title: msp1_S3_3

description:
small RNA
msp1 mutant, anther development stage 3 (S3), rep 3.
Raw files for smallRNA-Seq were not provided by submitter


title: MPAF Romidepsin 16h

status: Public on Sep 23 2016

type: RNA

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Universitätsstr. 1

department: Urology

country: Germany

institute: University Hospital Düsseldorf

description: MPAF treated with Romidepsin for 16h

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Bioconductor R. Normalized values were tranformed into log2-values.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: adult primary fibroblasts

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

growth_protocol: TCam-2 and NCCIT cells were grown in RPMI, while 2102EP and JAR were grown in DMEM. Both media were supplemented with 10 % fetal calf serum (FCS) (PAA, Pasching, Austria), 1 % Penicillin / streptomycin (P / S) (PAN, Aidenbach, Germany), 200 mM L-Glutamine (Glu) (PAN, Aidenbach, Germany). MPAF and ARZ were grown in DMEM medium (10 % FCS, 1 % P / S, 200 mM Glu, 1x non-essential amino acids (PAA, Pasching, Austria), 100 nM ß-Mercaptoethanol (Sigma-Aldrich, Taufkirchen, Germany). FS1 cells were grown DMEM medium (20 % FCS, 1 % P / S, 200 mM Glu, 1x non-essential amino acids, 100 nM ß-Mercaptoethanol). All cells were grown at 37 °C and 7.5 % CO2.

extract_protocol: RNA was isolate by the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell line

value: MPAF


title: patient 04, primary tumor, LOH status

type: genomic

city: Tokyo

first: Takuma

last: Morita

address: 1-5-45 Yushima, Bunkyo-ku

department: Maxillofacial Surgery

country: Japan

institute: Tokyo Medical and Dental University

description:
4-P_A_(OncoScan).CEL
4-P_C_(OncoScan).CEL
primary tumor of patient 04
LOH_04-P

hyb_protocol: The products were digested using HaeIII, mixed with the hybridization cocktail, denatured, and hybridized to the GeneChip OncoScan Arrays (Affymetrix)

scan_protocol: The hybridized arrays were finally washed and stained in a GeneChip Fluidics Station (Affymetrix) and scanned using a GeneChip Scanner (Affymetrix).

data_processing: Genome-wide copy number and loss of heterozygosity data were included in the .CEL files. The two files for each allele were collated for analysis in the .OSCHP files, which were quality checked using OncoScan Console Software (Affymetrix). Genome-wide copy number and CN-LOH data were visualized using Nexus Express for OncoScan Software (ver.3 BioDiscovery) and the Tuscan algorithm.  For statistical analysis, the status of copy number and LOH for each patient was calculated by Chromosome Analysis Suite (Affymetrix), and the obtained data in text file format was further analyzed by R statistical software (http://www.r-project.org/).

molecule: genomic DNA

source_name: primary tumor of patient 04

label_protocol: Genomic DNA (80 ng per each sample) was labeled by OncoScan FFPE Assay Kit (Affymetrix) according to manufacturer's instruction.

extract_protocol: All samples were formalin-fixed paraffin-embedded (FFPE) tissues. Sections of 4 μm were cut from each FFPE tissue and mounted onto slides. After confirmation of the tumor area by pathological examination, the viable cancer cell populations were isolated from each slide-mounted section using scalpels. Dissected samples were collected for each sample and DNA extraction was performed using the QIAamp DNA FFPE Tissue Kit (QIAGEN) according to the manufacturer’s protocol. For each sample, genomic DNA was isolated, purified, and then eluted in ATE buffer, low EDTA, pH 8.3. The double-stranded genomic DNA was quantified using a Qubit 2.0 Fluorometer (Life Technologies) and diluted to 12 ng/μL.

tag: disease state

value: oral tongue squamous cell carcinoma (OTSCC)

tag: individual

value: patient 04

tag: tissue

value: primary tumor (PT)

value: LOH


title: msp1_S3_2

type: SRA

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

country: USA

institute: Donald Danforth Plant Science Center

description:
small RNA
msp1 mutant, anther development stage 3 (S3), rep 2.
Raw files for smallRNA-Seq were not provided by submitter

library_source: transcriptomic

data_processing:
For data processing, the adapter sequences were trimmed from raw sequence reads. The small RNA sequences were further trimmed to the lengths between 18 and 34 nucleotides. RNA-seq sequences were maintained at the length after adapter trimming.
Sequence data processing was conducted using in-house Perl scripts developed by Meyers lab in University of Delaware
Genome_build: Rice Genome Annotation Project 7.0
Supplementary_files_format_and_content: tag count file

organism: Oryza sativa

source_name: Rice spikelets

extract_protocol:
Materials were collected and flash frozen in liquid nitrogen. Total RNA was extracted by TRIzol (Invitrogen) according to manufacturer's protocol.
Small RNA libraries were constructed from 1 microgram of  total RNA using Illumina Truseq small RNA sample preparation kit (RS-200-0012). RNA-seq libraries were constructed using the Illumina TruSeq RNA sample preparation kit (RS-122-2001).

tag: genotype

value: msp1 mutant

tag: developmental stage

value: anther development stage 3 (S3)


title: MPAF Solvent 16h

description: MPAF treated with DMSO for 16h


title: MPAF Romidepsin 8h

description: MPAF treated with Romidepsin for 8h


title: patient 03, metastatic lymph node, LOH status

description:
3-L_A_(OncoScan).CEL
3-L_C_(OncoScan).CEL
metastatic lymph node of patient 03
LOH_03-L

source_name: metastatic lymph node of patient 03

value: patient 03

value: metastatic lymph node (MLN)


title: patient 03, primary tumor, LOH status

description:
3-P_A_(OncoScan).CEL
3-P_C_(OncoScan).CEL
primary tumor of patient 03
LOH_03-P

source_name: primary tumor of patient 03


title: patient 01, primary tumor, LOH status

description:
1-P_A_(OncoScan).CEL
1-P_C_(OncoScan).CEL
primary tumor of patient 01
LOH_01-P

source_name: primary tumor of patient 01

value: patient 01


title: JAR Solvent 16h

description: JAR treated with DMSO for 16h

source_name: Choriocarcinoma-like cell line

value: JAR


title: rep1 AE GM-

city: La Jolla

first: Dong-Er

last: Zhang

state: CA

address: 3855 Health Sciences Drive

institute: UCSD Moores Cancer Center

description:
RE_1
Replicate 1

data_processing: The data was normalized using invariant set normalization with dCHIP.

organism: Mus musculus

source_name: RE Lin-/c-Kit+ HSPCs without GM-CSF treatment

label_protocol: Total RNAs were labeled and hybridized on Illumina Mouse Ref-8 v2.0 Expression BeadChips following manufacturer’s protocol

growth_protocol: Lineage negative bone marrow cells were isolated from C57B6/J mice. Cells were cultured in StemSpan SFEM with 15% FBS, 10 ng/ml rmIL-3, 50 ng/ml rmSCF, 50 ng/ml rmFLT3L, 1% penicillin-streptomycin, and 1% glutamine, at the concentration of 2 x 10^5 cells/ml, and prestimulated overnight. Cells were retrovirally transduced with control MigR1 (Mig) or MigR1-HA-RUX1-ETO (RE) for 24 hours. After transduction, cells were washed, resuspended in StemSpan SFEM with or without addition of 10ng/ml of rmGM-CSF for 24 hours. After a total of 48 hours of RUNX1-ETO expression and 24 hours of GM-CSF treatment, GFP+/Lineage-/c-Kit+ cells were sorted for RNA isolation.

extract_protocol: RNA was isolated using column purification with the QIAGEN RNeasy mini kit in accordance with the protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: strain

tag: cell type

value: MigR1-RUNX1-ETO (RE) HSPCs

tag: treatment

value: No Treatment


title: JAR Romidepsin 16h

description: JAR treated with Romidepsin for 16h


title: MPAF Solvent 8h

description: MPAF treated with DMSO for 8h


title: patient 01, metastatic lymph node, LOH status

description:
1-L6_A_(OncoScan).CEL
1-L6_C_(OncoScan).CEL
metastatic lymph node of patient 01
LOH_01-L

source_name: metastatic lymph node of patient 01


title: 9522_S7_3

description:
small RNA
Wild type 9522, anther development stage 7 (S7), rep 3.
Raw files for smallRNA-Seq were not provided by submitter

value: Wild type 9522

value: anther development stage 7 (S7)


title: 9522_S7_2

description:
small RNA
Wild type 9522, anther development stage 7 (S7), rep 2.
Raw files for smallRNA-Seq were not provided by submitter


title: msp1_S3_1

description:
small RNA
msp1 mutant, anther development stage 3 (S3), rep 1.
Raw files for smallRNA-Seq were not provided by submitter


title: 9522_S7_1

description:
small RNA
Wild type 9522, anther development stage 7 (S7), rep 1.
Raw files for smallRNA-Seq were not provided by submitter


title: JAR Solvent 8h

description: JAR treated with DMSO for 8h


title: ARZ Solvent 8h

description: ARZ treated with DMSO for 8h

source_name: neonatal primary fibroblasts

value: ARZ


title: NCCIT Romidepsin 16h

description: NCCIT treated with Romidepsin for 16h

source_name: Embryonal carcinoma-like cell line

value: NCCIT


title: patient 09, metastatic lymph node, copy number status

description:
15-L_A_(OncoScan).CEL
15-L_C_(OncoScan).CEL
metastatic lymph node of patient 09
CN_09-L

source_name: metastatic lymph node of patient 09

value: patient 09

value: copy number


title: NCCIT Romidepsin 8h

description: NCCIT treated with Romidepsin for 8h


title: patient 02, metastatic lymph node, LOH status

description:
2-L_A_(OncoScan).CEL
2-L_C_(OncoScan).CEL
metastatic lymph node of patient 02
LOH_02-L

source_name: metastatic lymph node of patient 02

value: oral tongue squamous cell carcinoma (OTSCC)

value: patient 02


title: NCCIT Solvent 16h

description: NCCIT treated with DMSO for 16h


title: wholeblood_healthycontrol_20

city: New Haven

first: Albert

middle: I

last: Ko

state: CT

address: 60 College St, PO Box 208034

department: Epidemiology of Microbial Diseases

institute: Yale University

hyb_protocol: 600ng of Cy3-labeled cRNA was fragmented and hybridized to SurePrint G3 Human Gene Expression 8x60K v2 Microarrays according to manufacturer’s specifications (Agilent, Cat#G4851B; 50,599 biological features).

scan_protocol: Arrays were scanned on an Agilent Microarray Scanner (Agilent Technologies).

data_processing: Features were extracted using Agilent Feature Extraction software (v10.7). Data was quantile normalized using limma, and data was retained in all instances in which the signal was >64 in at least 3 samples. Data from replicate probes were averaged.

source_name: Whole blood from healthy Brazilian volunteer 20

label_protocol: Aminoallyl-incorporated aRNA was conjugated to Cy3 dye (Life Technologies) for 1 h in sodium bicarbonate buffer and cleaned up on a spin column.

growth_protocol: None. Whole blood was collected directly into PAXgene solution and homogenized immediately, and frozen the same day of collection. Samples were stored at -70C until RNA was extracted.

extract_protocol: RNA was isolated with the Qiagen PAXgene Blood Kit according to the manufacturer’s protocol (Qiagen, Cat#762164).  22.5ng of total RNA (quality confirmed on Agilent Bioanalizer) was used from each sample, or the RNA spike in controls (Agilent; 10 x 32 E1A spike-in control probes), for initial cDNA synthesis.  Cy3-labeled cRNA was prepared using the Low Input QuickAmp Labeling Kit One-Color (Agilent, Cat#5190-2305) and RNA Spike-In Kit, One-Color (Agilent ,Cat#5188-5282).

