title: Rhesus cortex 2 (microRNA)

hyb_protocol: Hybridization mix was prepared using the Human miRNA Microarray kit (Agilent Technologies) following the manufacturer's instructions. Hybridization was performed at 55C for 20h. Washing was performed using the Gene Expression Wash Buffer kit (Agilent Technologies) following the manufacturer's instructions

scan_protocol: Scanning was performed by the Agilent Microarray Scanner and the Agilent's Scan Control Software v. A.7.0.1 (Agilent Technologies) using the XDR feature and the recommended parameter settings.

data_processing: Raw image data were processed by the Feature Extraction software 10.5.1.1  (Agilent Technologies).

source_name: Dissected Rhesus Macaque post-mortem superior frontal gyrus

label_protocol: 100ng Dephosphorylated RNA were labeled with Cyanine 3-pCp following standard Aglient protocols.

extract_protocol: mirVana RNA Isolation Kit( Applied Biosystem)was used to isolate total RNA from 100 mg of tissue according to the manufacturer's instructions.

value: superior frontal gyrus of the brain


title: SK-N-SH cell line with hsa-miR-299-3p transfection

status: Public on Oct 18 2011

type: RNA

city: shanghai

first: Song

last: Guo

address: 320 Yue Yang Road

country: China

institute: PICB

description:
SK-N-SH_hsa-miR-299-3p
Gene expression after miRNA transfection.

hyb_protocol: Hybridization was performed according to standard protocols for Affymetrix HG-U133 plus 2.0 arrays.

scan_protocol: Affymetrix GeneChIP Scanner 3000 7G.

data_processing: Prior to gene expression calculations, we made a custom CDF file based on Ensembl genes. This CDF file (HGU133Plus2_Hs_ENSG.cdf) was downloaded from http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/11.0.1/ensg.asp.  RMA processing was used without quantile normalization by RMA in the R Affy package (rma(normalize=F)).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: SK-N-SH neuroblastoma cell line, hsa-miR-299-3p

label_protocol: Labeling was performed according to standard Affymetrix protocols.

growth_protocol: Cells were plated in 0.5ml of growth medium, without antibiotics, 24h prior to transfection.

extract_protocol: Total RNA were extracted with Trizol reagent (Invitrogen).

treatment_protocol: miRNA mimics-Lipofectamine 2000 (Invitrogen) complexes were prepared freshly before  transfection according to the manufacturer's protocol.  SH-SY5Y and SK-N-SH cells were transfected in six-well plates using miRNA mimics-Lipofectamine 2000 with a final oligonucleotide concentration of 10nmol/L. In parallel, negative control transfections with mock oligonucleotides were conducted according to the manufacturer's protocol. For each cell line, transfections with negative control oligonucleotides were carried out in two independent replicates.

tag: cell line

value: SK-N-SH

tag: cell type

value: neuroblastoma cells

tag: miRNA transfection


title: SK-N-SH cell line with ptr-miR-299-3p transfection

description:
SK-N-SH_ptr-miR-299-3p
Gene expression after miRNA transfection.

source_name: SK-N-SH neuroblastoma cell line, ptr-miR-299-3p


title: Rhesus cortex 1 (microRNA)

organism: Macaca mulatta

treatment_protocol: All human postmortem brain tissue samples were obtained from the NICHD Brain and Tissue Bank for Developmental Disorders (NICHDBB)(Baltimore, MD, USA). All subjects were defined as normal controls by forensic pathologists at the NICHDBB. No subjects with prolonged agonal state were used. Chimpanzee samples were obtained from the Yerkes Primate Center (Atlanta, GA, USA), from the Biomedical Primate Research Centre (Rijswijk, Netherlands) and from the Anthropological Institute of the University of Zurich (Switzerland).

tag: tissue


title: T2DM_2_genomic_rep2

type: genomic

city: Jerusalem

first: Asaf

last: Hellman

address: Hadassah Medical School

department: Developmental Biology and Cancer Research

country: Israel

institute: Hebrew University

description: Hybridized to SNP 6.0

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

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

data_processing:
Affymetrix SNP6 microarrays were processed and scanned according to the manufacturer’s instructions (www.Affymetrix.com). Hybridization intensities were normalized using the dChip software package Build date: Jul 19 2010 (www.dchip.org). Methylation signals, defined as 1-log2 of the ratio between hybridization intensities before/after MSRE treatments were assigned to each one of the 1,461,753 DNA fragments with at least one MSRE site, probed on the Affymetrix SNP6 microarray.
The matrix file contain 20 columns. Each column presents the methylation signals obtained from one genomic and one MSRE cel files (1-log2 of the hybridization intensities before/after MSRE treatment), as presented in our paper. Please see the README file on the Series record for associations.

molecule: genomic DNA

source_name: T2DM 2 Genomic2

label_protocol: As per manufacturer (Affymetrix)

extract_protocol:
Genomic DNA samples were extracted from whole peripheral blood at various israel medical centers using standard DNA extraction protocols. For DNA pooling,  DNA samples were diluted in reduced EDTA buffer (10mM Tris-HCl, 0.5mM EDTA) to a precise concentration of 50+/-0.4 ng/µl and equivalent amounts of DNA from the participating individuals were assembled in DNA pools.
One microgram of pooled genomic DNA was digested at 37oC for16 hrs with a methylation sensitive restriction enzyme (MSRE) cocktail including AciI (20 units), BsaHI (1.3 units), HhaI (2.5 units), HpaII (2.5 units), and HpyCH4IV (10 units) (NewEngland Biolabs), in a 50 microliter reaction volume with 0.1 mg/ml BSA and 10% NEB buffer #4 (New England Biolabs), ethanol precipitated, and resuspended in TE at 50 ng/µl.

value: blood

tag: gender

value: pool


title: cl02200808.cel

city: Cambridge

first: Andrew

last: Hill

state: MA

address: 300 Technology Square

department: Research Business Technology

country: USA

institute: Pfizer

hyb_protocol: Affymetrix standard hybridization protocol

scan_protocol: Affymetrix standard scan protocol

data_processing: Affymetrix MAS 5.0 algorithm

organism: Rattus norvegicus

label_protocol: Affymetrix in-vitro labeling protocol

extract_protocol: RNA was extracted from L4 and L5 rat dorsal root ganglion (DRG)

tag: strain

value: Sprague-Dawley

value: male

tag: procedure

value: SNL

tag: contralateral or ipsilateral

value: c

tag: extract

tag: affy chip


title: Human cortex 3 (microRNA)

source_name: Dissected human post-mortem superior frontal gyrus


title: SK-N-SH cell line with hsa-miR-184 transfection

description:
SK-N-SH_hsa-miR-184
Gene expression after miRNA transfection.

source_name: SK-N-SH neuroblastoma cell line, hsa-miR-184


title: cl02150813.cel

value: Sham

value: i


title: cl02200806.cel


title: SK-N-SH cell line with hsa-miR-34c-5p transfection

description:
SK-N-SH_hsa-miR-34c-5p
Gene expression after miRNA transfection.

source_name: SK-N-SH neuroblastoma cell line, hsa-miR-34c-5p


title: cl02150830.cel


title: cl02150806.cel


title: Human cortex 2 (microRNA)


title: T2DM_1_genomic_rep2

description: Hybridized to SNP 6.0

source_name: T2DM 1 Genomic2


title: cl02150820.cel


title: SH-SY5Y cell line with hsa-miR-299-3p transfection

description:
SH-SY5Y_hsa-miR-299-3p
Gene expression after miRNA transfection.

source_name: SH-SY5Y neuroblastoma cell line, hsa-miR-299-3p


title: Human cortex 1 (microRNA)


title: T2DM_1_genomic_rep1

description: Hybridized to SNP 6.0

source_name: T2DM 1 Genomic1


title: T2DM_1_MSRE_rep2

description: Hybridized to SNP 6.0

source_name: T2DM 1 MSRE2


title: SH-SY5Y cell line with hsa-miR-383 transfection

description:
SH-SY5Y_hsa-miR-383
Gene expression after miRNA transfection.

source_name: SH-SY5Y neuroblastoma cell line, hsa-miR-383


title: SK-N-SH cell ine with hsa-miR-487a transfection

description:
SK-N-SH_hsa-miR-487a
Gene expression after miRNA transfection.

source_name: SK-N-SH neuroblastoma cell line, hsa-miR-487a


title: T2DM_2_genomic_rep1

description: Hybridized to SNP 6.0

source_name: T2DM 2 Genomic1


title: T2DM_1_MSRE_rep1

description: Hybridized to SNP 6.0

source_name: T2DM 1 MSRE1


title: SH-SY5Y cell line with ptr-miR-299-3p transfection

description:
SH-SY5Y_ptr-miR-299-3p
Gene expression after miRNA transfection.

source_name: SH-SY5Y neuroblastoma cell line, ptr-miR-299-3p


title: Chimpanzee cortex 2 (microRNA)

organism: Pan troglodytes

source_name: Dissected chimpanzee post-mortem superior frontal gyrus


title: cl02200809.cel


title: Chimpanzee cortex 3 (microRNA)


title: Day 5 endometria from cyclic heifers high progesterone biol rep 1

first: Jai Prakash

last: Mehta

address: Veterinary Science Center, University College Dublin

department: UCD School of Agriculture, Food Science & Veterinary Medicine

country: Ireland

institute: University College Dublin, Ireland

description: Gene expression data from Day 5 cyclic endometrium with high progesterone concentrations

hyb_protocol: 15 μg of fragmented cRNA were hybridized to the GeneChip® Bovine Genome Array. Each sample was added to a hybridization solution containing 100 mM 2-(N-morpholino) ethanesulfonic acid, 1 M Na+, and 20 mM of EDTA in the presence of 0.01% of Tween-20 to a final cRNA concentration of 0.05 μg/ml. Hybridization was performed for 16 h at 45ºC. Each microarray was washed and stained with streptavidin-phycoerythrin in a Fluidics station 450 (Affymetrix).

scan_protocol: Each array was scanned at 1.56 μm resolution in a GeneChip® Scanner 3000 7G System (Affymetrix).

data_processing: The raw data intensity files were read into R (http://www.r-project.org/) and preprocessed using functions of the Affymetrix and Gene Chip Robust Multi-array Average (GCRMA) packages of the BioConductor project (http://www.bioconductor.org/) (Gentleman et al Genome Biology 2004). Identification of differentially expressed genes from endoemtria between treatments on a given day and within a group across days was achieved using the Limma package employing linear modeling and an empirical Bayes framework to shrink the variance of measurements on each probe set. A modified t-test was carried out and P-values were adjusted for multiple testing using the Benjamini and Hochberg false discovery rate method. Lists of differentially expressed genes were selected on the basis of an adjusted P-value of <0.05.

organism: Bos taurus

source_name: Day 5 in vivo bovine endometrium

label_protocol: cDNA was synthesized from 2 µg of total RNA using One-cycle target labeling and control reagents (Affymetrix, Santa Clara, CA) to produce biotin labeled cRNA.

extract_protocol: Trizol was used to extract total RNA from 300 mg strips of endometira according to manufacturer´s instruction. On-column Dnase digestion and RNA cleanup was performed using hte Qiagen Rneasy mini kit as per manufacturers' instructions.

treatment_protocol: Following estrous synchronization, cross-bred beef heifers (n=210) were randomly assigned to either cyclic control group (n=70) or inseminated. Half of all heifers in both groups received a progesterone releasing intravaginal device (PRID) on day 3 of estrous cycle/early pregnancy to transiently elevate systemic progesterone concentrations in the range of 1 ng/ml. The PRID device remained in situ until the day of slaughter. This resulted in four treatment groups: 1) cyclic heifers normal progesterone (CN), 2) cyclic heifers high progesterone (CH), 3) confirmed pregnant heifers with normal progesterone (PN) and 4) confirmed pregnant heifers with high progesterone (PH). Heifers were randomly assigned to slaughter on either Day 5, 7, 13 or 16 of the estrous cycle/early pregnancy.

tag: time

value: Day 5

value: endometrium

tag: heifer status

value: cyclic

tag: progesterone

value: high progesterone


title: Chimpanzee cortex 1 (microRNA)


title: cl02200803.cel


title: SH-SY5Y cell line with hsa-miR-34c-5p transfection

description:
SH-SY5Y_has-miR-34c-5p
Gene expression after miRNA transfection.

source_name: SH-SY5Y neuroblastoma cell line, hsa-miR-34c-5p


title: cl02150827.cel


title: SH-SY5Y cell line with hsa-miR-184 transfection

description:
SH-SY5Y_hsa-miR-184
Gene expression after miRNA transfection.

source_name: SH-SY5Y neuroblastoma cell line, hsa-miR-184


title: SH-SY5Y cell line with hsa-miR-487a transfection

description:
SH-SY5Y_hsa-miR-487a
Gene expression after miRNA transfection.

source_name: SH-SY5Y neuroblastoma cell line, hsa-miR-487a


title: x112003RL2133HG133A

status: Public on Oct 17 2011

city: Cold Spring Harbor

first: Kazimierz

middle: O.

last: Wrzeszczynski

state: NY

address: One Bungtown Rd.

institute: Cold Spring Harbor Laboratory

description:
equivalent ROMA sample JB0178_ROMA
equivalent MOMA3 sample MJ001_MOMA3

hyb_protocol: The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates

scan_protocol: Standard Affymetrix protocol. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.

data_processing: RMA normalization method in affy package of R Bioconductor 2.5

source_name: female, ovarian, tumor

label_protocol: RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out.

