title: Mo-DC H4Ac LPS 1 hour rep 2.2

city: Lausanne

first: Mark

last: Ibberson

address: Genopode building

department: Vital-IT

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

description: comparison of DCi/ DCm H4ac after 1 hour LPS treatment

hyb_protocol: manufacturer's protocol

scan_protocol: manufacturer's protocol

data_processing:
manufacturer's data processing
normalized log2 ratios (Cy5/Cy3)

source_name: H4Ac ChIP DNA from immature DC

label_protocol: manufacturer's protocol

growth_protocol: monocytes were cultured in RPMI 10% FCS supplemented with 2-mercaptoethanol (50 μM), GM-CSF (600 U/ml), and IL-4 (750 U/ml)

extract_protocol: cells were fixed with 1% formaldehyde during 8 minutes followed by quenching with 0.18 M glycine.To isolate chromatin, the cell pellet was resuspended in 20 ml of TE supplemented with 0.5% NP-40, 1mM PMSF, 5mM benzamidine, 1ug/ml leupeptin, and 5ug/ml aprotinin, centrifuged as above, resuspended in 20 ml of TE supplemented with 1% Triton X-100, 0.5% Na-DOC, 0.5M NaCl, 1mM PMSF, 5mM benzamidine, 1ug/ml leupeptin, and 5ug/ml aprotinin. To break up the chromatin into ~300 to ~600bp fragments, the pellet was resuspended in 1.5ml of TEN (TE with 0.1M NaCl) and sonicated on ice. For one immunoprecipitation reaction, 10 ug of chromatin was diluted into 300ul of dilution/incubation buffer (20mM HEPES pH 7.9, 0.2M NaCl, 2mM EDTA, 0.1% Na-DOC, 0.1% SDS,1mg/ml BSA, Complete™ cocktail of protease inhibitors) and pre-cleared by the addition of 12ul of a 50:50 slurry of protein A Sepharose CL-4B beads (pre-washed in dilution/incubation buffer) and a 30 minute incubation with tumbling at room temperature. The supernatant was cleared by centrifugation and brought up to 1ml with dilution/incubation buffer. Antibodies were added and the reaction was incubated overnight with slow tumbling at 4 degress. The next day, the reactions were cleared by a 10 minute centrifugation at 10krpm at room temperature, 12 ul of a 50:50 slurry of protein A Sepharose CL-4B beads (pre-washed as before) was added and the reaction was incubated for 1h at room temperature with tumbling. The immunoprecipitates were washed twice in 20mM HEPES 7.9, 0.2M NaCl, 2mM EDTA, 0.1% Na-DOC, 0.1% SDS, twice in 20mM HEPES 7.9, 0.5M NaCl, 2mM EDTA, 0.1% Na-DOC, 0.1% SDS, twice in 20mM Tris-HCl 8.0, 0.25M LiCl, 2mM EDTA, 0.5% Na-DOC, 0.5% NP-40 and once in TE-0.1% NP-40. To reverse cross-links, 500ul of elution buffer (110mM Tris 8.0, 1.1% SDS) was added to the reaction and to a 10ug aliquot of non-immunoprecipitated chromatin (input). The sample was incubated for 10 minutes at 65 degress, 14ul of proteinase K (10mg/ml) and 11ul of 5M NaCl were added, the sample was cleared by centrifugation and then incubated at 42 degress for 2h and at 65 degress overnight. To extract DNA, one phenol-chloroform and one chloroform extraction were done. DNA was then precipitated by 20ug glycogen, 66ul NaAc (3M, pH 5.2) and 900 ul of isopropanol and resuspended in 100 ul of TE.

treatment_protocol: Untreated Monocyte-derived dendritic cells

value: Monocyte-derived denditric cells

tag: chip antibody

source_name: H4Ac ChIP DNA from 1h LPS DC

treatment_protocol: 1 hour LPS treated Monocyte-derived dendritic cells


title: IOR/OS14 transfected with backbone vector, clone 1

status: Public on Dec 31 2014

type: RNA

city: Oslo

first: Leonardo

middle: A.

last: Meza-Zepeda

address: Ullernchausseen 70

department: Department of Tumor Biology

country: Norway

institute: Oslo University Hospital

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was quantile normalisation in GenomeStudio

label: Biotin

molecule: total RNA

organism: Homo sapiens

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

growth_protocol: The cells were grown in DMEM (Lonza) supplemented with 10 % FBS (Fisher Scientific, Waltham, MA, USA), GlutaMAX (Invitrogen, CA, USA) and Geneticin (Invitrogen) , at 37 °C in a humidified atmosphere with 5 % CO2.

extract_protocol: RNA was isolated using miRNeasy mini kit (Qiagen), according to the manufacturers’ instructions.

tag: cell line

tag: gender

value: Male


title: Fish oil emulsion rep 2

city: Perth

first: Sam

last: Buckberry

state: WA

address: 35 Stirling Highway, Crawley

country: Australia

institute: The University of Western Australia

description:
Fish oil emulsion rep 2
D2

hyb_protocol: Illumina Whole-Genome Gene Expression Direct Hybridization Assay.

scan_protocol: Illumina iScan Scanner.

data_processing: Data pre-processed and quantile normalized using the beadarray package in R.

source_name: HTR8/SVneo cells

label_protocol: Illumina TotalPrep RNA Amplification Kit.

growth_protocol: 200,000 HTR8/SVneo cells per well were seeded in SRM in a 6-well plate and incubated for 24 hours at 37ºC in 20% oxygen and 5% CO2.

extract_protocol: Standard Trizol extraction.

treatment_protocol: After 24 hours, 2ml of either SRM (N), SRM containing 50μM Soy Oil emulsion (S), or SRM containing 50μM Fish Oil emulsion (D) were added to each well.

tag: treatment

value: Fish oil emulsion

tag: rep


title: GRANTA-519: GA101+Rituximab_rep3

city: Penzberg

first: Helmut

last: Burtscher

address: Nonnenwald 2

country: Germany

institute: Roche Pharma

description: gene expression data

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on Human Genome U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and scaling mean as normalization method.

label: biotin

source_name: GRANTA-519: GA101+Rituximab

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip 3' IVT Express Kit, 2008, Affymetrix).

growth_protocol: Mantle cell lymphoma cell lines were cultured at 37°C (5% CO2 in RPMI1640, 2mM L-glutamine and 20% fetal bovine serum).

extract_protocol: Total RNA was isolated using an RNeasy Mini Kit (Qiagen, Hilden, Germany)

treatment_protocol: MCL cells were treated with either obinutuzumab or rituximab or a combination of both at concentrations of 10 µg/ml each.

tag: tissue

value: mantle cell lymphoma


title: sample955

city: Homburg

first: Andreas

last: Keller

address: Building 60

institute: Saarland University

hyb_protocol: according to manufacturers instruction (febit biomed)

scan_protocol: Wizard software on standard Microsoft Windows Workstation PC

data_processing: Summarizing of technical replica by median and quantile normalization. Following BG correction, negative values were corrected to 1. R Version 3.0.2

source_name: RNA from blood

label_protocol: MPEA, microfluidic primer extension assay Biotin labeling

extract_protocol: Blood of controls and patients was extracted in PAXgene Blood RNA tubes (BD, Franklin Lakes, New Jersey USA). The content of blood sampling tubes of each patient and healthy donor was used for RNAe extraction. The total RNA including the miRNA was isolated using the miRNeasy kit (Qiagen GmbH, Hilden) according to manufacturers instructions..

