title: Neonatal male HHR heart 2_miRNA

description:
BHM2
microRNA expression from neonatal male HHR heart

value: 2 days old


title: OSKM_2

status: Public on Dec 01 2017

type: RNA

city: Kyoto

first: Kazutoshi

last: Takahashi

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

department: Center for iPS Cell Research and Application

country: Japan

institute: Kyoto University

description: Human dermal fibroblasts expressing OSKM, replicate 2

hyb_protocol: Manufature's protocol

scan_protocol: Slides were scanned on the G2565CA Microarray Scanner System (Agilent).

data_processing: GeneSpring GX. Signals were normalized to percentile.

molecule: total RNA

organism: Homo sapiens

label_protocol: Manufature's protocol

growth_protocol: Somatic cell lines were maintained in appropriate conditions according to manufacturer's recommendation.   TRA-1-60 (+) cells and iPSCs were maintained on SNL feeders in Primate ESC medium (ReproCELL) supplemented with 4 ng/ml basic fibroblast growth factor at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using the miReasy Purification kit (Qiagen) following the manufacturer's recommendations, and quantified using a NanoDrop-1000   spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: The samples on day3 were EGFP (+) cells collected by flow cytometry. TRA-1-60 (+) cells on days 7-28 were collected by magnetic activated cell sorting.

tag: cell type

value: Reprogramming cells


title: U937 cells transduced with pCDH-MSCV-puro-DNMT3A-R882H lentivirus vector_expression

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Normalize with RMA by Affymetrix Expression Console Ver 1.2

label: biotin

source_name: Human promyelocytic leukemia cell line_U937_DNMT3A-R882H

label_protocol: Standard Affymetrix protocol

growth_protocol: The human promyelocytic leukemia cells, U937 were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, and 1× antibiotic-antimycotic (Gibco by Life Technologies) in a humidified chamber with 5% CO2 atmosphere at 37°C

extract_protocol: Total RNA was isolated from LV appendages with the TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and was further purified and concentrated by using the WelPrep tissue RNA array (Welgene, Taipei, Taiwan). The quality and quantity of total RNA were analyzed by using a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA)

treatment_protocol: Cultured U937 cells were infected with lentivirus in the presence of 8 µg/ml polybrene (Sigma) and cultured for 72 hours. The infected cells were selected with 2 µg/mL puromycin for 2-weeks to obtain stable clones. DNMT3A WT/mutants expression was checked by immunoblot analysis and stable cells used for RNA extraction for microarray analysis.

tag: cell line

value: Human promyelocytic leukemia cell line

tag: tissue

value: Blood


title: SKM_1

description: Human dermal fibroblasts expressing SKM, replicate 1


title: Mock_3

description: Human dermal fibroblasts introduced empty vector (Mock), replicate 3


title: Neonatal male HHR heart 1_miRNA

city: Melbourne

first: Francine

last: Marques

state: VIC

address: Level 3, 75 Commercial Rd

country: Australia

institute: Baker IDI Heart and Diabetes

description:
BHM1
microRNA expression from neonatal male HHR heart

hyb_protocol: After fragmentation, samples were hybridized for 20 hr at 55°C to Agilent Rat miRNA Microarrays (V3, release 16.0). Chips were washed and stained in the Agilent Microarray Hybridization Chamber SureHyb. The Agilent’s miRNA Complete Labeling and Hyb Kit was used according to Agilent's manual.

scan_protocol: The chips were scanned on an Agilent G2565BA scanner.

data_processing: The samples were between array normalized so that expression intensities were similar across all arrays using the quantile method, in the R application (version 2.11.1). Differentially expressed miRNAs were identified using the moderated two-sample t-test in the Limma package.

organism: Rattus norvegicus

source_name: Neonatal male HHR heart

label_protocol: 100ng of total RNA was prepared for hybridisation according to the standard Agilent protocol (microRNA Labeling & Hybridization Kit Manual, Agilent, Version 1.7, October 2009).

growth_protocol: The whole heart from neonatal animals was obtained immediately after euthanasia.

extract_protocol: miRNeasy kit (Qiagen) was used for extraction of total RNA and microRNA according to the manufacturer's instructions.

treatment_protocol: Tissue was transferred either into microtubes and immediately frozen with liquid nitrogen. It was then preserved at -80°C before RNA extraction.

tag: gender

value: Male

value: heart

tag: strain

value: HHR

tag: age

tag: heart size

value: Hypetrophic


title: Mock_1

description: Human dermal fibroblasts introduced empty vector (Mock), replicate 1


title: OKM_3

description: Human dermal fibroblasts expressing OKM, replicate 3


title: U937 cells transduced with pCDH-MSCV-puro-DNMT3A-R882C lentivirus vector_expression

source_name: Human promyelocytic leukemia cell line_U937_DNMT3A-R882C


title: Neonatal female HHR heart 1_miRNA

description:
BHF1
microRNA expression from neonatal female HHR heart

source_name: Neonatal female HHR heart

value: Female


title: Primary NB tissue of NB2

city: Kitaadachi-gun Ina town

first: Takehiko

last: Kamijo

state: Saitama

address: 780, Komuro

institute: Saitama Cancer Center

description: Gene expression data from tumor tissue of NB2

hyb_protocol: Labeled samples were hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 Array, Affimetrix #900.

scan_protocol: GeneChip Scaner 3000 was used.

data_processing: Expression data were processed MAS5.0 algorithm and normalized using quantile normalization method.

source_name: Primary NB tissue isolated from patient No.2(NB2)

label_protocol: cDNA was synthesized using the GeneChIP 3′ IVT Express Kit (Affymetrix) according to the manufacturers’ protocols.

growth_protocol: Isolated from bone marrow aspirates using Lymphoprep and were cultured in sphere forming medium until form sphere.

extract_protocol: Total RNA was extracted using IsogenII according to the manufacture's instructions.

treatment_protocol: Cells were collected after isolation or sphere formation.

value: patient bone marrow

value: neuroblastoma

tag: tumor

value: stage4, MYCN amplified

tag: patient number

value: 31m, newly diagnose


title: U937 cells transduced with pCDH-MSCV-puro lentivirus vector_expression

source_name: Human promyelocytic leukemia cell line_U937_empty vector


title: SKM_2

description: Human dermal fibroblasts expressing SKM, replicate 2


title: SKM_3

description: Human dermal fibroblasts expressing SKM, replicate 3


title: U937 cells transduced with pCDH-MSCV-puro-DNMT3A-WT lentivirus vector_expression

source_name: Human promyelocytic leukemia cell line_U937_DNMT3A-WT


title: OSM_3

description: Human dermal fibroblasts expressing OSM, replicate 3


title: Neonatal female HHR heart 4_miRNA

description:
BHF4
microRNA expression from neonatal female HHR heart


title: Primary NB sphere of NB1

description: Gene expression data from tumor supere of NB1

source_name: Primary NB sphere isolated from patient No.1(NB1)

value: 120m, relapse


title: OSKM_1

description: Human dermal fibroblasts expressing OSKM, replicate 1


title: 15-C3C-Exon

city: Callaghan

first: Murray

middle: J

last: Cairns

state: NSW

address: University Drive

institute: University of Newcastle

description: RMA expression value derived from Expression Console software; core-gene analysis and core-exon analysis

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the Hunter Medical Research Institute (HMRI).

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Normalisation and summarisation were performed in Expression Console. The resulting gene and exon level CHP files were analysed using Genespring GX.

source_name: SH-SY5Y cells Cytoplasm, biological replicate 3

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Cells were grown in high-glucose DMEM with 10% FCS under standard conditions

extract_protocol: TRIzol extraction with addition of 2ul glycogen during precipitation step, and overnight precipitation.

treatment_protocol: Nucleus and Cytoplasm were fractionated by hypotonic lysis.

value: undifferentiated SH-SY5Y cells


title: 8-C2N-Exon

source_name: SH-SY5Y cells Nucleus, biological replicate 2


title: 14-C3N-Exon

source_name: SH-SY5Y cells Nucleus, biological replicate 3


title: 3-C1C-Exon

source_name: SH-SY5Y cells Cytoplasm, biological replicate 1


title: 2-C1N-Exon

source_name: SH-SY5Y cells Nucleus, biological replicate 1


title: OSM_2

description: Human dermal fibroblasts expressing OSM, replicate 2


title: HEK

description: Human embryonic karatinocytes

source_name: Human embryonic karatinocytes

value: Somatic cell line


title: 9-C2C-Exon

source_name: SH-SY5Y cells Cytoplasm, biological replicate 2


title: OKM_2

description: Human dermal fibroblasts expressing OKM, replicate 2


title: OSM_1

description: Human dermal fibroblasts expressing OSM, replicate 1


title: KM_2

description: Human dermal fibroblasts expressing KM, replicate 2


title: SM_3

description: Human dermal fibroblasts expressing SM, replicate 3


title: OSK_1

description: Human dermal fibroblasts expressing OSK, replicate 1


title: Primary NB tissue of NB1

description: Gene expression data from tumor tissue of NB1

source_name: Primary NB tissue isolated from patient No.1(NB1)


title: SM_2

description: Human dermal fibroblasts expressing SM, replicate 2


title: SK_1

description: Human dermal fibroblasts expressing SK, replicate 1


title: SK_2

description: Human dermal fibroblasts expressing SK, replicate 2


title: KM_1

description: Human dermal fibroblasts expressing KM, replicate 1


title: OM_1

description: Human dermal fibroblasts expressing OM, replicate 1


title: OKM_1

description: Human dermal fibroblasts expressing OKM, replicate 1


title: OSK_3

description: Human dermal fibroblasts expressing OSK, replicate 3


title: OK_3

description: Human dermal fibroblasts expressing OK, replicate 3


title: SK_3

description: Human dermal fibroblasts expressing SK, replicate 3


title: KM_3

description: Human dermal fibroblasts expressing KM, replicate 3


title: OSK_2

description: Human dermal fibroblasts expressing OSK, replicate 2


title: OK_2

description: Human dermal fibroblasts expressing OK, replicate 2


title: OM_2

description: Human dermal fibroblasts expressing OM, replicate 2


title: SM_1

description: Human dermal fibroblasts expressing SM, replicate 1


title: Primary NB sphere of NB2

description: Gene expression data from tumor supere of NB2

source_name: Primary NB sphere isolated from patient No.2(NB2)


title: OS_2

description: Human dermal fibroblasts expressing OS, replicate 2


title: OK_1

description: Human dermal fibroblasts expressing OK, replicate 1


title: OS_1

description: Human dermal fibroblasts expressing OS, replicate 1


title: K_3

description: Human dermal fibroblasts expressing K, replicate 3


title: OM_3

description: Human dermal fibroblasts expressing OM, replicate 3


title: OS_3

description: Human dermal fibroblasts expressing OS, replicate 3


title: M_1

description: Human dermal fibroblasts expressing M, replicate 1


title: Plakoglobin ChIP 1

type: genomic

city: Berne

first: Christian

last: Strauss

address: Laengassstrasse 122

country: Switzerland

institute: Institute of Animal Pathology

description: ChIP-chip mouse keratinocytes at onset of terminal differentiation using Plakoglobin antibodies

hyb_protocol: according to NimbleGen standart protocol, performed by NimbleGen

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

data_processing:
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.
Publication conclusions based on MEAN scaled, log2 (ChIP/Input) ratios.
Supplementary processed data files: "mean".txt and "peaks".txt.