extract_protocol: RNA was isolated using the trizol protocol.

value: female

tag: disease state

value: ovarian tumor


title: cl02150802.cel


title: x111903RL1796HG133A

description:
equivalent ROMA sample JB0174_ROMA
equivalent MOMA3 sample JB0754_MOMA3


title: x112003RL2059HG133A

description:
equivalent ROMA sample JB0175_ROMA
equivalent MOMA3 sample JB0743_MOMA3


title: x110603RL1650HG133A

description:
equivalent ROMA sample JB0172_ROMA
equivalent MOMA3 sample JB0750_MOMA3


title: x112003RL2061HG133A

description:
equivalent ROMA sample JB0176_ROMA
equivalent MOMA3 sample JB0745_MOMA3


title: x112003RL2186HG133A


title: 121503RL444HG133A

description: equivalent ROMA sample JB0785_ROMA


title: 111903RL891HG133A

description: equivalent ROMA sample JB0788_ROMA


title: 121503RL1924HG133A

description:
equivalent ROMA sample JB0715_ROMA
equivalent MOMA3 sample JB0485_MOMA3


title: 121503RL1032HG133A


title: 121503RL0919HG133A

description:
equivalent ROMA sample JB0738_ROMA
equivalent MOMA3 sample JB0479_MOMA3


title: 111903RL1037HG133A


title: x112003RL2113HG133A

description:
equivalent ROMA sample JB0177_ROMA
equivalent MOMA3 sample JB0747_MOMA3


title: 112003RL2087HG133A

description:
equivalent ROMA sample JB0736_ROMA
equivalent MOMA3 sample JB0632_MOMA3


title: 112003RL1957HG133A

description:
equivalent ROMA sample JB0737_ROMA
equivalent MOMA3 sample JB0620_MOMA3


title: 110503RL1585HG133A

description:
equivalent ROMA sample JB0724_ROMA
equivalent MOMA3 sample JB0495_MOMA3


title: 111903RL1900HG133A

description:
equivalent ROMA sample JB0787_ROMA
equivalent MOMA3 sample JB0664_MOMA3


title: x110503RL1654HG133A

description:
equivalent ROMA sample JB0173_ROMA
equivalent MOMA3 sample JB0752_MOMA3


title: 111903RL1340HG133A

description:
equivalent ROMA sample JB0781_ROMA
equivalent MOMA3 sample JB0656_MOMA3


title: 110503RL1535HG133A

description:
equivalent ROMA sample JB0727_ROMA
equivalent MOMA3 sample JB0493_MOMA3


title: 112003RL1944HG133A

description:
equivalent ROMA sample JB0795_ROMA
equivalent MOMA3 sample JB0634_MOMA3


title: 110603RL1805HG133A

description:
equivalent ROMA sample JB0735_ROMA
equivalent MOMA3 sample JB0481_MOMA3


title: 112003RL1028HG133A

description:
equivalent ROMA sample JB0732_ROMA
equivalent MOMA3 sample JB0497_MOMA3


title: 110603RL1841HG133A

description:
equivalent ROMA sample JB0725_ROMA
equivalent MOMA3 sample JB0483_MOMA3


title: 110603RL1679HG133A

description:
equivalent ROMA sample JB0791_ROMA
equivalent MOMA3 sample JB0654_MOMA3


title: 111903RL1013HG133A

description:
equivalent ROMA sample JB0726_ROMA
equivalent MOMA3 sample JB0471_MOMA3


title: 110403RL511HGU133A

description: equivalent ROMA sample JB0783_ROMA


title: 110503RL1412HG133A

description:
equivalent ROMA sample JB0717_ROMA
equivalent MOMA3 sample JB0491_MOMA3


title: 110403RL450HGU133A

description: equivalent ROMA sample JB0793_ROMA


title: 110503RL1209HG133A

description:
equivalent ROMA sample JB0786_ROMA
equivalent MOMA3 sample JB0618_MOMA3


title: 110303RL126HGU133A

description: equivalent ROMA sample JB0782_ROMA


title: 110403RL1133HGU133A

description:
equivalent ROMA sample JB0723_ROMA
equivalent MOMA3 sample JB0489_MOMA3


title: 110403RL0892HGU133A

description:
equivalent ROMA sample JB0734_ROMA
equivalent MOMA3 sample JB0467_MOMA3


title: 110403RL0951HGU133A

description:
equivalent ROMA sample JB0722_ROMA
equivalent MOMA3 sample JB0477_MOMA3


title: 042004RL1117HG133A

description:
equivalent ROMA sample JB0728_ROMA
equivalent MOMA3 sample JB0487_MOMA3


title: 110403RL0993HGU133A

description:
equivalent ROMA sample JB0733_ROMA
equivalent MOMA3 sample JB0473_MOMA3


title: 110403RL0877HGU133A

description:
equivalent ROMA sample JB0716_ROMA
equivalent MOMA3 sample JB0469_MOMA3


title: 110303RL107HGU133A

description: equivalent ROMA sample JB0794_ROMA


title: 110403RL1063HGU133A


title: 110403RL0980HGU133A

description:
equivalent ROMA sample JB0789_ROMA
equivalent MOMA3 sample JB0475_MOMA3


title: 042004RL118HG133A

description: equivalent ROMA sample JB0792_ROMA


title: 110303RL0095HGU133A

description:
equivalent ROMA sample JB0718_ROMA
equivalent MOMA3 sample JB0461_MOMA3


title: 110303RL0242HGU133A

description:
equivalent ROMA sampleJB0731_ROMA
equivalent MOMA3 sample JB0465_MOMA3


title: 041904RL736HG133A

description: equivalent ROMA sample JB0784_ROMA


title: Lymph-node (1118_Lymph-node)

city: Madrid

first: Cristina

last: Gomez-Abad

address: Melchor Fernández Almagro, 3

department: Molecular Pathology Program

country: Spain

institute: CNIO

description:
1118_Lymph-node
Raw data file:
US22502553_251485029246_S01_GE2-v5_95_Feb07_1_2_1118_GANGLIO.txt

hyb_protocol: The cDNA was fragmented, labeled and hybridized to Whole Human Genome Agilent 4X44K Oligonucleotide Microarray (Agilent Technologies, Inc., Santa Clara, CA)

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 9.0).

data_processing: Agilent Feature Extraction Software (version 9.0) was used for background subtraction and LOWESS normalization.

source_name: Lymph-node

label_protocol: Total RNA  amplification and labeling were performed according to the standard Agilent protocol.

extract_protocol: Total RNA was extracted using the Trizol reagent (Invitrogen, Carlsbad, CA, USA), and purified and treated with RNase-free DNase I using the RNeasy kit (Qiagen Inc., Valencia, CA)

value: freshly frozen lymph nodes

source_name: Universal Human Reference RNA from Stratagene

tag: reference composition

value: 10 human cell lines


title: Reactive Tonsils  (70413_Reactive Tonsil)

description:
70413_Reactive Tonsil
Raw data file:
US22502553_251485019374_S01_GE2-v5_95_Feb07_1_2_70413 total_AMIGDALA.txt

source_name: Reactive Tonsils


title: Reactive Tonsils  (11922_Reactive Tonsil)

description:
11922_Reactive Tonsil
Raw data file:
US22502553_251485019373_S01_GE2-v5_95_Feb07_1_3_11922_AMIGDALA.txt


title: Lymph-node (1010_Lymph-node)

description:
1010_Lymph-node
Raw data file:
US22502553_251485029246_S01_GE2-v5_95_Feb07_1_1_1010_GANGLIO.txt


title: Lymph-node (22382_Lymph-node)

description:
22382_Lymph-node
Raw data file:
US22502553_251485029245_S01_GE2-v5_95_Feb07_1_2_22382_GANGLIO.txt


title: 110303RL372HGU133A


title: Lymph-node (21688_Lymph-node)

description:
21688_Lymph-node
Raw data file:
US22502553_251485029245_S01_GE2-v5_95_Feb07_1_3_21688_GANGLIO.txt


title: Reactive Tonsils  (1070331_Reactive Tonsil)

description:
1070331_Reactive Tonsil
Raw data file:
US22502553_251485019374_S01_GE2-v5_95_Feb07_1_1_1070331_AMIGDALA.txt


title: Lymph-node (1123_Lymph-node)

description:
1123_Lymph-node
Raw data file:
US22502553_251485029246_S01_GE2-v5_95_Feb07_1_3_1123_GANGLIO.txt


title: Reactive Tonsils  (11907_Reactive Tonsil)

description:
11907_Reactive Tonsil
Raw data file:
US22502553_251485019373_S01_GE2-v5_95_Feb07_1_2_11907_AMIGDALA.txt


title: 110303RL0190HGU133A

description:
equivalent ROMA sample JB0721_ROMA
equivalent MOMA3 sample JB0463_MOMA3


title: Reactive Tonsils  (10700198_Reactive Tonsil)

description:
10700198_Reactive Tonsil
Raw data file:
US22502553_251485019373_S01_GE2-v5_95_Feb07_1_4_10700198_AMIGDALA.txt


title: Lymph-node (22464_Lymph-node)

description:
22464_Lymph-node
Raw data file:
US22502553_251485029245_S01_GE2-v5_95_Feb07_1_4_22464_GANGLIO.txt


title: Reactive Tonsils  (11906_Reactive Tonsil)

description:
11906_Reactive Tonsil
Raw data file:
US22502553_251485019373_S01_GE2-v5_95_Feb07_1_1_11906_AMIGDALA.txt


title: Lymph-node (3082_Lymph-node)

description:
3082_Lymph-node
Raw data file:
US22502553_251485029245_S01_GE2-v5_95_Feb07_1_1_3082_GANGLIO.txt


title: Nodal Marginal Zone Lymphoma  (NMZL2)

description:
NMZL2
Raw data file:
US22502553_251485056811_S01_GE2_107_Sep09_1_4_NMZL2.txt

source_name: Nodal Marginal Zone Lymphoma patient


title: Chronic Lymphocytic Leukemia  (2080383_CLLg)

description:
2080383_CLLg
Raw data file:
US22502553_251485043897_S01_GE2-v5_95_Feb07_1_4_2080383_CLLg.txt

source_name: Chronic Lymphocytic Leukemia patient


title: Chronic Lymphocytic Leukemia  (1060034_CLLg)

description:
1060034_CLLg
Raw data file:
US22502553_251485042598_S01_GE2-v5_95_Feb07_1_3_1060034_CLLg.txt


title: Chronic Lymphocytic Leukemia  (1030242_CLLg)

description:
1030242_CLLg
Raw data file:
US22502553_251485042599_S01_GE2-v5_95_Feb07_1_2_1030242_CLLg.txt


title: Chronic Lymphocytic Leukemia  (1040604_CLLg)

description:
1040604_CLLg
Raw data file:
US22502553_251485042600_S01_GE2-v5_95_Feb07_1_1_1040604_CLLg.txt


title: Chronic Lymphocytic Leukemia  (1060360_CLLg)

description:
1060360_CLLg
Raw data file:
US22502553_251485042598_S01_GE2-v5_95_Feb07_1_4_1060360_CLLg.txt


title: Chronic Lymphocytic Leukemia  (2080139_CLLg)

description:
2080139_CLLg
Raw data file:
US22502553_251485043897_S01_GE2-v5_95_Feb07_1_2_2080139_CLLg.txt


title: marginal zone lymphoma-MALT type  (MALT4)

description:
MALT4
Raw data file:
US22502553_251485056369_S01_GE2_107_Sep09_1_1_MALT4.txt

source_name: marginal zone lymphoma-MALT type patient


title: Chronic Lymphocytic Leukemia  (1040230_CLLg)

description:
1040230_CLLg
Raw data file:
US22502553_251485042599_S01_GE2-v5_95_Feb07_1_1_1040230_CLLg.txt


title: Chronic Lymphocytic Leukemia  (1090051_CLLg)

description:
1090051_CLLg
Raw data file:
US22502553_251485042599_S01_GE2-v5_95_Feb07_1_3_1090051_CLLg.txt


title: Chronic Lymphocytic Leukemia  (2070215_CLLg)

description:
2070215_CLLg
Raw data file:
US22502553_251485043897_S01_GE2-v5_95_Feb07_1_3_2070215_CLLg.txt


title: Nodal Marginal Zone Lymphoma  (NMZL1)

description:
NMZL1
Raw data file:
US22502553_251485056811_S01_GE2_107_Sep09_1_3_NMZL1.txt


title: Mantle Cell Lymphoma (MCL_2060252)

description:
MCL_2060252
Raw data file:
251485017063_S01_GE2-v5_95_Feb07_1_4_2060252.txt

source_name: Mantle Cell Lymphoma patient


title: Chronic Lymphocytic Leukemia  (4030015_CLLg)

description:
4030015_CLLg
Raw data file:
US22502553_251485042597_S01_GE2-v5_95_Feb07_1_1_4030015_CLLg.txt


title: Chronic Lymphocytic Leukemia  (2050158_CLLg)

description:
2050158_CLLg
Raw data file:
US22502553_251485043897_S01_GE2-v5_95_Feb07_1_1_2050158_CLLg.txt


title: Chronic Lymphocytic Leukemia  (1030208_CLLg)

description:
1030208_CLLg
Raw data file:
US22502553_251485042598_S01_GE2-v5_95_Feb07_1_1_1030208_CLLg.txt


title: Chronic Lymphocytic Leukemia  (1030378_CLLg)

description:
1030378_CLLg
Raw data file:
US22502553_251485042599_S01_GE2-v5_95_Feb07_1_4_1030378_CLLg.txt


