title: Oli-neu cells, differentiated_rep2

description: Mouse immortalized oligodendrocyte precursor cell line Oli-neu received from Dr. J. Trotter (University of Mainz, Mainz, Germany) differentiated in Iacobas lab by 10 days treatment with 1 mM dibutyryl-cAMP (Sigma, St. Louis, MO)

source_name: Oli-neu cells, differentiated

treatment_protocol: Differentiation of Oli-neu was induced by switching the cells for 10 days to a medium containing 1 mM dibutyryl-cAMP (Sigma, St. Louis, MO) following the protocol described in Gokhan et al. J Neurosci, 2005.

value: Oli-neu cells, differentiated


title: Oli-neu cells, control_rep3

status: Public on Oct 27 2009

type: RNA

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

country: USA

institute: Prairie View A&M University

description: mouse immortalized oligodendrocyte precursor cell line oli-neu received from Dr. J. Trotter (university of mainz, mainz, germany) that have been obtained as described in jung et al. eur j neurosci (1995) 7: 1245–1265

hyb_protocol: The labeled cDNA was co-hybridized with a distinct Alexa Fluor®_555-aha-dUTP labeled biological replica overnight at 50°C on a Duke Operon Mouse 30K oligonucleotide array V4.0. Hybridization design ("multiple yellow" strategy) was described in Iacobas et al. Biochem Biophys Res Commun. 2006.

scan_protocol: After washing (0.1% SDS and 1% SSC) to remove the non-hybridized cDNAs, each array was scanned WITH A 4000B scanner (MDS, Toronto, Canada)) and images were primarily analyzed with GenePixPro 6.0 (Axon Instruments, CA).

data_processing: Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al. Physiol Genomics 2005.

label: Alexa Fluor®_647

molecule: total RNA

organism: Mus musculus

source_name: Oli-neu cells, control

label_protocol: 20ug total RNA extracted from the culture dish were reverse transcribed into cDNA incorporating fluorescent Alexa Fluor®_647–aha-dUTP using SuperScriptTM Plus Direct cDNA Labeling System (Invitrogen, CA).

growth_protocol: Cells were seeded in culture flasks coated with 0.01% poly-L-lysine and cultured in DMEM medium + 1% B27, N2, PSG, SP and horse serum, and passed with Trypsin-EDTA.

extract_protocol: total RNA was extracted using the TRIzol® protocol (Invitrogen, CA). RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)

tag: cell type

value: Oli-neu cells, control


title: Oli-neu cells, differentiated_rep1


title: H3ac HSC rep3

status: Public on Nov 09 2009

type: genomic

city: Lund

first: Joanne

last: Attema

address: Tornavagen 10

department: Immunology

country: Sweden

institute: Lund University

description: miniChIP-chip HSCs H3ac replicate 3

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc.,Iceland following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Iceland, following their standard operating protocol. See www.nimblegen.com.

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan ChIP data extraction. Arrays were normalized using MA2C and quantile normalization as described in Weishaupt et al., 2009 (Blood).

molecule: genomic DNA

source_name: H3ac miniChIP DNA from HSC

label_protocol: Labeling was performed by NimbleGen Systems Inc., Iceland, following their standard operating protocol. See www.nimblegen.com.

extract_protocol: The miniChIP method is described in detail in the Supplementary Data file of Weishaupt et al., 2009 (Blood).

treatment_protocol: HSCs were FACS sorted from the bone marrow of 10-12 week old mice

tag: strain

tag: age

value: 10-12 weeks old

tag: tissue

value: bone marrow

value: hematopoieitic stem cells (HSC)

tag: antibody

source_name: Input DNA from HSC


title: Oli-neu cells, control_rep2

hyb_protocol: The labeled cDNA was co-hybridized with a distinct Alexa Fluor®_647-aha-dUTP labeled biological replica overnight at 50°C on a Duke Operon Mouse 30K oligonucleotide array V4.0. Hybridization design ("multiple yellow" strategy) was described in Iacobas et al. Biochem Biophys Res Commun. 2006.

label: Alexa Fluor®_555

label_protocol: 20ug total RNA extracted from the culture dish were reverse transcribed into cDNA incorporating fluorescent Alexa Fluor®_555–aha-dUTP using SuperScriptTM Plus Direct cDNA Labeling System (Invitrogen, CA).


title: H3K79me2 HSC rep2

description: miniChIP-chip HSCs H3K79me2 replicate 2

source_name: H3K79me2 miniChIP DNA from HSC


title: recil.log_phase_growth.T120 rep1

status: Public on Nov 01 2009

city: Villerubanne

first: Jean-François

last: Gout

address: 43 Bld du 11 Novembre 1918

country: France

institute: Laboratoire Biométrie et Biologie Evolutive

description:
Paramecium cells in log phase growth
Time point 120 minutes after deciliation (rep 1)

hyb_protocol: Hybridization by NimbleGen company

scan_protocol: Scanning by NimbleGen company

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM315905.pair file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes. The GSM315905_T120.norm_RMA.tab file contains the signals after background correction, but before applying across-array normalization.

label: biotin

organism: Paramecium tetraurelia

label_protocol: SuperScript Invitrogen (double strand labeling)

extract_protocol: Tri-reagent and Ambion column (ref AM1924)

treatment_protocol: A pellet of living paramecia is vortexed 30 sec. in TrisHCl 10mM pH 7.2, CaCl2 1mM, ethanol 5% v/v and centrifuged 1 min. 1000g. The pellet is essentially composed of living immobile deciliated paramecia that are transferred to fresh culture medium. Aliquotes are taken and pelleted at desired time after the treatment for total RNA extraction.

value: nd7 F2 1A5a

value: mutant strain unable to discharge trichocysts. Less background in deciliation experiments

tag: caryonide

value: polycaryonide

tag: medium

value: Klebsiella pneumoniae BHB

value: log-phase growth


title: H3K27me3 HSC rep2

description: miniChIP-chip HSCs H3K27me3 replicate 2

source_name: H3K27me3 miniChIP DNA from HSC


title: recil.log_phase_growth.T0 rep3

description:
Paramecium cells in log phase growth
Time point before deciliation (rep 4)

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM315903.pair file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes. The GSM315903_T0B.norm_RMA.tab file contains the signals after background correction, but before applying across-array normalization.

source_name: Time point before deciliation

treatment_protocol: deciliation


title: H3K9me3 HSC rep1

description: miniChIP-chip HSCs H3K9me3 replicate 1

source_name: H3K9me3 miniChIP DNA from HSC


title: H3K27me3 HSC rep1

description: miniChIP-chip HSCs H3K27me3 replicate 1


title: Oli-neu cells cocultured with cortical astrocytes in insert system _rep1

description: Mouse immortalized oligodendrocyte precursor cell line Oli-neu received from Dr. J. Trotter (University of Mainz, Mainz, Germany) co-cultured with mouse cortical astrocytes in FalconTM cell culture 6 wells insert system, with astrocytes in the insert and Oli-neu cells on the bottom of the system. The insert had pores of 0.4µm allowing the two types of cells to exchange neurotransmitters and other signaling molecules but preventing formation of gap junction channels.

growth_protocol: Oli-neu cells were seeded in culture flasks coated with 0.01% poly-L-lysine and cultured in DMEM medium + 1% B27, N2, PSG, SP and horse serum, and passed with Trypsin-EDTA. Preparation of primary astrocyte cultures: At E19 stage of pregnancy, C-sections were performed on C57Bl/6j mothers and brains from four pups were separately minced in 500μl of 0.05% trypsin-EDTA, transferred to 1 ml Eppendorf tubes containing 500μl culture medium  (Dulbecco’s Modified Eagle medium supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin and spun down at 2000 RPM for 10 min. Pellet was then re-suspended in culture medium and the cells were plated in 100 mm culture dishes and maintained in a humidified 5% CO2 incubator at 37°C. After 1 week in culture, primary confluent astrocyte cultures were trypsinized (0.05% trypsin) and replated (Iacobas et al. Cell Commun Adhes 2008).


