h-1, 96h]


title: S.mutans 48h biofilm, replicate 1

description:
Gene expression of 48h biofilm
[48h-1, 48h]


title: S.mutans 60h biofilm, replicate 2

description:
Gene expression of 60h biofilm
[60h-2, 60h]

source_name: S.mutans 60h biofilm


title: S.mutans 60h biofilm, replicate 1

description:
Gene expression of 60h biofilm
[60h-1, 60h]


title: Control_rep3

status: Public on Feb 26 2017

city: Victoria

first: Ben

middle: F

last: Koop

state: BC

address: PO Box 3020 STN CSC

country: Canada

institute: The University of Victoria

hyb_protocol: Samples were hybridized to oligonucleotide microarrays as per manufacturers' instructions for Low-Input Quick Amp kits (Agilent; v6.5). Arrays were designed using previously annotated ESTs from both Pacific and Atlantic L. salmonis (Yasuike et al. 2012; eArray design ID 024389; Agilent).

scan_protocol: Scanned at 5 micrometer resolution on a ScanArray Express (Perkin Elmer) and quantified on Imagene (v8.1; BioDiscovery).

data_processing: For each probe on the microarray, the background median was subtracted from the foreground median. Data analysis was performed using limma in R. The arrays were normalized by within array loess normalization and between array quantile normalization using the Cy3 reference channel. The probes present in the matrix file are those that passed quality and low expression filters: at least three samples in any condition were ≥ 500 for raw fluorescence in both channels, and not saturated in all samples.

organism: Lepeophtheirus salmonis

source_name: adult lice (Atlantic Canada)

label_protocol: Labeled cRNA was generated from 825ng total RNA using Low-Input Quick Amp kits (Agilent; v6.5). A Cy3-cRNA reference pool to hybridize alongside samples was created ensuring each experimental condition was included in the pool.

growth_protocol: Egg strings from L. salmonis were harvested from sea cage cultured Atlantic salmon (New Brunswick, Canada) from the BMA2A region (which contains lice with elevated EMB resistance), aerated in 13oC saltwater collected from the sea cage site and maintained at the Atlantic Animal Facility, Atlantic Veterinary College at 33-36 salinity through 10% daily water changes until nauplii hatched and molted to copepodids (~6-8 days).

extract_protocol: Lice were rapidly enumerated and staged, then flash frozen in dry ice. All tissues were stored at -80oC until required for gene expression analysis. Total RNA was extracted from lice infecting control diet fish and low dose diet fish (LD) from times T3 and T4 (Figure 1) using the TRIzol extraction method including QIAGEN spin column RNA purification and quality evaluation on a BioRad Experion automated electrophoresis machine. These individuals were used to hybridize to an L. salmonis 38K oligonucleotide microarray (Sutherland et al. 2012). Samples were pools of both male and female adult lice collected from the same fish (each sex in equal proportion within each sample; two-four individual per pool). Seven pools were used from the control fish and four pools from the LD.

treatment_protocol: Fish were infected following standard methods at Atlantic Veterinary College. Following seawater acclimatization, treatment tanks (total = 9 tanks) were randomly assigned to one of three treatment groups and placed on one of the following three diets: control/base feed, low dose (LD), or high dose immunostimulant treated feed (HD). Note that only the control and LD feed groups were used for transcriptome profiling. Fish were maintained on treated feed for 17 days and then sampled (T1). Seven days after T1, fish in all experimental tanks were exposed to L. salmonis copepodids at 10-12 lice/fish (initial exposure). Five days after the initial exposure, fish were sampled (T2). A second and a third lice exposure (also at 10-12 lice/fish) were conducted 14 and 28 days after the first exposure to mimic a more constant low-level exposure as expected in the field. Fish were sampled again at 40 and 47 days post initial infection (T3 and T4, respectively; Figure 1). Samples from T3 and T4, when they had the same number of males and females in the pools of samples, were used for transcriptomics.

value: Control

tag: sampling time (not used)

tag: number females in sample pool

tag: number males in sample pool

value: all condition pool


title: Control_rep17


title: lowdose_rep15

value: lowdose


title: lowdose_rep14


title: Control_rep6


title: lowdose_rep19


title: Control_rep7


title: L540_Ago2-T_dye swap

city: Groningen

first: Ye

last: Yuan

state: Groningen

address: Hanzeplein 1

department: pathology

country: Netherlands

institute: UMCG

description:
L540 Ago2 Total fraction labeled with Cy5
Raw data available in Cy5 channel of file:
US45102948_253973110006_S01_GE2_107_Sep09_1_4.txt

hyb_protocol: According to the manufacturers instructions

scan_protocol: Agilent DNA Microarray Scanner, Agilent Feature Extraction software version 10.7.3.1.

data_processing: GeneSpring GX 12.5 software (Agilent Technologies); quantile normalization without base line transformation.

source_name: HL cell line

label_protocol: Cy3 and Cy5 labelled using 50-100ng total RNA in combination with the LowInput QuickAmp Labelling Kit, Cyanine 3 CTP Dye Pack, Cyanine 5 CTP Dye Pack and RNA Spike-In kit (all Agilent Technologies).

growth_protocol: HL cell lines were cultured in RPMI-1640 medium at 37℃ in an atmosphere containing 5% CO2.

extract_protocol: Standard Trizol RNA isolation (Life Technologies)

value: Hodgkin lymphoma


title: KM-H2_Ago2-T_dye swap

description:
KM-H2 Ago2 Total fraction labeled with Cy3
Raw data available in Cy3 channel of file:
US45102948_253973110006_S01_GE2_107_Sep09_2_3.txt


title: Control_rep18


title: Control_rep10


title: lowdose_rep11


title: L540_Ago2-IP_dye swap

description:
L540 Ago2 IP fraction labeled with Cy3
Raw data available in Cy3 channel of file:
US45102948_253973110006_S01_GE2_107_Sep09_1_4.txt


title: Day0 Neuro2a cell (Total cDNA)

status: Public on Feb 25 2017

type: mixed

city: Klosterneuburg

first: Florian

middle: M

last: Pauler

address: Am Campus 1

country: Austria

institute: IST Austria

hyb_protocol: Hybridisation was performed by imaGenes GmbH (Berlin Germany). In brief: The labeled ds-cDNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC.

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol by imaGenes GmbH (Berlin Germany).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

source_name: Day0 Neuro2a cell

label_protocol: Labelling was performed by imaGenes GmbH (Berlin Germany). In brief: 1 µg ds-cDNA was directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers.

growth_protocol: Neuro2a cells were cultured in DMEM supplemented with 10% FCS, 2mM L-Glutamin, 100 unites/ml penicillin and 100ug/ml streptomycin in 5% CO2 atmosphere at 37°C.

extract_protocol: Total RNA was extracted from different tissues or cells. After the treatment of DNase I, total RNA was reverse transcribed, and synthesized to double-stranded cDNA. The genomic DNA isolated from CCE ES cell line was fragmented and used as Input DNA.

tag: time

value: day 0

tag: genotype/variation

value: wt

molecule: genomic DNA

source_name: Input (CCE Day0, sonicated genomic DNA)

label_protocol: Labelling was performed by imaGenes GmbH (Berlin Germany). In brief: 1 µg ds-cDNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers.

growth_protocol: ESCs were cultured in Hepes-buffered DMEM, supplemented with Leukaemia Inhibitory Factor (LIF), 15% FCS, 50µg/ml Gentamicin, 1× MEM, 1mM NaPyruvate, 2mM L-Glutamin and 2mM β-mercaptoethanol, in 5% CO2 atmosphere at 37°C. For feeder independent ES cell culture, all dishes and flasks were gelatinized with 0.2% Gelatin solution (diluted in DPBS) at RT for 20min before use.

value: CCE

value: Embryonic Stem Cell (ESC)


title: L540_Ago2-IP

description:
L540 Ago2 IP fraction labeled with Cy5
Raw data available in Cy5 channel of file:
US45102948_253973110006_S01_GE2_107_Sep09_1_2.txt


title: KM-H2_Ago2-T

description:
KM-H2 Ago2 Total fraction labeled with Cy5
Raw data available in Cy5 channel of file:
US45102948_253973110006_S01_GE2_107_Sep09_1_3.txt


title: L428_Ago2-T_dye swap

description:
L428 Ago2 Total fraction labeled with Cy3
Raw data available in Cy3 channel of file:
US45102948_253973110004_S01_GE2_107_Sep09_2_2.txt


title: L428_Ago2-T

description:
L428 Ago2 Total fraction labeled with Cy5
Raw data available in Cy5 channel of file:
US45102948_253973110004_S01_GE2_107_Sep09_1_1.txt


title: L1236_Ago2-T

description:
L1236 Ago2 Total fraction labeled with Cy3
Raw data available in Cy3 channel of file:
US45102948_253973110004_S01_GE2_107_Sep09_1_3.txt


title: L540_Ago2-T

description:
L540 Ago2 Total fraction labeled with Cy3
Raw data available in Cy3 channel of file:
US45102948_253973110006_S01_GE2_107_Sep09_1_2.txt


title: Slide 345013

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

description: Sample 1

hyb_protocol: The protocol was performed as described in Kloosterman et al., 2006 and Shafeeq et al., 2011.

