title: Deaf [Sample 60]


title: T26 [methylation]

status: Public on Feb 17 2017

type: genomic

city: Beijing

first: Jin

last: Gu

address: FIT Building 1-112C

department: Automation

country: China

institute: Tsinghua University

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 using standard recommended Illumina scanner setting

data_processing:
GenomeStudio Methylation Module v1.8, Methylated signal intensity/( Mehtylated signal intensity + Unmethylated signal intensity + 100 )
normalized data matrix (*.txt) contains Average Beta values

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary tumor from patient #26

label_protocol: Standard Illumina Protocol

growth_protocol: Fresh-frozen clinical tissue samples

extract_protocol: Sample DNA was extracted using DNeasy Blood &Tissue Kit (Cat#69506, QIAGEN, GmBH, Germany), following the manufacturer’s instructions. We used Nano Drop (Cat#ND-1000, Thermo Fisher, Waltham, MA, US) and ran a 1% agarose gel electrophoresis to check the quantity and quality of purified DNA.

tag: subject status

value: hepatocellular carcinoma (HCC) patient

tag: patient id

value: patient #26

tag: gender

value: Male

tag: age

tag: tumor size (cm)

tag: hbv infection

value: Yes

tag: cirrhosis

tag: tissue

value: Primary tumor


title: T25 [methylation]

source_name: Primary tumor from patient #25

value: patient #25

value: No


title: Deaf [Sample 58]

city: Miami

first: Denise

last: Yan

state: FL

address: 1601 NW 12th Ave

department: Otolaryngology

country: USA

institute: University of Miami

hyb_protocol: Each PCR reaction is prepared by combining 5 μl template DNA (15-150 ng), 10 μl mixture of amplification primer and 10 μl mixture of amplification reagent to the 25 μl reaction system individually. The amplification was performed in a Master Cycler nexus X2e (Oppendorf) by setting the temperature rate using the RAMP function of the PCR instrument under the following conditions: 37oC for 10min, 95oC for 15 min; 96oC for 1 min; then: 94oC for 30 sec, ramp (0.4 C/s) to 55oC, hold for 30 sec; ramp (0.2 C/s) to 70oC, hold for 45 sec for 32 cycles; followed by 60o C for 10 min, 4o C soak. Amplified products from the two tubes were mixed, and the amplicons were then captured by magnetic beads. Captured amplicons were denatured by NaOH, and only the single stranded DNA attached to the magnetic beads was collected and dissolved in hybridization buffer. First, an aliquot of 30 μg streptavidin-coated magnetic beads was washed twice with 2x binding and washing (B&W) buffer (10 mM Tris–HCl (pH 7.5), 1 mM EDTA, 2 M NaCl) and resuspended in 6 μL 2x B&W buffer after removing the supernatant with a external magnet. Then, an equal volume of biotinylated anti-tags solution was added, mixed gently with the magnetic beads suspension, incubated for 15 min at room temperature. After washing three times with 1x B&W buffer, the anti-tag-coated magnetic beads were resuspended in 15 μL hybridization buffer (9x SSC, 7.5x Denhardt's reagent, 37.5% (v/v) formamide, 0.15% (w/v) SDS). Approximately 30 µL of the hybridization solution was then injected into the sample inlet to cover the central hexagonal array region. The sample inlet and the air outlet were then sealed and the chip was placed into the Easy Array 3A (CapitalBio Corporation) for a dynamic hybridization at 55 oC for 20 min followed by washing at 42oC for 2 min.

scan_protocol: The hybridization results were recorded by a microarray scanner LuxScan™ 10K (CapitalBio), the laser power and photomultiplier tube (PMT) were set to 70 and 700, respectively.

data_processing: First, each microarray was scanned to obtain an image. Second, the absolute median signal intensities (AMSIs) for each spot, which were calculated by subtracting the local background from the median signal intensity, were extracted. Third, the system discriminated positive and negative signals according to the cut off value of each probe. On the basis of the distribution and the value of the signal, the reference values of the probes were made by ROC analysis. For a probe, if the detection signal value was greater than or equal to the reference value, the target was considered positive; if the detection signal value was less than the reference value of the probe, the target was considered negative.

label: Biotin

source_name: Deafness

label_protocol: The tag sequences in the tag-array were designed as described previously (Li et al., Hum. Mutat., 29 (2008), pp. 306-314). The tag probes were synthesized with a poly(dT) spacer and a 5' amino group for their immobilization onto the aldehyde-modified glass slides. The anti-tag probes complementary to the corresponding tag probes were synthesized with a poly(dT) spacer and a 5' biotin modification to validate the decoding performance of the tag-array. All probes and primers were dissolved in sterilized distilled and deionized water and quantified by UV absorbance at 260 nm. The tag probes were further diluted in 50% dimethyl sulfoxide (DMSO) to a final concentration of 15 μM and spotted with a SmartArrayer™ 136 spotter (CapitalBio, Beijing, China) on the aldehyde-functionalized glass slides (CapitalBio). Each tag probe was repeatedly spotted in triplicate.

extract_protocol: Genomic DNA was extracted from the whole blood using the Genetra Puregene DNA isolation kit (QIAGEN, Hilden, Germany) by following the instruction recommended by the manufacturer. Agarose gel and Qubit (Life Technologies, CA, USA) were used for DNA quantity and quality assessment.

tag: disease state

value: Deaf

tag: population

value: European descent

value: Whole blood

tag: genotype/variation


title: T24 [methylation]

source_name: Primary tumor from patient #24

value: patient #24


title: T22 [methylation]

source_name: Primary tumor from patient #22

value: patient #22


title: Deaf [Sample 57]


title: T21 [methylation]

source_name: Primary tumor from patient #21

value: patient #21


title: Deaf [Sample 56]


title: Deaf [Sample 55]


title: T19 [methylation]

source_name: Primary tumor from patient #19

value: patient #19


title: Deaf [Sample 59]


title: Thy1+LSK sorted bone marrow cells from NOL3+/+ mice rep2

type: RNA

city: Bronx

first: Robert

last: Stanley

state: New York

address: 1300 Morris Park Avenue, Chanin Building Rm 601

department: Cell Biology

institute: Albert Einstein College of Medicine

description: Gene expression data

hyb_protocol: Labeld cRNA of each individual samples was hybridized to Affymetrix Mouse Gene 2.0 ST microarray

scan_protocol: Scanned by GeneChip Scanner 3000 7G System (Affymetrix) according to standard protocols.

data_processing: Affymetrix Expression Console Software and Transcriptome Analysis Console

molecule: total RNA

organism: Mus musculus

label_protocol: Biotinylated cRNA were prepared using the GeneChip WT terminal labeling kit (Affymetrix) according to the manufacturer's instructions.

growth_protocol: uncultured primary cells

extract_protocol: Total mRNA was extracted using Qiagen's RNAeasy Micro kit according to the manufacturer's instructions; After checking the quality of the RNA with an Agilent 2100 Bioanalyzer, total RNA was amplified utilizing Single Primer Isothermal Amplification (SPIA Nugen Ovation pico WTA) system according the manufacturer's instructions.

treatment_protocol: No treatment

tag: cell type

tag: genotype

tag: background strain


title: Thy1+LSK sorted bone marrow cells from NOL3-/- MPN mice rep2

description: Gene expression data


title: T18 [methylation]

source_name: Primary tumor from patient #18

value: patient #18


title: Thy1+LSK sorted bone marrow cells from NOL3+/+ mice rep1

description: Gene expression data


title: Deaf [Sample 85]

value: WT


title: Deaf [Sample 54]


title: Deaf [Sample 52]


title: Thy1+LSK sorted bone marrow cells from NOL3-/- MPN mice rep1

description: Gene expression data


title: Deaf [Sample 86]


title: Deaf [Sample 51]


title: T16 [methylation]

source_name: Primary tumor from patient #16

value: patient #16


title: Deaf [Sample 50]


title: T15 [methylation]

source_name: Primary tumor from patient #15

value: hepatocellular carcinoma (HCC) patient

value: patient #15


title: T20 [methylation]

source_name: Primary tumor from patient #20

value: patient #20

value: Male


title: Deaf [Sample 49]


title: T14 [methylation]

source_name: Primary tumor from patient #14

value: patient #14

value: Female

value: Yes

value: Primary tumor


title: Deaf [Sample 48]

value: Deaf

value: European descent


title: T13 [methylation]

source_name: Primary tumor from patient #13

value: patient #13


title: H2228

city: Tokyo

first: Shinji

last: Nakamichi

address: 1-1-5, Sendagi, Bunkyo-ku

department: Department of Pulmonary Medicine and Oncology

country: Japan

institute: Graduate School of Medicine, Nippon Medical School

description: the parent cells

hyb_protocol: Biotin-labeled cDNA was injected into Genechip Human Gene 2.0 ST array and hybridized with probe in Genechip Hybridization Oven 645. The array was washed using Genechip Hybridization, Wash and Stain Kit and stained by phycoerythrin. GeneChip Fluidics Station 450 was used.

scan_protocol: Fluorescent signal by phycoerythrin staining of cDNA hybridized to the probe in the array was measured using a GeneChip Scanner 3000 7G. Data was acquired using analysis software GeneChip Command Console.

data_processing: Data was normalized in a data mining software (GeneSpring GX Version12.6) using the RMA 16 Summarization algorithm. Confidence level was all. Baseline transformation was not performed. All scanned transcript cluster data were obtained.

label: biotin

source_name: ALK positive

label_protocol: The purified, sense-strand cDNA is fragmented by uracil-DNA glycosylase (UDG) and  apurinic/apyrimidinic endonuclease 1 (APE 1) at the unnatural dUTP residues and breaks the DNA  strand. The fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the  Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin. 5.5 μg of singlestranded  cDNA is required for fragmentation and labeling.

extract_protocol: Total RNA from cells was extracted using Rneasy Plus Mini (QIAGEN) Kit according to the manufacturer’s protocol.

tag: cell line


title: H2228-CER

description: ceritinib resistant H2228

source_name: ceritinib resistant


title: T17 [methylation]

source_name: Primary tumor from patient #17

value: patient #17


title: H2228-CRR

description: crizotinib resistant H2228

source_name: crizotinib resistant


title: H2228-ALR

description: alectinib resistant H2228

source_name: alectinib resistant


title: T11 [methylation]

source_name: Primary tumor from patient #11

value: patient #11


title: Deaf [Sample 46]

source_name: Deafness

value: Whole blood


title: Deaf [Sample 44]


title: Deaf [Sample 45]


title: EHUH003_deltaVP30_48h_5_RNA

city: Richland

first: Natalie

last: Heller

address: 902 Battelle Blvd.

institute: PNNL

hyb_protocol: Hybridization was performed according to Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Scanned images were analyzed using Agilent Feature Extraction Software (v11.0.1.1). The limma package for R (available on Bioconductor) was used to perform background correction, quantile normalization (normalizeBetweenArrays), and summarization (avereps) to derive a single normalized intensity value per probe. Outlier samples were detected using PCA and by visual inspection of heatmaps, and all data was re-processed after removing outlier samples. All data processing for each of the biological replicates was performed independently of the other.

source_name: Primary human microvascular endothelial cells, deltaVP30-inoculated, 48h, bioreplicate 5

label_protocol: Total RNA was labeled according to Agilent’s Quick Amp Labeling protocol as part of the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). Total RNA from each sample was linearly amplified and labeled with Cy3-UTP.

extract_protocol: RNA was extracted with 1mL of Trizol.

treatment_protocol: Cells were infected with a multiplicity of infection of 5 PFU.

tag: time

tag: infection


title: N21

description:
Sample 16
Adjacent normal from patient #21

hyb_protocol: Prepare hybridization buffers and perform array hybridization at 50℃ in Hybridization Over (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US ) .After 16 hours hybridization, arrays were washed in Fluidics Station (Cat#00-0079, Affymetrix, Santa Clara, CA, US)according to Affymetrix CytoScan™ Assay User Manual (Cat#703038 Rev. 3, Affymetrix, Santa Clara, CA, US).

scan_protocol: Arrays were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing:
Raw data passed quality control were further analyzed by Affymetrix® Chromosome Analysis Suite (Affymetrix, Santa Clara, CA, US) .
In affymetrix CYCHP segmentation file format.

source_name: Adjacent normal from HCC patient

label_protocol: Sample DNA was digested by restriction enzymes NspI, adaptors were ligated to the fragment DNA to perform a PCR amplification. Amplified DNA was labeled and further fragmented using Affymetrix Cytoscan HD array kit and reagent kit bundle, (Cat#901835, Affymetrix, Santa Clara, CA,US)followed the manufacturer’s instruction Affymetrix CytoScan™ Assay User Manual (Cat#703038 Rev. 3, Affymetrix, Santa Clara, CA, US) to obtain biotin labeled DNA.