treatment_protocol: stored at -20 degree

tag: disease

value: others


title: IOR/OS14 transfected with backbone vector, clone 2


title: Mo-DC H4Ac LPS 1 hour rep 3.2

type: genomic

molecule: genomic DNA

tag: cell type


title: GRANTA-519: Isotype-control_rep1

description: gene expression data

source_name: GRANTA-519: Isotype-control


title: Mo-DC H4Ac LPS 1 hour rep 3.1


title: Mo-DC H4Ac LPS 1 hour rep 2.1


title: Soy oil emulsion rep 4

description:
Soy oil emulsion rep 4
S4

value: Soy oil emulsion


title: Fish oil emulsion rep 1

description:
Fish oil emulsion rep 1
D1


title: Soy oil emulsion rep 3

description:
Soy oil emulsion rep 3
S3


title: GRANTA-519: GA101+Rituximab_rep2

description: gene expression data


title: Mo-DC H4Ac LPS 1 hour rep 1.2


title: Mo-DC H4Ac LPS 1 hour rep 1.1


title: sample953


title: GRANTA-519: Isotype-control_rep2

description: gene expression data


title: sample951

value: psoriasis


title: sample952


title: sample954


title: Soy oil emulsion rep 2

description:
Soy oil emulsion rep 2
S2


title: sample949

value: lung cancer


title: sample950


title: GRANTA-519: GA101+Rituximab_rep1

description: gene expression data


title: Experiment 4

city: New Delhi

first: Pradeep

last: Sharma

email: praddybiotech@gmail.com, ravipathak@aol.in, raghuram98@hotmail.com, rvarshney@rediffmail.com, dwarakanathdrbs@gmail.com

state: Delhi

address: Lucknow Road, Timarpur

department: Division of radiation biosciences

country: India

institute: Institute of Nuclear medicine and allied sciences (INMAS, DRDO)

description: Combination (2-DG + 6-AN) treated irradiated (2 Gy)  Head and neck squamous carcinoma _cultured cells after 24 hours, Biological replicate  2 of 3. VS. Pooled sample of 3 biological replicates of untreated head and neck squamous carcinoma_cultured cells after 24hours

hyb_protocol: 825ng of cy3 labeled  samples and 825ng of cy5 labeled samples were pooled, fragmented and hybridized and data from these channels were used for comparison to test hybridizations of respective channels.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Agilent Microarray Scanner G Model G2565BA at 5 micron resolution.

data_processing: Data extraction done using Agilent Feature extraction software v 9.5.

label_protocol: The samples for Gene expression were labeled using Agilent Low RNA Input Linear amplification Kit (Part number:5184-3523).  Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 42°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dyes Cy3 CTP(Agilent) for control samples and Cy5 CTP(Agilent) for test samples were incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: KB (PE = 0.68) derived from head and neck squamous carcinoma was maintained as monolayer cultures at 37 ºC in a humidified CO2 incubator (5 % CO2, 95 % air). KB cells were maintained in high glucose DMEM supplemented with 10 % fetal bovine serum (FBS), HEPES (10 mM) and antibiotics (30 mg ml-1 penicillin G, 50 mg ml-1streptomycin and 2 mg ml-1 nystatin).

extract_protocol: RNA was extracted using Qiagen’s RNeasy minikit.

treatment_protocol: Monolayer KB, (1.0 × 106 cells were seeded in duplicate in 90 mm Petri dishes, each containing 8 ml of growth media) was grown for 24 h (exponential growth phase) in high glucose DMEM containing 10 % FBS. After 24 h of seeding,  6-AN (5 µM) and 2-DG (5 mM), obtained from SIGMA chemicals, were added to liquid-holding media (Hanks balanced salt solution, HBSS) just before irradiation (2 Gy) and removed after 4 h of incubation and fresh growth media was added to Petri dishes.

value: Head and neck squamous carcinoma


title: Soy oil emulsion rep 1

description:
Soy oil emulsion rep 1
S1


title: sample947

value: chronic obstructive pulmonary disease (COPD)


title: No treatment rep 4

description:
No treatment rep 4
N4

value: No treatment


title: GRANTA-519: Rituximab_rep2

description: gene expression data

source_name: GRANTA-519: Rituximab


title: GRANTA-519: Rituximab_rep3

description: gene expression data


title: GRANTA-519: Rituximab_rep1

description: gene expression data


title: No treatment rep: 3

description:
No treatment rep 3
N3


title: IOR/OS14 transfected with LSAMP open reading frame, clone 7


title: No treatment rep: 2

description:
No treatment rep 2
N2


title: sample948


title: No treatment rep: 1

description:
No treatment rep 1
N1


title: GRANTA-519: GA101_rep2

description: gene expression data

source_name: GRANTA-519: GA101


title: sample946


title: sample945

value: benign prostate hyperplasia


title: GRANTA-519: GA101_rep3

description: gene expression data


title: sample944


title: sample942


title: sample943

value: prostate cancer


title: sample941


title: sox10-NC sorted, biological rep 3 of 3

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

country: USA

institute: Memorial Sloan Kettering Cancer Center

description:
sox10-NC_C
Gene expression data from day 11 of differentiation from GFP+ FACS-sorted sox10::GFP cells.

hyb_protocol: Following fragmentation, cRNA were hybridized to Illumina GX HT12 Array. Slides were washed and stained in the Illumina instrument.

scan_protocol: Slides were scanned using the  Illumina iScanner.

data_processing: The data were analyzed with GenomeStudio using Illumina default analysis settings. No normalization or background correction are performed first, then quantile normalization and background correction are done.

source_name: H9 sox10::GFP hESCs, day 11 differentiation, wnt-induced neural crest cells

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: genotype/variation

tag: day of differentiation

tag: induction

value: wnt

value: neural crest cells

tag: facs sorting

value: GFP+


title: Z138: PBS-control_rep1

description: gene expression data

source_name: Z138: PBS-control


title: Experiment 1

description: Untreated head and neck squamous carcinoma_cultured cells after 24hours VS. Pooled sample of 3 Biological replicates of combination (2-DG + 6-AN) treated irradiated (2 Gy) head and neck squamous carcinoma_cultured cells after 24hours


title: NPC-NC sorted, biological rep 3 of 3

description:
NPC-NC_C
Gene expression data from day 18 of differentiation from HNK1+/p75+ FACS-sorted H9 cells.

source_name: H9 hESCs, day 18 differentiation, feeder-free-induced neural crest cells

value: feeder-free


title: sample940


title: GRANTA-519: GA101_rep1

description: gene expression data


title: Z138: PBS-control_rep3

description: gene expression data


title: Z138: PBS-control_rep2

description: gene expression data


title: NPC-NC sorted, biological rep 2 of 3

description:
NPC-NC_B
Gene expression data from day 18 of differentiation from HNK1+/p75+ FACS-sorted H9 cells.


title: NPC-NC sorted, biological rep 1 of 3

description:
NPC-NC_A
Gene expression data from day 18 of differentiation from HNK1+/p75+ FACS-sorted H9 cells.


title: sox10-NC sorted, biological rep 2 of 3

description:
sox10-NC_B
Gene expression data from day 11 of differentiation from GFP+ FACS-sorted sox10::GFP cells.


title: sox10-NC sorted, biological rep 1 of 3

description:
sox10-NC_A
Gene expression data from day 11 of differentiation from GFP+ FACS-sorted sox10::GFP cells.


title: Z138: Isotype-control_rep2

description: gene expression data

source_name: Z138: Isotype-control


title: Z138: GA101+Rituximab_rep3

description: gene expression data

source_name: Z138: GA101+Rituximab


title: MS5-NC sorted, biological rep 3 of 3

description:
MS5-NC_C
Gene expression data from day 35 of differentiation from HNK1+/p75+ FACS-sorted H9 cells.

source_name: H9 hESCs, day 35 differentiation, MS5-induced neural crest cells

value: MS5 feeder cells


title: Z138: Isotype-control_rep3

description: gene expression data


title: Z138: GA101+Rituximab_rep2

description: gene expression data


title: Z138: Isotype-control_rep1

description: gene expression data


title: MS5-NC sorted, biological rep 1 of 3

description:
MS5-NC_A
Gene expression data from day 35 of differentiation from HNK1+/p75+ FACS-sorted H9 cells.


title: MS5-NC sorted, biological rep 2 of 3

description:
MS5-NC_B
Gene expression data from day 35 of differentiation from HNK1+/p75+ FACS-sorted H9 cells.


title: ExVivoFoxp3-RORγt+_3

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

description: Gene expression of ex vivo FACS-purified CD4+ Foxp3-RORγt+ cells

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (Agilent 8x60k Human V1, AMID: 052800) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20120201) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

data_processing: log2 transformation; normalisation: shift to 75.0 percentile; baseline transformation: median of all samples

organism: Mus musculus

source_name: Foxp3-RORγt+_3, ex vivo

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Hilden, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: total RNA from FACS-sorted T cell subsets (see markers above) was isolated by using the RNeasy Plus Mini Kit (Qiagen).