title: H3K79me2 HSC rep1

description: miniChIP-chip HSCs H3K79me2 replicate 1


title: H3ac HSC rep2

description: miniChIP-chip HSCs H3ac replicate 2


title: recil.log_phase_growth.T0 rep2

description:
Paramecium cells in log phase growth
Time point before deciliation (rep 2)

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM315902.pair file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes. The  file GSM315902_T0A.norm_RMA.tab contains the signals after background correction, but before applying across-array normalization.


title: recil.log_phase_growth.T0 rep1

description:
Paramecium cells in log phase growth
Time point before deciliation (rep 1)

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM315848.pair file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes. The GSM315848_T0.norm_RMA.tab file contains the signals after background correction, but before applying across-array normalization.


title: H3K4me3 HSC rep2

description: miniChIP-chip HSCs H3K4me3 replicate 2

source_name: H3K4me3 miniChIP DNA from HSC


title: H3K4me3 HSC rep3

description: miniChIP-chip HSCs H3K4me3 replicate 3


title: Oli-neu cells, differentiated_rep3


title: normal prostate 34PN

status: Public on Sep 15 2009

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: Microarray experiments were carried out as one-color hybridizations on human catalog 8-plex 15K miRNA microarrays (AMADID 016436) from Agilent Technologies. Analyses were done initially with matched malignant and non-malignant sample pairs.

hyb_protocol: Labeled samples were hybridized on human catalog 8-plex 15K miRNA microarrays (AMADID 016436) from Agilent Technologies encoding probes for 470 human and 64 human viral microRNAs from the Sanger database v9.1. Microarrays were washed according to the supplier’s protocol.

scan_protocol: Microarrays were scanned at 5 µm resolution with DNA microarray laser scanner (Agilent Technologies) and processed according to the supplier’s protocol.

data_processing: Features were extracted with an image analysis tool version A.9.5.3 using default protocols and settings (Agilent Technologies). Data analysis was carried out on the Rosetta Inpharmics gene expression data management and analysis system Resolver Version 7.0. Intensity experiments were created with the Intensity Experiment Manager from Resolver by combining all hybridizations derived from malignant and non-malignant samples, respectively. ‘In silico’ ratio profiles and ratio experiments were generated by the Ratio Experiment Wizard after selection of either malignant and non-malignant samples derived from individual patients or by combining malignant and non-malignant intensity experiments. A two-sample Students t-test was applied on all intensity profiles, while a one-sample t-test was applied to the ratio experiments comprising individual patients. Principal Component Analysis (PCA) was used for data reduction on either experiment or reporter level. Cluster analysis was done on features or reporter levels with the 2D Matrix Wizard from Resolver with an agglomerative algorithm using average link as heuristic criteria and Manhattan distance as metric similarity measure on both, intensity profiles and ratio experiments. All analysis criteria were combined making the microarray results extremely robust and highly reproducible.

organism: Homo sapiens

source_name: human prostate

label_protocol: An amount of 100 ng total RNA was dephosphorylated with Calf Intestine Alkaline Phosphatase (GE Healthcare, Chalfont St. Giles, United Kingdom), denaturated with DMSO and used as RNA acceptor in a T4 RNA ligase mediated reaction with the RNA donor 3’, 5’-cytidine bisphosphate having a single Cy3 label attached to the 3’ phosphate of the nucleotide (Cy3-pCp). The labeling reaction was column purified, dried down using a speed-vac at 45°C and resuspended in blocking and hybridization buffer.

extract_protocol: Frozen matched malignant and non-malignant samples were collected in RNAlater Stabilization reagent (Qiagen GmbH, Hilden, Germany). RNA was extracted with the miRNeasy Mini Kit (Qiagen GmbH, Hilden, Germany). RNA yield and A260/280 ratio were monitored with a NanoDropND-100 spectrometer (NanoDrop Technologies, Wilmington, DE) and RNA integrity numbers were measured with the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Only RNA extracts with RNA integrity number values >6 were included in further analysis.

treatment_protocol: Tumor tissue and normal adjacent tissue were collected after radical prostatectomy between 2001 and 2005 at Charité University Hospital, Berlin. Tumor classification was determined according to the UICC 2002 TNM System and the tumor grading according to Gleason. Fresh prostate tissues were sampled directly after surgical removal. The fresh, cooled organ was sectioned according to standard histopathological grossing. For tissue asservation, one full frontal section, which was grossly tumor suspicious, was deep frozen in liquid nitrogen. A diagnostic H&E section was prepared to verify tumor content and margin status and to identify areas of normal and tumor tissue for further processing. These regions of interest were punch biopsied with a conventional single-use trephine needle. Then another frozen section was made to ascertain tumor content in the frozen tissue trephine and to assign a Gleason score. Only cases with more than 90% tumor tissue were considered for further analysis.

value: normal prostate


title: normal prostate 49PN


title: Embryonic Drosophila cells, Kc167 cells, nucleosome occupancy after white RNAi, replicate 2

status: Public on Oct 15 2009

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description: Nucleosome occupancy Kc167 cells w RNAi

hyb_protocol: 13 µg labeled DNA per, 2.4 µl alignment oligo and 24 µl NimbleGen hybridiziation component A and 1x hybridization buffer in a total volume of 120 µl were heated to 98°C for 5 min and hybridized in a TECAN hybridiaztion station for 16 hrs. at 42°C. Slides were washed sequentially with NimbleGen wash buffers I, II and III with 0.1 mM DTT at 42°C, 25°C, and 23°C, respectively.

scan_protocol: Slides were scanned on an Agilent scanner with 2 micron resolution at full intensity.

data_processing: Scans were processed with NimbleScan 2.4 using standard settings. Values of all reporters except NimbleGen control reporters were extracted from pair files and represented as log2-ratios and normalized using the the loess() function in R with parameter control=loess.control(trace.hat='approximate'). Values from 2 replicates were median centered and averaged and are represented in 'Nucleosomes_norm.txt'.

organism: Drosophila melanogaster

source_name: Embryonic Drosophila cells, Kc167 cells, white RNAi

label_protocol: 1 µg MNase digested DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy5/Cy3 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. On day 1, 3 and 5, cells were serum starved for 1h and treated with 15 μg/ul white dsRNA. On day 6, mononucleosomes were prepared.

extract_protocol: After micrococcal nuclease digestion, chromatin was treated with RNase A and Proteinase K, phenol/chloroform extracted, and ethanol precipitated.

treatment_protocol: Nuclei were isolated by pelleting 3 times in lysis buffer (10 mM Tris-HCl pH 8.0, 0.4% Triton X-100, 0.5 mM DTT, 15 mM NaCl, 4 mM MgCl2, 2 mM CaCl2, Complete Protease Inhibitors (Roche)). Nuclei from 13x10e6 cells were taken up in 200 μl MNase buffer (15 mM Tris-HCl pH 7.5, 60 mM KCl, 15 mM NaCl, 2 mM CaCl2, 0.5 mM DTT, 20% glycerol) and digested with micrococcal nuclease to yield predominantly mononucleosomes.

tag: cell line

treatment_protocol: Genomic DNA was isolated and digested with micrococcal nuclease to yield predominantly fragments of 100-1000 bp.


title: H3ac HSC rep1

description: miniChIP-chip HSCs H3ac replicate 1


title: prostate carcinoma 49PC

value: prostate carcinoma


title: Embryonic Drosophila cells, Kc167 cells, nucleosome occupancy after H3.3A+B RNAi, replicate 1

description: Nucleosome occupancy Kc167 cells H3.3A+B RNAi

source_name: Embryonic Drosophila cells, Kc167 cells, H3.3A+B RNAi

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. On day 1, 3 and 5, cells were serum starved for 1h and treated with 10 μg/ul H3.3A dsRNA and 10 μg/ul H3.3B dsRNA. On day 6, mononucleosomes were prepared.