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner.

data_processing: Dual-channel array images were analyzed with Genepix 6.  Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP software. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets. Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios  were calculated. Further analysis was performed with a Cyber-T Student T-test for paired data.

organism: Streptococcus pneumoniae D39

source_name: F550 Mean

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).

growth_protocol: Cells were grown in CDM and harvested at respective mid-exponential phase.

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Kloosterman et al., 2006). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

tag: dose

value: 0mM Aspirin

source_name: F650 Mean

value: 5mM Aspirin


title: Slide 345024

description: Sample 2


title: KM-H2_Ago2-IP

description:
KM-H2 Ago2 IP fraction labeled with Cy3
Raw data available in Cy3 channel of file:
US45102948_253973110006_S01_GE2_107_Sep09_1_3.txt


title: KM-H2_Ago2-IP_dye swap

description:
KM-H2 Ago2 IP fraction labeled with Cy5
Raw data available in Cy5 channel of file:
US45102948_253973110006_S01_GE2_107_Sep09_2_3.txt


title: L428_Ago2-IP_dye swap

description:
L428 Ago2 IP fraction labeled with Cy5
Raw data available in Cy5 channel of file:
US45102948_253973110004_S01_GE2_107_Sep09_2_2.txt


title: L428_Ago2-IP

description:
L428 Ago2 IP fraction labeled with Cy3
Raw data available in Cy3 channel of file:
US45102948_253973110004_S01_GE2_107_Sep09_1_1.txt


title: L1236_Ago2-T_dye swap

description:
L1236 Ago2 Total fraction labeled with Cy5
Raw data available in Cy5 channel of file:
US45102948_253973110004_S01_GE2_107_Sep09_2_1.txt


title: L1236_Ago2-IP_dye swap

description:
L1236 Ago2 IP fraction labeled with Cy3
Raw data available in Cy3 channel of file:
US45102948_253973110004_S01_GE2_107_Sep09_2_1.txt


title: L1236_Ago2-IP

description:
L1236 Ago2 IP fraction labeled with Cy5
Raw data available in Cy5 channel of file:
US45102948_253973110004_S01_GE2_107_Sep09_1_3.txt


title: Control_rep12


title: Neuron progenitor dpc 13.5 (Total cDNA)

description: Neuron progenitor dpc 13.5 (Total cDNA)

source_name: Neuron progenitor dpc 13.5 (Total cDNA)

growth_protocol: The cortex of mouse  embryos (dpc 13.5) was dissected in ice-cold PBS. After the removal of meninges, tissues were transferred into NS-A medium and dissociated into single cell suspension mechanically. Then, cells were cultured in NS-A stem cell medium supplemented with N-2 and 10ng/ml of EGF and 10ng/ml of FGF2. Medium was changed after three days to remove cell debris. Neural progenitors were maintained in stem cell medium and used for RNA isolation.

extract_protocol: Total RNA was extracted from different tissues or cells. After the treatment of DNase I, total RNA was reverse transcribed, and synthesized to double-stranded cDNA.

value: Neuron progenitor

extract_protocol: The genomic DNA isolated from CCE ES cell line was fragmented and used as Input DNA.


title: P6 Neonatal Heart (Total cDNA)

description: P6 Neonatal Heart

source_name: P6 Neonatal Heart

value: Neonatal heart


title: Dnmt3ab KO Day5 (Total cDNA, 2nd biological replicate)

description: Dnmt3ab KO Day5 (Total cDNA)

hyb_protocol: The labeled ds-cDNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

source_name: Dnmt3ab KO Day5 (Total cDNA)

label_protocol: 1 µg ds-cDNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

value: day 5

value: Dnmt3ab -/-

source_name: J1 Day5 (Total cDNA)


title: Day7 Neuro2a cell (Total cDNA)

description: Day7 Neuro2a cell

source_name: Day7 Neuro2a cell

treatment_protocol: Differentiation by retinoic acid was induced by deduction of FCS to 2% and addition of 20µM retinoic acid (RA) to the medium. After 7 days incubation, cells were harvested.

value: day 7


title: Dnmt3ab KO Day5 (Total cDNA, 1st biological replicate)

description: Dnmt3ab KO Day5 (Total cDNA)


title: 8.5dpc Dnmt1 null embryo (Total cDNA)

description: 8.5dpc Dnmt1 null embryo

source_name: 8.5dpc Dnmt1 null embryo

value: Embryo whole

value: dpc 8.5

value: Dnmt1 -/-

tag: number of embryos


title: Dnmt3ab KO Day0 (Total cDNA, 2nd biological replicate)

description: Dnmt3ab KO Day0 (Total cDNA)

source_name: Dnmt3ab KO Day0 (Total cDNA)

source_name: J1 Day0 (Total cDNA)


title: Day5 Suz12-/- ESC (Total cDNA)

description: Day5 Suz12-/- ESC (Total cDNA)

source_name: Day5 Suz12-/- ESC (Total cDNA)


title: E14Tg2a Day5 (Total cDNA)

description: E14Tg2a Day5 (Total cDNA)

source_name: E14Tg2a Day5 (Total cDNA)


title: Day5 Neuro2a cell (Total cDNA)

description: Day5 Neuro2a cell

source_name: Day5 Neuro2a cell

treatment_protocol: Differentiation by retinoic acid was induced by deduction of FCS to 2% and addition of 20µM retinoic acid (RA) to the medium. After 5 days incubation, cells were harvested.


title: 8.5dpc Dnmt1 null embryo (Double hyb1, KOvsWT)

description: 8.5dpc Dnmt1 null embryo

source_name: 8.5dpc Dmnt1 het embryo

value: Dnmt1 +/-


title: Day0 Suz12-/- ESC (Total cDNA)

description: Day0 Suz12-/- ESC (Total cDNA)

source_name: Day0 Suz12-/- ESC (Total cDNA)


title: Dnmt3b KO ESC Day5 (Total cDNA)

description: Dnmt3b KO ESC Day5 (Total cDNA)

source_name: Dnmt3b KO ESC Day5 (Total cDNA)

value: Dnmt3b -/-


title: 8.5dpc Dnmt1 null embryo (Double hyb1, WTvsKO)

description: 8.5dpc Dnmt1 null embryo


title: Dnmt3b KO ESC Day0 (Total cDNA)

description: Dnmt3b KO ESC Day0 (Total cDNA)

source_name: Dnmt3b KO ESC Day0 (Total cDNA)

source_name: Input (CCE Day0, sonicated genomic DNA)


title: E14Tg2a Day0 (Total cDNA)

description: E14Tg2a Day0 (Total cDNA)

source_name: E14Tg2a Day0 (Total cDNA)


title: P6 Neonatal Liver (Total cDNA)

description: P6 Neonatal Liver

hyb_protocol: Hybridisation was performed by imaGenes GmbH (Berlin Germany). In brief: The labeled ds-cDNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html).

source_name: P6 Neonatal Liver

value: Neonatal liver


title: Dnmt1KO Day5 (Total cDNA, 2nd biological replicate)

description: Dnmt1KO Day5 (Total cDNA)

source_name: Dnmt1KO Day5 (Total cDNA)


title: Dnmt1KO Day0 (Total cDNA, 2nd biological replicate)

description: Dnmt1KO Day0 (Total cDNA)

source_name: Dnmt1KO Day0 (Total cDNA)

value: day 0


title: Dnmt3a KO ESC Day5 (Total cDNA)

description: Dnmt3a KO ESC Day5 (Total cDNA)

source_name: Dnmt3a KO ESC Day5 (Total cDNA)

value: Dnmt3a -/-


title: Dnmt1KO Day5 (Total cDNA, 1st biological replicate)

description: Dnmt1KO Day5 (Total cDNA)

value: CCE


title: Dnmt1KO Day0 (Total cDNA, 1st biological replicate)

description: Dnmt1KO Day0 (Total cDNA)

value: D

value: Embryonic Stem Cell (ESC)


title: J1 Day5 (Total cDNA)

description: J1 Day5 (Total cDNA)

source_name: J1 Day5 (Total cDNA)


title: Eed-/-62-95 Day0 (Total cDNA)

description: Eed-/-62-95 Day0 (Total cDNA)

source_name: Eed-/-62-95 Day0 (Total cDNA)

value: Eed -/-


title: ΔSX Eed-/- Day0 (Total cDNA)

description: ΔSX Eed-/- Day0 (Total cDNA)

source_name: ΔSX Eed-/- Day0 (Total cDNA)

value: deltaSX Eed-/-


title: Eed-/-, Eed-GFP Day0 (Total cDNA)

description: Eed-/-, Eed-GFP Day0 (Total cDNA)

source_name: Eed-/-, Eed-GFP Day0 (Total cDNA)

value: Eed-/- Eed-GFP


title: 8.5dpc Dmnt1 het embryo (Total cDNA)

description: 8.5dpc Dmnt1 het embryo


title: Dnmt3ab KO Day0 (Total cDNA, 1st biological replicate)