treatment_protocol: PAXgene tubes were thawed quickly and RNA was extracted immediately

tag: cells

value: whole blood

value: healthy

tag: patient id

value: HealthyControl 20


title: patient 09, primary tumor, copy number status

description:
15-P_A_(OncoScan).CEL
15-P_C_(OncoScan).CEL
primary tumor of patient 09
CN_09-P

source_name: primary tumor of patient 09

value: primary tumor (PT)


title: patient 08, primary tumor, copy number status

description:
14-P_A_(OncoScan).CEL
14-P_C_(OncoScan).CEL
primary tumor of patient 08
CN_08-P

source_name: primary tumor of patient 08

value: patient 08


title: 9522_S5_3

description:
small RNA
Wild type 9522, anther development stage 5 (S5), rep 3.
Raw files for smallRNA-Seq were not provided by submitter

value: anther development stage 5 (S5)


title: wholeblood_healthycontrol_19

source_name: Whole blood from healthy Brazilian volunteer 19

value: HealthyControl 19


title: NCCIT Solvent 8h

description: NCCIT treated with DMSO for 8h


title: 2102EP Romidepsin 16h

description: 2102EP treated with Romidepsin for 16h


title: patient 07, primary tumor, copy number status

description:
11-P_A_(OncoScan).CEL
11-P_C_(OncoScan).CEL
primary tumor of patient 07
CN_07-P

source_name: primary tumor of patient 07

value: patient 07


title: patient 07, metastatic lymph node, copy number status

description:
11-L10_A_(OncoScan).CEL
11-L10_C_(OncoScan).CEL
metastatic lymph node of patient 07
CN_07-L

source_name: metastatic lymph node of patient 07

value: metastatic lymph node (MLN)


title: 9522_S3_3

description:
small RNA
Wild type 9522, anther development stage 3 (S3), rep 3.
Raw files for smallRNA-Seq were not provided by submitter

source_name: Rice spikelets

value: Wild type 9522

value: anther development stage 3 (S3)


title: JAR Romidepsin 8h

description: JAR treated with Romidepsin for 8h

value: JAR


title: 2102EP Romidepsin 8h

description: 2102EP treated with Romidepsin for 8h


title: 9522_S3_2

description:
small RNA
Wild type 9522, anther development stage 3 (S3), rep 2.
Raw files for smallRNA-Seq were not provided by submitter


title: patient 06, metastatic lymph node, copy number status

description:
7-L_A_(OncoScan).CEL
7-L_C_(OncoScan).CEL
metastatic lymph node of patient 06
CN_06-L

source_name: metastatic lymph node of patient 06

value: patient 06


title: 9522_S5_2

description:
small RNA
Wild type 9522, anther development stage 5 (S5), rep 2.
Raw files for smallRNA-Seq were not provided by submitter


title: wholeblood_healthycontrol_17

description: 2 technical replicates

source_name: Whole blood from healthy Brazilian volunteer 17

value: HealthyControl 17


title: 9522_S3_1

description:
small RNA
Wild type 9522, anther development stage 3 (S3), rep 1.
Raw files for smallRNA-Seq were not provided by submitter


title: 9522_S5_1

description:
small RNA
Wild type 9522, anther development stage 5 (S5), rep 1.
Raw files for smallRNA-Seq were not provided by submitter


title: 2102EP Solvent 16h

description: 2102EP treated with DMSO for 16h


title: 2102EP Solvent 8h

description: 2102EP treated with DMSO for 8h


title: wholeblood_healthycontrol_18

source_name: Whole blood from healthy Brazilian volunteer 18

value: HealthyControl 18


title: patient 08, metastatic lymph node, copy number status

description:
14-L_A_(OncoScan).CEL
14-L_C_(OncoScan).CEL
metastatic lymph node of patient 08
CN_08-L

source_name: metastatic lymph node of patient 08

value: oral tongue squamous cell carcinoma (OTSCC)

value: copy number


title: TCam-2 Romidepsin 16h

description: TCam-2 treated with Romidepsin for 16h

source_name: Seminoma-like cell line


title: wholeblood_convalescencesurvivor_patient13

source_name: Whole blood from convalescent phase from patient 13

value: whole blood

value: convalescent phase

value: Patient 13


title: wholeblood_convalescencesurvivor_patient12

source_name: Whole blood from convalescent phase from patient 12

value: Patient 12


title: patient 05, metastatic lymph node, copy number status

description:
5-L8_A_(OncoScan).CEL
5-L8_C_(OncoScan).CEL
metastatic lymph node of patient 05
CN_05-L

source_name: metastatic lymph node of patient 05

value: patient 05


title: patient 02, primary tumor, LOH status

description:
2-P_A_(OncoScan).CEL
2-P_C_(OncoScan).CEL
primary tumor of patient 02
LOH_02-P

source_name: primary tumor of patient 02

value: patient 02

value: primary tumor (PT)

value: LOH


title: wholeblood_convalescencesurvivor_patient11

source_name: Whole blood from convalescent phase from patient 11

value: Patient 11


title: TCam-2 Romidepsin 8h

description: TCam-2 treated with Romidepsin for 8h


title: patient 05, primary tumor, copy number status

description:
5-P_A_(OncoScan).CEL
5-P_C_(OncoScan).CEL
primary tumor of patient 05
CN_05-P

source_name: primary tumor of patient 05


title: patient 04, metastatic lymph node, copy number status

description:
4-L_A_(OncoScan).CEL
4-L_C_(OncoScan).CEL
metastatic lymph node of patient 04
CN_04-L

source_name: metastatic lymph node of patient 04

value: patient 04

value: metastatic lymph node (MLN)


title: wholeblood_convalescencesurvivor_patient8

source_name: Whole blood from convalescent phase from patient 8

value: Patient 8


title: wholeblood_convalescencesurvivor_patient7

description: 2 technical replicates

source_name: Whole blood from convalescent phase from patient 7

value: Patient 7


title: TCam-2 Solvent 8h

description: TCam-2 treated with DMSO for 8h


title: wholeblood_convalescencesurvivor_patient9

source_name: Whole blood from convalescent phase from patient 9

value: Patient 9


title: wholeblood_convalescencesurvivor_patient4

source_name: Whole blood from convalescent phase from patient 4

value: Patient 4


title: wholeblood_convalescencesurvivor_patient10

source_name: Whole blood from convalescent phase from patient 10

value: Patient 10


title: TCam-2 Solvent 16h

description: TCam-2 treated with DMSO for 16h


title: patient 03, primary tumor, copy number status

description:
3-P_A_(OncoScan).CEL
3-P_C_(OncoScan).CEL
primary tumor of patient 03
CN_03-P

source_name: primary tumor of patient 03

value: oral tongue squamous cell carcinoma (OTSCC)

value: patient 03

value: copy number


title: wholeblood_convalescencesurvivor_patient5

source_name: Whole blood from convalescent phase from patient 5

value: whole blood

value: convalescent phase

value: Patient 5


title: patient 03, metastatic lymph node, copy number status

description:
3-L_A_(OncoScan).CEL
3-L_C_(OncoScan).CEL
metastatic lymph node of patient 03
CN_03-L

source_name: metastatic lymph node of patient 03


title: patient 04, primary tumor, copy number status

description:
4-P_A_(OncoScan).CEL
4-P_C_(OncoScan).CEL
primary tumor of patient 04
CN_04-P

source_name: primary tumor of patient 04


title: wholeblood_convalescencesurvivor_patient6

source_name: Whole blood from convalescent phase from patient 6

value: Patient 6


title: crf6 mutant untreated rep1

city: Auburn

first: Aaron

middle: M

last: Rashotte

state: Alabama

address: 101 Rouse Life Sciences, Department of Biological Sciences, Auburn University

department: Biological Sciences

institute: Auburn University

description: untreated

hyb_protocol: The labeled cRNA was fragmented to between 35nt and 200nt segments by metal induced hydrolysis at 94ºC for 30 min.  The fragments were hybridized to the arrays in standard hybridization buffer by first heating to 95ºC for 5min then placed immediately at 45ºC for 5 min prior to loading into the arrays.  Hybridization was done using the Affymetrix rotating Hyb oven 640 at 60rpm for 16 hrs.

scan_protocol: The arrays were scanned using the Affymetrix 3000 7G scanner as described by the manufacturer.

data_processing:
Normalization and differential expression analyses were performed using the FlexArray 1.6 software package from McGill University and Genome Quebec. Normalization was performed using algorithms provided by Affymetrix.
Fold change in expression was calculated by Cyber-T analysis and adjusted p-values were determined using the Benjamini Hochberg method of False Discovery Rate.

organism: Arabidopsis thaliana

source_name: crf6 mutant untreated

label_protocol: RNA was converted to cRNA with an intermediate cDNA step as per the manufacturer’s instructions.  Briefly, one microgram of total RNA was reverse transcribed with an oligo-dT-T7 primer by first heating the total RNA and primer mixture to 65oC for 5min followed by incubation at 25oC for 5min.  Following primer annealing reverse transcription buffer, dNTPs, DTT and Reverse Transcriptase (SuperScript III, Invitrogen, Carlsbad CA) were incubated at 48oC for 90 min.  The cDNA second strand was synthesized using second strand reaction buffer, dNTPs, E. coli polymerase, E. coli ligase and RNAse H with incubation at 16oC for 2hrs immediately followed by addition of T4 DNA Polymerase and incubation for an additional 10min at 16oC.  Double stranded cDNA was purified using column purification by standard techniques.  To produce the labeled cRNA required for hybridization the cDNA was incubated with in vitro transcription (IVT) components including the biotin labeled uracil and T7 RNA polymerase for 16hrs at 37oC.  The cRNA was then cleaned using standard column purification as per the manufacturer’s instructions (Qiagen).

growth_protocol: Plants were grown for 10 days on MS medium and 1% sucrose buffered with MES at pH 5.7 in a controlled environmental chamber and grown under diurnal conditions of 16h light (100 µE) at 22°C, and 8h dark at 18°C.

extract_protocol: RNA was extracted using the Qiagen RNeasy Plant Mini-kit according to the manufacturer’s instructions

treatment_protocol: 10 day old plants were removed from plates and floated on 3mM MES buffer pH 5.7. After 1h treatment sample had H2O2 added to a final concentration of 20mM or cytokinin (benzyl adenine) to a concentration of 2uM. Treatment and control solutions both contained 0.2% DMSO.

tag: age

value: 10 day old Seedling


title: wholeblood_acutedead_patient16

description: 2 technical replicates

source_name: Whole blood from early acute disease from patient 16

value: acute

value: Patient 16


title: patient 02, primary tumor, copy number status

description:
2-P_A_(OncoScan).CEL
2-P_C_(OncoScan).CEL
primary tumor of patient 02
CN_02-P

value: patient 02

value: primary tumor (PT)


title: wholeblood_convalescencesurvivor_patient3

source_name: Whole blood from convalescent phasee from patient 3

value: Patient 3


title: patient 06, primary tumor, copy number status

description:
7-P_A_(OncoScan).CEL
7-P_C_(OncoScan).CEL
primary tumor of patient 06
CN_06-P

source_name: primary tumor of patient 06

value: patient 06


title: crf6 mutant + H2O2 rep2

description: 6h treatment with 20mM H2O2

source_name: crf6 mutant + H2O2


title: wholeblood_convalescencesurvivor_patient1

source_name: Whole blood from convalescent phase from patient 1

value: Patient 1


title: crf6 mutant untreated rep2

description: untreated


title: patient 01, metastatic lymph node, copy number status

description:
1-L6_A_(OncoScan).CEL
1-L6_C_(OncoScan).CEL
metastatic lymph node of patient 01
CN_01-L

source_name: metastatic lymph node of patient 01

value: patient 01

value: metastatic lymph node (MLN)


title: patient 01, primary tumor, copy number status

description:
1-P_A_(OncoScan).CEL
1-P_C_(OncoScan).CEL
primary tumor of patient 01
CN_01-P

source_name: primary tumor of patient 01

value: oral tongue squamous cell carcinoma (OTSCC)


title: wholeblood_acutedead_patient15

description: 2 technical replicates

source_name: Whole blood from early acute disease from patient 15

value: Patient 15


title: patient 02, metastatic lymph node, copy number status

description:
2-L_A_(OncoScan).CEL
2-L_C_(OncoScan).CEL
metastatic lymph node of patient 02
CN_02-L