treatment_protocol: CD4+ cells were enriched by CD4 (L3T4) MicroBeads (Miltenyi) followed by AutoMACS separation from spleen and lymph nodes of Foxp3-RFP/RORγt-GFP double reporter mice and stained for CD3, CD4, CD8, CD11c and CD19. Foxp3+/-RORγt+/- cell subsets were sorted from the CD3+CD4+ or CD4+CD8-CD11c-CD19- population according to the reporter signals .

tag: strain

value: Spleen and lymph nodes

tag: cell population

value: CD4+ Foxp3-RORγt+


title: LSB unsorted, biological rep 3 of 3

description:
LSB_C
Gene expression data from day 11 of differentiation, unsorted H9 cells.

source_name: H9 hESCs, day 11 differentiation

value: neuroepithelial cells


title: Z138: GA101+Rituximab_rep1

description: gene expression data

value: mantle cell lymphoma


title: sample939


title: Z138: Rituximab_rep3

description: gene expression data

source_name: Z138: Rituximab


title: ExVivoFoxp3+RORγt+_3

description: Gene expression of ex vivo FACS-purified CD4+ Foxp3+RORγt+ cells

source_name: Foxp3+RORγt+_3, ex vivo

value: CD4+ Foxp3+RORγt+


title: sample938


title: sample937


title: sample935

value: Wilms Tumor


title: sample934


title: sample933


title: Z138: GA101_rep2

description: gene expression data


title: LSB unsorted, biological rep 2 of 3

description:
LSB_B
Gene expression data from day 11 of differentiation, unsorted H9 cells.


title: Z138: Rituximab_rep2

description: gene expression data


title: ExVivoFoxp3-RORγt-_3

description: Gene expression of ex vivo FACS-purified CD4+ Foxp3-RORγt- cells

source_name: Foxp3-RORγt-_3, ex vivo

value: CD4+ Foxp3-RORγt-


title: Human none marrow-derived mesenchymal stromal primary culture (hMSC_Male)

data_processing: The data was quantile normalisation in GenomeStudio (Illumina)

growth_protocol: Primary hMSCs were obtained from the hip of a healthy donor after informed consent. Mononuclear cells from the bone marrow were isolated using standard density centrifugation and cultured in minimum essential medium (MEM) Alpha medium (cat. no. 22561) supplemented with 20% FBS (PAA Laboratories), GlutaMAX, penicillin (100U/mL), and streptomycin (100 mg/mL) (all from Life Technologies) at 37C and 5% CO2. Non-adherent cells were removed after approximately 24 h by replacement of the medium. Subsequently, the adherent cells were allowed to expand until 70% confluence (5–6 days) before they were harvested and further expanded. iMSC#3 were grown under the same condition as hMSCs, but the medium was supplemented with 10% FBS.

extract_protocol: RNA was isolated using the standard TRIzol procedure (Invitrogen), and further purified with an RNeasy mini column (Qiagen GmbH, Hilden, Germany), according to the manufacturers’ instructions.

value: hMSC

tag: sample origin

value: Human bone marrow-derived mesenchymal stromal cell

value: Male


title: ChIP FabR MOCK sample

city: Heverlee

first: Hans

last: Steenackers

address: Kasteelpark Arenberg 20, box 2460

country: Belgium

institute: KU Leuven

description: FabR ChIP-chip on Salmonella enterica subsp. enterica serovar Typhimurium SL1344

hyb_protocol: Samples were hybridized by Nimblegen (see http://www.nimblegen.com/products/lit/chip_userguide_v6p1.pdf)On S. Typhimurium LT2 whole genome tiling arrays. The arrays consisted of 387,000 unique 50-mer probes covering the whole S. Typhimurium LT2 genome and pSLT plasmid with a moving window overlap of 12 bases (Navarre et al., 2006).

scan_protocol: Arrays were scanned by nimblegen (see http://www.nimblegen.com/products/lit/chip_userguide_v6p1.pdf)

data_processing: Raw data were normalized by polynomial regression and log2 ratios of ChIP over reference (log2 enrichment ratios) were calculated (Matlab). To identify FabR-bound enriched regions in the ChIP-chip data, peak detection was performed with Mpeak (Zheng et al., 2007)  using the log2 enrichment ratios as input and performing first ‘simple cluster detection’ and then ‘peak detection’. All default parameter values were used, except for the ‘minimum number of probes’, which was set to 45 to account for the sonication process. Sonication produces DNA fragments of 800 bp on average, such that the ensemble of all retrieved FabR-bound DNA fragments for a specific target gene span a region of approximately 1700 bp, corresponding to ca. 45 probes in our tiling array design. The default Mpeak p-value is 0.01. Log2 enrichment ratios and identified peaks were visualized with SignalMap software (NimbleGen Systems, Inc.).

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: ChiP FabR Mock sample

label_protocol: ChIP-enriched DNA fragments were blunted and amplified via ligation-mediated (LM) PCR using PRO336 and PRO337 (Mueller & Wold, 1989), and sent to NimbleGen Systems, Inc. ChIP samples were labeled with Cy5 and hybridized against a genomic DNA reference, labeled with Cy3.

extract_protocol: Chromatin immunoprecipitation was performed as follows. DNA-binding proteins were cross-linked to their binding sites in vivo by the addition of formaldehyde (1%). After 20 min, cross-linking was quenched by the addition of glycine (125 mM). Cells were harvested from 50 ml of culture by centrifugation, washed twice with phosphate-buffered saline, resuspended in 500 µl of lysis buffer (10 mM Tris pH 8, 20% sucrose, 50 mM NaCl, Salmonella strains were cultured under free-living TSB conditions (TSB 1/20, 200 rpm, 25 °C) until an OD595 of 0.3 (ca. 2 x 108 cells) was reached (ca. 6h). ChIP experiments were performed as previously described (Thijs et al., 2007) on the fabR M9 S. Typhimurium SL1344 strain (CMPG5825). 10 mM EDTA with 10 mg/ml lysozyme) and incubated at 37°C for 30 min. Following lysis, 500 µl of 2X immunoprecipitation buffer (100 mM Tris pH 8, 300 mM NaCl, 2% NP-40, 1% Na-deoxycholate, 0.2% SDS) were added. Cellular DNA was then sheared by sonication (Labsonic U Braun) to an average size of 800 bp. Cell debris were removed by centrifugation and the supernatant was retained as input sample in immunoprecipitation experiments. A 750 µl aliquot of this input sample was incubated with 4 µl of anti-c-Myc monoclonal mouse antibody (M4439 Sigma) for 4 hrs at 4°C on a rotating wheel. Next, 30µl of protein G Dynabeads (Dynal, Invitrogen) were added and the mixture was incubated at 4°C for an additional hour. The beads were collected from each sample with the dedicated magnet and washed twice with 1X immunoprecipitation buffer, twice with wash buffer (10 mM Tris-HCl pH 8, 250 mM LiCl, 1 mM EDTA, 0.5% Nonidet-P40, 0.5% Na-deoxycholate) and once with TE buffer pH 8. Immunoprecipitated complexes were removed from the beads by treatment with elution buffer (50 mM TrisHCl pH 8, 10 mM EDTA, 1% SDS) at 65°C for 10 min. Cross-links in the eluted complexes were reversed by overnight incubation at 65°C. DNA was purified from the immunoprecipitate by proteinase K treatment and phenol-chloroform-isoamylalcohol (25:24:1) extraction and resuspended in 30 µl TE buffer pH 8. Leftover input sample was used as reference sample after removing cross links and purification.

tag: genotype

value: wildtype

tag: antibody

value: anti-Myc

source_name: Reference TSB 1/20


title: ChIP FabR IP sample

source_name: ChIP FabR IP sample

growth_protocol: Salmonella strains were cultured under free-living TSB conditions (TSB 1/20, 200 rpm, 25 °C) until an OD595 of 0.3 (ca. 2 x 108 cells) was reached (ca. 6h).