title: Embryonic Drosophila cells, Kc167 cells, nucleosome occupancy after H3.3A+B RNAi, replicate 2

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C.


title: prostate carcinoma 36PC


title: prostate carcinoma 37PC


title: normal prostate 36PN


title: H3K4me3 HSC rep1

description: miniChIP-chip HSCs H3K4me3 replicate 1


title: prostate carcinoma 25PC


title: prostate carcinoma 34PC


title: prostate carcinoma 22PC


title: normal prostate 22PN


title: prostate carcinoma 47PC


title: normal prostate 37PN


title: Oli-neu cells, differentiated_rep4


title: prostate carcinoma 21PC


title: normal prostate 18PN


title: normal prostate 47PN


title: Embryonic Drosophila cells, Kc167 cells, nucleosome occupancy after white RNAi, replicate 1

description: Nucleosome occupancy Kc167 cells w RNAi


title: Embryonic Drosophila cells, Kc167 cells, nucleosome occupancy, replicate 2

description: Nucleosome occupancy untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells


title: normal prostate 21PN


title: normal prostate 25PN


title: prostate carcinoma 18PC


title: NHEK_sample4

status: Public on Aug 24 2009

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

description: ENCODE_Broad_4_NHEK-2_06252009_(HuEx-1_0-st-v2)

data_processing: Raw CEL files were processed using Affymetrix Expression Console Software using RMA-Core-DABG

source_name: NHEK

label_protocol: 1ug of total RNA was labeled according to Standard Affymetrix WT protocol for Exon 1.0 ST arrays

extract_protocol: total RNA was extracted from cell pellets using Trizol protocol

treatment_protocol: cells were supplied as frozen pellets, pellets in trizol, pellets in RNA later or pellets in RLT buffer

value: NHEK


title: NHEK_sample7

hyb_protocol: Standard Affymetrix WT protocol for Exon 1.0 ST arrays

extract_protocol: total RNA was extracted from cell pellets using RNEasy protocol


title: NHEK_sample5

scan_protocol: Standard Affymetrix WT protocol for Exon 1.0 ST arrays


title: prostate carcinoma 11PC


title: HUVEC_sample5

source_name: HUVEC

value: HUVEC


title: NHEK_sample6


title: normal prostate 11PN


title: normal prostate 16PN


title: HepG2_sample9


title: normal prostate 09PN


title: HepG2_sample10


title: HUVEC_sample4

description: ENCODE_Broad_6_HUVEC-2_06252009_(HuEx-1_0-st-v2)


title: HUVEC_sample3

description: ENCODE_Broad_5_HUVEC-1_06252009_(HuEx-1_0-st-v2)


title: NHEK_sample3

description: ENCODE_Broad_3_NHEK-1_06252009_(HuEx-1_0-st-v2)


title: HUVEC_sample6


title: Embryonic Drosophila cells, Kc167 cells, nucleosome occupancy, replicate 1


title: prostate carcinoma 16PC


title: HepG2_sample7


title: HepG2_sample6


title: PATIENT_PBMC_rep1

status: Public on May 07 2009

city: Beijing

first: Zhaogang

last: Sun

state: Beijing

address: No. 97, Machang Road, Tongzhou District

department: Microbiology and Immunology

country: China

institute: Beijing Tuberculosis & Thotacic Tumor research Institute

description: microRNA level in PBMCS of the TB patients

hyb_protocol: The Cy3-labled RNA was dried for 1-2h at 45℃ to 55℃, then assembled the hybridization mixture  and hybridize for 20h at 55℃. Finally the hibridized slides were washed for scanning

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides [Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100% (XDR Hi) and 5%(XDR Lo)].

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent G4450AA) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: pulmonary patients, PBMCs, pool of 4 individuals

label_protocol: The microRNAs were labled using the miRNA Complete Labeling and Hyb Kit. Details were that 1005ng total RNA was treated with phosphatase at 37 ℃for 30min. The dephosphorylated RNA was labled as the kit instruction .

extract_protocol: RNA was prepared using the TRizol LS reagent (Invitrogen, CA, USA ) following the manufacturer's recommendations. RNA was quantified using spectrophotometer method and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The peripheral blood mononuclear cells were freshly extracted with the human lymphocyte separation medium  from the peripheral blood drawn from the volunteers of TB patients, latent-infected individuals and the completely healthy persons, respectively.

value: Peripheral Blood Mononuclear Cells

tag: gender

value: two males and two females


title: HEALTHY_PBMC_rep1

description: microRNA level in PBMCS of the complete healthy people

source_name: completely healthy, PBMCs, pool of 4 individuals


title: ASCRI_human adipose stem cells_miRNA_neuro_4

status: Public on Apr 07 2009

city: Seoul

first: Kyo Won

last: Lee

address: 108 Pyung-Dong, Jongro-Gu

department: Obsterics & Gynecology

country: South Korea

institute: Adult Stem Cell Research Institute

description:
Adipose stem cells were obtained from donors using lipoaspiration.
Donor 4.

hyb_protocol: Agilent protocol

scan_protocol: Agilent Scanner

data_processing: Agilent GeneSpring software

source_name: human adipose-derived stem cells, neurally differentiated

label_protocol: Agilent's miRNA Labeling Reagent & Hybridization Kit

extract_protocol: Trizol

value: adipose stem cell


title: HepG2_sample5

description: ENCODE_Broad_2_HepG2-2_06252009_(HuEx-1_0-st-v2)


title: LATENT_PBMC_rep1

description: microRNA level in PBMCS of the latent-infected individuals

source_name: latent infected, PBMCs, pool of 4 individuals


title: HeLa-S3_sample5


title: ASCRI_human adipose stem cells_miRNA_control_4

source_name: human adipose-derived stem cells, undifferentiated


title: HeLa-S3_sample4


title: ASCRI_human adipose stem cells_miRNA_neuro_2

description:
Adipose stem cells were obtained from donors using lipoaspiration.
Donor 2.

label_protocol: Agilent’s miRNA Labeling Reagent & Hybridization Kit


title: RAW264.7-50ug/ml AF-SWCNT-24hrs-replicate1

status: Public on Jul 08 2009

first: Bin

last: Wan

address: 18 shuangqing road, Haidian District

institute: Research centre for eco-environmental sciences, CAS

description: no

hyb_protocol: cDNA probes were dissolved in 3×SSC( 0.2%SDS, 5×Denhart’s, 25%Formamide), and hybrized for overnight at 42℃. after that, the arrays were washed for 5min with solution (0.2% SDS，2×SSC) at 42℃, followed by 5 min wash with 0.2×SSC at Room Temperature。The arrays were then centrifuged to dry for scanning.

scan_protocol: Arrays were scanned with a confocal LuxScan 10KA scanner (CapitalBio), and the data of obtained images were extracted with LuxScan 3.0 software (CapitalBio).

data_processing: A space and intensity-dependent normalization based on a LOWESS program was employed. Genes with the signal intensity (Cy3 or Cy5)>800 were regarded as the expressed ones. If there were only one valid observation for a gene within a condition, that datum was disregarded for analysis.

source_name: cy5 labelled treatment sample replicate1

label_protocol: Five micrograms DNase-treated total RNA was prepared and fluorescent dye (Cy5-dCTP)-labeled cDNA, produced through Eberwine’s linear RNA amplification method (Van Gelder et al., 1990) and subsequent enzymatic reaction, were then hybridized to an array.

extract_protocol: We extracted total cellular RNA from each sample using Trizol reagent according to the mannual provided by manufactor(Invitrogen) . The quality of purified total RNA was assessed by Nanodrop 1000 (Thermo Fisher Scientific Inc., MA, USA), and quantity was assessed by absorbance at 260 nm.