tag: subject status

value: patient #21

value: male

tag: age (yrs)

value: Adjacent normal


title: T12 [methylation]

source_name: Primary tumor from patient #12

value: hepatocellular carcinoma (HCC) patient

tag: patient id

value: patient #12

tag: gender


title: Deaf [Sample 47]


title: T10 [methylation]

source_name: Primary tumor from patient #10

value: patient #10

tag: age

tag: tumor size (cm)


title: EHUH003_deltaVP30_48h_2_RNA

source_name: Primary human microvascular endothelial cells, deltaVP30-inoculated, 48h, bioreplicate 2


title: EHUH003_deltaVP30_48h_3_RNA

source_name: Primary human microvascular endothelial cells, deltaVP30-inoculated, 48h, bioreplicate 3


title: EHUH003_Mock_48h_5_RNA

source_name: Primary human microvascular endothelial cells, mock-inoculated, 48h, bioreplicate 5

value: Mock


title: EHUH003_deltaVP30_48h_1_RNA

source_name: Primary human microvascular endothelial cells, deltaVP30-inoculated, 48h, bioreplicate 1


title: T8 [methylation]

source_name: Primary tumor from patient #8

value: patient #8

value: Male

tag: hbv infection

value: No

tag: cirrhosis


title: T7 [methylation]

source_name: Primary tumor from patient #7

value: patient #7

value: Yes

tag: tissue

value: Primary tumor


title: T6 [methylation]

source_name: Primary tumor from patient #6

value: patient #6


title: Deaf [Sample 41]

tag: disease state

value: Deaf

tag: population

value: European descent


title: N26 [methylation]

source_name: Adjacent normal from patient #26

value: patient #26


title: EHUH003_Mock_48h_4_RNA

source_name: Primary human microvascular endothelial cells, mock-inoculated, 48h, bioreplicate 4


title: T3 [methylation]

source_name: Primary tumor from patient #3

value: patient #3

value: Female


title: N25 [methylation]

source_name: Adjacent normal from patient #25

value: patient #25

value: Adjacent normal


title: N24 [methylation]

source_name: Adjacent normal from patient #24

value: hepatocellular carcinoma (HCC) patient

value: patient #24


title: EHUH003_Mock_48h_3_RNA

source_name: Primary human microvascular endothelial cells, mock-inoculated, 48h, bioreplicate 3

value: Mock


title: Deaf [Sample 43]

source_name: Deafness

value: Whole blood

tag: genotype/variation


title: Deaf [Sample 40]


title: N22 [methylation]

source_name: Adjacent normal from patient #22

value: patient #22

value: Male


title: Deaf [Sample 35]


title: Deaf [Sample 36]


title: P24 [methylation]

source_name: PVTT from patient #24

value: Portal vein tumor thrombosis (PVTT)


title: Deaf [Sample 39]


title: EHUH003_Mock_48h_1_RNA

source_name: Primary human microvascular endothelial cells, mock-inoculated, 48h, bioreplicate 1


title: N20 [methylation]

source_name: Adjacent normal from patient #20

value: patient #20

value: Yes


title: N21 [methylation]

source_name: Adjacent normal from patient #21

value: patient #21


title: Deaf [Sample 34]

value: Deaf


title: Deaf [Sample 33]

value: European descent


title: N19 [methylation]

source_name: Adjacent normal from patient #19

value: patient #19


title: EHUH003_deltaVP30_24h_3_RNA

source_name: Primary human microvascular endothelial cells, deltaVP30-inoculated, 24h, bioreplicate 3


title: EHUH003_deltaVP30_24h_1_RNA

source_name: Primary human microvascular endothelial cells, deltaVP30-inoculated, 24h, bioreplicate 1


title: EHUH003_deltaVP30_24h_2_RNA

source_name: Primary human microvascular endothelial cells, deltaVP30-inoculated, 24h, bioreplicate 2


title: N18 [methylation]

source_name: Adjacent normal from patient #18

value: patient #18


title: N17 [methylation]

source_name: Adjacent normal from patient #17

value: patient #17


title: EHUH003_deltaVP30_24h_4_RNA

source_name: Primary human microvascular endothelial cells, deltaVP30-inoculated, 24h, bioreplicate 4


title: EHUH003_deltaVP30_24h_5_RNA

source_name: Primary human microvascular endothelial cells, deltaVP30-inoculated, 24h, bioreplicate 5


title: Deaf [Sample 38]


title: Deaf [Sample 37]


title: N15 [methylation]

source_name: Adjacent normal from patient #15

value: patient #15


title: N16 [methylation]

source_name: Adjacent normal from patient #16

value: patient #16

value: Adjacent normal


title: N14 [methylation]

source_name: Adjacent normal from patient #14

value: hepatocellular carcinoma (HCC) patient

value: patient #14

value: Female


title: EHUH003_Mock_24h_2_RNA

source_name: Primary human microvascular endothelial cells, mock-inoculated, 24h, bioreplicate 2

value: Mock


title: Deaf [Sample 31]

source_name: Deafness

value: Whole blood


title: EHUH003_Mock_24h_4_RNA

source_name: Primary human microvascular endothelial cells, mock-inoculated, 24h, bioreplicate 4


title: Deaf [Sample 28]


title: Deaf [Sample 29]


title: Deaf [Sample 27]


title: EHUH003_Mock_24h_5_RNA

source_name: Primary human microvascular endothelial cells, mock-inoculated, 24h, bioreplicate 5


title: EHUH003_deltaVP30_8h_5_RNA

source_name: Primary human microvascular endothelial cells, deltaVP30-inoculated, 8h, bioreplicate 5


title: Deaf [Sample 32]


title: EHUH003_deltaVP30_8h_1_RNA

source_name: Primary human microvascular endothelial cells, deltaVP30-inoculated, 8h, bioreplicate 1


title: EHUH003_deltaVP30_8h_2_RNA

source_name: Primary human microvascular endothelial cells, deltaVP30-inoculated, 8h, bioreplicate 2


title: EHUH003_Mock_48h_2_RNA

source_name: Primary human microvascular endothelial cells, mock-inoculated, 48h, bioreplicate 2


title: Deaf [Sample 26]


title: N12 [methylation]

source_name: Adjacent normal from patient #12

value: patient #12


title: Deaf [Sample 30]


title: Deaf [Sample 25]


title: N10 [methylation]

source_name: Adjacent normal from patient #10

value: patient #10

value: Male


title: N8 [methylation]

source_name: Adjacent normal from patient #8

value: patient #8

value: No


title: Deaf [Sample 24]

value: Deaf

value: European descent


title: Deaf [Sample 23]


title: N7 [methylation]

source_name: Adjacent normal from patient #7

value: patient #7

value: Yes


title: EHUH003_Mock_8h_3_RNA

source_name: Primary human microvascular endothelial cells, mock-inoculated, 8h, bioreplicate 3


title: EHUH003_Mock_8h_5_RNA

source_name: Primary human microvascular endothelial cells, mock-inoculated, 8h, bioreplicate 5


title: N13 [methylation]

source_name: Adjacent normal from patient #13

value: patient #13


title: N6 [methylation]

source_name: Adjacent normal from patient #6

value: patient #6


title: N3 [methylation]

source_name: Adjacent normal from patient #3

value: patient #3

value: Adjacent normal


title: Deaf [Sample 20]


title: Deaf [Sample 22]


title: Deaf [Sample 21]


title: N11 [methylation]

source_name: Adjacent normal from patient #11

value: hepatocellular carcinoma (HCC) patient

value: patient #11


title: Deaf [Sample 17]

source_name: Deafness


title: Deaf [Sample 14]


title: Deaf [Sample 13]


title: Deaf [Sample 12]


title: Deaf [Sample 63]

value: WT


title: Deaf [Sample 18]

value: Whole blood


title: Deaf [Sample 19]


title: Deaf [Sample 11]


title: Deaf [Sample 7]


title: Deaf [Sample 10]


title: Deaf [Sample 9]


title: Deaf [Sample 8]


title: Deaf [Sample 16]


title: Deaf [Sample 6]


title: EHUH003_Mock_8h_1_RNA

source_name: Primary human microvascular endothelial cells, mock-inoculated, 8h, bioreplicate 1

value: Mock


title: Deaf [Sample 5]


title: 4mer3

city: Madrid

first: Marta

last: Berrocal-Lobo

state: Madrid

address: Antonio Nováis 10, s/n

department: System and Natural Resources

country: Spain

institute: School of Forestry Engineering and Natural Resources

hyb_protocol: The resulting biotin-tagged cRNA was fragmented to strands of less than 100 bases in length and the fragmented target cRNA (20 µg) was hybridized at 45°C with rotation at 60 rpm for 16 h (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix ATH1 GeneChip array. The GeneChip arrays were washed and then stained (streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 400.

scan_protocol: Scanning was performed on a Hewlett-Packard GeneArray scanner (Hewlett-Packard, Palo Alto, CA). Image analysis and pixel intensity were quantified using MicroArray Suite 5.0 software (Affymetrix, Inc., Santa Clara, CA).

data_processing: Data processing were performed as follows: First, values below 0.01 were set to 0.01.  Each measurement was then divided by the 50th percentile of all measurements in that sample.  Specific samples were then normalized to one another:  Three replicates at each treatment were normalized against the median of the control samples (water treatment). Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples. Raw data on all genes was then extracted and analyzed for significance using the Statistical Analysis of Microarrays (SAM) software (Tusher et al., 2001).  Genes determined to be statistically significant were listed and the resulting information was imported into TMEV for further analysis.  Genes were grouped by their biological function via their gene ontology (GO) annotation using the Bar Toronto Super viewer tool, MapMan tool (Usadel et al., 2008, http://mapman.mpimp-golm.mpg.de/pageman/) and  agriGO toolkit (Zhou et al., 2010, http://bioinfo.cau.edu.cn/agriGO/).

organism: Arabidopsis thaliana

source_name: seedlings, 4mer treatment

label_protocol: Single-stranded, then double-stranded cDNA was synthesized from the polyA+ mRNA present in the isolated total RNA (20 µg of total RNA starting material for each sample reaction) using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen Corp., Carlsbad, CA) and custom poly (T)-nucleotide primers that contained a sequence recognized by T7 RNA polymerase. All of the resulting double-stranded cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction, using the Bio-Array High-Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Inc., Farmingdale, NY).

growth_protocol: Arabidopsis seedlings were growth in liquid MS medium during 14 days before treatments.

extract_protocol: Total RNA samples were processed according to manufacturer’s protocols with the following modifications (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetrix, Inc., Santa Clara, CA).

treatment_protocol: Arabidopsis 14 days old seedlings were treated with a final concentration of 100 µg/ml with purified chitin oligomer tetramer in ddH2O (degree of polymerization, d.p. = 4, Seikagaku Corporation, Tokyo, Japan). The control seedlings were similarly treated with an equivalent amount of ddH2O.

tag: ecotype

value: whole seedling

tag: developmental stage

value: 14 days old seedlings


title: Deaf [Sample 15]


title: 4mer2


title: 4mer1


title: Mock3

source_name: seedlings, control


title: Spleen_ko

city: Shanghai

first: Eugene

last: Chin

address: Yueyang Road #320

department: Institute of Health Science

institute: Shanghai Institute of Biological Sciences

description: Gene expression in untreated Loxl3-/- mice spleen

hyb_protocol: Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242) was used for hybridization reaction by KangChen Bio-tech Inc., China according to provided protocol. Hybridization Chamber, stainless (Agilent p/n G2534A), Hybridization Chamber gasket slides (Agilent p/n G2534-60003), Hybridization oven (Agilent p/n G2545A) and Hybridization oven rotator for Agilent Microarray Hybridization Chambers (Agilent p/n G2530-60029) were used for experiment.

scan_protocol: Agilent Microarray Scanner (Agilent p/n G2565BA) was used for scanning by KangChen Bio-tech Inc., China.

data_processing: The scanned images were analyzed with Agilent Feature Extraction (FE) software by KangChen Bio-tech Inc., China.

source_name: Spleen

label_protocol: Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) was used for Cyanine-3 (Cy3) labelling, which is performed by KangChen Bio-tech Inc., China according to provided protocol.