title: Chronic Lymphocytic Leukemia  (1030171_CLLg)

description:
1030171_CLLg
Raw data file:
US22502553_251485042597_S01_GE2-v5_95_Feb07_1_3_1030171_CLLg.txt


title: Chronic Lymphocytic Leukemia  (1020055_CLLg)

description:
1020055_CLLg
Raw data file:
US22502553_251485042597_S01_GE2-v5_95_Feb07_1_4_1020055_CLLg.txt


title: Mantle Cell Lymphoma (MCL_40287)

description:
MCL_40287
Raw data file:
251485017063_S01_GE2-v5_95_Feb07_1_3_40287.txt


title: Mantle Cell Lymphoma (MCL__22601)

description:
MCL__22601
Raw data file:
251485017064_S01_GE2-v5_95_Feb07_1_1_22601.txt


title: Mantle Cell Lymphoma (MCL_40219)

description:
MCL_40219
Raw data file:
251485017064_S01_GE2-v5_95_Feb07_1_3_40219.txt


title: Chronic Lymphocytic Leukemia  (4011687_CLLg)

description:
4011687_CLLg
Raw data file:
US22502553_251485042597_S01_GE2-v5_95_Feb07_1_2_4011687_CLLg.txt


title: Mantle Cell Lymphoma (MCL_2060213)

description:
MCL_2060213
Raw data file:
251485017063_S01_GE2-v5_95_Feb07_1_2_2060213.txt


title: Chronic Lymphocytic Leukemia  (1030325_CLLg)

description:
1030325_CLLg
Raw data file:
US22502553_251485042598_S01_GE2-v5_95_Feb07_1_2_1030325_CLLg.txt


title: Mantle Cell Lymphoma (MCL_487)

description:
MCL_487
Raw data file:
251485017224_S01_GE2-v5_95_Feb07_1_1_487.txt


title: Mantle Cell Lymphoma (MCL_4010343)

description:
MCL_4010343
Raw data file:
251485017064_S01_GE2-v5_95_Feb07_1_4_4010343.txt


title: Mantle Cell Lymphoma (MCL_512)

description:
MCL_512
Raw data file:
251485017224_S01_GE2-v5_95_Feb07_1_2_512.txt


title: Mantle Cell Lymphoma (MCL_866)

description:
MCL_866
Raw data file:
251485017224_S01_GE2-v5_95_Feb07_1_3_866.txt


title: Mantle Cell Lymphoma (MCL_1126)

description:
MCL_1126
Raw data file:
251485017225_S01_GE2-v5_95_Feb07_1_2_1126.txt


title: Mantle Cell Lymphoma (MCL_5312)

description:
MCL_5312
Raw data file:
251485017226_S01_L_GE2-v5_95_Feb07_1_1_5312.txt


title: Mantle Cell Lymphoma (MCL_10063)

description:
MCL_10063
Raw data file:
251485017226_S01_L_GE2-v5_95_Feb07_1_4_10063.txt


title: Mantle Cell Lymphoma (MCL_1173)

description:
MCL_1173
Raw data file:
251485017225_S01_GE2-v5_95_Feb07_1_4_1173.txt


title: Mantle Cell Lymphoma (MCL_22073)

description:
MCL_22073
Raw data file:
251485017226_S01_L_GE2-v5_95_Feb07_1_3_22073.txt


title: Mantle Cell Lymphoma (MCL_993)

description:
MCL_993
Raw data file:
251485017225_S01_GE2-v5_95_Feb07_1_1_993.txt


title: Mantle Cell Lymphoma (MCL_11980)

description:
MCL_11980
Raw data file:
251485017227_S01_H_GE2-v5_95_Feb07_1_1_11980.txt


title: Diffuse Large B cell Lymphoma (DLBCL_60341)

description:
DLBCL_60341
Raw data file:
US22502553_251485023822_S01_GE2-v5_95_Feb07_1_2_DLBCL_60341.txt

source_name: Diffuse Large B cell Lymphoma patient


title: Mantle Cell Lymphoma (MCL_20690)

description:
MCL_20690
Raw data file:
251485017227_S01_H_GE2-v5_95_Feb07_1_3_20690.txt


title: Mantle Cell Lymphoma (MCL_1153)

description:
MCL_1153
Raw data file:
251485017225_S01_GE2-v5_95_Feb07_1_3_1153.txt


title: Mantle Cell Lymphoma (MCL_2060441)

description:
MCL_2060441
Raw data file:
251485017226_S01_L_GE2-v5_95_Feb07_1_2_2060441.txt


title: Mantle Cell Lymphoma (MCL_948)

description:
MCL_948
Raw data file:
251485017224_S01_GE2-v5_95_Feb07_1_4_948.txt


title: Diffuse Large B cell Lymphoma (DLBCL_700276)

description:
DLBCL_700276
Raw data file:
US22502553_251485024002_S01_GE2-v5_95_Feb07_1_3_DLBCL_700276.txt


title: Diffuse Large B cell Lymphoma (DLBCL_70096)

description:
DLBCL_70096
Raw data file:
US22502553_251485023999_S01_GE2-v5_95_Feb07_1_1_DLBCL_70096.txt


title: Mantle Cell Lymphoma (MCL_20691)

description:
MCL_20691
Raw data file:
251485017227_S01_H_GE2-v5_95_Feb07_1_2_20691.txt


title: Diffuse Large B cell Lymphoma (DLBCL_60523)

description:
DLBCL_60523
Raw data file:
US22502553_251485023999_S01_GE2-v5_95_Feb07_1_4_DLBCL_60523.txt


title: Diffuse Large B cell Lymphoma (DLBCL_60338)

description:
DLBCL_60338
Raw data file:
US22502553_251485023999_S01_GE2-v5_95_Feb07_1_3_DLBCL_60338.txt


title: Diffuse Large B cell Lymphoma (DLBCL_700270)

description:
DLBCL_700270
Raw data file:
US22502553_251485024002_S01_GE2-v5_95_Feb07_1_2_DLBCL_700270.txt


title: Diffuse Large B cell Lymphoma (DLBCL_2020318)

description:
DLBCL_2020318
Raw data file:
US22502553_251485024001_S01_GE2-v5_95_Feb07_1_2_DLBCL_2020318.txt


title: Diffuse Large B cell Lymphoma (DLBCL_20060196)

description:
DLBCL_20060196
Raw data file:
US22502553_251485024001_S01_GE2-v5_95_Feb07_1_3_DLBCL_20060196.txt


title: Diffuse Large B cell Lymphoma (DLBCL_60342)

description:
DLBCL_60342
Raw data file:
US22502553_251485023999_S01_GE2-v5_95_Feb07_1_2_DLBCL_60342.txt


title: Mantle Cell Lymphoma (MCL_21556)

description:
MCL_21556
Raw data file:
251485017227_S01_H_GE2-v5_95_Feb07_1_4_21556.txt


title: Diffuse Large B cell Lymphoma (DLBCL_60526)

description:
DLBCL_60526
Raw data file:
US22502553_251485023822_S01_GE2-v5_95_Feb07_1_4_DLBCL_60526.txt


title: Diffuse Large B cell Lymphoma (DLBCL_7030140)

description:
DLBCL_7030140
Raw data file:
US22502553_251485024001_S01_GE2-v5_95_Feb07_1_1_DLBCL_7030140.txt


title: Mantle Cell Lymphoma (MCL_4010139)

description:
MCL_4010139
Raw data file:
251485017063_S01_GE2-v5_95_Feb07_1_1_4010139.txt


title: Diffuse Large B cell Lymphoma (DLBCL_700269)

description:
DLBCL_700269
Raw data file:
US22502553_251485024002_S01_GE2-v5_95_Feb07_1_1_DLBCL_700269.txt


title: Diffuse Large B cell Lymphoma (DLBCL_506012)

description:
DLBCL_506012
Raw data file:
US22502553_251485023822_S01_GE2-v5_95_Feb07_1_3_DLBCL_506012.txt


title: Diffuse Large B cell Lymphoma (DLBCL_20031238)

description:
DLBCL_20031238
Raw data file:
US22502553_251485024002_S01_GE2-v5_95_Feb07_1_4_DLBCL_20031238.txt


title: Mantle Cell Lymphoma (MCL_4010341)

description:
MCL_4010341
Raw data file:
251485017064_S01_GE2-v5_95_Feb07_1_2_4010341.txt


title: Diffuse Large B cell Lymphoma (DLBCL_1040332)

description:
DLBCL_1040332
Raw data file:
US22502553_251485024003_S01_GE2-v5_95_Feb07_1_1_DLBCL_1040332.txt


title: Diffuse Large B cell Lymphoma (DLBCL_1040562)

description:
DLBCL_1040562
Raw data file:
US22502553_251485024003_S01_GE2-v5_95_Feb07_1_2_DLBCL_1040562.txt


title: Diffuse Large B cell Lymphoma (DLBCL_1050245)

description:
DLBCL_1050245
Raw data file:
US22502553_251485024004_S01_GE2-v5_95_Feb07_1_4_DLBCL_1050245.txt


title: Diffuse Large B cell Lymphoma (DLBCL_4040246)

description:
DLBCL_4040246
Raw data file:
US22502553_251485024005_S01_GE2-v5_95_Feb07_1_3_DLBCL_4040246.txt


title: Diffuse Large B cell Lymphoma (DLBCL_2030002)

description:
DLBCL_2030002
Raw data file:
US22502553_251485024005_S01_GE2-v5_95_Feb07_1_1_DLBCL_2030002.txt


title: marginal zone lymphoma-MALT type  (MALT_1106)

description:
MALT_1106
Raw data file:
US22502553_251485024006_S01_GE2-v5_95_Feb07_1_1_MALT_1106.txt


title: marginal zone lymphoma-MALT type  (MALT_1100)

description:
MALT_1100
Raw data file:
US22502553_251485024006_S01_GE2-v5_95_Feb07_1_3_MALT_1100.txt


title: Diffuse Large B cell Lymphoma (DLBCL_2030125)

description:
DLBCL_2030125
Raw data file:
US22502553_251485024005_S01_GE2-v5_95_Feb07_1_2_DLBCL_2030125.txt


title: marginal zone lymphoma-MALT type  (MALT_11536)

description:
MALT_11536
Raw data file:
US22502553_251485024006_S01_GE2-v5_95_Feb07_1_4_MALT_11536.txt


title: Nodal Marginal Zone Lymphoma  (2030091NMZL)

description:
2030091NMZL
Raw data file:
US22502553_251485024324_S01_GE2-v5_95_Feb07_1_2_2030091NMZL.txt


title: Nodal Marginal Zone Lymphoma  (11021NMZL)

description:
11021NMZL
Raw data file:
US22502553_251485024323_S01_GE2-v5_95_Feb07_1_1_11021NMZL.txt


title: marginal zone lymphoma-MALT type  (MALT_22545)

description:
MALT_22545
Raw data file:
US22502553_251485024007_S01_GE2-v5_95_Feb07_1_4_MALT_22545.txt


title: Diffuse Large B cell Lymphoma (DLBCL_700279)

description:
DLBCL_700279
Raw data file:
US22502553_251485024004_S01_GE2-v5_95_Feb07_1_2_DLBCL_700279.txt


title: marginal zone lymphoma-MALT type  (MALT_308)

description:
MALT_308
Raw data file:
US22502553_251485024006_S01_GE2-v5_95_Feb07_1_2_MALT_308.txt


title: Follicular Lymphoma (FL_802)

description:
FL_802
Raw data file:
US22502553_251485029170_S01_GE2-v5_95_Feb07_1_4_FL_802.txt

source_name: Follicular Lymphoma patient


title: Nodal Marginal Zone Lymphoma  (30109NMZL)

description:
30109NMZL
Raw data file:
US22502553_251485024324_S01_GE2-v5_95_Feb07_1_4_30109NMZL.txt


title: Nodal Marginal Zone Lymphoma  (2060229NMZL)

description:
2060229NMZL
Raw data file:
US22502553_251485024324_S01_GE2-v5_95_Feb07_1_3_2060229NMZL.txt


title: Nodal Marginal Zone Lymphoma  (20184NMZL)

description:
20184NMZL
Raw data file:
US22502553_251485024323_S01_GE2-v5_95_Feb07_1_3_20184NMZL.txt


title: marginal zone lymphoma-MALT type  (MALT_20432)

description:
MALT_20432
Raw data file:
US22502553_251485024007_S01_GE2-v5_95_Feb07_1_1_MALT_20432.txt


title: Nodal Marginal Zone Lymphoma  (2040336NMZL)

description:
2040336NMZL
Raw data file:
US22502553_251485024323_S01_GE2-v5_95_Feb07_1_4_2040336NMZL.txt


title: marginal zone lymphoma-MALT type  (MALT_22022)

description:
MALT_22022
Raw data file:
US22502553_251485024007_S01_GE2-v5_95_Feb07_1_3_MALT_22022.txt


title: Nodal Marginal Zone Lymphoma  (11953NMZL)

description:
11953NMZL
Raw data file:
US22502553_251485024323_S01_GE2-v5_95_Feb07_1_2_11953NMZL.txt


title: Follicular Lymphoma (FL_30568)

description:
FL_30568
Raw data file:
US22502553_251485029170_S01_GE2-v5_95_Feb07_1_1_FL_30568.txt


title: Nodal Marginal Zone Lymphoma  (119NMZL)

description:
119NMZL
Raw data file:
US22502553_251485024325_S01_GE2-v5_95_Feb07_1_1_119NMZL.txt