treatment_protocol: 50ug/ml acid functionalized single-wall carbon nanotubes for 24 hrs.

source_name: cy3 labelled control sample replicate1

label_protocol: Five micrograms DNase-treated total RNA was prepared and fluorescent dye (Cy3-dCTP)-labeled cDNA, produced through Eberwine’s linear RNA amplification method (Van Gelder et al., 1990) and subsequent enzymatic reaction, were then hybridized to an array.

treatment_protocol: incubated  24 hours without any treatment.


title: HepG2_sample8


title: RAW264.7-50ug/ml AF-SWCNT-24hrs-replicate2

description: no

source_name: cy5 labelled treatment sample replicate2

source_name: cy3 labelled control sample replicate2

treatment_protocol: incubated 24 hours without any treatment.


title: RAW264.7-50ug/ml AF-SWCNT-24hrs-replicate3

description: no

source_name: cy5 labelled treatment sample replicate3

source_name: cy3 labelled control sample replicate3


title: ASCRI_human adipose stem cells_miRNA_control_3

description:
Adipose stem cells were obtained from donors using lipoaspiration.
Donor 3.


title: ASCRI_human adipose stem cells_miRNA_neuro_3


title: ASCRI_human adipose stem cells_miRNA_neuro_1

description:
Adipose stem cells were obtained from donors using lipoaspiration.
Donor 1.

hyb_protocol: Agilent Protocol


title: ASCRI_human adipose stem cells_miRNA_control_2


title: HepG2_sample4

description: ENCODE_Broad_1_HepG2-1_06252009_(HuEx-1_0-st-v2)


title: ASCRI_human adipose stem cells_miRNA_control_1


title: 6697

status: Public on Mar 13 2009

city: Boston

first: Cheng

last: Li

state: MA

address: 44 Binney St

department: Biostatistics and Computational Biology

institute: Dana-Farber Cancer Institute

description: miRNA expression from frozen DLBCL sample

hyb_protocol: 100ng of Cy3-labelled cRNA were hybridized to microarray slides (8 complete microarrays/slide) and washed following manufacturer’s guidelines.

scan_protocol: The arrays were scanned and the intensity of the hybridization signals obtained using the Feature Extraction software (Agilent Technologies).

data_processing: The gene-level signal values of the miRNAs were extracted from individual text files generated by the Agilent software (we used the “gTotalGeneSignal” column”). 470 human miRNAs were used in the downstream analysis. To adjust for hybridization differences between arrays, normalization was performed to scale all the signal values in one array by a multiplicative factor, so that the 75th percentile of the signal values in each array is the same value.

source_name: Frozen DLBCL sample

label_protocol: Perfomed following manufacturer's guidelines

extract_protocol: Total RNA was isolated from 21 frozen primary DLBCL samples using Trizol Method.

tag: tumor site

value: Lymph node

tag: cell of origin defined by ihc

value: GCB

tag: infiltrating t-cells


title: 4236


title: 5204

value: extra-nodal


title: 6290


title: 4522


title: 5081


title: 3279

value: Non-GCB


title: 4021


title: Cellulose repB 15340102_532

status: Public on Mar 30 2009

city: Madison

first: Dan

last: Cullen

state: WI

address: One Gifford Pinchot Dr

institute: UW/FPL

description: Cellulose repB 15340102_532

hyb_protocol: Hybridization was carried out with 6ug of labeled cDNA suspended in NimbleGen hybridization solution for 17 hours at 42°C

scan_protocol: Arrays were scanned on the Axon4000B Scanner (Molecular Dynamics) and data was extracted from the scanned image using NimbleScan v2.4.

data_processing: Quantile normalization and robust multi-array averaging (RMA) applied

organism: Phanerodontia chrysosporium

source_name: mycelium

label_protocol: One ug of each cDNA sample was amplified and labeled with 1 unit per ul of Klenow Fragment (New England BioLabs) and 1 O.D unit of Cy3 fluorophore (TriLink Biotechnologies, Inc.) for 2 hours at 37°C

growth_protocol: 5 days growth in shake flasks at 37C

extract_protocol: RNA was converted to double-strand cDNA and labeled with the Cy3 fluorophore sample for hybridization to the array by Roche NimbleGen (Iceland).  In brief, 10ug of total RNA was incubated with 1X first strand buffer, 10 mM DTT, 0.5mM dNTPs, 100 pM oligo T7 d(T)24  primer, and 200 units of SuperScript II (Invitrogen) for 60 min at 42°C. Second strand cDNA was synthesized by incubation with 1X second strand buffer, 0.2mM dNTPs, 0.07 units per ul DNA ligase (Invitrogen), 0.27 units per ul DNA polymerase I (Invitrogen), 0.013 units per ul RNase H (Invitrogen), at 16°C for 2 hours.  Immediately following, 10 units T4 DNA polymerase (Invitrogen) was added for additional 5 minute incubation at 16°C.  Double-stranded cDNA was treated with 27ng/ul of RNase A (EpiCenter Technologies)  for 10 minutes at 37°C.  Treated cDNA was purified using an equal volume of phenol:chloroform:isoamyl alcohol (Ambion), ethanol precipitated, washed with 80% ethanol, and resuspended in 20ul water.

tag: condition

value: Cellulose


title: Cellulose repC 15340302_532

description: Cellulose repC 15340302_532


title: Glucose repA 15322902_532

description: Glucose repA 15322902_532

value: Glucose


title: 4450


title: 3832


title: 3522


title: 3271


title: 3416


title: Glucose repB 15336002_532

description: Glucose repB 15336002_532


title: Cellulose repA 15337202_532

description: Cellulose repA 15337202_532


title: 5935


title: 865


title: 1320


title: 642


title: 1143


title: Glucose repC 15336102_532

description: Glucose repC 15336102_532


title: 2633


title: 1326


title: SCC13_GFP_r12

status: Public on Feb 17 2009

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

description: Biological replicate 1, technical replicate 2. Biological replicates are different adenovirus infections. Technical replicates are different labelings and hybridizations

hyb_protocol: The labeled RNA was hybridized to Agilent human miRNA microarrays for 20 hours at 55°C with rotation.

scan_protocol: The arrays were scanned with an Agilent microarray scanner with high dynamic range settings as specified by the manufacturer.

data_processing: Agilent Feature Extraction Software was used to extract the data and different normalization procedures were applied to the Total Gene Signal intensity values

source_name: Total RNA from human SCC13 cells infected with the control GFP adenovirus for 24 hours

label_protocol: Each sample was prepared according to the Agilent’s miRNA Microarray System protocol. 100 ng of total RNA was dephosphorylated with calf intestine alkaline phosphatase (GE Healthcare Europe GmbH, Otelfingen, Switzerland), denatured with dimethyl sulfoxide and labeled with pCp-Cy3 using T4 RNA ligase (GE Healthcare Europe GmbH, Otelfingen, Switzerland).

growth_protocol: Cells were grown as described in Lefort et al. Genes & development, 21, 562-577.

extract_protocol: Cells were collected in Tri-Reagent (Sigma) and total RNA was extracted following manufacturer’s instructions (with the exception that three rounds of chloroform extraction were performed instead of one).

treatment_protocol: SCC13 cells were infected with adenovirus as described in Lefort et al. Genes & development, 21, 562-577.

