title: Fat-Crigler- Najjar-subjCN2

status: Public on Jul 31 2017

type: RNA

city: London

first: Matthew

last: Arno

state: LONDON

address: 150 Stamford Street

department: Genomics Centre

country: United Kingdom

institute: King's College London

description: sample 39

hyb_protocol: Samples were hybridised to Affymetrix Microarrays folllowing recommended procedures (3.4ug SPIA fragmented, biotinylated SPIA cDNA, 18 hours at 45oC using Affymetrix Hyb module, washing and staining in FS450 fluidics station using Affymetrix Hyb Wash Stain kit)

scan_protocol: Processed microarrays were scanned in GCS3000 scanner with 7G upgrade, using AGCC software. Automatic grid alignments in AGCC

data_processing:
CEL files were processed in Affymetrix Expression Console software, using RMA Sketch algorithm.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.0.38

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Crigler-Najjar_subcutaneous fat

label_protocol: RNA (50ng) was labelled and amplified using Nugen's Ovation Pico WTA V2 kit and Encore Biotin Module.

extract_protocol: RNA was extracted using TRIzol reagent (Life Technologies) and homogenisation using Tissuelyser II, followed by Qiagen RNeasy MinElute column cleanup

tag: subjectid

tag: disease

value: Crigler-Najjar

tag: tissue

value: subcutaneous fat


title: Muscle-Crigler- Najjar-subjCN1

description: sample 35

value: muscle (rectus abdominis)


title: Liver-chronic liver disease-BA-subj17

description: sample 31

source_name: chronic liver disease-BA_liver

value: chronic liver disease-BA

value: liver


title: Fat-Crigler- Najjar-subjCN1

description: sample 36


title: Fat-chronic liver disease-BA-subj3

description: sample 6

source_name: chronic liver disease-BA_subcutaneous fat


title: Liver-Crigler- Najjar-subjCN1

description: sample 34


title: Muscle-chronic liver disease-BA-subj4

description: sample 8

source_name: chronic liver disease-BA_muscle


title: Fat-chronic liver disease-BA-subj17

description: sample 33


title: Muscle-Crigler- Najjar-subjCN2

description: sample 38


title: Muscle-chronic liver disease-BC-subj15

description: sample 29

source_name: chronic liver disease-BC_muscle

value: chronic liver disease-BC


title: Liver-chronic liver disease-BA-subj12

description: sample 25


title: Fat-chronic liver disease-NSC-subj1

description: sample 3

source_name: chronic liver disease-NSC_subcutaneous fat

value: chronic liver disease-NSC


title: Muscle-chronic liver disease-BA-subj12

description: sample 26


title: Liver-chronic liver disease-BC-subj15

description: sample 28

source_name: chronic liver disease-BC_liver


title: Liver-Crigler- Najjar-subjCN2

description: sample 37


title: Liver-chronic liver disease-BA-subj4

description: sample 7


title: Fat-chronic liver disease-BA-subj4

description: sample 9


title: Muscle-chronic liver disease-BA-subj17

description: sample 32


title: Muscle-chronic liver disease-NSC-subj1

description: sample 2

source_name: chronic liver disease-NSC_muscle


title: Fat-chronic liver disease-BC-subj15

description: sample 30

source_name: chronic liver disease-BC_subcutaneous fat


title: Liver-chronic liver disease-BA-subj11

description: sample 22


title: Muscle-chronic liver disease-BA-subj11

description: sample 23


title: Muscle-chronic liver disease-BA-subj3

description: sample 5


title: Fat-chronic liver disease-BA-subj11

description: sample 24


title: Fat-chronic liver disease-BA-subj12

description: sample 27


title: Muscle-chronic liver disease-BA-subj10

description: sample 20


title: Fat-chronic liver disease-a1AT-subj9

description: sample 18

source_name: chronic liver disease-a1AT_subcutaneous fat

value: chronic liver disease-a1AT


title: Fat-chronic liver disease-BA-subj10

description: sample 21


title: Liver-chronic liver disease-a1AT-subj9

description: sample 16

source_name: chronic liver disease-a1AT_liver


title: Liver-chronic liver disease-BA-subj10

description: sample 19


title: Muscle-chronic liver disease-a1AT-subj9

description: sample 17

source_name: chronic liver disease-a1AT_muscle


title: Fat-chronic liver disease-BA-subj8

description: sample 15


title: Muscle-chronic liver disease-BA-subj8

description: sample 14


title: ST-C10-433 GRP ST-1 CONTROL

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

country: USA

institute: WRAIR

hyb_protocol: cRNA was hybridized to a whole mouse genome microarray (Agilent Technologies) following manufacturer's instructions

scan_protocol: Scanned on a Agilent Technologies Scanner G2600D Images were quantified using Agilent Feature Extraction Software

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction and GeneSpring v.10.1 (Agilent Technologies, Inc., CA) software was used to conduct the preliminary data filtration and statistical analysis.

organism: Mus musculus

source_name: Agilent's Universal Mouse Reference RNA composed of total RNA from 11 mouse cell lines

label_protocol: Total RNA (200-2000ng) was used as starting material, which was amplified using the Quick Amp Two-Color Kit (Agilent Technologies).The labelled cDNA was purified using an RNeasy Mini Kit (Qiagen, Hilden, Germany), and eluted, labelled cRNA was quantified using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific Inc, Waltham, MA, USA).

growth_protocol: growth protocol is not applicable

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

treatment_protocol: Three groups of C57BL/6j mice of 3 weeks age were introduced to one of the diet types for the subsequent 24 weeks

tag: gender

value: Male

source_name: Hemibrain

value: hemibrain

tag: strain

tag: diet

value: standard lab diet (STD, n3:n6= 1:6)


title: ST-C10-436 GRP ST-1 CONTROL


title: 58-C10-425 GRP 58-1 CONTROL

value: n-3 PUFA optimally balanced by n-6 PUFA (BLD, n3:n6= 1:1)


title: ST-C10-437 GRP ST-1 CONTROL


title: ST-C10-434 GRP ST-1 CONTROL


title: 58-C10-424 GRP 58-1 CONTROL


title: 57-C10-417 GRP 57-1 CONTROL

value: high n-3 PUFA enriched diet (ERD n3:n6= 7:1)


title: 58-C10-423 GRP 58-1 CONTROL


title: 57-C10-413 GRP 57-1 CONTROL


title: 57-C10-416 GRP 57-1 CONTROL


title: 57-C10-414 GRP 57-1 CONTROL


title: Fat-Alagille-subj6

description: sample 12

source_name: Alagille_subcutaneous fat

value: Alagille


title: 57-C10-415 GRP 57-1 CONTROL


title: Muscle-Alagille-subj6

description: sample 11


title: Liver-chronic liver disease-BA-subj8

description: sample 13


title: ST-C10-435 GRP ST-1 CONTROL


title: 58-C10-443 GRP 58-1 CONTROL


title: 58-C10-426 GRP 58-1 CONTROL


title: Liver-Alagille-subj6

description: sample 10


title: AMLcells_24h_DipGtreated_rep1-1

city: Nanjing

first: Jian

last: Gao

state: Jiangsu

address: 22 Han Kou Road

country: China

institute: Nanjing university

description: Gene expression of HL-60 cells after 24 hr 18 mM Dip G treated

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression（8*60K）for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: HL-60 cells, 24h, Dip G 15 mM, replicate 1-1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg 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: HL-60 cells were cultured in the presence of RPMI 1640 with 10% fetal bovine serum.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: The cells were incubated for 24 hours in the absence or presence of 15 M Dip G at 37 ºC in a humidified incubator with 5% CO2.

tag: cell line

tag: agent

value: Dip G (15 mM)


title: AMLcells_24h_DipGtreated_rep2-3

description: Gene expression of HL-60 cells after 24 hr 19 mM Dip G treated

source_name: HL-60 cells, 24h, Dip G 15 mM, replicate 2-3


title: AMLcells_24h_DipGtreated_rep3-2

description: Gene expression of HL-60 cells after 24 hr 20 mM Dip G treated

source_name: HL-60 cells, 24h, Dip G 15 mM, replicate 3-2


title: AMLcells_24h_NegtiveControl_rep3-1

description: Gene expression of HL-60 cells as control

source_name: HL-60 cells, 24h, Dip G 0 mM, replicate 3-1


title: AMLcells_24h_NegtiveControl_rep1-2

source_name: HL-60 cells, 24h, Dip G 0 mM, replicate 1-2


title: AMLcells_24h_NegtiveControl_rep2-3

source_name: HL-60 cells, 24h, Dip G 0 mM, replicate 2-3


title: 201328 -  Positive

type: genomic

hyb_protocol: We loaded 2.5 to 6µg DNA to the array

scan_protocol: Scanned on a Agilent Technologies SureScan Microarray Scanner G2600D

data_processing: Images were quantified using Agilent Feature Extraction Software (version11.5.1.1). Agilent Feature Extraction Software was used for background subtraction

molecule: genomic DNA

source_name: WCE (whole cell extract; reference)

label_protocol: Total Genomic DNA (5µg) was used as starting material, using the SureTag Complete DNA Labeling Kit (Agilent Technologies).  Labeled DNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific Inc, Waltham, MA, USA). The IP (sample of interest) samples were labeled with Cy5 and the WCE (reference) were labeled with Cy3.

extract_protocol: We extracted DNA from the PAXgene (Agilent, Inc.) tube; whole blood collected from the volenteers stored in Paxgen tube as per the vendor's recommendation.

tag: subject status

value: post-traumatic stress disorder (PTSD) positive (+)

tag: age (yrs)

tag: ethnicity

value: Non-Hispanic Black

tag: caps

value: Whole blood

source_name: Immunoprecipitated DNA

tag: age


title: 201418 - Positive

value: Non-Hispanic white


title: 202067 -  Positive


title: 202180 -  Positive

value: Hispanic


title: 201367-  Positive

value: Non-Hispanic Other


title: 202212 - Positive


title: 202068 - Positive


title: 202112 -  Positive


title: 201415 - Positive


title: 202223 - Positive


title: 202171 - Positive


title: 201410 - Positive


title: 201361 -  Positive


title: 202160 - Positive


title: 202188 - Positive


title: 202215 - Positive


title: 201356 -  Positive

value: Non-Hispanic Asian


title: 202211 - Positive


title: 201362 -  Positive


title: 201318 -  Positive


title: 202182 -  Positive


title: 201357 -  Positive


title: 231_siControl_48 hr

city: Baltimore

first: Pang-Kuo

last: Lo

state: Maryland

address: 108 N. Greene St.

department: Biochemistry and Molecular Biology

institute: University of Maryland School of Medicine

description: transfected with control siRNA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

label: biotin

source_name: Metastatic breast tumor

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

growth_protocol: Cells were cultured in the suitable medium according to the ATCC online instructions.

