title: Dam.mst2_spb2104_2

description: data column in DamID_results.txt file: Dam.mst2_spb2104_2_vs_Damonly_spb492_2


title: Dam.mst2_2104.1

status: Public on Jun 22 2017

type: genomic

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: data column in DamID_results.txt file: Dam.mst2_2104.1_vs_Damonly_492.1

hyb_protocol: Hybridization was performed for 16h at 45°C and 60rpm in an Affymetrix hybridization oven; washing steps were done in an Affymetrix Fluidics station with the Affymetrix protocol FS450_0002

scan_protocol: GeneChips were scanned with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip® Scanner 3000 with autoloader.

data_processing:
Oligo-level data was rma background corrected, quantile normalized and log2 transformed using Bioconductor packages tilingArray and preprocessCore on R. Contrasts were computed on the oligo level by subtracting respective columns of expression. Differential expression values for individual features in the file sPombegenomicelementsV02_ALL.txt were calculated by averaging enrichment values for all the oligos overlapping the individual features, considering only features covered by at least 50 oligos. This produces the DamID_results.txt file [contains all 8014 features for which DamID enrichment was calculated, with a separate column for each of the 4 contrasts].
All results file are summarised in DamID_results.txt file
DamID_results.txt is a table containing all 17910 features for which DamID enrichment was calculated with a separate column for each of the 14 contrasts

label: biotin

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: Dam fused to Mst2 in WT cells

label_protocol: The DNA was fragmented and labeled using the Affymetrix GeneChip® GeneChip Hybridization, Wash, and Stain Kit according to the manufactuer's instructions

growth_protocol: Cells were grown to early exponential phase (OD=0.4) and harvested.

extract_protocol: Genomic DNA isolated using Dneasy Blood and Tissue Kit (Qiagen)

treatment_protocol: Harvested cells were spheroplasted to remove cell wall

tag: expression

tag: genotype

value: WT

tag: strain number


title: 3420: Diagnosis AML

city: Rotterdam

first: Nicole

last: Larmonie

address: Wytemaweg

country: Netherlands

institute: ErasmusMC

description:
CpG island array screening
Reference: Please refer to Differential Methylation Hybridization (DMH) protocol by Dr. Tim H. Huang and coworkers. (PMID 18987809: Yan PS, Potter D, Deatherage DE, Huang TH, Lin S., Differential methylation hybridization: profiling DNA methylation with a high-density CpG island microarray.Methods Mol Biol. 2009;507:89-106.)

hyb_protocol: The Oligo aCGH/ChiP-on-chip Hybridization Kit was used according the protocol to hybridize the labeled gDNA onto the microarrays enclosed in the Agilent SureHyb-enabled hybridization chambers. After o/n hybridization, slides were washed according to protocol o/n.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (V10.5.1.1) for data extraction. The R and Bioconductor statistical environment (version 2.10.0) were used for quality control and LOESS normalization (limma package). No background correction was performed.

organism: Homo sapiens

source_name: Bone Marrow

label_protocol: 500ng genomic DNA was cut with MseI, generating 200-800bp fragments. These fragments were ligated to linkers and cut with two methylation-sensitive restriction enzymes (BstuI and HpaII), cutting all the unmethylated fragments. Methylated CpG-island fragments were afterwards amplified by linker-PCR. Amplicons were labeled with Cy5 (patient samples) and Cy3 (common reference samples) fluorescent dye using the BioPrime Array-CGH Genomic Labeling kit (Invitrogen, Carlsbad, USA).

extract_protocol: Genomic DNA  was extracted using Trizol reagent according to manufacturer's instructions.

tag: gender

value: Male

tag: diagniosis

value: AML

tag: fab

tag: type 2 molecular aberration

source_name: Common Reference Samples

tag: diagnosis

value: Normal


title: Damonly_spb492_4

source_name: Dam only in WT cells

value: Dam-only


title: Damonly_spb492_2


title: Damonly_spb492_1


title: 3433: Diagnosis AML

value: Female


title: Damonly_492.2


title: Damonly_492.1


title: 3400: Diagnosis AML

source_name: Peripheral Blood


title: 3418: Diagnosis AML

value: unknown


title: 3186: Diagnosis AML


title: 3165: Diagnosis AML


title: IP Ago2-Phos3E transfected Repl1

type: RNA

city: Regensburg

first: Gunter

last: Meister

state: Bayern

address: Am Biopark9

department: Institute of Biochemistry, Genetics and Microbiology

country: Germany

institute: University of Regensburg

description:
immunoprecipitated RNA FLAG-Antibody
Precipitated transcript data of HEK293T cells overexpressing wild type Ago2-Phos3E(Ago2-824-34E)
Phos3E1

hyb_protocol: Of the fragmented and biotin labeled ss cDNA 3.8 μg were hybridized to Affymetrix Human Gene 2.1 ST Array Plates. For hybridization, washing, staining an Affymetrix GeneTitan system, controlled by the Affymetrix GeneChip Command Console software v4.2, was used.

scan_protocol: For scanning an Affymetrix GeneTitan system, controlled by the Affymetrix GeneChip Command Console software v4.2, was used.

data_processing: Per probe intensity values from the microarray were read out by Affymetrix GeneChip Command Console software v4.2. The raw intensities were processed with the software R (version 3.3.0) using the oligo package [Carvalho2010] together with built-in Affymetrix annotation (pd.hugene.2.1.st_3.14.1). Normalization was performed using VSN on the ERCC spike-in probes [Huber2002]. Differential precipitation in RNA-IP (RIP) assays was analyzed using limma [Ritchie2015].

molecule: total RNA

source_name: HEK 293T transfected with FLAG/HA-tagged Ago2-Phos3E

label_protocol: Sample preparation for microarray hybridization was carried out as described in the Affymetrix GeneChip WT PLUS Reagent Kit User Manual (Affymetrix, Inc., Santa Clara, CA, USA). In brief, between 4 and 100 ng of IP- RNA were used to generate double-stranded cDNA. In addition ERCC spike-ins (Thermo Fisher Scientific) were added. For total RNA (50 ng) 1 μl ERCC (1:1000) was used and for IP RNA (40 ng) 0.8 μl ERCC (1:5000) was spiked-in. For samples with lower amounts of IP-RNA, the volume of the ERCC spike-in was adjusted accordingly. Of subsequently synthesized cRNA 15 μg were purified and reversely transcribed into sense-strand (ss) cDNA, where unnatural dUTP residues were incorporated. Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by a terminal labeling with biotin.

growth_protocol: HEK 293T were cultured under standard conditions (37 °C and 5% CO2) by using Dulbecco's modified Eagle's medium (DMEM, Sigma-Aldrich) supplemented with 10% FBS (Gibco) and 1 % penicillin-treptomycin (Sigma-Aldrich).

extract_protocol: Cells were harvested 48 h after transfection, washed with PBS and lysed with NET buffer (50 mM Tris/HCl, pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% (v/v) NP-40, 10 % Glycerol, 1 mM NaF, 0.5 mM DTT and 1 mM AEBSF) and incubated for 20 min. Lysates were cleared by centrifugation at 15,000g for 20 min at 4 °C before they were used in immunoprecipitations. Per IP sample, 30 μl packed volume of anti-FLAG-M2 agarose beads (Sigma-Aldrich) for Western detection and 100 μl of anti-FLAG-M2 agarose beads for FLAG-tagged proteins were used for microarray analysis. Before using, the beads were washed with PBS twice and incubated with lysate for 2.5 h at 4 °C. The samples were washed four times with wash buffer (50 mM Tris/HCl, pH 7.5, 300 mM NaCl, 5 mM EDTA, 0.5% (v/v) NP-40, 10 % Glycerol, 1 mM NaF, 0.5 mM DTT and 1 mM AEBSF) and once with 1 x PBS. The co-immunoprecipitated RNA and input RNA was extracted using TRIzol® (Thermo Fisher Scientific).

treatment_protocol: HEK 293T cells were grown on 15-cm plates and calcium phosphate-transfected with 10 μg of plasmid DNA per plate.

tag: cell line

tag: transfection plasmid

tag: ip antibody

value: FLAG-Antibody

tag: replicates

value: biological (1)


title: IP Ago2-Y529E transfected Repl3

description:
immunoprecipitated RNA FLAG-Antibody
Precipitated transcript data of HEK293T cells overexpressing wild type Ago2-529E(Ago2-Y529E)
Y529E3

source_name: HEK 293T transfected with FLAG/HA-tagged Ago2-Y529E

value: biological (3)


title: IP Ago2-Y529E transfected Repl1

description:
immunoprecipitated RNA FLAG-Antibody
Precipitated transcript data of HEK293T cells overexpressing wild type Ago2-529E(Ago2-Y529E)
Y529E1


title: 1886: Diagnosis AML


title: IP Ago2-Y529E transfected Repl2

description:
immunoprecipitated RNA FLAG-Antibody
Precipitated transcript data of HEK293T cells overexpressing wild type Ago2-529E(Ago2-Y529E)
Y529E2

value: biological (2)


title: IP Ago2-Phos3A transfected Repl3

description:
immunoprecipitated RNA FLAG-Antibody
Precipitated transcript data of HEK293T cells overexpressing wild type Ago2-Phos3A(Ago2-824-34A)
Phos3A3

source_name: HEK 293T transfected with FLAG/HA-tagged Ago2-Phos3A


title: IP Ago2-Phos3E transfected Repl3

description:
immunoprecipitated RNA FLAG-Antibody
Precipitated transcript data of HEK293T cells overexpressing wild type Ago2-Phos3E(Ago2-824-34E)
Phos3E3


title: IP wt Ago2 transfected Repl3

description:
immunoprecipitated RNA FLAG-Antibody
Precipitated transcript data of HEK293T cells overexpressing wild type Ago2
WT3

source_name: HEK 293T transfected with FLAG/HA-tagged Ago2 (wt)


title: IP Ago2-Phos3A transfected Repl2

description:
immunoprecipitated RNA FLAG-Antibody
Precipitated transcript data of HEK293T cells overexpressing wild type Ago2-Phos3A(Ago2-824-34A)
Phos3A2


title: 1583: Diagnosis AML

value: Unknown


title: Lcr35® restituo packet_1

city: Aurillac

first: Stephanie

last: Bornes

address: 100 rue de l'egalite

department: IUT genie biologique

country: France

institute: Universite d'Auvergne

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Lacticaseibacillus rhamnosus

source_name: Native strain_packet

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

growth_protocol: Lactobacillus rhamnosus Lcr35 native strain and formulations were grown overnight at 37°C in De Man Rogosa Sharpe (MRS) medium (BIORAD, Mitry Mory, France). 59(6):2075).

extract_protocol: Total RNA was extracted using the RNA L  kit (Macherey Nagel, Duren, Germany) and DNA was removed using DNase digestion with the RNase-Free Dnase kit (Ambion). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer.