extract_protocol: RNA was prepared using the standard procedures by KangChen Bio-tech Inc., China.  TRIzol® Reagent (Invitrogen life technologies) method was used. RNasey Mini Kit(Qiagen p/n 74104) was used for Total RNA clean-up and RNA quantification and quality was assured by NanoDrop ND-1000. RNA integrity and gDNA contamination test was performed by denaturing agarose gel electrophoresis. Biopulverizer(biospec) and Mini-Bead-Beater-16(biospec) were used for experiment.

treatment_protocol: Fresh spleens from healthy mice was directly used for RNA extraction.

value: Male

value: Loxl3 knock-out

value: Spleen


title: Mock2


title: Spleen_wt

description: Gene expression in untreated Loxl3+/+ mice spleen

value: Loxl3 wild-type


title: Deaf [Sample 3]

value: Deaf

value: European descent


title: OG1RF/rnjB Cy3/cy5 #3

city: Houston

first: Peng

last: Gao

state: Texas

address: SRB 301V, 1825 Pressler Street

department: IMM

institute: UTHealth

description: Cy3/Cy5 dye swap hybridized wildtype and mutant strain RNAs with microarray silde

hyb_protocol: Labelled cDNA hybridised using the MWG Gene-Frame system. Slides placed in shaking water bath for 16 h at 42 °C. Arrays then washed in 2x SSC (+0.1 % SDS), 1x SSC, 0.2x SSC and 0.1x SSC, each at 37 °C for 5 min prior to drying and scanning.

scan_protocol: Microarray slides were scanned using an GenePix 4000b scanner with GENPIXPRO 5.0 software

data_processing: Data analysis was carried out using Genepix Pro 5.0 and Genesight version 4 (Biodiscovery Inc).After quantitation and global normalization using the average spot intensity, Ratios of OG1RF to the rnjB mutant were calculated for each spot. For each open reading frame (ORF), ratios for each culture were calculated by averaging ratios for spots within a chip that met quality criteria and their averaging dye-swap hybridizations. The P value from a one-sample t test, testing whether the grand mean log ratio was different from 0.0, was significant at the 0.05 level or better

organism: Enterococcus faecalis

source_name: Steady-state continuous cultured experimental samples after 5 min oxygen depletion.

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript II Kit (Invitrogen) as manufacturers instructions. Samples purified using QIAGEN PCR purification kit before hybridization.

growth_protocol: Enterococcus faecalis cells were grown in BHI to mid-exponential phase at 37˚C 250rpm

extract_protocol: An equavelent of 1 OD600 cells were collected. RNAs were extracted from collected cells using NucleoSpin RNA II kit with on-colume DNase digestion

tag: strain

source_name: Steady-state continuous cultured control samples in presence of oxygen

value: rnjB deletion


title: Deaf [Sample 2]


title: OG1RF/rnjB Cy5/cy3 #2

description: Cy5/Cy3 dye swap hybridized wildtype and mutant strain RNAs with microarray silde

source_name: Steady-state continuous cultured experimental samples after 60 min oxygen depletion.


title: OG1RF/rnjB Cy5/cy3 #3

source_name: Steady-state continuous cultured experimental samples after 10 min oxygen depletion.


title: Deaf [Sample 4]


title: OG1RF/rnjB Cy3/cy5 #2

source_name: Steady-state continuous cultured experimental samples after 15 min oxygen depletion.


title: Mock1


title: OG1RF/rnjB Cy5/cy3 #1


title: Deaf [Sample 1]


title: OG1RF/rnjB Cy3/cy5 #1


title: Deaf [Sample 53]


title: RKO WT siCKIa 3

status: Public on Feb 16 2017

city: Heidelberg

first: Mohammed

last: Abba

address: Im Neuenheimer Feld 280

department: Molecular Oncology of Solid Tumors

country: Germany

institute: German Cancer Research Center (DKFZ)

description:
Chip ID: 254606412303_1_2
RKO cell line P53 Wildtype + CK1a knockdown, biological replicate 3

hyb_protocol: miRNA Microarray System with miRNA Complete Labeling and Hyb Kit protocol

scan_protocol: Slides were scanned using the SureScan Microaarray scanner with a scan resolution of 3uM

data_processing: Scanned images were analyzed with Feature Extraction Software FE version 9.5.3 (Agilent)

label_protocol: Standard Agilent labeling protocol

growth_protocol: P53 isogenic RKO cells(+/+ and -/-) were cultured in 6 well plates at 37 degrees celsius with McCoy medium supplemented with 10% FCS

extract_protocol: RNA was extracted using the miRNeasy kit (Qiagen) according to the given protocol

treatment_protocol: Isogenic cells were transfected with either CK1a or negative control siRNA at an end concentration of 100nM. Cells were harvested 48hrs after transfection after confirmation of CK1a knockdown by WB

tag: cell line

value: RKO cell line P53 Wildtype

tag: treatment

value: Cells treated with CK1a siRNA (100nM)

value: P53 Wildtype + CK1a knockdown


title: RKO WT NC 3

description:
Chip ID: 254606412303_1_1
RKO cell line P53 Wildtype, biological replicate 3

source_name: RKO cell line P53 Wildtype

value: Cells treated with negative control siRNA (100nM)

value: P53 Wildtype


title: RKO P53-/- siCKIa 3

description:
Chip ID: 254606412303_1_4
RKO cell line P53 null + CK1a knockdown, biological replicate 3

source_name: RKO cell line P53 null + CK1a knockdown

value: RKO cell line P53 null

value: P53 null + CK1a knockdown


title: RKO WT siCKIa 1

description:
Chip ID: 254606412302_1_2
RKO cell line P53 Wildtype + CK1a knockdown, biological replicate 1


title: RKO P53-/- NC 3

description:
Chip ID: 254606412303_1_3
RKO cell line P53 null, biological replicate 3

source_name: RKO cell line P53 null

value: P53 null


title: RKO P53-/- siCKIa 1

description:
Chip ID: 254606412302_1_4
RKO cell line P53 null + CK1a knockdown, biological replicate 1


title: RKO WT NC 2

description:
Chip ID: 254606412302_2_1
RKO cell line P53 Wildtype, biological replicate 2


title: RKO P53-/- NC 2

description:
Chip ID: 254606412302_2_3
RKO cell line P53 null, biological replicate 2


title: RKO WT siCKIa 2

description:
Chip ID: 254606412302_2_2
RKO cell line P53 Wildtype + CK1a knockdown, biological replicate 2


title: RKO WT NC 1

description:
Chip ID: 254606412302_1_1
RKO cell line P53 Wildtype, biological replicate 1


title: RKO P53-/- siCKIa 2

description:
Chip ID: 254606412302_2_4
RKO cell line P53 null + CK1a knockdown, biological replicate 2


title: RKO P53-/- NC 1

description:
Chip ID: 254606412302_1_3
RKO cell line P53 null, biological replicate 1


title: WT.SI.Veil.6.1.27.151#1

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

source_name: Small Intestine

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

value: 6 Weeks Old

tag: separation method

value: Dissection / Trimming

tag: Sex

tag: microbe

value: Veillonella 6_1_27

value: Small Intestine


title: Control Replicate 2

city: Ioannina

first: Katerina

middle: Periklis

last: Soupsana

address: Dourouti

department: Medical School

country: Greece

institute: University of Ioannina

hyb_protocol: Affymetrix protocols and procedures were followed

data_processing: Data were processed using GeneSpring software (Agilent). RMA16 normalization was performed and only probes above the background threshold were considered for further evaluation.

organism: Danio rerio

source_name: control larvae

growth_protocol: Embryos were bred under standard conditions

extract_protocol: none provided by the submitter

treatment_protocol: For exposure of zebrafish larvae to MC-LR, a control group was exposed to 0.05% ethanol served as control. At 3 dpf, 55 larvae were exposed to MC-LR for 4 days at 500 μg/L in 250-mL glass beakers containing 100 mL of MC-LR solution. Each concentration was studied using three independent biological replicates.

value: larvae


title: WT.SI.SPF.31#2

value: Male

value: Specific Pathogen Free (SPF)


title: MC-LR 500 Replicate 3

scan_protocol: Affymetrix protocols and procedures were followed

source_name: MC-LR treated larvae


title: WT.SI.Veil.6.1.27.151#2


title: WT.SI.SPF.31#1

value: Female


title: MC-LR 500 Replicate 2

label_protocol: Affymetrix protocols and procedures were followed


title: MC-LR 500 Replicate 1


title: WT.SI.Ssapr.DLK1.184#3

value: Staphylococcus saprophyticus DLK1


title: Control Replicate 3


title: WT.SI.Smiti.F0392.75#2

value: Streptococcus mitis F0392


title: WT.SI.Ssapr.DLK1.184#2


title: WT.SI.SPF#2


title: WT.SI.Ssapr.DLK1.184#1


title: WT.SI.Rgnav.ATCC29149.239#2

value: Ruminococcus gnavus ATCC29149


title: WT.SI.Pasac.AO33.68#2

value: Peptostreptococus asaccharolyticus AO33


title: WT.SI.Rgnav.ATCC29149.175#1


title: WT.SI.Pueno.UPII60-3.74#2

value: Porphyromonas uenonis UPII60-3


title: WT.SI.Pdist.ATCC8503.17#1

value: Parabacteroides distasonis ATCC8503


title: WT.SI.Rgnav.ATCC29149.239#1


title: Control Replicate 1


title: WT.SI.Pgran.AO42.43#1

value: Propionibacterium granulosum AO42


title: WT.SI.Pmagn.AO29.26#1

value: Peptostreptococcus magnus AO29


title: WT.SI.Rgnav.ATCC29149.175#2


title: WT.SI.Pueno.UPII60-3.74#1


title: WT.SI.Pasac.AO33.68#1


title: WT.SI.Pmerd.CL03T12C32.62#2

value: Parabacteroides merdae CL03T12C32


title: WT.SI.Lcase.AO47.21#2

value: 6 Weeks Old

value: Lactobacillus casei AO47


title: WT.SI.Pdist.ATCC8503.17#2

value: Dissection / Trimming


title: WT.SI.Lrham.LMS2-1.46#1

value: Lactobacillus rhamnosus LMS2-1

value: Small Intestine


title: WT.SI.Lcase.AO47.21#1

value: Male


title: WT.SI.Lach.2.1.58FAA.133#2

value: Lachnospiraceae sp_2_1_58FAA


title: WT.SI.Germfree.52#3

value: Female

value: Germ free


title: patient P020 two months after transplantation

city: Bergisch-Gladbach

first: Stefan

last: Tomiuk

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

institute: Miltenyi Biotec GmbH

description: RNA was extracted using the PAXgene Blood RNA Kit (QIAgen)

hyb_protocol: Whole blood samples were hybridized on the RISET 2.0 microarray platform. This is a custom Agilent 8×15K 60-mer oligonucleotide microarray comprising 5,069 probes represented in triplicate. Probes selected corresponded to 4,607 genes with a valid Entrez Gene ID and an additional 407 probes that could not be assigned to a valid Entrez Gene ID. The microarray is focused on the detection of genes relevant in the field of transplantation and was designed based on current literature and published and unpublished data provided by RISET consortium partners. Probe design was optimized for the detection of multiple transcript variants of a gene, on optimized hybridization properties of the probes, and avoiding cross-hybridization. The hybridization procedure was performed after control of RNA quality and integrity and according to ref. x* using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 0.6 μg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65°C) to RISET 2.0 microarrays. Following hybridization, the microarrays were washed once with Agilent Gene Expression Wash Buffer 1 for 1 minute at room temperature, followed by a second wash with preheated (37°C) Agilent Gene Expression Wash Buffer 2 containing 0.005% N-lauroylsarcosine for 1 minute. The last washing step was performed with acetonitrile for 30 seconds.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies, Inc.). The Agilent Feature Extraction Software (FES v10.5.1.1) was used to read out and process the microarray image files.

data_processing: In order to determine differential gene expression, FES derived output data files were further processed using the Rosetta Resolver gene expression data analysis system (v7.2.2.0.0., Rosetta Inpharmatics LLC).

source_name: peripheral vein blood

label_protocol: Sample labeling was performed as detailed in the “One-Colour Microarray-Based Gene Expression Analysis protocol (version 5.5, part number G4140-90040). Briefly, 0.5 µg of each total RNA sample was used for the amplification and labelling step using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies) in the presence of cyanine 3-CTP. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies, Inc.).

extract_protocol: Peripheral vein blood was drawn directly into PAXgene Blood RNA tubes (QIAgen, Crawley UK). Whole-blood RNA was extracted using the PAXgene Blood RNA Kit including DNAse I treatment (QIAgen). Quality and integrity of PAXgene RNA were determined using the Agilent RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was quantified by measuring absorbance at 260 nm on the ND-1000 Spectrophotometer (NanoDrop Technologies).