description: Dnmt3ab KO Day0 (Total cDNA)

source_name: Dnmt3ab KO Day0 (Total cDNA)


title: Dnmt3a KO ESC Day0 (Total cDNA)

description: Dnmt3a KO ESC Day0 (Total cDNA)

source_name: Dnmt3a KO ESC Day0 (Total cDNA)


title: J1 Day0 (Total cDNA)

description: J1 Day0 (Total cDNA)

source_name: J1 Day0 (Total cDNA)


title: 12.5dpc placenta (Total cDNA)

description: 12.5dpc placenta (Total cDNA)

source_name: 12.5dpc placenta (Total cDNA)

value: Placenta

value: wt


title: Adult spleen (Total cDNA)

description: Adult spleen (Total cDNA)

source_name: Adult spleen (Total cDNA)

value: Spleen

value: adult


title: Left dentate gyrus, FPI, 90 days, biological rep4 (mRNA)

city: Kuopio

first: Asla

last: Pitkänen

address: P.O.B. 1627 (Neulaniementie 2)

department: Department of Neurobiology

country: Finland

institute: University of Eastern Finland

description:
Left dentate gyrus from injured animal sacrificed after 90 days after FPI
HC6_mrna

hyb_protocol: Affymetrix guidelines for GeneAtlas instrument

scan_protocol: Affymetrix GeneAtlas System

data_processing: R/Bioconductor RMA algorithm implemented in oligo package ver 1.30.0 and pd.ragene.1.1.st.v1_3.10.0

organism: Rattus norvegicus

label_protocol: 100 ng of total mRNA was used for cDNA synthesis using Ambion WT Expression Kit (Life Technologies #4411974).

growth_protocol: Male Sprague-Dawley (Harlan Netherlands B.V., Horst, The Netherlands) weight 300-354 g were housed in a controlled enviroment (21-23 °C, 12h dark/light cycles; humidity 50-60%) with drinking and feeding ad libitum

extract_protocol: Brains were immediately removed from the skull and the left (ipsilateral) hippocampus was dissected out on ice (+4°C). Within 10 min after decapitation, the hippocampus was immersed into 1 ml of ice cold RNAlater RNA Stabilization Reagent (#76106, Qiagen, Hilden, Germany) and stored at -20°C until further processed. For RNA extraction, the hippocampus was cut into transverse slices. The dentate gyrus and hilus were then dissected along the hippocampal fissure under a dissection microscope (SZ-630T, Delta Optical, Poland) using a scalpel blade. Total RNA including miRNA was isolated from the left dentate gyrus region from hippocampi isolated on ice and placed in RNAlater solution (Ambion, AM7024) and stored at -20C until use. Isolation from dissected left dentate gyrus was performed by miRNease Mini kit (QIAGEN, 217004), according to the manufacturer's instructions.

treatment_protocol: The procedure for induction of lateral fluid-percussion injury (FPI). Animals (n = 28) were anesthetized with an intraperitoneal (i.p.) injection of a solution (6 ml/kg) containing sodium pentobarbital (58 mg/kg), chloral hydrate (60 mg/kg), magnesium sulfate (127.2 mg/kg), propylene glycol (42.8%) and absolute ethanol (11.6%), and placed in a Kopf stereotactic frame (David Kopf Instruments, Tujunga, CA, USA). The skull was exposed with a midline skin incision and the periosteum extracted. The left temporal muscle was gently detached from the lateral ridge. A circular craniectomy (Ø 5 mm) was performed over the left parietal lobe midway between lambda and bregma, leaving the dura mater intact. The edges of the craniectomy were sealed with a modified Luer lock cap that was filled with saline while the calvaria was covered with dental acrylate (Selectaplus CN, Dentsply DeTrey GmbH, Dreieich, Germany). Lateral FPI was produced 90 min after the induction of anesthesia by connecting the rat to a fluid-percussion device (AmScien Instruments, Richmond, VA, USA) via a female Luer lock fitting. The mean severity of the impact was 3.23±0.01 atm (min 3.13 - max 3.35 atm) in the group of animals used for the gene expression analysis (n=18) and 3.15±0.02 atm (min 3.05 - max 3.25 atm) in the group of animals used for immunohistochemistry (n=10). Control animals (n=18) received anesthesia and all surgical procedures without impact. From all surviving injured and sham-operated animals, we randomly selected 6 TBI and 5 control rats for gene expression analysis. Analysis of gene expression and miRNAs. At 3 months post-TBI, the rats were anesthetized with CO2 and decapitated with a guillotine.

value: Sprague-Dawley

tag: tissue

value: dentate gyrus

value: 90 days after stimulation

tag: gender

value: male

tag: treatment

value: FPI


title: Left dentate gyrus, FPI, 90 days, biological rep5 (mRNA)

description:
Left dentate gyrus from injured animal sacrificed after 90 days after FPI
HC13_mrna

tag: strain


title: Left dentate gyrus, FPI, 90 days, biological rep6 (mRNA)

description:
Left dentate gyrus from injured animal sacrificed after 90 days after FPI
HC15_mrna


title: Adult bone marrow (Total cDNA)

description: Adult bone marrow (Total cDNA)

source_name: Adult bone marrow (Total cDNA)

value: Bone marrow

value: day 0


title: Left dentate gyrus, FPI, 90 days, biological rep3 (mRNA)

description:
Left dentate gyrus from injured animal sacrificed after 90 days after FPI
HC4_mrna


title: Left dentate gyrus, FPI, 90 days, biological rep2 (mRNA)

description:
Left dentate gyrus from injured animal sacrificed after 90 days after FPI
HC2_mrna


title: Left dentate gyrus, FPI, 90 days, biological rep1 (mRNA)

description:
Left dentate gyrus from injured animal sacrificed after 90 days after FPI
HC1_mrna


title: p14 noxt 3

city: Bad Nauheim

first: Rory

last: Morty

address: Parkstr. 1

department: W.G. Kerckhoff-Institut

institute: MPI für Herz- und Lungenforschung

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray (GPL10787) for 18 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20150604) to obtain background subtracted and spatially detrended Processed Signal intensities. Features which were not positive and significant, not above background or were population outliers were flagged as “Compromised”. If features were flagged “Compromised” in all samples, than they were excluded.

source_name: lung tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick-Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Mice were euthanized with pentobarbital in the case of the P5.5 time-point or with isoflurane for the P14.5. Thoracic cavities were opened and lungs were perfused through the heart with PBS until lungs were white-colored. Lungs were harvested, placed into tubes containing RNA later (Qiagen 76104), stored at -20°C and homogenized with Precellys 24 homogenizer. RNA isolation was performed with the miRNeasy Kit (Qiagen 217004) following the manufacturer’s instructions.

treatment_protocol: Newborn mice were concomitantly treated with antagomiR-scrambled (SCR) or antagomiR-34a (A34a) and exposed either to normoxia (21% O2) or hyperoxia (85% O2).

value: antagomiR

tag: exposed

value: normoxia

tag: time point


title: Adult heart (Total cDNA)

description: Adult heart (Total cDNA)

source_name: Adult heart (Total cDNA)

value: Heart

tag: genotype

source_name: Input (CCE Day0, sonicated genomic DNA)

value: Embryonic Stem Cell (ESC)

value: CCE


title: Adult lung (Total cDNA)

description: Adult lung (Total cDNA)

source_name: Adult lung (Total cDNA)

tag: cell type

value: Lung


title: p14 noxt 4


title: Left dentate gyrus, sham operated, 90 days, biological rep5 (mRNA)

description:
Left dentate gyrus from sham operated animal, time matched control for animal sacrificed after 90 days after FPI
HC18_mrna

value: sham operated


title: Visceral Yolk Sac dpc14.5 (Total cDNA)

description: Visceral Yolk Sac dpc14.5 (Total cDNA)

source_name: Visceral Yolk Sac dpc14.5 (Total cDNA)

value: Visceral Yolk Sac (VYS)


title: Fetal head dpc14.5 (Total cRNA, 1st biological replicate)

description: Fetal head dpc14.5 (Total RNA)

source_name: Fetal head dpc14.5 (Total RNA)

value: Fetal head

value: wt


title: CCE Day5 (Total cDNA, 2nd biological replicate)

treatment_protocol: The differentiation of ESC by retinoic acid was induced by withdrawal of LIF and addition of 0.266µM retinoic acid (RA). Cells were plated at appropriate densities to be confluent at the day of harvesting. Cells were fed each third day and harvested at the indicated time points.

value: day 5

source_name: Input (CCE Day5, sonicated genomic DNA)

treatment_protocol: The differentiation of ESC by retinoic acid was induced by withdrawal of LIF and addition of 0.266µM retinoic acid (RA) to the medium (80ng/ml). Cells were plated at appropriate densities to be confluent at the day of harvesting. Cells were fed each third day and harvested at the indicated time points.