tag: strain

tag: manufacturing process

value: packet


title: IP Ago2-Phos3A transfected Repl1

description:
immunoprecipitated RNA FLAG-Antibody
Precipitated transcript data of HEK293T cells overexpressing wild type Ago2-Phos3A(Ago2-824-34A)
Phos3A1


title: IP wt Ago2 transfected Repl2

description:
immunoprecipitated RNA FLAG-Antibody
Precipitated transcript data of HEK293T cells overexpressing wild type Ago2
WT2


title: Input wt Ago2 transfected

description:
Gene expression data of HEK293T cells overexpressing wild type Ago2
Input1

value: no


title: Lcr35® restituo packet_2


title: Lcr35®_2

source_name: Native strain


title: Lcr35® restituo capsule_1

source_name: Native strain_capsule

value: capsule


title: Lcr35®_1


title: Lcr35® restituo capsule_3


title: Input Ago2-Phos3A transfected

description:
Gene expression data of HEK293T cells overexpressing wild type Ago2-Phos3A(Ago2-824-34A)
Input2


title: HCC037N

status: Public on Jun 21 2017

city: Beijing

first: Jin

last: Song

address: No.38 shengmingyuan Road

country: China

institute: Beijing Institute of Radiation Medicine

description: SAMPLE 75

hyb_protocol: Hybridization was performed for 16 hrs using the MES_EukGE-WS2v5_450-DEV fluidics wash and stain script.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip scanner 3000 7G

data_processing:
RMA (Robust Multiple chip Average) and quantile normalization integrated in Expression Console was used to extract the signal from core probes representing 22,012 transcript clusters and perform the preprocessing.
probe group file: HuEx-1_0-st-v2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label: Biotin

source_name: paired adjacent non-tumor tissue

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

growth_protocol: tumor tissues and non-tumor liver tissues from 38 HCC patients

extract_protocol: not applicable

tag: subject status

value: HCC patient

tag: subject id

tag: age

tag: tissue

value: liver

tag: tissue type

value: paired adjacent non-tumor tissue

tag: tnm staging


title: IP wt Ago2 transfected Repl1

description:
immunoprecipitated RNA FLAG-Antibody
Precipitated transcript data of HEK293T cells overexpressing wild type Ago2,biological replicate
WT1


title: Input Ago2-Phos3E transfected

description:
Gene expression data of HEK293T cells overexpressing wild type Ago2-Phos3E(Ago2-824-34E)
Input3


title: Lcr35® restituo capsule_2


title: Lcr35®_3


title: Lcr35® restituo packet_3


title: HCC038N

description: SAMPLE 76

tag: gender

value: Male


title: HCC034N

description: SAMPLE 72


title: HCC033N

description: SAMPLE 71


title: HCC035N

description: SAMPLE 73


title: HCC032N

description: SAMPLE 70


title: HCC030N

description: SAMPLE 68


title: HCC029N

description: SAMPLE 67


title: HCC031N

description: SAMPLE 69


title: HCC036N

description: SAMPLE 74


title: HCC024N

description: SAMPLE 62


title: HCC023N

description: SAMPLE 61


title: HCC022N

description: SAMPLE 60


title: HCC028N

description: SAMPLE 66


title: HCC021N

description: SAMPLE 59


title: HCC025N

description: SAMPLE 63


title: HCC017N

description: SAMPLE 55


title: HCC027N

description: SAMPLE 65


title: HCC026N

description: SAMPLE 64


title: HCC020N

description: SAMPLE 58


title: HCC019N

description: SAMPLE 57


title: HCC015N

description: SAMPLE 53


title: HCC018N

description: SAMPLE 56


title: HCC008N

description: SAMPLE 46


title: HCC012N

description: SAMPLE 50


title: HCC016N

description: SAMPLE 54


title: HCC013N

description: SAMPLE 51


title: HCC011N

description: SAMPLE 49


title: HCC010N

description: SAMPLE 48


title: HCC009N

description: SAMPLE 47


title: HCC006N

description: SAMPLE 44


title: HCC004N

description: SAMPLE 42


title: HCC007N

description: SAMPLE 45


title: HCC005N

description: SAMPLE 43


title: HCC014N

description: SAMPLE 52


title: HCC002N

description: SAMPLE 40


title: HCC038T

description: SAMPLE 38

source_name: tumor tissue

value: tumor tissue


title: HCC035T

description: SAMPLE 35


title: HCC034T

description: SAMPLE 34


title: HCC037T

description: SAMPLE 37


title: HCC032T

description: SAMPLE 32


title: HCC030T

description: SAMPLE 30


title: HCC003N

description: SAMPLE 41


title: HCC033T

description: SAMPLE 33


title: HCC024T

description: SAMPLE 24


title: HCC026T

description: SAMPLE 26


title: HCC022T

description: SAMPLE 22


title: HCC023T

description: SAMPLE 23


title: HCC001N

description: SAMPLE 39


title: HCC029T

description: SAMPLE 29


title: HCC021T

description: SAMPLE 21


title: HCC018T

description: SAMPLE 18


title: HCC031T

description: SAMPLE 31


title: HCC036T

description: SAMPLE 36


title: HCC019T

description: SAMPLE 19


title: HCC016T

description: SAMPLE 16


title: HCC015T

description: SAMPLE 15


title: HCC020T

description: SAMPLE 20


title: HCC028T

description: SAMPLE 28


title: HCC027T

description: SAMPLE 27


title: HCC025T

description: SAMPLE 25


title: HCC014T

description: SAMPLE 14


title: HCC013T

description: SAMPLE 13


title: HCC012T

description: SAMPLE 12


title: HCC008T

description: SAMPLE 8


title: HCC011T

description: SAMPLE 11


title: HCC006T

description: SAMPLE 6


title: HCC007T

description: SAMPLE 7


title: BEAS-2B CTRL, untreated

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

country: Japan

institute: Aichi Cancer Center

description:
Control
BEAS-2B CTRL 0h miRNA

data_processing: Normalization was carried out with the expression level of RNU44.

label: FAM

source_name: BEAS-2B cell line stably transduced with a CTRL vector, untreated

label_protocol: Total RNA was converted into cDNA using the megaplex reverse transcriptase reaction. The megaplex reaction contained a specific stem-loop primer for each of the mature target microRNA's. The cDNA was subjected to a pre-amplification PCR. The diluted pre-amplification products served as substrates for TaqMan quantitative PCR reactions.

growth_protocol: BEAS-2B cells were cultured with 1% (v/v) FCS-containing Ham F-12 supplemented with bovine insulin (5 ug/mL), human transferrin (5 ug/mL), 100 nM hydrocortisone, 200 pM triiode thyronine, penicillin (100 IU/mL), and streptomycin (100 ug/mL) at 37°C with 5% CO2

extract_protocol: Total RNA was extracted using the miRNeasy kit (Qiagen, Valencia, CA)

treatment_protocol: BEAS-2B CTRL and TTF-1 cell lines were treated with 1 ug/ml Doxycycline for 48 h before RNA was harvested

tag: protocol

value: control

tag: treatment

value: untreated


title: BEAS-2B CTRL, treated with doxycycline for 48h

description:
Control
BEAS-2B CTRL 48h miRNA

source_name: BEAS-2B cell line stably transduced with a CTRL vector, treated with doxycycline for 24h

value: doxycycline


title: BEAS-2B TTF-1, treated with doxycycline for 48h

description:
Test
BEAS-2B TTF-1 48h miRNA

source_name: BEAS-2B cell line stably transduced with a DOX-inducible TTF-1 expression vector, treated with doxycycline for 24h

value: transduced with a DOX-inducible TTF-1 expression construct


title: HCC004T

description: SAMPLE 4

value: Female


title: BEAS-2B TTF-1, untreated

description:
Control
BEAS-2B TTF-1 0h miRNA

source_name: BEAS-2B cell line stably transduced with a DOX-inducible TTF-1 expression vector, untreated


title: HCC005T

description: SAMPLE 5


title: HCC010T

description: SAMPLE 10


title: HCC009T

description: SAMPLE 9


title: HCC017T

description: SAMPLE 17


title: HCC003T

description: SAMPLE 3


title: HCC001T

description: SAMPLE 1


title: 325: Diagnosis AML

source_name: Bone Marrow

tag: diagniosis

value: AML

tag: fab

tag: type 2 molecular aberration

value: Normal


title: HCC002T

description: SAMPLE 2


title: eMC CIC-DUX4 5

city: Tokyo

first: Takuro

last: Nakamura

address: 3-8-31 Ariake, Koto-ku

department: The Cancer Institute

institute: Japanese Foundation for Cancer Research

description: Gene expression data from mesenchymal cells 48 hr after retroviral transduction

hyb_protocol: Following fragmentation, 7.5 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 PM Array. GeneChips were washed and stained in the Affymetrix GeneAtlas Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix GeneAtlas Imaging Station.

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

organism: Mus musculus

source_name: eMCs transduced with the CIC-DUX4 retrovirus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The tumor was grown subcutaneously in Balb/c nude mice. The mesenchymal cells were grown in Iscove's modified DMEM supplemented with 15% FBS.

extract_protocol: Total RNA was purified using RNA Easy kit (QIAGEN) according to the manufacturer's protocol

treatment_protocol: No treatment was provided to tumors. The mesenchymal cells were transduced with pMYs-CIC-DUX4-IRES-GFP or pMYs-IRES-GFP retroviruses by spinofection.

value: primary mesenchymal cell


title: ES 49

description: Gene expression data from mouse ES

source_name: Ewing sarcoma

value: Ewing sarcoma


title: eMC CIC-DUX4 6


title: eMC empty 6

source_name: eMCs transduced with the empty retrovirus


title: ES 51

description: Gene expression data from mouse ES


title: eMC CIC-DUX4 7


title: ES 47

description: Gene expression data from mouse ES


title: eMC CIC-DUX4 8


title: eMC empty 5


title: eMC empty 4


title: ES 48

description: Gene expression data from mouse ES


title: I475

city: Parkville

first: John

last: Hopper

state: Victoria

address: 207 Bouverie Street

department: Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health

country: Australia

institute: The University of Melbourne

description: SAMPLE 475

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

scan_protocol: Arrays were imaged using BeadArray Reader

data_processing:
Data was processed using minfi package, including Illumina’s reference factor-based normalization methods (preprocessIllumina) and subset-quantile within array normalization (SWAN) for type I and II probe bias correction (preprocessSWAN). ComBat was applied o minimize the technical variation across batches.
normalized_data.txt contains the normalised and batch-corrected average Beta and detection P-value
unmethylated_and_methylated_singal_intensities.txt contains the unmethylated and methylated signal intensities, and detection P-value

label: Cy5 and Cy3

source_name: Whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from dried blood spots using a method developed in-house.