treatment_protocol: The alemtuzumab 20 mg diluted in saline was given in two slow infusions doses before reperfusion and on the first day. Thirty minutes before the alemtuzumab each application, patients had received metylprednisolone 500mg i.v. The alemtuzumab dose was adopted from published literature. Infliximab was given as a single dose 5mg/kg diluted in 500 mL of saline and before application patients had received hydrocortisone 100mg as a local praxis. lnfliximab dose was chosen as for the Crohn disease therapy. Before the surgery, patients were randomized to receive either long-term tacrolimus monotherapy (control arm) or sirolimus monotherapy (investigational arm) from the 15 postoperative day while the first 14 days patients received tacrolimus monotherapy as in the control arm. Tacrolimus (Prograf®, Astellas) was given in standard doses 0,1mg/kg bid, the first dose was given before surgery. The second postoperative days, the whole blood through levels were evaluated and target levels were 10-15 ng/mL for the first month, 5-15 ng/ml for the first 3 months and 5-10 ng/ml later on. Sirolimus (Rapamune®, Wyeth) 4mg morning dose was given from the day 15. In this arm, the last tacrolimus dose was given 24 hours before. Long-term sirolimus through levels were 5-10 ng/mL. In patients with early acute rejection within the first 14 days or rejection in protocol biopsy, the study protocol allowed late sirolimus switch in the investigational arm. In a case of clinically relevant acute or chronic rejections in the case biopsies, patients were added mycophenolate mofetil.

tag: alternative sample name

tag: patient id

tag: time after transplantation

tag: drug

value: Tac

tag: acute or chronic rejection within 12 m 1= yes, 0= no

tag: proteinuria >1 g within 12m 1= yes, 0= no


title: patient P020 at least 12 months after transplantation


title: WT.SI.Germfree.144#1

tag: age

tag: tissue


title: WT.SI.Germfree.112#2


title: patient P019 M6 after transplantation


title: patient P019 three months after transplantation


title: WT.SI.Germfree.32#2


title: WT.SI.Germfree.144#2


title: WT.SI.Germfree.119#1

value: 8 Weeks Old


title: patient P019 two months after transplantation


title: patient P019 at least 12 months after transplantation


title: patient P018 at least 12 months after transplantation


title: patient P020 three months after transplantation


title: patient P018 M6 after transplantation


title: patient P018 three months after transplantation


title: patient P020 M6 after transplantation


title: patient P019 before transplantation

value: P19 [pre-Tx] [no]

value: pre

value: no


title: WT.SI.Fnucl.F0419.79#1

value: Fusobacterium nucleatum F0419


title: WT.SI.Germfree.246#1


title: patient P020 three weeks after transplantation


title: patient P019 three weeks after transplantation


title: WT.SI.Germfree.112#1


title: WT.SI.Germfree.174#1


title: patient P020 before transplantation

value: P20 [pre-Tx] [no]


title: WT.SI.Fmort.AO16.34#1

value: Fusobacterium mortiferum AO16


title: WT.SI.Fmort.AO16.249#2

value: 6 Weeks Old


title: WT.SI.Lach.2.1.58FAA.133#1


title: patient P018 two months after transplantation


title: WT.SI.Fmort.AO16.249#1


title: patient P017 two months after transplantation


title: patient P017 three weeks after transplantation


title: patient P017 before transplantation

value: P17 [pre-Tx] [no]


title: patient P017 at least 12 months after transplantation


title: patient P018 before transplantation

value: P18 [pre-Tx] [no]


title: patient P018 three weeks after transplantation


title: patient P017 M6 after transplantation

value: P17 [M6] [Tac/MMF]

value: Tac, MMF


title: patient P016 at least 12 months after transplantation


title: WT.SI.Efaec.TX0104.82#1

value: Dissection / Trimming

value: Male

value: Enterococcus faecalis TX0104

value: Small Intestine


title: WT.SI.Fmort.AO16.195#1


title: patient P016 M6 after transplantation

value: Tac


title: patient P016 before transplantation

value: P16 [pre-Tx] [no]


title: patient P016 two months after transplantation


title: WT.SI.Cjeju.AS-84-79.166#1

value: Campylobacter jejuni AS-84-79


title: patient P016 three weeks after transplantation


title: patient P016 three months after transplantation


title: WT.SI.Cperf.ATCC13124.69#2

value: Clostridium perfringens ATCC13124


title: WT.SI.Cperf.ATCC13124.69#1


title: WT.SI.Cramo.AO31.22#2

value: Clostridium ramosum AO31


title: WT.SI.Cjeju.AS-84-79.166#2


title: WT.SI.Copr.8.2.54BFAA.150#1

value: Coprobacillus 8_2_54BFAA


title: WT.SI.Efaec.TX0104.82#2


title: WT.SI.Chist.AO25.20#2

value: Clostridium histolyticum AO25


title: WT.SI.Chist.AO25.20#1


title: WT.SI.Bunif.ATCC8452.24#1

value: Bacteroides uniformis ATCC8492


title: WT.SI.Copr.8.2.54BFAA.150#2

value: 6 Weeks Old


title: WT.SI.Efaec.TX0104.78#3


title: patient P017 three months after transplantation


title: WT.SI.Bmass.DSM17679.71#2

value: Bacteroides massiliensis DSM17679


title: patient P015 at least 12 months after transplantation


title: patient P015 M6 after transplantation


title: patient P015 before transplantation

value: P15 [pre-Tx] [no]

value: pre

value: no


title: patient P014 three weeks after transplantation

value: Sir


title: patient P014 two months after transplantation


title: patient P014 at least 12 months after transplantation

value: Tac, MMF


title: WT.SI.Bfine.DSM17565.90#2

value: Dissection / Trimming

value: Male

value: Bacteroides finegoldii DSM17565


title: WT.SI.Badol.L2-32.80#4

value: Female

value: Bifidobacterium adolescentis L2-32

value: Small Intestine


title: patient P014 before transplantation

value: P14 [pre-Tx] [no]


title: WT.SI.Badol.L2-32.80#3


title: WT.SI.Bbrev.SK134.47#1

value: Bifidobacterium breve SK134


title: patient P013 at least 12 months after transplantation

value: Tac


title: patient P015 three months after transplantation


title: patient P013 three months after transplantation


title: WT.SI.Bmass.DSM17679.71#1


title: patient P013 two months after transplantation


title: WT.SI.Bfine.DSM17565.90#1


title: patient P013 M6 after transplantation


title: patient P015 two months after transplantation


title: WT.SI.Badol.L2-32.241#2


title: patient P014 M6 after transplantation


title: WT.SI.Bdore.DSM17855.73#2

value: Bacteroides dorei DSM17855


title: WT.Co.Veil.6.1.27.151#2

source_name: Colon

value: 6 Weeks Old

value: Veillonella 6_1_27

value: Colon


title: WT.SI.Badol.L2-32.241#3


title: patient P013 three weeks after transplantation


title: WT.SI.Abaum.ATCC17978.35#1

value: Acinetobacter baumannii ATCC17978


title: WT.SI.Alwof.F78.23#1

value: Acinetobacter lwoffii F78


title: patient P014 three months after transplantation

value: Sir


title: WT.SI.Badol.L2-32.241#1


title: WT.Co.Veil.6.1.27.151#1


title: WT.SI.Badol.L2-32.80#1


title: patient P013 before transplantation

value: P13 [pre-Tx] [no]

value: pre

value: no


title: patient P012 two months after transplantation


title: patient P012 three months after transplantation


title: patient P012 before transplantation

value: P12 [pre-Tx] [no]


title: patient P012 at least 12 months after transplantation


title: patient P012 M6 after transplantation


title: patient P011 at least 12 months after transplantation


title: WT.Co.SPF#2

value: Dissection / Trimming

value: Male

value: Specific Pathogen Free (SPF)


title: WT.Co.SPF#1


title: WT.Co.Rgnav.ATCC29149.239#2

value: Ruminococcus gnavus ATCC29149


title: WT.Co.Smiti.F0392.75#1

value: Streptococcus mitis F0392


title: WT.Co.Smiti.F0392.75#2


title: WT.Co.Pueno.UPII60-3.74#2

value: Porphyromonas uenonis UPII60-3


title: WT.Co.SPF.31#1

value: Female


title: patient P011 M6 after transplantation

value: Tac


title: WT.Co.Rgnav.ATCC29149.175#2

value: 6 Weeks Old


title: WT.Co.Rgnav.ATCC29149.175#1

value: Colon


title: patient P011 three months after transplantation


title: WT.Co.Pueno.UPII60-3.74#1


title: patient P011 three weeks after transplantation


title: patient P011 before transplantation

value: P11 [pre-Tx] [no]


title: WT.Co.Rgnav.ATCC29149.239#1


title: patient P011 two months after transplantation


title: PO_7P4

city: Illkirch/Strasbourg

first: Wolfgang

last: Raffelsberger

address: 1 rue Laurent Fries

department: DBGS

country: France

institute: IGBMC

description:
colon cancer mouse xenograft
SAMPLE 201

hyb_protocol: Following fragmentation, cRNA was hybridized on the GeneChip Array and the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2007, Affymetrix).

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

data_processing: Log2 GCRMA values were calculated using R&Bioconductor (version R-2.15.0, gcrma library version 2.28.0).

source_name: COLCATS consortium

label_protocol: Biotinylated cRNA was prepared from the total RNA according to the Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2007, Affymetrix)

growth_protocol: The human colorectal cancer HCT116 cell line was cultured in DMEM medium with 1g/l glucose, 10% Fetal Calf Bovine Serum, 50 mg/L Gentamicin sulfate. HT29 was cultured in RPMI medium (without Hepes), 10% Fetal Calf Bovine Serum, 2% Penicillin-Streptomycin.

extract_protocol: Totol RNA isolated using Trizol (Invitrogen) acording to the manufacturer's instructions, the resulting RNA was further purified using the RNeasy Mini Kit (Qiagen). Double-stranded cDNA was synthesized from the total RNA from these samples (colon cancer, colorectal tumor xenografts, colon cancer cell lines), and reverse transcription was carried out followed by biotin labeling. From each sample, 15 μg of biotin-labeled cRNA were hybridized onto Affymetrix HGU133 Plus 2.0 GeneChip arrays.

treatment_protocol: Freshly xenografted colon cancer tumors (57) were explanted and placed in PBS buffer for immediate preparation of single-cell suspensions for the clonogenic assay. Tumor clonogenic assays were performed as previously described (Fiebig et al., 2004).

value: colon cancer mouse xenograft


title: patient P010 at least 12 months after transplantation

value: Sir


title: POT_HT29

description:
colon cancer cell line
SAMPLE 203

value: colon cancer cell line HT29


title: POT_HCT116

description:
colon cancer cell line
SAMPLE 202

value: colon cancer cell line HCT116


title: PO_55P2

description:
colon cancer mouse xenograft
SAMPLE 200


title: patient P010 M6 after transplantation


title: PO_50P2

description:
colon cancer mouse xenograft
SAMPLE 197


title: WT.Co.Pgran.AO42.43#1

value: Propionibacterium granulosum AO42


title: patient P010 two months after transplantation


title: WT.Co.Pmagn.AO29.26#1

value: Peptostreptococcus magnus AO29


title: patient P010 three months after transplantation


title: patient P010 three weeks after transplantation


title: PO_52P1

description:
colon cancer mouse xenograft
SAMPLE 198


title: WT.Co.Pmerd.CL03T12C32.62#2

value: Dissection / Trimming

value: Parabacteroides merdae CL03T12C32


title: PO_53P1

description:
colon cancer mouse xenograft
SAMPLE 199


title: WT.Co.Pdist.ATCC8503.17#1

value: Male

value: Parabacteroides distasonis ATCC8503


title: PO_49P1

description:
colon cancer mouse xenograft
SAMPLE 195


title: WT.Co.Pasac.AO33.68#2

value: Peptostreptococus asaccharolyticus AO33


title: WT.Co.Pdist.ATCC8503.17#2


title: PO_4P2

description:
colon cancer mouse xenograft
SAMPLE 196


title: PO_46P2

description:
colon cancer mouse xenograft
SAMPLE 193


title: patient P09 at least 12 months after transplantation


title: PO_45P1

description:
colon cancer mouse xenograft
SAMPLE 192


title: PO_47P3

description:
colon cancer mouse xenograft
SAMPLE 194


title: patient P09 three months after transplantation


title: WT.Co.Pasac.AO33.68#1


title: WT.Co.Lrham.LMS2-1.46#1

value: Lactobacillus rhamnosus LMS2-1


title: patient P09 M6 after transplantation


title: patient P010 before transplantation

value: P10 [pre-Tx] [no]