title: ExVivoFoxp3+RORγt+_2

source_name: Foxp3+RORγt+_2, ex vivo


title: ExVivoFoxp3-RORγt+_2

source_name: Foxp3-RORγt+_2, ex vivo


title: Z138: Rituximab_rep1

description: gene expression data


title: sample936

source_name: RNA from blood

value: prostate cancer


title: Z138: GA101_rep3

description: gene expression data


title: Z138: GA101_rep1

description: gene expression data


title: ExVivoFoxp3-RORγt-_2

source_name: Foxp3-RORγt-_2, ex vivo


title: miR-27a rep 2b

city: Herston

first: Nicole

last: Cloonan

state: Queensland

address: 300 Herston Road

institute: QIMR Berghofer Medical Research Institute

description: replicate 2

data_processing: The data were preprocessed by Bioconductor lumi package (version 2.2.1). It was background adjusted, vst transformed and rsn normalized. Probes that did not have a detection p-value < 0.01 in all of the mock-transfected replicates were excluded from further analysis.

source_name: HEK293T cell

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

growth_protocol: HEK293T cells were grown in DMEM according to ATCC recommendations.

extract_protocol: Cells were harvested  24 hours post transfection, and the miRNAs and their bound targets were isolated using streptavidin myOne C1 Dynabeads. Beads were washed before RNA extraction using an RNeasy Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: 200pmols of synthetic biotin-labeled miRNA duplexes were transfected into HEK293T cells using HiPerFect Transfection Reagent (Qiagen).

tag: transfection molecule

tag: pull-down

value: pull-down


title: ExVivoFoxp3+RORγt-_3

description: Gene expression of ex vivo FACS-purified CD4+ Foxp3+RORγt- cells

source_name: Foxp3+RORγt-_3, ex vivo

value: CD4+ Foxp3+RORγt-


title: LSB unsorted, biological rep 1 of 3

description:
LSB_A
Gene expression data from day 11 of differentiation, unsorted H9 cells.

tag: cell line


title: Immortalized human bone marrow-derived mesenchymal stromal cell line iMSC#3 (Culture I)

tag: gender


title: Human none marrow-derived mesenchymal stromal primary culture (hMSC_Female)

value: Female


title: miR-27a input rep 2

description: replicate 2


title: sample932


title: 120646B_G3L13

city: Guangzhou

first: Lehang

last: Lin

address: 107, West Yanjiang Road

country: China

institute: Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University

description: liver of hPER1S714G mice at ZT13

hyb_protocol: labeled DNA were diluted with hybridization buffer(2X GEx Hyb Buffer（HI-RPM）, 25% formamide) and hybride at 45℃ overnight. Slides were wahsed with 0.2% SDS，2×SSC at  42℃ for 5 minutes, then washed in 0.2xSSC at room temperature for 5 minutes, then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA)

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

label_protocol: RNA were labeled with Jingxin cRNA labeling kit according to the manufacture's instruction.

growth_protocol: mice were grown in an AAALAC International (Association for Assessment and Accreditation of Laboratory Animal Care) accredited SPF animal facility, and all animal protocols were approved by the Animal Care and Use Committee of the Model Animal Research Center, the host for the National Resource Center for Mutant Mice in China, Nanjing University.

extract_protocol: total RNA were extracted with Trizol reagent.

treatment_protocol: mice were sacrificed at the indicated time point, and liver and white adipose tissue were taken immediately and frozen in liquid nitrigen, then stored at -80°C.

tag: strain background

value: hPER1 S714G mutant

value: male

tag: age

value: 2 months

value: liver

tag: time point


title: sample931

tag: disease


title: miR-27a input rep 1

description: replicate 1


title: sample928


title: sample929


title: sample927


title: sample930


title: control, biological rep11

city: Bethesda

first: Yanqin

last: Yang

state: Maryland

address: 10 Center Dr.

institute: NIH

hyb_protocol: Hybridization of the affymetrix microRNA arrays was done overnight at 45C for 16 hours in a hybridization oven.

scan_protocol: Scanning of the washed, stained arrays was done using Affymetrix 3000 7G scanner

data_processing: RMA normalization from Affymetrix Expression Console

source_name: PBMC

label_protocol: total RNA was used for target labeling procedure following affymtrix's IVT labeling kit.Briefly, total RNA was incubated with oligo dT/T7 primers and reverse-transcribed into double-stranded cDNA. In vitro transcription of the purified cDNA was performed with T7 RNA polymerase at 42°C for 6 hours. The amplified RNA was purified and subjected to a second round of amplification and biotin labeling with Affymetrix's IVT labeling kit according to the manufacturer's directions

growth_protocol: PBMCs were isolated from whole blood using CPT procedure

extract_protocol: RNA was isolated from PBMCs using qiagen's RNEasy kit

treatment_protocol: Blood samples were collected from sickle cell patients and control subjects

tag: diagnosis

value: normal

tag: tissue

value: PBMC


title: control, biological rep10


title: 120646B_G1L13

description: liver of hPER1S714G mice at ZT13

tag: genotype/variation


title: miR-23b input rep 2

description: replicate 2


title: miR-27a rep 1b

description: replicate 1


title: 120646B_G2L13

description: liver of hPER1S714G mice at ZT13


title: 120646B_G1W13

description: white adipose of hPER1S714G mice at ZT13

source_name: hPER1S714G_white adipose_ZT13

value: white adipose


title: miR-23b rep 2b

description: replicate 2


title: control, biological rep9


title: 120646B_G2W13


title: miR-23b input rep 1

description: replicate 1


title: miR-23b rep 1b

description: replicate 1


title: 120646B_G3W13


title: control, biological rep8


title: control, biological rep7


title: 120646B_W3L13

description: liver of hPER1S714 mice at ZT13

value: hPER1 S714 control


title: sample924

value: benign prostate hyperplasia


title: sample926


title: control, biological rep6


title: sample925


title: sample923


title: ExVivoFoxp3+RORγt-_2

source_name: Foxp3+RORγt-_2, ex vivo

value: Spleen and lymph nodes


title: control, biological rep5


title: control, biological rep4


title: 120646B_W2L13

description: liver of hPER1S714 mice at ZT13


title: miR-4307-3p input rep 3

description: replicate 3


title: sample920

value: lung cancer


title: sample921


title: sample922


title: miR-4307-3p rep 3

description: replicate 3


title: sample919

value: Wilms Tumor


title: 120646B_W1L13

description: liver of hPER1S714 mice at ZT13


title: sample918


title: control, biological rep1


title: 120646C_W2W13

description: white adipose of hPER1S714 mice at ZT13

source_name: hPER1S714_white adipose_ZT13


title: miR-4307-3p rep 2

description: replicate 2


title: miR-4307-3p input rep 2

description: replicate 2


title: groupA, biological rep24

value: sickle cell anemia (SCA)


title: 120646B_W3W13

description: white adipose of hPER1S714 mice at ZT13


title: miR-3118-3p input rep 2

description: replicate 2


title: 120646B_G2L1

description: liver of hPER1S714G mice at ZT1


title: groupA, biological rep22


title: sample916


title: miR-3118-3p input rep 3

description: replicate 3


title: miR-3118-3p rep 3

description: replicate 3


title: groupA, biological rep21


title: groupA, biological rep20


title: control, biological rep2


title: groupA, biological rep23


title: 120646B_G3L1

description: liver of hPER1S714G mice at ZT1


title: sample917


title: groupA, biological rep19


title: sample914


title: 120646B_G1L1

description: liver of hPER1S714G mice at ZT1


title: 120646B_G1W1

description: white adipose of hPER1S714G mice at ZT1

source_name: hPER1S714G_white adipose_ZT1


title: miR-4307-3p input rep 1

description: replicate 1


title: miR-4307-3p rep 1

description: replicate 1


title: 120646B_W1W13

description: white adipose of hPER1S714 mice at ZT13


title: sample915


title: 120646C_G2W1

description: white adipose of hPER1S714G mice at ZT1


title: miR-3118-3p rep 2

description: replicate 2


title: sample912


title: miR-3118-3p input rep 1

description: replicate 1


title: 120646C_G3W1

description: white adipose of hPER1S714G mice at ZT1


title: groupA, biological rep17


title: groupA, biological rep16


title: groupA, biological rep18


title: 120646B_W3L1

description: liver of hPER1S714 mice at ZT1


title: sample910

value: chronic obstructive pulmonary disease (COPD)