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

treatment_protocol: siRNA transfections were performed with 20 nM of each RNA oligonucleotide using OligofectamineTM RNAiMAX (Invitrogen) according to the instructions of the manufacturer.

tag: cell type

value: metastatic breast cancer cells

tag: transfection

value: control siRNA


title: MCF10A_siFOXF2_48 hr

description: transfected with FOXF2 siRNA

source_name: Breast tissue

value: immortalized breast epithelial cells

value: FOXF2 siRNA


title: 202041 -  Positive

value: Male


title: 231_siFOXF2_48 hr

description: transfected with FOXF2 siRNA


title: ExVivoBlood_control_peripheral blood_rep3

city: Beijing

first: Ying

last: Su

address: Tieyi Rd. No.10, Yangfangdian, Haidian district

institute: Capital Medical University affiliated Beijing Shijitan Hospital

description:
N3
lncRNAs and mRNAs expression profiles of peripheral blood leukocytes in control

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 9 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis (37,069 ID_REFs). Differentially expressed LncRNAs and mRNAs with statistical significance between two groups were identified through Volcano Plot filtering and differentially expressed LncRNAs/mRNAs were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show the distinguishable LncRNAs and mRNAs expression pattern among samples.

source_name: Peripheral Blood_control

label_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, 1ug RNA was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The Cyanine-3 (Cy3) labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000 Spectrophotometer.

extract_protocol: According to the manufacturer’s instructions, leukocytes were separated from whole blood using Red Blood Cell Lysis Buffer (TBD, Tianjin, China). Then RNA was extracted from leukocytes by Trizol reagent (Invitrogen, Carlsbad, CA, USA). A NanoDrop ND-1000 spectrophotometer was used for evaluating RNA quantity and quality. RNA integrity was assessed by standard denaturing agarose gel electrophoresis. Total RNA of the sample was used for lncRNA microarray analysis and the remaining sample was used for further RT-PCR validation.

value: control

value: Female

value: Peripheral Blood (PB)

value: leukocytes


title: MCF10A_siControl_48 hr

description: transfected with control siRNA


title: ExVivoBlood_paroxysmal atrial fibrillation_peripheral blood_rep3

description:
W5
lncRNAs and mRNAs expression profiles of peripheral blood leukocytes in paroxysmal atrial fibrillation patient

source_name: Peripheral Blood_paroxysmal atrial fibrillation

value: paroxysmal atrial fibrillation (pAF) patient


title: ExVivoBlood_paroxysmal atrial fibrillation_peripheral blood_rep2

description:
W4
lncRNAs and mRNAs expression profiles of peripheral blood leukocytes in paroxysmal atrial fibrillation patient


title: 201345 - Positive

value: post-traumatic stress disorder (PTSD) positive (+)


title: ExVivoBlood_control_peripheral blood_rep2

description:
N2
lncRNAs and mRNAs expression profiles of peripheral blood leukocytes in control


title: 202183 -  Positive

value: Non-Hispanic Black


title: 202072 -  Positive

value: Whole blood


title: ExVivoBlood_paroxysmal atrial fibrillation_peripheral blood_rep1

description:
W2
lncRNAs and mRNAs expression profiles of peripheral blood leukocytes in paroxysmal atrial fibrillation patient


title: ExVivoBlood_paroxysmal atrial fibrillation_coronary sinus blood_rep2

description:
C4
lncRNAs and mRNAs expression profiles of coronary sinus blood leukocytes in paroxysmal atrial fibrillation patient

source_name: Coronary Sinus Blood_paroxysmal atrial fibrillation

value: Coronary Sinus Blood (CSB)


title: 202064 -  Positive


title: 201327 -  Positive

value: Non-Hispanic white


title: 201349 -  Positive


title: 202155 - Negative

value: post-traumatic stress disorder (PTSD) negative (-)


title: ExVivoBlood_control_peripheral blood_rep1

description:
N1
lncRNAs and mRNAs expression profiles of peripheral blood leukocytes in control


title: 202175 -  Positive

value: Hispanic


title: 202143 - Positive


title: ExVivoBlood_paroxysmal atrial fibrillation_coronary sinus blood_rep3

description:
C5
lncRNAs and mRNAs expression profiles of coronary sinus blood leukocytes in paroxysmal atrial fibrillation patient


title: 202110 - Negative


title: 201229 - Negative


title: 201377 - Negative


title: 80mg/kg MPy liver day 24, biological rep3

city: Wuppertal

first: Heidrun

middle: Christine

last: Ellinger-Ziegelbauer

address: Aprather Weg 18a

country: Germany

institute: Bayer Pharma AG

description: Gene expression of liver tissue from rat treated with 80 mg/kg MPy

hyb_protocol: Following fragmentation, 12.5 µg of aRNA were hybridized for 16h at 45°C on GeneChip Rat Genome Arrays. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 running th Prime_450 protocol.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using GeneData Expressionist® Pro Refiner. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Rattus norvegicus

source_name: liver homogenate from rat treated with 80 mg/kg MPy

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 500 ng high quality total liver RNA (GeneChip® 3 IVT Express Kit).

growth_protocol: All animal experiments were performed according to the German guidelines for care and use of laboratory animals. Male Han Wistar rats, 8-10 weeks old, were purchased from Charles River laboratories (Sulzbach, Germany). Animals were individually housed in type III makrolon cages, with a 12h light-dark cycle. Standard rodent chow pellets and water were provided ad libitum.

extract_protocol: On days 4, 8, 15 and 24 (=14 days daily treatment +  10 days recovery) rats were euthanized and livers were removed for histopathological examination and RNA isolation. Liver tissue for RNA isolation was frozen in liquid nitrogen and then stored at -80°C. Total liver RNA was isolated with the RNeasy Mini Kit (Qiagen; Hilden, Germany) from 10 mg liver tissue,  according to the manufacturer’s instructions. The quality of isolated RNA was assessed using Bioanalyzer NanoRNA Kits (Agilent; Santa Clara, CA) and the quantity was determined with a spectrophotometer.

treatment_protocol: Male Han Wistar rats (8-10 weeks old) were randomly grouped (n = 6) and received oraly and daily 0, 30 or 80 mg/kg body weight methapyrilene (Sigma-Aldrich, Germany) diluted in caboxymethylcellulose. Control groups received appropriate amounts of the vehicle.

value: Han Wistar [Crl:WI(Han)]

value: male

value: liver


title: 80mg/kg MPy liver day 24, biological rep5


title: 201232 - Negative


title: 80mg/kg MPy liver day 15, biological rep5


title: 80mg/kg MPy liver day 24, biological rep4


title: 80mg/kg MPy liver day 24, biological rep2


title: 80mg/kg MPy liver day 15, biological rep3


title: 201402 - Negative


title: 202192 - Negative


title: 80mg/kg MPy liver day 24, biological rep1


title: 80mg/kg MPy liver day 15, biological rep4


title: ExVivoBlood_paroxysmal atrial fibrillation_coronary sinus blood_rep1

description:
C2
lncRNAs and mRNAs expression profiles of coronary sinus blood leukocytes in paroxysmal atrial fibrillation patient


title: 80mg/kg MPy liver day 15, biological rep2


title: 202125 - Negative


title: 201164 - Negative


title: 201409 - Negative


title: 80mg/kg MPy liver day 8, biological rep5


title: 80mg/kg MPy liver day 15, biological rep1


title: 80mg/kg MPy liver day 8, biological rep4


title: 201151 - Negative


title: 202144 - Negative


title: 201372 - Negative


title: 202197 - Negative

value: Non-Hispanic Other


title: BGC823_U6 (conU6)

city: beijing

first: lei

last: yan

state: beijing

address: Block 88 Kechuang 6th Street

department: sales

institute: capitalbiotech

description: Total RNA was extracted from Gastric cancer BGC823 cells

hyb_protocol: standard CapitalBio Methods: Labeled RNA was precipitated with 0.3 M sodium acetate, 2.5 volumes ethanol and resuspended in 15ul of hybridization buffer containing 3×SSC, 0.2% SDS and 15% formamide. The array was hybridized at 42℃ overnight and washed with two consecutive washing solutions (0.2% SDS, 2×SSC at 42°C for 5 min, and 0.2% SSC for 5 min at room temperature).

scan_protocol: Luxscan 3.0 (CapitalBio)

data_processing: Intensity data was extracted from the TIFF images using LuxScanTM 3.0 software (CapitalBio Corp, Peking, China). The low-intensity spots were removed for which fewer than 30% of the signal pixels exceeded the median background plus two times its standard deviation.

growth_protocol: All cells were cultured in a sterile incubator at 37˚C

extract_protocol: total RNA was extracted using Trizol Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions, and the low-molecular-weight RNA (LMW-RNA) be isolated using the PEG solution precipitation method

treatment_protocol: Before microarray analysis,the cells were incubated as usual.

value: gastric cancer cells

tag: genotype/variation

value: transfected with U6


title: 202069 - Negative

value: Male


title: BGC823_Pak1 knockdown (16)

description: Total RNA was extracted from Gastric cancer BGC823 cells with stable Pak1 knockdown

source_name: BGC823_Pak1 knockdown

value: stable Pak1 knockdown


title: 80mg/kg MPy liver day 8, biological rep3


title: 80mg/kg MPy liver day 8, biological rep2


title: 30mg/kg MPy liver day 24, biological rep4

description: Gene expression of liver tissue from rat treated with 30 mg/kg MPy

source_name: liver homogenate from rat treated with 30 mg/kg MPy


title: 80mg/kg MPy liver day 4, biological rep3


title: 30mg/kg MPy liver day 24, biological rep3


title: 201020 - Negative


title: H4 control cells 2 [MAS5]

city: Zagreb

first: Fran

last: Borovecki

address: Salata 2

department: Center for Translational anc Clinical Research

country: Croatia

institute: University of Zagreb School of Medicine

description: Gene expression data from H4 control cells

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

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

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

source_name: control

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: H4 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Life Tecnologies-Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS, PAA, Cölbe, Germany) and 1% Penicillin-Streptomycin (PS). H4 cells were grown at 37ºC in humidified 5% CO2 atmosphere.

extract_protocol: RNA was isolated from H4 control cells and WT asyn expressing H4 cells (myc-tagged) using the RNeasy kit (Qiagen) according to the manufacturer’s instructions. All samples were treated with the RNase-free DNase set (Qiagen).

treatment_protocol: H4 cells were transfected with plasmid psI-α-Syn_Myc (myc tagged alpha synuclein) using Fugene (Roche) according to manufacturer`s instructions.

tag: condition

value: expressing endogenous levels of asyn


title: 201368 - Negative


title: 80mg/kg MPy liver day 4, biological rep5


title: 201225 - Negative

value: Non-Hispanic Asian


title: 80mg/kg MPy liver day 8, biological rep1


title: 80mg/kg MPy liver day 4, biological rep2


title: 80mg/kg MPy liver day 4, biological rep4


title: H4 Myc tagged aSyn 2 [RMA]

description: Gene expression data from WT asyn expressing H4 cells (myc-tagged).

data_processing: The data were analyzed with RMA algortyhm default analysis settings and normalization methods.

source_name: MYC

value: transfected with plasmid psI-α-Syn_Myc (myc tagged alpha synuclein)


title: 201389 - Negative


title: 202184 - Negative

value: Non-Hispanic Black


title: H4 Myc tagged aSyn 1 [MAS5]


title: H4 Myc tagged aSyn 1 [RMA]


title: H4 Myc tagged aSyn 2 [MAS5]


title: H4 control cells 2 [RMA]


title: 30mg/kg MPy liver day 24, biological rep2


title: 202147 - Negative

value: Whole blood


title: H4 control cells 1 [MAS5]


title: 202101 - Negative


title: 201268 - Negative


title: 202195 - Negative


title: 201399 - Negative


title: 202111 - Negative


title: 202216 - Negative


title: 30mg/kg MPy liver day 24, biological rep1


title: 30mg/kg MPy liver day 15, biological rep3


title: 30mg/kg MPy liver day 15, biological rep4


title: H4 control cells 1 [RMA]


title: 7

city: Kashiwanoha, kashiwa

first: Tomohiro

last: Enokida

country: Japan

institute: National Cancer Center Hospital East

description: Human Tongue Tumor Tissue

hyb_protocol: The procedures for target hybridization, washing, and staining with signal amplification were conducted according to the supplier's protocols.

scan_protocol: The arrays were scanned with a GeneChip Scanner 3000 (Affymetrix).

data_processing: The intensity of each feature of the array was calculated using GeneSpring GX Software, version 12.6 (Agilent).

source_name: Tongue Tumor Tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA using a 3' IVT Express Kit.

extract_protocol: RNA extracted using Rneasy Plus Mini Kit / EZ1 RNA Universal Tissue Kit (Qiagen) according to the manufacturer's instructions.