title: Adult skeletal muscle (Total cDNA)

description: Adult skeletal muscle (Total cDNA)

source_name: Adult skeletal muscle (Total cDNA)

value: Muscle

value: adult


title: Fetal head dpc11.5 (Total cDNA)

description: Fetal head dpc11.5 (Total cDNA)

source_name: Fetal head dpc11.5 (Total cDNA)


title: CCE Day0 (Total cDNA, 2nd biological replicate)


title: Adult uterus (Total cDNA)

description: Adult uterus (Total cDNA)

source_name: Adult uterus (Total cDNA)

value: Uterus


title: Left dentate gyrus, sham operated, 90 days, biological rep3 (mRNA)

description:
Left dentate gyrus from sham operated animal, time matched control for animal sacrificed after 90 days after FPI
HC9_mrna

value: Sprague-Dawley

value: dentate gyrus

value: 90 days after stimulation

value: male


title: Fetal head dpc14.5 (Total cRNA, 2nd biological replicate)

description: Fetal head dpc14.5 (Total RNA)

value: day 0


title: Fetal liver dpc14.5 (Total cDNA)

description: Fetal liver dpc14.5 (Total cDNA)

source_name: Embryo liver dpc14.5 (Total cDNA)

value: Embryo liver


title: Visceral Yolk Sac dpc12.5 (Total cDNA, 2nd biological replicate)

value: Embryonic Stem Cell (ESC)


title: Adult liver (Total cDNA)

description: Adult liver (Total cDNA)

source_name: Adult liver (Total cDNA)

value: Liver

value: CCE


title: Fetal head dpc14.5 (Total cDNA)

description: Fetal head dpc14.5 (Total cDNA)

source_name: Fetal head dpc14.5 (Total cDNA)


title: Adult testis (Total cDNA)

description: Adult testis (Total cDNA)

source_name: Adult testis (Total cDNA)

value: Testis


title: Adult brain (Total cDNA)

description: Adult brain (Total cDNA)

source_name: Adult brain (Total cDNA)

value: Brain


title: Left dentate gyrus, sham operated, 90 days, biological rep2 (mRNA)

description:
Left dentate gyrus from sham operated animal, time matched control for animal sacrificed after 90 days after FPI
HC8_mrna

value: sham operated


title: CCE Day0 (Total cDNA, 1st biological replicate)


title: Wt MEF Nuclear cDNA

description:
ch1 molecule: nuclear cDNA
ch2 molecule: cytoplasmic cDNA
Wt MEF Nuclear cDNA

source_name: Wt MEF Nuclear cDNA

growth_protocol: MEF cells were cultured in DMEM supplemented with 10% FCS, 50µg/ml Gentamicin, 2mM L-Glutamin, in 5% CO2 atmosphere at 37°C. Cells were split every 3rd day by washing with DPBS and trypsinizing cells with 0.25% Trypsin-EDTA.

value: MEF

value: wt

source_name: Wt MEF Cytoplasmic cDNA


title: p14 noxs 3

source_name: lung tissue

value: scrambled

value: normoxia


title: Visceral Yolk Sac dpc12.5 (Total cDNA, 1st biological replicate)

value: Visceral Yolk Sac (VYS)


title: p14 noxt 2

value: antagomiR


title: CCE Day5 (Total cDNA, 1st biological replicate)

value: day 5


title: Embryo dpc12.5 (Total cDNA, 1st biological replicate)

value: Embryo whole

source_name: Input (Embryo dpc12.5, sonicated genomic DNA)

extract_protocol: The genomic DNA isolated from Embryo (12.5 dpc) was fragmented and used as Input DNA.


title: ThpM5 (Total cDNA, Thp/+ MEF)

description: ThpM5 (Total cDNA, Thp/+ MEF)

source_name: ThpM5 (Total cDNA, Thp/+ MEF)

value: Thp/+

source_name: Input (CCE Day0, sonicated genomic DNA)


title: ThpP5 (Total cDNA, +/Thp MEF)

description: ThpP5 (Total cDNA, +/Thp MEF)

source_name: ThpP5 (Total cDNA, +/Thp MEF)

value: +/Thp

value: day 0


title: p14 noxs 1


title: p14 hyxt 4

value: hyperoxia


title: Left dentate gyrus, FPI, 90 days, biological rep6 (miRNA)

description:
Left dentate gyrus from injured animal sacrificed after 90 days after FPI
HC15_mirna

hyb_protocol: The hybridization was performed according to the miRCURY LNATM microRNA Array Instruction manual using a Tecan HS4800TM hybridization station (Tecan, Austria). [Service conducted at Exiqon Services, Denmark.]

scan_protocol: The microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY LNATM microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 9.0 software (BioDiscovery, Inc., USA).  [Service conducted at Exiqon Services, Denmark.]

data_processing: The quantified signals were background corrected (Normexp with offset value 10, see Ritchie et al. 2007) and normalized using quantile normalization method. [Service conducted at Exiqon Services, Denmark.]

label_protocol: 750 ng total RNA from sample was labeled with Hy3TM fluorescent label, using the miRCURY LNATM microRNA Hi-Power Labeling Kit, Hy3TM/Hy5TM (Exiqon, Denmark) following the procedure described by the manufacturer. The Hy3TM-labeled samples were hybridized to the miRCURY LNATM microRNA Array 7'th (Exiqon, Denmark), which contains capture probes targeting all microRNAs for human, mouse or rat registered in the miRBASE 18.0. [Service conducted at Exiqon Services, Denmark.]

value: Sprague-Dawley

value: dentate gyrus

value: 90 days after stimulation

value: male

value: FPI


title: Embryo dpc12.5 (Total cDNA, 2nd biological replicate)


title: Left dentate gyrus, sham operated, 90 days, biological rep1 (mRNA)

description:
Left dentate gyrus from sham operated animal, time matched control for animal sacrificed after 90 days after FPI
HC7_mrna

value: sham operated


title: p14 noxs 4


title: Left dentate gyrus, FPI, 90 days, biological rep4 (miRNA)

description:
Left dentate gyrus from injured animal sacrificed after 90 days after FPI
HC6_mirna


title: Left dentate gyrus, FPI, 90 days, biological rep5 (miRNA)

description:
Left dentate gyrus from injured animal sacrificed after 90 days after FPI
HC13_mirna


title: p14 hyxt 1


title: p14 hyxt 2


title: p5 hyxt 2


title: p5 hyxs 4


title: Left dentate gyrus, sham operated, 90 days, biological rep4 (mRNA)

description:
Left dentate gyrus from sham operated animal, time matched control for animal sacrificed after 90 days after FPI
HC10_mrna


title: p5 hyxs 2


title: p5 hyxt 3


title: p14 hyxs 3


title: p14 hyxt 3


title: p14 hyxs 4


title: Left dentate gyrus, FPI, 90 days, biological rep3 (miRNA)

description:
Left dentate gyrus from injured animal sacrificed after 90 days after FPI
HC4_mirna


title: p5 hyxt 4


title: p5 hyxs 1


title: p14 hyxs 1


title: Left dentate gyrus, FPI, 90 days, biological rep2 (miRNA)

description:
Left dentate gyrus from injured animal sacrificed after 90 days after FPI
HC2_mirna


title: p14 hyxs 2


title: p5 hyxt 1


title: p5 hyxs 3


title: Left dentate gyrus, sham operated, 90 days, biological rep4 (miRNA)

description:
Left dentate gyrus from sham operated animal, time matched control for animal sacrificed after 90 days after FPI
HC10_mirna


title: Left dentate gyrus, FPI, 90 days, biological rep1 (miRNA)

description:
Left dentate gyrus from injured animal sacrificed after 90 days after FPI
HC1_mirna


title: Left dentate gyrus, sham operated, 90 days, biological rep5 (miRNA)

description:
Left dentate gyrus from sham operated animal, time matched control for animal sacrificed after 90 days after FPI
HC18_mirna


title: Left dentate gyrus, sham operated, 90 days, biological rep1 (miRNA)

description:
Left dentate gyrus from sham operated animal, time matched control for animal sacrificed after 90 days after FPI
HC7_mirna


title: Left dentate gyrus, sham operated, 90 days, biological rep2 (miRNA)

description:
Left dentate gyrus from sham operated animal, time matched control for animal sacrificed after 90 days after FPI
HC8_mirna


title: p14 noxt 1


title: Group 4,  Hyp, 31

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-035430 8x60K Mouse miRNA Rel17 Microarray (GPL15547) for 20 hours at 55°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol miRNA_107_Sep09 and Grid: 035430_D_F_20111226 ) to obtain background subtracted and spatially detrended Processed Signal intensities. Features which were not positive and significant, not above background or were population outliers were flagged as “Compromised”. If features were flagged “Compromised” in all samples, than they were excluded.

extract_protocol: Mice were euthanized with pentobarbital for early time-points (from P2.5 to P5.5) or with isoflurane for P14.5. Thoracic cavities were opened and lungs were perfused through the heart with PBS until lungs were white colored. Lungs were harvested, placed into tubes and immediately frozen to liquid nitrogen and homogenized with Precellys 24 homogenizer. RNA isolation was performed with the miRNeasy Kit (Qiagen 217004) following the manufacturer’s instructions.