tag: family id

tag: zygosity

value: Sister


title: I479

description: SAMPLE 479

value: MZ


title: I473

description: SAMPLE 473


title: I472

description: SAMPLE 472

value: DZ


title: I474

description: SAMPLE 474


title: I477

description: SAMPLE 477


title: I476

description: SAMPLE 476


title: eMC empty 7


title: I478

description: SAMPLE 478


title: I471

description: SAMPLE 471


title: CDS 2

description: Gene expression data from mouse CDS

source_name: CIC-DUX4 sarcoma

value: CIC-DUX4 sarcoma


title: ES 46

description: Gene expression data from mouse ES


title: CDS 1

description: Gene expression data from mouse CDS


title: CDS 5

description: Gene expression data from mouse CDS


title: I469

description: SAMPLE 469


title: I468

description: SAMPLE 468


title: I470

description: SAMPLE 470


title: CDS 6

description: Gene expression data from mouse CDS


title: CDS 4

description: Gene expression data from mouse CDS


title: ES 41

description: Gene expression data from mouse ES


title: I463

description: SAMPLE 463


title: I462

description: SAMPLE 462


title: CDS 3

description: Gene expression data from mouse CDS


title: I461

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title: I459

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title: I454

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description: SAMPLE 386


title: I385

description: SAMPLE 385


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description: SAMPLE 382


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description: SAMPLE 380


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description: SAMPLE 389


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description: SAMPLE 367


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description: SAMPLE 346


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description: SAMPLE 340


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description: SAMPLE 347


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description: SAMPLE 341


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description: SAMPLE 343


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description: SAMPLE 365


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description: SAMPLE 345


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description: SAMPLE 338


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description: SAMPLE 339


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description: SAMPLE 356


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description: SAMPLE 335


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description: SAMPLE 336


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description: SAMPLE 329


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description: SAMPLE 326


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description: SAMPLE 327


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description: SAMPLE 323


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description: SAMPLE 325


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description: SAMPLE 337


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description: SAMPLE 320


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description: SAMPLE 313


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description: SAMPLE 321


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description: SAMPLE 317


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description: SAMPLE 316


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description: SAMPLE 311


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description: SAMPLE 308


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description: SAMPLE 303


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description: SAMPLE 305


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description: SAMPLE 300


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description: SAMPLE 330


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description: SAMPLE 265


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description: SAMPLE 256


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description: SAMPLE 250


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description: SAMPLE 248


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description: SAMPLE 267


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description: SAMPLE 247


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description: SAMPLE 227


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description: SAMPLE 228


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description: SAMPLE 220


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description: SAMPLE 216


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description: SAMPLE 214


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description: SAMPLE 230


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description: SAMPLE 210


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title: I170

description: SAMPLE 170


title: I182

description: SAMPLE 182


title: I169

description: SAMPLE 169


title: I328

description: SAMPLE 328


title: Roemerine_0min_rep2

city: Udine

first: Dilara

last: Ayyıldız

address: p.le kolbe, 4

country: Italy

institute: University of Udine

description: Gene expression after 0 min. in Roemerine treated E.coli cells

hyb_protocol: 10X Blocking Agent supplied with the Agilent Gene Expression Hybridization Kit and 2x GEx Hybridization buffer HI-RPM were used in preparation of hybridization assembly by following manufacturers instructions.Hybridization was carried out at 65oC for 17 hours.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent C Scanner using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 3 µg, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Raw Microarray data evaluation including preprocessing, normalization, grouping the differentially expressed genes and statistical analyses with Moderated T-test and Bonferroni FWER was carried out with GeneSpring 13.0 Software.

organism: Escherichia coli

source_name: (-)-Roemerine treatment, 0 min, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  cRNA was quantitated using NanoDrop ND-1000 UV-VIS Spectrophotometer version 3.2.1.

growth_protocol: The pre-culture was the overnight propagated cells in 5 ml of LB medium at 37ºC and 180 rpm. The main bacterial culture was prepared by 1% inoculation from pre-culture when optical densities at 600 nm (i.e., OD600) reached 0.7. Growth was achieved in 50 ml of LB medium.

extract_protocol: Total RNA extraction was carried out based on the protocols given in the manual of QIAGEN - RNAprotect Bacteria Reagent Handbook, QIAGEN - RNeasy Mini Kit and QIAGEN - RNase-free DNase set. The concentration of each RNA sample was measured by Qubit® RNA BR Assay Kit (Invitrogen).

treatment_protocol: When OD600 of the culture reached 0.54±0.06, cells were treated with 100 µg/ml of (-)-Roemerine. Since the alkaloid was dissolved in DMSO, control cells were also treated with the same amount of DMSO.


title: I166

description: SAMPLE 166


title: I165

description: SAMPLE 165


title: Roemerine_0min_rep1

source_name: (-)-Roemerine treatment, 0 min, replicate 1


title: Roemerine_0min_rep3

source_name: (-)-Roemerine treatment, 0 min, replicate 3


title: I168

description: SAMPLE 168


title: DMSO_60min_rep3

description: Gene expression after 60 min. in DMSO treated E.coli cells

source_name: DMSO treatment, 60 min, replicate 3


title: I175

description: SAMPLE 175


title: Roemerine_60min_rep1

description: Gene expression after 60 min. in Roemerine treated E.coli cells

source_name: (-)-Roemerine treatment, 60 min, replicate 1


title: I164

description: SAMPLE 164


title: Roemerine_60min_rep2

source_name: (-)-Roemerine treatment, 60 min, replicate 2


title: I163

description: SAMPLE 163


title: Roemerine_60min_rep3

source_name: (-)-Roemerine treatment, 60 min, replicate 3


title: DMSO_60min_rep4

source_name: DMSO treatment, 60 min, replicate 4


title: I172

description: SAMPLE 172


title: DMSO_60min_rep2

source_name: DMSO treatment, 60 min, replicate 2


title: DMSO_60min_rep1

source_name: DMSO treatment, 60 min, replicate 1


title: DMSO_0min_rep3

description: Gene expression after 0 min. in DMSO treated E.coli cells

source_name: DMSO treatment, 0 min, replicate 3


title: I160

description: SAMPLE 160


title: I159

description: SAMPLE 159


title: I167

description: SAMPLE 167


title: I158

description: SAMPLE 158


title: DMSO_0min_rep2

source_name: DMSO treatment, 0 min, replicate 2


title: DMSO_0min_rep1

source_name: DMSO treatment, 0 min, replicate 1


title: I162

description: SAMPLE 162


title: I157

description: SAMPLE 157


title: I155

description: SAMPLE 155


title: I156

description: SAMPLE 156


title: I154

description: SAMPLE 154


title: I151

description: SAMPLE 151


title: I149

description: SAMPLE 149


title: I153

description: SAMPLE 153


title: I148

description: SAMPLE 148


title: I146

description: SAMPLE 146


title: I147

description: SAMPLE 147


title: I161

description: SAMPLE 161


title: I150

description: SAMPLE 150


title: Myopericytoma2

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

hyb_protocol: GeneChip® miRNA 2.0 arrays (Affymetrix) were hybridized with 100ng labelled microRNA, Hybridisation time was 18 hours.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project.  Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al..
probe group file: UnsupportedGeneChip® miRNA 2.0 Array CDF Files
meta-probeset file: miRNA 2.0 Annotations, Unsupported, CSV format from Affymetrix

source_name: Myopericytoma (tissue of whole sections)

label_protocol: miRNA was labeled with the Affymetrix FlashTag Biotin HSR RNA Labeling Kit

growth_protocol: none (primary cells were analyzed)

extract_protocol: miRNA was extracted with the miRNeasy FFPE Kit from Qiagen

treatment_protocol: no specific treatment was performed

tag: tissue/cell type

tag: molecule subtype

value: micro RNA


title: I144

description: SAMPLE 144


title: I142

description: SAMPLE 142


title: I143

description: SAMPLE 143


title: GC Bcells 5

source_name: Germinal center B cells (MACS-purified)

value: Germinal center B cells (MACS-purified)


title: I139

description: SAMPLE 139

source_name: Whole blood


title: I152

description: SAMPLE 152


title: I138

description: SAMPLE 138


title: I137

description: SAMPLE 137


title: Fibro4

source_name: fibroblasts isolated from circumcision

value: fibroblasts isolated from circumcision


title: I136

description: SAMPLE 136


title: I134

description: SAMPLE 134


title: I135

description: SAMPLE 135


title: I132

description: SAMPLE 132


title: GC Bcells 4


title: Fibro3


title: Fibro1


title: I133

description: SAMPLE 133


title: Myopericytoma1

value: Myopericytoma (tissue of whole sections)


title: I145

description: SAMPLE 145


title: Fibro5


title: I130

description: SAMPLE 130


title: I141

description: SAMPLE 141


title: GC Bcells 2


title: Fibro2


title: GC Bcells 3


title: I129

description: SAMPLE 129


title: GC Bcells 1


title: CD14 4

source_name: CD14-positive monocytes (FACS-sorted)

value: CD14-positive monocytes (FACS-sorted)


title: CD14 6


title: I128

description: SAMPLE 128


title: CD14 5


title: I127

description: SAMPLE 127


title: I126

description: SAMPLE 126


title: I125

description: SAMPLE 125


title: CD14 3


title: I131

description: SAMPLE 131


title: I124

description: SAMPLE 124


title: I120

description: SAMPLE 120


title: I123

description: SAMPLE 123


title: I122

description: SAMPLE 122


title: I118

description: SAMPLE 118


title: I119

description: SAMPLE 119


title: I116

description: SAMPLE 116


title: I117

description: SAMPLE 117


title: I121

description: SAMPLE 121


title: I115

description: SAMPLE 115


title: CD14 2


title: I112

description: SAMPLE 112


title: I113

description: SAMPLE 113


title: I114

description: SAMPLE 114


title: FDC Sarcoma31

source_name: FDC sarcoma (tissue of whole sections)

value: follicular dendritic cell (FDC) sarcomas

value: FDC sarcoma (tissue of whole sections)


title: CD14 1


title: FDC Sarcoma30


title: I111

description: SAMPLE 111


title: CD1c 1

source_name: CD1c dendritic cells (FACS-sorted)

value: CD1c dendritic cells (FACS-sorted)