value: tongue

tag: disease state

value: tumor

tag: pt-stage

tag: pn-stage


title: 30mg/kg MPy liver day 15, biological rep5

tag: gender

tag: tissue


title: 201189 - Negative

value: post-traumatic stress disorder (PTSD) negative (-)


title: 30mg/kg MPy liver day 15, biological rep2

tag: strain


title: 30mg/kg MPy liver day 15, biological rep1


title: 4

description: Human Tongue Tumor Tissue


title: 30mg/kg MPy liver day 8, biological rep4


title: 30mg/kg MPy liver day 8, biological rep3


title: 5

description: Human Tongue Tumor Tissue


title: 6

description: Human Tongue Normal Tissue

source_name: Tongue Normal Tissue

value: normal

value: Female


title: 9

description: Human Tongue Tumor Tissue


title: 201324 - Negative

value: Hispanic


title: 8

description: Human Tongue Normal Tissue


title: 30mg/kg MPy liver day 8, biological rep5

value: Han Wistar [Crl:WI(Han)]

value: male

value: liver


title: 31

description: Human Tongue Tumor Tissue


title: 30mg/kg MPy liver day 8, biological rep1


title: 3

description: Human Tongue Tumor Tissue


title: 30

description: Human Tongue Tumor Tissue


title: B16F0 exosomes isolated from serum-free media media conditioned by B16F0 cells for 24 hr, rep 4

city: Morgantown

first: David

middle: John

last: Klinke

state: WV

department: Chemical Engineering

institute: West Virginia University

description: 8 exosome 24h_(MoEx-1_0-st-v1)

hyb_protocol: The entire reaction of fragmented and biotin-labeled cDNA (50 mu) with added hybridization controls was hybridized to the mouse GeneChip 1.0 ST Exon Arrays (Affymetrix) at 45oC for 17 hours in GeneChip Hybridization Oven 640 (Affymetrix).

scan_protocol: Mouse GeneChip 1.0 ST Exon Arrays were stained using FS 450_0001 protocol in Affymetrix GeneChip Fluidics Station 450. Phycoerythrin labeling was detected within the Affymetrix GeneChip Scanner 3000 7G plus using 532 nm light and detected by a photomultiplier tube.

data_processing:
Expression Console software (Affymetrix) was used to check quality controls of hybridized chips.  All chips that passed quality controls were RMA normalized using Expression Console software.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm8.mps

source_name: B16F0 exosomes

label_protocol: Each reaction yielded between 6 to 9 micrograms of cDNA, whereby 5.5 mug of cDNA was fragmented and labeled with biotin by the GeneChip WT Terminal Labeling Kit (Affymetrix). The efficiency of fragmentation reaction was checked via Agilent Bioanalyzer.

growth_protocol: Cultured for 24 hours in serum-free media

extract_protocol: Total RNA isolated from B16F0 exosomes and cells by RNeasy Plus kit (Qiagen) was quantified using Nanodrop and analyzed by on-chip-electrophoresis using the Agilent Bioanalyzer and was processed by the Ambion WT Expression Kit.

tag: cell line

tag: sample type

value: exosomes isolated from B16F0 conditioned media

tag: molecule subtype

value: exosomal RNA


title: 30mg/kg MPy liver day 8, biological rep2


title: B16F0 exosomes isolated from serum-free media media conditioned by B16F0 cells for 24 hr, rep 3

description: 7 exosome 24h_(MoEx-1_0-st-v1)


title: B16F0 exosomes isolated from serum-free media media conditioned by B16F0 cells for 24 hr, rep 2

description: 6 exosome 24h_(MoEx-1_0-st-v1)


title: B16F0 exosomes isolated from serum-free media media conditioned by B16F0 cells for 24 hr, rep 1

description: 5 exosome 24h_(MoEx-1_0-st-v1)


title: 28

description: Human Tongue Tumor Tissue


title: 29

description: Human Tongue Tumor Tissue

value: Male


title: RKO_parental_rep2

city: Uppsala

first: Chatarina

last: Larsson

address: Rudbeck Laboratory

department: Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

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

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

data_processing: Color balance adjustment and background correction was performed in the R methylumi package, and the “pfilter” function with default settings from the wateRmelon package was used to remove sites with bead count <3 in >5% of the samples and sites where >1% of samples had a detection p-value >0.05. Quantile normalization of the pooled signal intensities of methylated and unmethylated probes was done before calculation of β-values with the “nanet” method from the same R-package. The probe type bias in the Illumina Infinium technology was eliminated by beta mixture quantile dilation (BMIQ).

label: Cy5 [Alexa647] and Cy3 [Alexa555]

source_name: Cell culture

label_protocol: Standard Illumina Protocol

growth_protocol: RKO parental (ATCC CRL-2577) and DIP2C knockout cells were cultured in McCoys 5A medium supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol: DNA was isolated using the NucleoSpin Tissue kit from Macherey-Nagel (Düren, Germany)

value: RKO colorectal cancer cells

tag: genotype/variant

value: non modified


title: B16F0 cells cultured for 24 hr in serum-free media, rep 4

description: 4 cell 24h_(MoEx-1_0-st-v1)

source_name: B16F0 cells

value: parental B16F0 cells

value: total RNA


title: 30mg/kg MPy liver day 4, biological rep1


title: B16F0 cells cultured for 24 hr in serum-free media, rep 3

description: 3 cell 24h_(MoEx-1_0-st-v1)


title: 30mg/kg MPy liver day 4, biological rep4


title: B16F0 cells cultured for 24 hr in serum-free media, rep 1

description: 1 cell 24h_(MoEx-1_0-st-v1)


title: RKO_DIP2C-/-_Cl.1-1_rep1

description: Clone designation C10/#1-1


title: RKO_DIP2C+/-_Cl. 1_rep1

description: Clone designation F6-A7/#1


title: 30mg/kg MPy liver day 4, biological rep3


title: 30mg/kg MPy liver day 4, biological rep5


title: 25

description: Human Tongue Tumor Tissue


title: 23

description: Human Tongue Tumor Tissue


title: 26

description: Human Tongue Tumor Tissue


title: mouse embryonic stem cell [ESC-H]

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

data_processing: Data normalization was calculated with the Quantile normalization algorithm implemented in the BioConductor lumi package.

source_name: mouse embryonic stem cell

growth_protocol: Mouse ESC and iPSC were cultured in ESC media containing 15% FBS and 1,000 U/ml of LIF (ESGRO® Leukemia Inhibitory Factor [LIF], 1 million units/1 mL). Doxycycline-inducible ZSCAN10 was induced in media supplemented with 2 μg/ml doxycycline (MP Biomedicals, doxycycline hyclate). Human iPSC were cultured in human ESC media (DMEM/F12, 20% knockout serum replacement, 10 ng/ml bFGF, and 0.1 mM -mercaptoethanol) on irradiated mouse embryonic feeders. Human and mouse fibroblasts were cultured in DMEM media with 10% FBS.

extract_protocol: Total RNA was reverse transcribed using the M-MuLV Reverse Transcriptase system (New England Biolabs), and the resulting cDNA was diluted. Synthesized cDNA solution was used for analysis.

treatment_protocol: Fibroblasts were collected from B6CBAF1 mouse E17.5 embryonic skin and 1.5-year-old tail tip skin. 10E6 fibroblasts were infected with retrovirus generated from pMX-mOCT4, pMX-mSOX2, pMX-mKLF4, and pEYK-mMYC in 6-well dishes with 0.5 ml of each viral supernatant (total 2 ml per well) and spun at 2500 rpm at RT for 90 min (BenchTop Centrifuge, BeckmanCoulter, Allegra-6R). For the generation of A-iPSC-ZSCAN10, the procedure was identical but in addition to the four reprogramming factors, we added a doxycycline-inducible system to overexpress ZSCAN10.”

value: mouse embryonic stem cell


title: 22

description: Human Tongue Tumor Tissue

value: tongue


title: Control liver day 24, biological rep5

description: Gene expression of liver tissue from control rat

source_name: liver homogenate from control rat


title: 27

description: Human Tongue Tumor Tissue

value: tumor


title: 30mg/kg MPy liver day 4, biological rep2


title: RKO_DIP2C-/-_Cl. 1-2_rep1

description: Clone designation E3/#1-2


title: B16F0 cells cultured for 24 hr in serum-free media, rep 2

description: 2 cell 24h_(MoEx-1_0-st-v1)


title: Control liver day 24, biological rep4


title: RKO_parental_rep1


title: mouse embryonic stem cell [ESC-D]


title: 21

description: Human Tongue Tumor Tissue


title: Control liver day 24, biological rep3


title: 20

description: Human Tongue Tumor Tissue


title: Control liver day 15, biological rep5


title: iPSC wih ZSCAN10 from aged somatic cell [A-iPSC-ZSCAN10-7]

source_name: iPSC wih ZSCAN10 from aged somatic cell

value: iPSC

value: aged


title: Control liver day 15, biological rep4


title: iPSC from aged somatic cell [A-iPSC-16]

source_name: iPSC from aged somatic cell


title: Control liver day 24, biological rep2


title: iPSC from young somatic cell [Y-iPSC-4]

source_name: iPSC from young somatic cell

value: young


title: 19

description: Human Tongue Tumor Tissue


title: iPSC wih ZSCAN10 from aged somatic cell [A-iPSC-ZSCAN10-3]


title: Control liver day 8, biological rep5


title: 16

description: Human Tongue Tumor Tissue

value: Female


title: Control liver day 15, biological rep1

value: Han Wistar [Crl:WI(Han)]


title: Control liver day 15, biological rep3

value: male


title: 2

description: Human Tongue Tumor Tissue


title: RKO_DIP2C+/-_Cl. 2_rep1

description: Clone designation A9-A12/#2


title: somatic cell from aged donor [A-SC-1.4]

source_name: somatic cell from aged donor

value: somatic cell


title: iPSC from aged somatic cell [A-iPSC-19]


title: 15

description: Human Tongue Tumor Tissue


title: 14

description: Human Tongue Tumor Tissue


title: somatic cell from aged donor [A-SC-1.3]


title: iPSC from young somatic cell [Y-iPSC-12]


title: Control liver day 8, biological rep3

value: liver


title: Control liver day 8, biological rep4


title: 18

description: Human Tongue Tumor Tissue


title: 13

description: Human Tongue Tumor Tissue


title: somatic cell from aged donor [A-SC]


title: 17

description: Human Tongue Tumor Tissue


title: Control liver day 15, biological rep2


title: Control liver day 8, biological rep2


title: somatic cell from young donor [Y-SC-17]

source_name: somatic cell from young donor


title: Control liver day 4, biological rep5


title: Control liver day 4, biological rep4


title: 11

description: Human Tongue Tumor Tissue


title: 1

description: Human Tongue Tumor Tissue


title: 10

description: Human Tongue Normal Tissue

value: normal


title: somatic cell from young donor [Y-SC-16]


title: NFAT1 KO pam3 12hr_2

city: Pohang

first: Sinhyeog

last: Im

state: Hyoja-dong Namgu

address: POSTECH, postech biotech center Rm 430, Hyoja-dong Namgu, pohang

country: South Korea

institute: POSTECH/IBS

description: Sample name: SAMPLE 12

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0). R 2.15.1 (www.r-project.org).

source_name: Bone marrow

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX)

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with Ribospin II RNA purification kit (GeneAll biotechnology, Seoul, Korea) according to the manufacturer's instructions.