treatment_protocol: Pups were randomized on the day of birth and litters were balanced. 4 cages were placed in normoxia whereas 4 cages in hyperoxia. Then, pups of the same age being placed in normoxia or hyperoxia were sacrificed on the same time-point.

tag: age

value: harvested at P14.5


title: Group 4,  Hyp, 32


title: Group 4,  Hyp, 30


title: p5 noxt 2


title: p5 noxt 4


title: p5 noxt 3


title: p5 noxs 4

value: scrambled


title: p5 noxs 2

value: normoxia


title: p5 noxt 1


title: p5 noxs 1


title: Left dentate gyrus, sham operated, 90 days, biological rep3 (miRNA)

description:
Left dentate gyrus from sham operated animal, time matched control for animal sacrificed after 90 days after FPI
HC9_mirna


title: Group 4, Nox , 28


title: Group 4, Nox , 27


title: Group 4,  Hyp, 29


title: Group 4, Nox , 26


title: Group 3,  Hyp, 24

value: harvested at P5.5


title: Group 3,  Hyp, 23


title: p5 noxs 3


title: Group 4, Nox , 25


title: Group 3,  Hyp, 22


title: 20mGyAA3/ reference male mouse8

type: genomic

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: OGURA

state: Aomori

address: Takahoko, Hacchasawa,

department: Department of Radiobiology

country: Japan

institute: Institute for Environmental Science

description: 20mGyAA3 Cy5

hyb_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing: Agilent Genomic Workbench Software (v 7.0.) was used.

extract_protocol: PI-50a (Kurabo Industries LTD.) tissue DNA extraction protocol.

value: tail

source_name: reference male mouse8


title: reference male mouse8/ 20mGyAA4

description: 20mGyAA4 Cy3

label_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8


title: reference male mouse8/ 20mGyAA5

description: 20mGyAA5 Cy3


title: 20mGyAA2/ reference male mouse8

description: 20mGyAA2 Cy5


title: 20mGyAA5/ reference male mouse8

description: 20mGyAA5 Cy5


title: reference male mouse8/ 20mGyAA3

description: 20mGyAA3 Cy3


title: 20mGyAA4/ reference male mouse8

description: 20mGyAA4 Cy5


title: 20mGyAA1/ reference male mouse8

description: 20mGyAA1 Cy5


title: reference male mouse8/ 20mGyAAF

description: 20mGyAAF Cy3


title: reference male mouse8/ 20mGyAA2

description: 20mGyAA2 Cy3


title: Group 3,  Hyp, 21


title: Group 3, Nox , 20


title: HA-Rec8 ChIP in rec8 overexpression_rep2

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

description: HA-rec8 rec8OE_rep2

hyb_protocol: Equal amounts of Cy5-labeled ChIP DNA and Cy3-labeled  whole-cell extract DNA were mixed and combined with human Cot1 DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density  microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Data were extracted using Agilent Feature Extraction Software (CHIP-v1_95_May07 or ChIP-v1_10_Apr08 protocol). Signal was normalized by combined rank consistency filtering with LOWES intensity normalization.

organism: Schizosaccharomyces pombe

source_name: log. growing cells_ChIP

label_protocol: ChIP and whole-cell extract DNA was amplified by random-primed PCR and conjugated with Cy5 (ChIP DNA) or Cy3 (whole-cell extract DNA).

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YEA). Cultures were grown at 30˚C.

extract_protocol: Fixed cells were lysed with glass-beads, DNA sheared by sonication to 500-1000bp fragments and immunoprecipitated with Anti-HA (12CA5, Roche), Anti-HA (16B12, Biolegend) and Anti-GFP (ab290, Abcam) . Immunoprecipitated DNA was recovered by incubation with protein A/G slurry and reversed-crosslinked at 65˚C.

treatment_protocol: Exponentially growing cells were fixed in 3% paraformaldehyde at 30˚C. Prior fixation cells were incubated at 18˚C for 2h.

tag: strain information

tag: molecule subtype

value: HA-Rec8 immunoprecipitated DNA (16B12)

source_name: log. growing cells_WCE

value: Whole-cell extract DNA


title: Rec11-ChIP ChIP in mmi1D cells

source_name: log. growing cells

extract_protocol: Fixed cells were lysed with glass-beads, DNA sheared by sonication to 500-1000bp fragments and immunoprecipitated with GFP antibody (Abcam, ab290). Immunoprecipitated DNA was recovered by incubation with protein A/G slurry and reversed-crosslinked at 65˚C.

treatment_protocol: Exponentially growing cells were fixed in 3% paraformaldehyde at 30˚C. Prior fixation cells were incubated at 18˚C for 2h

value: mmi1D cells

tag: fraction

value: Rec11-GFP immunoprecipitated DNA


title: HA-Rec8 ChIP in rec8 overexpression_rep1

description: HA-rec8 rec8OE_rep1

value: HA-Rec8 immunoprecipitated DNA (12CA5)


title: 20mGyAAF/ reference male mouse8

description: 20mGyAAF Cy5


title: p14 noxs 2


title: Group 3, Nox ,19


title: reference male mouse8/ 20mGyAA1

description: 20mGyAA1 Cy3


title: reference male mouse8/ 20mGyAAM

description: 20mGyAAM Cy3


title: HA-Rec8 ChIP in wt_rep1

description: HA-rec8 wt_rep1

value: wild type


title: Rad21-GFP ChIP in mmi1d

description: Rad21-GFP ChIP mmi1∆

value: mei4 mmi1∆

value: Rad21-GFP immunoprecipitated DNA


title: HA-Rec8 ChIP in mmi1d_rep1

description: HA-rec8 mmi1∆_rep1


title: Rec11-ChIP in wt cells


title: Group 3, Nox ,18


title: HA-Rec8 ChIP in wt_rep2

description: HA-rec8 wt_rep2


title: Group 2,  Hyp, 16

value: harvested at P3.5

value: hyperoxia


title: Group 2,  Hyp, 15


title: Group 2,  Hyp, 14


title: Psc3-GFP ChIP in mmi1d rec8d

description: Psc3-GFP ChIP mmi1∆ rec8∆

value: mei4 mmi1∆ rec8∆

value: Psc3-GFP immunoprecipitated DNA


title: Psc3-GFP ChIP in wt

description: Psc3-GFP ChIP wt_rep2


title: 20mGyT2/ reference male mouse4

description: 20mGyT2 Cy5

source_name: reference male mouse4


title: Psc3-GFP ChIP in mmi1d

description: Psc3-GFP ChIP mmi1∆


title: reference male mouse4/ 20mGyT2

description: 20mGyT2 Cy3


title: Rad21-GFP ChIP in wt

description: Rad21-GFP ChIP wt


title: H3K9me2 ChIP in mmi1d cells

source_name: H3K9me2 ChIP DNA

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YEA) for H3K9me2 and Psc3-GFP and minimal medium PMG for Rec8-GFP. Cultures were grown at 30˚C.

extract_protocol: Fixed cells were lysed with glass-beads, DNA sheared by sonication to 500-1000bp fragments and immunoprecipitated with H3K9dime antibody (Abcam,ab1220) or GFP antibody (Abcam, ab290). Immunoprecipitated DNA was recovered by incubation with protein A/G slurry and reversed-crosslinked at 65˚C.

treatment_protocol: Exponentially growing cells were fixed in 3% paraformaldehyde at 30˚C. Prior fixation cells were incubated at 18˚C for 2h (Psc3 and Rec8 ChIPs)