molecule: genomic DNA

organism: Mus musculus

source_name: Plakoglobin (PG) ChIP DNA from mouse keratinocytes

growth_protocol: keratinocytes were grown till confluency, then four days in high calcium medium and harvested

extract_protocol: Four days after calcium switch, keratinocytes grown in 4x75cm2 flasks were washed with PBS(+) and proteins cross-linked with 2mM di-succinimidyl-glutarate(5) for 45min at RT followed by 1% formaldehyde for 15min at RT. Cells were scraped into 3ml PBS(+), centrifuged at 1,000rpm for 10min at RT and cell pellets lysed with 500μl lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.0). To shear DNA, lysates were sonicated in a Covaris S2 water bath sonicator (Covaris; Raublingen, Germany) with settings for 500bp DNA fragment length, confirmed by BioAnalyzer©. Samples were diluted 1:1 with 70mM HEPES, pH 7.5, 2.5mM NaCl, 1.5mM EDTA, 1.5% Triton-X100, 0.6% Deoxycholate (DOC) and centrifuged for 30min at 14,000rpm (Centrifuge 5417R, Eppendorf). The supernatant was pre-cleared with tRNA blocked Dynabeads® (Invitrogen Switzerland) for 2h at 4°C by rotation (Input). Immunoprecipitation was performed by rotating with 5µg antibody (PG, β-catenin (BD Biosciences)) per 1ml lysate at 4°C overnight, and 30µl Dynabeads® (pre-blocked with 1mg/ml tRNA for 1h at 4°C rotating) were added the next day for 3h at 4°C. Beads were washed twice with 1ml mixed micelle washing buffer (150mM NaCl, 100mM Tris-HCl, pH 8.1, 100mM EDTA, pH 8.0, 5% w/v sucrose, 0.02% NaN3, 1% Triton X-100, 0.2% SDS), twice with 1ml buffer 500 (0.1% DOC, 1mM EDTA, pH 8.0, 50mM HEPES, pH 7.5, 500mM NaCl, 1% Triton X-100, 0.2% NaN3), twice with 1ml LiCl buffer (0.5% DOC, 1mM EDTA, pH 8.0, 250mM LiCl, 0.5% NP-40, 10mM Tris-HCl, pH 8.0, 0.2% NaN3) and once with 1ml TE buffer. Protein-DNA complexes were eluted with 100µl elution buffer (1% SDS, 1mM NaHCO3) for 2x30min at 60°C. Samples were diluted 1:1 with TE buffer and NaCl (0.5M final concentration), reverse cross-linked overnight at 65°C followed by 100ng/µl proteinase K and 100ng/µl RNase A treatment for 1h at 55°C. A tenth volume 4M LiCl was added and proteins extracted with phenol:chloroform:isoamyl alcohol. DNA was precipitated with 100% ice cold ethanol and washed with 70% ethanol before resuspending in 50µl dH2O. The input sample was treated in the same way. The DNA amount was determined using NanoDrop

treatment_protocol: at confluency, terminal differentiation was initiated with high calcium medium

value: keratinocytes

tag: chip antibody

value: Plakoglobin

tag: chip antibody vendor

value: BD Biosciences

tag: chip antibody catalog#

source_name: Input DNA from mouse keratinocytes

value: none, input DNA


title: S_2

description: Human dermal fibroblasts expressing S, replicate 2

value: Reprogramming cells


title: O_3

description: Human dermal fibroblasts expressing O, replicate 3


title: S_3

description: Human dermal fibroblasts expressing S, replicate 3


title: M_2

description: Human dermal fibroblasts expressing M, replicate 2


title: K_1

description: Human dermal fibroblasts expressing K, replicate 1


title: HPrEC_d28_2

description: TRA-1-60 (+) cells expressing OSKM on day 28 derived from Human prostate epithelial cells, replicate2


title: HPrEC_d28_1

description: TRA-1-60 (+) cells expressing OSKM on day 28 derived from Human prostate epithelial cells, replicate1


title: HPrEC_d20_2

description: TRA-1-60 (+) cells expressing OSKM on day 20 derived from Human prostate epithelial cells, replicate2


title: HPrEC_d20_3

description: TRA-1-60 (+) cells expressing OSKM on day 20 derived from Human prostate epithelial cells, replicate3


title: S_1

description: Human dermal fibroblasts expressing S, replicate 1


title: HPrEC_d15_3

description: TRA-1-60 (+) cells expressing OSKM on day 15 derived from Human prostate epithelial cells, replicate3


title: HPrEC_d28_3

description: TRA-1-60 (+) cells expressing OSKM on day 28 derived from Human prostate epithelial cells, replicate3


title: HPrEC_d20_1

description: TRA-1-60 (+) cells expressing OSKM on day 20 derived from Human prostate epithelial cells, replicate1


title: HPrEC_d11_3

description: TRA-1-60 (+) cells expressing OSKM on day 11 derived from Human prostate epithelial cells, replicate3


title: HPrEC_d15_2

description: TRA-1-60 (+) cells expressing OSKM on day 15 derived from Human prostate epithelial cells, replicate2


title: O_2

description: Human dermal fibroblasts expressing O, replicate 2


title: M_3

description: Human dermal fibroblasts expressing M, replicate 3


title: HPrEC_d11_1

description: TRA-1-60 (+) cells expressing OSKM on day 11 derived from Human prostate epithelial cells, replicate1


title: HPrEC_d15_1

description: TRA-1-60 (+) cells expressing OSKM on day 15 derived from Human prostate epithelial cells, replicate1


title: HPrEC_d7_3

description: TRA-1-60 (+) cells expressing OSKM on day 7 derived from Human prostate epithelial cells, replicate3


title: HPrEC_d11_2

description: TRA-1-60 (+) cells expressing OSKM on day 11 derived from Human prostate epithelial cells, replicate2


title: P60_EMI2_ko-1

city: Singapore

first: Diana

middle: HP

last: Low

address: #03-06, 61 Biopolis Drive, Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with limma and beadarray in R

source_name: Testis

label_protocol: cRNA was prepared with Illumina® TotalPrep RNA kit according to the manufacturer's protocol  Illumina Total Prep RNA Amplification Kit

growth_protocol: Mouse whole testis were isolated from either wildtype or Emi2 KO mice at various timepoints : p12,p21,p30,p60

extract_protocol: RNA was isolated with Life Technologies' PureLink RNA mini kit according to the manufacturer's protocol.

tag: genotype/variation


title: P30_EMI2_ko-2


title: HPrEC_d3_3

description: EGFP (+) cells expressing OSKM on day 3 derived from Human prostate epithelial cells, replicate3


title: P60_EMI2_ko-2


title: P60_wt-2

value: wild type


title: P60_wt-1


title: HPrEC_d7_1

description: TRA-1-60 (+) cells expressing OSKM on day 7 derived from Human prostate epithelial cells, replicate1


title: P30_EMI2_ko-1


title: P30_wt-2


title: P30_wt-1


title: P21_EMI2_ko-2


title: P21_wt-1


title: HPrEC_d0_2

description: Human prostate epithelial cells, replicate2

value: Parental cell line


title: HPrEC_d0_3

description: Human prostate epithelial cells, replicate3


title: HPrEC_d3_2

description: EGFP (+) cells expressing OSKM on day 3 derived from Human prostate epithelial cells, replicate2


title: HPrEC_d7_2

description: TRA-1-60 (+) cells expressing OSKM on day 7 derived from Human prostate epithelial cells, replicate2


title: P21_EMI2_ko-1


title: HPrEC_d3_1

description: EGFP (+) cells expressing OSKM on day 3 derived from Human prostate epithelial cells, replicate1


title: HPrEC_d0_1

description: Human prostate epithelial cells, replicate1


title: P15_wt-2


title: P15_EMI2_ko-2


title: HBEC_d28_3

description: TRA-1-60 (+) cells expressing OSKM on day 28 derived from Human bronchial epithelial cells, replicate3


title: P21_wt-2


title: HBEC_d20_3

description: TRA-1-60 (+) cells expressing OSKM on day 20 derived from Human bronchial epithelial cells, replicate3


title: HBEC_d28_2

description: TRA-1-60 (+) cells expressing OSKM on day 28 derived from Human bronchial epithelial cells, replicate2


title: P15_wt-1


title: Reactive hyperleukocytosis leucocytes, sample #2

city: BORDEAUX

first: Bruno

last: CARDINAUD

address: 146 rue Leo Saignat

department: INSERM U1035

country: France

institute: Bordeaux University

hyb_protocol: The totality of the labeled RNA were resuspended in 45ul of a mix containing 18ul of nuclease-free water, 4.5 ul of 10X GE Blocking agent, 22.5ul of 2xHi-RPM Hybridization buffer. After a 100°C/5min incubation, the labeled RNA were hybridized to Agilent-019118 Human miRNA Microarray 2.0 for 16 hours at 55°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minutes at room temperature with GE Wash Buffer 1 (Agilent) then 5 minutes with 37°C GE Wash buffer 2 (Agilent). Slides were then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent B DNA Microarray Scanner using settings for 4x44k one color slides (eXtended Dynamic Range, scan area 61x21.6 mm, Scan resolution 5um, dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol miRNA_V1_95_May07_Feb07 and Grid: 019118_D_20080214) to obtain background subtracted and spatially detrended Processed Signal intensities.  Quantile normalization with BRB array tools.

source_name: blood leukocytes

label_protocol: 200ng of total RNA were Cy3-labeled using the miRNA complete labeling kit (5190-0456), following the manufacturer's instructions. After removal of the unincorporated nucleotides using a BioRad micro Bio-Spin 6 columns (Biorad), the labeled RNA were dried using a vacuum concentrator at 45°C

extract_protocol: RNA was prepared using the Trizol kit ThermoFisher). The first steps of the extraction were performed following the manufacturer's recommendations. After phases separation, Ethanol (1.5volume) was added to the aqueous phase and the mix was deposited onto a RNeasy column (Qiagen) and RNA were purified following the RNA cleanup protocol supplied by the manufacturer. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored using agarose gel electrophoresis.

value: blood

value: leukocytes

tag: diagnosis

value: Reactive hyperleukocytosis


title: Reactive hyperleukocytosis leucocytes, sample #3


title: Reactive hyperleukocytosis leucocytes, sample #4


title: Reactive hyperleukocytosis leucocytes, sample #1


title: HBEC_d28_1

description: TRA-1-60 (+) cells expressing OSKM on day 28 derived from Human bronchial epithelial cells, replicate1


title: HBEC_d20_2

description: TRA-1-60 (+) cells expressing OSKM on day 20 derived from Human bronchial epithelial cells, replicate2


title: chronic myeloid leukemia leucocytes, sample#9

value: chronic myeloid leukemia


title: P15_EMI2_ko-1


title: HBEC_d15_3

description: TRA-1-60 (+) cells expressing OSKM on day 15 derived from Human bronchial epithelial cells, replicate3


title: HBEC_d20_1

description: TRA-1-60 (+) cells expressing OSKM on day 20 derived from Human bronchial epithelial cells, replicate1


title: chronic myeloid leukemia leukocytes, sample#8


title: chronic myeloid leukemia leukocytes, sample#7


title: HBEC_d15_2

description: TRA-1-60 (+) cells expressing OSKM on day 15 derived from Human bronchial epithelial cells, replicate2


title: HBEC_d11_2

description: TRA-1-60 (+) cells expressing OSKM on day 11 derived from Human bronchial epithelial cells, replicate2


title: chronic myeloid leukemia leukocytes, sample#6


title: K_2

description: Human dermal fibroblasts expressing K, replicate 2


title: HBEC_d11_1

description: TRA-1-60 (+) cells expressing OSKM on day 11 derived from Human bronchial epithelial cells, replicate1


title: HBEC_d7_3

description: TRA-1-60 (+) cells expressing OSKM on day 7 derived from Human bronchial epithelial cells, replicate3


title: HBEC_d11_3

description: TRA-1-60 (+) cells expressing OSKM on day 11 derived from Human bronchial epithelial cells, replicate3


title: HBEC_d15_1

description: TRA-1-60 (+) cells expressing OSKM on day 15 derived from Human bronchial epithelial cells, replicate1


title: breast_tissue_17_oxBS

city: Hanover

first: Kevin

middle: Crowley

last: Johnson

state: NH

address: 72 College Street

department: Epidemiology

country: USA

institute: Geisel School of Medicine at Dartmouth College

description: tissue17_oxBS derived from the same biological sample

hyb_protocol: 1.4ug was carried forward through oxBS conversion with the TrueMethyl protocol, and 1.05ug through the bisulfite conversion arm of the protocol with manufacturer recommended mass and volume.  DNA was then hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