tag: keratinocyte-derived squamous cell carcinoma (SCC) cell line


title: SCC13_p53_r12

source_name: Total RNA from human SCC13 cells infected with the p53 adenovirus for 24 hours


title: 1309


title: SCC13_GFP_r32

description: Biological replicate 3, technical replicate 2. Biological replicates are different adenovirus infections. Technical replicates are different labelings and hybridizations


title: SCC13_GFP_r31

description: Biological replicate 3, technical replicate 1. Biological replicates are different adenovirus infections. Technical replicates are different labelings and hybridizations


title: SCC13_GFP_r11

description: Biological replicate 1, technical replicate 1. Biological replicates are different adenovirus infections. Technical replicates are different labelings and hybridizations


title: SCC13_p53_r32


title: SCC13_p53_r11


title: SCC13_p53_r31


title: SCC13_GFP_r22

description: Biological replicate 2, technical replicate 2. Biological replicates are different adenovirus infections. Technical replicates are different labelings and hybridizations


title: SCC13_p53_r22


title: SCC13_GFP_r21

description: Biological replicate 2, technical replicate 1. Biological replicates are different adenovirus infections. Technical replicates are different labelings and hybridizations


title: Brain-Heart_50-50_r2

description: Technical replicate 2 (labeling and hybridization)

source_name: Stratagene human heart and brain total RNA (50%-50% mixture)


title: Brain-Heart_95-05_r2

source_name: Stratagene human heart and brain total RNA (95% brain - 5% heart mixture)


title: Brain-Heart_75-25_r2

source_name: Stratagene human heart and brain total RNA (75% brain - 25% heart mixture)


title: SCC13_p53_r21


title: Brain-Heart_50-50_r1

description: Technical replicate 1 (labeling and hybridization)


title: Brain-Heart_75-25_r1


title: Brain-Heart_95-05_r1


title: Heart_r3

description: Technical replicate 3 (labeling and hybridization)

source_name: Stratagene human heart total RNA

tag: Heart


title: Brain_r1

source_name: Stratagene human brain total RNA

tag: Brain


title: Heart_r1


title: prostate carcinoma 09PC

description: Microarray experiments were carried out as one-color hybridizations on human catalog 8-plex 15K miRNA microarrays (AMADID 016436) from Agilent Technologies. Analyses were done initially with matched malignant and non-malignant sample pairs.

source_name: human prostate


title: Brain_r2


title: Brain_r3


title: Incipient AD 702

status: Public on Jan 10 2009

city: Los Angeles

first: Celia

last: Williams

state: CA

address: 2011 Zonal Ave

department: Pathology

institute: Keck School of Medicine, USC

hyb_protocol: Hybridization to the HG-U133A (Affymetrix) was performed according to standard Affymetrix protocols. Probe-sets consist of 11 probe-pairs, distributed across the array, which are typically designed with bias towards the 3'-end of each gene and include a mismatched pair for quantification and subtraction of non-specific hybridization. Escherichia coli internal spike controls are also included to determine hybridization efficiency. The hybridized array was washed, labeled with phycoerythrin-conjugated streptavidin and scanned in the Affymetrix scanner.

scan_protocol: The hybridized array was washed, labeled with phycoerythrin-conjugated streptavidin and scanned in the Affymetrix scanner. Microarray Analysis Suite 5.0 (MAS 5.0) was used for the initial signal analysis which generates a signal detection value based on the difference between the perfect match (PM) and mismatch (MM) probes in a probe set. A ‘present’ or ‘absent’ call was assigned to each gene by MAS 5.0 according to certain threshold and the detection p-values. The microarray data was checked for RNA degradation, visible defects in images, and Affymetrix hybridization control by Bioconductor Affymetrix package (http://www.bioconductor.org/)

data_processing: Model-Based Expression Index (dChip) (Li and Wong, 2001) implemented in Bioconductor, was used for signal normalization within an individual chip and across all samples. For high-level analysis, statistics tests were conducted to find significantly expressed genes, and this small set of genes was applied for clustering and pathway analysis. Probe sets that were differentially expressed among control and IAD were identified using ANOVA. Benjamini and Hochberg’s False Discovery Rate (FDR) was used for adjusting for multiple testing. The genes with significant change in expression were subject to hierarchical clustering using dChip.

source_name: Frontal cortex synaptoneurosome

label_protocol: Biotinylation and amplification of cDNA was accomplished by the use of an Enzo BioArray High Yield RNA Transcript Labeling Kit followed by purification by absorption over an RNeasy column.

extract_protocol: Total RNA from synaptoneurosome preparations was extracted with Trizol LS and purified with RNeasy columns. The RNA was quantified and checked for purity by comparison of absorbance at 260 and 280nm in the Nanodrop Spectrophotometer. Total RNA and mRNA were analyzed for integrity and concentration by microanalysis in an Agilent bioanalyzer.

treatment_protocol: Synaptoneurosomes were prepared by a standard method (Banko et al., 2004; Johnson et al., 1997; Villasana et al., 2006; Westmark and Malter, 2007). with slight modifications. Frontal cortex (0.5gm-2.5gm) was thawed and homogenized with a Teflon-homogenizer (4 strokes at 1000 rpm) in buffer (1/10wt/vol), containing 0.35M sucrose pH7.4, 10mM HEPES, 1mM EDTA, 0.25mM dithiothreitol, 30U/ml RNAse inhibitor and a protease inhibitor cocktail (Pierce, Rockford, Il). Cell debris and nuclei were removed by centrifugation at 1000g for 10 min at 4°C yielding pellet P1 and supernatant S1. The S1 fraction was passed sequentially through a series of screens with decreasing pore sizes of 100, 80, 30 and 10m. The final filtrate was resuspended in 3 volumes of buffer without sucrose and centrifuged at 2000xg, for 15 minutes at 4°C to yield a pellet containing synaptoneurosomes. Total preparation time did not exceed 1 hour.

tag: Synaptoneurosomes isolated from human brain frontal cortex of a patient with incipient Alzheimer's Disease with MMSE 26


title: Incipient AD 733

description: The microarray data was checked for RNA degradation, visible defects in images, and Affymetrix hybridization control by Bioconductor Affymetrix package (http://www.bioconductor.org/)

tag: Synaptoneurosomes isolated from human brain frontal cortex of a patient with incipient Alzheimer's Disease with MMSE 27


title: Glucose rep3 10550202-532

status: Public on Jan 09 2009

description: Glucose rep3 10550202-532

organism: Rhodonia placenta

source_name: mycelium, glucose

growth_protocol: Six days growth in shaking flasks at room temperature.

extract_protocol: RNA was converted to double-strand cDNA and labeled with the Cy3 fluorophore sample for hybridization to the XX-array by Roche NimbleGen (Iceland).  In brief, 10ug of total RNA was incubated with 1X first strand buffer, 10 mM DTT, 0.5mM dNTPs, 100 pM oligo T7 d(T)24  primer, and 200 units of SuperScript II (Invitrogen) for 60 min at 42°C. Second strand cDNA was synthesized by incubation with 1X second strand buffer, 0.2mM dNTPs, 0.07 units per ul DNA ligase (Invitrogen), 0.27 units per ul DNA polymerase I (Invitrogen), 0.013 units per ul RNase H (Invitrogen), at 16°C for 2 hours.  Immediately following, 10 units T4 DNA polymerase (Invitrogen) was added for additional 5 minute incubation at 16°C.  Double-stranded cDNA was treated with 27ng/ul of RNase A (EpiCenter Technologies)  for 10 minutes at 37°C.  Treated cDNA was purified using an equal volume of phenol:chloroform:isoamyl alcohol (Ambion), ethanol precipitated, washed with 80% ethanol, and resuspended in 20ul water.

tag: stain


title: Incipient AD 678

tag: Synaptoneurosomes isolated from human brain frontal cortex of a patient with incipient Alzheimer's Disease with MMSE 25


title: Control 585

data_processing: Model-Based Expression Index (dChip) (Li and Wong, 2001) implemented in Bioconductor, was used for signal normalization within an individual chip and across all samples. For high-level analysis, statistics tests were conducted to find significantly expressed genes, and this small set of genes was applied for clustering and pathway analysis. Probe sets that were differentially expressed among control and IAD were identified using ANOVA. Benjamini and Hochberg’s False Discovery Rate (FDR) was used for adjusting for multiple testing. The genes with significant change in expression were subject to  hierarchical clustering using dChip.