source_name: metastatic lymph node of patient 02

value: copy number


title: crf6 mutant + H2O2 rep1

description: 6h treatment with 20mM H2O2


title: patient 10, metastatic lymph node, copy number status

description:
16-L53_A_(OncoScan).CEL
16-L53_C_(OncoScan).CEL
metastatic lymph node of patient 10
CN_10-L

source_name: metastatic lymph node of patient 10

value: patient 10


title: wholeblood_convalescencesurvivor_patient2

source_name: Whole blood from convalescent phase from patient 2

value: whole blood

value: convalescent phase

value: Patient 2


title: patient 10, primary tumor, copy number status

description:
16-P4_A_(OncoScan).CEL
16-P4_C_(OncoScan).CEL
primary tumor of patient 10
CN_10-P

source_name: primary tumor of patient 10


title: crf6 mutant + BA rep2

description: 6h treatment with 2uM Benzyl Adenine

source_name: crf6 mutant + BA

value: 10 day old Seedling


title: wholeblood_acutedead_patient14

source_name: Whole blood from early acute disease from patient 14

value: acute

value: Patient 14


title: wholeblood_acutesurvivor_patient13

source_name: Whole blood from early acute disease from patient 13

value: Patient 13


title: wholeblood_acutesurvivor_patient12

source_name: Whole blood from early acute disease from patient 12

value: Patient 12


title: WT (Col-0) + H202 rep1

description: 6h treatment with 20mM H2O2


title: wholeblood_acutesurvivor_patient7

source_name: Whole blood from early acute disease from patient 7

value: Patient 7


title: WT (Col-0) untreated rep2

description: untreated

source_name: WT (Col-0) untreated


title: WT (Col-0) + BA rep1

description: 6h treatment with 2uM Benzyl Adenine

source_name: WT (Col-0) + BA


title: wholeblood_acutesurvivor_patient6

source_name: Whole blood from early acute disease from patient 6

value: Patient 6


title: wholeblood_acutesurvivor_patient9

description: 2 technical replicates

source_name: Whole blood from early acute disease from patient 9

value: Patient 9


title: CRF6oe + H202 rep2

description: 6h treatment with 20mM H2O2

source_name: CRF6oe 6h treatment with 20mM H2O2


title: WT (Col-0) + H202 rep2

description: 6h treatment with 20mM H2O2


title: crf6 mutant + BA rep1

description: 6h treatment with 2uM Benzyl Adenine


title: CRF6oe untreated rep1

description: untreated

source_name: CRF6oe untreated


title: wholeblood_acutesurvivor_patient10

source_name: Whole blood from early acute disease from patient 10

value: Patient 10


title: CRF6oe + BA rep2

description: 6h treatment with 2uM Benzyl Adenine

source_name: CRF6oe 6h treatment with 2uM Benzyl Adenine


title: wholeblood_acutesurvivor_patient8

source_name: Whole blood from early acute disease from patient 8

value: Patient 8


title: wholeblood_acutesurvivor_patient2

source_name: Whole blood from early acute disease from patient 2


title: wholeblood_acutesurvivor_patient3

source_name: Whole blood from early acute disease from patient 3

value: Patient 3


title: CRF6oe untreated rep2

description: untreated


title: CRF6oe + H202 rep1

description: 6h treatment with 20mM H2O2


title: WT (Col-0) + BA rep2

description: 6h treatment with 2uM Benzyl Adenine


title: wholeblood_acutesurvivor_patient5

source_name: Whole blood from early acute disease from patient 5

value: Patient 5


title: wholeblood_acutesurvivor_patient4

source_name: Whole blood from early acute disease from patient 4

value: Patient 4


title: A204 pazopanib resistant cell line

city: Salt Lake City

first: Aik Choon

last: Tan

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: Huntsman Cancer Institute

description:
A204 treated to induce resistance to Pazopanib
A204PazR

hyb_protocol: Denatured DNA samples were applied to the microarray under a coverslip and hybridized at 37 °C for 18 h. After hybridization, the coverslips were removed by washing slides in 2× SSC/1% SDS for 15 min at 45 °C. Slides were then washed in 50% deionised formamide/2× SSC for 15 min at 45 °C, followed by 2× SSC/1% SDS for 30 min at 45 °C and twice in 0.2× SSC for 15 min at room temperature [28, 29]. After washing, the arrays were dried by centrifugation at 2000 r.p.m. for 2 min.

scan_protocol: Slides were accned using an Axon 4000B scanner and images were processed using Genepix Pro Image analysis software.

data_processing: Raw Log2 ratios of intensity between samples and pooled female genomic DNA were read without background subtraction and normalized in the LIMMA package in R using PrinTipLoess. Outliers were removed based upon their deviation from neighboring genomic probes, using an estimation of the genome-wide median absolute deviation of all probes. Log2 ratios were rescaled using the genome wide median absolute deviation in each sample and then smoothed using circular binary segmentation (cbs) in the DNACopy package. After filtering polymorphic BACs and BACs mapping to chromosome Y, a final dataset of 31,157 clones with unambiguous mapping information according to build hg19 of the human genome (http://www.ensembl.org). A categorical analysis was applied to the BACs after classifying them as representing amplification (>0.45), gain (>0.08 and ≤0.45), loss (<−0.08) or no change, according to their cbs-smoothed log2 ratio values.

source_name: A204 pazopanib resistant cell line

label_protocol: Reference (normal DNA extracted from blood lymphocytes pooled from 24 females) and cell line DNA samples (300ng aliquots) were labelled with Cy3- or Cy5-conjugated dCTP respectively (Amersham Biosciences, Buckinghamshire, UK) using random primed BioPrime DNA labelling (Invitrogen Life Technologies) according to the manufacturer's protocol, modified to incorporate 1.0 mM Cy dye, 0.6 mM dCTP and 1.2 mM dATP, dGTP and dTTP. After labelling at 37 °C for 16 h, non-incorporated reaction constituents were removed by MinElute Reaction Cleanup (Qiagen Ltd, Crawley, UK). Labelled reference and tumor DNA were co-ethanol precipitated with 100 µg human Cot-1 DNA (Invitrogen Life Technologies) and re-suspended in 45 µl hybridization buffer (50% deionised formamide, 10% w/v dextran sulphate, 2× SSC, 2% SDS, 20 µg yeast tRNA). Labelled DNA was denatured at 70 °C for 15 min, followed by a 30 min incubation at 37 °C to allow blocking of repetitive sequences by human Cot-1 DNA.

growth_protocol: Dasatinib, Pazopanib, and Sunitinib (LC laboratories) were used to induce resistance in the A204 cells. Cells were grown initially in DMEM media containing drug concentration of 500 nM. The drug was incremented when the cells had proliferated to near-confluency alongside minimal visible cell death. Drug concentration was incremented from 2µM, 3µM, and 5µM in a stepwise manner over 6 weeks. A final drug concentration of 5µM was maintained in resistant cells. Media and drug were replenished twice weekly.

extract_protocol: DNA was extracted using the DNeasy Blood and Tissue Kit.

value: A204 pazopanib-resistant cell line

source_name: Pooled normal samples

tag: reference


title: wholeblood_acutesurvivor_patient1

source_name: Whole blood from early acute disease from patient 1

value: whole blood

value: Patient 1


title: A204 parental cell line

description:
Parental cell line A204
A204_parental

source_name: A204 parental cell line

value: A204 parental cell line

value: normal DNA extracted from blood lymphocytes pooled from 24 females


title: WT (Col-0) untreated rep1

description: untreated

source_name: WT (Col-0) untreated

value: 10 day old Seedling


title: HaCaT WT-actin line rep2

status: Public on Sep 22 2016

city: London

first: John

last: Connelly

address: 4 Newark Street

department: Centre for Cell Biology and Cutaneous Research

country: United Kingdom

institute: Queen Mary University of London

description: HaCaT WT-actin cell line

hyb_protocol: cRNA were hybridized to the human U133 plus 2.0 arrays

scan_protocol: Arrays were scanned using the GeneChip 3000

data_processing: MAS5 analysis implemented in Bioconductor

source_name: HaCaT WT-actin cell line

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

extract_protocol: Agilent absolutely RNA miniprep

value: HaCaT

value: epidermis

value: immortalised keratinocytes


title: HaCaT WT-actin line rep1

description: HaCaT WT-actin cell line


title: HaCaT NLS-actin line rep1

description: HaCaT NLS-actin cell line

source_name: HaCaT NLS-actin cell line


title: CRF6oe + BA rep1

description: 6h treatment with 2uM Benzyl Adenine


title: HaCaT parental line rep3

description: HaCaT parental cell line

source_name: HaCaT parental cell line


title: A204 sunitinib resistant cell line

description:
A204 treated to induce resistance to Sunitinib
A204SunR

source_name: A204 sunitinib resistant cell line

value: A204 sunitinib-resistant cell line


title: HaCaT parental line rep1

description: HaCaT parental cell line


title: A204 dasatinib resistant cell line

description:
A204 treated to induce resistance to Dasatinib
A204DasR

source_name: A204 dasatinib resistant cell line

value: A204 dasatinib-resistant cell line


title: HaCaT WT-actin line rep3

description: HaCaT WT-actin cell line


title: Male HP_sham_rep2

city: Covilhã

first: Telma

last: Quintela

address: Av. Infante D. Henrique

department: Health Sciences Research Centre

country: Portugal

institute: University of Beira Interior

description: HP gene expression in sham males

hyb_protocol: Hybridizations were carried out on an Agilent-based microarray platform using custom-designed whole genome Rat GE 4x4K v3 microarrays

scan_protocol: Scanned images on an Agilent microarray scanner were analyzed by Feature extraction software (Agilent Technologies) using GE1_105_Dec08 protocol.

data_processing: The signal intensity was normalized by centering the median of the signal distribution using BRB-ArrayTools v3.8.1 (http://linus.nci.nih.gov/BRB-ArrayTools.html).

organism: Rattus norvegicus

source_name: Male hippocampus_sham

label_protocol: Equal amounts of RNA extract (200 ng) from the HP of sham or OOX animals, in a total of three biological replicates, were amplified and Cy- 3-labeled using the Low Input Quick Amp Labeling kit (Agilent Technologies).