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

data_processing:
minfi, Aryee et al Bioinformatics 2014
minfi, Aryee et al Bioinformatics 2014
We used maximum likelihood to fit the data generating model under the constraints of each C modification (5C, 5mC, 5hmC) > 0, 5C + 5mC + 5hmC = 1, thus estimating parameters 5C (unmethylated proportion), 5mC  (5mC proportion), and 5hmC (5hmC proportion)

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: Tumor DNA was extracted with the QIAmp DNeasy tissue kit (Qiagen) according to the manufacturer’s instructions.

value: Breast tissue

tag: Sex

value: Female

tag: subject bmi

tag: subject age


title: chronic myeloid leukemia leukocytes, sample#5

tag: cell type


title: breast_tissue_14_oxBS

description: tissue14_oxBS derived from the same biological sample


title: chronic myeloid leukemia leukocytes, sample#3


title: breast_tissue_15_oxBS

description: tissue15_oxBS derived from the same biological sample


title: chronic myeloid leukemia leukocytes, sample#4


title: chronic myeloid leukemia leukocytes, sample#2


title: HBEC_d7_2

description: TRA-1-60 (+) cells expressing OSKM on day 7 derived from Human bronchial epithelial cells, replicate2


title: breast_tissue_16_oxBS

description: tissue16_oxBS derived from the same biological sample


title: HBEC_d7_1

description: TRA-1-60 (+) cells expressing OSKM on day 7 derived from Human bronchial epithelial cells, replicate1


title: chronic myeloid leukemia leukocytes, sample#1


title: chronic myeloid leukemia leukocytes, sample#10


title: atypical MPN leukocytes, sample#9

value: Atypical Myeloproliferative Neoplasms


title: HBEC_d3_1

description: EGFP (+) cells expressing OSKM on day 3 derived from Human bronchial epithelial cells, replicate1


title: atypical MPN leukocytes, sample#8


title: HBEC_d3_2

description: EGFP (+) cells expressing OSKM on day 3 derived from Human bronchial epithelial cells, replicate2


title: breast_tissue_18_oxBS

description: tissue18_oxBS derived from the same biological sample


title: atypical MPN leukocytes, sample#5


title: breast_tissue_7_oxBS

description: tissue7_oxBS derived from the same biological sample


title: atypical MPN leukocytes, sample#7


title: atypical MPN leukocytes, sample#6


title: breast_tissue_11_oxBS

description: tissue11_oxBS derived from the same biological sample


title: breast_tissue_13_oxBS

description: tissue13_oxBS derived from the same biological sample


title: atypical MPN leukocytes, sample#4


title: HBEC_d0_3

description: Human bronchial epithelial cells, replicate3


title: breast_tissue_6_oxBS

description: tissue6_oxBS derived from the same biological sample


title: HBEC_d0_1

description: Human bronchial epithelial cells, replicate1


title: HBEC_d0_2

description: Human bronchial epithelial cells, replicate2


title: HA_d28_2

description: TRA-1-60 (+) cells expressing OSKM on day 28 derived from Human astrocytes, replicate2


title: atypical MPN leukocytes, sample#3


title: HA_d28_1

description: TRA-1-60 (+) cells expressing OSKM on day 28 derived from Human astrocytes, replicate1


title: O_1

description: Human dermal fibroblasts expressing O, replicate 1


title: HBEC_d3_3

description: EGFP (+) cells expressing OSKM on day 3 derived from Human bronchial epithelial cells, replicate3


title: HA_d28_3

description: TRA-1-60 (+) cells expressing OSKM on day 28 derived from Human astrocytes, replicate3


title: atypical MPN leukocytes, sample#2


title: atypical MPN leukocytes, sample#15


title: atypical MPN leukocytes, sample#14


title: atypical MPN leukocytes, sample#16


title: breast_tissue_12_oxBS

description: tissue12_oxBS derived from the same biological sample


title: breast_tissue_8_oxBS

description: tissue8_oxBS derived from the same biological sample


title: breast_tissue_9_oxBS

description: tissue9_oxBS derived from the same biological sample


title: breast_tissue_2_oxBS

description: tissue2_oxBS derived from the same biological sample


title: atypical MPN leukocytes, sample#11


title: atypical MPN leukocytes, sample#12


title: HA_d20_3

description: TRA-1-60 (+) cells expressing OSKM on day 20 derived from Human astrocytes, replicate3


title: atypical MPN leukocytes, sample#13


title: atypical MPN leukocytes, sample#10


title: atypical MPN leukocytes, sample#1


title: HA_d20_2

description: TRA-1-60 (+) cells expressing OSKM on day 20 derived from Human astrocytes, replicate2


title: HA_d11_2

description: TRA-1-60 (+) cells expressing OSKM on day 11 derived from Human astrocytes, replicate2


title: HA_d15_3

description: TRA-1-60 (+) cells expressing OSKM on day 15 derived from Human astrocytes, replicate3


title: HA_d11_1

description: TRA-1-60 (+) cells expressing OSKM on day 11 derived from Human astrocytes, replicate1


title: HA_d7_3

description: TRA-1-60 (+) cells expressing OSKM on day 7 derived from Human astrocytes, replicate3


title: HA_d15_2

description: TRA-1-60 (+) cells expressing OSKM on day 15 derived from Human astrocytes, replicate2


title: HA_d15_1

description: TRA-1-60 (+) cells expressing OSKM on day 15 derived from Human astrocytes, replicate1


title: breast_tissue_4_oxBS

description: tissue4_oxBS derived from the same biological sample


title: HA_d20_1

description: TRA-1-60 (+) cells expressing OSKM on day 20 derived from Human astrocytes, replicate1


title: HA_d11_3

description: TRA-1-60 (+) cells expressing OSKM on day 11 derived from Human astrocytes, replicate3


title: breast_tissue_5_oxBS

description: tissue5_oxBS derived from the same biological sample


title: breast_tissue_1_oxBS

description: tissue1_oxBS derived from the same biological sample


title: HA_d7_2

description: TRA-1-60 (+) cells expressing OSKM on day 7 derived from Human astrocytes, replicate2


title: MELA_0226

city: North Sydney

first: Graham

middle: J.

last: Mann

address: Poche Centre, 40 Rocklands Road

institute: Melanoma Institute Australia

description: HumanWG-6 v3 Expression BeadChip

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: NEQC normalisation (default parameters) was separately applied to each of the AJCC stage II and AJCC stage IV datasets (http://nar.oxfordjournals.org/content/38/22/e204). Probes for which there were no samples with a detection p-value of less than 0.01 were removed.

source_name: AJCC stage IV melanoma

label_protocol: Labeling was performed per manufacturer’s instructions.

growth_protocol: Total RNA was extracted from 20-30mg of fresh frozen tissue.

extract_protocol: The RNA was isolated and purified with an RNeasy purification kit (Qiagen RNeasy purification kit- Qiagen Pty Ltd., Clifton Hill, Victoria, Australia) with DNAse I digestion on the column. The quality of the RNA preparations was assessed using the Agilent 2100 Bioanalyser (Agilent Technologies, Palo Alto, CA, USA). RNA integrity scores were >8 for all samples analyzed.

treatment_protocol: Tissue samples were homogenized using a high-speed agitation polytron blender (Kinematica, Luzern, Switzerland) in the presence of Trizol.

tag: region

value: Lymph nodes- Axilla


title: MELA_0040

description: HumanWG-6 v3 Expression BeadChip

value: Lymph nodes- Groin


title: HA_d3_2

description: EGFP (+) cells expressing OSKM on day 3 derived from Human astrocytes, replicate2


title: HA_d0_3

description: Human astrocytes, replicate3

source_name: Human astrocytes, replicate3

value: Somatic cell line


title: HA_d3_1

description: EGFP (+) cells expressing OSKM on day 3 derived from Human astrocytes, replicate1


title: MELA_0052

description: HumanWG-6 v3 Expression BeadChip


title: MELA_0163

description: HumanWG-6 v3 Expression BeadChip


title: HA_d0_2

description: Human astrocytes, replicate2

source_name: Human astrocytes, replicate2


title: MELA_0078

description: HumanWG-6 v3 Expression BeadChip

value: Lymph nodes- Inguinal


title: MELA_0044

description: HumanWG-6 v3 Expression BeadChip


title: HA_d3_3

description: EGFP (+) cells expressing OSKM on day 3 derived from Human astrocytes, replicate3


title: HA_d0_1

description: Human astrocytes, replicate1

source_name: Human astrocytes, replicate1


title: HAdMSC_d28_1

description: TRA-1-60 (+) cells expressing OSKM on day 28 derived from Human adipose-derived mesenchymal stem cells, replicate1


title: HA_d7_1

description: TRA-1-60 (+) cells expressing OSKM on day 7 derived from Human astrocytes, replicate1


title: HAdMSC_d28_3

description: TRA-1-60 (+) cells expressing OSKM on day 28 derived from Human adipose-derived mesenchymal stem cells, replicate3


title: Neonatal female NHR heart 2

description: Gene expression from neonatal female NHR heart

hyb_protocol: After fragmentation, ssDNA was hybridized for 17 hr at 45°C to GeneChip Human Gene 1.0 ST Arrays. Chips were washed and stained in the Affymetrix GeneChip® Fluidics Stations 450. For all these steps, the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix) was used according to manufacturer’s recommendations (GeneChip® Whole Transcript (WT) Sense Target Labelling Assay Manual, version 4, Affymetrix).

scan_protocol: The chips were scanned using the GeneChip® Scanner 3000 7G 4C (Affymetrix) according to manufacturer’s recommendations (GeneChip® Whole Transcript (WT) Sense Target Labelling Assay Manual, version 4, Affymetrix).

data_processing: The samples were individually normalized using robust-multi-array analysis (RMA) in the R application (version 2.11.1). Differentially expressed genes were identified using the moderated two-sample t-test in the Limma package.

source_name: Neonatal female NHR heart

label_protocol: 100ng of total RNA was prepared for hybridisation according to the standard Affymetrix protocol (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual, version 4, Affymetrix).

tag: tissue

value: heart

value: NHR

value: 2 days old

value: Normal


title: Neonatal male NHR heart 3

description: Gene expression from neonatal male NHR heart

source_name: Neonatal male NHR heart

tag: gender

value: Male


title: HAdMSC_d28_2

description: TRA-1-60 (+) cells expressing OSKM on day 28 derived from Human adipose-derived mesenchymal stem cells, replicate2

value: Reprogramming cells


title: HAdMSC_d20_3

description: TRA-1-60 (+) cells expressing OSKM on day 20 derived from Human adipose-derived mesenchymal stem cells, replicate3


title: Neonatal male HHR heart 4

description: Gene expression from neonatal male HHR heart

source_name: Neonatal male HHR heart

tag: strain

value: HHR

value: Hypetrophic


title: Neonatal female NHR heart 4

tag: age


title: Neonatal male NHR heart 2

tag: heart size


title: HAdMSC_d20_2

description: TRA-1-60 (+) cells expressing OSKM on day 20 derived from Human adipose-derived mesenchymal stem cells, replicate2


title: Neonatal male NHR heart 1


title: Neonatal female NHR heart 1


title: HAdMSC_d15_2

description: TRA-1-60 (+) cells expressing OSKM on day 15 derived from Human adipose-derived mesenchymal stem cells, replicate2


title: Neonatal female NHR heart 3


title: HAdMSC_d15_3

description: TRA-1-60 (+) cells expressing OSKM on day 15 derived from Human adipose-derived mesenchymal stem cells, replicate3


title: HAdMSC_d20_1

description: TRA-1-60 (+) cells expressing OSKM on day 20 derived from Human adipose-derived mesenchymal stem cells, replicate1


title: Neonatal male HHR heart 2


title: HAdMSC_d11_3

description: TRA-1-60 (+) cells expressing OSKM on day 11 derived from Human adipose-derived mesenchymal stem cells, replicate3


title: Neonatal male HHR heart 1


title: Healthy sample_9 Dnase-treated

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Circulatory miRNAs expression was analyzed

hyb_protocol: The labelled samples were hybridized on the Human miRNA 8x60K Arrays at 55°C for 20 hours. The wahing was performed using Gene Expression Wash Buffer1 (Agilent Technologies, Part Number 5188-5325) at room temperature for 5 minutes and Gene Expression Wash Buffer 2 (Agilent Technologies, Part Number 5188-5326) at 37oC for 5 minutes.