label_protocol: Biotinylation and amplification of cDNA was accomplished by the use of an Enzo BioArray High Yield RNA Transcript Labeling Kit  followed by purification by absorption over an RNeasy column.

treatment_protocol: Synaptoneurosomes were prepared by a standard method (Banko et al., 2004; Johnson et al., 1997; Villasana et al., 2006; Westmark and Malter, 2007). with slight modifications. Frontal cortex (0.5gm-2.5gm) was thawed and homogenized with a Teflon-homogenizer (4 strokes at 1000 rpm)  in buffer (1/10wt/vol), containing 0.35M sucrose pH7.4, 10mM HEPES, 1mM EDTA, 0.25mM dithiothreitol, 30U/ml RNAse inhibitor and a protease inhibitor cocktail (Pierce, Rockford, Il). Cell debris and nuclei were removed by centrifugation at 1000g for 10 min at 4°C yielding pellet P1 and supernatant S1. The S1 fraction was passed sequentially through a series of screens with decreasing pore sizes of 100, 80, 30 and 10m. The final filtrate was resuspended in 3 volumes of buffer without sucrose and centrifuged at 2000xg, for 15 minutes at 4°C to yield a pellet containing synaptoneurosomes. Total preparation time did not exceed 1 hour.

tag: Synaptoneurosomes isolated from human brain frontal cortex of control patient with MMSE 29


title: Control 632


title: 8hr 10mM menadione-1

status: Public on Nov 03 2008

city: Novato

first: Christina

last: Yau

address: 8001 Redwood Blvd

institute: Buck Institute of Age Research

description: Gene expression data from MCF7 after 8hr 10mM menadione treatment

hyb_protocol: Affymetrix Comm Hyb Setup 21 & Affymetrix Comm Wash Stain 21  (performed by  HTArray Genomics Core Facility of Lawrence Berkeley National Laboratory)

scan_protocol: GeneChip HT Scanner protocol v2.2.09  (performed by  HTArray Genomics Core Facility of Lawrence Berkeley National Laboratory)

data_processing: RMA normalization with affy package in Bioconductor R

source_name: MCF7, 10mM menadione, 8hr

label_protocol: Affymetrix Gene Expression TP 21 (performed by  HTArray Genomics Core Facility of Lawrence Berkeley National Laboratory)

growth_protocol: Cells are maintained routinely at 37C and 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin, and 10ng/ml insulin prior to treatments

extract_protocol: Qiagen RNAesy purification

tag: ER+/PR+


title: Control 715

tag: Synaptoneurosomes isolated from human brain frontal cortex of control patient with MMSE 28


title: Glucose rep1 10555502-532

description: Glucose rep1 10555502-532


title: Control 405


title: Cellulose rep3 8693502-532

description: Cellulose rep3 8693502-532

source_name: mycelium, cellulose


title: 8hr 10mM menadione-2


title: Control 688

tag: Synaptoneurosomes isolated from human brain frontal cortex of control patient with MMSE 25


title: Incipient AD 224


title: Control 679


title: 8hr 0.5mM H2O2-2

description: Gene expression data from MCF7 after 8hr 0.5mM H2O2 treatment

source_name: MCF7, 0.5mM H2O2, 8hr


title: Glucose rep2 10554902-532

description: Glucose rep2 10554902-532


title: 8hr 275mM diamide-2

description: Gene expression data from MCF7 after 8hr 275mM diamide treatment

source_name: MCF7, 275mM diamide, 8hr


title: Cellulose rep2 8694202-532

description: Cellulose rep2 8694202-532


title: Control 530

extract_protocol:
NA isolation
Total RNA from synaptoneurosome preparations was extracted with Trizol LS and purified with RNeasy columns. The RNA was quantified and checked for purity by comparison of absorbance at 260 and 280nm in the Nanodrop Spectrophotometer. Total RNA and mRNA were analyzed for integrity and concentration by microanalysis in an Agilent bioanalyzer.


title: Incipient AD 385

tag: Synaptoneurosomes isolated from human brain frontal cortex of a patient with incipient Alzheimer's Disease with MMSE 21


title: Control 564

tag: Synaptoneurosomes isolated from human brain frontal cortex of control patient with MMSE 27


title: 8hr 0.5mM H2O2-1


title: Incipient AD 606


title: Cellulose rep1 8694802-532

description: Cellulose rep1 8694802-532


title: 72hr E2 deprivation-2

description: Gene expression data from MCF7 after 72hr E deprivation

source_name: MCF7, E2 deprivation, 72hr


title: 72hr antiERalpha siRNA-1

description: Gene expression data from MCF7 after 72hr anti-Eralpha siRNA knockdown

source_name: MCF7, anti-ERa siRNA treatment, 72hr


title: 72hr E2 deprivation-1


title: 72hr antiERalpha siRNA-2


title: 8hr 275mM diamide-1


title: Hyperplasia tissue FFPE 2623 extraction 2

status: Public on Nov 01 2008

city: Kingston

first: Harriet

last: Feilotter

state: Ontario

address: 88 Stuart St

department: Pathology and molecular department

country: Canada

institute: Queen's University

description: slide 4

hyb_protocol: labeled RNA was hybridized to Agilent miRNA array ( 8 arrays per slide) at 55°C for 22h in rotisserie in a hybridization oven. Disassembled arrays was washed in GE wash buffer 1&2 for 5 minutes each.

scan_protocol: Images was scanned with Agilent scanner at 5µm resolution

data_processing: The raw data for same gene was then summarized automatically in Agilent feature extraction protocol to generate Gene view file, providing expression data for each gene probed on the array. Features interogating same miRNA were summarized together based on their weight. No interarray normalization method was employed. See pdf file linked to Series for more information.

label: Cy3 pCp

source_name: lymphoid hyperplasia tissue

label_protocol: 100ng total RNA was dephosphorylated at the presence of calf intestine alkaline phsphatase, then a Cy3-pCp molecule was then ligated to the 3' end of the RNA molecule according to Agilent miRNA protocol version 1.0

extract_protocol: All samples contained at least 75% hyperplasia tissues without necrosis, which was confirmed by pathologist. The miRNAeasy kit (Qiagen, Mississauga, Canada) was used to extract total RNA (including miRNA) from frozen samples, The RecoverAll total RNA Isolation kit (Ambion, Streetsville, Canada) was used to extract total RNA (including miRNA) from FFPE samples