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following manufacturer’s instructions. RNA was quantified using a NanoDrop spectrophotometer (NanoDrop Technologies), and RNA integrity was assessed by Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). All RNA samples used in this study had an A260/A280 ratio of.1.9

treatment_protocol: Wistar rats were housed under a 12-h light, 12-h dark cycle, with food and water ad libitum during the course of the experiment. Male rats (2 months) were orchidectomized or sham-operated. Two weeks after surgery, castrated and sham animals were anesthetized with a mixture of ketamine and medetomidine. Cerebral hemispheres were separated and HP collected.

value: Wistar

tag: gender

value: male

tag: experimental procedure

value: sham-operated

value: brain

tag: brain region

value: Hippocampus


title: Male HP_sham_rep1

description: HP gene expression in sham males


title: Male HP_OOX_rep2

description: HP gene expression in orchidectomized males

source_name: Male hippocampus_orchidectomized

value: orchidectomy


title: Male HP_sham_rep3

description: HP gene expression in sham males


title: HaCaT NLS-actin line rep3

description: HaCaT NLS-actin cell line


title: Liver, Mgl2-DTR, rep2

city: Newark

first: Yosuke

last: Kumamoto

state: NJ

address: 205 South Orange Ave

department: Center for Immunity and Inflammation

institute: Rutgers University

description: Liver gene expression data from CD301b+ MNP-depleted Mgl2-DTR mouse.

hyb_protocol: cRNAs were hybridized to Affymetrix GeneChip Mouse Gene 2.0 ST arrays for 16 hours at 45C. Hybridization was performed by the Yale Center for Genome Analysis.

scan_protocol: Arrays were scanned by GeneChip Scanner 3000 at the Yale Center for Genome Analysis.

data_processing: The differential analysis was done by limma package with defaults.

source_name: Liver from Mgl2-DTR mouse treated with diphtheria toxin for 10 days

label_protocol: The isolated total RNA was amplified and labeled with GeneChip WT PLUS Reaget Kit (Affymetrix) by the Yale Center for Genome Analysis.

growth_protocol: Mouse colonies were maintained in a specific pathogen-free facility at Yale University.

extract_protocol: All tissues were directly homogenized in Trizol reagent and frozen at -80 C. Total RNA was isolated with chloroform and isopropanol according to manufacturer's protocol. The isolated RNA was treated with DNase I and purified with RNeasy column (Qiagen).

treatment_protocol: Male Mgl2-DTR mice or age-matched male wild-type C57BL/6N mice were intraperitoneally injected with diphtheria toxin (500 ng per mouse per dose) every three days for for times. On day 10, the epididymal and inguinal adipose tissues and the liver were harvested for RNA isolation.

tag: background strain

value: Liver


title: Liver, wild-type, rep1

description: Liver gene expression data from CD301b+ MNP-intact wild-type mouse.

source_name: Liver from wild-type C57BL/6N mouse treated with diphtheria toxin for 10 days

value: Wild-type


title: Liver, wild-type, rep2


title: HaCaT parental line rep2

description: HaCaT parental cell line

tag: cell line


title: Liver, Mgl2-DTR, rep1


title: Male HP_OOX_rep3


title: Inguinal white adipose tissue, Mgl2-DTR, rep1

description: Inguinal adipose tissue gene expression data from CD301b+ MNP-depleted Mgl2-DTR mouse.

source_name: Inguinal adipose tissue from Mgl2-DTR mouse treated with diphtheria toxin for 10 days

value: Inguinal white adipose


title: Inguinal white adipose tissue, wild-type, rep2

description: Inguinal adipose tissue gene expression data from CD301b+ MNP-intact wild-type mouse.

source_name: Inguinal adipose tissue from wild-type C57BL/6N mouse treated with diphtheria toxin for 10 days


title: Inguinal white adipose tissue, Mgl2-DTR, rep2


title: Epididymal white adipose tissue, wild-type, rep1

description: Epididymal adipose tissue gene expression data from CD301b+ MNP-intact wild-type mouse.

source_name: Epididymal adipose tissue from wild-type C57BL/6N mouse treated with diphtheria toxin for 10 days

value: Epididymal white adipose


title: Epididymal white adipose tissue, wild-type, rep2


title: HaCaT NLS-actin line rep2

description: HaCaT NLS-actin cell line


title: Inguinal white adipose tissue, wild-type, rep1


title: Muscle_tissue_from_WT_mice_rep2

city: Bethesda

first: Haiming

last: Cao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description:
Gene expression in liver tissue from WT mice
OB_M14

hyb_protocol: 1 μg of each labeled cRNA was  fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 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 G2505B).

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Genes with average normalized signal intensity >= 7.64 in at least one biological group regardless of tissue type were retained and regarded as expressed genes.

source_name: Muscle tissue from WT mice

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

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

treatment_protocol: Male C57BL/6 mice from the Jackson Laboratory were used for all experiments. Groups of co-housed mice were randomly assigned to experimental groups with age and weight matched between groups. For the fasting and refeeding regimen, mice of around 20 weeks of age were either allowed free access to food or were subjected to a 24-hour fast before being euthanized for tissue harvest (sacrificed at 10am). A third group was fasted for 24 hours and then allowed to feed ad libitum for another 4 hours before tissue harvest (sacrificed at 2pm). For high fat diet feeding (20% kcal from protein, 60% kcal from fat, and 20% kcal from carbohydrate, D12492, Research Diets Inc.), 6 week old mice were fed for a total of 12 weeks, a second group of mice of 18 weeks old were fed for 48h. Mice fed with a normal chow diet were used as controls (sacrificed at 2pm). For the genetic obesity model, 10 week old Ob/Ob mice and their lean control were used. All mice were subjected to a 4-5h food withdrawal before tissue harvest unless specified otherwise.

value: Male

value: Muscle

tag: condition

value: WT

tag: group


title: Muscle_tissue_from_WT_mice_rep4

description:
Gene expression in liver tissue from WT mice
OB_M20

tag: tissue


title: Muscle_tissue_from_ob/ob_mice_rep2

description:
Gene expression in liver tissue from ob/ob mice
OB_M9

source_name: Muscle tissue from ob/ob mice

value: ob/ob


title: Muscle_tissue_from_ob/ob_mice_rep4

description:
Gene expression in liver tissue from ob/ob mice
OB_M15


title: Male HP_OOX_rep1


title: Muscle_tissue_from_ob/ob_mice_rep3

description:
Gene expression in liver tissue from ob/ob mice
OB_M13


title: Epididymal white adipose tissue, Mgl2-DTR, rep2

description: Epididymal adipose tissue gene expression data from CD301b+ MNP-depleted Mgl2-DTR mouse.

source_name: Epididymal adipose tissue from Mgl2-DTR mouse treated with diphtheria toxin for 10 days

tag: genotype


title: Adipose_tissue_from_ob/ob_mice_rep3

description:
Gene expression in liver tissue from ob/ob mice
OB_F9

source_name: Adipose tissue from ob/ob mice

value: Adipose


title: Muscle_tissue_from_WT_mice_rep1

description:
Gene expression in liver tissue from WT mice
OB_M2


title: Adipose_tissue_from_ob/ob_mice_rep2

description:
Gene expression in liver tissue from ob/ob mice
OB_F7


title: Adipose_tissue_from_WT_mice_rep5

description:
Gene expression in liver tissue from WT mice
OB_F20

source_name: Adipose tissue from WT mice


title: Adipose_tissue_from_ob/ob_mice_rep4

description:
Gene expression in liver tissue from ob/ob mice
OB_F13


title: Adipose_tissue_from_WT_mice_rep3

description:
Gene expression in liver tissue from WT mice
OB_F14


title: Adipose_tissue_from_WT_mice_rep4

description:
Gene expression in liver tissue from WT mice
OB_F18


title: Epididymal white adipose tissue, Mgl2-DTR, rep1


title: Adipose_tissue_from_WT_mice_rep1

description:
Gene expression in liver tissue from WT mice
OB_F2


title: Liver_tissue_from_ob/ob_mice_rep4

description:
Gene expression in liver tissue from ob/ob mice
OB_L13

source_name: Liver tissue from ob/ob mice


title: Adipose_tissue_from_WT_mice_rep2

description:
Gene expression in liver tissue from WT mice
OB_F6


title: Liver_tissue_from_ob/ob_mice_rep5

description:
Gene expression in liver tissue from ob/ob mice
OB_L15


title: Adipose_tissue_from_ob/ob_mice_rep5

description:
Gene expression in liver tissue from ob/ob mice
OB_F15


title: Muscle_tissue_from_WT_mice_rep3

description:
Gene expression in liver tissue from WT mice
OB_M18


title: Liver_tissue_from_ob/ob_mice_rep1

description:
Gene expression in liver tissue from ob/ob mice
OB_L3


title: Adipose_tissue_from_ob/ob_mice_rep1

description:
Gene expression in liver tissue from ob/ob mice
OB_F3


title: Muscle_tissue_from_ob/ob_mice_rep1

description:
Gene expression in liver tissue from ob/ob mice
OB_M7


title: Liver_tissue_from_ob/ob_mice_rep3

description:
Gene expression in liver tissue from ob/ob mice
OB_L9


title: Muscle_tissue_from_12w_high_fat_diet_mice_rep3

description:
Gene expression in Muscle tissue from 12w high fat diet mice
HD_M31

value: 12w high fat diet


title: Liver_tissue_from_WT_mice_rep1

description:
Gene expression in liver tissue from WT mice
OB_L2

source_name: Liver tissue from WT mice


title: Muscle_tissue_from_12w_high_fat_diet_mice_rep1

description:
Gene expression in Muscle tissue from 12w high fat diet mice
HD_M25


title: Liver_tissue_from_WT_mice_rep4

description:
Gene expression in liver tissue from WT mice
OB_L18


title: Liver_tissue_from_WT_mice_rep2

description:
Gene expression in liver tissue from WT mice
OB_L6


title: Liver_tissue_from_WT_mice_rep5

description:
Gene expression in liver tissue from WT mice
OB_L20


title: Muscle_tissue_from_48h_high_fat_diet_mice_rep4

description:
Gene expression in Muscle tissue from 48h high fat diet mice
HD_M16

value: 48h high fat diet


title: Muscle_tissue_from_12w_high_fat_diet_mice_rep2

description:
Gene expression in Muscle tissue from 12w high fat diet mice
HD_M30


title: Muscle_tissue_from_48h_high_fat_diet_mice_rep2

description:
Gene expression in Muscle tissue from 48h high fat diet mice
HD_M13


title: Muscle_tissue_from_normal_diet_mice_rep2

description:
Gene expression in Muscle tissue from normal fat diet mice
HD_M15

source_name: Muscle tissue from normal fat diet mice

value: Normal fat diet


title: Muscle_tissue_from_12w_high_fat_diet_mice_rep4

description:
Gene expression in Muscle tissue from 12w high fat diet mice
HD_M33


title: Liver_tissue_from_ob/ob_mice_rep2

description:
Gene expression in liver tissue from ob/ob mice
OB_L7


title: Adipose_tissue_from_12w_high_fat_diet_mice_rep3

description:
Gene expression in Adipose tissue from 12w high fat diet mice
HD_F30


title: Adipose_tissue_from_12w_high_fat_diet_mice_rep1

description:
Gene expression in Adipose tissue from 12w high fat diet mice
HD_F19


title: Muscle_tissue_from_normal_diet_mice_rep3

description:
Gene expression in Muscle tissue from normal fat diet mice
HD_M26


title: Adipose_tissue_from_12w_high_fat_diet_mice_rep4

description:
Gene expression in Adipose tissue from 12w high fat diet mice
HD_F31


title: Adipose_tissue_from_48h_high_fat_diet_mice_rep5

description:
Gene expression in Adipose tissue from 48h high fat diet mice
HD_F17


title: Adipose_tissue_from_48h_high_fat_diet_mice_rep1

description:
Gene expression in Adipose tissue from 48h high fat diet mice
HD_F7


title: Adipose_tissue_from_48h_high_fat_diet_mice_rep3

description:
Gene expression in Adipose tissue from 48h high fat diet mice
HD_F14


title: Adipose_tissue_from_12w_high_fat_diet_mice_rep2

description:
Gene expression in Adipose tissue from 12w high fat diet mice
HD_F25


title: Muscle_tissue_from_normal_diet_mice_rep1

description:
Gene expression in Muscle tissue from normal fat diet mice
HD_M9


title: Muscle_tissue_from_48h_high_fat_diet_mice_rep3

description:
Gene expression in Muscle tissue from 48h high fat diet mice
HD_M14


title: Adipose_tissue_from_48h_high_fat_diet_mice_rep2

description:
Gene expression in Adipose tissue from 48h high fat diet mice
HD_F13


title: wholeblood_acutesurvivor_patient11

source_name: Whole blood from early acute disease from patient 11

value: whole blood

tag: disease state

value: acute

value: Patient 11


title: Muscle_tissue_from_normal_diet_mice_rep4

description:
Gene expression in Muscle tissue from normal fat diet mice
HD_M32

tag: strain


title: Adipose_tissue_from_normal_diet_mice_rep5

description:
Gene expression in Adipose tissue from normal fat diet mice
HD_F32


title: Adipose_tissue_from_normal_diet_mice_rep4

description:
Gene expression in Adipose tissue from normal fat diet mice
HD_F26


title: Adipose_tissue_from_48h_high_fat_diet_mice_rep4

description:
Gene expression in Adipose tissue from 48h high fat diet mice
HD_F16


title: Adipose_tissue_from_normal_diet_mice_rep2

description:
Gene expression in Adipose tissue from normal fat diet mice
HD_F9


title: Muscle_tissue_from_48h_high_fat_diet_mice_rep1

description:
Gene expression in Muscle tissue from 48h high fat diet mice
HD_M7


title: Adipose_tissue_from_normal_diet_mice_rep1

description:
Gene expression in Adipose tissue from normal fat diet mice
HD_F6


title: Liver_tissue_from_12w_high_fat_diet_mice_rep2

description:
Gene expression in liver tissue from 12w high fat diet mice
HD_L25

source_name: Liver tissue from 12w high fat diet mice


title: Liver_tissue_from_12w_high_fat_diet_mice_rep3

description:
Gene expression in liver tissue from 12w high fat diet mice
HD_L30


title: After pre-differentiation, biological rep1

city: Columbus

first: Shuting

last: zhao

state: Ohio

address: Room 340H, 460 West 12th Ave., Biomedical research

institute: The ohio state university

description: Gene expression data

hyb_protocol: Samples were hybridized using Herring sperm DNA, Acetylated BSA (50mg/mL), Eukaryotic Hybridization Controls (Affymetrix) •Heat 65oC for 5 minutes, 99oC for 5 minutes, 45oC for 5 minutes centrifuge top speed for 5 minutes  •Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene Chip Scanner 3000 7G using AGCC (Affymetrix GeneChip Command Console)

data_processing: The data were analyzed with Affymetrix® Transcriptome Analysis Console (TAC) Softwareusing Affymetrix default analysis settings

source_name: Mouse embryonic stem cell aggregates

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Cell aggregates cultured in ES complete medium for 7 days (with LIF)

extract_protocol: RNA was extracted using RNeasy Plus Mini Kit (Qiagen) following the manufacture’s instruction

treatment_protocol: On day 7, medium was changed to pre-differentiation protocol (with BMP4 and bFGF) for 3 days.