scan_protocol: Scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D) at 5 micron resolution.

data_processing: Images were quantified using Feature Extraction Software (Agilent). Data was analyzed using GeneSpring GX Software. 75th Percentile Normalization and miRNA-based anaysis was performed.

source_name: healthy_peripheral  blood

label_protocol: The miRNA labeling was performed using miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Part Number: 5190-0456).The total RNA sample was diluted to 100ng/ul in nuclease free water. About 200ng of total RNA was dephosphorylated using Calf Intestinal Alkaline Phosphatase (CIP) master mix (Agilent Technologies, Part Number: 5190-0456) by incubating at 37°C for 30 minutes. The dephosphorylated miRNA sample was denatured by adding Dimethyl Sulfoxide and heating at 100 °C for 10 minutes and transferred to ice-water bath. The Ligation master mix (Agilent Technologies, Part Number: 5190-0456) containing Cyanine 3-pCp was added to the denatured miRNA sample and incubated at 16°C for 2 hours. The Cyanine 3-pCp labeled miRNA sample was dried completely in the vacuum concentrator (Eppendorf, Concentrator Plus, Catalog Number 5305000) at 45°C for 2 hour. The dried sample was resuspended in nuclease free water and mixed with Hybridization Mix containing blocking solution (Agilent Technologies, Part Number: 5190-0456) and Hi-RPM Hybridization Buffer (Agilent Technologies, Part Number: 5190-0456) and incubated at 100°C for 5 minutes followed by snap chill on ice for 5 minutes.

extract_protocol: RNA was extracted using Qiamp Circulating Nucleic acid kit Catalog no. 55114

tag: subject status

value: healthy subject

value: Whole Blood


title: HAdMSC_d15_1

description: TRA-1-60 (+) cells expressing OSKM on day 15 derived from Human adipose-derived mesenchymal stem cells, replicate1


title: HAdMSC_d7_3

description: TRA-1-60 (+) cells expressing OSKM on day 7 derived from Human adipose-derived mesenchymal stem cells, replicate3


title: Neonatal male HHR heart 3


title: breast_tissue_3_oxBS

description: tissue3_oxBS derived from the same biological sample

value: Breast tissue


title: HAdMSC_d11_1

description: TRA-1-60 (+) cells expressing OSKM on day 11 derived from Human adipose-derived mesenchymal stem cells, replicate1


title: Neonatal female HHR heart 2

description: Gene expression from neonatal female HHR heart

source_name: Neonatal female HHR heart

value: Female


title: Neonatal female HHR heart 3


title: Neonatal female HHR heart 1


title: Patient sample_5A

source_name: patient_peripheral  blood

value: chronic kidney disease patient


title: HAdMSC_d7_1

description: TRA-1-60 (+) cells expressing OSKM on day 7 derived from Human adipose-derived mesenchymal stem cells, replicate1


title: Patient sample_4A_Pooled


title: Patient sample_3A


title: Patient sample_7A


title: breast_tissue_10_oxBS

description: tissue10_oxBS derived from the same biological sample


title: Neonatal female HHR heart 4


title: Patient sample_2A


title: Patient sample_6A & 6B Pooled


title: HAdMSC_d11_2

description: TRA-1-60 (+) cells expressing OSKM on day 11 derived from Human adipose-derived mesenchymal stem cells, replicate2


title: HAdMSC_d3_3

description: EGFP (+) cells expressing OSKM on day 3 derived from Human adipose-derived mesenchymal stem cells, replicate3


title: HAdMSC_d7_2

description: TRA-1-60 (+) cells expressing OSKM on day 7 derived from Human adipose-derived mesenchymal stem cells, replicate2


title: HAdMSC_d0_3

description: Human adipose-derived mesenchymal stem cells, replicate3


title: HAdMSC_d3_1

description: EGFP (+) cells expressing OSKM on day 3 derived from Human adipose-derived mesenchymal stem cells, replicate1


title: HAdMSC_d3_2

description: EGFP (+) cells expressing OSKM on day 3 derived from Human adipose-derived mesenchymal stem cells, replicate2


title: HDF_d28_2

description: TRA-1-60 (+) cells expressing OSKM on day 28 derived from Human dermal fibroblasts, replicate2


title: HDF_d28_3

description: TRA-1-60 (+) cells expressing OSKM on day 28 derived from Human dermal fibroblasts, replicate3


title: HAdMSC_d0_1

description: Human adipose-derived mesenchymal stem cells, replicate1


title: Patient sample_1A

description: Circulatory miRNAs expression was analyzed


title: HDF_d28_1

description: TRA-1-60 (+) cells expressing OSKM on day 28 derived from Human dermal fibroblasts, replicate1


title: HDF_d15_1

description: TRA-1-60 (+) cells expressing OSKM on day 15 derived from Human dermal fibroblasts, replicate1


title: Hoxa9_MIY _2

city: Gothenburg

first: Lars

last: Palmqvist

address: Sahlgrenska University Hospital

department: Institute of Biomedicine

country: Sweden

institute: University of Gothenburg

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Expression Console software. Probe intensities, gene level expression were RMA summarized and then quantile normalized.
MoEx-1_0-st-v1.r2.pgf'
MoEx-1_0-st-v1.r2.mps

label: Biotin

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

extract_protocol: Qiagens RNeasy Plus mini kit

value: Cells from 12 week old 5-FU treated mice

value: Bone marrow

tag: developmental stage

value: Progenitor cells

value: Primary bone marrow culture

tag: genetic modification

value: Transduced with MSCV construct

tag: genetic characteristics

value: Overexpression of HOXA9 in WT mouse

tag: growth condition

value: DMEM 15% FCS, IL3, SCF, IL6


title: HDF_d15_3

description: TRA-1-60 (+) cells expressing OSKM on day 15 derived from Human dermal fibroblasts, replicate3


title: HDF_d20_1

description: TRA-1-60 (+) cells expressing OSKM on day 20 derived from Human dermal fibroblasts, replicate1


title: HA9_mir155_WT_II

value: Overexpression of HOXA9 and miR-155 in WT mouse


title: HDF_d11_2

description: TRA-1-60 (+) cells expressing OSKM on day 11 derived from Human dermal fibroblasts, replicate2


title: HDF_d11_3

description: TRA-1-60 (+) cells expressing OSKM on day 11 derived from Human dermal fibroblasts, replicate3


title: HA9_mir155_WT_III


title: HDF_d20_2

description: TRA-1-60 (+) cells expressing OSKM on day 20 derived from Human dermal fibroblasts, replicate2


title: HA9_mir155_WT_I


title: HDF_d3_3

description: EGFP (+) cells expressing OSKM on day 3 derived from Human dermal fibroblasts, replicate3


title: HDF_d20_3

description: TRA-1-60 (+) cells expressing OSKM on day 20 derived from Human dermal fibroblasts, replicate3


title: HA9_MIG_KO_III

value: Overexpression of HOXA9 in miR-155 KO mouse


title: HDF_d7_3

description: TRA-1-60 (+) cells expressing OSKM on day 7 derived from Human dermal fibroblasts, replicate3

value: Reprogramming cells


title: HDF_d15_2

description: TRA-1-60 (+) cells expressing OSKM on day 15 derived from Human dermal fibroblasts, replicate2


title: Hoxa9_MIY _1


title: HDF_d7_1

description: TRA-1-60 (+) cells expressing OSKM on day 7 derived from Human dermal fibroblasts, replicate1


title: HA9_MIG_WT_III


title: HDF_d11_1

description: TRA-1-60 (+) cells expressing OSKM on day 11 derived from Human dermal fibroblasts, replicate1


title: HDF_d7_2

description: TRA-1-60 (+) cells expressing OSKM on day 7 derived from Human dermal fibroblasts, replicate2


title: HA9_MIG_KO_I


title: HDF_d3_2

description: EGFP (+) cells expressing OSKM on day 3 derived from Human dermal fibroblasts, replicate2


title: HA9_MIG_KO_II


title: HA9_MIG_WT_II


title: HDF_d3_1

description: EGFP (+) cells expressing OSKM on day 3 derived from Human dermal fibroblasts, replicate1


title: Brain-Tumor-W55-1-1

city: Seattle

first: Ralph

middle: B.

last: Puchalski

state: WA

address: 550 17th Ave., Suite 570

institute: Swedish Neuroscience Institute

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing:
CHP files were created from CEL file intensities using the Affymetrix Genotyping Console using the BIRDSEED V2 algorithm with default settings. CHP files were imported into Partek Genomics Suite v6.6. Genotype Call (SNP call): AA, AB, BB, or NC (No Call).
Call Codes:Genotype Call (SNP call): AA, AB, BB, NC, and NoCall;        Confidence:confidence level;    Forced Call Codes:Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; Signal A:Signal intensity for Allele A; Signal B:Signal intensity for Allele B; Forward Strand Base Calls:Genotype Call (A,T,C,G)       Forced Forward Strand Base Calls:Genotype Call (A,T,C,G)

source_name: Glioblastoma

label_protocol: DNA labeling, hybridization (Genome-Wide Human SNP Array 6.0, Affymetrix®), and data extraction were performed by the Genome Technology Access Center, Washington University School of Medicine, St. Louis, MO.

extract_protocol: Genomic DNA was extracted from tumor tissues by using ChargeSwitch gDNA mini tissue kit (Life Tech, CA) per company protocol. Measurement of quality and quantity of genomic DNA was carried out by using Nanodrop ND-1000.

value: male


title: Brain-Tumor-W53-1-1-D


title: Brain-Tumor-W53-1-1-A


title: HDF_d0_3

description: Human dermal fibroblasts, replicate3

source_name: Human dermal fibroblasts, replicate3

value: Somatic cell line


title: Brain-Tumor-W54-1-1


title: Brain-Tumor-W50-1-1


title: Brain-Tumor-W22-2-1

value: female


title: Brain-Tumor-W42-1-1


title: Brain-Tumor-W43-1-1


title: Brain-Tumor-W48-2-1


title: Brain-Tumor-W45-1-1


title: Brain-Tumor-W48-1-1


title: Neonatal male NHR heart 4

description: Gene expression from neonatal male NHR heart

value: Male

value: heart

value: NHR

value: 2 days old

value: Normal


title: Brain-Tumor-W39-1-1


title: HDF_d0_1

description: Human dermal fibroblasts, replicate1

source_name: Human dermal fibroblasts, replicate1


title: HA9_MIG_WT_I

value: Female

value: Cells from 12 week old 5-FU treated mice

value: Bone marrow


title: HDF_d0_2

description: Human dermal fibroblasts, replicate2

source_name: Human dermal fibroblasts, replicate2


title: Seedling Replicate 1

city: Shanghai

first: Weihua

last: Tang

address: 300 Fenglin Rd

country: China

institute: Shanghai Inst. Plant Phys. & Eco.