title: I110

description: SAMPLE 110

value: Female


title: I108

description: SAMPLE 108


title: FDC Sarcoma29


title: I107

description: SAMPLE 107


title: I106

description: SAMPLE 106


title: FDC Sarcoma28


title: FDC Sarcoma27


title: I105

description: SAMPLE 105


title: I102

description: SAMPLE 102


title: I103

description: SAMPLE 103


title: I100

description: SAMPLE 100


title: FDC Sarcoma16b


title: I101

description: SAMPLE 101


title: I104

description: SAMPLE 104


title: FDC Sarcoma5b


title: FDC Sarcoma26


title: I096

description: SAMPLE 96


title: I099

description: SAMPLE 99


title: CD1c 2


title: I095

description: SAMPLE 95


title: I094

description: SAMPLE 94


title: I109

description: SAMPLE 109


title: I093

description: SAMPLE 93


title: I092

description: SAMPLE 92


title: I091

description: SAMPLE 91


title: I090

description: SAMPLE 90


title: FDC Sarcoma25


title: FDC Sarcoma22


title: FDC Sarcoma21


title: FDC Sarcoma23


title: I088

description: SAMPLE 88


title: FDC Sarcoma24


title: I089

description: SAMPLE 89


title: FDC Sarcoma20


title: I086

description: SAMPLE 86


title: I087

description: SAMPLE 87


title: I098

description: SAMPLE 98


title: I085

description: SAMPLE 85


title: I097

description: SAMPLE 97


title: I084

description: SAMPLE 84


title: I083

description: SAMPLE 83


title: FDC Sarcoma19


title: FDC Sarcoma18


title: FDC Sarcoma16


title: FDC Sarcoma17


title: I078

description: SAMPLE 78


title: I079

description: SAMPLE 79


title: I077

description: SAMPLE 77


title: I080

description: SAMPLE 80


title: I076

description: SAMPLE 76


title: I074

description: SAMPLE 74


title: I073

description: SAMPLE 73


title: FDC Sarcoma15


title: I072

description: SAMPLE 72


title: FDC Sarcoma14


title: I071

description: SAMPLE 71


title: I070

description: SAMPLE 70


title: I075

description: SAMPLE 75


title: FDC Sarcoma13


title: FDC Sarcoma12


title: I082

description: SAMPLE 82


title: FDC Sarcoma11


title: I081

description: SAMPLE 81


title: I068

description: SAMPLE 68


title: I069

description: SAMPLE 69


title: I067

description: SAMPLE 67


title: FDC Sarcoma10


title: I066

description: SAMPLE 66


title: I064

description: SAMPLE 64


title: I065

description: SAMPLE 65


title: I063

description: SAMPLE 63


title: I062

description: SAMPLE 62


title: FDC Sarcoma8


title: I061

description: SAMPLE 61


title: I058

description: SAMPLE 58


title: I059

description: SAMPLE 59


title: I060

description: SAMPLE 60


title: FDC Sarcoma9


title: I057

description: SAMPLE 57


title: I055

description: SAMPLE 55


title: I054

description: SAMPLE 54


title: I056

description: SAMPLE 56


title: I053

description: SAMPLE 53


title: I051

description: SAMPLE 51


title: I052

description: SAMPLE 52


title: I050

description: SAMPLE 50


title: FDC Sarcoma6


title: FDC Sarcoma4


title: FDC Sarcoma5


title: I049

description: SAMPLE 49


title: FDC Sarcoma3


title: FDC Sarcoma2


title: FDC Sarcoma7


title: FDC Sarcoma1


title: I048

description: SAMPLE 48


title: Castleman5

source_name: microdissected FDCs from Castleman´s disease


title: I046

description: SAMPLE 46


title: Castleman4

value: microdissected FDCs from Castleman´s disease


title: I047

description: SAMPLE 47


title: I045

description: SAMPLE 45


title: I043

description: SAMPLE 43


title: I038

description: SAMPLE 38


title: I037

description: SAMPLE 37


title: I041

description: SAMPLE 41


title: I039

description: SAMPLE 39


title: I042

description: SAMPLE 42


title: I040

description: SAMPLE 40


title: Castleman1


title: Castleman2


title: I036

description: SAMPLE 36


title: I035

description: SAMPLE 35


title: I034

description: SAMPLE 34


title: Castleman3


title: I030

description: SAMPLE 30


title: I028

description: SAMPLE 28


title: I032

description: SAMPLE 32


title: I029

description: SAMPLE 29


title: I026

description: SAMPLE 26


title: I025

description: SAMPLE 25


title: I031

description: SAMPLE 31


title: I027

description: SAMPLE 27


title: I024

description: SAMPLE 24


title: I021

description: SAMPLE 21


title: I023

description: SAMPLE 23


title: I020

description: SAMPLE 20


title: I022

description: SAMPLE 22


title: I044

description: SAMPLE 44


title: I019

description: SAMPLE 19


title: I018

description: SAMPLE 18


title: I016

description: SAMPLE 16


title: I017

description: SAMPLE 17


title: I013

description: SAMPLE 13


title: I014

description: SAMPLE 14


title: I015

description: SAMPLE 15


title: I012

description: SAMPLE 12


title: I010

description: SAMPLE 10


title: I011

description: SAMPLE 11


title: I033

description: SAMPLE 33


title: I007

description: SAMPLE 7


title: I008

description: SAMPLE 8


title: I006

description: SAMPLE 6


title: I140

description: SAMPLE 140


title: I005

description: SAMPLE 5


title: I003

description: SAMPLE 3


title: I004

description: SAMPLE 4


title: I001

description: SAMPLE 1


title: I002

description: SAMPLE 2


title: I009

description: SAMPLE 9


title: Cy5-H1299_miR-532-5p_Cy3-20CL

description: NCI-H1299 miR-532-5p

hyb_protocol: 300 ng of Cy5-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) and Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) were fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K v2 Microarrays (G4851B) for 17 hours at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: SurePrint G3 Human GE 8x60K v2 Microarray with 60k distinct probes was scanned using an Agilent DNA microarray scanner (G2539A, Agilent Technologies). Images were quantified using Agilent Scan Control Software (version 10.7.1.1. or 10.10.1.1).

data_processing: LOWESS normalized, background subtracted VALUE data obtained from ratio of processed Red signal/processed Green signal using Agilent Scan Control Software (version 10.7.1.1. or 10.10.1.1).

source_name: miR-532-5p-transfection in NCI-H1299

label_protocol: Cy5-sample cRNA and Cy3-sample cRNA were generated and hybridized to a SurePrint G3 Human GE 8x60K v2 Microarray kit (Agilent Technologies) with 60k distinct probes.

growth_protocol: BEAS-2B cells were cultured with 1% (v/v) FCS-containing Ham F-12 supplemented with bovine insulin (5 ug/mL), human transferrin (5 ug/mL), 100 nM hydrocortisone, 200 pM triiode thyronine, penicillin (100 IU/mL), and streptomycin (100 ug/mL) at 37°C with 5% CO2. NCI-H23, NCI-H1299 and PC-9 cells were cultured with 10% (v/v) FCS-containing RPMI 1640 at 37°C with 5% CO2.

extract_protocol: Total RNA was extracted using the miRNeasy kit (Qiagen, Valencia, CA), followed by treatment with DNase I. Double-stranded cDNA was synthesized from 100 ng of total RNA using MMLV-RT and poly dT primer incorporating the T7 promoter.

treatment_protocol: BEAS-2B, NCI-H23, NCI-H1299 and PC-9 CTRL and TTF-1 cell lines were treated with 1 ug/ml Doxycycline for 24 h before RNA was harvested; NCI-H23 and NCI-H1299 cells were transfected with miR-532-5p mimics or a negative control and incubated for 48h before harvest

tag: cell line

value: transfected with miR-532-5p mimics

tag: reference

value: mixture of 20 cell ines


title: Cy5-H23_miR-532-5p_Cy3-20CL

description: NCI-H23 miR-532-5p

source_name: miR-532-5p-transfection in NCI-H23


title: Cy5-H23_NC_Cy3-20CL

description: NCI-H23 NC

source_name: NC-transfection in NCI-H23

value: transfection control


title: Cy5-PC-9_TTF-1_24h_Cy3-20CL

description: PC-9 TTF-1 24h

source_name: PC-9 cell line stably transduced with a DOX-inducible TTF-1 expression vector, treated with doxycycline for 24h

value: transduced with a DOX-inducible TTF-1 expression construct

value: doxycycline


title: Cy5-PC-9_CTRL_24h_Cy3-20CL

description: PC-9 CTRL 24h

source_name: PC-9 cell line stably transduced with a CTRL vector, treated with doxycycline for 24h

value: control


title: Cy5-PC-9_TTF-1_0h_Cy3-20CL

description: PC-9 TTF-1 0h

source_name: PC-9 cell line stably transduced with a DOX-inducible TTF-1 expression vector, untreated

value: untreated


title: Cy5-H1299_TTF-1_24h_Cy3-20CL

description: NCI-H1299 TTF-1 24h

source_name: NCI-H1299 cell line stably transduced with a DOX-inducible TTF-1 expression vector, treated with doxycycline for 24h


title: Cy5-H1299_TTF-1_0h_Cy3-20CL

description: NCI-H1299 TTF-1 0h

source_name: NCI-H1299 cell line stably transduced with a DOX-inducible TTF-1 expression vector, untreated


title: Cy5-H23_CTRL_0h_Cy3-20CL

description: NCI-H23 CTRL 0h

source_name: NCI-H23 cell line stably transduced with a CTRL vector, untreated


title: Cy5-H1299_NC_Cy3-20CL

description: NCI-H1299 NC

source_name: NC-transfection in NCI-H1299


title: Adenocarcinoma 087

scan_protocol: SurePrint G3 Human GE 8x60K v2 Microarray with 60k distinct probes was scanned using an Agilent DNA microarray scanner (G2539A, Agilent Technologies). Images were quantified using Agilent Scan Control Software (version 10.10.1.1).

data_processing: LOWESS normalized, background subtracted VALUE data obtained from ratio of processed Red signal/processed Green signal using Agilent Scan Control Software (version 10.10.1.1).

source_name: Primary lung tumor

growth_protocol: Tumors of 75 lung adenocarcinoma patients which successfully underwent potential curative resection at Aichi Cancer Center, Nagoya, Japan, were investigated. All tumors were histologically categorized according to the IASLC/ATS/ERS classification. Approval of the institutional review boards of Nagoya University Graduate School of Medicine and Aichi Cancer Center and written informed consent from the patients were obtained.

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen, Valencia, CA), followed by treatment with DNase I. Double-stranded cDNA was synthesized from 100 ng of total RNA using MMLV-RT and poly dT primer incorporating the T7 promoter.

treatment_protocol: All tumor specimens were embedded in OCT compound and stored at −80°C.

value: F

tag: histology

value: AD

tag: stage (pathological)

value: IIB


title: Cy5-H1299_CTRL_0h_Cy3-20CL

description: NCI-H1299 CTRL 0h

source_name: NCI-H1299 cell line stably transduced with a CTRL vector, untreated


title: Adenocarcinoma 086

tag: age

value: IIIA


title: Cy5-H23_TTF-1_24h_Cy3-20CL

description: NCI-H23 TTF-1 24h

source_name: NCI-H23 cell line stably transduced with a DOX-inducible TTF-1 expression vector, treated with doxycycline for 24h


title: Cy5-H23_TTF-1_0h_Cy3-20CL

description: NCI-H23 TTF-1 0h

source_name: NCI-H23 cell line stably transduced with a DOX-inducible TTF-1 expression vector, untreated


title: Cy5-H23_CTRL_24h_Cy3-20CL

description: NCI-H23 CTRL 24h

source_name: NCI-H23 cell line stably transduced with a CTRL vector, treated with doxycycline for 24h


title: Cy5-PC-9_CTRL_0h_Cy3-20CL

description: PC-9 CTRL 0h

source_name: PC-9 cell line stably transduced with a CTRL vector, untreated


title: Adenocarcinoma 084

value: M

value: IB


title: Cy5-H1299_CTRL_24h_Cy3-20CL

description: NCI-H1299 CTRL 24h

source_name: NCI-H1299 cell line stably transduced with a CTRL vector, treated with doxycycline for 24h


title: Adenocarcinoma 079


title: Cy5-BEAS-2B_CTRL_24h_Cy3-20CL

description: BEAS-2B CTRL 24h

source_name: BEAS-2B cell line stably transduced with a CTRL vector, treated with doxycycline for 24h


title: Cy5-BEAS-2B_TTF-1_0h_Cy3-20CL

description: BEAS-2B TTF-1 0h

source_name: BEAS-2B cell line stably transduced with a DOX-inducible TTF-1 expression vector, untreated


title: Adenocarcinoma 082

value: IA


title: Adenocarcinoma 088


title: Cy5-BEAS-2B_TTF-1_24h_Cy3-20CL

description: BEAS-2B TTF-1 24h

source_name: BEAS-2B cell line stably transduced with a DOX-inducible TTF-1 expression vector, treated with doxycycline for 24h