value: Cell aggregates


title: Liver_tissue_from_12w_high_fat_diet_mice_rep4

description:
Gene expression in liver tissue from 12w high fat diet mice
HD_L31


title: Adipose_tissue_from_12w_high_fat_diet_mice_rep5

description:
Gene expression in Adipose tissue from 12w high fat diet mice
HD_F33


title: After pre-differentiation, biological rep2

description: Gene expression data


title: Liver_tissue_from_12w_high_fat_diet_mice_rep1

description:
Gene expression in liver tissue from 12w high fat diet mice
HD_L19


title: After pre-differentiation, biological rep3

description: Gene expression data


title: normal aortic valve 12

city: Quebec

first: Yohan

last: Bossé

state: Quebec

address: 2725, chemin Sainte-Foy

country: Canada

institute: Laval University

data_processing: Data was processed by log2-transformation and quantile normalized using the lumi package in R (Du et al 2008)

source_name: human normal aortic valve

label_protocol: IlluminaTotalPrep™-96 RNA Amplification Kit (Ambion)

extract_protocol: RNA extraction was performed using 45 to 100 mg and 82 to 192 mg of tissue from one leaflet of normal and calcified valves, respectively, under a modified TRIzol protocol (Lee JTY et al. J Biomater Nanobiotechnol 2011;2:41-48) followed by a purification step on QIAGEN RNeasy columns (QIAGEN).

tag: subject status

value: individual who underwent primary aortic valve replacement

value: male

value: tricuspid valves without aortic valve stenosis (TAVn)


title: Before pre-differentiation, biological rep2

description: Gene expression data


title: Before pre-differentiation, biological rep3

description: Gene expression data


title: Before pre-differentiation, biological rep1

description: Gene expression data


title: Liver_tissue_from_48h_high_fat_diet_mice_rep5

description:
Gene expression in liver tissue from 48h high fat diet mice
HD_L17

source_name: Liver tissue from 48h high fat diet mice

value: Liver


title: normal aortic valve 7


title: Liver_tissue_from_48h_high_fat_diet_mice_rep2

description:
Gene expression in liver tissue from 48h high fat diet mice
HD_L13


title: Liver_tissue_from_48h_high_fat_diet_mice_rep3

description:
Gene expression in liver tissue from 48h high fat diet mice
HD_L14


title: Liver_tissue_from_48h_high_fat_diet_mice_rep4

description:
Gene expression in liver tissue from 48h high fat diet mice
HD_L16


title: normal aortic valve 2


title: normal aortic valve 6


title: Liver_tissue_from_48h_high_fat_diet_mice_rep1

description:
Gene expression in liver tissue from 48h high fat diet mice
HD_L7


title: normal aortic valve 1


title: normal aortic valve 3


title: normal aortic valve 4


title: stenotic aortic valve 11

source_name: human stenotic aortic valve

value: tricuspid valves with aortic valve stenosis (TAVc)


title: stenotic aortic valve 10


title: Liver_tissue_from_normal_diet_mice_rep3

description:
Gene expression in liver tissue from normal fat diet mice
HD_L15

source_name: Liver tissue from normal fat diet mice

value: Male


title: stenotic aortic valve 9


title: Liver_tissue_from_normal_diet_mice_rep2

description:
Gene expression in liver tissue from normal fat diet mice
HD_L9


title: Muscle_tissue_from_4h_refeeding_following_24h_fasting_mice_rep3

description:
Gene expression in Muscle tissue from 4h refeeding following 24h fasting mice
FR_M19

value: Muscle

value: 4h refeeding following 24h fasting


title: stenotic aortic valve 3


title: Liver_tissue_from_normal_diet_mice_rep5

description:
Gene expression in liver tissue from normal fat diet mice
HD_L32


title: Muscle_tissue_from_4h_refeeding_following_24h_fasting_mice_rep4

description:
Gene expression in Muscle tissue from 4h refeeding following 24h fasting mice
FR_M20


title: stenotic aortic valve 6


title: Muscle_tissue_from_24h_fasting_mice_rep4

description:
Gene expression in Muscle tissue from 24h fasting mice
FR_M12

source_name: Muscle tissue from 24h fasting mice

value: 24h fasting


title: Muscle_tissue_from_24h_fasting_mice_rep3

description:
Gene expression in Muscle tissue from 24h fasting mice
FR_M11


title: Liver_tissue_from_normal_diet_mice_rep1

description:
Gene expression in liver tissue from normal fat diet mice
HD_L6


title: bicuspid aortic valve 12

source_name: human bicuspid aortic valve

value: calcified bicuspid aortic valves (BAV)


title: stenotic aortic valve 7


title: bicuspid aortic valve 9


title: Muscle_tissue_from_24h_fasting_mice_rep1

description:
Gene expression in Muscle tissue from 24h fasting mice
FR_M9


title: Muscle_tissue_from_4h_refeeding_following_24h_fasting_mice_rep1

description:
Gene expression in Muscle tissue from 4h refeeding following 24h fasting mice
FR_M17


title: Muscle_tissue_from_24h_fasting_mice_rep2

description:
Gene expression in Muscle tissue from 24h fasting mice
FR_M10


title: bicuspid aortic valve 10


title: stenotic aortic valve 4


title: Liver_tissue_from_normal_diet_mice_rep4

description:
Gene expression in liver tissue from normal fat diet mice
HD_L26


title: stenotic aortic valve 1


title: bicuspid aortic valve 11


title: Muscle_tissue_from_4h_refeeding_following_24h_fasting_mice_rep2

description:
Gene expression in Muscle tissue from 4h refeeding following 24h fasting mice
FR_M18


title: stenotic aortic valve 2


title: Muscle_tissue_from_ad_libitum_mice_rep3

description:
Gene expression in Muscle tissue from ad libitum mice
FR_M3

source_name: Muscle tissue from ad libitum mice

value: Ad libitum


title: bicuspid aortic valve 6


title: Liver_tissue_from_WT_mice_rep3

description:
Gene expression in liver tissue from WT mice
OB_L14

value: WT


title: Liver_tissue_from_12w_high_fat_diet_mice_rep5

description:
Gene expression in liver tissue from 12w high fat diet mice
HD_L33

value: 12w high fat diet


title: bicuspid aortic valve 4


title: Muscle_tissue_from_ad_libitum_mice_rep4

description:
Gene expression in Muscle tissue from ad libitum mice
FR_M4


title: Muscle_tissue_from_ad_libitum_mice_rep2

description:
Gene expression in Muscle tissue from ad libitum mice
FR_M2


title: Adipose_tissue_from_4h_refeeding_following_24h_fasting_mice_rep4

description:
Gene expression in Adipose tissue from 4h refeeding following 24h fasting mice
FR_A20

value: Adipose


title: Adipose_tissue_from_24h_fasting_mice_rep1

description:
Gene expression in Adipose tissue from 24h fasting mice
FR_A9

source_name: Adipose tissue from 24h fasting mice


title: Liver_tissue_from_4h_refeeding_following_24h_fasting_mice_rep4

description:
Gene expression in liver tissue from 4h refeeding following 24h fasting mice
CH-20

source_name: Liver tissue from 4h refeeding following 24h fasting mice


title: Liver_tissue_from_4h_refeeding_following_24h_fasting_mice_rep3

description:
Gene expression in liver tissue from 4h refeeding following 24h fasting mice
CH-19


title: Adipose_tissue_from_ad_libitum_mice_rep3

description:
Gene expression in Adipose tissue from ad libitum mice
FR_A3

source_name: Adipose tissue from ad libitum mice


title: Adipose_tissue_from_ad_libitum_mice_rep2

description:
Gene expression in Adipose tissue from ad libitum mice
FR_A2


title: Muscle_tissue_from_ad_libitum_mice_rep1

description:
Gene expression in Muscle tissue from ad libitum mice
FR_M1


title: Adipose_tissue_from_4h_refeeding_following_24h_fasting_mice_rep2

description:
Gene expression in Adipose tissue from 4h refeeding following 24h fasting mice
FR_A18


title: Adipose_tissue_from_4h_refeeding_following_24h_fasting_mice_rep3

description:
Gene expression in Adipose tissue from 4h refeeding following 24h fasting mice
FR_A19


title: Adipose_tissue_from_24h_fasting_mice_rep4

description:
Gene expression in Adipose tissue from 24h fasting mice
FR_A12


title: bicuspid aortic valve 2


title: Adipose_tissue_from_ad_libitum_mice_rep1

description:
Gene expression in Adipose tissue from ad libitum mice
FR_A1


title: Liver_tissue_from_4h_refeeding_following_24h_fasting_mice_rep2

description:
Gene expression in liver tissue from 4h refeeding following 24h fasting mice
CH-18


title: bicuspid aortic valve 7


title: bicuspid aortic valve 1


title: Adipose_tissue_from_24h_fasting_mice_rep2

description:
Gene expression in Adipose tissue from 24h fasting mice
FR_A10


title: normal aortic valve 10


title: Adipose_tissue_from_24h_fasting_mice_rep3

description:
Gene expression in Adipose tissue from 24h fasting mice
FR_A11


title: bicuspid aortic valve 3


title: Adipose_tissue_from_ad_libitum_mice_rep4

description:
Gene expression in Adipose tissue from ad libitum mice
FR_A4


title: Adipose_tissue_from_4h_refeeding_following_24h_fasting_mice_rep1

description:
Gene expression in Adipose tissue from 4h refeeding following 24h fasting mice
FR_A17


title: Liver_tissue_from_ad_libitum_mice_rep4

description:
Gene expression in liver tissue from ad libitum mice
CH-4

source_name: Liver tissue from ad libitum mice


title: Liver_tissue_from_24h_fasting_mice_rep1

description:
Gene expression in liver tissue from 24h fasting mice
CH-9

source_name: Liver tissue from 24h fasting mice


title: Liver_tissue_from_24h_fasting_mice_rep2

description:
Gene expression in liver tissue from 24h fasting mice
CH-10


title: Liver_tissue_from_ad_libitum_mice_rep2

description:
Gene expression in liver tissue from ad libitum mice
CH-2


title: Liver_tissue_from_4h_refeeding_following_24h_fasting_mice_rep1

description:
Gene expression in liver tissue from 4h refeeding following 24h fasting mice
CH-17


title: Liver_tissue_from_ad_libitum_mice_rep3

description:
Gene expression in liver tissue from ad libitum mice
CH-3


title: Adipose_tissue_from_normal_diet_mice_rep3

description:
Gene expression in Adipose tissue from normal fat diet mice
HD_F15

value: Normal fat diet


title: Clams collected  in Marghera (Venice lagoon) exposed to 50 µg Cu l-1 for 7 day [PM_Cu_T3_4]