hyb_protocol: Each Slide was hybridized with 60pmol Cy3-labeled cRNA and 30pmol Cy-5 labeled cRNA in Hybridization Oven. After 17 hours hybridization, slides were washed in staining dishes.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565BA, Agilent technologies, Santa Clara, CA, US)and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings. Raw data were normalized by Lowess(locally weighted scatter plot smoothing) algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

data_processing: Lowess

organism: Zea mays

source_name: Seedling Replicate 1

label_protocol: Total RNA were labeled by Cy3 NHS ester (Cat#PA13105, GE healthcare Biosciences, Pittsburgh, PA, US) ，Cy5 NHS ester (Cat#PA15100, GE healthcare Biosciences, Pittsburgh, PA, US)followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Maize ( Zea mays ) B73 inbred line plants were grown in the greenhouse under 14h light and 10h dark in a growth chamber at 22-26℃ with 65% relative humidity.

extract_protocol: Total RNA from Laser microdissection samples were extracted with the PicoPure RNA isolation kit (Applied Biosystems), Amino-ally1 aRNA was recovered through 2-round amplification using a Target Amp™ 2-Round Aminoallyl-aRNA Amplification Kit.

value: Seedling

value: 14-days-old seedling


title: Pollen Mother Cells Replicate 3

source_name: Pollen Mother Cells Replicate 3

value: Pollen Mother Cell

value: 1.8-2.0 mm anther


title: Pollen Mother Cells Replicate 1

source_name: Pollen Mother Cells Replicate 1


title: Archesporial Cells Replicate 2

source_name: Archesporial Cells Replicate 2

value: Archesporial Cell

value: 0.7-0.9 mm anther


title: Parenchyma Cells Replication 1

source_name: Parenchyma Cells Replication 1

value: Parenchyma Cell

value: 2-months-old B73


title: Tapetal Cells Replicate 2

source_name: Tapetal Cells Replicate 2

value: Tapetal Cell


title: Seedling Replicate 3

source_name: Seedling Replicate 3


title: Early Pollen Mother Cells Replicate 3

source_name: Early Pollen Mother Cells Replicate 3

value: Early Pollen Mother Cell

value: 1.2-1.5 mm anther


title: Brain-Tumor-W50-2-1

value: male


title: Archesporial Cells Replicate 1

source_name: Archesporial Cells Replicate 1


title: Brain-Tumor-W40-1-1


title: Tapetal Cells Replicate 1

source_name: Tapetal Cells Replicate 1


title: Seedling Replicate 2

source_name: Seedling Replicate 2


title: Brain-Tumor-W38-1-1

value: female


title: Brain-Tumor-W37-1-1

source_name: Glioma


title: Brain-Tumor-W36-1-1


title: Brain-Tumor-W35-1-1


title: Mature Pollen Replicate 3

source_name: Mature Pollen Replicate 3

value: Mature Pollen

value: 75-day-old maize panicles


title: Brain-Tumor-W34-1-1

source_name: Glioblastoma


title: Parenchyma Cells Replication 2

source_name: Parenchyma Cells Replication 2


title: Mature Pollen Replicate 1

source_name: Mature Pollen Replicate 1


title: Brain-Tumor-W30-1-1


title: Brain-Tumor-W31-1-1


title: Brain-Tumor-W8-1-1


title: Brain-Tumor-W7-1-1


title: Brain-Tumor-W18-1-1


title: Brain-Tumor-W19-1-1


title: Brain-Tumor-W3-2-1


title: Brain-Tumor-W26-1-1


title: Mature Pollen Replicate 2

source_name: Mature Pollen Replicate 2


title: Early Pollen Mother Cells Replicate 2

source_name: Early Pollen Mother Cells Replicate 2


title: Brain-Tumor-W29-1-1


title: Brain-Tumor-W4-2-1


title: Brain-Tumor-W10-1-1


title: Archesporial Cells Replicate 3

source_name: Archesporial Cells Replicate 3


title: Brain-Tumor-W5-1-1


title: Tapetal Cells Replicate 3

source_name: Tapetal Cells Replicate 3


title: Early Pollen Mother Cells Replicate 1

source_name: Early Pollen Mother Cells Replicate 1


title: Brain-Tumor-W4-1-1


title: Pollen Mother Cells Replicate 2

source_name: Pollen Mother Cells Replicate 2


title: Brain-Tumor-W2-1-1


title: G2-8 OBM

city: chiyodaku misakichou

first: Shoko

last: Onodera

state: Tokyo

department: biochemistry

institute: Tokyo Dental collage

description: Autosomal dominant inheritance

data_processing:
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Matrix normalized worksheet reports normalized signal (against housekeeping genes). Fold Change worksheet reports test/control ratios.

label: SYBR Green

source_name: iPSc established by my lablatory

label_protocol: PCR assays were performed using RT² Profiler™ PCR Array Human Hedgehog Signaling Pathway (PAHS-078Z, SA Biosciences, Frederick, MD) following the Manufacturer’s instructions. Reverse transcription was performed from 500 ng total RNA using the RT2 First Strand Kit (SA Biosciences). Quantitative real-time PCR were performed (ABI7500, ABI).

extract_protocol: Total RNA was extracted with QIAZOL

treatment_protocol: Protocl was weritten in PloS one 2014 vol: 9 (6) pp: e99534

value: oral muccosal fibroblast

value: disease specific iPSc

tag: treatment

value: After EB formation, sample was treated 10 day with OBM medium


title: APAP + copper m3.1

city: Rancagua

first: Mauricio

middle: Alejandro

last: Latorre

state: VI

address: Av. Libertador Bernardo OHiggins 611

department: ICI

country: Chile

institute: Universidad de OHiggins

description: biological replicate 3. technical replicate 1.

hyb_protocol: Three different set of hybridizations experiments were made (12 in total): a) aRNA from control (placebo condition) versus aRNA from copper (chronic loading); b) aRNA from control (placebo condition) versus aRNA from acetaminophen (acute-challenge); c) aRNA from control (placebo condition) versus aRNA from copper + acetaminophen (chronic loading and acute-challenge). For each experiment the two dye probes were mixed and concentrated to a volume of 50 ul in a solution containing 20% formamide, 5x SSC and 0.1% SDS, and hybridization was performed essentially according to the microarray manufacturer’s instructions. Slides were incubated for 16 hours at 42°C. For detection of the fluorescent derivatives, we used a ScanArray GX laser reader (Perkin Elmer).

scan_protocol: Spot identification and quantification were performed with Scanarray Express software (Perkin Elmer). Array data were analyzed using the R statistical language and environment (http:// www.r-project.org), specifically with the microarray analysis tools available from the Bioconductor Project (http://www.bioconductor.org).

data_processing:
Data were background subtracted and normalized using the LIMMA Bioconductor package.
Differentially expressed genes were determined using Significance Analysis of Microarrays (SAM) (Tusher VG et al. 2001), with a false discovery rate (FDR) < 10%.

organism: Cebus capucinus

source_name: control

label_protocol: Two channels microarray (Cy3-Cy5) were performed following previous published data (Iyer VR, et al. 1999). Control (placebo) was used as common reference probe in all the hybridization, labeled with Cy3 dye. Experimental conditions samples (copper and/or acetaminophen) were labeled independently (four monkeys per each experiment) with Cy5 dye. Five micrograms of aRNA from each sample was coupled with the dyes, according to the manufacturer’s instructions.

growth_protocol: All experiments were carried out humanely and with respect for alleviation of suffering following protocols approved by the institutional Animal Care Committee, Institute of Nutrition and Food Technology, University of Chile, which is based on the Declaration of Helsinki and follows the NIH Guide for the Care and Use of Laboratory Animals. Protocols were also approved by Pontificia Universidad Catolica de Chile Institutional Animal Care Committee. Adult tufted capuchin monkeys were obtained from the Catholic University Primate Center, Santiago, Chile, where the monkeys were housed. Eight (four males and four females) adult monkeys were maintained indoors under the constant care of nursery and veterinary staff in temperature-controlled rooms with 12-h light cycles.

extract_protocol: Total RNA extraction from Cebus capucinus liver was carried out using Tri-reagent (Ambion, Austin, TX, USA), following manufacturer recommendations (four independent subjects, two females and two males monkeys per each conditions). Genomic DNA in the RNA samples was digested with RNase-free DNase I  (Ambion, Austin, TX, USA). The concentration, 28S/18S ribosomal RNA (rRNA) ratio, and RNA integrity number (RIN) of the purified RNA samples were measured using the 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA) with the RNA 6000 Pico Chip kit (Agilent). After confirming the purity of RNA samples, one microgram of total RNA was used to synthesize aRNA using the MessageAmp II mRNA amplification kit (Ambion, Austin, TX, USA).

treatment_protocol: Copper dosing started at 5 mg Cu × kg-1 x d-1 and progressively increased to 7.5 mg × kg-1 × d-1 over a 2-month period. Then, this final concentration of copper was administrated for 3 year. After the copper treatment, an unique dose of 120 mg APAP /kg was administrated.

value: Liver

value: Female

value: control (placebo condition)

source_name: APAP + copper m3

value: APAP + copper


title: 201B7 OBM

description: Autosomal dominant inheritance

source_name: derived by RIKEN

value: fibroblast

value: control iPS


title: APAP + copper m4.1

description: biological replicate 4. technical replicate 1.

source_name: APAP + copper m4


title: APAP + copper m4.2

description: biological replicate 4. technical replicate 2.


title: G2-8 iPS

description: Autosomal dominant inheritance

value: After EB formation, sample was collected


title: HAdMSC_d0_2

description: Human adipose-derived mesenchymal stem cells, replicate2

data_processing: GeneSpring GX. Signals were normalized to percentile.

value: Somatic cell line


title: Brain-Tumor-W3-1-1


title: G2-5 OBM

description: Autosomal dominant inheritance


title: APAP + copper m2.2

description: biological replicate 2. technical replicate 2.

value: Male

source_name: APAP + copper m2


title: APAP + copper m3.2

description: biological replicate 3. technical replicate 2.


title: APAP + copper m1.2

description: biological replicate 1. technical replicate 2.

source_name: APAP + copper m1


title: APAP + copper m2.1

description: biological replicate 2. technical replicate 1.


title: 201B7 iPS

description: Autosomal dominant inheritance


title: APAP + copper m1.1

description: biological replicate 1. technical replicate 1.


title: APAP m4.2

source_name: APAP m4

value: APAP


title: Brain-Tumor-W12-1-1

source_name: Glioblastoma


title: HA9_Meis1_II_3w

value: Cells from 12 week old 5-FU treated mice

value: Bone marrow

value: Progenitor cells

value: Primary bone marrow culture

value: Transduced with MSCV construct

value: Overexpression of HOXA9 and Meis1 in WT mouse

value: DMEM 15% FCS, IL3, SCF, IL6


title: APAP m3.1

value: Liver

source_name: APAP m3


title: HeyA8 treated MFH 3

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V4.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Sample Gene Profile option of this software was used.

source_name: Ovarian cancer cells

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 300 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

tag: cell line

value: Parental cells treated with MFH


title: APAP m4.1

value: Female

value: control (placebo condition)


title: stable Six8, biological rep1

city: Amsterdam

first: Oskar

last: Bruning

address: Science Park 904

department: SILS

country: Netherlands

institute: University of Amsterdam

description: Gene expression data from 4 weeks old stable transformant plant leaves

hyb_protocol: Resulting amplified RNA was hybridized to GeneChip Arabidopsis ATH1 Genome arrays. The arrays were subsequently washed and stained on a GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: GeneChips were scanned on a GeneChip Scanner 3000 7G (Affymetrix). Feature extraction was performed using Affymetrix GCOS Software v1.4.0.036.