value: Bone marrow

value: dendritic

tag: genotype

value: NFAT1 KO

tag: stimulation

tag: stimulation duration

value: 12 hours


title: Control liver day 8, biological rep1


title: somatic cell from young donor [Y-SC]

tag: cell type

tag: age


title: Control liver day 4, biological rep3


title: NFAT1 KO W/O_2

description: Sample name: SAMPLE 8


title: Control liver day 4, biological rep2


title: NFAT1 KO pam3 2hr_2

description: Sample name: SAMPLE 10

value: 2 hours


title: WT pam3 12hr_2

description: Sample name: SAMPLE 6

value: wildtype


title: Control liver day 4, biological rep1


title: NFAT1 KO W/O_1

description: Sample name: SAMPLE 7


title: WT W/O_2

description: Sample name: SAMPLE 2


title: NFAT1 KO pam3 2hr_1

description: Sample name: SAMPLE 9


title: WT pam3 2hr_1

description: Sample name: SAMPLE 3


title: NFAT1 KO pam3 12hr_1

description: Sample name: SAMPLE 11


title: WT pam3 12hr_1

description: Sample name: SAMPLE 5


title: WT W/O_1

description: Sample name: SAMPLE 1


title: DCs No treatment rep3

city: Chicago

first: Yuk Man

last: Lei

state: IL

institute: University of Chicago

description: Ctrl Rep3

hyb_protocol: Hybridization step was done at the University of Chicago by the Genomics Core Facility

scan_protocol: Scanning step was done at the University of Chicago by the Genomics Core Facility

data_processing: Quantile normalized

source_name: Mouse lymph node

label_protocol: Labeling step was done at the University of Chicago by the Genomics Core Facility

extract_protocol: RNA was extracted using QIAGEN Rnasy microb kit

treatment_protocol: Mouse were treated with broad-spectrum antibiotics for 10 days through oral gavage. After isolation from peripheral LNs, cells were stained and FACS-sorted

value: dendritic cells

tag: treatment

value: no treatment


title: human_female_GBM_U87MG_clone#1_shRNA/CDCA7L(1)

city: Frederick

first: Karlyne

middle: M

last: Reilly

address: West 7th St at Fort Detrick, PO Box B

department: Mouse Cancer Genetics Program

institute: National Cancer Institute, Center for Cancer Research

hyb_protocol: Labeled cDNA of each sample was hybridized to Affymetrix human Gene ST 1.0 GeneChip in Affymetrix hybridization oven at 45C, 60rpm for 16 hrs. Wash and stain were performed on Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned on Affymetrix GeneChip scanner 3000 and data were collected using Affymetrix AGCC software.

data_processing: Data was normalized in Partek Genomics Suite v6.5 using RMA normalization algorithm. Scrambled shRNA control samples were selected for M vs F comparison. LN18 and U87 samples were selected for CDCA7L knockdown analysis, due to weak/incomplete knockdown in U118MG and SF539

source_name: human female U87MG GBM cells, CDCA7L depleted

label_protocol: RNA (100 ng) was reverse transcribed and amplified using Ambion WT expression kit following manufacturer’s suggested protocol. Sense strand cDNA was fragmented and labeled using Affymetrix WT terminal labeling kit.

growth_protocol: Human male and female GBM cells, established from human patients with malignant gliomas, were obtained from ATCC and cultured in DMEM + 10% FBS + antibiotics.

extract_protocol: Total RNA was extracted from human GBM cells using RNeasy Mini Kit (Qiagen) and treated with TURBO DNAfree (Ambion). RNA quality was checked on Agilent Bioanalyzer. All samples used for microarray analysis have high quality score (RIN >9).

treatment_protocol: Human male and female GBM cells were transfected using the Lipofectamine 2000 transfection protocol (Invitrogen) with either scrambled shRNA or shRNA against CDCA7L. Each well of a 6-well plate received 3.5 μg of total DNA for two days. Cells were seeded in 6-well plates with 3 X 10^5 cells per well and transduced with pLKO.1-puro CDCA7L-shRNA or pLKO.1-puro non-target shRNA the following day. After 8 hrs of incubation, the supernatant was removed, and 2 ml of DMEM complete medium was added. After 16 hrs, the transfection was repeated a second time and medium was not changed. 48 hrs post-transfection, puromycin selection was initiated to make the CDCA7L-depleted stable cell lines.

tag: Sex

value: female

tag: transfection


title: WT pam3 2hr_2

description: Sample name: SAMPLE 4


title: 12

description: Human Tongue Normal Tissue

value: tongue

tag: disease state

value: Male

tag: pt-stage


title: human_female_GBM_U87MG_clone#2_shRNA/CDCA7L(1)


title: DCs No treatment rep2

description: Ctrl Rep2


title: human_female_GBM_SF539_clone#1_shRNA/CDCA7L(1)

source_name: human female SF539 GBM cells, CDCA7L depleted


title: human_female_GBM_U87MG_clone#2_scrambled shRNA

source_name: human female U87MG GBM cells, non-targeting scrambled shRNA

value: Scrambled shRNA control


title: DCs Abx-treated rep2

description: Abx Rep2

value: broad-spectrum antibiotics


title: DCs Abx-treated rep3

description: Abx Rep3


title: human_female_GBM_U87MG_clone#1_scrambled shRNA


title: human_male_GBM_U118MG_clone#3_scrambled shRNA

source_name: human male U118MG GBM cells, non-targeting scrambled shRNA

value: male


title: human_female_GBM_SF539_clone#1_scrambled shRNA

source_name: human female SF539 GBM cells, non-targeting scrambled shRNA


title: 57-C10-417 GRP 57-1 CONTROL

hyb_protocol: Labeled DNA was hybridized to Mouse 105K CpG Island Microarrays (Design ID:015279)  using conditions specified my manufacture's instructions

scan_protocol: Scanned on a Agilent Technologies Scanner G2505C

data_processing: Agilent Feature Extraction Software (v 9.0) was used to extract data and Genomic Workbench (v 7.0.4) was used to apply the Z-score-based algorithm to find methylation events.

source_name: input DNA

label_protocol: Genomic DNA 5ug was used as starting material with the Genomic DNA Enzymatic Labeling Kit and following the Agilent Microarray Analysis of Methylated DNA Immunoprecipitation protocol

extract_protocol: DNA was extracted using TRIzol Reagent following the manufacturer's instructions

value: Hemibrain

tag: gender

tag: diet

value: high n-3 PUFA enriched diet (ERD n3:n6= 7:1)

source_name: Immunoprecipitated DNA


title: human_male_GBM_U118MG_clone#2_shRNA/CDCA7L(1)

source_name: human male U118MG GBM cells, CDCA7L depleted


title: human_male_GBM_LN18_clone#4_shRNA/CDCA7L(1)

source_name: human male LN18 GBM cells, CDCA7L depleted


title: 57-C10-416 GRP 57-1 CONTROL

tag: tissue

tag: strain


title: human_male_GBM_U118MG_clone#1_scrambled shRNA


title: DCs No treatment rep1

description: Ctrl Rep1


title: ST-C10-434 GRP ST-1 CONTROL

value: standard lab diet (STD, n3:n6= 1:6)


title: ST-C10-437 GRP ST-1 CONTROL


title: DCs Abx-treated rep1

description: Abx Rep1


title: 58-C10-425 GRP 58-1 CONTROL

value: n-3 PUFA optimally balanced by n-6 PUFA (BLD, n3:n6= 1:1)


title: human_male_GBM_LN18_clone#1_scrambled shRNA

source_name: human male LN18 GBM cells, non-targeting scrambled shRNA


title: human_male_GBM_LN18_clone#6_shRNA/CDCA7L(1)


title: human_male_GBM_LN18_clone#5_scrambled shRNA


title: ST-C10-435 GRP ST-1 CONTROL


title: 58-C10-423 GRP 58-1 CONTROL


title: human_male_GBM_U118MG_clone#6_shRNA/CDCA7L(1)


title: 57-C10-415 GRP 57-1 CONTROL


title: 58-C10-424 GRP 58-1 CONTROL


title: WM164 CR DMSO

type: protein

city: Toronto

first: Hezhe

last: Lu

state: Ontario

address: 600 University Ave

country: Canada

institute: The Lunenfeld-Tanenbaum Research Institute

description: DMSO

hyb_protocol: cell were washed by PBS for 3 times before lysis

scan_protocol: the array were performed by the protocol from RPPA Core Facility, MD Anderson Cancer Center

data_processing: All the data points were normalized for protein loading and transformed to linear value.Normalized Linear value was transformed to Log2  value, and then median-centered for Hierarchical Cluster analysis. Median-Centered values were then formatted for heatmap generation. The average value for three repeats for each sample were submitted.

label: antibody

molecule: protein

source_name: melanoma

label_protocol: 50ul protein lysis (1ug/ul) were analyzed by RPPA

growth_protocol: 3 BRAF/MEK inhibitor resistance melanoma cells were growth in RPMI1640 (5% FBS, 3uM PLX4720 and 300nM PD0325901)

extract_protocol: cell were lysised by Cell Lysis Buffer: 1% Triton X-100, 50mM HEPES, pH 7.4, 150mM NaCl, 1.5mM MgCl2, 1mM EGTA, 100mM NaF, 10mM Na pyrophosphate, 1mM Na3VO4, 10% glycerol, containing freshly added protease and phosphatase inhibitors from Roche Applied Science Cat. # 05056489001 and 04906837001, respectively

treatment_protocol: Cells were treated with DMSO or 1uM PAK inhibitor PF3758309 for 48 hr, the cell lysis were analyzed by RPPA

value: melanoma


title: WM164 CR PF3758309


title: 1205Lu CR PF3758309


title: UACC-903 CR PF3758309


title: 57-C10-413 GRP 57-1 CONTROL


title: UACC-903 CR DMSO

description: DMSO


title: skin E17.5 control rep4

city: Lausanne

first: Federica

last: Gilardi

address: chemin de la Vulliette 4

department: University Center of Legal Medicine

country: Switzerland

institute: University of Lausanne

description: gene expression data

hyb_protocol: Affymetrix mouse gene 1.0ST arrays (Affymetrix, Santa Clara, CA, USA) were hybridized with 2.3μg of fragmented target, at 45°C for 16 hours washed and stained according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007).

scan_protocol: The arrays were scanned with the GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: RMA algorithm was applied to data, using Affymetrix Expression Console software.

source_name: mouse full thickness skin

label_protocol: For each sample, 100ng of total RNA were amplified using the Ambion® WT Expression Kit (4411973, life technologies) kit. 5.5μg of the cDNA was fragmented and labeled with GeneChip® WT Terminal Labeling kit (901525, Affymetrix).

growth_protocol: pregnant mice were housed in standard 12h Light/12h dark light regimen

extract_protocol: Trizol extraction of total RNA, followed by purification with the RNeasy Mini Kit (Qiagen).

treatment_protocol: at the indicated developmental stage  mice were decapitated and full thickness skin was collected for RNA extraction

value: Mixed C57BL6/SV129

tag: developmental stage

tag: genotype/variation

value: PPARgamma wildtype


title: 1205Lu CR DMSO

description: DMSO


title: WT at 6 h high light, biological replicate 4

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

description:
S_WT_4
Gene expression data from shoots of 28-day-old Arabidopsis wildtype grown in 6 h high light

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of Aragene_1.0st-type from Affymetrix. A Custom CDF Version 20 with TAIR based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

organism: Arabidopsis thaliana

source_name: WT at 6 h high light_shoot

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

growth_protocol: Arabidopsis thaliana wildtype and mutants were grown in soil for total 4 weeks under short-day conditions (8 h light / 16 h dark)

extract_protocol: RNA was extracted using the peqGOLD Total RNA Kit according to the manufacturer´s instruction

treatment_protocol: Plants were grown under normal light conditions (80 µmol quanta m-2s-1) or treated with 6 h high light (800 µmol quanta m-2s-1)

value: WT

tag: sample group

value: 6 h high light

value: shoot


title: serat2;1 at 6 h high light, biological replicate 4

description:
S_serat2_1_4
Gene expression data from shoots of 28-day-old Arabidopsis serat2;1 grown in 6 h high light

source_name: serat2;1 at 6 h high light_shoot

tag: genotype


title: skin E17.5 PpargΔ/Δ rep3

description: gene expression data

value: PPARgamma null


title: skin E17.5 PpargΔ/Δ rep4

description: gene expression data


title: skin E17.5 PpargΔ/Δ rep1

description: gene expression data


title: skin E17.5 control rep3

description: gene expression data


title: WT at 6 h high light, biological replicate 1

description:
S_WT_1
Gene expression data from shoots of 28-day-old Arabidopsis wildtype grown in 6 h high light


title: skin E17.5 PpargΔ/Δ rep2

description: gene expression data


title: oastlB at 6 h high light, biological replicate 4

description:
S_oastlB_4
Gene expression data from shoots of 28-day-old Arabidopsis oastlB grown in 6 h high light

source_name: oastlB at 6 h high light_shoot

value: oastlB


title: serat2;1 at 6 h high light, biological replicate 2

description:
S_serat2_1_2
Gene expression data from shoots of 28-day-old Arabidopsis serat2;1 grown in 6 h high light


title: skin E17.5 control rep1

description: gene expression data


title: serat2;1 at 6 h high light, biological replicate 3

description:
S_serat2_1_3
Gene expression data from shoots of 28-day-old Arabidopsis serat2;1 grown in 6 h high light