title: marginal zone lymphoma-MALT type  (MALT_464)

description:
MALT_464
Raw data file:
US22502553_251485029242_S01_GE2-v5_95_Feb07_1_2_MALT_464.txt


title: Nodal Marginal Zone Lymphoma  (2040450NMZL)

description:
2040450NMZL
Raw data file:
US22502553_251485024324_S01_GE2-v5_95_Feb07_1_1_2040450NMZL.txt


title: Follicular Lymphoma (FL_30305)

description:
FL_30305
Raw data file:
US22502553_251485029170_S01_GE2-v5_95_Feb07_1_2_FL_30305.txt


title: Nodal Marginal Zone Lymphoma  (2050469NMZL)

description:
2050469NMZL
Raw data file:
US22502553_251485024325_S01_GE2-v5_95_Feb07_1_3_2050469NMZL.txt


title: Follicular Lymphoma (FL_423)

description:
FL_423
Raw data file:
US22502553_251485029170_S01_GE2-v5_95_Feb07_1_3_FL_423.txt


title: Nodal Marginal Zone Lymphoma  (21904NMZL)

description:
21904NMZL
Raw data file:
US22502553_251485024325_S01_GE2-v5_95_Feb07_1_2_21904NMZL.txt


title: marginal zone lymphoma-MALT type  (MALT_992)

description:
MALT_992
Raw data file:
US22502553_251485029242_S01_GE2-v5_95_Feb07_1_4_MALT_992.txt


title: marginal zone lymphoma-MALT type  (MALT_826)

description:
MALT_826
Raw data file:
US22502553_251485029242_S01_GE2-v5_95_Feb07_1_3_MALT_826.txt


title: marginal zone lymphoma-MALT type  (MALT_1066)

description:
MALT_1066
Raw data file:
US22502553_251485029244_S01_GE2-v5_95_Feb07_1_1_MALT_1066.txt


title: Follicular Lymphoma (FL_20182)

description:
FL_20182
Raw data file:
US22502553_251485032193_S01_GE2-v5_95_Feb07_1_2_FL_20182.txt


title: Follicular Lymphoma (FL_22196)

description:
FL_22196
Raw data file:
US22502553_251485032192_S01_GE2-v5_95_Feb07_1_2_FL_22196.txt


title: marginal zone lymphoma-MALT type  (MALT_1109)

description:
MALT_1109
Raw data file:
US22502553_251485029244_S01_GE2-v5_95_Feb07_1_3_MALT_1109.txt


title: Follicular Lymphoma (FL_20612)

description:
FL_20612
Raw data file:
US22502553_251485032193_S01_GE2-v5_95_Feb07_1_3_FL_20612.txt


title: marginal zone lymphoma-MALT type  (MALT_21782)

description:
MALT_21782
Raw data file:
US22502553_251485029244_S01_GE2-v5_95_Feb07_1_4_MALT_21782.txt


title: Follicular Lymphoma (FL_31048)

description:
FL_31048
Raw data file:
US22502553_251485032192_S01_GE2-v5_95_Feb07_1_3_FL_31048.txt


title: Follicular Lymphoma (FL_21804t)

description:
FL_21804t
Raw data file:
US22502553_251485032193_S01_GE2-v5_95_Feb07_1_1_FL_21804t.txt


title: Follicular Lymphoma (FL_811)

description:
FL_811
Raw data file:
US22502553_251485032192_S01_GE2-v5_95_Feb07_1_1_FL_811.txt


title: MM96L

city: Brisbane

first: Mitchell

last: Stark

address: 300 Herston Rd Herston

country: Australia

institute: QIMR

hyb_protocol: See Agilent Technologies website for miRNA microarray hybridization and wash protocol: http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=50500

scan_protocol: Scanned on an Agilent G2505B Scanner

data_processing: Agilent Feature Extraction v9.5.1, default miRNA parameters

source_name: Melanoma Cell Line

label_protocol: Direct labeling with Cy3-pCp. See Agilent Technologies website for miRNA labeling protocol: http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=50500

growth_protocol: Cell Lines were grown in 10%FBS and RPMI.

extract_protocol: QIAGEN miRNA kit


title: SKMEL28


title: MM649


title: marginal zone lymphoma-MALT type  (MALT_1107)

description:
MALT_1107
Raw data file:
US22502553_251485029244_S01_GE2-v5_95_Feb07_1_2_MALT_1107.txt


title: Follicular Lymphoma (FL_20298)

description:
FL_20298
Raw data file:
US22502553_251485032195_S01_GE2-v5_95_Feb07_1_3_FL_20298.txt


title: Follicular Lymphoma (FL_20899)

description:
FL_20899
Raw data file:
US22502553_251485032193_S01_GE2-v5_95_Feb07_1_4_FL_20899.txt


title: SKMEL5


title: Follicular Lymphoma (FL_20542)

description:
FL_20542
Raw data file:
US22502553_251485032194_S01_GE2-v5_95_Feb07_1_1_FL_20542.txt


title: Follicular Lymphoma (FL_11881)

description:
FL_11881
Raw data file:
US22502553_251485032194_S01_GE2-v5_95_Feb07_1_4_FL_11881.txt


title: Diffuse Large B cell Lymphoma (DLBCL_60528)

description:
DLBCL_60528
Raw data file:
US22502553_251485023822_S01_GE2-v5_95_Feb07_1_1_DLBCL_60528.txt


title: Follicular Lymphoma (FL_10064)

description:
FL_10064
Raw data file:
US22502553_251485032196_S01_GE2-v5_95_Feb07_1_1_FL_10064.txt


title: Follicular Lymphoma (FL_31266)

description:
FL_31266
Raw data file:
US22502553_251485032196_S01_GE2-v5_95_Feb07_1_4_FL_31266.txt


title: Follicular Lymphoma (FL_22092)

description:
FL_22092
Raw data file:
US22502553_251485032194_S01_GE2-v5_95_Feb07_1_2_FL_22092.txt


title: Follicular Lymphoma (FL_11873.2)

description:
FL_11873.2
Raw data file:
US22502553_251485032195_S01_GE2-v5_95_Feb07_1_1_FL_11873.2.txt


title: Follicular Lymphoma (FL_22588)

description:
FL_22588
Raw data file:
US22502553_251485032195_S01_GE2-v5_95_Feb07_1_2_FL_22588.txt


title: Follicular Lymphoma (FL_11094)

description:
FL_11094
Raw data file:
US22502553_251485032196_S01_GE2-v5_95_Feb07_1_3_FL_11094.txt


title: Follicular Lymphoma (FL_20426)

description:
FL_20426
Raw data file:
US22502553_251485032194_S01_GE2-v5_95_Feb07_1_3_FL_20426.txt


title: Follicular Lymphoma (FL_1013)

description:
FL_1013
Raw data file:
US22502553_251485032196_S01_GE2-v5_95_Feb07_1_2_FL_1013.txt


title: MM473


title: MM466


title: MM485


title: Follicular Lymphoma (FL_918.1)

description:
FL_918.1
Raw data file:
US22502553_251485032195_S01_GE2-v5_95_Feb07_1_4_FL_918.1.txt


title: MM603


title: MM426


title: MM622


title: MM648


title: MM537


title: MM595


title: MM540


title: MM548


title: MM200


title: D29


title: MELA_1_replicate_1

source_name: Primary Melanocyte Pool

value: Primary Melanocyte


title: MELB_1_replicate_1


title: HT144


title: MM415


title: MM229


title: MM370


title: D40


title: MM386


title: MELA_2_replicate_2


title: D32


title: D41


title: D22


title: D36


title: MM253


title: MM329


title: MELB_2_replicate_2


title: D35


title: D24


title: D28


title: D25


title: MM127


title: D17


title: D14


title: D20


title: D08


title: D05


title: A13


title: D01


title: D04


title: D10


title: A15


title: A04


title: CJM

value: CJM


title: A06


title: A02_2_replicate_2


title: D11


title: C-32


title: AF6


title: A02_1_replicate_1


title: BR6_G17_240min_R2

city: Trondheim

first: Arnar

last: Flatberg

address: Postboks 8905

department: Department of Cancer Research and Molecular Medicine

country: Norway

institute: Norwegian University of Science and Technology

description: AR42J gastrin response

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.4.0). It was log2 transformed and quantile normalized.