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing:
Data processed with FeatureExtraction v9.5 and normalized using R2.6.1 statistical software
Normalized intensities (null corresponds to missing spot; 'blank' corresponds to control spot not included in the normalization). Gene expression values are reported in LOG base 2 transformed.

label: Cyanine 3

organism: Ruditapes philippinarum

source_name: digestive gland of Manila clam exposed to 50 µg Cu l-1 for 7 day

label_protocol: Amplified and labeled according to Agilent Low input One-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: Extracted according to QiAgen RNeasy MiniKit protocol for tissue samples (pools of 5 digestive gland)


title: Liver_tissue_from_24h_fasting_mice_rep3

description:
Gene expression in liver tissue from 24h fasting mice
CH-11


title: Clams collected  in Marghera (Venice lagoon) exposed to 50 µg Cu l-1 for 7 day [PM_Cu_T3_5]

value: Manila clam exposed to 50 µg Cu l-1 for 7 day


title: Liver_tissue_from_ad_libitum_mice_rep1

description:
Gene expression in liver tissue from ad libitum mice
CH-1


title: Clams collected  in Marghera (Venice lagoon) exposed to 50 µg Cu l-1 for 7 day [PM_Cu_T3_1]


title: Clams collected  in Marghera (Venice lagoon) exposed to 50 µg Cu l-1 for 7 day [PM_Cu_T3_2]


title: Clams collected  in Marghera (Venice lagoon) representing control group (day 7) [PM_CNTR_T3_5]

source_name: digestive gland of Manila clam maintained in normal condition (14 days)

value: Clams collected  in Marghera (Venice lagoon) representing control group (day 1) corresponding to 14 days of acclimation


title: Liver_tissue_from_24h_fasting_mice_rep4

description:
Gene expression in liver tissue from 24h fasting mice
CH-12


title: Septic cardiomyopathy heart, patient sample 20308

city: Indianapolis

first: Scot

middle: J

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

hyb_protocol: Following fragmentation with NuGen Encore Biotin Module, 2.5 ug of cDNA were hybridized onto Human Gene 1.0 ST Arrays in the GeneChip Hybridization Oven 640 for 18 hr at 45C. Arrays were then washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Raw data scans (in the form of .CEL files) were imported into Partek Genomics Suite 6.6 (Partek, St. Louis, MO) using RMA and quantile normalization together with corrections for %GC content and probe sequences, and probesets were summarized using median polish.

label: Biotin

source_name: Cardiac tissue, diseased heart (sepsis) post-mortem

label_protocol: 50 ng of total RNA was used to generate biotinylated cDNA, according to the standard NuGen WT-Ovation Pico RNA Amplification kit.

extract_protocol: Total RNA was extracted from frozen tissue, which was thawed in QIAzol (Qiagen, Valencia, CA) and homogenized with a TissueRuptor (Qiagen). RNA was purified by using a Qiagen RNeasy kit according to the manufacturer’s instructions.

value: Left ventricular free wall

value: septic cardiomyopathy


title: Septic cardiomyopathy heart, patient sample 20304


title: Clams collected  in Marghera (Venice lagoon) representing control group (day 7) [PM_CNTR_T3_1]


title: Septic cardiomyopathy heart, patient sample 20303


title: Clams collected  in Marghera (Venice lagoon) representing control group (day 7) [PM_CNTR_T3_2]


title: Clams collected  in Marghera (Venice lagoon) exposed to 50 µg Cu l-1 for 3 day [PM_Cu_T2_5]

source_name: digestive gland of Manila clam exposed to 50 µg Cu l-1 for 3 day


title: Clams collected  in Marghera (Venice lagoon) representing control group (day 7) [PM_CNTR_T3_4]


title: Septic cardiomyopathy heart, patient sample 20294


title: Septic cardiomyopathy heart, patient sample 20293


title: Septic cardiomyopathy heart, patient sample 20311


title: Septic cardiomyopathy heart, patient sample 20299


title: Septic cardiomyopathy heart, patient sample 20289


title: Septic cardiomyopathy heart, patient sample 20290


title: 3O-7d

city: Beijing

first: 思

last: 陈

address: 22 Zhongguancun South Avenue, Haidian District

department: Prosthodontics

country: China

institute: Peking University School and Hospital of Stomatology

description: Gene expression data from human adipose tissue-mesenchymal stem cells transfected with pre-miR-375

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome primeview with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: Cells were cultured in osteogenic media comprised DMEM with 10% FBS, 1% antibiotics, 100nM dexamethasone, 10mM β-glycerophosphate and 0.2 mM L-ascorbic acid.

treatment_protocol: hASCs cultured in the third passage were transfected with pre-miR-375 and control vector, then select with Puromycin.

value: adipose

tag: cell type

value: mesenchymal stem cells


title: NO-7d

description: Gene expression data from human adipose tissue-mesenchymal stem cells transfected with control vector


title: Clams collected  in Marghera (Venice lagoon) exposed to 50 µg Cu l-1 for 3 day [PM_Cu_T2_1]

value: Manila clam exposed to 50 µg Cu l-1 for 3 day


title: Clams collected  in Marghera (Venice lagoon) exposed to 50 µg Cu l-1 for 3 day [PM_Cu_T2_4]


title: Septic cardiomyopathy heart, patient sample 20288


title: Clams collected  in Marghera (Venice lagoon) representing control group (day 3) [PM_CNTR_T2_5]

source_name: digestive gland of Manila clam maintained in normal condition (10 days)

value: Clams collected  in Marghera (Venice lagoon) representing control group (day 1) corresponding to 10 days of acclimation


title: Clams collected  in Marghera (Venice lagoon) exposed to 50 µg Cu l-1 for 3 day [PM_Cu_T2_2]


title: Clams collected  in Marghera (Venice lagoon) representing control group (day 3) [PM_CNTR_T2_4]


title: Septic cardiomyopathy heart, patient sample 20284


title: Septic cardiomyopathy heart, patient sample 20280


title: Clams collected  in Marghera (Venice lagoon) representing control group (day 3) [PM_CNTR_T2_1]


title: Septic cardiomyopathy heart, patient sample 20272


title: Clams collected  in Marghera (Venice lagoon) exposed to 50 µg Cu l-1 for 1 day [PM_Cu_T1_5]

source_name: digestive gland of Manila clam exposed to 50 µg Cu l-1 for 1 day


title: Clams collected  in Marghera (Venice lagoon) exposed to 50 µg Cu l-1 for 1 day [PM_Cu_T1_4]

value: Manila clam exposed to 50 µg Cu l-1 for 1 day


title: Clams collected  in Marghera (Venice lagoon) representing control group (day 1) [PM_CNTR_T1_5]

source_name: digestive gland of Manila clam maintained in normal condition (8 days)

value: Clams collected  in Marghera (Venice lagoon) representing control group (day 1) corresponding to 8 days of acclimation


title: Clams collected  in Marghera (Venice lagoon) exposed to 50 µg Cu l-1 for 1 day [PM_Cu_T1_2]


title: Septic cardiomyopathy heart, patient sample 20275


title: Clams collected  in Marghera (Venice lagoon) representing control group (day 1) [PM_CNTR_T1_2]


title: Nonfailing donor heart, patient sample 21139

source_name: Cardiac tissue, donor heart not suitable for transplant

value: nonfailing heart


title: Septic cardiomyopathy heart, patient sample 20265


title: Clams collected  in Marghera (Venice lagoon) representing control group (day 1) [PM_CNTR_T1_4]


title: Clams collected  in Marghera (Venice lagoon) representing control group (day 3) [PM_CNTR_T2_2]


title: Septic cardiomyopathy heart, patient sample 20276


title: Septic cardiomyopathy heart, patient sample 20268


title: Clams collected  in Marghera (Venice lagoon) exposed to 50 µg Cu l-1 for 1 day [PM_Cu_T1_1]


title: Clams collected  in Marghera (Venice lagoon) representing control group (day 1) [PM_CNTR_T1_1]


title: Nonfailing donor heart, patient sample 21137


title: Nonfailing donor heart, patient sample 21138


title: Septic cardiomyopathy heart, patient sample 20264


title: Septic cardiomyopathy heart, patient sample 20277


title: Septic cardiomyopathy heart, patient sample 20263


title: Clams collected  in Marghera (Venice lagoon) and acclimated for 7 days [PM_ACCL_4]

source_name: digestive gland of  Manila clam after 7 days of acclimation

value: clams collected in Marghera and acclimated 7 days in controlled condition


title: Clams collected  in Marghera (Venice lagoon) and acclimated for 7 days [PM_ACCL_3]


title: Clams collected  in Marghera (Venice lagoon) and acclimated for 7 days [PM_ACCL_1]


title: Clams collected  in Marghera (Venice lagoon) and acclimated for 7 days [PM_ACCL_2]


title: Nonfailing donor heart, patient sample 20305


title: Nonfailing donor heart, patient sample 20295


title: Nonfailing donor heart, patient sample 20297


title: Clams collected in wild in Marghera (Venice lagoon) [PM_WILD_6]

source_name: digestive gland of wild Manila clam

value: clams collected in Marghera


title: Nonfailing donor heart, patient sample 20307


title: Clams collected in wild in Marghera (Venice lagoon) [PM_WILD_5]


title: Clams collected  in Chioggia (Venice lagoon) exposed to 50 µg Cu l-1 for 7 day [CH_Cu_T3_5]


title: Clams collected in wild in Marghera (Venice lagoon) [PM_WILD_4]


title: Nonfailing donor heart, patient sample 20287


title: Clams collected  in Chioggia (Venice lagoon) exposed to 50 µg Cu l-1 for 7 day [CH_Cu_T3_1]


title: Clams collected  in Chioggia (Venice lagoon) exposed to 50 µg Cu l-1 for 7 day [CH_Cu_T3_4]


title: Ischemic heart disease, patient sample 20285

source_name: Cardiac tissue, diseased heart (IHD) pre-transplant

value: ischemic heart disease


title: Clams collected  in Chioggia (Venice lagoon) exposed to 50 µg Cu l-1 for 7 day [CH_Cu_T3_2]


title: Nonfailing donor heart, patient sample 20266


title: Ischemic heart disease, patient sample 20306


title: Ischemic heart disease, patient sample 20282


title: Clams collected in wild in Marghera (Venice lagoon) [PM_WILD_3]


title: Ischemic heart disease, patient sample 20281


title: Ischemic heart disease, patient sample 20302


title: Nonfailing donor heart, patient sample 20274


title: Clams collected  in Chioggia (Venice lagoon) representing control group (day 7) [CH_CNTR_T3_5]

value: Clams collected  in Chioggia (Venice lagoon) representing control group (day 1) corresponding to 14 days of acclimation


title: Ischemic heart disease, patient sample 20310


title: Clams collected  in Chioggia (Venice lagoon) representing control group (day 7) [CH_CNTR_T3_2]


title: Ischemic heart disease, patient sample 20291


title: Clams collected  in Chioggia (Venice lagoon) representing control group (day 7) [CH_CNTR_T3_1]


title: Clams collected  in Chioggia (Venice lagoon) representing control group (day 7) [CH_CNTR_T3_4]


title: Clams collected in wild in Marghera (Venice lagoon) [PM_WILD_1]


title: Ischemic heart disease, patient sample 20298


title: Clams collected in wild in Marghera (Venice lagoon) [PM_WILD_2]


title: Nonfailing donor heart, patient sample 20278


title: Ischemic heart disease, patient sample 20271


title: Ischemic heart disease, patient sample 20262


title: Ischemic heart disease, patient sample 20279


title: Nonischemic (dilated) cardiomyopathy, patient sample 20312

source_name: Cardiac tissue, diseased heart (DCM) pre-transplant

value: nonischemic dilated cardiomyopathy


title: Clams collected  in Chioggia (Venice lagoon) exposed to 50 µg Cu l-1 for 3 day [CH_Cu_T2_5]