title: skin E17.5 control rep2

description: gene expression data


title: 2cysprx at 6 h high light, biological replicate 4

description:
S_2CP_4
Gene expression data from shoots of 28-day-old Arabidopsis 2cysprx grown in 6 h high light

source_name: 2cysprx at 6 h high light_shoot


title: WT at 6 h high light, biological replicate 3

description:
S_WT_3
Gene expression data from shoots of 28-day-old Arabidopsis wildtype grown in 6 h high light


title: cyp20-3 at 6 h high light, biological replicate 3

description:
S_CYP20_3_3
Gene expression data from shoots of 28-day-old Arabidopsis cyp20-3 grown in 6 h high light

source_name: cyp20-3 at 6 h high light_shoot


title: oastlB at 6 h high light, biological replicate 1

description:
S_oastlB_1
Gene expression data from shoots of 28-day-old Arabidopsis oastlB grown in 6 h high light


title: cyp20-3 at 6 h high light, biological replicate 1

description:
S_CYP20_3_1
Gene expression data from shoots of 28-day-old Arabidopsis cyp20-3 grown in 6 h high light


title: serat2;1 at 6 h high light, biological replicate 1

description:
S_serat2_1_1
Gene expression data from shoots of 28-day-old Arabidopsis serat2;1 grown in 6 h high light


title: oastlB at 6 h high light, biological replicate 3

description:
S_oastlB_3
Gene expression data from shoots of 28-day-old Arabidopsis oastlB grown in 6 h high light


title: WT at 6 h high light, biological replicate 2

description:
S_WT_2
Gene expression data from shoots of 28-day-old Arabidopsis wildtype grown in 6 h high light


title: cyp20-3 at 6 h high light, biological replicate 4

description:
S_CYP20_3_4
Gene expression data from shoots of 28-day-old Arabidopsis cyp20-3 grown in 6 h high light


title: oastlB at 6 h high light, biological replicate 2

description:
S_oastlB_2
Gene expression data from shoots of 28-day-old Arabidopsis oastlB grown in 6 h high light


title: cyp20-3 at 6 h high light, biological replicate 2

description:
S_CYP20_3_2
Gene expression data from shoots of 28-day-old Arabidopsis cyp20-3 grown in 6 h high light


title: glomeruli from JAK2 Akita diabetic glomeruli + JAK1/2 inhibitor 1

city: Ann Arbor

first: Viji

last: Nair

address: 1152 West Medical Centre Dr.

institute: University of Michigan

description: Gene expression data from JAK2 mice (JAK1/2 )  glomeruli (16 weeks old)

hyb_protocol: Affymetrix Standard protocol

scan_protocol: GeneChip arrays were scanned by GeneChip Scanner 3000 7G according to the Affymetrix Expression Analysis Technical Manual.

data_processing: The data were analyzed using ChipInspector which carries out significance analysis on the single probe level. Normalized probe set level data not provided for individual Sample records. ChipInspector gives the log2 based fold change ratio between two group samples for each gene

source_name: glomeruli from diabetic JAK2 mouse treated with JAK1/2 inhibitor

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

extract_protocol: Total RNA was isolated using RNeasy Mini Kit (Qiagen, Hilden, Germany)

treatment_protocol: 129S6 Akita podocyte-JAK2 transgenic mice were implanted with osmotic minipumps that infused angiontensin II subcutaneously at a rate of 700 ng/min/kg for 4 wks.  During the final 2 wks of this infusion the experimental mice received a JAK1/2 inhibitor at 3 mg/kg/day in acidified water, while the control mice received vehicle alone. The JAK1/2 inhibitor reduced mesangial expansion and albuminuria in the diabetic hypertensive mice without affecting glycemia or blood pressure.

value: Glomeruli

value: diabetic

value: JAK1/2 inhibitor


title: glomeruli from JAK2 Akita diabetic glomeruli + JAK1/2 inhibitor 2


title: glomeruli from JAK2 Akita diabetic glomeruli + JAK1/2 inhibitor 5


title: glomeruli from JAK2 Akita diabetic glomeruli + JAK1/2 inhibitor 3


title: glomeruli from JAK2 Akita diabetic glomeruli + JAK1/2 inhibitor 4


title: glomeruli from JAK2 Akita diabetic glomeruli + vehicle 5

description: Gene expression data from JAK2 mice (vehicle)  glomeruli (16 weeks old)

source_name: glomeruli from diabetic JAK2 mouse

value: vehicle


title: WM3903 PF3758309

hyb_protocol: cell were washed by PBS for 3 times before lysis, Samples were probed with antibodies by CSA amplification approach and visualized by DAB colorimetric reaction.

scan_protocol: the array were performed by the protocol from RPPA Core Facility, MD Anderson Cancer Center, Slides were scanned on a flatbed scanner to produce 16-bit tiff image. Spots from tiff images were identified and the density was quantified by Array-Pro Analyzer.

data_processing: Relative protein levels for each sample were determined by interpolation of each dilution curves from the standard curve (supercurve) of the slide (antibody).  Supercurve is constructed by a script in R written by Bioinformatics.  These values (given as Log2 values) are defined as Supercurve Log2 (Raw) value

label_protocol: 50ul protein lysis (1ug/ul) were analyzed by RPPA,Tumor or cell  lysates were two-fold-serial diluted for 5 dilutions (from undiluted to 1:16 dilution) and arrayed on nitrocellulose-coated slide in 11x11 format

growth_protocol: 22 BRAF inhibitor resistance cells were growth in RPMI1640 (5% FBS, 3uM PLX4720)

treatment_protocol: Cells were treated with  or 1uM PAK inhibitor PF3758309 for 48 hr, the cell lysis were analyzed by RPPA

tag: agent


title: 2cysprx at 6 h high light, biological replicate 3

description:
S_2CP_3
Gene expression data from shoots of 28-day-old Arabidopsis 2cysprx grown in 6 h high light


title: glomeruli from JAK2 Akita diabetic glomeruli + vehicle 3


title: WM3936

value: DMSO


title: 2cysprx at 6 h high light, biological replicate 2

description:
S_2CP_2
Gene expression data from shoots of 28-day-old Arabidopsis 2cysprx  grown in 6 h high light


title: 2cysprx at 6 h high light, biological replicate 1

description:
S_2CP_1
Gene expression data from shoots of 28-day-old Arabidopsis 2cysprx grown in 6 h high light


title: WM3903


title: WM3936 PF3758309


title: glomeruli from JAK2 Akita diabetic glomeruli + vehicle 1


title: WM3901 PF3758309


title: glomeruli from JAK2 Akita diabetic glomeruli + vehicle 2


title: WM164BR PF3758309


title: WT at normal light, biological replicate 4

description:
C_WT_4
Gene expression data from shoots of 28-day-old Arabidopsis wildtype grown in normal light

source_name: WT at normal light_shoot

value: Control


title: WM164BR


title: WM989BR PF3758309


title: glomeruli from JAK2 Akita diabetic glomeruli + vehicle 4


title: WM3901


title: WM989BR


title: WM983BR


title: WM983BR PF3758309


title: WT at normal light, biological replicate 1

description:
C_WT_1
Gene expression data from shoots of 28-day-old Arabidopsis wildtype grown in normal light


title: WT at normal light, biological replicate 2

description:
C_WT_2
Gene expression data from shoots of 28-day-old Arabidopsis wildtype grown in normal light


title: serat2;1 at normal light, biological replicate 2

description:
C_serat2_1_2
Gene expression data from shoots of 28-day-old Arabidopsis serat2;1 grown in normal light

source_name: serat2;1 at normal light_shoot


title: oastlB at normal light, biological replicate 4

description:
C_oastlB_4
Gene expression data from shoots of 28-day-old Arabidopsis oastlB grown in normal light

source_name: oastlB at normal light_shoot


title: UACC903BR


title: serat2;1 at normal light, biological replicate 3

description:
C_serat2_1_3
Gene expression data from shoots of 28-day-old Arabidopsis serat2;1 grown in normal light


title: SK-MEL-28BR PF3758309


title: serat2;1 at normal light, biological replicate 1

description:
C_serat2_1_1
Gene expression data from shoots of 28-day-old Arabidopsis serat2;1 grown in normal light


title: UACC903BR PF3758309


title: LOX-IMVIBR_PF3758309


title: oastlB at normal light, biological replicate 2

description:
C_oastlB_2
Gene expression data from shoots of 28-day-old Arabidopsis oastlB grown in normal light


title: WT at normal light, biological replicate 3

description:
C_WT_3
Gene expression data from shoots of 28-day-old Arabidopsis wildtype grown in normal light


title: oastlB at normal light, biological replicate 3

description:
C_oastlB_3
Gene expression data from shoots of 28-day-old Arabidopsis oastlB grown in normal light


title: SK-MEL-28BR


title: LOX-IMVIBR


title: serat2;1 at normal light, biological replicate 4

description:
C_serat2_1_4
Gene expression data from shoots of 28-day-old Arabidopsis serat2;1 grown in normal light


title: 451LUBR


title: 1205LUBR_PF3758309


title: 1205LuBR


title: 451LUBR_PF3758309


title: cyp20-3 at normal light, biological replicate 2

description:
C_CYP20_3_2
Gene expression data from shoots of 28-day-old Arabidopsis cyp20-3 grown in normal light

source_name: cyp20-3 at normal light_shoot


title: oastlB at normal light, biological replicate 1

description:
C_oastlB_1
Gene expression data from shoots of 28-day-old Arabidopsis oastlB grown in normal light


title: cyp20-3 at normal light, biological replicate 1

description:
C_CYP20_3_1
Gene expression data from shoots of 28-day-old Arabidopsis cyp20-3 grown in normal light


title: cyp20-3 at normal light, biological replicate 3

description:
C_CYP20_3_3
Gene expression data from shoots of 28-day-old Arabidopsis cyp20-3 grown in normal light


title: 2cysprx at normal light, biological replicate 3

description:
C_2CP_3
Gene expression data from shoots of 28-day-old Arabidopsis 2cysprx grown in normal light

source_name: 2cysprx at normal light_shoot


title: 2cysprx at normal light, biological replicate 1

description:
C_2CP_1
Gene expression data from shoots of 28-day-old Arabidopsis 2cysprx grown in normal light


title: 2cysprx at normal light, biological replicate 4

description:
C_2CP_4
Gene expression data from shoots of 28-day-old Arabidopsis 2cysprx grown in normal light


title: 2cysprx at normal light, biological replicate 2

description:
C_2CP_2
Gene expression data from shoots of 28-day-old Arabidopsis 2cysprx grown in normal light


title: cyp20-3 at normal light, biological replicate 4

description:
C_CYP20_3_4
Gene expression data from shoots of 28-day-old Arabidopsis cyp20-3 grown in normal light


title: N_ERGO_T1_1

status: Public on Jul 30 2017

city: Montpellier

first: Bruno

last: Blondin

address: 2 place Pierre Viala

country: France

institute: INRA

description: Gene expression in sample from EC1118 strain, biological rep 1, at 1 g/L released CO2 under nitrogen plus ergsoterol starvation

hyb_protocol: Agilent gene expression microarrays 8x15k was used for the micro array hybridization, with one-color method. Array design is based on ID 038619 completed with the regions A, B and C + KHR1 + MPR1 from the new regions of EC1118  (Agilent Technologies, Santa Clara, CA, USA). 600ng of labeled cRNA were hybridized for 17h in 65°C in a rotative hybridization oven (Corning) using the Expression Hybridization kit (Agilent Technologies, 5188-5242). Plates were washed with expression wash buffer kit (Agilent Technologies, 5188-5325 5188-5326).

scan_protocol: The array pictures were analyzed on a GenePix 4000B laser Scanner (Axon Instruments) and with the GenePix software Pro7.

data_processing: Data normalization and statistical analysis were performed using the R 3.1.3 software and the limma package. Normalization was done by the quantile method considering all arrays.