tag: sample age 1-2 years


title: Hyperplasia tissue FFPE 2623 extraction 1

description: slide 4


title: Hyperplasia tissue Frozen 2623 extraction 2

description: slide 4


title: Hyperplasia tissue Frozen 2623 extraction 1

description: slide 4


title: Untreated MCF7 RNA-2

description: Gene expression data from untreated MCF7


title: Hyperplasia tissue FFPE 19322 extraction 2

description: slide 3


title: Hyperplasia tissue Frozen 19322 extraction 1

description: slide 3


title: Hyperplasia tissue FFPE 11826 extraction 1

description: slide 3


title: Hyperplasia tissue Frozen 19322 extraction 2

description: slide 3


title: Hyperplasia tissue FFPE 11826 extraction 2

description: slide 3


title: Hyperplasia tissue Frozen 11826 extraction 2

description: slide 3


title: Hyperplasia tissue Frozen 2248 extraction 2

description: slide 2


title: Untreated MCF7 RNA-1


title: Hyperplasia tissue Frozen 17176 extraction 2 replica

description: slide 2


title: Hyperplasia tissue FFPE 17176 extraction 2 replica

description: slide 2


title: Hyperplasia tissue FFPE 19322 extraction 1

description: slide 3


title: Hyperplasia tissue FFPE 2248 extraction 2 replica

description: slide 2


title: Hyperplasia tissue FFPE 17176 extraction 2

description: slide 2


title: Hyperplasia tissue Frozen 2248 extraction 2 replica

description: slide 2


title: Hyperplasia tissue FFPE 2248 extraction 2

description: slide 2


title: Hyperplasia tissue Frozen 11826 extraction 1

description: slide 3


title: Hyperplasia tissue Frozen 17176 extraction 2

description: slide 2


title: Hyperplasia tissue FFPE 11903 extraction 1

description: slide 1


title: Hyperplasia tissue FFPE 17176 extraction 1

description: slide 1


title: Hyperplasia tissue FFPE 2248 extraction 1

description: slide 1


title: Hyperplasia tissue FFPE 2817 extraction 1

description: slide 1


title: Hyperplasia tissue Frozen 11903 extraction 1

description: slide 1


title: Hyperplasia tissue Frozen 2248 extraction 1

description: slide 1


title: Hyperplasia tissue Frozen 2817 extraction 1

description: slide 1


title: Hyperplasia tissue Frozen 17176 extraction 1

description: slide 1


title: Expression data of CCMS_84

status: Public on Oct 18 2006

city: Bunkyo-ku

first: Toshiaki

last: Watanabe

state: Tokyo

department: Department of Surgical Oncology

country: Japan

institute: University of Tokyo

description:
MSS, distal
Training-Lymph(+)

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

label_protocol: Approximately 8 ug of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Surgically isolated colorectal cancers were immediately frozen in liquid nitrogen. Tissues were lysed and total RNA was isolated using RNeasy Mini Kit (QIAGEN, Chatswort,CA) according to the manufacturer's instructions.

tag: Tissue

value: Colorecal Cancer


title: Expression data of CCMS_67

description:
MSI, distal
Training-Lymph(+)


title: Expression data of CCMS_70

description:
MSI, proximal
Training-Lymph(-)


title: Expression data of CCMS_77

description:
MSI, proximal
Training-Lymph(+)


title: Expression data of CCMS_80

description:
MSI, proximal
Training-Lymph(+)


title: Expression data of CCMS_74

description:
MSI, distal
Training-Lymph(-)


title: Expression data of CCMS_83

description:
MSS, distal
Training-Lymph(+)


title: Expression data of CCMS_75

description:
MSI, proximal
Training-Lymph(+)


title: Expression data of CCMS_64

description:
MSI, proximal
Training-Lymph(-)


title: Expression data of CCMS_78

description:
MSI, proximal
Training-Lymph(+)


title: Expression data of CCMS_73

description:
MSI, distal
Training-Lymph(-)


title: Expression data of CCMS_59

description:
MSS, distal
Training-Lymph(+)


title: Expression data of CCMS_76

description:
MSI, proximal
Training-Lymph(+)


title: Expression data of CCMS_71

description:
MSI, distal
Training-Lymph(-)


title: Expression data of CCMS_81

description:
MSI, distal
Training-Lymph(-)


title: Expression data of CCMS_61

description:
MSI, unknown
Training-Lymph(-)


title: Expression data of CCMS_69

description:
MSI, proximal
Training-Lymph(-)


title: Expression data of CCMS_68

description:
MSI, proximal
Training-Lymph(-)


title: Expression data of CCMS_65

description:
MSI, proximal
Training-Lymph(+)


title: Expression data of CCMS_82

description:
MSI, proximal
Training-Lymph(-)


title: Expression data of CCMS_62

description:
MSI, unknown
Training-Lymph(-)


title: Expression data of CCMS_60

description:
MSI, proximal
Training-Lymph(-)


title: Expression data of CCMS_57

description:
MSS, proximal
Training-Lymph(-)


title: Expression data of CCMS_79

description:
MSI, proximal
Training-Lymph(+)


title: Expression data of CCMS_58

description:
MSS, distal
Training-Lymph(-)


title: Expression data of CCMS_56

description:
MSS, distal
Training-Lymph(-)


title: Expression data of CCMS_66

description:
MSI, proximal
Training-Lymph(-)


title: Expression data of CCMS_72

description:
MSI, proximal
Training-Lymph(+)


title: Expression data of CCMS_63

description:
MSI, proximal
Training-Lymph(-)


title: Expression data of CCMS_50

description:
MSS, distal
Test-Lymph(+)


title: Expression data of CCMS_47

description:
MSI, distal
Test-Lymph(-)


title: Expression data of CCMS_43

description:
MSS, distal
Test-Lymph(-)


title: Expression data of CCMS_35

description:
MSS, distal
Training-Lymph(+)


title: Expression data of CCMS_33

description:
MSS, distal
Training-Lymph(-)


title: Expression data of CCMS_32

description:
MSS, distal
Training-Lymph(+)


title: Expression data of CCMS_49

description:
MSS, proximal
Test-Lymph(-)


title: Expression data of CCMS_44

description:
MSS, distal
Test-Lymph(-)


title: Expression data of CCMS_42

description:
MSS, distal
Test-Lymph(-)


title: Expression data of CCMS_40

description:
Training-Lymph(-)
MSS, distal


title: Expression data of CCMS_39

description:
MSS, distal
Training-Lymph(-)


title: Expression data of CCMS_34

description:
MSS, distal
Training-Lymph(-)


title: Expression data of CCMS_41

description:
MSS, distal
Training-Lymph(-)


title: Expression data of CCMS_29

description:
MSS, distal
Training-Lymph(-)


title: Expression data of CCMS_25

description:
MSS, distal
Training-Lymph(-)


title: Expression data of CCMS_48

description:
MSI, distal
Test-Lymph(-)


title: Expression data of CCMS_30

description:
MSS, distal
Training-Lymph(-)


title: Expression data of CCMS_24

description:
MSS, distal
Test-Lymph(-)


title: Expression data of CCMS_31

description:
MSS, distal
Training-Lymph(-)


title: Expression data of CCMS_26

description:
MSS, distal
Training-Lymph(-)


title: Expression data of CCMS_28

description:
MSS, distal
Training-Lymph(+)


title: Expression data of CCMS_23

description:
MSS, distal
Test-Lymph(-)


title: Expression data of CCMS_37

description:
MSS, distal
Training-Lymph(-)


title: Expression data of CCMS_22

description:
MSI, proximal
Training-Lymph(+)


title: Expression data of CCMS_38

description:
MSS, distal
Training-Lymph(-)


title: Expression data of CCMS_27

description:
MSS, distal
Training-Lymph(-)


title: Expression data of CCMS_36

description:
MSS, distal
Training-Lymph(-)


title: Expression data of CCMS_19

description:
MSI, proximal
Test-Lymph(-)


title: Expression data of CCMS_21

description:
MSS, proximal
Test-Lymph(-)


title: Expression data of CCMS_18

description:
MSS, proximal
Test-Lymph(+)


title: Expression data of CCMS_16

description:
MSI, proximal
Test-Lymph(+)


title: Expression data of CCMS_09

description:
MSS, proximal
Training-Lymph(+)


title: Expression data of CCMS_13

description:
MSS, distal
Test-Lymph(+)


title: Expression data of CCMS_08

description:
MSS, proximal
Training-Lymph(+)


title: Expression data of CCMS_05

description:
MSI, distal
Training-Lymph(-)


title: Obese M 07 subAv2

status: Public on Jan 01 2006

city: Phoenix

first: Yong-Ho

state: AZ

department: Phoenix Epidemiology and Clinical Research Branch

institute: NIDDK, NIH

description:
Adipocytes were isolated using collagenase digestion of abdominal subcutaneous fat needle biopsies. Array type: HG_U95Av2. Subject: obese male Pima Indian (OM07).
Keywords = adipocyte
Keywords = obesity
Keywords = inflammation
Keywords = gene expression

source_name: adipocytes


title: Expression data of CCMS_06

description:
MSS, distal
Training-Lymph(+)