title: miR-3118-3p rep 1

description: replicate 1

value: pull-down


title: sample913


title: sample911


title: 120646B_W1L1

description: liver of hPER1S714 mice at ZT1


title: groupA, biological rep15


title: groupA, biological rep14


title: sample908


title: groupA, biological rep13


title: sample907


title: sample906

value: colon cancer


title: 120646B_W2L1

description: liver of hPER1S714 mice at ZT1


title: groupA, biological rep12


title: 120646B_W3W1

description: white adipose of hPER1S714 mice at ZT1

source_name: hPER1S714_white adipose_ZT1


title: groupA, biological rep11


title: 120646B_W2W1

description: white adipose of hPER1S714 mice at ZT1


title: groupA, biological rep9


title: sample909


title: groupA, biological rep10


title: sample905


title: 120646B_W1W1

description: white adipose of hPER1S714 mice at ZT1


title: sample903


title: sample904


title: groupA, biological rep8


title: groupA, biological rep7


title: groupA, biological rep5


title: sample901

value: Renal cancer


title: sample902


title: groupA, biological rep6


title: groupA, biological rep3


title: sample900


title: groupA, biological rep2


title: H3K27me3 of CpG island in HMEC

city: Shinagawa-ku

first: Hideyuki

last: Takeshima

state: Tokyo

department: Institute for Advanced Life Sciences

country: Japan

institute: Hoshi University

description: Untreated cells

hyb_protocol: Labelled DNA mixed with cot-1 DNA and Agilent blocking solution was hybridized to microarray for 40 hours at 67℃ and 20 rpm rotation. Microarrays was washed according to Agilent protocol.

scan_protocol: The microarray was scanned with an Agilent G2565BA microarray scanner (Agilent Technologies).

data_processing: Scanned data was analyzed with Feature Extraction Ver.9.1 and normalized (Background subtraction) using Agilent G4477AA ChIP Analytics 1.3 software.

source_name: Sonicated HMEC chromatin (WCE)

label_protocol: Solubilized chromatin was diluted 10-fold in dilution buffer [50 mM Tris-HCl, pH 8.0, 167 mM NaCl, 1.1 % (w/v) Triton X-100, 0.11 % (w/v) sodium deoxycholate (DOC)], and incubated with antibody against H3K27me3 (07-449, Millipore) at 4ºC overnight. Immuno-complexes were collected with Dynabeads Protein A, washed with 1 x RIPA buffer [50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, 1 % (w/v) Triton X-100, 0.1 % (w/v) SDS, 0.1 % (w/v) DOC] containing 150 mM NaCl, 1 x RIPA buffer containing 500 mM NaCl, LiCl wash buffer [10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5 % (w/v) NP-40, 0.5 % (w/v) DOC] and 1 x TE containing 50 mM NaCl. After cross-link reversal, DNA was recovered with RNaseA and proteinase K treatment, followed by phenol extraction and ethanol precipitation, and dissolved in 30 μl of 1 x TE. 500 ng of DNA was labeled using Agilent Genomic DNA labeling Kit PLUS (5188-5309).

growth_protocol: Du145, PC3, MCF7, MDA-MB-231, and RKO were maintained in RPMI1640 medium.  HCT116 was maintained in McCoy's 5A medium.  RWPE1 was maintained in keratinocyte-SFM.  HMEC was maintained in mammary epithelial cell serum-free growth medium.  FHC was maintained in mixture of Ham's F12 and DMEM (1:1).

extract_protocol: About 1 x 10e7 cells were cross-linked with 1 % formaldehyde, lysed, and sonicated with a Bioruptor UCD-250 (Cosmo Bio, Tokyo, Japan).

value: HMEC

tag: cell fraction

value: WCE

source_name: Sonicated HMEC chromatin (IP)

value: IP


title: groupA, biological rep1


title: H3K27me3 of CpG island in RKO

description: Untreated cells

source_name: Sonicated RKO chromatin (WCE)

value: RKO

source_name: Sonicated RKO chromatin (IP)


title: sample897

value: others


title: H3K27me3 of CpG island in HCT116

description: Untreated cells

source_name: Sonicated HCT116 chromatin (WCE)

source_name: Sonicated HCT116 chromatin (IP)


title: H3K27me3 of CpG island in FHC

description: Untreated cells

source_name: Sonicated FHC chromatin (WCE)

value: FHC

source_name: Sonicated FHC chromatin (IP)


title: H3K27me3 of CpG island in MCF7

description: Untreated cells

source_name: Sonicated MCF7 chromatin (WCE)

source_name: Sonicated MCF7 chromatin (IP)


title: H3K27me3 of CpG island in MDA-MB-231

description: Untreated cells

source_name: Sonicated MDA-MB-231 chromatin (WCE)

source_name: Sonicated MDA-MB-231 chromatin (IP)


title: sample895

source_name: RNA from blood


title: sample896


title: LNCaP cell line

city: Alcala de Henares

first: Nadia

last: Ashour

address: S/N

department: Biochemistry

country: Spain

institute: Universidad de Alcala

description: Cancer sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Golden Gate Methylation Cancer Panel  I Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: Prostate left supraclavicular lymph node

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

value: Male

tag: sample type

value: cell line


title: DU145 cell line

description: Cancer sample

source_name: Brain metastasis


title: PC3 cell line

description: Cancer sample

source_name: Bone metastasis of grade IV


title: sample899


title: sample894


title: Control 10

description: normal prostate sample

source_name: genomic DNA from prostate

value: Prostate tissue

tag: disease state

value: normal


title: Control 9

description: normal prostate sample


title: Control 8

description: normal prostate sample


title: Control 7

description: normal prostate sample


title: groupA, biological rep4

source_name: PBMC

value: PBMC


title: HSC-60Luc (Luciferase-expressing HSC-60) -1

city: Chuo-ku

first: Hiroki

last: Sasaki

institute: National Cancer Center Reseach Institute

description: Gene expression data from diffuse-type gastric cancer cell line using GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 ﾟC on GeneChip Human Genome Array U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using GeneSpring GX version11

label_protocol: Biotinylated cRNA were prepared according to Affymetrix protocol for two-cycle terget labeling assay with 100 ng of total RNA using Two-Cycle Terget Labeling and Control Reagents (Affymetrix P/N 900432) and MEGAscript High Yield Transcription Kit (Ambion Inc P/N 1334).

growth_protocol: All cell lines were maintained in an RPMI1640 medium supplemented with 10% fetal calf serum.

extract_protocol: ISOGEN (Nippon Gene, Toyama, Japan) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: A human gastric cancer cell line, HSC-60 was established by a collaborator using the procedure as described previously (Yanagihara et al., Cancer Sci. Vol. 95, 575–582, 2004). A highly peritoneal-seeding cell line, 60As6 was established from HSC-60 using orthotopic tissue implantation into SCID/SCID mice as briefly follows: the xenografted tumor of HSC-60 cells was transplanted into the gastric wall of a mouse. We repeated six cycles of harvesting ascitic tumor cells and the orthotopic inoculation of these cells, in turn, into the animals to establish a highly metastatic 60As6 cell line (Fujita et al., Cancer Sci., Vol. 104, 214–222, 2013). In this study, we also used luciferase- or green fluorescence protein (GFP)-expressing transfectants (HSC-60 and 60As6Luc). Total RNA of 60As6, luciferase-expressing 60As6Luc, HSC-60, and luciferase-expressing HSC-60 cells were isolated by suspending the cells in an ISOGEN lysis buffer (Nippon Gene, Toyama, Japan) followed by precipitation with isopropanol.