organism: Saccharomyces cerevisiae

source_name: N_ERGO_T1_biological repetition 1

label_protocol: Cy3-labeled cRNA was synthesized with the One color RNA Spike-In kit (Agilent Technologies) and purified with RNeasy kit (Qiagen). Quality and quantity of RNA were controlled at each step by spectrometry (NanoDrop 1000, Thermo Scientific).

growth_protocol: Yeast cells were first pre-cultured with shaking (180rpm) overnight at 28°C  in 50ml flasks containing YNB medium. After centrifugation, pellets were washed with synthetic must. These pre-cultures were used to inoculate fermentations (10^6 cells/ml) in synthetic must. Fermentation experiments were performed at 24°C in fermenters with a working volume of 1.1l. The synthtetic must used contains 230g/l of sugars ( (115g/L glucose and 115g/l of fructose), and either 71 or 425 mg/L of yeast assimilable nitrogen (free amino acids and ammonium).

extract_protocol: Total RNA extraction were performed with Trizol reagent (Gibco BRL, Life Technologies), purified by isopropanol precipitation then using RNeasy kit (Qiagen).

treatment_protocol: Cells were sampled at 4 time-point during the alcoholic fermentation (20 106cells/ml, 12 g of CO2 released, 40 g of CO2 released and 75 g of CO2 released). 10^9 cells were pelleted, washed with DEPC-treated water and freezed in methanol at -80°C.

tag: released co2 (g/l)

tag: array

tag: block

tag: condition

value: nitrogen plus ergsoterol starvation


title: ERGO_T1_3

description: Gene expression in sample from EC1118 strain, biological rep 3, at 1 g/L released CO2 under ergosterol starvation

source_name: ERGO_T1_biological repetition 3

value: ergosterol starvation


title: TWN_T3_1

description: Gene expression in sample from EC1118 strain, biological rep 1, at 40 g/L released CO2 under oleic acid starvation

source_name: TWN_T3_biological repetition 1

value: oleic acid starvation


title: TWN_T1_3

description: Gene expression in sample from EC1118 strain, biological rep 3, at 1 g/L released CO2 under oleic acid starvation

source_name: TWN_T1_biological repetition 3


title: NICO_T3_1

description: Gene expression in sample from EC1118 strain, biological rep 1, at 40 g/L released CO2 under nicotinic acid starvation

source_name: NICO_T3_biological repetition 1

value: nicotinic acid starvation


title: ERGO_T4_1

description: Gene expression in sample from EC1118 strain, biological rep 1, at 75 g/L released CO2 under ergosterol starvation

source_name: ERGO_T4_biological repetition 1


title: PANTO_T2_3

description: Gene expression in sample from EC1118 strain, biological rep 3, at 12 g/L released CO2 under pantothenic acid starvation

source_name: PANTO_T2_biological repetition 3

value: pantothenic acid starvation


title: NICO_T3_2

description: Gene expression in sample from EC1118 strain, biological rep 2, at 40 g/L released CO2 under nicotinic acid starvation

source_name: NICO_T3_biological repetition 2


title: ERGO_T2_3

description: Gene expression in sample from EC1118 strain, biological rep 3, at 12 g/L released CO2 under ergosterol starvation

source_name: ERGO_T2_biological repetition 3


title: N_ERGO_T3_3

description: Gene expression in sample from EC1118 strain, biological rep 3, at 40 g/L released CO2 under nitrogen plus ergsoterol starvation

source_name: N_ERGO_T3_biological repetition 3


title: N_ERGO_T2_1

description: Gene expression in sample from EC1118 strain, biological rep 1, at 12 g/L released CO2 under nitrogen plus ergsoterol starvation

source_name: N_ERGO_T2_biological repetition 1


title: MS71_T2_1

description: Gene expression in sample from EC1118 strain, biological rep 1, at 12 g/L released CO2 under nitrogen starvation

source_name: MS71_T2_biological repetition 1

value: nitrogen starvation


title: MS71_T3_1

description: Gene expression in sample from EC1118 strain, biological rep 3, at 1 g/L released CO2 under nitrogen starvation

source_name: MS71_T3_biological repetition 1


title: MS71_T4_1

description: Gene expression in sample from EC1118 strain, biological rep 1, at 75 g/L released CO2 under nitrogen starvation

source_name: MS71_T4_biological repetition 1


title: N_ERGO_T3_2

description: Gene expression in sample from EC1118 strain, biological rep 2, at 40 g/L released CO2 under nitrogen plus ergsoterol starvation

source_name: N_ERGO_T3_biological repetition 2


title: TWN_T4_1

description: Gene expression in sample from EC1118 strain, biological rep 1, at 75 g/L released CO2 under oleic acid starvation

source_name: TWN_T4_biological repetition 1


title: TWN_T1_1

description: Gene expression in sample from EC1118 strain, biological rep 1, at 1 g/L released CO2 under oleic acid starvation

source_name: TWN_T1_biological repetition 1


title: PANTO_T2_1

description: Gene expression in sample from EC1118 strain, biological rep 1, at 12 g/L released CO2 under pantothenic acid starvation

source_name: PANTO_T2_biological repetition 1


title: PANTO_T3_3

description: Gene expression in sample from EC1118 strain, biological rep 3, at 40 g/L released CO2 under pantothenic acid starvation

source_name: PANTO_T3_biological repetition 3


title: MS71_T1_3

source_name: MS71_T1_biological repetition 3


title: NICO_T4_3

description: Gene expression in sample from EC1118 strain, biological rep 3, at 75 g/L released CO2 under nicotinic acid starvation

source_name: NICO_T4_biological repetition 3


title: ERGO_T4_3

description: Gene expression in sample from EC1118 strain, biological rep 3, at 75 g/L released CO2 under ergosterol starvation

source_name: ERGO_T4_biological repetition 3


title: N_ERGO_T2_2

description: Gene expression in sample from EC1118 strain, biological rep 2, at 12 g/L released CO2 under nitrogen plus ergsoterol starvation

source_name: N_ERGo_T2_biological repetition 2


title: NICO_T1_1

description: Gene expression in sample from EC1118 strain, biological rep 1, at 1 g/L released CO2 under nicotinic acid starvation

source_name: NICO_T1_biological repetition 1


title: ERGO_T2_1

description: Gene expression in sample from EC1118 strain, biological rep 1, at 12 g/L released CO2 under ergosterol starvation

source_name: ERGO_T2_biological repetition 1


title: TWN_T2_3

description: Gene expression in sample from EC1118 strain, biological rep 3, at 40 g/L released CO2 under oleic acid starvation

source_name: TWN_T2_biological repetition 3


title: TWN_T2_1

description: Gene expression in sample from EC1118 strain, biological rep 1, at 12 g/L released CO2 under oleic acid starvation

source_name: TWN_T2_biological repetition 1


title: ERGO_T1_1

description: Gene expression in sample from EC1118 strain, biological rep 1, at 1 g/L released CO2 under ergosterol starvation

source_name: ERGO_T1_biological repetition 1


title: PANTO_T4_1

description: Gene expression in sample from EC1118 strain, biological rep 1, at 75 g/L released CO2 under pantothenic acid starvation

source_name: PANTO_T4_biological repetition 1


title: MS71_T2_2

description: Gene expression in sample from EC1118 strain, biological rep 2, at 12 g/L released CO2 under nitrogen starvation

source_name: MS71_T2_biological repetition 2


title: MS71_T3_2

description: Gene expression in sample from EC1118 strain, biological rep 2, at 40 g/L released CO2 under nitrogen starvation

source_name: MS71_T3_biological repetition 2


title: TWN_T4_3

description: Gene expression in sample from EC1118 strain, biological rep 3, at 75 g/L released CO2 under oleic acid starvation

source_name: TWN_T4_biological repetition 3


title: ERGO_T3_2

description: Gene expression in sample from EC1118 strain, biological rep 2, at 40 g/L released CO2 under ergosterol starvation

source_name: ERGO_T3_biological repetition 2


title: ERGO_T4_2

description: Gene expression in sample from EC1118 strain, biological rep 2, at 75 g/L released CO2 under ergosterol starvation

source_name: ERGO_T4_biological repetition 2


title: NICO_T4_2

description: Gene expression in sample from EC1118 strain, biological rep 2, at 75 g/L released CO2 under nicotinic acid starvation

source_name: NICO_T4_biological repetition 2


title: NICO_T2_3

description: Gene expression in sample from EC1118 strain, biological rep 3, at 12 g/L released CO2 under nicotinic acid starvation

source_name: NICO_T2_biological repetition 3


title: N_ERGO_T1_2

description: Gene expression in sample from EC1118 strain, biological rep 2, at 1 g/L released CO2 under nitrogen plus ergsoterol starvation

source_name: N_ERGO_T1_biological repetition 2


title: PANTO_T1_2

description: Gene expression in sample from EC1118 strain, biological rep 2, at 1 g/L released CO2 under pantothenic acid starvation

source_name: PANTO_T1_biological repetition 2


title: PANTO_T4_3

description: Gene expression in sample from EC1118 strain, biological rep 3, at 75 g/L released CO2 under pantothenic acid starvation

source_name: PANTO_T4_biological repetition 3


title: MS71_T3_3

description: Gene expression in sample from EC1118 strain, biological rep 3, at 40 g/L released CO2 under nitrogen starvation

source_name: MS71_T3_biological repetition 3


title: NICO_T1_2

description: Gene expression in sample from EC1118 strain, biological rep 2 at 1 g/L released CO2 under nicotinic acid starvation

source_name: NICO_T1_biological repetition 2


title: NICO_T3_3

description: Gene expression in sample from EC1118 strain, biological rep 3, at 40 g/L released CO2 under nicotinic acid starvation

source_name: NICO_T3_biological repetition 3


title: MS71_T1_2

description: Gene expression in sample from EC1118 strain, biological rep 2, at 1 g/L released CO2 under nitrogen starvation

source_name: MS71_T1_biological repetition 2


title: ERGO_T3_1

description: Gene expression in sample from EC1118 strain, biological rep 1, at 40 g/L released CO2 under ergosterol starvation

source_name: ERGO_T3_biological repetition 1


title: PANTO_T3_1

description: Gene expression in sample from EC1118 strain, biological rep 1, at 40 g/L released CO2 under pantothenic acid starvation

source_name: PANTO_T3_biological repetition 1


title: N_ERGO_T3_1

description: Gene expression in sample from EC1118 strain, biological rep 1, at 40 g/L released CO2 under nitrogen plus ergsoterol starvation

source_name: N_ERGO_T3_biological repetition 1


title: N_ERGO_T2_3

description: Gene expression in sample from EC1118 strain, biological rep 3, at 12 g/L released CO2 under nitrogen plus ergsoterol starvation

source_name: N_ERGO_T2_biological repetition 3


title: ERGO_T1_2

description: Gene expression in sample from EC1118 strain, biological rep 2, at 1 g/L released CO2 under ergosterol starvation

source_name: ERGO_T1_biological repetition 2


title: MS71_T4_2

description: Gene expression in sample from EC1118 strain, biological rep 2, at 75 g/L released CO2 under nitrogen starvation

source_name: MS71_T4_biological repetition 2


title: PANTO_T4_2

description: Gene expression in sample from EC1118 strain, biological rep 2, at 75 g/L released CO2 under pantothenic acid starvation

source_name: PANTO_T4_biological repetition 2


title: TWN_T4_2

description: Gene expression in sample from EC1118 strain, biological rep 2, at 75 g/L released CO2 under oleic acid starvation

source_name: TWN_T4_biological repetition 2


title: MS71_T1_1

description: Gene expression in sample from EC1118 strain, biological rep 1, at 1 g/L released CO2 under nitrogen starvation

source_name: MS71_T1_biological repetition 1


title: PANTO_T1_3

description: Gene expression in sample from EC1118 strain, biological rep 3, at 1 g/L released CO2 under pantothenic acid starvation

source_name: PANTO_T1_biological repetition 3


title: NICO_T2_2

description: Gene expression in sample from EC1118 strain, biological rep 2, at 12 g/L released CO2 under nicotinic acid starvation