value: pre

value: no


title: PO_43P2

description:
colon cancer mouse xenograft
SAMPLE 190


title: PO_44P1

description:
colon cancer mouse xenograft
SAMPLE 191


title: WT.Co.Lcase.AO47.21#2

value: 6 Weeks Old

value: Lactobacillus casei AO47

value: Colon


title: WT.Co.Lach.2.1.58FAA.133#2

value: Lachnospiraceae sp_2_1_58FAA


title: WT.Co.Lcase.AO47.21#1


title: patient P09 two months after transplantation

value: Tac


title: patient P09 before transplantation

value: P09 [pre-Tx] [no]


title: patient P08 M6 after transplantation

value: Sir


title: patient P08 three months after transplantation


title: PO_41P1

description:
colon cancer mouse xenograft
SAMPLE 188

value: colon cancer mouse xenograft


title: patient P08 at least 12 months after transplantation


title: PO_42P2

description:
colon cancer mouse xenograft
SAMPLE 189


title: WT.Co.Germfree.93#3

value: Dissection / Trimming

value: Female

value: Germ free


title: PO_40P2

description:
colon cancer mouse xenograft
SAMPLE 187


title: WT.Co.Lach.2.1.58FAA.133#1

value: Male


title: patient P08 two months after transplantation


title: WT.Co.Germfree.65#1


title: PO_38P1

description:
colon cancer mouse xenograft
SAMPLE 185


title: PO_39P4

description:
colon cancer mouse xenograft
SAMPLE 186


title: PO_37P4

description:
colon cancer mouse xenograft
SAMPLE 184


title: PO_36PTC

description:
colon cancer mouse xenograft
SAMPLE 183


title: PO_36M1C

description:
colon cancer mouse xenograft
SAMPLE 182


title: WT.Co.Germfree.32#2


title: patient P08 before transplantation

value: P08 [pre-Tx] [no]


title: patient P07 at least 12 months after transplantation


title: WT.Co.Germfree.52#3


title: patient P07 three weeks after transplantation


title: WT.Co.Germfree.174#1


title: WT.Co.Germfree.246#1


title: patient P07 two months after transplantation


title: patient P06 at least 12 months after transplantation

value: Tac, MMF


title: patient P07 M6 after transplantation


title: WT.Co.Germfree.119#1

value: 8 Weeks Old


title: patient P07 before transplantation

value: P07 [pre-Tx] [no]

value: pre


title: patient P06 three months after transplantation


title: patient P06 two months after transplantation


title: patient P06 three weeks after transplantation


title: PO_35P4

description:
colon cancer mouse xenograft
SAMPLE 181


title: WT.Co.Fnucl.F0419.79#2

value: 6 Weeks Old

value: Fusobacterium nucleatum F0419


title: WT.Co.Germfree.112#2

value: Colon


title: PO_33P1

description:
colon cancer mouse xenograft
SAMPLE 179


title: WT.Co.Germfree.112#1


title: WT.Co.Fnucl.F0419.79#1


title: WT.Co.Germfree.144#2


title: WT.Co.Germfree.144#1


title: patient P06 before transplantation

value: P06 [pre-Tx] [no]

value: no


title: WT.Co.Fmort.AO16.34#1

value: Fusobacterium mortiferum AO16


title: E7R_040a05

description:
colon cancer mouse xenograft
SAMPLE 71


title: PO_34P4

description:
colon cancer mouse xenograft
SAMPLE 180


title: WT.Co.Fmort.AO16.249#2


title: PO_21C

description:
colon cancer mouse xenograft
SAMPLE 176


title: patient P07 three months after transplantation

value: Tac


title: PO_17C

description:
colon cancer mouse xenograft
SAMPLE 174

value: colon cancer mouse xenograft


title: PO_32P2

description:
colon cancer mouse xenograft
SAMPLE 178


title: E7R_032m01

description:
colon cancer mouse xenograft
SAMPLE 69


title: patient P05 at least 12 months after transplantation


title: PO_30P2

description:
colon cancer mouse xenograft
SAMPLE 177


title: patient P05 three months after transplantation


title: WT.Co.Fmort.AO16.249#1

value: Dissection / Trimming


title: patient P05 two months after transplantation


title: E7R_018a19

description:
colon cancer mouse xenograft
SAMPLE 68


title: PO_20P10

description:
colon cancer mouse xenograft
SAMPLE 175


title: E7R_040a04

description:
colon cancer mouse xenograft
SAMPLE 70


title: E7R_018a13

description:
colon cancer mouse xenograft
SAMPLE 67


title: patient P05 before transplantation

value: P05 [pre-Tx] [no]


title: patient P05 three weeks after transplantation


title: E6R_033a04

description:
colon cancer mouse xenograft
SAMPLE 66


title: patient P04 at least 12 months after transplantation


title: WT.Co.Cperf.ATCC13124.69#4

value: Female

value: Clostridium perfringens ATCC13124


title: WT.Co.Efaec.TX0104.78#1

value: Male

value: Enterococcus faecalis TX0104


title: E6R_033a02

description:
colon cancer mouse xenograft
SAMPLE 64


title: WT.Co.Fmort.AO16.195#1


title: patient P04 two months after transplantation

value: Sir


title: E6R_033a03

description:
colon cancer mouse xenograft
SAMPLE 65


title: WT.Co.Efaec.TX0104.82#2


title: patient P04 three months after transplantation


title: patient P04 three weeks after transplantation


title: WT.Co.Cperf.ATCC13124.69#3


title: patient P04 before transplantation

value: P04 [pre-Tx] [no]


title: E6R_028b04

description:
colon cancer mouse xenograft
SAMPLE 62


title: WT.Co.Cperf.ATCC13124.69#1


title: E6R_028b05

description:
colon cancer mouse xenograft
SAMPLE 63


title: E5R_071b10

description:
colon cancer mouse xenograft
SAMPLE 60


title: E6R_028b02

description:
colon cancer mouse xenograft
SAMPLE 61


title: patient P03 at least 12 months after transplantation


title: WT.Co.Copr.8.2.54BFAA.150#2

value: Coprobacillus 8_2_54BFAA


title: patient P03 three months after transplantation


title: WT.Co.Cperf.ATCC13124.69#2

value: 6 Weeks Old


title: WT.Co.Copr.8.2.54BFAA.150#1


title: WT.Co.Cjeju.AS-84-79.166#2

value: Campylobacter jejuni AS-84-79


title: E5R_071b09

description:
colon cancer mouse xenograft
SAMPLE 59


title: E5R_071b06

description:
colon cancer mouse xenograft
SAMPLE 57


title: WT.Co.Cjeju.AS-84-79.166#1

value: Colon


title: patient P03 three weeks after transplantation


title: patient P03 before transplantation

value: P03 [pre-Tx] [no]

value: pre


title: WT.Co.Chist.AO25.20#1

value: Clostridium histolyticum AO25


title: E5R_071b05

description:
colon cancer mouse xenograft
SAMPLE 56


title: WT.Co.Chist.AO25.20#2


title: E5R_071b08

description:
colon cancer mouse xenograft
SAMPLE 58


title: patient P03 two months after transplantation

value: Tac


title: WT.Co.Bvulg.ATCC8482.16#2

value: Bacteroides vulgatus ATCC8482


title: E5R_071b02

description:
colon cancer mouse xenograft
SAMPLE 53

value: colon cancer mouse xenograft


title: WT.Co.Bunif.ATCC8452.24#1

value: Dissection / Trimming

value: Bacteroides uniformis ATCC8492


title: patient P02 three weeks after transplantation

value: P02 [W3] [Tac/MMF]

value: Tac, MMF


title: patient P02 two months after transplantation

value: MMF


title: E5R_071b03

description:
colon cancer mouse xenograft
SAMPLE 54


title: patient P02 three months after transplantation


title: E5R_071b04

description:
colon cancer mouse xenograft
SAMPLE 55


title: E5R_057a16

description:
colon cancer mouse xenograft
SAMPLE 51


title: E5R_021a17

description:
colon cancer mouse xenograft
SAMPLE 49


title: E5R_071b01

description:
colon cancer mouse xenograft
SAMPLE 52


title: patient P02 before transplantation

value: P02 [pre-Tx] [no]

value: no


title: patient P02 at least 12 months after transplantation


title: patient P01 two months after transplantation

value: P01 [M2] [Tac/MMF]


title: patient P01 at least 12 months after transplantation


title: patient P01 three months after transplantation


title: WT.Co.Bvulg.ATCC8482.16#1

value: 6 Weeks Old

value: Male


title: WT.Co.Bthet.ATCC29148.84#2

value: Female

value: Bacteroides thetaiotaomicron ATCC29148

value: Colon


title: WT.Co.Bovat.ATCC8483.15#2

value: Bacteroides ovatus ATCC8483


title: WT.Co.Bthet.ATCC29148.84#1


title: patient P01 before transplantation

value: P01 [pre-Tx] [no]

value: pre


title: WT.Co.Cramo.AO31.22#2

value: Clostridium ramosum AO31


title: WT.Co.Bsala.DSM18170.72#1

value: Dissection / Trimming

value: Bacteroides salanitronis DSM18170


title: WT.Co.Bovat.ATCC8483.15#1


title: patient P01 three weeks after transplantation

value: P01 [W3] [Tac/MMF]


title: WT.Co.Bsala.DSM18170.72#2


title: E5R_021a16

description:
colon cancer mouse xenograft
SAMPLE 48

value: colon cancer mouse xenograft


title: WT.Co.Bsala.DSM18170.83#4


title: WT.Co.Bsala.DSM18170.83#3


title: E5R_021a15

description:
colon cancer mouse xenograft
SAMPLE 47


title: E5R_057a06

description:
colon cancer mouse xenograft
SAMPLE 50


title: E4R_072c5

description:
colon cancer mouse xenograft
SAMPLE 43


title: E5R_021a13

description:
colon cancer mouse xenograft
SAMPLE 45


title: AD_917

description:
colon cancer
SAMPLE 40

value: colon cancer


title: WT.Co.Bmass.DSM17679.71#2

value: Bacteroides massiliensis DSM17679


title: WT.Co.Bmass.DSM17679.71#1


title: E4R_072c6

description:
colon cancer mouse xenograft
SAMPLE 44


title: AD_944

description:
colon cancer
SAMPLE 41


title: WT.Co.Bfine.DSM17565.90#1

value: Bacteroides finegoldii DSM17565


title: E5R_021a14

description:
colon cancer mouse xenograft
SAMPLE 46


title: AD_950

description:
colon cancer
SAMPLE 42


title: WT.Co.Bfine.DSM17565.90#2


title: WT.Co.Bbrev.SK134.47#1

value: Bifidobacterium breve SK134


title: WT.Co.Badol.L2-32.80#2

value: 6 Weeks Old

value: Bifidobacterium adolescentis L2-32


title: WT.Co.Bdore.DSM17855.73#2

value: Male

value: Bacteroides dorei DSM17855


title: AD_875

description:
colon cancer
SAMPLE 38


title: WT.Co.Badol.L2-32.80#1

value: Colon


title: AD_797

description:
colon cancer
SAMPLE 37


title: MDAMB231 ZEB 6

first: William Evan

last: Johnson

address: 72 E Concord Street

department: Computational Biomedicine

institute: Boston University

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: standard Illumina protocol

source_name: ATCC Cell line

label_protocol: standard Illumina protocol

tag: sample type

value: ATCC Cell line

tag: disease state

value: Zebularine treated


title: AD_885

description:
colon cancer
SAMPLE 39


title: WT.Co.Alwof.F78.23#2

value: Acinetobacter lwoffii F78


title: WT.Co.Badol.L2-32.241#1


title: AD_658

description:
colon cancer
SAMPLE 34


title: HCC1428 ZEB 6


title: CAMA-1 ZEB 6


title: AD_459

description:
colon cancer
SAMPLE 31


title: WT.Co.Badol.L2-32.241#2


title: AD_694

description:
colon cancer
SAMPLE 35


title: AD_793

description:
colon cancer
SAMPLE 36


title: AD_476

description:
colon cancer
SAMPLE 32


title: AD_498

description:
colon cancer
SAMPLE 33


title: AD_416

description:
colon cancer
SAMPLE 30


title: WT.Co.Alwof.F78.23#1


title: MDAMB435s ZEB 6


title: WT.Co.Abaum.ATCC17978.35#1

value: Acinetobacter baumannii ATCC17978


title: SKBR3 VPA 6

value: VPA treated


title: AD_414

description:
colon cancer
SAMPLE 29


title: T47D VPA 6


title: HS578T VPA 6


title: AD_1512

description:
colon cancer
SAMPLE 24


title: AD_1516

description:
colon cancer
SAMPLE 27


title: D0 NEO 1-2

city: New Haven

first: Smita

last: Gopinath

state: CT

address: 300 Cedar St., TAC S640

department: Immunobiology

institute: Yale University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: These data were normalized using Illumina quantile normalization run by the Yale Center for Genomics Analyses.