title: Clams collected  in Chioggia (Venice lagoon) exposed to 50 µg Cu l-1 for 3 day [CH_Cu_T2_2]


title: Clams collected  in Chioggia (Venice lagoon) exposed to 50 µg Cu l-1 for 3 day [CH_Cu_T2_4]


title: Clams collected  in Chioggia (Venice lagoon) exposed to 50 µg Cu l-1 for 3 day [CH_Cu_T2_1]


title: Nonischemic (dilated) cardiomyopathy, patient sample 20301


title: Nonischemic (dilated) cardiomyopathy, patient sample 20309


title: Clams collected  in Chioggia (Venice lagoon) representing control group (day 3) [CH_CNTR_T2_4]

value: Clams collected  in Chioggia (Venice lagoon) representing control group (day 1) corresponding to 10 days of acclimation


title: Clams collected  in Chioggia (Venice lagoon) representing control group (day 3) [CH_CNTR_T2_5]


title: Clams collected  in Chioggia (Venice lagoon) representing control group (day 3) [CH_CNTR_T2_2]


title: Nonischemic (dilated) cardiomyopathy, patient sample 20283


title: Clams collected  in Chioggia (Venice lagoon) representing control group (day 3) [CH_CNTR_T2_1]


title: Clams collected  in Chioggia (Venice lagoon) exposed to 50 µg Cu l-1 for 1 day [CH_Cu_T1_1]


title: Clams collected  in Chioggia (Venice lagoon) exposed to 50 µg Cu l-1 for 1 day [CH_Cu_T1_2]


title: Nonischemic (dilated) cardiomyopathy, patient sample 20270


title: Nonischemic (dilated) cardiomyopathy, patient sample 20286


title: Nonischemic (dilated) cardiomyopathy, patient sample 20296


title: Clams collected  in Chioggia (Venice lagoon) exposed to 50 µg Cu l-1 for 1 day [CH_Cu_T1_5]


title: Clams collected  in Chioggia (Venice lagoon) representing control group (day 1) [CH_CNTR_T1_5]

value: Clams collected  in Chioggia (Venice lagoon) representing control group (day 1) corresponding to 8 days of acclimation


title: Clams collected  in Chioggia (Venice lagoon) representing control group (day 1) [CH_CNTR_T1_4]


title: Nonischemic (dilated) cardiomyopathy, patient sample 20267


title: Clams collected  in Chioggia (Venice lagoon) representing control group (day 1) [CH_CNTR_T1_2]


title: Nonischemic (dilated) cardiomyopathy, patient sample 20273


title: AML12_5mM_Oct_replicate_4

city: Durham

first: Matthew

last: Hirschey

state: NC

address: 300 N. Duke Street

department: Department of Medicine

institute: Duke University Medical Center

data_processing: Illumina expression microarray data underwent a strict quality control evaluation using the lumi Bioconductor package from the R statistical programming environment.  Raw data underwent a variance stabilizing transformation followed by robust spline normalization to eliminate systematic differences across the arrays.

source_name: AML12 cells, treated 24h

label_protocol: Standard Illumina labeling protocol

growth_protocol: AML12 immortalized hepatocytes (ATCC) were plated at 350,000 cells per well in 6-well plates and allowed seed overnight.

extract_protocol: Cells were washed with PBS, lysed with Bio-Rad Aurum RNA lysis buffer and frozen at -80°C. RNA was collected using the Bio-Rad Aurum mini kit.

treatment_protocol: The following day cells were treated with PBS, 1 mM, 2 mM or 5 mM octanoate for 24 hours added to complete DMEM media with 10% FBS.

tag: agent

value: 5 mM octanoate

value: AML12 cells, immortalized mouse hepatocytes


title: Clams collected  in Chioggia (Venice lagoon) exposed to 50 µg Cu l-1 for 1 day [CH_Cu_T1_4]


title: AML12_5mM_Oct_replicate_2


title: AML12_5mM_Oct_replicate_3


title: AML12_5mM_Oct_replicate_1


title: 4 - High [15_159]

city: Darlinghurst

first: Tim

last: Molloy

state: NSW

address: Level 8, 405 Liverpool St

department: Haematology

country: Australia

institute: St Vincent's Centre for Applied Medical Research

hyb_protocol: GeneChip hybridisation oven 640 at a final concentration of 23 ng/µL using a GeneChip Hybridization, Wash and Stain Kit (both Affymetrix) in accordance with manufacturer’s instructions.

scan_protocol: Arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GeneChip 3000 7G+ scanner and using GeneChip Command Console Software (all Affymetrix), following manufacturer’s instructions.

data_processing: Microarray data were pre-processed using the robust multi-array average (RMA) algorithm, background correction, quartile normalisation and gene-level probe set summation19. Genes differentially expressed between the two groups were identified by Significance Analysis of Microarrays (SAM) analysis with a false discovery rate (FDR) of 0.1 using BRBArrayTools Version 4.4 software Gene networks were generated by Ingenuity Pathway Analysis (IPA) software (Qiagen, Redwood City, CA).

organism: Ovis aries

source_name: Lung tissue

label_protocol: WTPlus Kit (Affymetrix)

growth_protocol: Ovis arise (merino cross) singleton fetuses at 115 d gestational age

extract_protocol: TRIZOL LYSIS OF 100MG TISSUE USING A DRY ICE-COOLED PRECELLYS HOMOGENISER

treatment_protocol: 48 h post-op recovery followed by 2 x maternal IV betamethasone infusions (start time separated by 48h) with euthanasia at 122 d

tag: treatment

value: 2 x 0.125 mg/kg Maternal IV Betamethasone Phosphate Infusions


title: 4 - High [15_157]


title: AML12_2mM_Oct_replicate_4

value: 2 mM octanoate


title: AML12_2mM_Oct_replicate_5


title: AML12_2mM_Oct_replicate_2


title: 3 - Medium [15_163]

value: 2 x 0.04 mg/kg Maternal IV Betamethasone Phosphate Infusions


title: Clams collected  in Chioggia (Venice lagoon) representing control group (day 1) [CH_CNTR_T1_1]


title: Clams collected  in Chioggia (Venice lagoon) and acclimated for 7 days [CH_ACCL_4]

value: clams collected in Chioggia and acclimated 7 days in controlled condition


title: 4 - High [15_158]


title: Clams collected  in Chioggia (Venice lagoon) and acclimated for 7 days [CH_ACCL_3]


title: Clams collected  in Chioggia (Venice lagoon) and acclimated for 7 days [CH_ACCL_1]


title: AML12_2mM_Oct_replicate_3


title: 3 - Medium [15_143]


title: AML12_2mM_Oct_replicate_1


title: 3 - Medium [15_141]


title: 2 - Low [15_150]

value: 2 x 0.0125mg/kg Maternal IV Betamethasone Phosphate Infusions


title: 4 - High [15_139]


title: AML12_1mM_Oct_replicate_4

value: 1 mM octanoate


title: 2 - Low [15_151]


title: 3 - Medium [15_142]


title: AML12_1mM_Oct_replicate_2


title: AML12_1mM_Oct_replicate_1


title: Clams collected in wild in Chioggia (Venice lagoon) [CH_WILD_5]

value: clams collected in Chioggia


title: Clams collected  in Chioggia (Venice lagoon) and acclimated for 7 days [CH_ACCL_2]


title: Clams collected in wild in Chioggia (Venice lagoon) [CH_WILD_3]


title: replumless-1_inflorescence_replicate1

city: NORWICH

first: Robert

last: Sablowski

state: Norfolk

address: The John Innes Centre

department: CDB

institute: JIC

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 50 C on AGRONOMICS1 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing:
The affylmGUI package (http://bioinf.wehi.edu.au/affylmGUI/about.html) was used to run LIMMA (Linear Models for MicroArray data). Normalization was performed with Robust Probe-level Linear Model and BH was used for multiple test correction.
[rpl-1_X_wt_inflorescence_PLM.csv] Comma-separated values table with gene identifier (AGI), Affymetrix probe number, normalized intensity for each replicate, log2 ratio (M), average log intensity (A), moderated t statistic, p-value, B statistic, Gene model name, Gene model description, Gene Symbols.

source_name: replumless-1, inflorescence

label_protocol: Probes were prepared using a standard Affymetrix protocol (GeneChip © 3’  IVT Express kit)

growth_protocol: Plants were grown in a controlled environment room at 20-22 °C, 16 h light (100 µE) until they flowered and the inflorescences were around 12 cm tall.

extract_protocol: Immediately after dissecting the terminal 1-2 cm of the inflorescences (1-2 g fresh tissue per sample), total RNA was extracted RNA was extracted with Trizol (Sigma) and purified using QIAGEN RNAeasy columns (QIAGEN) according to the manufacturer's instructions

treatment_protocol: No treatment - straightforward comparison of genotypes

tag: genotype/variation

value: inflorescence apices


title: replumless-1_inflorescence_replicate3


title: 1 - Saline [15_147]

value: 2 x Maternal IV Saline Infusions


title: replumless-1_inflorescence_replicate2


title: 2 - Low [15_149]


title: Clams collected in wild in Chioggia (Venice lagoon) [CH_WILD_4]


title: AML12_PBS_replicate_4

value: PBS


title: AML12_1mM_Oct_replicate_3


title: AML12_PBS_replicate_5


title: Clams collected in wild in Chioggia (Venice lagoon) [CH_WILD_2]


title: Clams collected in wild in Chioggia (Venice lagoon) [CH_WILD_1]


title: Reactive hyperplasia 9

status: Public on Sep 21 2016

city: Barcelona

first: Itziar

last: Salaverria

address: Rossello 153

country: Spain

institute: Hospital Clínic

description: Hybridized to Affymetrix OncoScan FFPE Assay

hyb_protocol: Affymetrix OncoScan™ FFPE Assay kit

scan_protocol: Affymetrix® GeneChip® Scanner 3000G to detect target bound to Oncoscan array after staining with Biotin.

data_processing:
Nexus biodiscovery software
Gains and losses were evaluated with visual inspection by 2 different observers using Nexus Biodiscovery software (Biodiscovery, Hawthorne CA, USA). The CNAs with a minimum size of 100kb were considered real. Loss of heterozigosity regions where considered when size was >5Mb.

source_name: Axilar Lymh Node

label_protocol: Affymetrix OncoScan™ FFPE Assay kit

extract_protocol: DNA from formalin-fixed paraffin-embedded (FFPE) tissue was extracted after dewaxing and proteinase K digestion applying standard phenol/chloroform purification procedures

tag: diagnosis

value: Reactive hyperplasia

value: Female

value: FFPE


title: Reactive hyperplasia 10

source_name: Palatine Tonsil

tag: gender

value: Male


title: Reactive hyperplasia 8

source_name: Rectal polipus, exeresis


title: 1 - Saline [15_134]


title: Reactive hyperplasia 1

source_name: Lymph node


title: Pediatric type Follicular Lymphoma 41

source_name: parotid gland

value: Pediatric type Follicular Lymphoma


title: wild-type_Landsberg_inflorescence_replicate3

source_name: wild-type, Landsberg, inflorescence

value: wt


title: 1 - Saline [15_135]


title: Pediatric type Follicular Lymphoma 42

source_name: Cervical Lymph Node


title: wild-type_Landsberg_inflorescence_replicate2


title: AML12_PBS_replicate_2

value: AML12 cells, immortalized mouse hepatocytes


title: Pediatric type Follicular Lymphoma 40


title: Pediatric type Follicular Lymphoma 7


title: AML12_PBS_replicate_1


title: Pediatric type Follicular Lymphoma 39

source_name: Intraglandular parotid Lymph Node


title: Pediatric type Follicular Lymphoma 5

source_name: Left cervical Lymph Node


title: Clams collected in wild in Chioggia (Venice lagoon) [CH_WILD_6]


title: wild-type_Landsberg_inflorescence_replicate1


title: 1 - Saline [15_133]


title: Serum_suckling

city: Hangzhou

first: Xin

last: Tao

address: Shiqiao Road 145

description: suckling

hyb_protocol: Hybridization was performed on a μParaflo microfluidic chip using a micro-circulation pump overnight (Atactic Technologies). On the microfluidic chip, each probe consisted of a chemically modified nucleotide coding segment complementary to its target miRNA and a spacer segment composed of polyethylene glycol to enlarge the encoding segment away from the substrate. The detection probes were made by in situ synthesis using photogenerated reagent (PGR) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 μL 6×SSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) with 25% formamide at 34°C. Fluorescence labeling with tag-conjugating Cy3 dye was used after hybridization detection.