title: Adenocarcinoma 083

value: IIA


title: Adenocarcinoma 078


title: Adenocarcinoma 081


title: Adenocarcinoma 080


title: Cy5-BEAS-2B_CTRL_0h_Cy3-20CL

description: BEAS-2B CTRL 0h

source_name: BEAS-2B cell line stably transduced with a CTRL vector, untreated


title: Adenocarcinoma 077


title: Adenocarcinoma 075


title: Adenocarcinoma 066


title: Adenocarcinoma 067


title: Adenocarcinoma 065


title: Adenocarcinoma 072


title: Adenocarcinoma 073


title: Adenocarcinoma 076


title: Adenocarcinoma 074


title: Adenocarcinoma 071


title: Adenocarcinoma 064


title: Adenocarcinoma 059


title: Adenocarcinoma 058


title: Adenocarcinoma 060


title: Adenocarcinoma 055


title: Adenocarcinoma 056


title: Adenocarcinoma 069


title: Adenocarcinoma 063


title: Adenocarcinoma 053


title: Adenocarcinoma 054

value: IIIB


title: Adenocarcinoma 062


title: Adenocarcinoma 052


title: Adenocarcinoma 061


title: Adenocarcinoma 057


title: Adenocarcinoma 051


title: Adenocarcinoma 050


title: Adenocarcinoma 047


title: Adenocarcinoma 046


title: Adenocarcinoma 049


title: Adenocarcinoma 045


title: Adenocarcinoma 043


title: Adenocarcinoma 034


title: Adenocarcinoma 042


title: Adenocarcinoma 040


title: Adenocarcinoma 037


title: Adenocarcinoma 041


title: Adenocarcinoma 035


title: Adenocarcinoma 044


title: Adenocarcinoma 030


title: Adenocarcinoma 039


title: Adenocarcinoma 032


title: Adenocarcinoma 026


title: Adenocarcinoma 020


title: Adenocarcinoma 033


title: Adenocarcinoma 018


title: Adenocarcinoma 027


title: Adenocarcinoma 011


title: Adenocarcinoma 036


title: Adenocarcinoma 029


title: Adenocarcinoma 014


title: Adenocarcinoma 031


title: Adenocarcinoma 012


title: Adenocarcinoma 025


title: Adenocarcinoma 010


title: Adenocarcinoma 009


title: Adenocarcinoma 019


title: Adenocarcinoma 023


title: Adenocarcinoma 008


title: Adenocarcinoma 006


title: Adenocarcinoma 007


title: Blood_normalHDLC [10010719]

city: Philadelphia

first: Sumeet

last: Khetarpal

address: 3400 Civic Center Blvd, 11-166 SCTR

country: USA

institute: University of Pennsylvania

description:
10010719
Genomic DNA extracted form whole blood was genotyped using the  Illumina HumanExome-12 v1.0 BeadChip system

hyb_protocol: standard Illumina protocol

scan_protocol: Illumina HiScan scanner

data_processing: SNP calling was performed with GenomeStudio (2010.3); processed data files include: Plus/Minus Alleles, Genotype, Score, Theta, R, B Allele Frequency, and Log R Ratio

label: Cy3, Cy5

source_name: Blood, normal HDLC

label_protocol: Illumina Infinium HD Assay Kit

extract_protocol: genomic DNA was extracted from peripheral blood according to standard procedures.

tag: tissue

value: Blood

tag: hdlc status

value: normal


title: Blood_normalHDLC [10003647]

description:
10003647
Genomic DNA extracted form whole blood was genotyped using the  Illumina HumanExome-12 v1.0 BeadChip system


title: Blood_normalHDLC [10010993]

description:
10010993
Genomic DNA extracted form whole blood was genotyped using the  Illumina HumanExome-12 v1.0 BeadChip system


title: IPA_D

city: Suita

first: Chiara

last: Furusawa

state: Osaka

address: Furuedai

institute: RIKEN Quantitative Biology Center

description: Transcriptome data of Isopropanol tolerant strain D without stress

hyb_protocol: After confirmation of yields (> 825 ng) and specific activities (> 15 pmol/μg) of the Cy3-labbeled cRNAs using NanoDrop ND-2000, 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GE Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to custom designed the Agilent 8× 60K arrays for E. coli W3110, E.coli_K12_Expression_Ver.1, for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G4900DA) using one color scan setting for 8x60k array slides (AgilentG3_GX_1Color, Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: ExternalFullGEML_043017_D_F_20120907) to obtain background subtracted and spatially detrended Processed Signal intensities.

label_protocol: One hundred ng of purified total RNAs was labeled using the Low Input Quick Amp WT Labeling Kit (Agilent Technologies) with Cyanine3 (Cy3) in accordance with the manufacturer’s instructions.

growth_protocol: The cells were precultured for overnight. Then, 5×10^7 cells in the exponential growth phase were used to transcriptome analysis.

extract_protocol: Total RNA was isolated and purified from cells using an RNeasy micro kit with on-column DNA digestion (Qiagen) in accordance with the manufacturer’s instructions. The quality of the purified RNA was evaluated using Agilent 2100 Bioanalyzer with an RNA 6000 Nano kit (Agilent Technologies). Only purified RNAs that had RIN (RNA integrity number) of 9.0 or more were utilized. The purified RNAs were stored at −80°C prior to transcriptome analysis.

treatment_protocol: Exponential cultures were withdrawn rapidly, and cells were killed immediately by the addition of an equal volume of ice-cold ethanol that contained 10% (w/v) phenol. The cells were collected by centrifugation at 20,000 × g at 4 °C for 5 min, and the pelleted cells were stored at −80 °C prior to RNA extraction.

tag: strain


title: IPA_C

description: Transcriptome data of Isopropanol tolerant strain C without stress


title: Blood_normalHDLC [10000196]

description:
10000196
Genomic DNA extracted form whole blood was genotyped using the  Illumina HumanExome-12 v1.0 BeadChip system


title: IPA_B

description: Transcriptome data of Isopropanol tolerant strain B without stress


title: IPA_E

description: Transcriptome data of Isopropanol tolerant strain E without stress


title: Parent_rep2

description: Transcriptome data of Parent without stress replicate 2

source_name: Parent without stress replicate 2


title: Parent_rep1

description: Transcriptome data of Parent without stress replicate 1

source_name: Parent without stress replicate 1


title: IPA_A

description: Transcriptome data of Isopropanol tolerant strain A without stress


title: Blood_normalHDLC [10000292]

description:
10000292
Genomic DNA extracted form whole blood was genotyped using the  Illumina HumanExome-12 v1.0 BeadChip system


title: HCC031N [lncRNA expression]

description: SAMPLE 69

hyb_protocol: HMicroarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3/Cy5 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA).

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000 B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon). Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and intensity extraction.

data_processing: Raw signal intensities were normalized in RMA method by NimbleScan v2.5

label: cy3, experiment

source_name: paired adjacent non-tumor liver tissue

label_protocol: Double-strand cDNA (ds-cDNA) was synthesized from 5 μg of total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100 pmol oligo dT primers. ds-cDNA was cleaned and labeled in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., USA). Briefly, ds-cDNA was incubated with 4 μg RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using a NanoDrop ND-1000. For Cy3/Cy5 labeling of cDNA, the NimbleGen Dual-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). One μg ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3/Cy5-9mer primer. Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled ds-cDNA was purified by isopropanol / ethanol precipitation.

growth_protocol: Tumor tissues and non-tumor liver tissues from 38 HCC patients

extract_protocol: The total RNAs were extract with Qiagen Rneasy mini kit according to the manufacturer’s protocols.

treatment_protocol: not applicable

tag: subject status

value: HCC patient

tag: subject id

tag: gender

value: Male

tag: tnm staging

value: liver

tag: tissue subytpe

value: paired adjacent non-tumor tissue

label: cy5, reference

source_name: adjacent non-tumor liver tissues

tag: sample type

value: pooled reference


title: Adenocarcinoma 001

value: mixture of 20 cell ines


title: Blood_highHDLC [PDHS2216]

description:
PDHS2216
Genomic DNA extracted form whole blood was genotyped using the  Illumina HumanExome-12 v1.0 BeadChip system

source_name: Blood, high HDLC

value: high


title: Adenocarcinoma 002

source_name: Primary lung tumor

value: F

value: AD


title: Adenocarcinoma 003

value: IIIA


title: Adenocarcinoma 005


title: Blood_normalHDLC [10004010]

description:
10004010
Genomic DNA extracted form whole blood was genotyped using the  Illumina HumanExome-12 v1.0 BeadChip system


title: IPA_F

description: Transcriptome data of Isopropanol tolerant strain F without stress


title: Adenocarcinoma 004


title: HCC037N [lncRNA expression]

description: SAMPLE 75


title: HCC036N [lncRNA expression]

description: SAMPLE 74


title: HCC038N [lncRNA expression]

description: SAMPLE 76


title: HCC033N [lncRNA expression]

description: SAMPLE 71


title: HCC034N [lncRNA expression]

description: SAMPLE 72


title: HCC035N [lncRNA expression]

description: SAMPLE 73


title: HCC032N [lncRNA expression]

description: SAMPLE 70


title: Blood_highHDLC [PAM1340]

description:
PAM1340
Genomic DNA extracted form whole blood was genotyped using the  Illumina HumanExome-12 v1.0 BeadChip system


title: Blood_highHDLC [HHDL1574]

description:
HHDL1574
Genomic DNA extracted form whole blood was genotyped using the  Illumina HumanExome-12 v1.0 BeadChip system


title: Blood_highHDLC [HHDL0398]

description:
HHDL0398
Genomic DNA extracted form whole blood was genotyped using the  Illumina HumanExome-12 v1.0 BeadChip system


title: Blood_highHDLC [HHDL0166]

description:
HHDL0166
Genomic DNA extracted form whole blood was genotyped using the  Illumina HumanExome-12 v1.0 BeadChip system


title: Blood_highHDLC [PAM0567]

description:
PAM0567
Genomic DNA extracted form whole blood was genotyped using the  Illumina HumanExome-12 v1.0 BeadChip system


title: HCC029N [lncRNA expression]

description: SAMPLE 67


title: Blood_highHDLC [HHDL2248]

description:
HHDL2248
Genomic DNA extracted form whole blood was genotyped using the  Illumina HumanExome-12 v1.0 BeadChip system


title: Blood_highHDLC [HHDL1658]

description:
HHDL1658
Genomic DNA extracted form whole blood was genotyped using the  Illumina HumanExome-12 v1.0 BeadChip system


title: HCC030N [lncRNA expression]

description: SAMPLE 68

value: Female


title: Blood_highHDLC [HHDL1088]

description:
HHDL1088
Genomic DNA extracted form whole blood was genotyped using the  Illumina HumanExome-12 v1.0 BeadChip system


title: Blood_highHDLC [HHDL1656]

description:
HHDL1656
Genomic DNA extracted form whole blood was genotyped using the  Illumina HumanExome-12 v1.0 BeadChip system


title: Blood_highHDLC [HHDL2221]

description:
HHDL2221
Genomic DNA extracted form whole blood was genotyped using the  Illumina HumanExome-12 v1.0 BeadChip system


title: Blood_highHDLC [HHDL1087]

description:
HHDL1087
Genomic DNA extracted form whole blood was genotyped using the  Illumina HumanExome-12 v1.0 BeadChip system


title: Blood_highHDLC [CCS0570]

description:
CCS0570
Genomic DNA extracted form whole blood was genotyped using the  Illumina HumanExome-12 v1.0 BeadChip system


title: HCC026N [lncRNA expression]

description: SAMPLE 64


title: HCC028N [lncRNA expression]

description: SAMPLE 66


title: HCC027N [lncRNA expression]

description: SAMPLE 65


title: HCC024N [lncRNA expression]