tag: growth stage

value: log growing cells

value: mmi1d cells

tag: antibody

source_name: Whole-cell extract DNA

value: whole-cell extract


title: HA-Rec8 ChIP in mmi1d_rep2

description: HA-rec8 mmi1∆_rep2


title: 20mGyT1/ reference male mouse4

description: 20mGyT1 Cy5


title: Group 2, Nox , 12

value: normoxia


title: Psc3-GFP ChIP in WT cells

source_name: Psc3-GFP ChIP DNA

tag: genotype/variation


title: Psc3-GFP ChIP in dcr1d cells

value: dcr1d cells


title: H3K9me2 ChIP in WT cells


title: reference male mouse4/ 20mGyT1

description: 20mGyT1 Cy3

value: tail


title: 20mGyTF/ reference male mouse4

description: 20mGyTF Cy5


title: H3K9me2 ChIP in mei4 cells

value: mei4 cells


title: 20mGyTM/ reference male mouse4

description: 20mGyTM Cy5


title: 20mGyZ5/ reference male mouse8

description: 20mGyZ5 Cy5


title: reference male mouse4/ 20mGyTF

description: 20mGyTF Cy3


title: reference male mouse8/ 20mGyZ5

description: 20mGyZ5 Cy3


title: Group 2,  Hyp, 13


title: reference male mouse4/ 20mGyTM

description: 20mGyTM Cy3


title: 20mGyZ3/ reference male mouse8

description: 20mGyZ3 Cy5


title: Psc3-GFP ChIP in clr4d cells

value: clr4d cells


title: 20mGyAAM/ reference male mouse8

description: 20mGyAAM Cy5


title: Group 2, Nox , 11


title: 20mGyZ4/ reference male mouse8

description: 20mGyZ4 Cy5


title: Group 3, Nox , 17

value: harvested at P5.5


title: 20mGyZ2/ reference male mouse8

description: 20mGyZ2 Cy5


title: Group 2, Nox , 10


title: reference male mouse8/ 20mGyZ2

description: 20mGyZ2 Cy3


title: reference male mouse8/ 20mGyZ4

description: 20mGyZ4 Cy3


title: Group 2, Nox , 9


title: Group 1,  Hyp, 8

value: harvested at P2.5


title: Group 1,  Hyp, 7


title: 20mGyS3/ reference male mouse4

description: 20mGyS3 Cy5


title: reference male mouse8/ 20mGyZ3

description: 20mGyZ3 Cy3


title: reference male mouse4/ 20mGyS3

description: 20mGyS3 Cy3


title: 20mGyZ1/ reference male mouse8

description: 20mGyZ1 Cy5


title: reference male mouse8/ 20mGyZ1

description: 20mGyZ1 Cy3


title: 20mGyY6/ reference male mouse8

description: 20mGyY6 Cy5


title: 20mGyZF/ reference male mouse8

description: 20mGyZF Cy5


title: reference male mouse8/ 20mGyZF

description: 20mGyZF Cy3


title: 20mGyZM/ reference male mouse8

description: 20mGyZM Cy5


title: 20mGyS2/ reference male mouse4

description: 20mGyS2 Cy5


title: Group 1,  Hyp, 6


title: reference male mouse8/ 20mGyY6

description: 20mGyY6 Cy3


title: reference male mouse4/ 20mGyS2

description: 20mGyS2 Cy3


title: reference male mouse4/ 20mGyS1

description: 20mGyS1 Cy3


title: Group 1,  Hyp, 5


title: 20mGyY5/ reference male mouse8

description: 20mGyY5 Cy5


title: 20mGyS1/ reference male mouse4

description: 20mGyS1 Cy5


title: Group 1, Nox, 4


title: 20mGySF/ reference male mouse4

description: 20mGySF Cy5


title: Group 1, Nox, 2


title: reference male mouse8/ 20mGyY5

description: 20mGyY5 Cy3


title: reference male mouse4/ 20mGySM

description: 20mGySM Cy3


title: reference male mouse8/ 20mGyZM

description: 20mGyZM Cy3


title: 20mGyY4/ reference male mouse8

description: 20mGyY4 Cy5


title: 20mGyY2/ reference male mouse8

description: 20mGyY2 Cy5


title: reference male mouse8/ 20mGyY2

description: 20mGyY2 Cy3


title: reference male mouse4/ 20mGySF

description: 20mGySF Cy3


title: Group 1, Nox, 1


title: 20mGyY3/ reference male mouse8

description: 20mGyY3 Cy5


title: reference male mouse8/ 20mGyY3

description: 20mGyY3 Cy3


title: reference male mouse8/ 20mGyY4

description: 20mGyY4 Cy3


title: 20mGyY1/ reference male mouse8

description: 20mGyY1 Cy5


title: reference male mouse8/ 20mGyY1

description: 20mGyY1 Cy3


title: 20mGyYF/ reference male mouse8

description: 20mGyYF Cy5


title: 20mGyX6/ reference male mouse7

description: 20mGyX6 Cy5

source_name: reference male mouse7


title: reference male mouse8/ 20mGyYM

description: 20mGyYM Cy3


title: reference male mouse8/ 20mGyYF

description: 20mGyYF Cy3


title: reference male mouse7/ 20mGyX6

description: 20mGyX6 Cy3


title: 20mGyV6/ reference male mouse9

description: 20mGyV6 Cy5

source_name: reference male mouse9


title: SKM-1_RPL23-KD_rep3

city: Shanghai

first: Yuekun

last: Qi

state: Shanghai

address: No.600 Yishan Road

department: Department of Hematology

institute: Shanghai Jiao Tong University Affiliated Sixth People’s Hospital

description: an human acute myeloid leukaemia cell line established in the leukaemic phase during the progression from MDS to AML (MDS/AML)

hyb_protocol: Following fragmentation, 130 ul preliminary hybrid liquid was hybridized for 16 hr at 45℃ on a GeneChip® PrimeView™ Human Gene Expression Array (Affymetrix, Santa Clara, USA). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Background correction, normalization, and expression calculations were performed using Robust Multichip Average (RMA).

source_name: SKM-1 cells transfected with vectors carrying LV-RPL23-RNAi-EGFP (KD).

label_protocol: cDNA and biotinylated cRNA were synthesized according to the manufacturer’ instructions (GeneChip 3’IVT Express Kit) from 500 ng total RNA.

growth_protocol: SKM-1 (an acute myeloid leukaemia cell line established in the leukaemic phase during the progression from MDS to AML (MDS/AML)) cells (Health Science Research Resources Bank, Japan) were grown in RPMI-1640 medium (Gibco, US) containing 10% heat-inactivated foetal bovine serum, 100 IU/ml penicillin, and 100 μg/ml streptomycin in a humidified atmosphere of 5% CO2 at 37℃.

extract_protocol: Transfected SKM-1 cells were harvested 3 days after lentiviral infection. Total RNA was extracted using TRIzol® reagent (Invitrogen) and passed quality tests (NanoDrop 2000 and Agilent Bioanalyzer 2100) according to the manufacturer's instructions.

treatment_protocol: lentiviral vectors carrying LV-RPL23-RNAi-EGFP (KD group) and LV-RPL23-NC-EGFP (NC group) were constructed to produce lentivirus venom (Genechem, Shanghai, China). The supernatants of different virus-producing cells were used to transfect SKM-1 cells in combination with 5 mg/ml Polybrene (Genechem, Shanghai, China) at an appropriate MOI of 20 according to the manufacturer’s instructions. GFP expression was examined by performing flow cytometry after 48 h of infection, and knockdown efficiency was testified by qRT-PCR and western blotting as over 90%.

tag: tumor stage


title: reference male mouse7/ 20mGyX7

description: 20mGyX7 Cy3


title: 20mGyX5/ reference male mouse7

description: 20mGyX5 Cy5


title: SKM-1_RPL23-NC_rep3

source_name: SKM-1 cells transfected with vectors carrying LV-RPL23-NC-EGFP (NC).

value: an acute myeloid leukaemia cell line established in the leukaemic phase during the progression from MDS to AML (MDS/AML)