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by subtracting the background, and normalizing the signals using a LOWESS filter (Locally-Weighted Regression) (Bolstad et al, 2003). Differentially expressed miRNAs using the ratio of detected signals log2-fold changes and the Student’ t-test was used to calculate P values.

organism: Sus scrofa

source_name: serum

label_protocol: The assay started from 5μg total RNA from each sample, which was size fractionated using an YM-100 microcon filter(Millipore, Bedford, USA) and the small RNAs (<300 nt) isolated were 3’-extended with a poly (A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for fluorescent dye staining later.

growth_protocol: Animal studies were conducted in accordance with the principles and guidelines of the Zhejiang Farm Animal Welfare Council of China and approved by the ethics committee of Zhejiang Academy of Agricultural Sciences. In this experiment, a total of 8 piglets from four newborn litters of crossbred piglets (DYL, originating from mating Duroc boars with Yorkshire-Landrace sows) and their respective sows were housed separately in pens with farrowing crates. 4 piglets (one per litter) were removed at 25 d of age. The remaining 4 piglets were allowed to continue suckling with their sows.

extract_protocol: Total RNA from serum samples was extracted using miRNeasy mini kit according to the manufacturer’s protocol (Qiagen, Hilden, Germany). Total RNA concentration was determined on a NanoDrop1000 spectrophotometer (Thermo Fisher Scientific, Wilmington, USA). RNA quality was assessed by electrophoresis on a formaldehyde-containing, ethidium bromide-stained 1% (w/v) agarose gel. And RNA integrity was evaluated on Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA).

treatment_protocol: Blood samples were collected from the jugular vein into 10-ml EDTA-containing vacuum tubes and taken from the four suckling piglets at 29 d of age and from another four weaning piglets at 4 d after weaning. Serum from whole blood samples was obtained by centrifugation at 3,500 g for 10 min at 4°C and stored at -80°C.

value: serum

tag: developmental stage

value: suckling

tag: age

value: 29 days old

tag: Sex

value: female


title: Serum_weaning

institute: Zhejiang Academy of Agricultural Sciences

description: weaning at 25 days old

value: weaned (at 25 days old)

value: 29 days old (4 days after weaning)


title: Pig 21, SA MCT

city: bologna

first: PAOLO

middle: o

last: BOSI

state: BOLOGNA

address: Viale Fanin, 46

department: DISTAL

institute: UNIVERSITY OF BOLOGNA

description:
Gene expression data from oxyntic mucosa
Twelve piglets from sows [(Great York × Pietrain) × ‘Dalland’ cross] were obtained by caesarean delivery (CD) (day 0) and were divided over two microbiota association treatments, housed in separate clean, non-sterile rooms and balanced for BW and litter of origin. Piglets were housed in two pens per room suited with an automatic feeding system for supply of a moist diet.

hyb_protocol: Total mRNA was hybridized on  Affymetrix©Porcine Gene 1.1 ST array strips.  Affymetrix hybridization, wash, and stain Kit for WT Array Strips were used.

scan_protocol: Quantification of transcript expression on a GeneAtlas imaging station (Affymetrix).

data_processing: Performance quality tests of the arrays including the labelling, hybridization, scanning and background signals by a Robust Multichip Analysis were performed on the CEL files using Affymetrix Expression ConsoleTM.

source_name: Pig 21,simple microbial association, MCT diet, oxyntic mucosa

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

extract_protocol: Total mRNA was isolated, according to Qiagen RNeasy® Midi Kit protocol (Qiagen, Hilden, Germany). Purity and integrity evaluation was assessed just before analysis by Agilent Bioanalyzer 2100.

treatment_protocol: Pigs received pasteurized sow colostrum at birth (d0), 2 mL of starter microbiota (10^7 CFU of each Lactob. Amylovorus (LAM), Clostr. glycolicum, and Parabacteroides spp.) on d1-d3 of age and either a placebo inoculant (simple association, SA) or an inoculant consisting of diluted feces of an adult sow (complex association, CA) on d3-d4 of age. On days 26-37 of age, jejunal loops were perfused for 8 h with either enterotoxigenic E. coli F4 (ETEC), F4 fimbriae (F4), LAM or saline (CTRL) and jejunal samples were obtained from each piglet immediately afterwards. For each loop in each subject, the jejunum tract was removed, opened,  washed in ice-cold PBS, and tissue sample was collected and immediately frozen in liquid nitrogen and stored at -80°C until use.

value: oxyntic mucosa

value: (Great York x Pie) x 'Dalland' cross

value: artificially fed pig, 3 weeks of age


title: Pig 17, SA CON

source_name: Pig 17,simple microbial association, control diet, oxyntic mucosa


title: Pig 15, SA CON

source_name: Pig 15,simple microbial association, control diet, oxyntic mucosa


title: Pig 22, SA MCT

source_name: Pig 22,simple microbial association, MCT diet, oxyntic mucosa


title: Pig 19, SA MCT

source_name: Pig 19,simple microbial association, MCT diet, oxyntic mucosa


title: Pig 24, SA MCT

source_name: Pig 24,simple microbial association, MCT diet, oxyntic mucosa


title: Pig 23, SA MCT

source_name: Pig 23,simple microbial association, MCT diet, oxyntic mucosa


title: Pig 18, SA CON

source_name: Pig 18,simple microbial association, control diet, oxyntic mucosa


title: Pig 13, SA CON

source_name: Pig 13,simple microbial association, control diet, oxyntic mucosa


title: Pig 14, SA CON

source_name: Pig 14,simple microbial association, control diet, oxyntic mucosa


title: Pig 20, SA MCT

source_name: Pig 20,simple microbial association, MCT diet, oxyntic mucosa


title: Pig 16, SA CON

source_name: Pig 16,simple microbial association, control diet, oxyntic mucosa


title: Pig 8, CA MCT

source_name: Pig 8,complex microbial association,  MCT diet, oxyntic mucosa


title: Pig 5, CA CON

source_name: Pig 5,complex microbial association, control diet, oxyntic mucosa


title: Pig 10, CA MCT

source_name: Pig 10,complex microbial association,  MCT diet, oxyntic mucosa


title: Pig 9, CA MCT

source_name: Pig 9,complex microbial association,  MCT diet, oxyntic mucosa


title: Pig 7, CA MCT

source_name: Pig 7,complex microbial association,  MCT diet, oxyntic mucosa


title: Pig 4, CA CON

source_name: Pig 4,complex microbial association, control diet, oxyntic mucosa


title: Pig 3, CA CON

source_name: Pig 3,complex microbial association, control diet, oxyntic mucosa


title: Pig 2, CA CON

source_name: Pig 2,complex microbial association, control diet, oxyntic mucosa


title: Pig 10, SA

source_name: Pig 10,simple microbial association, oxyntic mucosa

value: artificially fed pig, 2 weeks of age


title: Pig 11, SA

source_name: Pig 11,simple microbial association, oxyntic mucosa


title: Pig 6, CA CON

source_name: Pig 6,complex microbial association, control diet, oxyntic mucosa


title: Pig 12, SA

source_name: Pig 12,simple microbial association, oxyntic mucosa


title: Pig 12, CA MCT

source_name: Pig 12,complex microbial association,  MCT diet, oxyntic mucosa


title: Pig 11, CA MCT

source_name: Pig 11,complex microbial association,  MCT diet, oxyntic mucosa


title: Pig 8, SA

source_name: Pig 8,simple microbial association, oxyntic mucosa


title: Pig 1, CA CON

source_name: Pig 1,complex microbial association, control diet, oxyntic mucosa


title: Pig 2, CA

source_name: Pig 2,complex microbial association, , oxyntic mucosa


title: Pig 1, CA

source_name: Pig 1,complex microbial association, , oxyntic mucosa


title: Pig 3, CA

source_name: Pig 3,complex microbial association, , oxyntic mucosa


title: YapTaz1

city: Los Angeles

first: Jimmy

last: Hu

address: 10833 Le Conte Ave.

institute: UCLA

description:
9482912062_F_Grn.idat
quadruplate 1
mutant labial cervical loops

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Preprocessing of data was performed within the R statistical computing environment. The SampleNetwork R function was used to perform data normalization. A technical batch affect was corrected for using the ComBat R function

source_name: Mouse incisor cervical loops

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

growth_protocol: Mice were group housed and maintained using standard protocols.

extract_protocol: RNA was extracted with QIAGEN RNeasy micro kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Both control and mutant mice were injected with 5mg of tamoxifen at 8 weeks old for consecutive 2 days and samples were extracted 48 hours after the second injection

value: labial cervical loops


title: Pig 9, SA

source_name: Pig 9,simple microbial association, oxyntic mucosa


title: Pig 7, SA

source_name: Pig 7,simple microbial association, oxyntic mucosa


title: Pig 6, CA

source_name: Pig 6,complex microbial association, , oxyntic mucosa


title: Pig 4, CA

source_name: Pig 4,complex microbial association, , oxyntic mucosa


title: Pig 5, CA

source_name: Pig 5,complex microbial association, , oxyntic mucosa


title: YapTaz2

description:
9482912062_G_Grn.idat
quadruplate 2
mutant labial cervical loops


title: YapTaz3

description:
9482912063_E_Grn.idat
quadruplate 3
mutant labial cervical loops


title: YapTaz4

description:
9482912063_H_Grn.idat
quadruplate 4
mutant labial cervical loops


title: WT3

description:
9482912063_A_Grn.idat
triplicate 3
control labial cervical loops

value: Yap/Tazf/f


title: WT1

description:
9482912062_A_Grn.idat
triplicate 1
control labial cervical loops


title: WT2

description:
9482912062_B_Grn.idat
triplicate 2
control labial cervical loops


title: control4

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the Illumina beadarray Assay System Manual

data_processing: For each probe, replicated mesurements (beads) were averaged after removing outliers. Data were were then normalized using quantilenormalization by using GenomeStudio software v.3 (Illumina).

source_name: mouse, stellate cell, control,4

extract_protocol: RNA was isolated from primary mouse hepatic stellate cell (Passage 0) with Triazol reagent (Invitrogen) followed by a cleanup procedure using QIAGEN RNeasy minicolumns according to manufacturer’s protocol.

treatment_protocol: Six week-old female IL-15RaKO and wild type (WT) B6/129 mice were purchased from Jackson Laboratories (Bar Harbor, ME). All procedures were performed in accordance with the Institutional Animal Care and Use Committee Protocols of the Mount Sinai School of Medicine. Mouse HSCs were isolated from WT and IL-15RKO mice using an established method with modifications. Briefly, the mouse liver was perfused in situ with pronase and collagenase, followed by Percoll (GE) density gradient centrifugation. HSC cultures were maintained in Dulbecco's Modified Eagle Medium with 20% Fetal Bovine Serum.

value: stellate cell

value: control


title: IL15RaKO4

scan_protocol: Refer to the Illumina beadarray Assay System Manual

source_name: mouse, stellate cell, IL15Ra-knockout,4


title: control1

source_name: mouse, stellate cell, control,1

label_protocol: Refer to the Illumina beadarray Assay System Manual


title: IL15RaKO2

source_name: mouse, stellate cell, IL15Ra-knockout,2


title: IL15RaKO3

source_name: mouse, stellate cell, IL15Ra-knockout,3