description: SAMPLE 62


title: HCC025N [lncRNA expression]

description: SAMPLE 63


title: HCC020N [lncRNA expression]

description: SAMPLE 58


title: HCC021N [lncRNA expression]

description: SAMPLE 59


title: HCC023N [lncRNA expression]

description: SAMPLE 61


title: HCC022N [lncRNA expression]

description: SAMPLE 60


title: HCC018N [lncRNA expression]

description: SAMPLE 56


title: HCC012N [lncRNA expression]

description: SAMPLE 50


title: HCC010N [lncRNA expression]

description: SAMPLE 48


title: HCC019N [lncRNA expression]

description: SAMPLE 57


title: HCC014N [lncRNA expression]

description: SAMPLE 52


title: HCC011N [lncRNA expression]

description: SAMPLE 49


title: HCC009N [lncRNA expression]

description: SAMPLE 47


title: HCC015N [lncRNA expression]

description: SAMPLE 53


title: HCC017N [lncRNA expression]

description: SAMPLE 55


title: HCC008N [lncRNA expression]

description: SAMPLE 46


title: HCC013N [lncRNA expression]

description: SAMPLE 51


title: HCC006N [lncRNA expression]

description: SAMPLE 44


title: HCC016N [lncRNA expression]

description: SAMPLE 54


title: 22Rv1-WCE rep1

city: Taipei

first: Chin-Hsien

last: Tsai

state: Others

address: Nan-Kang

department: ABRC

country: Taiwan

institute: Academia Sinica

description: SAMPLE 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

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

extract_protocol: RNA was extracted with ZYMO research mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell type

value: prostate cancer cell line

tag: treatment

value: 10 μg/mL WCE


title: HCC005N [lncRNA expression]

description: SAMPLE 43


title: 22Rv1-WCE rep2

description: SAMPLE 4


title: HCC007N [lncRNA expression]

description: SAMPLE 45


title: HCC004N [lncRNA expression]

description: SAMPLE 42


title: HCC037T [lncRNA expression]

description: SAMPLE 37

source_name: primary hepatocellular carcinoma tissue

value: tumor tissue


title: 22Rv1 rep2

description: SAMPLE 2

value: Vehicle


title: 22Rv1 rep1

description: SAMPLE 1


title: HCC001N [lncRNA expression]

description: SAMPLE 39


title: HCC002N [lncRNA expression]

description: SAMPLE 40


title: HCC003N [lncRNA expression]

description: SAMPLE 41


title: HCC038T [lncRNA expression]

description: SAMPLE 38


title: HCC036T [lncRNA expression]

description: SAMPLE 36


title: HCC033T [lncRNA expression]

description: SAMPLE 33


title: HCC030T [lncRNA expression]

description: SAMPLE 30


title: HCC027T [lncRNA expression]

description: SAMPLE 27


title: HCC026T [lncRNA expression]

description: SAMPLE 26


title: HCC034T [lncRNA expression]

description: SAMPLE 34


title: HCC032T [lncRNA expression]

description: SAMPLE 32


title: HCC031T [lncRNA expression]

description: SAMPLE 31


title: HCC029T [lncRNA expression]

description: SAMPLE 29


title: HCC022T [lncRNA expression]

description: SAMPLE 22


title: HCC024T [lncRNA expression]

description: SAMPLE 24


title: HCC025T [lncRNA expression]

description: SAMPLE 25


title: HCC028T [lncRNA expression]

description: SAMPLE 28


title: HCC035T [lncRNA expression]

description: SAMPLE 35


title: HCC023T [lncRNA expression]

description: SAMPLE 23


title: HCC018T [lncRNA expression]

description: SAMPLE 18


title: HCC021T [lncRNA expression]

description: SAMPLE 21


title: HCC020T [lncRNA expression]

description: SAMPLE 20


title: HCC019T [lncRNA expression]

description: SAMPLE 19


title: HCC015T [lncRNA expression]

description: SAMPLE 15


title: HCC013T [lncRNA expression]

description: SAMPLE 13


title: HCC016T [lncRNA expression]

description: SAMPLE 16


title: HCC017T [lncRNA expression]

description: SAMPLE 17


title: HCC008T [lncRNA expression]

description: SAMPLE 8


title: HCC014T [lncRNA expression]

description: SAMPLE 14


title: HCC010T [lncRNA expression]

description: SAMPLE 10


title: HCC007T [lncRNA expression]

description: SAMPLE 7


title: HCC006T [lncRNA expression]

description: SAMPLE 6


title: HCC012T [lncRNA expression]

description: SAMPLE 12


title: HCC005T [lncRNA expression]

description: SAMPLE 5


title: HCC009T [lncRNA expression]

description: SAMPLE 9


title: HCC004T [lncRNA expression]

description: SAMPLE 4


title: HCC003T [lncRNA expression]

description: SAMPLE 3


title: HCC001T [lncRNA expression]

description: SAMPLE 1


title: Tumor_200627

status: Public on Jun 20 2017

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

hyb_protocol: Hybridization was performed on a human GE 4x44K formatted expression array spotted with 60-mer oligonucleotides representing over 43,000 well-characterized coding and non-coding sequences (G4112F, Agilent Technologies, Amstelveen, The Netherlands).  Input: 825 ng RNA

scan_protocol: Scanning was performed using a microarray scanner G2505B (Agilent Technologies). Feature Extraction v9.5 using the manufacturers protocols (Agilent Technologies).

data_processing: Preprocessing of the gene expression data comprised of RMA background correction, loess within-array normalization and A-quantile between-array normalization (as implemented in the Limma-package)

source_name: HNSCC

label_protocol: cDNA synthesis and labeling were performed according to the recommendations of the manufacturer (Agilent Technologies, Amstelveen, The Netherlands), including quality controls (QCs) using a low input labeling and amplification kit (Agilent)

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen).

treatment_protocol: Tumors and Matched Mucosas were collected immediately after surgery and stored in liquid nitrogen.

tag: individual

value: Tumor

source_name: reference

value: Universal Human Reference RNA (Stratagene)


title: Tumor_9937


title: Tumor_9942


title: Tumor_200704


title: Tumor_9959


title: Tumor_200603


title: Tumor_200701


title: Tumor_200708


title: HCC002T [lncRNA expression]

description: SAMPLE 2

value: HCC patient


title: Tumor_200505


title: Tumor_200615


title: Liver_alcohol treated_pool1

city: Yangzhou

first: Manhong

last: Ye

state: Jiangsu

address: East Wenhui road 12#

department: College of Bioscience and Biotechnology

institute: Yangzhou University

hyb_protocol: Array hybridization was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). 0.875 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μL containing 25×Agilent fragmentation buffer and 10×Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 55 μL of 2×Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent microarray scanner G2565BA (Scan resolution 5μm).

data_processing:
The Agilent Feature Extraction Software version 9.5 was used to read out and  process the microarray image files. Raw expression data were normalized using the quantile normalization method. Microarray datasets were obtained from one-color hybridization of rat RNAs on Agilent Whole Rat Genome Microarrays. The magnitude of expression difference (fold change) was applied in order to identify genes with differential expression between groups. Data analysis focused on these differentially expressed genes (DEGs) with a present flag value for both samples.

This GEO submission has no raw data because the raw data files can not be found.

organism: Rattus norvegicus

source_name: liver tissue

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Cyanine-3 (Cy3) labeled cRNA was prepared from 2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Hilden, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from liver samples using the TRIzol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) and the RNeasy Mini Kit (Qiagen, Hilden, Germany). Genomic DNA was eliminated using the RNase-free DNase Digest Set (Qiagen, Hilden, Germany) and RNA was quantified using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, USA). The integrity of the total RNA sample was evaluated using an Agilent 2100 Bioanalyzer (Agilent, Foster City, CA, USA). RNA samples with integrity number larger than 8.5 were then subjected to next process of pooling. 5 μg of total RNA isolated from six individuals of the same sub-group were pooled into a single sample. Microarray analysis was performed on two pooled RNA samples from sub-groups AT-EEP and AT-NS.

treatment_protocol: Chronic alcoholic fatty liver was induced by administration of 52% alcohol to Wistar rats at the dose of 1% body weight for 7 weeks (group AT). Then animals were simultaneously treated with 50% ethanol solutions of EEP (sub-group AT-EEP) or normal saline (sub-group AT-NS) at the dose of 0.1% body weight for 4 further weeks.

tag: Sex

value: male

value: 22-week old

tag: condition

value: chronic alcoholic fatty liver


title: Tumor_200509

tag: reference


title: Tumor_200523


title: Tumor_200504


title: Tumor_200614


title: Liver_alcohol and EEP treated_pool1

value: liver


title: Tumor_200002


title: Tumor_200035


title: Tumor_200005


title: Mucosa_9959

source_name: Matched Normal Mucosa

value: Mucosa


title: Tumor_200001


title: Tumor_200021


title: Mucosa_9942


title: Mucosa_200708


title: Tumor_200044


title: Tumor_200521


title: Mucosa_200704


title: Mucosa_9937


title: Tumor_200041


title: Mucosa_200614


title: Mucosa_200521


title: Mucosa_200523


title: Mucosa_200627


title: Mucosa_200615


title: Mucosa_200509


title: Mucosa_200603


title: Mucosa_200701


title: Mucosa_200035


title: Mucosa_200041


title: Mucosa_200002


title: Mucosa_200021


title: Mucosa_200504


title: UK-Z-3-EB-R-2X DAY 16

city: Sheffield

first: Paul

last: Gokhale

address: Western Bank

department: Biomedical Science

country: United Kingdom

institute: University of Sheffield

description: Test

data_processing: Low-quality data was removed and raw Ct values were capped (Ct_max=35), scaled to the level of control genes (GAPDH, ACTB), quantile-normalized and finally inverted by subtracting each value from the maximum Ct_max.