source_name: NICO_T2_biological repetition 2


title: PANTO_T2_2

description: Gene expression in sample from EC1118 strain, biological rep 2, at 12 g/L released CO2 under pantothenic acid starvation

source_name: PANTO_T2_biological repetition 2


title: N_ERGO_T4_1

description: Gene expression in sample from EC1118 strain, biological rep 1, at 75 g/L released CO2 under nitrogen plus ergsoterol starvation

source_name: N_ERGO_T4_biological repetition 1


title: ERGO_T3_3

description: Gene expression in sample from EC1118 strain, biological rep 3, at 40 g/L released CO2 under ergosterol starvation

source_name: ERGO_T3_biological repetition 3


title: NICO_T1_3

description: Gene expression in sample from EC1118 strain, biological rep 3, at 1 g/L released CO2 under nicotinic acid starvation

source_name: NICO_T1_biological repetition 3


title: TWN_T3_2

description: Gene expression in sample from EC1118 strain, biological rep 2, at 40 g/L released CO2 under oleic acid starvation

source_name: TWN_T3_biological repetition 2


title: N_ERGO_T4_3

description: Gene expression in sample from EC1118 strain, biological rep 3, at 75 g/L released CO2 under nitrogen plus ergsoterol starvation

source_name: N_ERGO_T4_biological repetition 3


title: MS71_T2_3

description: Gene expression in sample from EC1118 strain, biological rep 3, at 12 g/L released CO2 under nitrogen starvation

source_name: MS71_T2_biological repetition 3


title: TWN_T2_2

description: Gene expression in sample from EC1118 strain, biological rep 2, at 12 g/L released CO2 under oleic acid starvation

source_name: TWN_T2_biological repetition 2


title: N_ERGO_T4_2

description: Gene expression in sample from EC1118 strain, biological rep 2, at 75 g/L released CO2 under nitrogen plus ergsoterol starvation

source_name: N_ERGO_T4_biological repetition 2


title: NICO_T4_1

description: Gene expression in sample from EC1118 strain, biological rep 1, at 75 g/L released CO2 under nicotinic acid starvation

source_name: NICO_T4_biological repetition 1


title: TWN_T1_2

description: Gene expression in sample from EC1118 strain, biological rep 1, at 1 g/L released CO2 under oleic acid starvation

source_name: TWN_T1_biological repetition 2


title: PANTO_T1_1

description: Gene expression in sample from EC1118 strain, biological rep 1, at 1 g/L released CO2 under pantothenic acid starvation

source_name: PANTO_T1_biological repetition 1


title: ERGO_T2_2

description: Gene expression in sample from EC1118 strain, biological rep 2, at 12 g/L released CO2 under ergosterol starvation

source_name: ERGO_T2_biological repetition 2


title: N_ERGO_T1_3

description: Gene expression in sample from EC1118 strain, biological rep 3, at 1 g/L released CO2 under nitrogen plus ergsoterol starvation

source_name: N_ERGO_T1_biological repetition 3


title: MS71_T4_3

description: Gene expression in sample from EC1118 strain, biological rep 2, at 75 g/L released CO2 under nitrogen starvation

source_name: MS71_T4_biological repetition 3


title: PANTO_T3_2

description: Gene expression in sample from EC1118 strain, biological rep 2, at 40 g/L released CO2 under pantothenic acid starvation

source_name: PANTO_T3_biological repetition 2


title: NICO_T2_1

description: Gene expression in sample from EC1118 strain, biological rep 1, at 12 g/L released CO2 under nicotinic acid starvation

source_name: NICO_T2_biological repetition 1


title: TWN_T3_3

description: Gene expression in sample from EC1118 strain, biological rep 3, at 40 g/L released CO2 under oleic acid starvation

source_name: TWN_T3_biological repetition 3


title: Col0 vs. Ila3 replicate 2

city: Valencia

first: Jose

last: Gadea

address: Ingeniero Fausto Elio

department: Stress

country: Spain

institute: IBMCP

hyb_protocol: Hybridization and slide washing were performed with the Gene Expression Hybridization Kit and Gene Expression Wash Buffers, respectively.

scan_protocol: slides were scanned in a GenePix 4000B microarray scanner, at 5 μm resolution and using the double scanning

data_processing: Feature Extraction software 9.5.1. was used for background substraction and normalization

source_name: wildtype Col0 seedlings

label_protocol: Sample RNA (0.5 μg) was amplified and labeled with the Agilent Low Input Quick Amp Labeling Kit.

growth_protocol: Arabidopsis plants were grown on MS plates for 20 days after sowing

extract_protocol: Total RNA extracted using Qiagen RNA extraction kit following manufacturer's instructions

tag: ecotype

value: seedlings

value: ila3 wild-type

source_name: ila3 mutant seedlings

value: ila3 mutant


title: Col0 vs. Ila3 replicate 1


title: Col0 vs. Ila3 replicate 3


title: Normal_7_Hy5

status: Public on Jul 29 2017

city: Oslo

first: Vandana

last: Sandhu

state: oslo

address: Ullernchausseen 70

department: Department of Genetics

country: Norway

institute: Radiumhospitalet, Oslo

description:
miRNA expression of adjacent normal sample from pancreatic cancer patient 7
Normal_7

hyb_protocol: The Hy3TM-labeled samples and a Hy5TM-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNATM microRNA Array 7'th (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human (n=2042), mouse or rat registered in the miRBASE 18.0. The hybridization was performed according to the miRCURY LNATM microRNA Array Instruction manual using a Tecan HS4800TM hybridization station (Tecan, Austria).

scan_protocol: The miRCURY LNATM microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA).

data_processing: The image analysis was carried out using the ImaGene® 9 (miRCURY LNATM microRNA Array Analysis Software, Exiqon, Denmark).

source_name: Adjacent normal

label_protocol: A total of 700 ng total RNA from both the tumor and stroma  was labeled with Hy3TM and Hy5TM fluorescent label, respectively, using the miRCURY LNATM microRNA Hi-Power Labeling Kit, Hy3TM/Hy5TM (Exiqon, Denmark) as described by the manufacturer.

extract_protocol: RNA was extracted from FFPE (Formalin-Fixed Paraffin-Embedded) samples using the Qiagen miRNeasy FFPE kit. 1-2 sections of 10 μm were transferred to a 1.5 mL tube and 1mL xylene was added. The tube was inverted ten times to mix, and centrifuged at full speed for 2 min at room temperature. The supernatant was removed and 1 mL 100 % ethanol was added. Mixing and centrifugation was repeated. Supernatant was removed and the tube was spun at full speed for 30 sec and residual ethanol was removed. The tube was incubated at room temperature with open lid for 10 min to evaporate ethanol. The pellet was resuspended in 150 μL buffer PKD, and 10 μL proteinase K was added. The sample was mixed and incubated for 3 hours at 55 °C. The sample was mixed again and incubated at 80 °C for 15 min. The lower clear phase was transferred to a new tube, transferred to ice, and incubated for 3 min. The sample was then centrifuges at 20,000 x g for 15 min. The supernatant was transferred to a new tube and 16μL DNase booster buffer and 15 μL DNase I stock solution was added and the tube was mixed prior to incubation at room temperature for 15 min. 320 μL Buffer RBC was added. 1120 μL of 99.9 % ethanol was added. The sample was transferred to a spin-column until the entire sample had passed through the column. The column was washed twice with 500 μL RPE buffer using a vacuum-manifold. The column was transferred to a 2 mL collection tube and spun for 5 min at full speed. The dry columns were transferred to a new collection tube and 30 μL RNase free H2O was added directly on the membrane of the spin column. The column was incubated for 1 min at room temperature prior to centrifugation at 11,000 x g. The RNA was stored in -80 °C freezer.

tag: subject status

value: pancreatic cancer patient

tag: patient id

value: patient 7

tag: tissue type

value: Adjacent normal


title: Normal_8_Hy5

description:
miRNA expression of adjacent normal sample from pancreatic cancer patient 8
Normal_8

value: patient 8


title: Normal_6_Hy5

description:
miRNA expression of adjacent normal sample from pancreatic cancer patient 6
Normal_6

value: patient 6


title: Normal_4_Hy5

description:
miRNA expression of adjacent normal sample from pancreatic cancer patient 4
Normal_4

value: patient 4


title: Normal_3_Hy5

description:
miRNA expression of adjacent normal sample from pancreatic cancer patient 3
Normal_3

value: patient 3


title: Normal_2_Hy5

description:
miRNA expression of adjacent normal sample from pancreatic cancer patient 2
Normal_2

value: patient 2


title: Normal_1_Hy5

description:
miRNA expression of adjacent normal sample from pancreatic cancer patient 1
Normal_1

value: patient 1


title: Panc_stroma20_Hy5

description:
miRNA expression of pancreatic cancer patient 20 stroma sample
Panc_stroma20

source_name: FFPE stroma tissue

value: patient 20

value: FFPE stroma tissue


title: Panc_stroma17_Hy5

description:
miRNA expression of pancreatic cancer patient 17 stroma sample
Panc_stroma17

value: patient 17


title: Panc_stroma15_Hy5

description:
miRNA expression of pancreatic cancer patient 15 stroma sample
Panc_stroma15

value: patient 15


title: Panc_stroma16_Hy5

description:
miRNA expression of pancreatic cancer patient 16 stroma sample
Panc_stroma16

value: patient 16


title: Panc_stroma19_Hy5

description:
miRNA expression of pancreatic cancer patient 19 stroma sample
Panc_stroma19

value: patient 19


title: Panc_stroma18_Hy5

description:
miRNA expression of pancreatic cancer patient 18 stroma sample
Panc_stroma18

value: patient 18


title: Panc_stroma13_Hy5

description:
miRNA expression of pancreatic cancer patient 13 stroma sample
Panc_stroma13

value: patient 13


title: Panc_stroma12_Hy5

description:
miRNA expression of pancreatic cancer patient 12 stroma sample
Panc_stroma12

value: pancreatic cancer patient

value: patient 12


title: Panc_stroma14_Hy5

description:
miRNA expression of pancreatic cancer patient 14 stroma sample
Panc_stroma14

value: patient 14


title: Panc_stroma9_Hy5

description:
miRNA expression of pancreatic cancer patient 9 stroma sample
Panc_stroma9

value: patient 9


title: Panc_stroma11_Hy5

description:
miRNA expression of pancreatic cancer patient 11 stroma sample
Panc_stroma11

value: patient 11


title: Normal_5_Hy5

description:
miRNA expression of adjacent normal sample from pancreatic cancer patient 5
Normal_5

value: patient 5

value: Adjacent normal


title: Panc_stroma1_Hy5

description:
miRNA expression of pancreatic cancer patient 1 stroma sample
Panc_stroma1


title: Panc_tumor19_Hy5

description:
miRNA expression of pancreatic cancer patient 19 tumor sample
Panc_tumor19

source_name: FFPE tumor tissue

value: FFPE tumor tissue


title: Panc_stroma5_Hy5

description:
miRNA expression of pancreatic cancer patient 5 stroma sample
Panc_stroma5


title: Panc_stroma2_Hy5

description:
miRNA expression of pancreatic cancer patient 2 stroma sample
Panc_stroma2

value: patient 2


title: Panc_stroma3_Hy5

description:
miRNA expression of pancreatic cancer patient 3 stroma sample
Panc_stroma3

value: patient 3


title: Panc_stroma7_Hy5

description:
miRNA expression of pancreatic cancer patient 7 stroma sample
Panc_stroma7

value: patient 7

value: FFPE stroma tissue


title: Panc_stroma4_Hy5

description:
miRNA expression of pancreatic cancer patient 4 stroma sample
Panc_stroma4

value: patient 4


title: Panc_tumor17_Hy5

description:
miRNA expression of pancreatic cancer patient 17 tumor sample
Panc_tumor17

value: patient 17


title: Panc_tumor18_Hy5

description:
miRNA expression of pancreatic cancer patient 18 tumor sample
Panc_tumor18


title: Panc_stroma8_Hy5

description:
miRNA expression of pancreatic cancer patient 8 stroma sample
Panc_stroma8

value: patient 8


title: Panc_tumor16_Hy5

description:
miRNA expression of pancreatic cancer patient 16 tumor sample
Panc_tumor16