source_name: AR42J cells, gastrin, 240 min

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

tag: batch

tag: stimuli

value: gastrin

tag: technical replicate

value: yes


title: BR5_G17_240min

description: AR42J gastrin response

value: no


title: BR6_CHXandG17_240min_R2

description: AR42J gastrin response

source_name: AR42J cells, gastrin+chx, 240 min

value: gastrin, chx


title: BR6_Un_240min

description: AR42J gastrin response

source_name: AR42J cells, control, 240 min


title: BR6_G17_240min

description: AR42J gastrin response


title: BR5_Un_240min

description: AR42J gastrin response


title: BR5_CHXandG17_240min

description: AR42J gastrin response


title: BR4_Un_240min

description: AR42J gastrin response


title: BR5_G17_60min

description: AR42J gastrin response

source_name: AR42J cells, gastrin, 60 min


title: BR6_CHX_240min

description: AR42J gastrin response

source_name: AR42J cells, chx, 240 min

value: chx


title: BR6_CHXandG17_240min

description: AR42J gastrin response


title: BR5_CHX_240min

description: AR42J gastrin response


title: BR4_CHX_240min

description: AR42J gastrin response


title: BR4_G17_240min

description: AR42J gastrin response


title: BR5_Un_60min

description: AR42J gastrin response

source_name: AR42J cells, control, 60 min


title: BR4_CHXandG17_240min

description: AR42J gastrin response


title: BR4_Un_60min

description: AR42J gastrin response


title: BR4_G17_60min

description: AR42J gastrin response


title: BR5_Un_360min_42

description: AR42J gastrin response

source_name: AR42J cells, control, 360 min


title: BR5_CHXandG17_360min_38

description: AR42J gastrin response

source_name: AR42J cells, gastrin+chx, 360 min


title: BR5_CHXandG17_120min_26

description: AR42J gastrin response

source_name: AR42J cells, gastrin+chx, 120 min


title: BR5_ G17_360min_41

description: AR42J gastrin response

source_name: AR42J cells, gastrin, 360 min


title: BR5_ G17_120min_29

description: AR42J gastrin response

source_name: AR42J cells, gastrin, 120 min


title: BR5_Un_120min_30

description: AR42J gastrin response

source_name: AR42J cells, control, 120 min


title: BR5_CHX _120min_27

description: AR42J gastrin response

source_name: AR42J cells, chx, 120 min


title: BR5_CHX _360min_39

description: AR42J gastrin response

source_name: AR42J cells, chx, 360 min


title: BR5_CHX _60min_21

description: AR42J gastrin response

source_name: AR42J cells, chx, 60 min


title: BR4_Un_360min_42

description: AR42J gastrin response


title: BR5_Un_60min_24

description: AR42J gastrin response


title: BR4_Un_60min_24

description: AR42J gastrin response


title: BR4_ G17_360min_41

description: AR42J gastrin response


title: BR4_ G17_120min_29

description: AR42J gastrin response


title: BR5_CHXandG17_60min_20

description: AR42J gastrin response

source_name: AR42J cells, gastrin+chx, 60 min


title: BR4_CHX _60min_21

description: AR42J gastrin response


title: BR4_CHX _360min_39

description: AR42J gastrin response


title: BR4_CHXandG17_360min_38

description: AR42J gastrin response


title: BR4_ G17_60min_23

description: AR42J gastrin response


title: BR4_Un_120min_30

description: AR42J gastrin response


title: BR4_CHXandG17_120min_26

description: AR42J gastrin response


title: BR4_CHXandG17_60min_20

description: AR42J gastrin response


title: BR5_ G17_60min_23

description: AR42J gastrin response


title: BR4_CHX _120min_27

description: AR42J gastrin response


title: BR3_Un_720min_22

description: AR42J gastrin response

source_name: AR42J cells, gastrin, 720 min


title: BR1_Un_840min_24

description: AR42J gastrin response

source_name: AR42J cells, control, 840 min


title: BR3_G17_840min_23

description: AR42J gastrin response

source_name: AR42J cells, gastrin, 840 min


title: BR3_Un_600min_20

description: AR42J gastrin response

source_name: AR42J cells, control, 600 min


title: BR3_Un_840min_24

description: AR42J gastrin response


title: BR3_Un_480min_18

description: AR42J gastrin response

source_name: AR42J cells, control, 480 min


title: BR3_G17_600min_19

description: AR42J gastrin response

source_name: AR42J cells, gastrin, 600 min


title: BR3_G17_720min_21

description: AR42J gastrin response

source_name: AR42J cells, control, 720 min


title: BR3_G17_240min_13

description: AR42J gastrin response

source_name: AR42J cells, gastrin, 240 min


title: BR3_Un_360min_16

description: AR42J gastrin response

source_name: AR42J cells, control, 360 min


title: BR3_G17_120min_11

description: AR42J gastrin response


title: BR3_Un_90min_10

description: AR42J gastrin response

source_name: AR42J cells, control, 90 min


title: BR3_Un_240min_14

description: AR42J gastrin response

source_name: AR42J cells, control, 240 min


title: BR3_Un_30min_6

description: AR42J gastrin response

source_name: AR42J cells, control, 30 min


title: BR3_G17_90min_9

description: AR42J gastrin response

source_name: AR42J cells, gastrin, 90 min


title: BR3_Un_60min_8

description: AR42J gastrin response

source_name: AR42J cells, control, 60 min


title: BR3_G17_480min_17

description: AR42J gastrin response

source_name: AR42J cells, gastrin, 480 min


title: BR3_Un_120min_12

description: AR42J gastrin response

source_name: AR42J cells, control, 120 min


title: BR3_G17_15min_3

description: AR42J gastrin response

source_name: AR42J cells, gastrin, 15 min


title: BR3_Un_15min_4

description: AR42J gastrin response

source_name: AR42J cells, control, 15 min


title: BR3_G17_60min_7

description: AR42J gastrin response

source_name: AR42J cells, gastrin, 60 min


title: BR3_G17_360min_15

description: AR42J gastrin response

source_name: AR42J cells, gastrin,360 min


title: BR3_G17_30min_5

description: AR42J gastrin response

source_name: AR42J cells, gastrin, 30 min


title: BR3_Un_0min_1

description: AR42J gastrin response

source_name: AR42J cells, control, 0 min


title: BR2_G17_840min_23

description: AR42J gastrin response

source_name: AR42J cells, gastrin, 840 min


title: BR2_Un_720min_22

description: AR42J gastrin response

source_name: AR42J cells, control, 720 min


title: BR1-G17_840min_23

description: AR42J gastrin response


title: BR2_G17_720min_21

description: AR42J gastrin response

source_name: AR42J cells, gastrin, 720 min


title: BR2_Un_600min_20

description: AR42J gastrin response

source_name: AR42J cells, control, 600 min


title: BR2_Un_840min_24

description: AR42J gastrin response

source_name: AR42J cells, control, 840 min


title: BR2_Un_480min_18

description: AR42J gastrin response

source_name: AR42J cells, control, 480 min


title: BR2_G17_240min_13

description: AR42J gastrin response

source_name: AR42J cells, gastrin, 240 min


title: BR2_G17_600min_19

description: AR42J gastrin response

source_name: AR42J cells, gastrin, 600 min


title: BR2_Un_360min_16

description: AR42J gastrin response

source_name: AR42J cells, control, 360 min


title: BR2_G17_480min_17

description: AR42J gastrin response

source_name: AR42J cells, gastrin, 480 min


title: BR2_Un_120min_12

description: AR42J gastrin response

source_name: AR42J cells, control, 120 min


title: BR2_G17_360min_15

description: AR42J gastrin response

source_name: AR42J cells, gastrin, 360 min


title: BR2_G17_120min_11

description: AR42J gastrin response

source_name: AR42J cells, gastrin, 120 min


title: BR2_Un_90min_10

description: AR42J gastrin response

source_name: AR42J cells, control, 90 min


title: BR2_Un_30min_6

description: AR42J gastrin response

source_name: AR42J cells, control, 30 min


title: BR2_Un_240min_14

description: AR42J gastrin response

source_name: AR42J cells, control, 240 min


title: BR2_G17_90min_9

description: AR42J gastrin response

source_name: AR42J cells, gastrin, 90 min


title: BR2_Un_60min_8

description: AR42J gastrin response

source_name: AR42J cells, control, 60 min


title: BR2_G17_30min_5

description: AR42J gastrin response

source_name: AR42J cells, gastrin, 30 min


title: BR2_G17_15min_3

description: AR42J gastrin response

source_name: AR42J cells, gastrin, 15 min


title: BR2_Un_15min_4

description: AR42J gastrin response

source_name: AR42J cells, control, 15 min


title: BR2_Un_0min_1

description: AR42J gastrin response

source_name: AR42J cells, control, 0 min


title: JB0535N_MOMA3

description: Genomic DNA was first digested with MspI and ligated with adaptors; for ch1 the sample was then subjected to McrBC treatment while mock treatment for ch2, both followed by PCR amplification. Then a dye (label) swap was performed on the split sample. Additional raw files for each labeliing are provided as .ftr files.

hyb_protocol: The primary restriction endonuclease used is MspI. After the digestion the following linkers were ligated: MspI24mer CAGCATCGAGACTGAACGCAGCAG, and MspI12mer CGCTGCTGCGTT. The 12 mer is not phosphorylated and does not ligate. After ligation the material is cleaned by phenol chloroform, precipitated, centrifuged, and resuspended. The material is divided in two, half being digested by the endonuclease McrBC and the other half being mock digested according to specification by New England Biolabs. The digestion time is 3 hours. As few as four 250-μL tubes were used for each sample pair for amplification of the representation in a 100ul volume reaction.  The cycle conditions were 95°C for 1 min, 72°C for 3 min, for 15 cycles, followed by a 10-min extension at 72°C. The contents of the tubes for each pair were pooled when completed. Representations were cleaned by phenol-chloroform extraction, precipitated, resuspended, and the concentration determined. Representations were run on a gel to check for content, the McrBC digested representation being approximately 100-150bp shorter on average than the mock. DNA was labeled as described with minor changes (Lucito, Healy et al. 2003). Briefly, 2μg of DNA template was placed (dissolved in TE at pH 8) in a 0.2-mL PCR tube. 5 μL of random nanomers (Sigma Genosys) were added brought up to 25 μL with dH2O, and mixed. The tubes were placed in Tetrad at 100°C for 5 min, then on ice for 5 min.  To this 5 μL of NEB Buffer2, 5 μL of dNTPs (0.6nm dCTP, 1.2nm dATP, dTTP, dGTP), 5 μL of label (Cy3-dCTP or Cy5-dCTP) from GE Healthcare, 2 μL of NEB Klenow fragment, and 2 μL dH2O was added. Procedures for hybridization and washing were followed as reported previously (As previously reported Chen, S. et. al. Cancer Biol Ther. 2008 Nov;7(11):1793-802. PMID: 18836286 ) with the exception that the oven temperature for hybridization was increased to 50°C.

scan_protocol: Microarray Images were scanned on GenePix 4000B scanner and data extracted using Nimblescan software (Nimblegen Systems Inc).

data_processing: For each probe, the geometric mean of the ratios (GeoMeanRatio) of McrBc and control treated samples were then calculated for each experiment and its associated dye swap. The GeoMeanRatios of all the samples in a dataset were then normalized using quantile normalization method (Bolstad, B.M., Irizarry, R.A., Astrand, M. and Speed, T.P. (2003) Bioinformatics, 19, 185-193).

source_name: Ovarian Normal

label_protocol: Take 5ug of DNA template and place in a 0.2mL PCR tube and add 5uL of primer solution and bring volume up to 40uL with diH20, mix gently and quickly spin. Then place the tubes in thermal cycler at 100 C for 5 minutes, quickly spin and immediately place on ice for 5 minutes. After this add 6uL of Klenow Buffer, 4uL Cy3-dCTP and 4uL Cy5-dCTP, 2uL klenow fragment, 6uL dNTPs and 2uL diH2O in a total volume of 60uL. Mix by pipetting, quickly spin and incubate at 37 C for 2 hours in thermal cycler. After the incubation combine the labeled samples into one Eppendorf tube and add 50uL Human Cot-I DNA, 10uL yeast tRNA and 200uL low TE. Load this into a Microcon YM-30 filter and spin at 12,600 rcf for 10 minutes. Discard deep purple flow through and add 450uL low TE and spin again. Repeat this until flow through is clear and then invert filter into new tube and spin for 2 minutes. Transfer the sample into a new 0.2mL PCR tube and adjust volume to 10uL with low TE.

extract_protocol: DNA was extracted by first homogenizing tissue in lysis buffer and incubating for 60 minutes followed by 3 phenol extractions and precipitation.

value: ovarian normal

tag: treatment

value: McrBC restriction enzyme

value: untreated, Mock digestion control


title: JB0526N_MOMA3


title: JB0539N_MOMA3


title: BR2_G17_60min_7

description: AR42J gastrin response

source_name: AR42J cells, gastrin, 60 min


title: JB0533N_MOMA3


title: JB0795_ROMA

description: CBS Segmentation Data provided as a supplementary file.

hyb_protocol: Hybridizations consisted of 35 uL of hybridization solution (37% formamide, 4x SSC, 0.1%SDS, and labeled DNA). Samples were denatured in an MJ Research Tetrad (Bio-Rad, Hercules, CA) at 95 degrees C for 5 min, and then pre-annealed at 37 degrees C for no more than 30 min. The solution was then applied to the microarray and hybridized under a coverslip in an oven at 42 degrees C for 14 to 16 h. Thereafter, slides were washed 1 min in 0.2% SDS/0.2x SSC, 30 sec in 0.2x SSC, and 30 sec in 0.05x SSC. Slides were dried by centrifugation and scanned immediately (As previously reported Chen, S. et. al. Cancer Biol Ther. 2008 Nov;7(11):1793-802. PMID: 18836286 ).

scan_protocol: Scanned on an Axon GenePix 4000B scanner using a pixel size of 5 um.  Microarrays were scanned and gridded using GenePix Pro 4.0 software (MDS Analytical Technologies, Toronto, Canada) and data were imported into S-Plus 2000 analysis software (Insightful, Seattle, WA).

data_processing:
The normalized log ratios from each color reversal experiment were averaged for each segmentation. We then applied the CBS algorithm to this data. The CBS segmentation method is the circular binary segmentation algorithm as described in "Circular binary segmentation for the analysis of array-based DNA copy number data.", Olshen AB, Venkatraman ES, Lucito R, Wigler M., Biostatistics. 2004 Oct;5:557-72 (PMID:15475419).
Seg.mean.txt is the average of normalized log ratios for each experiment.
chrom: Chromosome
loc.start: Chromosome Segment Start Location (1000kb)
loc.end: Chromoseom Segment End Location (1000kb)
num.mark: Number of Markers in the Segment
seg.mean: The Segment Mean

label_protocol: Briefly, complexity-reduced representations consisting of small (200-1200 bp) fragments were amplified by adapter-mediated PCR of genomic DNA. DNA samples (2 ug) were labeled either with Cy5-dCTP or Cy3-dCTP using Amersham-Pharmacia MegaPrime labeling kit (Amersham Biosciences, Piscataway, NJ), and competitively hybridized to each other on the same slide. (As previously reported Chen, S. et. al. Cancer Biol Ther. 2008 Nov;7(11):1793-802. PMID: 18836286 ).

tag: primary cells

value: Fibroblasts

value: male

value: normal

value: Ovarian tumor


title: JB0564N_MOMA3

value: female


title: JB0632_MOMA3

source_name: Ovarian Tumor

value: ovarian tumor


title: JB0792_ROMA


title: JB0794_ROMA


title: JB0743_MOMA3


title: JB0747_MOMA3


title: MJ013_MOMA3


title: JB0537N_MOMA3


title: JB0789_ROMA


title: MJ001_MOMA3


title: JB0745_MOMA3


title: JB0793_ROMA


title: JB0485_MOMA3


title: JB0620_MOMA3


title: JB0634_MOMA3


title: JB0785_ROMA


title: JB0788_ROMA


title: JB0529N_MOMA3


title: JB0791_ROMA


title: JB0787_ROMA


title: JB0784_ROMA


title: JB0483_MOMA3


title: JB0783_ROMA


title: JB0782_ROMA


title: JB0664_MOMA3


title: JB0786_ROMA


title: JB0781_ROMA


title: JB0752_MOMA3


title: JB0737_ROMA


title: Lean (sample 1095, Cy5) VS Fat (sample 1076, Cy3)

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

description: Direct comparison of mouse liver samples from Lean (sample 1095, Cy5) and Fat lines (sample 1076, Cy3)

hyb_protocol: Channel 1 sample was mixed with channel 2 sample hybridization buffer was added (final concentration was 3xSSC, 0.2% SDS) and samples were denatured. Using LifterSlip cover glasses (Erie Scientific Company, Portsmouth, NH, USA) samples were hybridized for 16h at 65ºC in a water bath using humidified hybridization chambers (HybChambers, GeneMachines, San Carlos, CA, USA). Prior hybridizations Steroltalk v2 slides were pre-hybridized for 1 hour at 42ºC in 5xSSC, 0.1%SDS and 1%BSA, then washed at room temperature for 5 min in 2xSSC and 0.1%SDS, 3 min in 0.2xSSC and 2 min in MilliQ water and dried by centrifugation. After hybridization slides were washed at room temperature for 5 min in 2xSSC and 0.5%SDS, 5 min in 0.5xSSC, 5 min in 0.05xSSC, and then dried using vacuum centrifuge.

scan_protocol: Arrays scanned on an Tecan LS200 scanner; images analyzed using MediaCybernetics Array-Pro Analyzer software.

data_processing: Raw data deposited to BASE (BioArray Software Environment) and normalized using OWNormalize, a widget for explorative normalization of focused microarrays, implemented within Orange, a component based machine learning library for Python developed at Laboratory of Artificial Intelligence, Faculty of Computer and Information Science, University of Ljubljana, Slovenia. LOWESS fit to spike in control RNAs according to their average intensity. For normalization, two types of spike in controls were used: custom-made Firefly luciferase and commercial Lucidea Universal ScoreCard.