tag: cell type

value: Gastric cancer cell line


title: 60As6Luc (Luciferase-expressing 60As6) -2


title: HSC-60Luc (Luciferase-expressing HSC-60) -2


title: sample898


title: H3K27me3 of CpG island in PC3

description: Untreated cells

source_name: Sonicated PC3 chromatin (WCE)

source_name: Sonicated PC3 chromatin (IP)


title: HSC-60 (No.60 of cell line derived from diffuse-type gastric cancer) -2


title: 60As6Luc (Luciferase-expressing 60As6) -1


title: sample893


title: HSC-60 (No.60 of cell line derived from diffuse-type gastric cancer) -1


title: Control 6

description: normal prostate sample


title: H3K27me3 of CpG island in RWPE1

description: Untreated cells

source_name: Sonicated RWPE1 chromatin (WCE)

source_name: Sonicated RWPE1 chromatin (IP)


title: sample892


title: sample891

value: Wilms Tumor


title: sample889


title: Control 5

description: normal prostate sample


title: sample890


title: sample888


title: Control 4

description: normal prostate sample


title: sample887


title: Control 2

description: normal prostate sample


title: Control 3

description: normal prostate sample


title: Control 1

description: normal prostate sample


title: Prostate Tumor 83

description: Prostate tumor sample

value: Prostate tumor

tag: total gleason score

tag: t clinical stage

tag: ki-67 index (%)

tag: radical prostatectomy

value: yes

tag: biochemical progression (bp)

tag: bp free interval (months)

tag: death of prostate cancer

tag: follow-up (months)


title: EpCAM positive HCCLM3 cells, Antagomir-429

city: Shanghai

first: Liang

last: Li

state: Shanghai

address: 225 Changhai Road

institute: Eastern Hepatobiliary Surgery Hospital

description: Gene expression data from  40μM Antagomir-429 treated magnetically sorted EpCAM  positive cells

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides 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 were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US). of each array was arbitrarily set to 100.

source_name: EpCAM positive HCCLM3 liver cancer cells, Antagomir-429, 40μM

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Magnetically sorted EpCAM  negative and positive cells were maintained at 37°C in an atmosphere containing 5% CO2 in Dulbecco’s modified Eagle’s medium (Gibco) supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Mimics  transfection was performed with INTERFERin reagents (Poly plus) according to the manufacturers’ instructions. Briefly, for each well (6 well, for example), dilute 100nM of mimics  duplexes into 200 μl of medium without serum. Mix by pipetting up and down. Then, add 12 μl of INTERFERin into the 200 μl of mimics duplexes, homogenize by vortex immediately for 10 seconds. Incubate for 10 minutes at room temperature to allow transfection complexes to form between mimics duplexes and INTERFERin. Finally, Add 200 μl of transfection mix onto the cells and homogenize by gently swirling the plate.  Followed the manufacturers’ instructions (Ribobio Co.), the cholesterol-conjugated Antagomir-429 was diluted into the medium without serum and added onto the cells. About 4 hours after incubation, serum was added and incubates for another 8 hours.

tag: cell line

value: Magnetically sorted EpCAM (epithelial cell adhesion molecule) positive cells

tag: treatment

value: 40μM Antagomir-429


title: EpCAM negative HCCLM3 cells, miR-NC mimics

description: Gene expression data from 100nM miR-NC mimics treated magnetically sorted EpCAM  negative cells

source_name: EpCAM negative HCCLM3 liver cancer cells, miR-NC mimics, 100nM

value: Magnetically sorted EpCAM (epithelial cell adhesion molecule) negative cells

value: 100nM miR-NC mimics


title: EpCAM positive HCCLM3 cells, Antagomir-NC

description: Gene expression data from  40μM Antagomir-NC treated magnetically sorted EpCAM  positive cells

source_name: EpCAM positive HCCLM3 liver cancer cells, Antagomir-NC, 40μM

value: 40μM Antagomir-NC


title: 60As6 (Highly peritoneal-metastatic subline of HSC-60) -1


title: EpCAM negative HCCLM3 cells, miR-429 mimics

description: Gene expression data from 100nM miR-429 mimics treated magnetically sorted EpCAM  negative cells

source_name: EpCAM negative HCCLM3 liver cancer cells, miR-429 mimics, 100nM

value: 100nM miR-429 mimics


title: 60As6 (Highly peritoneal-metastatic subline of HSC-60) -2


title: sample885

tag: disease

value: others


title: sample886


title: sample884


title: H3K27me3 of CpG island in Du145

description: Untreated cells

source_name: Sonicated Du145 chromatin (WCE)

value: WCE

source_name: Sonicated Du145 chromatin (IP)

value: IP

tag: antibody


title: Prostate Tumor 82

description: Prostate tumor sample

tag: gender

value: Male

tag: age

value: no


title: Prostate Tumor 81

description: Prostate tumor sample

tag: sample type

value: Prostate tissue


title: sample883

value: lung cancer


title: Prostate Tumor 80

description: Prostate tumor sample

tag: disease state


title: sample882


title: Prostate Tumor 78

description: Prostate tumor sample


title: Prostate Tumor 79

description: Prostate tumor sample


title: sample881


title: sample880


title: sample879


title: Prostate Tumor 77

description: Prostate tumor sample


title: Prostate Tumor 76

description: Prostate tumor sample


title: MCF10A_SC_R4

city: Manchester

first: Ged

last: Brady

address: Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Rd

department: Clinical and Experimental Pharmacology

country: United Kingdom

institute: Caner Research UK Manchester Institute

hyb_protocol: The hybridisation cocktail containing 5mg of biotin cDNA was heated to 99°C for 5 mins. The hybridisation cocktail was then transferred to 45°C for 5 mins and centrifuged at maximum speed for 5 mins to remove insoluble material. Samples were then hybridised to Affymetrix Human HGU133 Plus 2 arrays for 16 hours overnight and then stained with SAPE using a biotin targeted antibody step and washed according to the EukGE_Ws2v4_450 fluidics protocol from Affymetrix.

scan_protocol: Samples were scanned in an Affymetrix 3000 scanner.

data_processing: Data were normalised and summarised using RMA, as implemented by Affymetrix Power Tools (APT) software package (http://www.affymetrix.com/estore/partners_programs/programs/developer/tools/powertools.affx) using the 'apt-probeset-summarize' default parameter setting. In subsequent analysis, gene level summaries (not included here) were computed as the geometric mean of all probesets mapping to a gene, as defined by annmap, using ENSEMBL version 70 as the source of underlying genome annotation. The empirical Bayes statistics implemented in the Bioconductor package LIMMA were used to identify protein-coding genes showing differential levels in MCF7 and MCF10A samples (FDR < 0.05; absolute fold change > 2)

source_name: MCF10A single cell

label_protocol: Following amplification the cDNA was Biotin-labeled using the EpiStem RNA-Amp labeling kit (EpiStem, Manchester, UK)

growth_protocol: The human epithelial cell lines MCF7 and MCF10A were grown in DMEM (Gibco, Paisley, Scotland) supplemented with 10% heat-inactivated FCS, 2.5% HEPES buffer (pH 7.2), 0.1% β-mercaptoethanol and 2mM L-glutamine (all from Sigma, UK). Both cell lines were maintained in a 5% CO2 humidified incubator at 37°C and were routinely tested for the presence of mycoplasma.

extract_protocol: RNA (1ng-25pg) or cell lysates in CLS were adjusted to 6.75ml volume and RNA-amplified using the EpiStem RNA-Amp Kit according to the manufacturers protocols (EpiStem, Manchester, UK). Briefly the samples underwent oligo-dT priming and 5’ capping prior to x35 cycles of PCR amplification using the conditions 90ºC 30 sec, 42ºC 2 min and 72ºC 6 min. Following amplification all samples were purified using a MoBio UltraClean® PCR Clean-Up Kit (Carlsbad, CA, USA) and quantified on a NanoDrop spectrophotometer.

value: Amplified cDNA from single cell


title: MCF10A_SC_R5


title: MCF10A_SC_R3


title: MCF7_SC_R4

source_name: MCF7 single cell


title: MCF10A_SC_R2


title: MCF10A_SC_R1


title: MCF7_SC_R5


title: Prostate Tumor 74

description: Prostate tumor sample


title: Prostate Tumor 75

description: Prostate tumor sample


title: sample877

source_name: RNA from blood


title: MCF7_SC_R3


title: sample878


title: sample876

value: chronic obstructive pulmonary disease (COPD)


title: Prostate Tumor 72

description: Prostate tumor sample

value: Prostate tumor


title: MCF7_SC_R2


title: sample874


title: sample875


title: Prostate Tumor 73

description: Prostate tumor sample

value: yes


title: Prostate Tumor 71

description: Prostate tumor sample


title: Prostate Tumor 70

description: Prostate tumor sample


title: sample873


title: MCF10A_1ng_R5

source_name: MCF10A cells

value: Amplified cDNA from 1ng RNA


title: CMT-U309 cell line rep2

city: Warsaw

first: Magdalena

last: Król

address: Nowoursynowska 159

department: Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences

description: dye-swap

hyb_protocol: The hybridization was performed with canine-specific AMADID Release GE 4x44K microarrays (Agilent, USA) using Gene Expression Hybridization Kit (Agilent, USA) according to the manufacturer`s protocol.