data_processing: The data were analyzed with the R statistical programming language (http://cran.r-project.org/) and the bioconductor affy package. The raw data were normalized and summarized using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003; Biostatistics 4: 249-264)

organism: Arabidopsis thaliana

source_name: Arabidopsis stable Six8 transformant plant leave

label_protocol: All procedures were performed per manufacturer’s instructions. Briefly, for each test sample, 125 ng total RNA was amplified and labeled using the 3' IVT Express Kit (Affymetrix Inc., Santa Clara, CA, USA)

growth_protocol: the plants were grown in an 11-h photoperiod at 70% relative humidity and 22°C for four weeks

extract_protocol: Approximately 25 mg A. thaliana leaf tissue was disrupted using a tissue lyzer (Qiagen) for 1 min at 25 Hz. RNA was isolated using the TRIzol LS Reagent (Life Technologies) followed by an extraction with chloroform and a 1:1 mixture of phenol:chloroform.  Subsequently, RNA was precipitated with 0,1 volume of 3 M NaAc pH 5,2 plus 2-2,5 volume 96% ethanol at -20°C. After centrifugation the pellet was washed with 1 ml 70 % ethanol, air-dried and dissolved in 100 µl RNase free water for 10 min at 55-60°C. A cleanup was performed using the RNeasy Mini Kit (Qiagen) according to the manufacture’s protocol. Digestion of DNases was done with the RNase-free DNase set (Qiagen) and additional RNA cleanup with RPE. RNA was eluted with 40 µl RNase free water. The RNA quality was analysed on an agorse gel and quantified using a NanoDrop spectrophotometer.

treatment_protocol: no treament was applied to these plants

tag: ecotype background

tag: genotype/variation

value: stable Six8 transformant

value: leaf


title: APAP m2.2

source_name: APAP m2


title: stable Six8, biological rep2


title: HeyA8 treated MFH 2


title: G1-6 OBM

description: Autosomal dominant inheritance

value: oral muccosal fibroblast

value: disease specific iPSc

value: After EB formation, sample was treated 10 day with OBM medium


title: APAP m3.2

value: APAP


title: stable Six8, biological rep3


title: stable Six6 line 1.37, biological rep3

source_name: Arabidopsis stable Six6 transformant line 37 plant leave

value: stable Six6 transformant


title: G1-1 OBM

description: Autosomal dominant inheritance


title: stable Six8, biological rep4


title: G2-5 iPS

description: Autosomal dominant inheritance

value: After EB formation, sample was collected


title: HeyA8 treated MFH 1


title: G1-6 iPS

description: Autosomal dominant inheritance


title: APAP m2.1

value: Male


title: HeyA8 untreated 3

value: Parental cells, untreated


title: stable Six6 line 1.37, biological rep1

source_name: Arabidopsis stable Six8 transformant line 37 plant leave


title: stable Six6 line 1.37, biological rep2


title: KD iPS

description: Autosomal dominant inheritance

value: lip fibroblast  (cell line)

value: control iPS


title: KD OBM

description: Autosomal dominant inheritance


title: HeyA8 untreated 2


title: APAP m1.1

source_name: APAP m1


title: APAP m1.2


title: stable Six6 line 1.36, biological rep3

source_name: Arabidopsis stable Six6 transformant line 36 plant leave


title: copper m4.1

source_name: copper m4

value: copper


title: HeyA8 untreated 1


title: G1-1 iPS

description: Autosomal dominant inheritance

source_name: iPSc established by my lablatory


title: stable Six6 line 1.36, biological rep2


title: WM9-48HR-DMSO-B

city: Philadelphia

first: Jianglan

last: Liu

state: PA

address: 3601 Spruce Street

institute: The Wistar Institute

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

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

growth_protocol: Melanoma cells were grown in Tumor 2% medium before they reach the 70% confluency.

extract_protocol: Cells were washed again with HBSS and lysed directly in TRI Reagent® RNA Isolation Reagent (Sigma) and stored at -20°C.

treatment_protocol: Melanoma cells were treated with 5uM HA130 or vehicle control (DMSO) for 48h.

value: Melanoma cell line

tag: treated with

value: DMSO for 48 hours


title: copper m4.2

source_name: control

value: Liver

value: Female


title: WM9-48HR-DMSO-A

tag: cell type


title: WM9-48HR-HA130-C

value: HA130 for 48 hours


title: WM9-48HR-HA130-B


title: stable Six6 line 1.36, biological rep1

value: leaf


title: copper m3.2

value: control (placebo condition)

source_name: copper m3


title: copper m2.2

source_name: copper m2


title: copper m3.1


title: wildtype Col-0, biological rep4

description: Gene expression data from 4 weeks old wildtype plant leaves

source_name: Arabidopsis wildtype Col-0 plant leave

value: wildtype


title: wildtype Col-0, biological rep2


title: MELA_0081

description: HumanHT-12 v4 Expression BeadChip

source_name: AJCC stage II melanoma

tag: region

value: Little Finger


title: copper m2.1

tag: tissue


title: copper m1.2

tag: gender

source_name: copper m1


title: MELA_0079

description: HumanHT-12 v4 Expression BeadChip

value: Scalp


title: wildtype Col-0, biological rep3


title: stable Avr2 line 6.4, biological rep3

source_name: Arabidopsis stable Avr2 transformant line 6 plant leave

value: stable Avr2 transformant


title: copper m1.1


title: MELA_0210

description: HumanHT-12 v4 Expression BeadChip

value: Thorax (Query Upper Arm Lateral)


title: stable Avr2 line 23.5, biological rep4

source_name: Arabidopsis stable Avr2 transformant line 23 plant leave


title: stable Avr2 line 6.4, biological rep4


title: stable Avr2 line 6.4, biological rep2


title: MELA_0218

description: HumanHT-12 v4 Expression BeadChip

value: Lower Lip


title: MELA_0208

description: HumanHT-12 v4 Expression BeadChip

value: Thigh


title: MELA_0189

description: HumanHT-12 v4 Expression BeadChip

value: Shoulder


title: RAW264.7 Melatonin LPS3h

city: Tsukuba

first: Yutaro

last: Kumagai

state: Ibaraki

address: Central 5-41, Higashi 1-1-1

department: BRD

institute: AIST

description: Gene expression of RAW264.7 cell line, stimulated with LPS for 3 h after pretreated with melatonin for 1 h

hyb_protocol: Hybridization was done by using Gene Expression Hybridization Kit (Agilent) according to the manufacturer's instruction.

scan_protocol: Scanning was performed by Agilent Microarray Scanner with 3 micro meter Scan Resolution and 20 bit TIFF dynamic range.

data_processing: Spot intensities were measured by using Agilent Feature Extraction 12.0.3.1.

source_name: RAW264.7 cell line, Melatonin 1 h, LPS, 3 h

label_protocol: Laballing was performed by using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instruction.

growth_protocol: RPMI1640 medium with 5 % FBS

extract_protocol: Total RNA was extracted by using TRIzol reagent (Invitrogen).

treatment_protocol: RAW 264.7 macrophage were pretreated with 1mM of melatonin (Nacalai tesque) for 1 hour or left untreated. The cells were stimulated with 100 ng/ml LPS (E. coli O55:B5, purchased from Sigma) for 1, 3 or 5 hours after pretreatment.

value: 1mM of melatonin for 1h and 100 ng/ml LPS for 5h


title: RAW264.7 Melatonin LPS5h

description: Gene expression of RAW264.7 cell line, stimulated with LPS for 5 h after pretreated with melatonin for 1 h

source_name: RAW264.7 cell line, Melatonin 1 h, LPS, 5 h


title: stable Avr2 line 6.4, biological rep1


title: RAW264.7 Melatonin

description: Gene expression of RAW264.7 cell line, treated with melatonin for 1 h

source_name: RAW264.7 cell line, Melatonin 1 h

value: 1mM of melatonin for 1h and 100 ng/ml LPS for 1h


title: stable Avr2 line 23.5, biological rep3


title: RAW264.7 control

description: Gene expression of RAW264.7 cell line, unstimulated

source_name: RAW264.7 cell line, unstimulated

value: control


title: RAW264.7 LPS1h

description: Gene expression of RAW264.7 cell line, stimulated with LPS for 1 h

source_name: RAW264.7 cell line, LPS, 1 h

value: 100 ng/ml LPS for 1h


title: stable Avr2 line 23.5, biological rep2


title: RAW264.7 Melatonin LPS1h

description: Gene expression of RAW264.7 cell line, stimulated with LPS for 1 h after pretreated with melatonin for 1 h

source_name: RAW264.7 cell line, Melatonin 1 h, LPS, 1 h

value: 1mM of melatonin for 1h and 100 ng/ml LPS for 3h


title: MELA_0188

description: HumanHT-12 v4 Expression BeadChip


title: RAW264.7 LPS5h

description: Gene expression of RAW264.7 cell line, stimulated with LPS for 5 h

source_name: RAW264.7 cell line, LPS, 5 h

value: 100 ng/ml LPS for 5h


title: MELA_0209

description: HumanHT-12 v4 Expression BeadChip

value: Ear


title: MELA_0207

description: HumanHT-12 v4 Expression BeadChip

value: Shin


title: MELA_0212

description: HumanHT-12 v4 Expression BeadChip

value: Thorax


title: MELA_0178

description: HumanHT-12 v4 Expression BeadChip

value: Upper Arm


title: RAW264.7 LPS3h

description: Gene expression of RAW264.7 cell line, stimulated with LPS for 3 h

source_name: RAW264.7 cell line, LPS, 3 h

value: 100 ng/ml LPS for 3h


title: stable Avr2 line 23.5, biological rep1

value: leaf


title: RAW264.7-S.oralis_SpxBKO16h

description:
Gene expression of RAW264.7 cell line, infected with S. oralis SpxB KO for 16h
KO16h

source_name: RAW264.7 cell line, S. oralis SpxB KO, 16h

growth_protocol: RPMI1640 medium with 10 % FBS

treatment_protocol: RAW264.7 cells were stimulated with LPS (E coli O55:B5, Sigma) at the conc of 100 ng/ml with or without pretreatment with 1mM of H2O2 for 1 hour, or infected with S. oralis WT or SpxB KO strains at MOI=5 for 16 hours.

tag: infection

value: S. oralis SpxB KO


title: MELA_0211

description: HumanHT-12 v4 Expression BeadChip


title: RAW264.7-S.oralis_WT16h

description:
Gene expression of RAW264.7 cell line, infected with S. oralis WT for 16h
WT16h

source_name: RAW264.7 cell line, S. oralis WT, 16h

value: S. oralis WT


title: wildtype Col-0, biological rep1

value: wildtype


title: MELA_0240

description: HumanHT-12 v4 Expression BeadChip

value: Abdomen


title: MELA_0214

description: HumanHT-12 v4 Expression BeadChip

value: Thigh


title: RAW264.7-H2O2-LPS3h

description:
Gene expression of RAW264.7 cell line, stimulated with LPS for 3h after pretreated with H2O2 for 1 hr
H2O2LPS3h

source_name: RAW264.7 cell line, H2O2, 1 hr, LPS, 3h

value: pretreated with H2O2, then stimulated with LPS

tag: stimulation time


title: MELA_0082

description: HumanHT-12 v4 Expression BeadChip


title: RAW264.7-H2O2-LPS1h

description:
Gene expression of RAW264.7 cell line, stimulated with LPS for 1h after pretreated with H2O2 for 1 hr
H2O2LPS1h

source_name: RAW264.7 cell line, H2O2, 1 hr, LPS, 1h


title: RAW264.7-H2O2

description:
Gene expression of RAW264.7 cell line, pretreated with H2O2 for 1 hr
H2O2

source_name: RAW264.7 cell line, H2O2, 1 hr

value: pretreated with H2O2


title: MELA_0221

description: HumanHT-12 v4 Expression BeadChip

source_name: AJCC stage II melanoma

value: Chin


title: MELA_0080

description: HumanHT-12 v4 Expression BeadChip


title: RAW264.7-LPS3h

description:
Gene expression of RAW264.7 cell line, stimulated with LPS for 3h
LPS3h