source_name: mouse vaginal tissue

label_protocol: Illumina Protocol

growth_protocol: not applicable

extract_protocol: RNA was extracted with RLT lysis buffer as per the Qiagen RNeasy kit  protocol with on-column DNase I treatment. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: No treatment, tissues were harvested, flash frozen using dry ice and ethanol for RNA extraction.

tag: agent

value: neomycin

value: female


title: HCC38 ZEB 6


title: MDAMB453 VPA 6


title: MCF7 VPA 6


title: MDAMB231 ZEB 2


title: CAMA-1 VPA 6


title: D0 NEO 3

tag: strain


title: D0 PBS 2

value: pbs


title: AD_1515

description:
colon cancer
SAMPLE 26

value: colon cancer


title: AD_1517

description:
colon cancer
SAMPLE 28


title: AD_1514

description:
colon cancer
SAMPLE 25


title: D0 PBS 3


title: D0 NEO 1-1


title: HCC1428 ZEB 2


title: BT483 ZEB 6


title: CAMA-1 ZEB 2


title: MDAMB435s ZEB 2


title: BT483 ZEB 2


title: HCC38 ZEB 2


title: AD_1433

description:
colon cancer
SAMPLE 19


title: AD_1434

description:
colon cancer
SAMPLE 20


title: AD_1437

description:
colon cancer
SAMPLE 21


title: SKBR3 VPA 2


title: WT.Co.Badol.L2-32.241#3

value: Dissection / Trimming


title: AD_1413

description:
colon cancer
SAMPLE 17


title: AD_1412

description:
colon cancer
SAMPLE 16


title: AD_1511

description:
colon cancer
SAMPLE 23


title: AD_1414

description:
colon cancer
SAMPLE 18


title: AD_1376

description:
colon cancer
SAMPLE 14


title: AD_1384

description:
colon cancer
SAMPLE 15


title: AD_1473

description:
colon cancer
SAMPLE 22


title: CAMA-1 VPA 2


title: MDAMB453 VPA 2


title: AD_1361

description:
colon cancer
SAMPLE 13


title: AD_1339

description:
colon cancer
SAMPLE 12


title: T47D VPA 2


title: AD_1337

description:
colon cancer
SAMPLE 11


title: HS578T VPA 2


title: MDAMB435s cont

value: control


title: AD_1325

description:
colon cancer
SAMPLE 10


title: AD_1311

description:
colon cancer
SAMPLE 9


title: CAMA-1 cont


title: MDAMB231 cont


title: AD_1294

description:
colon cancer
SAMPLE 7


title: D0 PBS 1


title: AD_1261

description:
colon cancer
SAMPLE 6


title: AD_1259

description:
colon cancer
SAMPLE 5


title: SKBR3 cont


title: BT483 cont


title: HCC38 cont


title: AD_1183

description:
colon cancer
SAMPLE 4


title: HCC1428 cont


title: MCF7 VPA 2


title: AD_1178

description:
colon cancer
SAMPLE 3


title: AD_1136

description:
colon cancer
SAMPLE 2


title: MDAMB453 cont


title: T47D Cont


title: 320p2 zeb6 6 h

source_name: Mouse Xenograft

value: Mouse Xenograft


title: HS578T Cont


title: 320p2 zeb4 6 h


title: AD_1023

description:
colon cancer
SAMPLE 1


title: AD_1301

description:
colon cancer
SAMPLE 8


title: BE(2)-C HDAC11 siRNA no. 2 54h replicate 1

city: Berlin

first: Theresa

middle: Maria

last: Thole

address: Augustenburger Platz 1

department: Klinik für Pädiatrie mit Schwerpunkt Onkologie, Hämatologie und STZ

institute: Charite Universitätsmedizin Berlin

description:
SAMPLE 33
replicate 1

hyb_protocol: Standard Illumina hybridization protocol, (Whole-Genome Gene Expression Direct Hybridization Assay Guide), 750 ng of cRNA were hybridized for 17 hr at 58°C on Illumina Human HT-12-Microarray

scan_protocol: Gene Expression Microarrays were scanned using the Illumina iScan-Scanner according to Standard Illumina Scanning Protocol (Whole-Genome Gene Expression Direct Hybridization Assay Guide)

data_processing: The data were normalized using quantile normalization with R using function normalize.quantiles from Bioconductor package preprocessCore

source_name: BE(2)-C HDAC11 siRNA no. 2 54h

label_protocol: The Illumina TotalPrep RNA Amplification Kit (life technologie) is used to generate single-stranded cRNA from input amounts of 200ng total RNA Label: Biotin, Cy3-Streptavidin

growth_protocol: cells were grown at 37°C, 5%CO2 in DMEM containing 10% FCS and 1% non-essential aminoacids

extract_protocol: total RNA was extracted using the Rneasy Mini Kit (Quiagen, Hilden, Germany) Quality of cRNA was controlled using the RNA Nano Chip Assay on an Agilent 2100 Bioanalyzer and spectrophotometrically quantified (NanoDrop)

treatment_protocol: samples and negative controls were transfected with HDAC11 or negative control siRNA using the HiPerfect system (Qiagen)

tag: cell line

tag: sirna

value: siHDAC11_7 Qiagen #SI03105186

tag: time

tag: genotype/variation

value: HDAC11 depletion


title: BE(2)-C HDAC11 siRNA no. 2 54h replicate 2

description:
SAMPLE 36
replicate 2


title: BE(2)-C Neg Co. No. 1 54h replicate 2

description:
SAMPLE 34
replicate 2

source_name: BE(2)-C Neg Co. No. 1 54h

value: AllStars Qiagen #1027280


title: MCF7 Cont


title: 320p2 zeb45 6 h


title: CAMA-1 Cont


title: BE(2)-C Neg Co. No. 1 54h replicate 1

description:
SAMPLE 31
replicate 1


title: BE(2)-C HDAC11 siRNA no. 1 54h replicate 2

description:
SAMPLE 35
replicate 2

source_name: BE(2)-C HDAC11 siRNA no. 1 54h

value: siHDAC11_3 Ambion #130749


title: BE(2)-C HDAC11 siRNA no. 2 48h replicate 2

description:
SAMPLE 30
replicate 2

source_name: BE(2)-C HDAC11 siRNA no. 2 48h


title: 320p2 vpa5 6 h


title: 320p2 zeb2 2 h


title: BE(2)-C HDAC11 siRNA no. 1 48h replicate 2

description:
SAMPLE 29
replicate 2

source_name: BE(2)-C HDAC11 siRNA no. 1 48h


title: 320p2 vpa6 6 h


title: 320p2 vpa3 2 h


title: BE(2)-C HDAC11 siRNA no. 2 48h replicate 1

description:
SAMPLE 27
replicate 1


title: 320p2 zeb1 2 h


title: BE(2)-C Neg Co. No. 1 48h replicate 2

description:
SAMPLE 28
replicate 2

source_name: BE(2)-C Neg Co. No. 1 48h


title: BE(2)-C Neg Co. No. 1 48h replicate 1

description:
SAMPLE 25
replicate 1


title: 320p2 ck6 6 h


title: BE(2)-C HDAC11 siRNA no. 1 42h replicate 2

description:
SAMPLE 23
replicate 2

source_name: BE(2)-C HDAC11 siRNA no. 1 42h


title: BE(2)-C HDAC11 siRNA no. 1 54h replicate 1

description:
SAMPLE 32
replicate 1


title: BE(2)-C HDAC11 siRNA no. 1 48h replicate 1

description:
SAMPLE 26
replicate 1


title: 320p2 vpa2 2 h


title: BE(2)-C HDAC11 siRNA no. 2 42h replicate 2

description:
SAMPLE 24
replicate 2

source_name: BE(2)-C HDAC11 siRNA no. 2 42h


title: 320p2 vpa1 2 h


title: 320p2 ck5 6 h


title: 320p2 ck4 6 h


title: BE(2)-C HDAC11 siRNA no. 2 42h replicate 1

description:
SAMPLE 21
replicate 1


title: 320p2 vpa4 6 h


title: 320p2 ck2 2 h


title: 320p2 ck3 2 h


title: 110p5 zeb6 6 h


title: BE(2)-C HDAC11 siRNA no. 1 42h replicate 1

description:
SAMPLE 20
replicate 1


title: 320p2 zeb3 2 h


title: 320p2 ck1 2 h


title: BE(2)-C Neg Co. No. 1 42h replicate 2

description:
SAMPLE 22
replicate 2

source_name: BE(2)-C Neg Co. No. 1 42h


title: IMR-32 HDAC11 siRNA no. 2 54h replicate 2

description:
SAMPLE 18
replicate 2

source_name: IMR-32 HDAC11 siRNA no. 2 54h


title: BE(2)-C Neg Co. No. 1 42h replicate 1

description:
SAMPLE 19
replicate 1


title: IMR-32 HDAC11 siRNA no. 1 54h replicate 2

description:
SAMPLE 17
replicate 2

source_name: IMR-32 HDAC11 siRNA no. 1 54h


title: 110p5 zeb4 6 h


title: 110p5 zeb2 2 h


title: IMR-32 HDAC11 siRNA no. 2 54h replicate 1

description:
SAMPLE 15
replicate 1


title: 110p5 zeb5 6 h


title: IMR-32 HDAC11 siRNA no. 2 48h replicate 2

description:
SAMPLE 12
replicate 2

source_name: IMR-32 HDAC11 siRNA no. 2 48h


title: IMR-32 HDAC11 siRNA no. 1 54h replicate 1

description:
SAMPLE 14
replicate 1


title: IMR-32 Neg Co. No. 1 54h replicate 2

description:
SAMPLE 16
replicate 2

source_name: IMR-32 Neg Co. No. 1 54h


title: 110p5 vpa6 6 h


title: IMR-32 Neg Co. No. 1 54h replicate 1

description:
SAMPLE 13
replicate 1


title: 110p5 zeb3 2 h


title: 110p5 zeb1 2 h


title: 110p5 vpa5 6 h


title: IMR-32 HDAC11 siRNA no. 2 48h replicate 1

description:
SAMPLE 9
replicate 1


title: 110p5 ck6 6 h


title: IMR-32 Neg Co. No. 1 48h replicate 2

description:
SAMPLE 10
replicate 2

source_name: IMR-32 Neg Co. No. 1 48h


title: IMR-32 Neg Co. No. 1 42h replicate 1

description:
SAMPLE 1
replicate 1

source_name: IMR-32 Neg Co. No. 1 42h


title: 110p5 vpa1 2 h


title: IMR-32 HDAC11 siRNA no. 1 42h replicate 1

description:
SAMPLE 2
replicate 1

source_name: IMR-32 HDAC11 siRNA no. 1 42h


title: 110p5 vpa4 6 h

source_name: Mouse Xenograft


title: keratinocytes_pre-miR-Ctrl_rep2

status: Public on Feb 15 2017

city: Stockholm

first: Ning

last: Xu

address: CMM L8:02

country: Sweden

institute: Karolinska Institutet

hyb_protocol: The samples were hybridized to a Human Gene 2.1 ST Array Plate according to standard Affymetrix GeneTitan protocol.

scan_protocol: The array plate was scanned using the Affymetrix GeneTitan Scanner.

data_processing: Generated CEL files were analyzed using Affymetrix Expression Console v. 1.4 and the RMA method

source_name: keratinocytes with control/scrambled oligos sequence

label_protocol: Total RNA was labeled using the Whole Transcript (WT) Sense Target Labeling Assay according to the manufacturer’s (Affymetrix) instructions.

growth_protocol: Human adult epidermal keratinocytes were purchased from Cascade Biologics and cultured in EpiLife® serum-free keratinocyte growth medium including Human Keratinocyte Growth Supplement at a final Ca2+ concentration of 0.06mM (Cascade Biologics) at 37°C in 5% CO2.