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

organism: Canis lupus familiaris

source_name: CMT-U309 cells grown as monoculture

label_protocol: The Quick Amp Labeling Kit (Agilent, USA) was used to amplify and label target RNA to generate complementary RNA (cRNA) for oligo microarrays used in gene expression profiling and other downstream analyses.

growth_protocol: Cells were cultured in optimal conditions: a medium (RPMI-1640) enriched with 10% (v/v) heat-inactivated fetal bovine serum (FBS), penicillin-streptomycin (50 iU mL–1), and fungizone (2.5 mg mL–1) (reagents obtained from Sigma Aldrich, USA), in an atmosphere of 5% CO2 and 95% humidified air at 37°C, and routinely subcultured every second day.

extract_protocol: The total RNA from the samples was isolated using a Total RNA kit (A&A Biotechnology, Poland) according to the manufacturer’s protocol.

treatment_protocol: Canine mammary neoplastic cells were grown and sorted myeloid-derived supressor cells (MDSC) were then layered in tissue culture plate inserts. The co-culture was maintained for at least 72 hrs. After the 72 hrs of co-culture the cells were harvested by trypsynization t-RNA was isolated.

value: monoculture

source_name: CMT-U309 cells grown as co-culture with MDSC

value: MDSC co-cuture


title: sample872


title: sample871


title: MCF10A_1ng_R3


title: Prostate Tumor 69

description: Prostate tumor sample

source_name: genomic DNA from prostate


title: Prostate Tumor 68

description: Prostate tumor sample


title: MCF7_SC_R1


title: sample870


title: Prostate Tumor 66

description: Prostate tumor sample


title: CMT-U27 cell line rep1

description: culture condition

source_name: CMT-U27 cells grown as co-culture with MDSC

value: MDSC co-culture

source_name: CMT-U27 cells grown as monoculture


title: CMT-U27 cell line rep2

description: dye-swap


title: MCF10A_1ng_R2


title: sample869


title: MCF7_1ng_R5

source_name: MCF7 cells


title: MCF10A_1ng_R4


title: MCF10A_1ng_R1


title: P114 cell line rep2

description: dye-swap

source_name: P114 cells grown as mono-culture

source_name: P114 cells grown as co-culture with MDSC


title: MCF7_1ng_R4


title: P114 cell line rep1

description: culture condition


title: sample868


title: Prostate Tumor 65

description: Prostate tumor sample


title: Prostate Tumor 64

description: Prostate tumor sample


title: Prostate Tumor 67

description: Prostate tumor sample


title: sample867


title: Prostate Tumor 63

description: Prostate tumor sample


title: AE_2_Unfertilized_CumulusCells

city: Ljubljana

first: Ales

last: Maver

address: Slajmerjeva 3

country: Slovenia

institute: Clinical institute of medical genetics Ljubljana Slovenia

hyb_protocol: For comparative microarray hybridization, a universal reference RNA experimental design was employed. Agilent Universal Human Reference RNA was labelled with Cy3 and each isolated test RNA sample was labelled with Cy5. Afterwards, labeled reference RNA sample and labeled test RNA samples were co-hybridized on the array.

scan_protocol: Chips were scanned using the Agilent Surescan Microarray Scanner.

data_processing: Post-processing steps included intra-array loess and inter-array quantile normalization to correct for potential bias resulting from differential stability of cyanine dyes (Limma version 2.12 in Bioconductor 2.12 environment).

label_protocol: Labeling of RNA samples was performed according to manufacturer's instructions (Agilent Low Input Quick Amp Labeling protocol).

extract_protocol: Immediately after oocyte retrieval CC of each oocyte were removed by a needle and a glass denudation pipette (Swemed, Sweden), washed in PBS, snap frozen in liquid nitrogen and stored at -80°C until RNA isolation.  For GC isolation Dynabeads® CD45 Magnetic Beads (Invitrogen Dynal AS, Oslo, Norway) were used for depletion of CD45+ cells according to manufacturer's protocol with some adjustements. The beads were used to separate GC from leukocyte CD45+ cells to exclude the risk of contamination [Assou,2010]. Follicular fluids were centrifuged at 800x g, 4°C for 10 minutes. Follicular fluids were than snap frozen in liquid nitrogen and stored at -80°C. The sediment was resuspended in 2 ml of lysis solution (NH4Cl) to remove red blood cells, incubated for 10 minutes and centrifuged at 600x g, 4°C for 10 minutes. The supernatant was discarded and the sediment resuspended in 1 ml PBS with 0,1% BSA and 0,002 EDTA . The suspension was added to the tubes with 50 μl of Dynabeads® CD45 and incubated at 4°C for 30 minutes with gentle tilting and rotation of the mixer. The tubes were pre-coated with 2 ml of RPMI with 1% FCS for 5 minutes. After incubation, the samples were diluted to 4 ml with PBS with 0,1% BSA and 0,002 EDTA and placed in a magnet for 10 minutes. The supernatant was transfered to a new pre-coated tube and centifuged at 800x g, 4°C for 15 minutes. The supernatant was discarded and sediment resuspended in 1 ml of PBS. The samples were then centrifuged at 2000 x g for 5 minutes, supernatant discharged and sediment snap frozen in liquid nitrogen and stored at -80°C. The purity of the samples was checked with flow cytometry. The samples were prepared from GCs suspension before isolation and compared to cell suspension after GCs isolation. The contamination with leucocytes was investigated using antibodies CD45 conjugated with Fluorescein Isothiocyanate (FITC) and CD14 Phycoerythrin (PE) ( both from BD Bioscience, San Jose, USA). Samples were washed and resuspended in phosphate-buffered saline with 1% bovine serum albumin added and incubated with antibodies for 20 minutes. The purity of the samples were characterised by FSC vs SSC followed by gating on CD45 and CD14. Data were collected on FACSCanto flow cytometer (BD Bioscience, San Jose, USA) and expression of various markers was assessed using FlowJo (TreeStar Inc, Ashland, USA) analysis software.

tag: ivf outcome

value: Unfertilized

tag: cell type

value: Cumulus cells

source_name: Agilent Universal Human Reference RNA

tag: reference

value: Agilent Universal Human Reference RNA


title: Prostate Tumor 62

description: Prostate tumor sample

tag: total gleason score

tag: t clinical stage

tag: ki-67 index (%)


title: N_1_Unfertilized_GranulosaCells

value: Granulosa cells


title: MCF7_1ng_R3


title: sample865

value: others


title: MCF7_1ng_R2


title: MCF7_1ng_R1


title: Skin_osteoma_area_control2

city: Oulu

first: Riina

middle: M

last: Myllylä

address: Aapistie 7 A

country: Finland

institute: University of Oulu

description: RM C2 O

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000.