title: Obese M 09 subAv2

description:
Adipocytes were isolated using collagenase digestion of abdominal subcutaneous fat needle biopsies. Array type: HG_U95Av2. Subject: obese male Pima Indian (OM09).
Keywords = adipocyte
Keywords = obesity
Keywords = inflammation
Keywords = gene expression


title: Expression data of CCMS_15

description:
MSI, distal
Training-Lymph(+)


title: Expression data of CCMS_20

description:
MSI, proximal
Test-Lymph(-)


title: Obese M 06 subAv2

description:
Adipocytes were isolated using collagenase digestion of abdominal subcutaneous fat needle biopsies. Array type: HG_U95Av2. Subject: obese male Pima Indian (OM06).
Keywords = adipocyte
Keywords = obesity
Keywords = inflammation
Keywords = gene expression


title: Obese M 08 subAv2

description:
Adipocytes were isolated using collagenase digestion of abdominal subcutaneous fat needle biopsies. Array type: HG_U95Av2. Subject: obese male Pima Indian (OM08).
Keywords = adipocyte
Keywords = obesity
Keywords = inflammation
Keywords = gene expression


title: Expression data of CCMS_17

description:
MSS, distal
Training-Lymph(-)


title: Expression data of CCMS_02

description:
MSS, distal
Training-Lymph(+)


title: Expression data of CCMS_04

description:
MSS, distal
Training-Lymph(+)


title: Expression data of CCMS_12

description:
MSS, distal
Test-Lymph(-)

source_name: Colorecal Cancer, Patient_12

tag: tissue

tag: treatment response


title: Expression data of CCMS_14

description:
MSS, proximal
Test-Lymph(+)


title: Expression data of CCMS_03

description:
MSI, proximal
Training-Lymph(-)


title: Obese F 09 subAv2

description:
Adipocytes were isolated using collagenase digestion of abdominal subcutaneous fat needle biopsies. Array type: HG_U95Av2. Subject: obese female Pima Indian (OF09).
Keywords = adipocyte
Keywords = obesity
Keywords = inflammation
Keywords = gene expression


title: Obese F 10 subAv2

description:
Adipocytes were isolated using collagenase digestion of abdominal subcutaneous fat needle biopsies. Array type: HG_U95Av2. Subject: obese female Pima Indian (OF10).
Keywords = adipocyte
Keywords = obesity
Keywords = inflammation
Keywords = gene expression


title: Obese F 08 subAv2

description:
Adipocytes were isolated using collagenase digestion of abdominal subcutaneous fat needle biopsies. Array type: HG_U95Av2. Subject: obese female Pima Indian (OF08).
Keywords = adipocyte
Keywords = obesity
Keywords = inflammation
Keywords = gene expression


title: P205 pheochromocytoma

status: Public on Aug 12 2005

city: San Antonio

first: Patricia

middle: L.

last: Dahia

address: 7703 Floyd Curl Dr MC7880

department: Medicine/Cel&Struct Biology

institute: UTHSCSA

description: sample: P205

data_processing: This sample has been excluded from the analysis due to lower quality compared to remaining samples.

source_name: flash-frozen tumor specimen

label_protocol: Approximately 10 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Trizol as described in Monti S et al. Blood. 2005 Mar 1;105(5):1851-61.

value: adrextraadrenal paragangliomanal

tag: genetic class

tag: tumor type

value: pheochromocytoma


title: Obese F 07 subAv2

description:
Adipocytes were isolated using collagenase digestion of abdominal subcutaneous fat needle biopsies. Array type: HG_U95Av2. Subject: obese female Pima Indian (OF07).
Keywords = adipocyte
Keywords = obesity
Keywords = inflammation
Keywords = gene expression


title: Expression data of CCMS_01

description:
MSS, distal
Training-Lymph(+)


title: Obese M 05 subAv2

description:
Adipocytes were isolated using collagenase digestion of abdominal subcutaneous fat needle biopsies. Array type: HG_U95Av2. Subject: obese male Pima Indian (OM05).
Keywords = adipocyte
Keywords = obesity
Keywords = inflammation
Keywords = gene expression


title: Lean M 10 subAv2

description:
Adipocytes were isolated using collagenase digestion of abdominal subcutaneous fat needle biopsies. Array type: HG_U95Av2. Subject: lean male Pima Indian (LM10).
Keywords = adipocyte
Keywords = obesity
Keywords = inflammation
Keywords = gene expression


title: Obese F 06 subAv2

description:
Adipocytes were isolated using collagenase digestion of abdominal subcutaneous fat needle biopsies. Array type: HG_U95Av2. Subject: obese female Pima Indian (OF06).
Keywords = adipocyte
Keywords = obesity
Keywords = inflammation
Keywords = gene expression


title: Expression data of CCMS_10

description:
MSS, distal
Training-Lymph(-)


title: Lean M 09 subAv2

description:
Adipocytes were isolated using collagenase digestion of abdominal subcutaneous fat needle biopsies. Array type: HG_U95Av2. Subject: lean male Pima Indian (LM09).
Keywords = adipocyte
Keywords = obesity
Keywords = inflammation
Keywords = gene expression


title: Lean M 06 subAv2

description:
Adipocytes were isolated using collagenase digestion of abdominal subcutaneous fat needle biopsies. Array type: HG_U95Av2. Subject: lean male Pima Indian (LM06).
Keywords = adipocyte
Keywords = obesity
Keywords = inflammation
Keywords = gene expression


title: Lean M 08 subAv2

description:
Adipocytes were isolated using collagenase digestion of abdominal subcutaneous fat needle biopsies. Array type: HG_U95Av2. Subject: lean male Pima Indian (LM08).
Keywords = adipocyte
Keywords = obesity
Keywords = inflammation
Keywords = gene expression


title: Lean F 08 subAv2

description:
Adipocytes were isolated using collagenase digestion of abdominal subcutaneous fat needle biopsies. Array type: HG_U95Av2. Subject: lean female Pima Indian (LF08).
Keywords = adipocyte
Keywords = obesity
Keywords = inflammation
Keywords = gene expression


title: Lean F 09 subAv2

description:
Adipocytes were isolated using collagenase digestion of abdominal subcutaneous fat needle biopsies. Array type: HG_U95Av2. Subject: lean female Pima Indian (LF09).
Keywords = adipocyte
Keywords = obesity
Keywords = inflammation
Keywords = gene expression


title: Lean F 07 subAv2

description:
Adipocytes were isolated using collagenase digestion of abdominal subcutaneous fat needle biopsies. Array type: HG_U95Av2. Subject: lean female Pima Indian (LF07).
Keywords = adipocyte
Keywords = obesity
Keywords = inflammation
Keywords = gene expression


title: Expression data of CCMS_07

description:
MSS, proximal
Training-Lymph(-)


title: Lean F 06 subAv2

description:
Adipocytes were isolated using collagenase digestion of abdominal subcutaneous fat needle biopsies. Array type: HG_U95Av2. Subject: lean female Pima Indian (LF06).
Keywords = adipocyte
Keywords = obesity
Keywords = inflammation
Keywords = gene expression


title: Lean M 07 subAv2

description:
Adipocytes were isolated using collagenase digestion of abdominal subcutaneous fat needle biopsies. Array type: HG_U95Av2. Subject: lean male Pima Indian (LM07).
Keywords = adipocyte
Keywords = obesity
Keywords = inflammation
Keywords = gene expression


title: Lean F 10 subAv2

description:
Adipocytes were isolated using collagenase digestion of abdominal subcutaneous fat needle biopsies. Array type: HG_U95Av2. Subject: lean female Pima Indian (LF10).
Keywords = adipocyte
Keywords = obesity
Keywords = inflammation
Keywords = gene expression


title: Heart_r2

description: Technical replicate 2 (labeling and hybridization)

tag: Heart