extract_protocol: 24 hours after transfection, the total RNA was extracted with miRNeasy Mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: The third passage keratinocytes at 30-50% confluence were transfected with 20nM miR-19a, miR-19b, miR-20a mimics or control oligos (Ambion) using Lipofectamine 2000 (Invitrogen).

value: skin

tag: cell type

value: adult epidermal keratinocytes

tag: transfected with

value: pre-miR-Ctrl


title: 110p5 vpa3 2 h


title: IMR-32 HDAC11 siRNA no. 1 42h replicate 2

description:
SAMPLE 5
replicate 2


title: IMR-32 Neg Co. No. 1 48h replicate 1

description:
SAMPLE 7
replicate 1


title: IMR-32 HDAC11 siRNA no. 2 42h replicate 2

description:
SAMPLE 6
replicate 2

source_name: IMR-32 HDAC11 siRNA no. 2 42h


title: keratinocytes_pre-miR-Ctrl_rep3


title: keratinocytes_pre-miR-Ctrl_rep1


title: IMR-32 HDAC11 siRNA no. 2 42h replicate 1

description:
SAMPLE 3
replicate 1


title: keratinocytes_pre-miR-20a_rep3

source_name: keratinocytes with miR-20a overexpression


title: 110p5 vpa2 2 h


title: 110p5 ck-1 2 h


title: keratinocytes_pre-miR-20a_rep1


title: 110p5 ck-2 2 h


title: keratinocytes_pre-miR-20a_rep2


title: 110p5 ck4 6 h


title: keratinocytes_pre-miR-19b_rep1

source_name: keratinocytes with miR-19b overexpression


title: IMR-32 HDAC11 siRNA no. 1 48h replicate 2

description:
SAMPLE 11
replicate 2

source_name: IMR-32 HDAC11 siRNA no. 1 48h


title: 110p5 ck 2 h


title: keratinocytes_pre-miR-19a_rep3

source_name: keratinocytes with miR-19a overexpression


title: Post11271055

city: Cambridge

first: Karl

middle: George

last: Wassmann

address: 245 First Street Suite 1800-109

institute: CheckPoint Sciences Inc.

description: Phase IIb biomarker study, Advanced Melanoma, 15 mg/kg dose, previous chemotherapy

data_processing:
The normalized data is reported in delta CT units. 18S rRNA is the sole endogenous control gene. With each heating/cooling cycle, the real time PCR assay detects fluorescent signal accumulation. The Ct (cycle threshold) is the number of cycles required for the fluorescent signal to exceed background level. Thermal cycling goes through 40 cycles, and 18S rRNA is measured at the 14th cycle. Delta Ct is measured up to 26 cycles from the point endogenous control is recognized. Raw CT data is automatically processed to delta CT data by a software program subtracting the 18S CT value from the raw data CT value for each triplicate well. Triplicate test results are used to identify and eliminate data points that are statistical “outliers”; such data points are those that differ by a percentage greater than 3% of the average of all three values. If more than one data point in a set of three is excluded by this procedure, then all data for the relevant constituent is discarded.
Normalized signal (against 18S housekeeping gene). All normalized data was reported and analyzed as delta CT units and fold change was not calculated.

source_name: Whole Blood, 30 days Post tremelimumab treatment

label_protocol: First-strand complementary DNA was synthesized from random hexamer-primed RNA templates using TaqMan® reverse-transcription reagents. Synthesis of first strand cDNA for use in PCR amplification used Applied Biosystems TAQMAN Reverse Transcription Reagents Kit (P/N 808-0234). Individual target-gene amplification was multiplexed with the 18S rRNA endogenous control and run in triplicate in 384-well format on the 7900HT fast real-time PCR system.  PCR procedures followed ABI Prism® 7900 Sequence Detection System instructions. Applied Biosystems (Foster City, Calif.)

extract_protocol: Total RNA was stabilized in PAXgene tubes and was extracted using vendor PreAnalytics PAXgene™ Blood RNA System to process the RNA to meet quality and integrity standards (RNA integrity number ≥6.3) per the Bioanalyzer 2100 in combination with the RNA 6000 Nano or Pico Series II LabChip

treatment_protocol: Post-treatment blood samples taken 30-days after immunotherapy treatment with 15 mg/kg dose of tremelimumab

value: Venous blood from arm

tag: gender

value: MALE

tag: cancer stage

value: IV M1C

tag: worst diarrhea grade

tag: immunotherapy response (responder=1 nonresponder=0)

tag: survival status 12 months (1=alive 0=dead)


title: keratinocytes_pre-miR-19a_rep2


title: Post11271054

value: FEMALE

tag: age

value: IV M1A


title: Post11141002

tag: tissue

value: IV M1B


title: Post11191002


title: Post11191006


title: Post10921007


title: Post11171001


title: Post11181004


title: Post11271051


title: Post11191005


title: Post10921004


title: CD138_relapse

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: Gene expression profiling data of CD138+ cells from MM patient 1 purified from bone marrow aspirate at relapse

hyb_protocol: Following fragmentation, 15 micrograms of cRNA were hybridized for 16 hr  at 45°C on GeneChip HG-U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: HG-U133 2.0 Plus arrays were scanned using the Scanner G3000 7G (Affymetrix).

data_processing: The probe-level signals were converted to expression values using the Bioconductor function for Robust Multi-array Analysis (RMA), in which perfect match intensities are background adjusted, normalized by means of quantile-quantile normalization and log2-transformed. Custom GeneAnnot-based Chip Annotation Files (Version 2.2.0) were used for annotation procedure ( Ferrari F. et al., BMC Bioinformatics. 2007).

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms of total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: CD138+ cells from bone marrow of MM patient at diagnosis and relapse. The CD138+ cell fraction was obtained by immunomagnetic cells sorting using anti-CD138 monoclonal antibody-coated microbeads (MACS, Miltenyi Biotec., Bergish-Gladbach, Germany). Samples with a purity of more than 93%, tested via flow-cytometry (BD biosciences, San Josè, CA) were analyzed. These samples were evaluated immediately after purification.

extract_protocol: Total RNA was extracted from CD138+ cells with Rneasy Mini Kit (Qiagen, Valencia, CA)

treatment_protocol: No treatment was applied to CD18+ cells.

tag: individual

value: MM patient 1

value: bone marrow

value: plasma cells

value: male

value: 54 years

value: at relapse


title: IMR-32 Neg Co. No. 1 42h replicate 2

description:
SAMPLE 4
replicate 2

value: AllStars Qiagen #1027280

value: control


title: Post10921003

value: IIIC


title: Post10921006


title: Post10871001


title: Post10861007


title: Post10861008


title: CD138_diagnosis

description: Gene expression profiling data of CD138+ cells from MM patient 1 purified from bone marrow aspirate at diagnosis

value: at diagnosis


title: Post10861006


title: keratinocytes_pre-miR-19b_rep3

value: skin

value: adult epidermal keratinocytes


title: Post10861001

value: Venous blood from arm


title: Post10861003

value: MALE

value: IV M1C


title: Post10851002

value: FEMALE

value: IV M1A


title: Post10921005


title: Post10851001


title: Post10841012


title: Post10841013


title: Post10791005

value: IV M1B


title: Post10771001


title: Post10841008


title: Post10791002


title: 110p5 ck5 6 h

tag: sample type

value: Mouse Xenograft

tag: disease state


title: Post10761010


title: Post10761007


title: Post10761008


title: Post10761009


title: Post10761005


title: Post10761006


title: Post10761001


title: Post10761002


title: Post10741007


title: Post10741008


title: Post10741002


title: Post10741004


title: Post10741001


title: Post10841011


title: Post10721009


title: Post10721006


title: keratinocytes_pre-miR-19a_rep1


title: Post10721007


title: Post10721004


title: IMR-32 HDAC11 siRNA no. 1 48h replicate 1

description:
SAMPLE 8
replicate 1

value: siHDAC11_3 Ambion #130749

value: HDAC11 depletion


title: Post10721003


title: Post10711001


title: Post10701011


title: Post10751001


title: keratinocytes_pre-miR-19b_rep2


title: Post10701004


title: Post10701008


title: Post10701009


title: Post10601005


title: Post10701002


title: Post10601003


title: Post10681003


title: Post10681004


title: Post10621001


title: Post10601008


title: Post10701001


title: Post10681005


title: Post10601006


title: Post10691004


title: Post10591001


title: Post10681001


title: Post10581004


title: Post10581003


title: Post10701005


title: Post10581001


title: Post10571006


title: Post10571005


title: Post10581002


title: Post10571001


title: Post10571003


title: Post10541002


title: Post10541001


title: Post10531016


title: Post10531018


title: Post10601004


title: Post10531011


title: Post10501001


title: Post10521008


title: Post10521002


title: Post10531009


title: Post10521001


title: Post10531007


title: Post10531015


title: Post10531010


title: Post10501004


title: Post10521005


title: Post10521009


title: Post10521004


title: Post10491008


title: Post10501003


title: Post10491007


title: Post10531001


title: Post10491010


title: Post10491006


title: Post10491005


title: Post10491004


title: Post10491003


title: Post10421002


title: Post10421003


title: Post10531012


title: Post10361009


title: Post10531014


title: Post10401003


title: Post10361008


title: Post10341005


title: Post10471002


title: Post10361006


title: Post10321006


title: Post10321004


title: Post10361007


title: Post10361002


title: Post10271017


title: Post10321005


title: Post10271013


title: Post10361005


title: Post10341003


title: Post10311001


title: Post10321003


title: Post10341004


title: Post10341006


title: Post10271008


title: Post10271012


title: Post10271007


title: Post10241003


title: Post10271006


title: Post10271005


title: Post10361001


title: Post10271014


title: Post10241004


title: Post10271015


title: Post10271004


title: Post10241001


title: Post10241006


title: Post10301005


title: Post10221001


title: Post10091003


title: Post10211002


title: Post10101003


title: Post10101001


title: Post10181003


title: Post10091004


title: Pre11271054

description: Phase IIb biomarker study, Advanced Melanoma, previous chemotherapy

source_name: Whole Blood, Pretreatment


title: Post10011001


title: Pre11181004


title: Post10031003


title: Pre11171001


title: Post10011002


title: Pre11271051


title: Pre11191002


title: Pre10921007


title: Pre10921005


title: Pre10861007


title: Pre10861006


title: Pre10921004


title: Pre10921003


title: Pre10921001


title: Pre10861008


title: Pre10861003


title: Pre11271055


title: Pre11191006


title: Post10091002


title: Pre11191005


title: Pre10861001


title: Pre11141002


title: Pre10851001


title: Pre10851002


title: Pre10841012


title: Pre10771001


title: Pre10761008


title: Pre10761007


title: Pre10791002


title: Pre10791005


title: Pre10841011


title: Pre10761009


title: Pre10921006


title: Pre10761006


title: Pre10841013


title: Pre10761005


title: Pre10841008


title: Pre10761002


title: Pre10701008


title: Pre10741007


title: Pre10701009


title: Pre10721007


title: Pre10721006


title: Pre10721004


title: Pre10741001


title: Pre10741008


title: Pre10741002


title: Pre10761001


title: Pre10721009


title: Pre10701011


title: Pre10751001


title: Pre10741004


title: Pre10711001


title: Pre10721003


title: Pre10761010


title: Pre10701002


title: Pre10701005


title: Pre10681005


title: Pre10701004


title: Pre10691004


title: Pre10681003


title: Pre10701001


title: Pre10621001


title: Pre10601008


title: Pre10601006


title: Pre10601005


title: Pre10601004


title: Pre10581002


title: Pre10681004


title: Pre10541002


title: Pre10571003


title: Pre10571005


title: Pre10541001


title: Pre10571006


title: Pre10581003


title: Pre10531016


title: Pre10681001


title: Pre10571001


title: Pre10581001


title: Pre10601003


title: Pre10531015


title: Pre10581004


title: Pre10531018


title: Pre10531014


title: Pre10531011


title: Pre10531010


title: Pre10521009


title: Pre10521008


title: Pre10521004


title: Pre10531007


title: Pre10531001


title: Pre10531009


title: Pre10601001


title: Pre10531012


title: Pre10521002


title: Pre10521001


title: Pre10491010


title: Pre10501004


title: Pre10491006


title: Pre10501001


title: Pre10521005


title: Pre10491007


title: Pre10361009


title: Pre10361008


title: Pre10491004


title: Pre10491003


title: Pre10421003


title: Pre10491008


title: Pre10361006


title: Pre10501003


title: Pre10491002


title: Pre10361001


title: Pre10361005


title: Pre10341005


title: Pre10491005


title: Pre10361007


title: Pre10421002


title: Pre10341006


title: Pre10341004


title: Pre10341003


title: Pre10401003


title: Pre10321004


title: Pre10321005


title: Pre10321003


title: Pre10311001


title: Pre10321006


title: Pre10271017


title: Pre10271015


title: Pre10271013


title: Pre10361002


title: Pre10301005


title: Pre10271014


title: Pre10271012


title: Pre10271008


title: Pre10271004


title: Pre10271006


title: Pre10271007


title: Pre10271005


title: Pre10241006


title: Pre10241004


title: Pre10241001


title: Pre10241003


title: Pre10221001


title: Pre10181003


title: Pre10211002


title: Pre10101001


title: Pre10101003


title: Pre10091003


title: Pre10091004


title: Pre10091002


title: Pre10031003


title: Pre10011002


title: Pre10011001

description: Phase IIb biomarker study, Advanced Melanoma,  previous chemotherapy