source_name: RAW264.7 cell line, LPS, 3h

value: stimulated with LPS


title: MELA_0165

description: HumanHT-12 v4 Expression BeadChip

value: Shoulder (Query Thorax)


title: MELA_0182

description: HumanHT-12 v4 Expression BeadChip

value: Forearm (Query Upper Arm)


title: MELA_0186

description: HumanHT-12 v4 Expression BeadChip

value: Forearm


title: MELA_0164

description: HumanHT-12 v4 Expression BeadChip

value: Foot - Sole


title: MELA_0206

description: HumanHT-12 v4 Expression BeadChip


title: MELA_0204

description: HumanHT-12 v4 Expression BeadChip

value: Vulva


title: Patient 7 surgical resection - post treatment

status: Public on Nov 29 2017

type: SRA

city: Chapel Hill

first: Gary

middle: L

state: NC

address: 4009 Genetic Medicine Building, 120 Mason Farm Road

department: Pharmacology

institute: University of North Carolina School of Medicine

description:
150501_UNC15-SN850_0404_AC5JF0ACXX_2_TGACCA_L002
LCCC1122_rawRSEM.txt
LCCC1122_normalizedLog2RSEM.txt

library_source: transcriptomic

data_processing:
Reads were aligned to the human reference genome hg19_M_rCRS using MapSplice v2.1.4; alignment profile was determined by Picard Tools v1.88.
Aligned reads were sorted and indexed using SAMtools v1.2 and translated to transcriptome coordinates and filtered for indels, large inserts, and zero mapping quality using UNC Bioinformatics Utilities v1.2.
Transcript abundance estimates were determined using RSEM and upper-quartile normalized.
For DESeq differential expression analysis comparing pre-treatment and post-treatment patient tumors: RSEM gene-level expected read counts were imported into R version 3.2.2. and were analyzed using DESeq2 v1.12.3 to detect genes that were differentially expressed between pre-treatment and post-treatment conditions.  Default DESeq2 parameters were used for the analysis, specifying sample ID in addition to pre and post treatment status to account for pairing between samples in the specification of the model design matrix.
Genome_build: hg19
Supplementary_files_format_and_content: Processed files contain raw or log2-transformed upper-quartile normalized RSEM transcript abundance estimates, organized by official gene symbol and Entrez Gene ID.

molecule: polyA RNA

source_name: breast carcinoma

extract_protocol:
Total RNA was isolated with Qiagen RNeasy Mini kit.
mRNA libraries were made with Illumina TruSeq RNA Sample Prep Kit starting with 0.5-1 micrograms of total RNA.

tag: disease state

value: TNBC

tag: individual

value: Patient 7

tag: protocol

value: post-treatment surgical resection

tag: tumor sample subtype

value: normal breast


title: Patient 6 needle core biospy - pre treatment_2

description:
150501_UNC15-SN850_0404_AC5JF0ACXX_1_ATCACG_L001
LCCC1122_rawRSEM.txt
LCCC1122_normalizedLog2RSEM.txt

value: Patient 6

value: pre-treatment needle core biospy

value: claudin low


title: MELA_0216

description: HumanHT-12 v4 Expression BeadChip

value: Cheek


title: RAW264.7-control

description:
Gene expression of RAW264.7 cell line, unstimulated
con

value: unstimulated


title: Patient 5 surgical resection - post treatment_2

description:
150424_UNC12-SN629_0406_AC5HCRACXX_7_AGTCAA_L007
LCCC1122_rawRSEM.txt
LCCC1122_normalizedLog2RSEM.txt
DESeq2_trametinibresponse.txt

value: Patient 5

value: basal


title: MELA_0181

description: HumanHT-12 v4 Expression BeadChip

value: Shoulder


title: HBC Mutant Mature Green_rep 2_1

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60°C and hybridized on to a Genotypic designed Tomato_GXP_8x60K (AMADID:65951). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65° C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327).

scan_protocol: Slides were scanned using the Agilent Microarray Scanner G2600D.

data_processing: Data extraction from Images was done using Feature Extraction software Version 11.5.1.1  and Normalization of the data was done in GeneSpring GX V 12.0

organism: Solanum lycopersicum

source_name: HBC Mutant Mature Green stage of Fruit ripening

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Solanum lycopersicum (cv. Arka Vikas) and HBC (High Beta Carotene) Mutant tomato plants were grown in a greenhouse with supplementary lighting providing an irradiance of 250–400 l mol m-2 s-1. Individual tomato plants were grown in pots (20 cm diameter) containing compost supplemented with appropriate ferrtilizer. Plants were watered daily and fruit were tagged at anthesis and harvested when they had reached the appropriate developmental stage. Individual fruit were removed from the plant, weighed, kept in RNA Later, and stored at -80 c until required.

extract_protocol: Isolation of RNA from Tomato fruit was carried out by using Ambion RNAaqueous Phenol free total RNA isolation Kit (Cat # AM1912) with Ambion plant RNA isolation Aid (P/N: AM9690) as per the manufacturer’s protocols.

treatment_protocol: Pericarp tissue was selected for microarray analysis. The tissue was collected at Mature Green (MG), Breaker (BR), Turning (TR), and Fully Ripen (FR) stages from HBC (High Beta Carotene) Mutant and Wild type (cv. Arka Vikas). Fruits were collected from green house and transfer immediately into thermocouple boxes. Sterile working area was prepared by wiping the working area surface with 1% hypochlorite bleach. Samples were dissected wearing new Nitrile gloves which were wiped with 1% hypochlorite. Pre labelled RNA free 2 ml tubes filled with 1.5 ml RNALater (RLT) solution were placed in working area for sample collection. The samples were kept in sterile petri plate and the tissue was sliced 3 mm or less in size and then transferred immediately in labelled vial containing RNALater (1.5 ml) and this step was finished within 90 seconds (Long time might degrade RNA). Each sample was prepared in triplicates containing 10-15 small pieces and the tissue was stored at -80 °C until to carry out the further experiment.

value: Fruit

value: HBC Mutant

tag: Stage

value: mature green


title: HBC Mutant Turning_rep 2_3

source_name: HBC Mutant Turning stage of Fruit ripening

value: turning


title: HBC Mutant Breaker_rep 2_2

source_name: HBC Mutant Breaker stage of Fruit ripening

value: breaker


title: RAW264.7-LPS1h

description:
Gene expression of RAW264.7 cell line, stimulated with LPS for 1h
LPS1h

source_name: RAW264.7 cell line, LPS, 1h

value: stimulated with LPS


title: MELA_0018

description: HumanHT-12 v4 Expression BeadChip


title: MELA_0225

description: HumanHT-12 v4 Expression BeadChip

value: Great toe (Query Toenail)


title: Wild Type Turning_rep 1_3

source_name: Wild type Turning stage of fruit ripening

value: wild type


title: Patient 5 needle core biopsy - pre treatment

description:
150424_UNC12-SN629_0406_AC5HCRACXX_6_CTTGTA_L006
LCCC1122_rawRSEM.txt
LCCC1122_normalizedLog2RSEM.txt

value: TNBC


title: Wild Type Ripening_ rep 1-4

source_name: Wild type Ripening stage of Fruit ripening

value: ripening


title: Patient 5 needle core biopsy - pre treatment_2

description:
150424_UNC12-SN629_0406_AC5HCRACXX_GGCTAC_L006
LCCC1122_rawRSEM.txt
LCCC1122_normalizedLog2RSEM.txt
DESeq2_trametinibresponse.txt

value: pre-treatment needle core biospy


title: Patient 6 surgical resection - post treatment

description:
150424_UNC12-SN629_0406_AC5HCRACXX_TAGCTT_L005
LCCC1122_rawRSEM.txt
LCCC1122_normalizedLog2RSEM.txt

value: Patient 6

value: post-treatment surgical resection

value: claudin low


title: Wild Type Breaker_rep 1_2

source_name: Wild type Breaker stage of fruit ripening


title: HBC Mutant Ripening_rep 2_4

source_name: HBC Mutant Ripening stage of Fruit ripening


title: Patient 7 needle core biopsy - pre treatment

description:
150501_UNC15-SN850_0404_AC5JF0ACXX_2_TTAGGC_L002
LCCC1122_rawRSEM.txt
LCCC1122_normalizedLog2RSEM.txt

value: Patient 7

value: normal breast


title: Patient 6 surgical resection - post treatment_2

description:
150501_UNC15-SN850_0404_AC5JF0ACXX_1_CGATGT_L001
LCCC1122_rawRSEM.txt
LCCC1122_normalizedLog2RSEM.txt


title: Patient 5 surgical resection - post treatment

description:
150424_UNC12-SN629_0406_AC5HCRACXX_7_AGTTCC_L007
LCCC1122_rawRSEM.txt
LCCC1122_normalizedLog2RSEM.txt

value: Patient 5

value: basal


title: Patient 6 needle core biospy - pre treatment

description:
150424_UNC12-SN629_0406_AC5HCRACXX_GATCAG_L005
LCCC1122_rawRSEM.txt
LCCC1122_normalizedLog2RSEM.txt


title: Wild Type Mature Green_ rep 1_1

source_name: Wild type Mature green stage of  fruit ripening

value: Fruit


title: E12-HpInfected-Rep2

status: Public on Sep 21 2017

city: Galway

first: Michael

address: University Road

department: NCBES

country: Ireland

institute: NUI Galway

hyb_protocol: All hybridizations were carried out using the hybridization and wash solutions as recommended in the Affymetrix 3' IVT Express Protocol. Carried out by DNA Vision, Charleroi, BE.

scan_protocol: Agilent Technologies Scanner G2505C (5 micron reolution). Carried out by DNA Vision, Charleroi, BE

data_processing: Carried out by DNA Vision, Charleroi, BE. Images were processed using GenePix Pro 6.1.0.4. Spot intensities  were normalized and analyzed in GeneSpring (Ver 12.3). Data were log transformed and quantile normalized. Subsequently all normalized data was baseline transformed to the median of all samples.

source_name: HT29-MTX-E12 cell line

label_protocol: Affymetrix 3' IVT Express Protocol. Carried out by DNA Vision, Charleroi, BE starting from 100 ng of eukaryotic RNA

growth_protocol:
E12 cells were maintained in flasks in complete Dulbecco's modified Eagle's medium (DMEM) supplemented with 10 % foetal calf serum, 2 mM L-glutamine, 1 % nonessential amino acids and antibiotics (penicillin (50 U/ml) and streptomycin (50 μg/ml). Cells (2 x 106) were seeded on transwell filters (0.4 micometer pore polycarbonate membrane insert) in 6-well plates. Cells were incubated at 37 oC in a humidified 5 % CO2 atmosphere and media was added every second day. TEER measurements were taken at 20 days. Antibiotics were removed from the cells at least 24 h before infection assays.
Bacteria were plated on Columbia blood agar (Oxoid) plates and grown for 48 h in a microaerophilic environment using gas packs (Oxoid, BR0038). Bacteria were harvested from plates into Brucella broth and the OD600 adjusted to 0.1 and grown in T25 tissue culture flasks at 37 oC under microaerophilic conditions with shaking at 70-80 rpm until the OD600 reached 0.6. Gram staining of bacterial cultures was used to check coccoid levels were less than 5 %. Washed bacteria were resuspended to an OD600 of 1.8 with antibiotic-free RPMI.

extract_protocol: RNA for microarray hybridizations was isolated by TRIzol extraction followed by standard RNA purification protocols using the RNeasy Mini Kit (Qiagen). RNA quality control was carried by a commercial company (DNA Vision, Charleroi, BE) using an Agilent Bioanalyzer 2100. The amount of eukaryotic RNA was corrected across samples using the 28S RNA peak because of the variable presence of prokaryotic RNA (infecting Helicobacter pylori).