organism: Mus musculus

source_name: Liver tissue from Lean mouse line, sample 1095

label_protocol: Total RNA from 10 Lean and Fat line animals, respectively, was individually labeled using Cy3 and Cy5 dye. To 20 μg of Lean and Fat line total RNA sample we added spike of control RNAs: 250 pg of Firefly Luciferase mRNA (Promega, Madison, WI, USA), and 0.5 μL of either test or reference spike mix from Lucidea Universal Scorecard kit (Amersham Biosciences, GE Healthcare UK limited, Little Chalfont, UK). mRNA was reverse transcribed to amino-allyl cDNA using 2.5 μg of Oligo dT (Invitrogen, Carlsbad, CA, USA), 400U of SuperScriptTM III Reverse Transcriptase (Invitrogen, Carlsbad, CA, USA) and 1μL of 10mM amino-allyl dUTP (Sigma, St Louis, MI, USA) according to the manufacturer’s protocol. Reaction was stopped after 2 hours by addition of 10 μL of 0.5 M EDTA and of 1M NaOH and further incubated at 65ºC for 15 min. 10 μL of 1 M HCl was added and cDNA was purified using MinElute PCR Purification Kit (Qiagen GmBH, Hilden, D) according to manufacturer’s protocol with exception of using a phosphate buffer (5mM KPO4 pH 8.5 in 80% ethanol) for washing step and MilliQ water for elution. Purified amino-allyl cDNA was dried and resuspended in 4.5 μL of 0.2 M Na2CO3 (pH 9.0) and 4.5 μL of cyanin-3 or cyanin-5 dye in DMSO (Amersham Biosciences, GE Healthcare UK limited, Little Chalfont, UK). Labeling reaction was incubated at room temperature for two hours. Next we added 35 μL of 0.1 M Na acetate (pH 5.2) and purified reaction using MinElute PCR Purification Kit (Qiagen GmBH, Hilden, D) according to manufacturer’s protocol. Labeled cDNA was eluted in water and 1 μL was used for analyses using ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, Delaware, USA).

growth_protocol: Lean and Fat mouse lines were developed from the same base population upon long-term (over 60 generations) divergent selection on low or high body fat% [Bunger L, Hill WG: Inbred lines of mice derived from long-term divergent selection on fat content and body weight. Mamm Genome 1999, 10(6):645-648].

extract_protocol: Total RNA was isolated from mouse livers using TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions. The RNA was precipitated using ethanol.

tag: tissue

value: Liver

tag: sample id

tag: raw data label

value: {Smpl}

tag: phenotype

value: lean

tag: genetic background

value: CBA, JU, and CFLP

source_name: Liver tissue from Fat mouse line, sample 1076

value: {Ref}

value: high body fat


title: JB0754_MOMA3

tag: gender


title: JB0750_MOMA3


title: JB0738_ROMA


title: JB0734_ROMA


title: JB0495_MOMA3


title: JB0733_ROMA


title: Lean (sample 1437, Cy5) VS Fat (sample 1336, Cy3)

description: Direct comparison of mouse liver samples from Lean (sample 1437, Cy5) and Fat lines (sample 1336, Cy3)

source_name: Liver tissue from Lean mouse line, sample 1437

source_name: Liver tissue from Fat mouse line, sample 1336


title: JB0481_MOMA3


title: Lean (sample 1876, Cy5) VS Fat (sample 1861, Cy3)

description: Direct comparison of mouse liver samples from Lean (sample 1876, Cy5) and Fat lines (sample 1861, Cy3)

source_name: Liver tissue from Lean mouse line, sample 1876

source_name: Liver tissue from Fat mouse line, sample 1861


title: JB0493_MOMA3


title: JB0736_ROMA


title: JB0728_ROMA


title: Lean (sample 2777, Cy5) VS Fat (sample 2883, Cy3)

description: Direct comparison of mouse liver samples from Lean (sample 2777, Cy5) and Fat lines (sample 2883, Cy3)

source_name: Liver tissue from Lean mouse line, sample 2777

source_name: Liver tissue from Fat mouse line, sample 2883


title: JB0732_ROMA


title: JB0489_MOMA3


title: JB0618_MOMA3


title: JB0656_MOMA3


title: JB0735_ROMA


title: JB0491_MOMA3


title: JB0487_MOMA3


title: Lean (sample 2800, Cy5) VS Fat (sample 2915, Cy3)

description: Direct comparison of mouse liver samples from Lean (sample 2800, Cy5) and Fat lines (sample 2915, Cy3)

source_name: Liver tissue from Lean mouse line, sample 2800

source_name: Liver tissue from Fat mouse line, sample 2915


title: JB0654_MOMA3


title: JB0731_ROMA


title: JB0459_MOMA3


title: JB0726_ROMA


title: Lean (sample 3462, Cy5) VS Fat (sample 3556, Cy3)

description: Direct comparison of mouse liver samples from Lean (sample 3462, Cy5) and Fat lines (sample 3556, Cy3)

source_name: Liver tissue from Lean mouse line, sample 3462

source_name: Liver tissue from Fat mouse line, sample 3556


title: JB0724_ROMA


title: JB0727_ROMA


title: JB0725_ROMA


title: JB0497_MOMA3


title: JB0723_ROMA


title: Lean (sample 3301, Cy5) VS Fat (sample 3400, Cy3)

description: Direct comparison of mouse liver samples from Lean (sample 3301, Cy5) and Fat lines (sample 3400, Cy3)

source_name: Liver tissue from Lean mouse line, sample 3301

source_name: Liver tissue from Fat mouse line, sample 3400


title: 15-2KO#1 [Lung study]

city: Kyoto

first: Shinya

last: Yamanaka

address: 53 Kawahara-machi, Shogoin, Sakyo-ku

country: Japan

institute: Center for iPS Cell Research and Applicaton (CiRA), Kyoto University

description:
Gene expression of E18.5 ECAT15-2KO lung.
Raw data file: 4838#5KO.txt
The mouse strain used in our study is complicated mixture of several strains.
In detail, the chimeric mice were generated from 129Sv ES cells. Then the germ line transmitted F1 mouse were obtained from the chimeric mice and C57/BL6 intercross. The F1 mice were mated at least two times with C57/BL6, and one time with Cre or FLPe expressing transgenic mice, whose background is unknown.

hyb_protocol: Standard Agilent protocol

scan_protocol: Standard Agilent protocol

data_processing: GeneSpring GX. Normalized to Quantile.

source_name: ECAT15-2KO lung at E18.5 #1

label_protocol: Standard Agilent protocol

extract_protocol: Frozen tissues were quickly homogenized in Trizol reagent.Total RNA was isolated according to the manufacturer's instruction.

treatment_protocol: Embryos from 15-1+/Flox, 15-2+/- intercorss at E18.5 were digested, and their lungs were removed and frozen.

tag: genotype of ecat15-1

tag: genotype of ecat15-2


title: 15-2KO#3 [Lung study]

description:
Gene expression of E18.5 ECAT15-2KO lung.
Raw data file: 4938#1KO.txt
The mouse strain used in our study is complicated mixture of several strains.
In detail, the chimeric mice were generated from 129Sv ES cells. Then the germ line transmitted F1 mouse were obtained from the chimeric mice and C57/BL6 intercross. The F1 mice were mated at least two times with C57/BL6, and one time with Cre or FLPe expressing transgenic mice, whose background is unknown.

source_name: ECAT15-2KO lung at E18.5 #3


title: 15-2KO#2 [Lung study]

description:
Gene expression of E18.5 ECAT15-2KO lung.
Raw data file: 4838#7KO.txt
The mouse strain used in our study is complicated mixture of several strains.
In detail, the chimeric mice were generated from 129Sv ES cells. Then the germ line transmitted F1 mouse were obtained from the chimeric mice and C57/BL6 intercross. The F1 mice were mated at least two times with C57/BL6, and one time with Cre or FLPe expressing transgenic mice, whose background is unknown.

source_name: ECAT15-2KO lung at E18.5 #2


title: JB0471_MOMA3

source_name: Ovarian Tumor


title: JB0614_MOMA3


title: JB0722_ROMA


title: JB0473_MOMA3


title: JB0477_MOMA3


title: WT#3 [Lung study]

description:
Gene expression of E18.5 wild type lung.
Raw data file: 4938#5WT.txt
The mouse strain used in our study is complicated mixture of several strains.
In detail, the chimeric mice were generated from 129Sv ES cells. Then the germ line transmitted F1 mouse were obtained from the chimeric mice and C57/BL6 intercross. The F1 mice were mated at least two times with C57/BL6, and one time with Cre or FLPe expressing transgenic mice, whose background is unknown.

source_name: WT lung at E18.5 #3


title: Lean (sample 3438, Cy5) VS Fat (sample 3380, Cy3)

description: Direct comparison of mouse liver samples from Lean (sample 3438, Cy5) and Fat lines (sample 3380, Cy3)

source_name: Liver tissue from Lean mouse line, sample 3438

source_name: Liver tissue from Fat mouse line, sample 3380


title: Lean (sample 3476, Cy5) VS Fat (sample 3540, Cy3)

description: Direct comparison of mouse liver samples from Lean (sample 3476, Cy5) and Fat lines (sample 3540, Cy3)

source_name: Liver tissue from Lean mouse line, sample 3476

source_name: Liver tissue from Fat mouse line, sample 3540


title: Lean (sample 1095, Cy3) VS Fat (sample 1076, Cy5)

description: Direct comparison of mouse liver samples from Lean (sample 1095, Cy3) and Fat lines (sample 1076, Cy5)

source_name: Liver tissue from Lean mouse line, sample 1095

source_name: Liver tissue from Fat mouse line, sample 1076


title: WT#2 [Lung study]

description:
Gene expression of E18.5 wild type lung.
Raw data file: 4839#6WT.txt
The mouse strain used in our study is complicated mixture of several strains.
In detail, the chimeric mice were generated from 129Sv ES cells. Then the germ line transmitted F1 mouse were obtained from the chimeric mice and C57/BL6 intercross. The F1 mice were mated at least two times with C57/BL6, and one time with Cre or FLPe expressing transgenic mice, whose background is unknown.

source_name: WT lung at E18.5 #2


title: JB0475_MOMA3

description: Genomic DNA was first digested with MspI and ligated with adaptors; for ch1 the sample was then subjected to McrBC treatment while mock treatment for ch2, both followed by PCR amplification. Then a dye (label) swap was performed on the split sample. Additional raw files for each labeliing are provided as .ftr files.


title: JB0718_ROMA

description: CBS Segmentation Data provided as a supplementary file.


title: Lean (sample 1437, Cy3) VS Fat (sample 1336, Cy5)

description: Direct comparison of mouse liver samples from Lean (sample 1437, Cy3) and Fat lines (sample 1336, Cy5)

source_name: Liver tissue from Lean mouse line, sample 1437

source_name: Liver tissue from Fat mouse line, sample 1336


title: JB0721_ROMA


title: 15-2KO_Flag15-2#2 [KOrescue study]

description:
Flag tagged ECAT15-2 transcudted ECAT15-2 deficient ESC, derived from the blastocyst of mother #875
Raw data file: 875#2_F15-2.txt
The mouse strain used in our study is complicated mixture of several strains.
In detail, the chimeric mice were generated from 129Sv ES cells. Then the germ line transmitted F1 mouse were obtained from the chimeric mice and C57/BL6 intercross. The F1 mice were mated at least two times with C57/BL6, and one time with Cre or FLPe expressing transgenic mice, whose background is unknown.

data_processing: GeneSpring GX. Signals were normalized to Quantile.

source_name: 15-2KO 875#2 Flag15-2 transduction

growth_protocol: ESCs were cultivated with 15% FCS ES medium supplemented with LIF on gelatin coated plate, passage by Trypsin

extract_protocol: Total RNA was isolated by Trizol according to the manufacturer's instruction.

treatment_protocol: Blastocysts from two pairs of 15-1+/CT, 15-2+/- intercorss were cultured in vitro, and the ESCs were were established. piggyBac-CAG-IP (mock) or piggyBac-CAG-Flag15-2-IP (Flag15-2) were introduced into the ECAT15-2 deficient ESCs.

tag: transduction


title: WT#1 [Lung study]

description:
Gene expression of E18.5 wild type lung.
Raw data file: 4839#5WT.txt
The mouse strain used in our study is complicated mixture of several strains.
In detail, the chimeric mice were generated from 129Sv ES cells. Then the germ line transmitted F1 mouse were obtained from the chimeric mice and C57/BL6 intercross. The F1 mice were mated at least two times with C57/BL6, and one time with Cre or FLPe expressing transgenic mice, whose background is unknown.

source_name: WT lung at E18.5 #1


title: JB0717_ROMA


title: JB0715_ROMA


title: Lean (sample 3462, Cy3) VS Fat (sample 3556, Cy5)

description: Direct comparison of mouse liver samples from Lean (sample 3462, Cy3) and Fat lines (sample 3556, Cy5)

source_name: Liver tissue from Lean mouse line, sample 3462

source_name: Liver tissue from Fat mouse line, sample 3556


title: Lean (sample 1876, Cy3) VS Fat (sample 1861, Cy5)

description: Direct comparison of mouse liver samples from Lean (sample 1876, Cy3) and Fat lines (sample 1861, Cy5)

source_name: Liver tissue from Lean mouse line, sample 1876

source_name: Liver tissue from Fat mouse line, sample 1861


title: JB0479_MOMA3

source_name: Ovarian Tumor


title: Lean (sample 3317, Cy3) VS Fat (sample 3039, Cy5)

description: Direct comparison of mouse liver samples from Lean (sample 3317, Cy3) and Fat lines (sample 3039, Cy5)

source_name: Liver tissue from Lean mouse line, sample 3317

source_name: Liver tissue from Fat mouse line, sample 3039


title: 15-2KO_mock#2 [KOrescue study]

description:
Mock transcudted ECAT15-2 deficient ESC, derived from the blastocyst of mother #875
Raw data file: 875#2_mock.txt
The mouse strain used in our study is complicated mixture of several strains.
In detail, the chimeric mice were generated from 129Sv ES cells. Then the germ line transmitted F1 mouse were obtained from the chimeric mice and C57/BL6 intercross. The F1 mice were mated at least two times with C57/BL6, and one time with Cre or FLPe expressing transgenic mice, whose background is unknown.