title: SKM-1_RPL23-KD_rep2


title: SKM-1_RPL23-KD_rep1


title: reference male mouse9/ 20mGyV5

description: 20mGyV5 Cy3


title: reference male mouse7/ 20mGyX4

description: 20mGyX4 Cy3


title: 20mGyYM/ reference male mouse8

description: 20mGyYM Cy5


title: 20mGyI6/ reference male mouse3

source_name: reference male mouse3


title: 20mGyI5/ reference male mouse3


title: 20mGyX4/ reference male mouse7

description: 20mGyX4 Cy5


title: reference male mouse3/ 20mGyI7


title: 20mGyI7/ reference male mouse3


title: reference male mouse3/ 20mGyI5


title: reference male mouse3/ 20mGyI6


title: reference male mouse7/ 20mGyX5

description: 20mGyX5 Cy3


title: 20mGyX7/ reference male mouse7

description: 20mGyX7 Cy5


title: 20mGyV4/ reference male mouse9

description: 20mGyV4 Cy5


title: reference male mouse9/ 20mGyV6

description: 20mGyV6 Cy3


title: 20mGyV5/ reference male mouse9

description: 20mGyV5 Cy5


title: Group 1, Nox, 3

source_name: lung tissue


title: SKM-1_RPL23-NC_rep1


title: reference male mouse7/ 20mGyX3

description: 20mGyX3 Cy3


title: 20mGyX1/ reference male mouse7

description: 20mGyX1 Cy5


title: SKM-1_RPL23-NC_rep2


title: reference male mouse9/ 20mGyV4

description: 20mGyV4 Cy3


title: 20mGyV3/ reference male mouse9

description: 20mGyV3 Cy5


title: 20mGyI3/ reference male mouse3


title: 20mGyXF/ reference male mouse7

description: 20mGyXF Cy5


title: reference male mouse9/ 20mGyV2

description: 20mGyV2 Cy3


title: reference male mouse9/ 20mGyV3

description: 20mGyV3 Cy3


title: reference male mouse4/ 20mGyR4

description: 20mGyR4 Cy3


title: reference male mouse7/ 20mGyX1

description: 20mGyX1 Cy3


title: 20mGySM/ reference male mouse4

description: 20mGySM Cy5


title: 20mGyX2/ reference male mouse7

description: 20mGyX2 Cy5


title: 20mGyX3/ reference male mouse7

description: 20mGyX3 Cy5


title: reference male mouse3/ 20mGyI3


title: reference male mouse7/ 20mGyX2

description: 20mGyX2 Cy3


title: reference male mouse3/ 20mGyI1


title: 20mGyV2/ reference male mouse9

description: 20mGyV2 Cy5


title: 20mGyI1/ reference male mouse3


title: 20mGyR4/ reference male mouse4

description: 20mGyR4 Cy5


title: reference male mouse3/ 20mGyI4


title: reference male mouse9/ 20mGyV1

description: 20mGyV1 Cy3


title: 20mGyVF/ reference male mouse9

description: 20mGyVF Cy5


title: 20mGyR3/ reference male mouse4

description: 20mGyR3 Cy5


title: reference male mouse7/ 20mGyXF

description: 20mGyXF Cy3


title: 20mGyI2/ reference male mouse3


title: reference male mouse3/ 20mGyI2


title: 20mGyI4/ reference male mouse3


title: 20mGyV1/ reference male mouse9

description: 20mGyV1 Cy5


title: reference male mouse9/ 20mGyVF

description: 20mGyVF Cy3


title: 20mGyXM/ reference male mouse7

description: 20mGyXM Cy5


title: reference male mouse4/ 20mGyR3

description: 20mGyR3 Cy3


title: 20mGyIF/ reference male mouse3


title: 20mGyM7/ reference male mouse3

description: 20mGyM7 Cy5


title: reference male mouse4/ 20mGyR2

description: 20mGyR2 Cy3


title: reference male mouse3/ 20mGyM7

description: 20mGyM7 Cy3


title: 20mGyVM/ reference male mouse9

description: 20mGyVM Cy5


title: 20mGyR2/ reference male mouse4

description: 20mGyR2 Cy5


title: 20mGyN6/ reference male mouse3

description: 20mGyN6 Cy5


title: 20mGyN5/ reference male mouse3

description: 20mGyN5 Cy5


title: reference male mouse3/ 20mGyIM


title: reference male mouse3/ 20mGyN5

description: 20mGyN5 Cy3


title: 20mGyH5/ reference male mouse3


title: reference male mouse4/ 20mGyRF

description: 20mGyRF Cy3


title: 20mGyR1/ reference male mouse4

description: 20mGyR1 Cy5


title: reference male mouse4/ 20mGyR1

description: 20mGyR1 Cy3


title: 20mGyIM/ reference male mouse3


title: reference male mouse3/ 20mGyH6


title: 20mGyRF/ reference male mouse4

description: 20mGyRF Cy5


title: 20mGyH6/ reference male mouse3


title: 20mGyM8/ reference male mouse3

description: 20mGyM8 Cy5


title: reference male mouse9/ 20mGyVM

description: 20mGyVM Cy3


title: reference male mouse3/ 20mGyN4

description: 20mGyN4 Cy3


title: reference male mouse3/ 20mGyN6

description: 20mGyN6 Cy3


title: 20mGyM6/ reference male mouse3

description: 20mGyM6 Cy5


title: reference male mouse3/ 20mGyM6

description: 20mGyM6 Cy3


title: reference male mouse7/ 20mGyXM

description: 20mGyXM Cy3


title: reference male mouse3/ 20mGyH5


title: reference male mouse3/ 20mGyM8

description: 20mGyM8 Cy3


title: 20mGyRM/ reference male mouse4

description: 20mGyRM Cy5


title: reference male mouse3/ 20mGyIF


title: 20mGyN4/ reference male mouse3

description: 20mGyN4 Cy5


title: 20mGyH4/ reference male mouse3


title: 20mGyM5/ reference male mouse3

description: 20mGyM5 Cy5


title: reference male mouse4/ 20mGyRM

description: 20mGyRM Cy3


title: reference male mouse3/ 20mGyM5

description: 20mGyM5 Cy3


title: 20mGyN3/ reference male mouse3

description: 20mGyN3 Cy5


title: reference male mouse3/ 20mGyH4


title: 20mGyM4/ reference male mouse3

description: 20mGyM4 Cy5


title: reference male mouse3/ 20mGyN1

description: 20mGyN1 Cy3


title: reference male mouse3/ 20mGyM4

description: 20mGyM4 Cy3


title: 20mGyN2/ reference male mouse3

description: 20mGyN2 Cy5


title: reference male mouse3/ 20mGyH3


title: reference male mouse3/ 20mGyH2


title: 20mGyH3/ reference male mouse3


title: 20mGyQ3/ reference male mouse3

description: 20mGyQ3 Cy5


title: reference male mouse3/ 20mGyN3

description: 20mGyN3 Cy3


title: 20mGyNF/ reference male mouse3

description: 20mGyNF Cy5


title: 20mGyQ4/ reference male mouse3

description: 20mGyQ4 Cy5


title: 20mGyM3/ reference male mouse3

description: 20mGyM3 Cy5


title: 20mGyH2/ reference male mouse3


title: reference male mouse3/ 20mGyH1


title: 20mGyQ2/ reference male mouse3

description: 20mGyQ2 Cy5


title: 20mGyN1/ reference male mouse3

description: 20mGyN1 Cy5


title: reference male mouse3/ 20mGyN2

description: 20mGyN2 Cy3


title: 20mGyH1/ reference male mouse3


title: 20mGyM2/ reference male mouse3

description: 20mGyM2 Cy5


title: reference male mouse3/ 20mGyM2

description: 20mGyM2 Cy3


title: reference male mouse3/ 20mGyQ3

description: 20mGyQ3 Cy3


title: reference male mouse3/ 20mGyQ2

description: 20mGyQ2 Cy3


title: 20mGyHF/ reference male mouse3


title: 20mGyNM/ reference male mouse3

description: 20mGyNM Cy5


title: reference male mouse3/ 20mGyHF


title: 20mGyM1/ reference male mouse3

description: 20mGyM1 Cy5


title: reference male mouse3/ 20mGyQ1

description: 20mGyQ1 Cy3


title: 20mGyQ1/ reference male mouse3

description: 20mGyQ1 Cy5


title: reference male mouse3/ 20mGyM1

description: 20mGyM1 Cy3


title: 20mGyHM/ reference male mouse3


title: reference male mouse3/ 20mGyHM


title: 20mGyMF/ reference male mouse3

description: 20mGyMF Cy5


title: reference male mouse3/ 20mGyMF

description: 20mGyMF Cy3


title: 20mGyMM/ reference male mouse3

description: 20mGyMM Cy5


title: 20mGyG6/ reference male mouse2

description: 20mGyG6 Cy5

source_name: reference male mouse2


title: 20mGyL8/ reference male mouse3

description: 20mGyL8 Cy5


title: reference male mouse3/ 20mGyQ4

description: 20mGyQ4 Cy3


title: 20mGyG7/ reference male mouse2

description: 20mGyG7 Cy5


title: reference male mouse2/ 20mGyG7

description: 20mGyG7 Cy3


title: 20mGyQF/ reference male mouse3

description: 20mGyQF Cy5


title: reference male mouse3/ 20mGyQF

description: 20mGyQF Cy3


title: 20mGyL7/ reference male mouse3

description: 20mGyL7 Cy5


title: 20mGyQM/ reference male mouse3

description: 20mGyQM Cy5


title: 20mGyO6/ reference male mouse3

description: 20mGyO6 Cy5


title: reference male mouse3/ 20mGyQM

description: 20mGyQM Cy3


title: reference male mouse3/ 20mGyMM

description: 20mGyMM Cy3


title: reference male mouse3/ 20mGyNM

description: 20mGyNM Cy3


title: reference male mouse3/ 20mGyL7

description: 20mGyL7 Cy3


title: reference male mouse3/ 20mGyM3

description: 20mGyM3 Cy3


title: 20mGyJ6/ reference male mouse3

description: 20mGyJ6 Cy5


title: 20mGyO5/ reference male mouse3

description: 20mGyO5 Cy5


title: reference male mouse3/ 20mGyL6

description: 20mGyL6 Cy3


title: reference male mouse3/ 20mGyO6

description: 20mGyO6 Cy3


title: reference male mouse3/ 20mGyJ6

description: 20mGyJ6 Cy3


title: 20mGyJ5/ reference male mouse3

description: 20mGyJ5 Cy5


title: reference male mouse2/ 20mGyG6

description: 20mGyG6 Cy3