value: patient 16


title: Panc_tumor11_Hy5

description:
miRNA expression of pancreatic cancer patient 11 tumor sample
Panc_tumor11


title: Panc_tumor10_Hy5

description:
miRNA expression of pancreatic cancer patient 10 tumor sample
Panc_tumor10

value: patient 10


title: Panc_tumor12_Hy5

description:
miRNA expression of pancreatic cancer patient 12 tumor sample
Panc_tumor12

value: pancreatic cancer patient


title: Panc_tumor14_Hy5

description:
miRNA expression of pancreatic cancer patient 14 tumor sample
Panc_tumor14


title: Panc_tumor15_Hy5

description:
miRNA expression of pancreatic cancer patient 15 tumor sample
Panc_tumor15

value: patient 15


title: Panc_tumor9_Hy5

description:
miRNA expression of pancreatic cancer patient 9 tumor sample
Panc_tumor9


title: Panc_tumor6_Hy5

description:
miRNA expression of pancreatic cancer patient 6 tumor sample
Panc_tumor6

value: patient 6


title: Panc_tumor8_Hy5

description:
miRNA expression of pancreatic cancer patient 8 tumor sample
Panc_tumor8


title: Panc_tumor7_Hy5

description:
miRNA expression of pancreatic cancer patient 7 tumor sample
Panc_tumor7


title: Panc_tumor3_Hy5

description:
miRNA expression of pancreatic cancer patient 3 tumor sample
Panc_tumor3


title: Panc_tumor4_Hy5

description:
miRNA expression of pancreatic cancer patient 4 tumor sample
Panc_tumor4


title: Panc_tumor5_Hy5

description:
miRNA expression of pancreatic cancer patient 5 tumor sample
Panc_tumor5


title: Normal_2_Hy3

description:
miRNA expression of adjacent normal sample from pancreatic cancer patient 2
Normal_2


title: Panc_tumor2_Hy5

description:
miRNA expression of pancreatic cancer patient 2 tumor sample
Panc_tumor2


title: Panc_tumor1_Hy5

description:
miRNA expression of pancreatic cancer patient 1 tumor sample
Panc_tumor1

value: patient 1


title: Normal_3_Hy3

description:
miRNA expression of adjacent normal sample from pancreatic cancer patient 3
Normal_3


title: Normal_6_Hy3

description:
miRNA expression of adjacent normal sample from pancreatic cancer patient 6
Normal_6


title: Normal_8_Hy3

description:
miRNA expression of adjacent normal sample from pancreatic cancer patient 8
Normal_8


title: Normal_7_Hy3

description:
miRNA expression of adjacent normal sample from pancreatic cancer patient 7
Normal_7


title: Normal_5_Hy3

description:
miRNA expression of adjacent normal sample from pancreatic cancer patient 5
Normal_5


title: Normal_1_Hy3

description:
miRNA expression of adjacent normal sample from pancreatic cancer patient 1
Normal_1


title: Normal_4_Hy3

description:
miRNA expression of adjacent normal sample from pancreatic cancer patient 4
Normal_4


title: Panc_stroma18_Hy3

description:
miRNA expression of pancreatic cancer patient 18 stroma sample
Panc_stroma18

value: patient 18


title: Panc_stroma20_Hy3

description:
miRNA expression of pancreatic cancer patient 20 stroma sample
Panc_stroma20

value: patient 20


title: Panc_stroma19_Hy3

description:
miRNA expression of pancreatic cancer patient 19 stroma sample
Panc_stroma19

value: patient 19


title: Panc_stroma17_Hy3

description:
miRNA expression of pancreatic cancer patient 17 stroma sample
Panc_stroma17


title: Panc_stroma16_Hy3

description:
miRNA expression of pancreatic cancer patient 16 stroma sample
Panc_stroma16


title: Panc_stroma12_Hy3

description:
miRNA expression of pancreatic cancer patient 12 stroma sample
Panc_stroma12

value: patient 12


title: Panc_stroma14_Hy3

description:
miRNA expression of pancreatic cancer patient 14 stroma sample
Panc_stroma14

value: patient 14


title: Panc_stroma13_Hy3

description:
miRNA expression of pancreatic cancer patient 13 stroma sample
Panc_stroma13

value: patient 13


title: Panc_stroma8_Hy3

description:
miRNA expression of pancreatic cancer patient 8 stroma sample
Panc_stroma8


title: Panc_stroma15_Hy3

description:
miRNA expression of pancreatic cancer patient 15 stroma sample
Panc_stroma15


title: Panc_stroma9_Hy3

description:
miRNA expression of pancreatic cancer patient 9 stroma sample
Panc_stroma9

value: patient 9


title: Panc_stroma4_Hy3

description:
miRNA expression of pancreatic cancer patient 4 stroma sample
Panc_stroma4

value: FFPE stroma tissue


title: Panc_stroma5_Hy3

description:
miRNA expression of pancreatic cancer patient 5 stroma sample
Panc_stroma5

value: patient 5


title: Panc_stroma7_Hy3

description:
miRNA expression of pancreatic cancer patient 7 stroma sample
Panc_stroma7

value: patient 7


title: Panc_stroma3_Hy3

description:
miRNA expression of pancreatic cancer patient 3 stroma sample
Panc_stroma3

value: patient 3


title: Panc_stroma2_Hy3

description:
miRNA expression of pancreatic cancer patient 2 stroma sample
Panc_stroma2

value: patient 2


title: Panc_stroma11_Hy3

description:
miRNA expression of pancreatic cancer patient 11 stroma sample
Panc_stroma11

value: patient 11


title: Panc_tumor17_Hy3

description:
miRNA expression of pancreatic cancer patient 17 tumor sample
Panc_tumor17

value: pancreatic cancer patient

value: patient 17

value: FFPE tumor tissue


title: Panc_tumor19_Hy3

description:
miRNA expression of pancreatic cancer patient 19 tumor sample
Panc_tumor19


title: Panc_tumor15_Hy3

description:
miRNA expression of pancreatic cancer patient 15 tumor sample
Panc_tumor15

value: patient 15


title: Panc_tumor18_Hy3

description:
miRNA expression of pancreatic cancer patient 18 tumor sample
Panc_tumor18

value: patient 18


title: Panc_stroma1_Hy3

description:
miRNA expression of pancreatic cancer patient 1 stroma sample
Panc_stroma1

value: patient 1


title: Panc_tumor14_Hy3

description:
miRNA expression of pancreatic cancer patient 14 tumor sample
Panc_tumor14


title: Panc_tumor11_Hy3

description:
miRNA expression of pancreatic cancer patient 11 tumor sample
Panc_tumor11


title: Panc_tumor9_Hy3

description:
miRNA expression of pancreatic cancer patient 9 tumor sample
Panc_tumor9


title: Panc_tumor10_Hy3

description:
miRNA expression of pancreatic cancer patient 10 tumor sample
Panc_tumor10

value: patient 10


title: Panc_tumor12_Hy3

description:
miRNA expression of pancreatic cancer patient 12 tumor sample
Panc_tumor12

value: patient 12


title: Panc_tumor6_Hy3

description:
miRNA expression of pancreatic cancer patient 6 tumor sample
Panc_tumor6

value: patient 6


title: Panc_tumor7_Hy3

description:
miRNA expression of pancreatic cancer patient 7 tumor sample
Panc_tumor7


title: Panc_tumor8_Hy3

description:
miRNA expression of pancreatic cancer patient 8 tumor sample
Panc_tumor8

value: patient 8


title: MCF-7 treated 0.1% EtOH

city: goyang

first: seungyeon

last: lee

address: dongguk-ro 32

department: life science

institute: dongguk unversity

description:
SAMPLE 1
breast cancer
mammary gland, breast; derived from metastatic site: pleural effusion

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human MethylationEPIC 850K Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina procedures using Illumina iScan scanner

data_processing: Background correction, Extraction of CpGs with detection p-value ≥ 0.05 more than 25% of all samples, and BMIQ normalization

label: Cy3, Cy5

source_name: MCF-7, 0.1% EtOH

extract_protocol: genomic DNA was extracted and purified from MCF-7 using ZR Dyet DNA/RNA kit (Zymo research) according to standard instructions

tag: cell line

tag: cell type

value: epithelial

tag: gender

value: female

tag: disease

value: adenocarcinoma

value: control


title: Panc_tumor16_Hy3

description:
miRNA expression of pancreatic cancer patient 16 tumor sample
Panc_tumor16

value: patient 16


title: MCF-7 treated Ginsenoside Rh2

description:
SAMPLE 2
breast cancer
mammary gland, breast; derived from metastatic site: pleural effusion

source_name: MCF-7, Ginsenoside Rh2

value: Ginsenoside Rh2


title: Panc_tumor5_Hy3

description:
miRNA expression of pancreatic cancer patient 5 tumor sample
Panc_tumor5

value: patient 5


title: Panc_tumor4_Hy3

description:
miRNA expression of pancreatic cancer patient 4 tumor sample
Panc_tumor4

value: pancreatic cancer patient

value: patient 4


title: Panc_tumor1_Hy3

description:
miRNA expression of pancreatic cancer patient 1 tumor sample
Panc_tumor1

value: FFPE tumor tissue


title: Panc_tumor3_Hy3

description:
miRNA expression of pancreatic cancer patient 3 tumor sample
Panc_tumor3

value: patient 3


title: Panc_tumor2_Hy3

description:
miRNA expression of pancreatic cancer patient 2 tumor sample
Panc_tumor2

value: patient 2


title: Lung, anti-H-2Kb, day 1, rep 1

city: Phoenix

first: Deepak

middle: K

last: Nayak

state: Arizona

address: 475 N. 5th Street

institute: University of Arizona College of Medicine

description: Gene expression after one day in anti-H-2Kb Ab treated lungs

hyb_protocol: Hybridization of the labeled cDNAs was done in Agilent 2x gene expession hybrization buffer, agilent 10x blocking reagent and kreatech Kreablock onto Agilent 4x44K V2 microarrays at 65oC for 20 min

scan_protocol: Slides were scanned on an Agilent C-class Microarray scanner.

data_processing: Gridding and analysis of images was performed using Agilent Feature Extraction V11.5.1.1.

source_name: Lung RNA, 4 hr post intrabronchial anti-H-2Kb challenge, day 1, replicate1

label_protocol: cDNAs were chemically labeled with Kreatech ULS RNA labeling kit (Kreatech Diagnostics) and Cy5-labeled cDNAs were hybridized to Agilent Mouse v2 4x44K microarrays (G4846A-026655).

extract_protocol: Total RNA was extracted by PureLink RNA kit (Ambion), DNase I treated and evaluated by an Agilent 2100 Bioanalyzerfor for RNA integrity number >7 indicating good quality RNA . Full-length mRNA was enriched by MessageAmpII aRNA Amplification kit (Life Technologies) and reverse transcribed into cDNA.

treatment_protocol: Wildtype C57BL/6 (H-2Kb) mice were administered with intrabronchial delivery of Abs (anti-H-2Kb or isotype control) on days 1, 2, 3 and 6. Four hrs post Ab administration, lungs were perfused with phosphate-buffered saline, pH 7.4 to remove circulating leukocytes and lung tissues were harvested and stored in RNALater (Lifetechnologies) at -20ºC.

tag: strain

tag: tissue

value: Whole lungs (perfused)

value: Male

tag: age

value: 8 wk


title: Lung, isotype, day 6, rep 2

description: Gene expression after six days in isotype treated lungs

source_name: Lung RNA, 4 hr post intrabronchial Ab isotype challenge, day 6, replicate2


title: Lung, isotype, day 6, rep 1

source_name: Lung RNA, 4 hr post intrabronchial Ab isotype challenge, day 6, replicate1


title: Lung, isotype, day 6, rep 3

source_name: Lung RNA, 4 hr post intrabronchial Ab isotype challenge, day 6, replicate3


title: Lung, isotype, day 3, rep 1

description: Gene expression after three days in isotype treated lungs

source_name: Lung RNA, 4 hr post intrabronchial Ab isotype challenge, day 3, replicate1