source_name: 15-2KO 875#2 mock transduction

value: Mock


title: JB0179_ROMA


title: Lean (sample 3301, Cy3) VS Fat (sample 3400, Cy5)

description: Direct comparison of mouse liver samples from Lean (sample 3301, Cy3) and Fat lines (sample 3400, Cy5)

source_name: Liver tissue from Lean mouse line, sample 3301

source_name: Liver tissue from Fat mouse line, sample 3400


title: 15-2KO_mock#1 [KOrescue study]

description:
Mock transcudted ECAT15-2 deficient ESC, derived from the blastocyst of mother #1046
Raw data file: 1046#3_mock.txt
The mouse strain used in our study is complicated mixture of several strains.
In detail, the chimeric mice were generated from 129Sv ES cells. Then the germ line transmitted F1 mouse were obtained from the chimeric mice and C57/BL6 intercross. The F1 mice were mated at least two times with C57/BL6, and one time with Cre or FLPe expressing transgenic mice, whose background is unknown.

source_name: 15-2KO 1046#3 mock transduction


title: WT#2 [KOrescue study]

description:
Wild type ESC derived from the blastocyst of mother #875
Raw data file: 875#5.txt
The mouse strain used in our study is complicated mixture of several strains.
In detail, the chimeric mice were generated from 129Sv ES cells. Then the germ line transmitted F1 mouse were obtained from the chimeric mice and C57/BL6 intercross. The F1 mice were mated at least two times with C57/BL6, and one time with Cre or FLPe expressing transgenic mice, whose background is unknown.

source_name: WT ESC 875#5


title: JB0662_MOMA3


title: JB0469_MOMA3


title: Lean (sample 3476, Cy3) VS Fat (sample 3540, Cy5)

description: Direct comparison of mouse liver samples from Lean (sample 3476, Cy3) and Fat lines (sample 3540, Cy5)

source_name: Liver tissue from Lean mouse line, sample 3476

source_name: Liver tissue from Fat mouse line, sample 3540


title: JB0467_MOMA3


title: SD Day 14 vs SD Day 0

city: Edmonton

first: Chelsea

last: Ju

state: Alberta

address: CW 405, Biological Sciences Centre

department: Biological Sciences

country: Canada

institute: University of Alberta

description: 4 biological replicates were used, and raw data file 'HA013-017.gpr' and 'HA013-015.gpr' were dye-swap [i.e. ch1 labeled with Alexa555 and ch2 with Alexa647].

hyb_protocol: Microarray slides were incubated for 2 hours at 65°C in pre-hybridization buffer (5 × SSC, 0.1% sodium dodecyl sulphate (SDS), 0.2 mg ml−1 bovine serum albumin (BSA), and 0.1 mg ml−1 herring sperm DNA) to prevent nonspecific binding.  Slides were washed twice with 0.1 × SSC, and twice with water at room temperature, and were then transferred to a water bath at 85°C for 90 seconds before drying by centrifugation for 2 minutes at 480 g in a bench top centrifuge (Eppendorf 5804). Alexa Fluor® 555 and Alexa Fluor® 647 labeled aRNA were denatured at 95°C for 2 minutes, cooled on ice and centrifuged. 51 µl of hybridization buffer (50% formamide, 5 × SSC, 0.1% SDS and 0.1 mg ml−1 herring sperm DNA) was preheated to 46°C, and added to the labeled aRNAs (referred as aRNA probes). The aRNA probes were kept at 46°C until applying to each slide.  Cover-slip (Erie Scientific Company, Portsmouth, NH, USA) was placed on each slide over the subarrays, and aRNA probes were added to one edge of the cover-slip, which allowed the probe to wick underneath it. The slides were put into the hybridization chambers (Corning, New York, NY, USA), with a drop of water being added to dedicated wells to maintain humidity, and incubated for 18 hours in a hybridization oven at 45°C. Cover-slips were then removed by floating the slides in a Coplin jar (Bel-Art Products Inc, Pequannock, NJ, USA) containing 2 × SSC and 0.5% SDS preheated to 45°C. The slides were incubated in the hybridization oven at 45°C for three periods of 15 minutes, with shaking every few minutes: once in 2 × SSC, 0.5% SDS, and twice in 0.5 × SSC, 0.1% SDS. The slides were then washed at room temperature twice with 0.1 × SSC for 1 minute and twice with water for 20 seconds before drying by centrifugation for 2 minutes at 480 g in Eppendorf 5804.

scan_protocol: Microarray images were obtained using a GenePix 4000B microarray scanner and analyzed with Genepix Pro 6.0 (Axon Instruments). Adaptive circles were used to indicate spots (spot diameter resize feature, 80 to 150%; composite pixel intensity, 300). After manual elimination of bad spots (highly irregular spot shape, dust, or salt particles), the median background intensity was subtracted from the mean spot intensity applying the local method (default option).

data_processing:
Within-array data normalization was first applied using print-tip loess detrending procedure, followed by between-array scale normalization to enforce the data having the same median-absolute-deviation across arrays from the same experiment. Taking the normalized data, linear models were fitted using duplicate correlation for each sequence. To reduce the false discovery rate, a nonspecific filtering was applied by removing invalid and low intensity sequences prior statistical analysis.  A moderated t-statistic, empirical Bayes statistic, was used to obtain p-values, and these p-values were further adjusted by Benjamini-Hochberg procedure.  A list of statistically significant differentially expressed (DE) sequences was selected by an adjusted p-value cut-off at 0.01, and this list was further filtered to include sequences with fold change greater than 1.5 or smaller than 0.67.
The VALUEs in the data table represent the averaged values of 4 biological replicates.

label: Alexa647, Alexa555

organism: Picea glauca

source_name: SD day 70

label_protocol: Two micrograms of total RNA was amplified with the amino allyl antisense RNA (aRNA) procedure (Superscript Indirect RNA Amplification System, Invitrogen). Five micrograms of aRNA was directly labeled using Alexa Fluor® 555 and/or 647 Dyes, (Invitrogen). Alexa fluor 647 conjugates virtually match those of the Cy5 dye, and spectra of the Alexa fluor 555 conjugates virtually match those of the Cy3 dye. Coupling efficiency was evaluated using the NanoDrop 1000 (Thermo Scientific).

growth_protocol: Seedlings were received from CFS, Quebec. Trees are surplus individuals from starting association population being created by N. Isabel, LFC-CFS. The two-years-old plants were grown using a complete randomized block design in controlled-environment chambers at 20°C and 50-60% humidity, with full illumination for 16 hours and 8 hours of dark.  At 6 to 8 weeks (46-58 days), part of the plant population was switched from long daylight photoperiod (16h) to short daylight photoperiod with 8 hours of light and 16 hours of dark for 18 to 25 weeks. A subset was subsequently transferred to low temperature at 2°C to 4°C for 3 to 4 weeks under short daylight photoperiod. During the long daylight photoperiod, plants were fertilized with 0.5 g/L of 20-20-20. After switching to short daylight photoperiod, 1.0 g/L of 15-30-15 fertilizations were applied for the first two weeks, 0.5 g/L of 20-20-20 from week 3 to week 8, and 0.5 g/L of 8-20-30 after week 8.

extract_protocol: Total RNA was extracted according to a modified procedure of Chang et al. 1993, a simple and efficient method for isolating RNA from pine trees [Plant Molecular Biology Reporter, 11(2):113-116].  Ground tissue was treated with 750 µL CTAB + b-ME extraction buffer, and incubated in water bath at 65°C for 10 minutes, vortexed periodically.  Each tube received 500 µl of chloroform:isoamyl alcohol (24:1 v/v), vortexed vigorously, and centrifuged at 14000 rpm for 15 minutes.  The aqueous phase was transferred to new tubes, and purified with chloroform:isoamyl alcohol again.  The volume of aqueous phase recovered after the second purification was determined, and mixed with an equal volume of LiCl-EDTA (7.5 M LiCl, 50mM EDTA) gently by inverting the tubes several times.  These tubes were placed at -20°C freezer for one hour, and centrifuged for 15 minutes at 14000 rpm at 4ºC. Pellet from each tube was collected, and washed with 800 µL of 80% ethanol, followed by a brief vortex.  Another 5 minutes of centrifugation at 14000 rpm at room temperature was applied to separate out the ethanol.  After drying the pellet by removing the supernatant, the pellet was resuspended in sterile water. NanoDrop 1000 (Thermo Scientific, ON, Canada) and 2100 Bioanalyzer (Agilent, ON, Canada) were used to determine the relative quality and quantity of the extracted RNA.

tag: time point

value: Day 70

tag: daylight

value: Short day

value: Lignified stems

tag: developmental stage

value: Plants were grown for the SD time course experiment. Lignified stems were harvested 70 days after the photoperiod was switched from LD to SD.

label: Alexa555, Alexa647

source_name: SD day 0

value: Day 0

value: Plants were grown for the SD time course experiment. Lignified stems were harvested right after switching the photoperiod from LD to SD.


title: Lean (sample 3438, Cy3) VS Fat (sample 3380, Cy5)

description: Direct comparison of mouse liver samples from Lean (sample 3438, Cy3) and Fat lines (sample 3380, Cy5)

source_name: Liver tissue from Lean mouse line, sample 3438

source_name: Liver tissue from Fat mouse line, sample 3380


title: 15-2KO#2 [KO study]

description:
ECAT15-2 deficient ESC derived from the blastocyst of mother #875
Raw data file: 875#2.txt
The mouse strain used in our study is complicated mixture of several strains.
In detail, the chimeric mice were generated from 129Sv ES cells. Then the germ line transmitted F1 mouse were obtained from the chimeric mice and C57/BL6 intercross. The F1 mice were mated at least two times with C57/BL6, and one time with Cre or FLPe expressing transgenic mice, whose background is unknown.

source_name: ECAT15-2 deficient ESC, 875#2

treatment_protocol: Blastocysts from 15-1+/CT, 15-2+/- intercorss were cultured in vitro, and the ESCs were were established.


title: JB0177_ROMA

value: Fibroblasts

value: male

tag: disease state

value: normal


title: WT#1 [KOrescue study]

description:
Wild type ESC derived from the blastocyst of mother #1046
Raw data file: 1046#1.txt
The mouse strain used in our study is complicated mixture of several strains.
In detail, the chimeric mice were generated from 129Sv ES cells. Then the germ line transmitted F1 mouse were obtained from the chimeric mice and C57/BL6 intercross. The F1 mice were mated at least two times with C57/BL6, and one time with Cre or FLPe expressing transgenic mice, whose background is unknown.


title: LT vs SD Day 0

source_name: LT

value: LT

value: Plants were grown for the SD time course experiment. About 18-23 weeks after switching the photoperiod from LD to SD, they were exposed to low temperature (2°C to 4°C) for another 3 to 4 weeks. Lignified stems were harvested after the low temperatures treatment.


title: JB0622_MOMA3

description: Genomic DNA was first digested with MspI and ligated with adaptors; for ch1 the sample was then subjected to McrBC treatment while mock treatment for ch2, both followed by PCR amplification. Then a dye (label) swap was performed on the split sample. Additional raw files for each labeliing are provided as .ftr files.

value: ovarian tumor

value: female

value: McrBC restriction enzyme

value: untreated, Mock digestion control


title: JB0178_ROMA

description: CBS Segmentation Data provided as a supplementary file.

value: Ovarian tumor


title: 15-2KO#1 [KO study]

description:
ECAT15-2 deficient ESC derived from the blastocyst of mother #1046
Raw data file: 1046#3.txt
The mouse strain used in our study is complicated mixture of several strains.
In detail, the chimeric mice were generated from 129Sv ES cells. Then the germ line transmitted F1 mouse were obtained from the chimeric mice and C57/BL6 intercross. The F1 mice were mated at least two times with C57/BL6, and one time with Cre or FLPe expressing transgenic mice, whose background is unknown.

source_name: ECAT15-2 deficient ESC, 1046#3


title: JB0465_MOMA3

source_name: Ovarian Tumor


title: JB0176_ROMA


title: SD Day 7 vs SD Day 0

source_name: SD day 14

value: Day 14

value: Plants were grown for the SD time course experiment. Lignified stems were harvested 14 days after the photoperiod was switched from LD to SD.


title: JB0716_ROMA


title: JB0463_MOMA3


title: WT#2 [KO study]

source_name: Wild type ESC, 875#5


title: JB0616_MOMA3


title: SD Day 3 vs SD Day 0

source_name: SD day 3

value: Day 3

value: Short day

value: Plants were grown for the SD time course experiment. Lignified stems were harvested 3 days after the photoperiod was switched from LD to SD.


title: WT#1 [KO study]

source_name: Wild type ESC, 1046#1


title: DMSO_control

city: Uppsala

first: Mårten

last: Fryknäs

address: Akademiska sjh ingång 61

department: Medical sciencies

country: Sweden

institute: Uppsala university

description: Gene expression data from MCF7 cells treated 0.1% DMSO for 6 hours.

hyb_protocol: Affymetrix GeneChip® expression arrays (Human Genome U133 Plus 2.0 Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm.

scan_protocol: According to the GeneChip® Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA) the arrays were then washed and stained using the Fluidics Station 450 and finally scanned using the GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

source_name: Breast cancer cell line MCF7

label_protocol: 2 micrograms of total RNA from each sample were used to prepare biotinylated fragmented cRNA according to the GeneChip® Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA).