label: EvaGreen

label_protocol: High-Capacity cDNA Archive Kit (ThermoFisher Scientific) following manufacturers protocols with 10 cycles of amplification

extract_protocol: PicoPure RNA Isolation Kit (Arcturus Bioscience), QCed with 2100 Bioanalyzer (Agilent Technologies)

tag: cell line

value: ES

tag: cell line code

tag: starting culture conditions

value: mTeSR1, Matrigel

tag: teratoma, injected cell number(106)

tag: teratoma, volume of injection (ul)

tag: teratoma injection site

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

tag: teratoma, mouse sex

tag: replicate

tag: time point (days)

value: EMBYOID BODY

tag: differentiation condition

value: NEUTRAL

tag: differentiation condition (details)

value: APEL


title: Mucosa_200001

tag: individual

tag: tissue


title: UK-Z-3-EB-R-3-M-16

description: Test

tag: cell type

value: hESC

value: Z

value: MESODERM

value: APEL, 20ng/ml Activin A, 20ng/ml BMP4


title: UK-Z-3-EB-R-3-C-16

description: Test

tag: cell line


title: UK-Z-3-EB-R-3-EC-16

description: Test

tag: cell line code

value: ECTODERM

value: APEL, 10uM Dorsomorphin, 10uM SB431542, 100ng/ml bFGF


title: UK-Z-3-EB-R-2-EN-16

description: Test

tag: starting culture conditions

value: ENDODERM

value: APEL, 100ng/ml Activin A, 1ng/ml BMP4


title: UK-Z-3-EB-R-2-EC-16

description: Test

tag: teratoma, injected cell number(106)


title: UK-Z-3-EB-R-2-C-16

description: Test

tag: teratoma, volume of injection (ul)


title: Mucosa_200005

tag: reference

value: Universal Human Reference RNA (Stratagene)


title: Mucosa_200505


title: UK-Z-3-EB-R-1-M-16

description: Test

tag: teratoma injection site

tag: teratoma injection position


title: UK-Z-3-EB-R-1-C-16

description: Test

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)


title: UK-Z-3-EB-R-1-EN-16

description: Test

tag: teratoma, mouse sex

tag: replicate


title: UK-Z-3-EB-R-1-EC-16

description: Test

tag: time point (days)

tag: differentiation condition


title: UK-Z-2-EB-R-3-M-10

description: Test

tag: differentiation condition (details)


title: Erg-knockdown HSPCs from mouse 279

city: Boston

first: Zhe

last: Li

state: MA

address: 77 Avenue Louis Pasteur, Room 466

department: Medicine, Genetics Division

institute: Brigham and Women's Hospital

description:
Adult Mx1Cre;Ergkd/+;R26Y mouse, mixed 129-B6 background
Gene expression data for sorted YFP- Erg-knockdown (~40% reduction) LSK HSPCs

hyb_protocol: The biotinylated cDNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C

scan_protocol: Each cDNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured

data_processing:
The raw CEL files were imported, normalized and analyzed with genepattern analysis tools (dCHIP, GSEA) from Broad institiute
After normalization, the model-based expression values were calculated by dCHIP and exported

source_name: Erg-knockdown HSPCs from mouse 279

label_protocol: Labeling, hybridization and scan were performed at the Dana-Farber Cancer Institute Microaraay Core Facility. The NuGEN Ovation V2 Amplification System was used to amplify and label the samples, according to manufacturer's protocol.

growth_protocol: Bone marrow cells were prepared from adult Mx1Cre;Ergkd/+;R26Y mice

extract_protocol: RNAeasy kit (Qiagen, #74134) was used according to manufacturer's protocol

treatment_protocol: YFP+ and YFP- LSK cells were sorted from bone marrow cell preparations

tag: genetic background

value: mixed 129-B6 background

tag: genotype

value: Erg-knockdown

value: LSK HPSCs


title: Erg-knockdown HSPCs from mouse 278

source_name: Erg-knockdown HSPCs from mouse 278

tag: cell type


title: Erg-knockdown HSPCs from mouse 281

source_name: Erg-knockdown HSPCs from mouse 281


title: Erg-restored HSPCs from mouse 281

description:
Adult Mx1Cre;Ergkd/+;R26Y mouse, mixed 129-B6 background
Gene expression data for sorted YFP+ Erg-restored (to wild type level) LSK HSPCs

source_name: Erg-restored HSPCs from mouse 281

value: Erg-restored


title: Erg-restored HSPCs from mouse 279

source_name: Erg-restored HSPCs from mouse 279


title: UK-Z-2-EB-R-3-EN-10

description: Test

tag: cell line

tag: cell line code

value: mTeSR1, Matrigel


title: UK-Z-2-EB-R-2-EN-10

description: Test

tag: starting culture conditions

tag: teratoma, injected cell number(106)

value: EMBYOID BODY


title: Erg-restored HSPCs from mouse 278

source_name: Erg-restored HSPCs from mouse 278


title: UK-Z-2-EB-R-2-M-10

description: Test

tag: teratoma, volume of injection (ul)


title: UK-Z-2-EB-R-2-C-10

description: Test

tag: teratoma injection site

value: NEUTRAL


title: UK-Z-2-EB-R-1-M-10

description: Test

tag: teratoma injection position


title: UK-Z-2-EB-R-3-EC-10

description: Test

tag: teratoma, mouse strain


title: UK-Z-2-EB-R-1-EC-10

description: Test

tag: teratoma, mouse age (weeks)


title: UK-Z-2-EB-R-1-EN-10

description: Test

tag: teratoma, mouse sex


title: UK-Z-2-EB-R-1-C-10

description: Test

tag: replicate

value: APEL


title: UK-Z-1-T-R-1

description: Test

value: hESC

value: in-between shoulder blades

value: SCID

value: Female

tag: time point (days)

value: TERATOMA


title: HCC011T [lncRNA expression]

description: SAMPLE 11

tag: subject status

value: HCC patient

tag: subject id

tag: gender

value: Male

tag: age

tag: tnm staging

tag: tissue

value: liver

tag: tissue subytpe

value: tumor tissue

tag: sample type

value: pooled reference


title: UK-Z-1-EB-R-3-M-4

description: Test

tag: cell line

tag: cell type

tag: cell line code

value: Z

tag: starting culture conditions

tag: teratoma, injected cell number(106)

tag: differentiation condition

value: MESODERM

tag: differentiation condition (details)

value: APEL, 20ng/ml Activin A, 20ng/ml BMP4


title: UK-Z-1-EB-R-3-EC-4

description: Test

value: mTeSR1, Matrigel

tag: teratoma, volume of injection (ul)

tag: teratoma injection site

tag: teratoma injection position

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)

tag: teratoma, mouse sex

tag: replicate

value: ECTODERM

value: APEL, 10uM Dorsomorphin, 10uM SB431542, 100ng/ml bFGF


title: UK-Z-1-EB-R-3-C-4

description: Test

tag: time point (days)

value: EMBYOID BODY

value: NEUTRAL

value: APEL


title: UK-Z-1-EB-R-2-EN-4

description: Test

value: hESC

value: ENDODERM

value: APEL, 100ng/ml Activin A, 1ng/ml BMP4


title: UK-Z-1-EB-R-2-M-4

description: Test


title: UK-Z-1-EB-R-3-EN-4

description: Test


title: UK-Z-1-EB-R-2-EC-4

description: Test


title: UK-Z-1-EB-R-2-C-4

description: Test


title: UK-Z-1-EB-R-1-M-4

description: Test


title: UK-Z-1-EB-R-1-EC-4

description: Test


title: UK-Z-001-P-R-1

description: Test

value: START


title: UK-Z-003-P-R-1

description: Test


title: UK-Z-1-EB-R-1-C-4

description: Test

value: EMBYOI BOY


title: UK-Z-002-P-R-1

description: Test


title: UK-S3-3-EB-R-3-M-16

description: Test

value: ES


title: UK-S3-3-T-R-1

description: Test

value: in-between shoulder blades

value: SCID

value: Female

value: TERATOMA


title: UK-S3-3-EB-R-3-EN-16

description: Test


title: UK-S3-3-EB-R-3-EC-16

description: Test


title: UK-S3-3-EB-R-2-EC-16

description: Test


title: UK-S3-3-EB-R-3-C-16

description: Test


title: UK-S3-3-EB-R-2-M-16

description: Test

value: MESODERM

value: APEL, 20ng/ml Activin A, 20ng/ml BMP4


title: UK-S3-3-EB-R-2-EN-16

description: Test

value: mTeSR1, Matrigel


title: UK-S3-3-EB-R-2-C-16

description: Test


title: UK-S3-3-EB-R-1-EN-16

description: Test


title: UK-S3-3-EB-R-1-M-16

description: Test


title: UK-S3-3-EB-R-1-EC-16

description: Test

value: ECTODERM

value: APEL, 10uM Dorsomorphin, 10uM SB431542, 100ng/ml bFGF


title: UK-S3-2-EB-R-3-M-10

description: Test

value: EMBYOID BODY


title: UK-S3-3-EB-R-1-C-16

description: Test

value: NEUTRAL

value: APEL


title: UK-S3-2-EB-R-3-EN-10

description: Test

value: hESC

value: ENDODERM


title: UK-S3-2-EB-R-3-EC-10

description: Test


title: UK-S3-2-EB-R-2-EN-10

description: Test

value: APEL, 100ng/ml Activin A, 1ng/ml BMP4


title: UK-S3-2-EB-R-3-C-10

description: Test


title: UK-S3-2-EB-R-2-EC-10

description: Test


title: UK-S3-2-EB-R-2-M-10

description: Test


title: UK-S3-2-EB-R-2-C-10

description: Test


title: UK-S3-2-EB-R-1-M-10

description: Test


title: UK-S3-2-EB-R-1-EN-10

description: Test


title: UK-S3-2-EB-R-1-EC-10

description: Test


title: UK-S3-2-EB-R-1-C-10

description: Test


title: UK-S3-1-T-R-1

description: Test


title: UK-S3-1-EB-R-3-M-4

description: Test


title: UK-S3-1-EB-R-3-C-4

description: Test


title: UK-S3-1-EB-R-3-EN-4

description: Test


title: UK-S3-1-EB-R-3-EC-4

description: Test


title: UK-S3-1-EB-R-2-M-4

description: Test


title: UK-S3-2-T-R-2

description: Test


title: UK-S3-1-EB-R-2-C-4

description: Test


title: UK-S3-1-EB-R-2-EN-4

description: Test


title: UK-S3-1-EB-R-1-M-4

description: Test


title: UK-S3-1-EB-R-1-EN-4

description: Test


title: UK-S3-1-EB-R-1-C-4

description: Test


title: UK-S3-003-P-R-1

description: Test

value: START


title: UK-S3-1-EB-R-1-EC-4

description: Test


title: UK-OX2-3-EB-R-3-EN-16

description: Test


title: UK-S3-001-P-R-1

description: Test


title: UK-OX2-3-EB-R-3-C-16

description: Test


title: UK-OX2-3-EB-R-2-EN-16

description: Test


title: UK-OX2-3-EB-R-2-EC-16

description: Test


title: UK-S3-1-EB-R-2-EC-4

description: Test


title: UK-OX2-3-EB-R-1-M-16

description: Test


title: UK-OX2-2-T-R-1

description: Test


title: UK-OX2-2-EB-R-3-M-10

description: Test


title: UK-OX2-3-EB-R-1-C-16

description: Test


title: UK-OX2-2-EB-R-3-EN-10

description: Test


title: UK-OX2-3-EB-R-1-EC-16

description: Test


title: UK-OX2-2-EB-R-2-EN-10

description: Test


title: UK-OX2-2-EB-R-2-M-10

description: Test


title: UK-S3-002-P-R-1

description: Test


title: UK-OX2-3-EB-R-2-C-16

description: Test


title: UK-OX2-2-EB-R-3-EC-10

description: Test


title: UK-OX2-2-EB-R-2-C-10

description: Test


title: UK-OX2-2-EB-R-1-EN-10

description: Test


title: UK-OX2-3-EB-R-3-M-16

description: Test


title: UK-OX2-2-EB-R-1-C-10

description: Test


title: UK-OX2-3-EB-R-2-M-16

description: Test


title: UK-OX2-1-EB-R-3-EN-4

description: Test


title: UK-OX2-3-EB-R-1-EN-16

description: Test


title: UK-OX2-1-T-R-1

description: Test


title: UK-OX2-1-EB-R-3-M-4

description: Test


title: UK-OX2-1-EB-R-3-C-4

description: Test


title: UK-OX2-1-EB-R-3-EC-4

description: Test


title: UK-OX2-1-EB-R-2-M-4

description: Test


title: Mucosa_200044

tag: individual

tag: tissue

value: Mucosa

tag: reference

value: Universal Human Reference RNA (Stratagene)