title: reference male mouse2/ 20mGyG5

description: 20mGyG5 Cy3


title: 20mGyO3/ reference male mouse3

description: 20mGyO3 Cy5


title: 20mGyG5/ reference male mouse2

description: 20mGyG5 Cy5


title: reference male mouse3/ 20mGyO5

description: 20mGyO5 Cy3


title: reference male mouse3/ 20mGyL8

description: 20mGyL8 Cy3


title: 20mGyL5/ reference male mouse3

description: 20mGyL5 Cy5


title: 20mGyJ4/ reference male mouse3

description: 20mGyJ4 Cy5


title: 20mGyG4/ reference male mouse2

description: 20mGyG4 Cy5


title: 20mGyO4/ reference male mouse3

description: 20mGyO4 Cy5


title: 20mGyL3/ reference male mouse3

description: 20mGyL3 Cy5


title: reference male mouse3/ 20mGyO3

description: 20mGyO3 Cy3


title: reference male mouse3/ 20mGyO4

description: 20mGyO4 Cy3


title: reference male mouse3/ 20mGyL5

description: 20mGyL5 Cy3


title: 20mGyO2/ reference male mouse3

description: 20mGyO2 Cy5


title: reference male mouse3/ 20mGyJ5

description: 20mGyJ5 Cy3


title: 20mGyL4/ reference male mouse3

description: 20mGyL4 Cy5


title: reference male mouse2/ 20mGyG3

description: 20mGyG3 Cy3


title: reference male mouse3/ 20mGyL3

description: 20mGyL3 Cy3


title: reference male mouse3/ 20mGyO2

description: 20mGyO2 Cy3


title: reference male mouse3/ 20mGyJ3

description: 20mGyJ3 Cy3


title: reference male mouse3/ 20mGyL4

description: 20mGyL4 Cy3


title: 20mGyG2/ reference male mouse2

description: 20mGyG2 Cy5


title: 20mGyL1/ reference male mouse3

description: 20mGyL1 Cy5


title: reference male mouse2/ 20mGyG2

description: 20mGyG2 Cy3


title: 20mGyJ3/ reference male mouse3

description: 20mGyJ3 Cy5


title: reference male mouse3/ 20mGyO1

description: 20mGyO1 Cy3


title: 20mGyL2/ reference male mouse3

description: 20mGyL2 Cy5


title: reference male mouse3/ 20mGyL2

description: 20mGyL2 Cy3


title: reference male mouse3/ 20mGyJ2

description: 20mGyJ2 Cy3


title: 20mGyJ1/ reference male mouse3

description: 20mGyJ1 Cy5


title: 20mGyG1/ reference male mouse2

description: 20mGyG1 Cy5


title: 20mGyO1/ reference male mouse3

description: 20mGyO1 Cy5


title: reference male mouse2/ 20mGyG1

description: 20mGyG1 Cy3


title: reference male mouse3/ 20mGyNF

description: 20mGyNF Cy3


title: reference male mouse2/ 20mGyG4

description: 20mGyG4 Cy3


title: reference male mouse3/ 20mGyJ1

description: 20mGyJ1 Cy3


title: reference male mouse3/ 20mGyJ4

description: 20mGyJ4 Cy3


title: reference male mouse3/ 20mGyL1

description: 20mGyL1 Cy3


title: 20mGyGF/ reference male mouse2

description: 20mGyGF Cy5


title: 20mGyOF/ reference male mouse3

description: 20mGyOF Cy5


title: 20mGyLF/ reference male mouse3

description: 20mGyLF Cy5


title: reference male mouse3/ 20mGyJF

description: 20mGyJF Cy3


title: 20mGyJ2/ reference male mouse3

description: 20mGyJ2 Cy5


title: 20mGyGM/ reference male mouse2

description: 20mGyGM Cy5


title: reference male mouse2/ 20mGyGF

description: 20mGyGF Cy3


title: PB_FA_042976

status: Public on Feb 24 2017

city: Barcelona

first: Luis Alberto

middle: Perez

last: Jurado

state: Barcelona

address: Doctor Aiguader, 88 (PRBB)

department: Department of Experimental and Health Sciences

country: Spain

institute: Universitat Pompeu Fabra

hyb_protocol: According to the manufacturer’s specifications

data_processing: LRR and BAF values were obtained by using Illumina GenomeStudio software

source_name: Peripheral Blood

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using standard phenol-chloroform extraction method or the Puregene DNA Isolation Kit (QiagenInc, US)

tag: disease state

value: Fanconi Anemia

value: Peripheral Blood

tag: age at sampling

tag: cancer diagnosis

value: Yes

tag: age at cancer diagnosis

tag: evolution

value: Exitus

tag: age of exitus


title: PB_FA_010315

scan_protocol: According to the manufacturer’s specifications

tag: tissue

value: Alive


title: PB_FA_041869

label_protocol: According to the manufacturer’s specifications


title: PB_FA_041607


title: 20mGyJM/ reference male mouse3

description: 20mGyJM Cy5

tag: strain


title: reference male mouse3/ 20mGyOF

description: 20mGyOF Cy3


title: 20mGyOM/ reference male mouse3

description: 20mGyOM Cy5


title: 20mGyG3/ reference male mouse2

description: 20mGyG3 Cy5


title: 20mGyLM/ reference male mouse3

description: 20mGyLM Cy5


title: reference male mouse3/ 20mGyJM

description: 20mGyJM Cy3


title: PB_FA_FA88

value: No


title: PB_FA_FA90


title: reference male mouse3/ 20mGyLM

description: 20mGyLM Cy3


title: reference male mouse2/ 20mGyGM

description: 20mGyGM Cy3


title: PB_FA_FA82


title: PB_FA_900058


title: PB_FA_FA74


title: PB_FA_000644


title: PB_FA_FA72


title: reference male mouse3/ 20mGyOM

description: 20mGyOM Cy3


title: PB_FA_FA71


title: PB_FA_FA70


title: PB_FA_042668


title: PB_FA_FA69


title: PB_FA_FA648


title: PB_FA_FA649


title: PB_FA_FA647


title: PB_FA_FA642


title: PB_FA_FA625


title: PB_FA_FA630


title: PB_FA_FA616


title: PB_FA_FA62


title: PB_FA_FA84


title: PB_FA_FA611


title: PB_FA_FA610


title: PB_FA_FA596


title: PB_FA_FA574


title: PB_FA_FA562


title: PB_FA_FA558


title: PB_FA_FA55


title: PB_FA_FA549


title: PB_FA_FA537


title: PB_FA_FA548


title: PB_FA_FA535


title: PB_FA_FA530


title: PB_FA_FA53


title: PB_FA_FA486


title: PB_FA_FA527


title: PB_FA_FA438


title: PB_FA_FA466


title: PB_FA_FA460


title: PB_FA_FA434


title: PB_FA_FA388


title: PB_FA_FA617


title: PB_FA_FA382


title: PB_FA_FA374


title: PB_FA_FA378


title: PB_FA_FA609


title: PB_FA_FA387


title: PB_FA_FA569


title: PB_FA_FA363


title: PB_FA_FA357


title: PB_FA_FA354


title: PB_FA_FA351


title: PB_FA_FA344


title: PB_FA_FA337


title: PB_FA_FA334


title: PB_FA_FA306


title: PB_FA_FA328


title: PB_FA_FA331


title: PB_FA_FA300

value: Not Available


title: PB_FA_FA304


title: PB_FA_FA281


title: PB_FA_FA23


title: PB_FA_FA202


title: PB_FA_FA360


title: PB_FA_FA184


title: PB_FA_FA183


title: PB_FA_FA178


title: PB_FA_FA345


title: PB_FA_FA170


title: PB_FA_FA177


title: PB_FA_FA164


title: PB_FA_FA155


title: PB_FA_FA126


title: PB_FA_FA124


title: PB_FA_FA122


title: PB_FA_FA121

value: Missing


title: PB_FA_FA123


title: PB_FA_FA117


title: PB_FA_FA116


title: PB_FA_FA192


title: PB_FA_FA203


title: PB_FA_FA109


title: PB_FA_FA112


title: PB_FA_FA106


title: PB_FA_FA105


title: PB_FA_FA13


title: PB_FA_EGF119


title: PB_FA_EGF063


title: PB_FA_EGF058


title: PB_FA_EGF047


title: PB_FA_072960


title: PB_FA_EGF045


title: PB_FA_FA103


title: MCS_2

city: Yokohama

first: Jing-Ru

last: Li

state: Kanagawa

address: 1-7-22 Suehiro-cho,

department: Devision of Genomic Technology

institute: RIKEN Center for Life Science Technologies,

description: replicate 5

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: Mock control overexpressed HEK293T cells

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

growth_protocol: HEK293T cells, standard culture method

extract_protocol: RNA was isolated using NucleoSpin® kit (Macherey-Nagel, Germany) according to the user manual

tag: cell line

value: Mock control overexpressed


title: MCS_3

description: replicate 6


title: 20mGyL6/ reference male mouse3

description: 20mGyL6 Cy5


title: RUNX1_2

description: replicate 2

source_name: RUNX1 overexpressed HEK293T cells

value: RUNX1 overexpressed


title: MCS_1

description: replicate 4


title: RUNX1_3

description: replicate 3


title: P7-PBMC

city: Prague 2

first: Vojtěch

last: Kulvait

address: U Nemocnice 5

department: Institute of Pathological Physiology

country: Czech Republic

institute: Charles University in Prague - 1st Faculty of Medicine

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Image data was read by beadarray package (there are no detection p-values). Further data processing was performed using blima Bioconductor package. Averaged foreground values GrnF after background correction was used for Matrix non-normalized data.

source_name: Patient's primary lymphoma cells obtained from leukemized blood.

label_protocol: Standard Illumina protocol

extract_protocol: RNA extraction using Trizol, as per manufacturer's protocol

tag: cell type


title: RUNX1_1

description: replicate 1


title: P2-A2

source_name: Patient's primary lymphoma cells obtained from malignant ascites.


title: 20mGyJF/ reference male mouse3

description: 20mGyJF Cy5