extract_protocol: Extraction of total RNA was performed using Qiagen Rneasy minikit according to the manufacturer's instructions

treatment_protocol: MCF7 control cells treated with 0.1% DMSO for 6 hours.

value: DMSO

tag: cell line


title: JB0666_MOMA3


title: 15-2KO_Flag15-2#1 [KOrescue study]

description:
Flag tagged ECAT15-2 transcudted ECAT15-2 deficient ESC, derived from the blastocyst of mother #1046
Raw data file: 1046#3_F15-2.txt
The mouse strain used in our study is complicated mixture of several strains.
In detail, the chimeric mice were generated from 129Sv ES cells. Then the germ line transmitted F1 mouse were obtained from the chimeric mice and C57/BL6 intercross. The F1 mice were mated at least two times with C57/BL6, and one time with Cre or FLPe expressing transgenic mice, whose background is unknown.

source_name: 15-2KO 1046#3 Flag15-2 transduction


title: JB0652_MOMA3


title: b-AP15

description: Gene expression data from MCF7 cells treated with b-AP15 for 6 hours.

extract_protocol: Extraction of total RNA was performed using Qiagen Rneasy minikit according to the manufacturer's instructions.

treatment_protocol: MCF7 cells treated with 1 microM b-AP15 for 6 hours.


title: JB0658_MOMA3


title: JB0461_MOMA3


title: ID3 knockout mouse CD8+ T cells, pooled sample#4, exon-level

status: Public on Oct 16 2011

city: Budapest

first: Zoltan

last: Pos

address: 4 Nagyvarad ter

department: Dept. of Genetics, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

description:
ID3 KO- 4
Id3 KO-4_(MoGene-1_0-st-v1).CEL
mouse  ID3-/- CD8+ T cells, pooled sample derived from four mice, sample #4

hyb_protocol: Samples were hybridized to WT Human Gene 1.0 ST arrays using Affymetrix hybridization kit materials, according to the manufacturrer's instructions. Sample cocktails were heated at 99°C for 5 minutes, then 45°C for 5 minutes, centrifuged at max speed for 1 minute. Eighty ul of hyb solution was transferred to each array, and hybridized 17 hours at 45°C at 60rpm. Fluidics washing protocol used was FS450_0007.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data from .CEL files were imported into Partek Genomincs Suite using the RMA method. For gene level analyses, probeset level data were merged using the median probeset expression level.
probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.r4.mps

source_name: CD8+ T cells

label_protocol: WT expression kit (Ambion), WT Terminal Labeling Kit (Affymetrix), according to the manufatcturer's instructions

extract_protocol: RNEasy Micro kit (Qiagen), following manufatcturer's instructions

tag: strain

tag: genotype/variation

value: ID3 knockout

tag: batch

value: Array batch 2


title: ID3 wild type mouse CD8+ T cells, pooled sample#3, gene-level

description:
ID3 WT- 3
WT-8_(MoGene-1_0-st-v1).CEL
mouse  ID3+/+ CD8+ T cells, pooled sample derived from four mice, sample #3

value: Wild type


title: ID3 wild type mouse CD8+ T cells, pooled sample#4, exon-level

description:
ID3 WT- 4
WT-9_(MoGene-1_0-st-v1).CEL
mouse  ID3+/+ CD8+ T cells, pooled sample derived from four mice, sample #4


title: ID3 wild type mouse CD8+ T cells, pooled sample#2, gene-level

description:
ID3 WT- 2
WT-7_(MoGene-1_0-st-v1).CEL
mouse  ID3+/+ CD8+ T cells, pooled sample derived from four mice, sample #2


title: JB0630_MOMA3

tag: treatment


title: ID3 wild type mouse CD8+ T cells, pooled sample#3, exon-level


title: ID3 wild type mouse CD8+ T cells, pooled sample#4, gene-level


title: ID3 wild type mouse CD8+ T cells, pooled sample#2, exon-level


title: JB0174_ROMA

tag: primary cells

value: Fibroblasts

value: male

value: normal


title: ID3-transduced mouse CD8+ T cells, pooled sample #2

description: Pmel-1 mouse CD8+ T cells transduced with pMSGV1-ID32aThy1.1, pooled sample derived from four mice, sample #2

growth_protocol: On day zero, transgenic mouse Pmel-1 CD8+ cells expressing a TCR specific for gp100, were enriched with a MACS negative selection kit (Miltenyi Biotech). Cells were activated on plates coated with 2 g/ml anti-CD3 antibody and 1 g/ml of soluble anti-CD28 antibody in culture medium containing 10 ng/ml of IL-2 (Chiron Corporation).

treatment_protocol: Twenty four hours after activation, cells were transduced with pMSGV1-ID32aThy1.1 (ID3-transduced group) or pMSGV1-Thy1.1 (mock-transduced group) retrovirus following standard protocol. On day 5, 3e5 cells were transferred into C57BL/6 mice in conjunction with 2E7 pfu rvvhgp100 virus. Five days later, Thy1.1+CD8+ cells were sorted out from CD8+ enriched splenocytes and analyzed using microarrays.

value: Array batch 1


title: ID3 knockout mouse CD8+ T cells, pooled sample#4, gene-level


title: Mock-transduced mouse CD8+ T cells, pooled sample#3

description: Pmel-1 mouse CD8+ T cells transduced with pMSGV1-Thy1.1, pooled sample derived from four mice, sample #3

value: Mock-transduced


title: ID3 knockout mouse CD8+ T cells, pooled sample#3, exon-level

description:
ID3 KO- 3
Id3 KO-3_(MoGene-1_0-st-v1).CEL
mouse  ID3-/- CD8+ T cells, pooled sample derived from four mice, sample #3


title: ID3 knockout mouse CD8+ T cells, pooled sample#1, exon-level

description:
ID3 KO- 1
Id3 KO-1_(MoGene-1_0-st-v1).CEL
mouse  ID3-/- CD8+ T cells, pooled sample derived from four mice, sample #1


title: ID3-transduced mouse CD8+ T cells, pooled sample #3

description: Pmel-1 mouse CD8+ T cells transduced with pMSGV1-ID32aThy1.1, pooled sample derived from four mice, sample #3


title: ID3 wild type mouse CD8+ T cells, pooled sample#1, gene-level

description:
ID3 WT- 1
WT-6_(MoGene-1_0-st-v1).CEL
mouse  ID3+/+ CD8+ T cells, pooled sample derived from four mice, sample #1


title: ID3 wild type mouse CD8+ T cells, pooled sample#1, exon-level


title: Mock-transduced mouse CD8+ T cells, pooled sample#1

description: Pmel-1 mouse CD8+ T cells transduced with pMSGV1-Thy1.1, pooled sample derived from four mice, sample #1


title: ID3-transduced mouse CD8+ T cells, pooled sample #1

description: Pmel-1 mouse CD8+ T cells transduced with pMSGV1-ID32aThy1.1, pooled sample derived from four mice, sample #1


title: JB0660_MOMA3

description: Genomic DNA was first digested with MspI and ligated with adaptors; for ch1 the sample was then subjected to McrBC treatment while mock treatment for ch2, both followed by PCR amplification. Then a dye (label) swap was performed on the split sample. Additional raw files for each labeliing are provided as .ftr files.

value: ovarian tumor

value: female

value: McrBC restriction enzyme


title: ID3-transduced mouse CD8+ T cells, pooled sample #4

description: Pmel-1 mouse CD8+ T cells transduced with pMSGV1-ID32aThy1.1, pooled sample derived from four mice, sample #4


title: ID3 knockout mouse CD8+ T cells, pooled sample#2, gene-level

description:
ID3 KO- 2
Id3 KO-2_(MoGene-1_0-st-v1).CEL
mouse  ID3-/- CD8+ T cells, pooled sample derived from four mice, sample #2


title: ID3 knockout mouse CD8+ T cells, pooled sample#2, exon-level


title: Mock-transduced mouse CD8+ T cells, pooled sample#2

description: Pmel-1 mouse CD8+ T cells transduced with pMSGV1-Thy1.1, pooled sample derived from four mice, sample #2


title: ID3 knockout mouse CD8+ T cells, pooled sample#3, gene-level


title: JB0173_ROMA

description: CBS Segmentation Data provided as a supplementary file.

value: Ovarian tumor


title: JB0175_ROMA


title: JB0172_ROMA


title: Mock-transduced mouse CD8+ T cells, pooled sample#4

description: Pmel-1 mouse CD8+ T cells transduced with pMSGV1-Thy1.1, pooled sample derived from four mice, sample #4


title: Ganglion Poola

city: Caen

first: Nolwenn

middle: Marie

last: Dheilly

address: Esplanade de la Paix

department: Biological sciences

country: France

institute: Universite de caen

description: Ganglions Visceraux, Pool a

hyb_protocol: Hybridization was performed using the Agilent’s Gene expression hybridization kit as described by the purchaser with 1.65μg of aRNA samples labeled with Cy3. Subsequently, slides were washed with Gene expression wash buffer kit (Agilent Technologies), dried and stablilized in Stabilization and Drying solution (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565AA) using one color scan setting for 4x44k array slides (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 6.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. A matrix of gene expression levels was generated, where each row corresponds to a different gene and each column to one sample. The expression level of each gene was then logarithmically transformed, centered, and reduced, so that relative variations rather than absolute values were used for interpretation.

organism: Magallana gigas

source_name: Ganglions Visceraux, Pool a

label_protocol: 200 ng of total RNA was indirectly labeled with Cy3 using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions. Qiagen's RNeasy mini spin columns were used for purifying amplified RNA (aRNA) samples. After purification, aRNA amplification and dye incorporation rates were controlled using a ND-1000 spectrophotometer (Nanodrop Technologies) and were comprised respectively between 200 and 500 ng/μL (concentration) and between 20 and 50 pmol/μg aRNA (dye incorporation).

extract_protocol: Total RNA was extracted from the tissues with Tri-Reagent kit (Sigma) and subsequently cleaned with nucleospin RNA Clean-up (Macherev Nagel) isolation columns. After homogenisation of the N2 grinding powder in Tri-reagent and the first centrifugation, the aqueous phase was extracted to directly isolate the tota RNA on the column as described by the provide. RNA concentrations were measured using an ND-1000 spectrophotometer (Nanodrop Technologies) and RNA integrity was controlled on the Agilent bioanalyser using RNA 6000 nano kit (Agilent Technologies)

treatment_protocol: Oysters were sampled in july 2010 in Locamriaquer (brittany, France) and their tissues were immediately dissected, snap-frozen in liquid nitrogen, and stored at -80 degrees celcius for total RNA extraction

tag: individual

value: a

tag: tissue

value: Visceral Ganglion

tag: array


title: Ganglion Poolc

description: Ganglions Visceraux, Pool c

source_name: Ganglions Visceraux, Pool c

value: c


title: Hemocytes Poold

description: Hemocytes, Poold

source_name: Hemocytes, Poold

value: d

value: Hemocytes


title: Labial Palps ind6 F

description: Labial Palps, ind6, F

source_name: Labial Palps, ind6, F

tag: gender

value: F

value: Labial palps


title: Hemocytes Poolb

description: Hemocytes, Poolb

source_name: Hemocytes, Poolb

value: b


title: Ganglion Poolb

description: Ganglions Visceraux, Pool b

source_name: Ganglions Visceraux, Pool b


title: Ganglionx Poold

description: Ganglions Visceraux, Pool d

source_name: Ganglions Visceraux, Pool d


title: iPS cell abrogated iHAC2 F-N7

city: Yonago

first: Masaharu

last: Hiratsuka

state: Tottori

address: Nishicho 86

department: Molecular and Cellular Biology

institute: Tottori university, Faculty of Medicine

hyb_protocol: Cy3-labeled cRNA 1.65 g was combined with spiked in control probes specific for targets on the arrays and hybridized for 17 hours at 65 deg C to Agilent Mouse Whole Genome 44K Oligo Microarrays (Agilent Technologies, Palo Alto, CA). The arrays were washed with Agilent Gene Expression Washing Buffer 1 at room temperature and Agilent Gene Expression Washing Buffer 2 at 37 deg C. The slides were then air-dried.

scan_protocol: Arrays were scanned at a 5um resolution using an Agilent Microarray Scanner, G2505C.

data_processing: Signals were processed by 75% Percentile Shift Normalization in GeneSpring GX11.

source_name: mouse iPS

label_protocol: total RNA 500 ng was labeled with Cy3 using Quick Amp Labeling Kit (Agilent Technologies, Palo Alto, CA) according to manufacturer’s instructions. Qiagen RNeasy columns (Qiagen Valencia, CA) were used to purify the labeled cRNA.

extract_protocol: For each array sample, the RNA was prepared by using the RNeasy Midi Kit (Qiagen, Valencia, CA). Quality and quantity of the total RNA was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: cell type

value: mouse induced pluripotent stem cells abrogated iHAC2 vector after generation using iHAC2 vector

tag: genetic background


title: iPS cell abrogated iHAC2 F-B1


title: Labial Palps ind2 F

description: Labial Palps, ind2, F

source_name: Labial Palps, ind2, F


title: Labial Palps ind5 F

description: Labial Palps, ind5, F

source_name: Labial Palps, ind5, F


title: ID3 knockout mouse CD8+ T cells, pooled sample#1, gene-level

value: ID3 knockout

value: Array batch 2


title: iPS cell abrogated iHAC2 F-C5