title: UK-OX2-2-EB-R-2-EC-10

description: Test

tag: cell line

tag: cell type


title: UK-OX2-2-EB-R-1-EC-10

description: Test

tag: cell line code

tag: starting culture conditions


title: UK-OX2-2-EB-R-1-M-10

description: Test

tag: teratoma, injected cell number(106)

tag: differentiation condition


title: UK-I9-3-EB-R-1-M-16

description: Test

value: IPS

tag: teratoma, volume of injection (ul)

tag: differentiation condition (details)


title: UK-I9-3-EB-R-3-C-16

description: Test

tag: teratoma injection site

tag: teratoma injection position


title: UK-OX2-1-EB-R-1-EN-4

description: Test

tag: teratoma, mouse strain

tag: teratoma, mouse age (weeks)


title: UK-OX2-001-P-R-1

description: Test

tag: teratoma, mouse sex

tag: replicate


title: UK-I9-3-EB-R-1-EN-16

description: Test

tag: time point (days)


title: UK-OX2-1-EB-R-1-C-4

description: Test


title: UK-I9-3-EB-R-2-C-16

description: Test


title: UK-OX2-1-EB-R-2-EC-4

description: Test


title: UK-OX2-1-EB-R-2-EN-4

description: Test


title: UK-I9-3-EB-R-1-EC-16

description: Test


title: UK-OX2-1-EB-R-1-M-4

description: Test


title: UK-OX2-1-EB-R-2-C-4

description: Test


title: UK-I9-2-T-R-1

description: Test

value: iPSC

value: in-between shoulder blades

value: SCID

value: Female


title: UK-I9-3-EB-R-1-C-16

description: Test

value: mTeSR1, Matrigel


title: UK-I9-2-T-R-2

description: Test

value: TERATOMA


title: UK-I9-3-EB-R-3-EN-16

description: Test


title: UK-I9-3-EB-R-2-EN-16

description: Test


title: UK-OX2-003-P-R-1

description: Test


title: UK-OX2-002-P-R-1

description: Test


title: UK-I9-3-EB-R-3-EC-16

description: Test

value: ECTODERM

value: APEL, 10uM Dorsomorphin, 10uM SB431542, 100ng/ml bFGF


title: UK-I9-3-EB-R-3-M-16

description: Test

value: EMBYOID BODY

value: MESODERM

value: APEL, 20ng/ml Activin A, 20ng/ml BMP4


title: UK-I9-3-EB-R-2-EC-16

description: Test


title: UK-I9-2-EB-R-3-EN-10

description: Test

value: ENDODERM


title: UK-I9-2-EB-R-3-M-10

description: Test


title: UK-I9-2-EB-R-3-EC-10

description: Test


title: UK-I9-3-EB-R-2-M-16

description: Test


title: UK-I9-2-EB-R-2-M-10

description: Test


title: UK-I9-2-EB-R-2-EN-10

description: Test

value: APEL, 100ng/ml Activin A, 1ng/ml BMP4


title: UK-I9-2-EB-R-1-EN-10

description: Test


title: UK-I9-2-EB-R-1-EC-10

description: Test


title: UK-I9-2-EB-R-2-C-10

description: Test

value: NEUTRAL

value: APEL


title: UK-I9-1-EB-R-3-M-4

description: Test


title: UK-I9-1-T-R-1

description: Test


title: UK-I9-1-EB-R-3-C-4

description: Test


title: UK-I9-2-EB-R-2-EC-10

description: Test


title: UK-I9-2-EB-R-1-C-10

description: Test


title: UK-I9-1-EB-R-1-M-4

description: Test


title: UK-I9-1-EB-R-2-C-4

description: Test


title: UK-I9-2-EB-R-1-M-10

description: Test


title: UK-I9-1-EB-R-2-EC-4

description: Test


title: UK-I9-1-EB-R-2-M-4

description: Test


title: UK-I9-1-EB-R-1-EC-4

description: Test


title: UK-I9-1-EB-R-3-EN-4

description: Test


title: UK-I9-1-EB-R-2-EN-4

description: Test


title: UK-I9-002-P-R-1

description: Test

value: START


title: MC-Z-7-EB-R-1

description: Test

source_name: HES3/MIXL1 GFP

value: ES

value: DMEM/F-12 + 20% KOSR, 10ng/ml FGF2, MEF feeders


title: UK-I9-001-P-R-1

description: Test

value: IPS


title: MC-Z-8-EB-R-1

description: Test


title: UK-I9-003-P-R-1

description: Test


title: MC-Z-38-EB-R-3

description: Test


title: MC-Z-3-T-R-3

description: Test

value: Z

value: subcutaneous

value: Back of the neck   or  Caudal flank near the hip.

value: NOD/SCID IL2R


title: MC-Z-37-EB-R-3

description: Test

value: ECTODERM


title: UK-I9-1-EB-R-3-EC-4

description: Test

value: mTeSR1, Matrigel

value: APEL, 10uM Dorsomorphin, 10uM SB431542, 100ng/ml bFGF


title: MC-Z-36-EB-R-3

description: Test

value: EMBYOID BODY


title: MC-Z-9-EB-R-1

description: Test

value: MESODERM

value: APEL, 20ng/ml Activin A, 20ng/ml BMP4


title: MC-Z-6-EB-R-1

description: Test


title: MC-Z-5-EB-R-1

description: Test


title: MC-Z-35-EB-R-3

description: Test


title: MC-Z-34-EB-R-3

description: Test

value: ENDODERM

value: APEL, 100ng/ml Activin A, 1ng/ml BMP4


title: MC-Z-39-EB-R-3

description: Test


title: MC-Z-27-EB-R-3

description: Test


title: MC-Z-31-EB-R-3

description: Test


title: MC-Z-25-EB-R-2

description: Test


title: MC-Z-2-EB-R-1

description: Test

value: NEUTRAL

value: APEL


title: MC-Z-28-EB-R-3

description: Test

value: ES


title: MC-Z-33-EB-R-3

description: Test

value: DMEM/F-12 + 20% KOSR, 10ng/ml FGF2, MEF feeders


title: MC-Z-30-EB-R-3

description: Test


title: MC-Z-26-EB-R-2

description: Test


title: MC-Z-32-EB-R-3

description: Test

value: NEUTRAl


title: MC-Z-19-EB-R-2

description: Test


title: MC-Z-1-T-R-1

description: Test

value: Z

value: Female

value: TERATOMA


title: MC-Z-17-EB-R-2

description: Test


title: MC-Z-22-EB-R-2

description: Test


title: MC-Z-1-EB-R-1

description: Test

value: START


title: MC-Z-20-EB-R-2

description: Test

value: ECTODERM


title: MC-Z-16-EB-R-2

description: Test


title: MC-Z-18-EB-R-2

description: Test


title: MC-Z-14-EB-R-2

description: Test


title: MC-Z-15-EB-R-2

description: Test


title: MC-Z-13-EB-R-1

description: Test


title: MC-Z-29-EB-R-3

description: Test


title: MC-Z-12-EB-R-1

description: Test


title: MC-Z-11-EB-R-1

description: Test


title: MC-Z-24-EB-R-2

description: Test


title: MC-Z-23-EB-R-2

description: Test


title: MC-Z-10-EB-R-1

description: Test


title: MC-03-5-EB-R-1

description: Test

value: IPS


title: MC-03-7-EB-R-1

description: Test

value: APEL, 10uM Dorsomorphin, 10uM SB431542, 100ng/ml bFGF


title: MC-03-9-EB-R-1

description: Test

value: EMBYOID BODY


title: MC-03-3-EB-R-1

description: Test


title: MC-03-4-EB-R-1

description: Test


title: MC-03-36-EB-R-3

description: Test


title: MC-03-37-EB-R-3

description: Test


title: MC-03-39-EB-R-3

description: Test

value: MESODERM


title: MC-03-3-T-R-3

description: Test

value: iPS

value: subcutaneous

value: Back of the neck   or  Caudal flank near the hip.

value: NOD/SCID IL2R


title: MC-03-38-EB-R-3

description: Test

value: ENDODERM

value: APEL, 100ng/ml Activin A, 1ng/ml BMP4


title: MC-03-32-EB-R-3

description: Test

value: DMEM/F-12 + 20% KOSR, 10ng/ml FGF2, MEF feeders

value: NEUTRAL

value: APEL


title: MC-03-33-EB-R-3

description: Test


title: MC-03-26-EB-R-2

description: Test

value: APEL, 20ng/ml Activin A, 20ng/ml BMP4


title: MC-03-29-EB-R-3

description: Test


title: MC-03-28-EB-R-3

description: Test


title: MC-03-2-T-R-2

description: Test

value: Female

value: TERATOMA


title: MC-03-27-EB-R-3

description: Test

value: START


title: MC-03-30-EB-R-3

description: Test

value: IPS


title: MC-03-25-EB-R-2

description: Test


title: MC-03-21-EB-R-2

description: Test


title: MC-03-20-EB-R-2

description: Test

value: ECTODERM

value: APEL, 10uM Dorsomorphin, 10uM SB431542, 100ng/ml bFGF


title: MC-03-1-T-R-1

description: Test


title: MC-03-35-EB-R-3

description: Test

value: EMBYOID BODY

value: MESODERM


title: MC-03-34-EB-R-3

description: Test


title: MC-03-22-EB-R-2

description: Test


title: MC-03-18-EB-R-2

description: Test


title: MC-03-1-EB-R-1

description: Test


title: MC-03-17-EB-R-2

description: Test


title: MC-03-19-EB-R-2

description: Test


title: MC-03-23-EB-R-2

description: Test


title: MC-03-13-EB-R-1

description: Test


title: MC-03-15-EB-R-2

description: Test


title: MC-03-14-EB-R-2

description: Test


title: MC-03-24-EB-R-2

description: Test


title: MC-02-9-EB-R-1

description: Test

source_name: MEL1/INS GFP

value: MEL1/INS GFP

value: ES


title: MC-02-8-EB-R-1

description: Test


title: MC-03-11-EB-R-1

description: Test


title: MC-02-7-EB-R-1

description: Test


title: MC-02-6-EB-R-1

description: Test


title: MC-02-4-EB-R-1

description: Test


title: MC-02-3-T-R-3

description: Test

value: subcutaneous

value: Back of the neck   or  Caudal flank near the hip.

value: NOD/SCID IL2R


title: MC-02-39-EB-R-3

description: Test

value: DMEM/F-12 + 20% KOSR, 10ng/ml FGF2, MEF feeders


title: MC-02-37-EB-R-3

description: Test


title: MC-02-3-EB-R-1

description: Test


title: MC-03-16-EB-R-2

description: Test


title: MC-02-38-EB-R-3

description: Test

value: ENDODERM

value: APEL, 100ng/ml Activin A, 1ng/ml BMP4


title: MC-02-34-EB-R-3

description: Test


title: MC-02-33-EB-R-3

description: Test


title: MC-02-35-EB-R-3

description: Test

value: APEL, 20ng/ml Activin A, 20ng/ml BMP4


title: MC-02-36-EB-R-3

description: Test

value: NEUTRAL

value: APEL


title: MC-02-31-EB-R-3

description: Test


title: MC-02-30-EB-R-3

description: Test


title: MC-02-32-EB-R-3

description: Test


title: MC-02-2-T-R-2

description: Test

value: Female

value: TERATOMA