title: Post 12251004

description: Phase III biomarker study, Advanced Melanoma, chemotherapy naïve


title: Post 12211018


title: Post 12241002


title: Post 12211023


title: Post 12211011


title: Post 12211013


title: Post 12211003


title: Post 12211006


title: Post 12211007


title: Post 12211017


title: Post 12201002


title: Post 12171001


title: Post 12201004


title: Post 12091017


title: Post 12171004


title: Post 12091006


title: Post 12091015


title: Post 12091004


title: Post 12261002


title: Post 12041001


title: Post 12051001


title: Post 12031003


title: Post 12021005


title: Post 12021010


title: Post 12021002


title: Post 12011001


title: Post 12001004


title: Post 11991004


title: Post 11981001


title: Post 11981004


title: Post 12011005


title: Post 11961003


title: Post 11951002


title: Post 12091019


title: Post 11941015


title: Post 11951005


title: Post 11951004


title: Post 11941019


title: Post 11941021


title: Post 11921015


title: Post 11941003


title: Post 11931005


title: Post 11921011


title: Post 11921010


title: Post 11951003


title: Post 11921008


title: Post 11891003


title: Post 11941012


title: Post 11761005


title: Post 11721006


title: Post 11731002


title: Post 11721005


title: Post 11721002


title: Post 11571001


title: Post 11721001


title: Post 11721003


title: Post 11891002


title: Post 11921007


title: Post 11481003


title: Post 11481002


title: Post 11481004


title: Post 11541003


title: Post 11471009


title: Post 11471005


title: Post 11481001


title: Post 11471003


title: Post 11451007


title: Post 11451004


title: Post 11441002


title: Post 11441004


title: Post 11431001


title: Post 11421009


title: Post 11421011


title: Post 11421008


title: Post 11421010


title: Post 11401012


title: Post 11411006


title: Post 11401011


title: Post 11421001


title: Post 11471007


title: Post 11401009


title: Post 11381005


title: Post 11401001


title: Post 11341001


title: Post 11401008


title: Post 11331001


title: Post 11321004


title: Post 11291002


title: Post 11311002


title: Post 11271011


title: Post 11231006


title: Post 11201002


title: Post 11231001


title: Post 11201001


title: Post 11231005


title: Post 11191006


title: Post 11151023


title: Post 11191002


title: Post 11161001


title: Post 11181004


title: Post 11321005


title: Post 11151020


title: Post 11151022


title: Post 11211003


title: Post 11151016


title: Post 11151008


title: Post 11151013


title: Post 11151017


title: Post 11271016


title: Post 11151007


title: Post 11151005


title: Post 11091007


title: Post 11071014


title: Post 11151006


title: Post 11071011


title: Post 11071002


title: Post 11011009


title: Post 11011002


title: Post 10991002


title: Post 10961001


title: Post 10961002


title: Post 10941003


title: Post 10941001


title: Post 10941005


title: Post 10931006


title: Post 10921018


title: Post 10921021


title: Post 10931003


title: Post 10921015


title: Post 10921013


title: Post 10921005


title: Post 10841007


title: Post 10841009


title: Post 10921002


title: Post 10881001


title: Post 10921012


title: Post 10841003


title: Post 10811010


title: Post 10811015


title: Post 10811016


title: Post 10991001


title: Post 10791011


title: Post 10811003


title: Post 10921017


title: Post 10801003


title: Post 10811004


title: Post 10791010


title: Post 10791006


title: Post 10791008


title: Post 10791003


title: Post 10811008


title: Post 10811005


title: Post 10761005


title: Post 10761002


title: Post 10761008


title: Post 10741018


title: Post 10701018


title: Post 10741017


title: Post 10751002


title: Post 10751003


title: Post 10701011


title: Post 10701008


title: Post 10701005


title: Post 10701003


title: Post 10681011


title: Post 10681008


title: Post 10681005


title: Post 10681003


title: Post 10681002


title: Post 10601001


title: Post 10661003


title: Post 10791001


title: Post 10561004


title: Post 10561003


title: Post 10781001


title: Post 10561002


title: Post 10781006


title: Post 10501004


title: Post 10471001


title: Post 10291001


title: Post 10271001


title: Post 10211005


title: Post 10161015


title: Post 10081012


title: Post 10081001


title: Post 10081006


title: Post 10081004


title: Post 10041011


title: Post 10041012


title: Post 10041003


title: Post 10041001


title: Post 10041002


title: Post 10021016


title: Post 10361001


title: Post 10021013


title: Post 10021007


title: Post 10021009


title: Post 10021006


title: Post 10021010


title: Post 10161011


title: Post 10161005


title: Post 10081014


title: Post 10211003


title: Post 10021001


title: Post 10021004


title: Post 10011001


title: Post 10021003


title: Pre 12261002


title: Post 10161014


title: Post 10081002


title: Pre 12251004


title: Post 10021015


title: Pre 12211013


title: Pre 12211023


title: Pre 12211017


title: Pre 12241002


title: Pre 12211018


title: Pre 12211011


title: Pre 12171004


title: Pre 12171001


title: Pre 12201002


title: Pre 12201004


title: Pre 12211006


title: Pre 12211007


title: Pre 12091019


title: Pre 12211003


title: Pre 12091006


title: Pre 12091004


title: Pre 12091015


title: Pre 11991004


title: Pre 12021002


title: Pre 12021005


title: Pre 12041001


title: Pre 12011001


title: Pre 12051001


title: Pre 12021010


title: Pre 12001004


title: Pre 12031003


title: Pre 12011005


title: Pre 12091017


title: Pre 11961003


title: Pre 11951005


title: Pre 11981001


title: Pre 11951003


title: Pre 11951002


title: Pre 11941019


title: Pre 11921008


title: Pre 11921011


title: Pre 11941003


title: Pre 11921015


title: Pre 11921007


title: Pre 11931005


title: Pre 11941012


title: Pre 11981004


title: Pre 11941015


title: Pre 11951004


title: Pre 11731002


title: Pre 11761005


title: Pre 11891002


title: Pre 11941021


title: Pre 11571001


title: Pre 11721003


title: Pre 11481004


title: Pre 11721006


title: Pre 11721005


title: Pre 11541003


title: Pre 11721001


title: Pre 11921010


title: Pre 11481003


title: Pre 11891003


title: Pre 11481002


title: Pre 11721002


title: Pre 11481001


title: Pre 11451007


title: Pre 11471003


title: Pre 11471007


title: Pre 11471009


title: Pre 11471005


title: Pre 11451004


title: Pre 11441002


title: Pre 11441001


title: Pre 11421010


title: Pre 11421011


title: Pre 11411006


title: Pre 11421008


title: Pre 11421009


title: Pre 11401012


title: Pre 11421001


title: Pre 11401011


title: Pre 11321004


title: Pre 11401009


title: Pre 11331001


title: Pre 11311002


title: Pre 11291002


title: Pre 11381005


title: Pre 11321005


title: Pre 11401008


title: Pre 11371001


title: Pre 11401001


title: Pre 11271016


title: Pre 11441004


title: Pre 11271011


title: Pre 11231006


title: Pre 11231005


title: Pre 11231001


title: Pre 11211003


title: Pre 11151013


title: Pre 11161001


title: Pre 11151020


title: Pre 11151016


title: Pre 11151023


title: Pre 11151017


title: Pre 11151022


title: Pre 11181004


title: Pre 11191002


title: Pre 11151007


title: Pre 11201001


title: Pre 11191006


title: Pre 11151008


title: Pre 11201002


title: Pre 11071002


title: Pre 10961002


title: Pre 11071011


title: Pre 10941003


title: Pre 10961001


title: Pre 11151006


title: Pre 10931006


title: Pre 11071014


title: Pre 11011009


title: Pre 10941001


title: Pre 10941005


title: Pre 10991002


title: Pre 11151005


title: Pre 10991001


title: Pre 11011002


title: Pre 11091007


title: Pre 10921021


title: Pre 10931003


title: Pre 10921013


title: Pre 10921018


title: Pre 10921012


title: Pre 10921005


title: Pre 10921017


title: Pre 10841003


title: Pre 10841007


title: Pre 10841009


title: Pre 10921015


title: Pre 10921002


title: Pre 10811016


title: Pre 10811005


title: Pre 10811015


title: Pre 10811008


title: Pre 10811004


title: Pre 10921001


title: Pre 10811010


title: Pre 10811003


title: Pre 10801003


title: Pre 10791011


title: HSC_Chrm1KO_1

first: Halley

middle: C

last: Pierce

state: NY

address: 1301 Morris Park Ave.

department: Ruth L. and David S. Gottesman Stem Cell Institutue

institute: Albert Einstein College of Medicine

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Analysis was performed by first processing the chip through Transcriptome analysis center (TAC) software (Affymetrix) to determine fold changes and p-values which were then analyzed by gene set enrichment analysis (GSEA).

source_name: steady state bone marrow HSC (LSKF) Chrm1-/-

label_protocol: Affymetrix protocol

extract_protocol: Qiagen Rneasy plus microkit RNA extraction from FACS sorted HSCs

treatment_protocol: steady state bone marrow sorted HSCs

tag: strain

value: bone marrow HSC


title: THP-1 macrophages incubated with LPL hydrolysis products_replicate 1

city: St. John's

first: Sherri

middle: L

last: Christian

state: Newfoundland

address: 232 Elizabeth Ave

department: Biochemistry

country: Canada

institute: Memorial University of Newfoundland

description: LPL hydrolysis_1

hyb_protocol: After terminal labeling with biotin, cRNA were hybridized for 16-18 hours at 45°C on Affymetrix GeneChips by TCAG.

scan_protocol: GeneChips were scanned at TCAG using an Affymetrix GeneChip Scanner 3000.

data_processing: Microarray data analysis was performed using the Oligo package (v1.32.0) from Bioconductor using R (v3.2.0). The data were normalized using the RMA.

source_name: THP-1 monocyte-derived macrophages_LPL hydrolysis products

label_protocol: Biotinylated cRNA were prepared at The Centre for Applied Genomics (TCAG; Toronto, Ontario, Canada) from 250 ng of total RNA using the Affymetrix WT PLUS Reagent Kit, according to manufacturer's instructions.

growth_protocol: THP-1 monocytes were cultured in RPMI media supplemented with 10% fetal bovine serum and 1% Antibiotic/Antimycotic (Hyclone). Cells were incubated at 37°C with 5% CO2.

extract_protocol: Total RNA was isolated from cells using TRIzol; genomic DNA contamination was removed using the TURBO DNA-free kit (Ambion). The DNase-treated RNA samples were further purified using a Qiagen spin column.

treatment_protocol: THP-1 monocytes were differentiated into macrophages using 100 nM PMA for 72 hours. The differentiated macrophages were incubated for 18 hours with total lipoproteins that were treated with heparinized media from control HEK-293T cells or HEK-293T cells that expressed human LPL.

value: THP-1 monocyte-derived macrophages

tag: incubated with

value: LPL hydrolysis products for 18hrs


title: Pre 10791010


title: Pre 10791008


title: Pre 10791006


title: THP-1 macrophages incubated with LPL hydrolysis products_replicate 3

description: LPL hydrolysis_3


title: Pre 10791003


title: THP-1 macrophages incubated with LPL hydrolysis products_replicate 2

description: LPL hydrolysis_2


title: Pre 10791001


title: THP-1 macrophages incubated with non-hydrolysis products_replicate 1

description: Non-hydrolysis _1

source_name: THP-1 monocyte-derived macrophages_non-hydrolysis products

value: non-hydrolysis products for 18hrs


title: HSC_Chrm1KO_2

city: Bronx


title: THP-1 macrophages incubated with non-hydrolysis products_replicate 3