treatment_protocol: On day 20 E12 cells in transwells were washed with HBSS and 2 ml antibiotic-free complete DMEM media was added to the base of each well and 1 ml of RPMI to the apical surface of each well. On day 21 200ml bacteria (6 x 108) were added to each well at an MOI of 300. Plates were incubated at 37 oC for 24 h. Replicate transwells were used to determine the number of bacteria (CFU/ml) that were associated with the cells. Cells were harvested for RNA isolation.

tag: cell line_1

value: Derivative of the human cell line HT29 from an original adenocarcinoma of the colon

tag: cell line_2

value: Selected from HT29-MTX on the basis of tight junction formation and adherent mucus production, having many of the characteristics of a gastric cell (Behrens et al., 2001, DOI:10.1023/A:1010974909998)

value: H. pylori strain 26695


title: E12-HpInfected-Rep3

tag: cell line


title: Low_FA 015

status: Public on Mar 08 2017

city: Ann Arbor

first: Jeffrey

middle: F

last: Horowitz

state: Michigan

address: CCRB, 401 Washtenaw Ave

institute: University of Michigan

hyb_protocol: Following Labeling procedure, 3.75 ug of biotinylated cDNA were hybridized at 48C – WT on Human Gene ST 2.1 strip arrays, and were washed and stained using the Affymetrix Gene Atlas system (software version 1.0.4.267)

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system (software version 1.0.4.267)

data_processing: Data was analyzed using the limma and oligo Bioconductor packages implemented in the R-statistical environment version 3.3.0. RMA was used to fit log2 transformed expression values

source_name: subcutaneous adipose from sedentary, obese female

label_protocol: cDNA were prepared according to the Nugen Ovation PicoSL WTA System V2 kit protocol from 10 ng total RNA (Ovation PicoSL WTA System V2 Manual, P/N M01226 v4).  Subsequently, Biotinylated cDNA were prepared according to the Nugen Encore Biotin Module from 3.75 ug of cDNA (Encore Biotin Module Manual, P/N M01111 v6)

extract_protocol: Qiazol RNA extraction

value: subcutaneous adipose

value: female

tag: phenotype

value: high rate of fatty acid release


title: E12-HpInfected-Rep1

last: Cairns


title: E12-Control-Rep2

value: uninfected


title: Low_FA 019


title: Low_FA 011


title: E12-Control-Rep1


title: CTRL

status: Public on Feb 24 2017

city: Prague 2

first: Vojtěch

last: Kulvait

address: U Nemocnice 5

department: Institute of Pathological Physiology

country: Czech Republic

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

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

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

source_name: Non-malignant B-cells isolated from peripheral blood of 5 healthy donors.

label_protocol: Standard Illumina protocol

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


title: UPF1G-SC

source_name: Cells established by xenotransplantation of UPF1G cell line isolated ex vivo from subcutaneously growing lymphoma.


title: UPF1G-A

source_name: Cells established by xenotransplantation of UPF1G cell line isolated ex vivo from malignant murine ascites.


title: UPF1H-D85

source_name: Lymphoma cell line named UPF1H established from the pateint's primary lymphoma cells after cytarabine-based therapy after 85 days of in vitro cultivation.


title: UPF7U-D166

source_name: Lymphoma cell line named UPF7U established from the patient's primary lymphoma cells after 166 days of in vitro cultivation.


title: VFN-M3-LN3

source_name: Patient-derived xenograft (PDX) cells named VFN-M3 established by xenotransplantation of primary lymphoma cells into immunodeficient mice isolated ex vivo from the lymph node like tumor.


title: Low_FA 014

source_name: subcutaneous adipose from sedentary, obese male

value: male


title: VFN-M3-SC3

source_name: Patient-derived xenograft (PDX) cells named VFN-M3 established by xenotransplantation of primary lymphoma cells into immunodeficient mice isolated ex vivo from subcutaneously growing lymphoma.


title: Low_FA 004

value: low rate of fatty acid release


title: Low_FA 013


title: P6-PBMC2

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


title: UPF1H-SC

source_name: Cells established by xenotransplantation of UPF1H cell line isolated ex vivo from subcutaneously growing lymphoma.


title: Low_FA 007


title: UPF1H-D185

source_name: Lymphoma cell line named UPF1H established from the pateint's primary lymphoma cells after cytarabine-based therapy after 185 days of in vitro cultivation.


title: UPF1G-D63

source_name: Lymphoma cell line named UPF1G established from the patient's primary lymphoma cells before cytarabine-based therapy after 63 days of in vitro cultivation.


title: Low_FA 006


title: P6-PBMC1

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


title: Low_FA 001


title: UPF1G-D163

source_name: Lymphoma cell line named UPF1G established from the patient's primary lymphoma cells before cytarabine-based therapy after 163 days of in vitro cultivation.


title: E12-Control-Rep3


title: Low_FA 005


title: VFN-M3-CTRL2

value: Non-malignant B-cells isolated from peripheral blood of 5 healthy donors.


title: UPF4D-D75

source_name: Lymphoma cell line named UPF4D established from the patient's primary lymphoma cells after 75 days of in vitro cultivation.


title: UPF7U-D226

source_name: Lymphoma cell line named UPF7U established from the patient's primary lymphoma cells after 226 days of in vitro cultivation.


title: VFN-M3-CTRL1


title: CTRL2

source_name: Patient's non-malignant B-cells.

value: Patient's non-malignant B-cells.


title: VFN-D2-K2

source_name: Patient-derived xenograft (PDX) cells named VFN-D2 established by xenotransplantation of primary lymphoma cells into immunodeficient mice isolated from the infiltrated murine kidneys.


title: VFN-D2-SC

source_name: Patient-derived xenograft (PDX) cells named VFN-D2 established by xenotransplantation of primary lymphoma cells  into immunodeficient mice isolated ex vivo from subcutaneously growing lymphoma.


title: VFN-M3-SC1

value: Patient-derived xenograft (PDX) cells named VFN-M3 established by xenotransplantation of primary lymphoma cells into immunodeficient mice isolated ex vivo from subcutaneously growing lymphoma.


title: UPF4D-D15B

source_name: Lymphoma cell line named UPF4D established from the patient's primary lymphoma cells after 15 days of in vitro cultivation.


title: CTRL1


title: VFN-D2-K1

value: Patient-derived xenograft (PDX) cells named VFN-D2 established by xenotransplantation of primary lymphoma cells into immunodeficient mice isolated from the infiltrated murine kidneys.


title: UPF4D-SC

source_name: Cells established by xenotransplantation of UPF4D cell line isolated ex vivo from subcutaneously growing lymphoma.


title: UPF4D-D15A

value: Lymphoma cell line named UPF4D established from the patient's primary lymphoma cells after 15 days of in vitro cultivation.


title: Ras replicate 2

status: Public on Jan 13 2017

city: Barcelona

first: William

middle: M

last: Keyes

address: Carrer del Dr. Aiguader, 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Centre for Genomic Regulation (CRG)

hyb_protocol: After fragmentation, 600 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 3um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent). The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

source_name: primary mouse keratinocytes

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNA using the LowInputQuick Amp Labeling kit – Agilent 5190-2305 according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated 6 days post infection using an RNA-easy mini RNA extraction kit (Qiagen).

tag: agent

value: primary mouse keratinocytes


title: Patient 5 T197728

status: Public on Nov 01 2016

first: Zhang

last: Zi-Zhen

address: Department of General Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, 1630 Dongfang Road, Shanghai 200127, China

institute: Department of General Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, P.R. China

description: gastric cancer tissue of patient 5

hyb_protocol: The labeled cRNAs were hybridized onto the Human LncRNA Array v2.0 (8 x 60K, Arraystar)

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505B.Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images.

data_processing: Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package

source_name: Gastric Cancer

label_protocol: 1 µg of total RNA were primed with 1.2 μL of T7 Promoter Primer at 65°C for 10 min, then prepare labeling reaction at 40°C for 2 h in the presence of 8.5 μL of cDNA Master Mix, Add 60 μL of Transcription Master Mix to each sample tube. Gently mix by pipetting. Incubate samples at 40°C for 2 hours. And then purify the labeled/amplified RNA and labeled cRNA QC, finally do the hybridaztion.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. RNA quality was measured by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: The samples were stored in -80 degrees prior to extract preparation

value: tumor


title: Ras replicate 4


title: Patient 5 N197728

description: adjacent normal tissue of patient 5

value: adjacent normal


title: Vector replicate 3

value: empty vector (MSCV)


title: Vector replicate 1


title: Patient 4 T197359

description: gastric cancer tissue of patient 4


title: Patient 1 T197507

description: gastric cancer tissue of patient 1


title: Patient 2 N196955

description: adjacent normal tissue of patient 2


title: Patient 3 N197046

description: adjacent normal tissue of patient 3


title: Patient 4 N197359

description: adjacent normal tissue of patient 4


title: Ras replicate 3


title: Patient 2 T196955

description: gastric cancer tissue of patient 2


title: UPF4D-K

source_name: Cells established by xenotransplantation of UPF4D cell line isolated ex vivo from infiltrated murine kidney.


title: Ras replicate 1


title: Patient 3 T197046

description: gastric cancer tissue of patient 3


title: meningioma sample Jed13_MN

city: Jeddah

first: Hans-Juergen

last: Schulten

department: Center of Excellence in Genomic Medicine Research

country: Saudi Arabia

institute: King Abdulaziz University

description: GSE77259_GSM2046759; Gene expression data from primary brain tumor

hyb_protocol: Following fragmentation, 6 ug of cDNA were hybridized for 17 hr at 45C on GeneChip HuGene-1.0-st arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Data were generated using the Affymetrix Expression Console Software using Affymetrix default analysis settings.

source_name: meningioma, meningothelial  histology

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA from biospecimens was extracted using the Quagen RNeasy mini kit according to the manufacturer's instructions and integrity of RNA was checked using the Agilent Bioanalyzer.

tag: grade

value: I

value: F


title: meningioma sample Jed57_MN

description: GSE77259_GSM2046767; Gene expression data from primary brain tumor

source_name: meningioma, transitional histology


title: Patient 1 N197507

description: adjacent normal tissue of patient 1


title: Patient #189, Day 0

status: Public on May 26 2016

city: Singapore

first: Allen Eng Juh

last: Yeoh

address: 14 Medical Drive, MD6 #09-02

department: Paediatrics

institute: National University of Singapore

description: gene expression data at Day 0

hyb_protocol: Hybridization step was performed according to the Affymetrix 3' IVT PLUS Reagent Kit User Manual. Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A or -U133 Plus 2.0 array.

scan_protocol: Arrays were washed and stained using the Affymetrix Fluidics Station 450, and scanned using the GeneChip Scanner 3000 7G accroding to the manufacturer's instruction.

data_processing: Gene expression signal intensities were interrogated using the Affymetrix Expression Console software. Expression values were scaled to the target of 500 within the 22,277 probe sets that are common to both platforms. To reduce noise, a probe set was only retained if it is present in >30% of the samples. The remaining probe sets were then log transformed and quantile normalized.

source_name: bone marrow sample from child with acute lymphoblastic leukemia

label_protocol: Labeling step was performed according to the Affymetrix 3' IVT PLUS Reagent Kit User Manual.

extract_protocol: Total RNA was isolated using TRIzol reagent and purified using RNeasy Mini Kit according to respective manufacturer's instruction.

tag: diagnosis

value: acute lymphoblastic leukemia

value: bone marrow

tag: time point

value: Day 0

tag: patient id

tag: dataset

value: Test set


title: meningioma sample Jed64_MN

description: GSE77259_GSM2046769; Gene expression data from primary brain tumor

source_name: meningioma, fibroblastic histology

tag: gender


title: Patient #190, Day 8

description: gene expression data at Day 8

tag: tissue

value: Day 8


title: Patient #188, Day 8

description: gene expression data at Day 8