data_processing: The data were analyzed with dCip software.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

treatment_protocol: Skin biopsies were taken from upper chest (osteoma area) and lower abdomen (unaffected area)

value: male

tag: tissue

value: osteoma affected skin area


title: AR_4_NonPregnant_GranulosaCells

value: NonPregnant


title: Prostate Tumor 60

description: Prostate tumor sample

value: Male

value: Prostate tissue

tag: radical prostatectomy

value: no

tag: biochemical progression (bp)

tag: bp free interval (months)

tag: death of prostate cancer


title: Prostate Tumor 61

description: Prostate tumor sample

value: Prostate tumor

tag: follow-up (months)


title: sample864

data_processing: Summarizing of technical replica by median and quantile normalization. Following BG correction, negative values were corrected to 1. R Version 3.0.2

tag: disease

value: psoriasis


title: sample863


title: sample866


title: Prostate Tumor 59

description: Prostate tumor sample

tag: gender

value: yes


title: sample862

value: Wilms Tumor


title: Prostate Tumor 58

description: Prostate tumor sample

tag: age


title: CMT-U309 cell line rep1

description: culture condition

tag: cell line

tag: treatment

value: monoculture


title: sample861

value: benign prostate hyperplasia


title: N_1_Unfertilized_CumulusCells

tag: ivf outcome

value: Unfertilized


title: AJ_3_Unfertilized_GranulosaCells

tag: cell type


title: 2G_2_Pregnant_CumulusCells

value: Pregnant

value: Cumulus cells

tag: reference


title: Skin_osteoma_area_patient2

description: RM P2 O


title: AK_1_Pregnant_CumulusCells

value: Agilent Universal Human Reference RNA


title: Skin_unaffected_area_control2

description: RM C2 K

value: unaffected healthy skin area


title: H_2_Pregnant_CumulusCells


title: Skin_unaffected_area_patient3

description: RM P3 K

value: male


title: AJ_2_NonPregnant_GranulosaCells

value: Granulosa cells


title: Prostate Tumor 57

description: Prostate tumor sample

tag: sample type

tag: disease state

tag: total gleason score


title: Prostate Tumor 56

description: Prostate tumor sample

tag: t clinical stage

tag: ki-67 index (%)


title: sample859

value: lung cancer


title: Skin_osteoma_area_patient3

description: RM P3 O

tag: tissue

value: osteoma affected skin area


title: sample858

value: others


title: Prostate Tumor 55

description: Prostate tumor sample

value: Male

value: Prostate tissue

tag: radical prostatectomy

tag: biochemical progression (bp)

tag: bp free interval (months)

value: no


title: Prostate Tumor 54

description: Prostate tumor sample

value: Prostate tumor

value: yes

tag: death of prostate cancer

tag: follow-up (months)


title: sample857

tag: disease


title: sample856


title: Skin_osteoma_area_patient4

description: RM P4 O

tag: gender


title: Skin_unaffected_area_patient4

description: RM P4 K


title: Skin_unaffected_area_patient2

description: RM P2 K


title: Skin_unaffected_area_control1

description: RM C1 K


title: Prostate Tumor 52

description: Prostate tumor sample

tag: age


title: Skin_osteoma_area_control1

description: RM C1 O


title: sample855

value: colon cancer


title: P_1_NonPregnant_CumulusCells

tag: ivf outcome

value: NonPregnant


title: AB_7_Unfertilized_GranulosaCells

value: Unfertilized

tag: cell type


title: AG_3_Pregnant_GranulosaCells

value: Pregnant

tag: reference


title: AM_8_Pregnant_GranulosaCells


title: Prostate Tumor 50

description: Prostate tumor sample

tag: sample type


title: sample854


title: AI_5_Pregnant_GranulosaCells


title: Prostate Tumor 53

description: Prostate tumor sample

tag: disease state


title: Prostate Tumor 51

description: Prostate tumor sample

tag: total gleason score


title: AP_1_Pregnant_CumulusCells

value: Cumulus cells


title: sample853

value: Renal cancer


title: sample852


title: Prostate Tumor 49

description: Prostate tumor sample

tag: t clinical stage


title: Prostate Tumor 47

description: Prostate tumor sample

tag: ki-67 index (%)


title: Prostate Tumor 48

description: Prostate tumor sample


title: sample849

value: Wilms Tumor


title: colonic mucosal biopsy from pancolitis 17

city: Herlev

first: Jacob

middle: Tveiten

last: Bjerrum

address: Herlev Ringvej 75

department: Department of Gastroenterology, Medical Section

country: Denmark

institute: Herlev Hospital

hyb_protocol: The cRNA was fragmented and a hybridization mix was prepared, which included the fragmented target, probe array controls, bovine serum albumin, and herring sperm DNA. In this experiment, the Affymetrix GeneChip Human Genome U133 Plus 2.0 was applied.

scan_protocol: The hybridized probe array was subsequently stained with fluorescent protein streptavidin-phycoerythirn and scanned with a GeneArray scanner at the excitation wavelength of 488 nm. The amount of light emitted at 570 nm was proportional to the bound target at each location on the probe array.

data_processing: By employing the robust multi-array analysis procedure with quantile normalization implemented in the Affymetrix library for the R statistical environment, a single log2 scale expression measure for each probe set was attained from the low level data files (CEL files). Principal component analysis (PCA) was used in order to reduce data complexity. This was performed with the R package pcaGoPromoter, The Hotelling T2 test, which is the multivariate counterpart of a Student’s t-test, was conducted on the two-component PCA model. In brief the scores for each sample were applied to a multiple linear regression model using a dummy variable to encode the classes (left-sided colitis, pancolitis, and dysplasia, respectively). The calculations were performed in R. Dysplasia was tested against pancolitis and left-sided colitis, respectively.

source_name: Colonic mucosal biopsy from patient with pancolitis

label_protocol: In accordance with the Affymetrix protocol and the one-cycle eukaryotic target labelling assay, biotin-labelled cRNA was produced

extract_protocol: RNA was extracted with the NucleoSpin® RNA/Protein mini kit (Macherey-Nagel, Düren, Germany) in accordance with the manufactures protocol. Integrity (only samples with a RNA integrity number above 7 were included) and purity were verified with an Agilent Bioanalyzer (Palo Alto, CA, USA).

tag: tissue

value: Colonic mucosal biopsy from the left side of the colon

value: pancolitis


title: V_5_Pregnant_CumulusCells

value: Agilent Universal Human Reference RNA


title: Prostate Tumor 46

description: Prostate tumor sample

tag: radical prostatectomy


title: sample850

city: Homburg

first: Andreas

last: Keller

institute: Saarland University

label_protocol: MPEA, microfluidic primer extension assay Biotin labeling

extract_protocol: Blood of controls and patients was extracted in PAXgene Blood RNA tubes (BD, Franklin Lakes, New Jersey USA). The content of blood sampling tubes of each patient and healthy donor was used for RNAe extraction. The total RNA including the miRNA was isolated using the miRNeasy kit (Qiagen GmbH, Hilden) according to manufacturers instructions..


title: R_5_Pregnant_GranulosaCells

value: Granulosa cells


title: colonic mucosal biopsy from pancolitis 18


title: M_2_NonPregnant_GranulosaCells


title: colonic mucosal biopsy from pancolitis 19


title: O_5_Unfertilized_GranulosaCells


title: V_5_Pregnant_GranulosaCells


title: sample848


title: Prostate Tumor 44

description: Prostate tumor sample

tag: biochemical progression (bp)


title: AB_2_Unfertilized_GranulosaCells


title: colonic mucosal biopsy from pancolitis 14


title: sample851


title: colonic mucosal biopsy from pancolitis 13


title: AA_4_NonPregnant_GranulosaCells


title: sample847


title: colonic mucosal biopsy from pancolitis 16


title: Prostate Tumor 45

description: Prostate tumor sample

tag: bp free interval (months)


title: colonic mucosal biopsy from pancolitis 15


title: C_1_NonPregnant_CumulusCells


title: colonic mucosal biopsy from pancolitis 11


title: Prostate Tumor 43

description: Prostate tumor sample

tag: death of prostate cancer


title: colonic mucosal biopsy from pancolitis 12


title: sample845


title: colonic mucosal biopsy from pancolitis 8


title: sample844


title: colonic mucosal biopsy from pancolitis 9


title: colonic mucosal biopsy from pancolitis 10


title: sample843


title: AK_1_Pregnant_GranulosaCells


title: Prostate Tumor 41

description: Prostate tumor sample

tag: follow-up (months)


title: sample846

tag: disease


title: sample842


title: Prostate Tumor 38

description: Prostate tumor sample

tag: gender


title: sample841

value: psoriasis


title: Prostate Tumor 40

description: Prostate tumor sample

value: Male

tag: age


title: Prostate Tumor 37

description: Prostate tumor sample

value: Prostate tissue


title: Prostate Tumor 42

description: Prostate tumor sample


title: Prostate Tumor 39

description: Prostate tumor sample

value: no


title: sample840


title: AB_2_Unfertilized_CumulusCells

tag: ivf outcome


title: Prostate Tumor 36

description: Prostate tumor sample

value: Prostate tumor


title: M_1_Unfertilized_CumulusCells

tag: cell type


title: P_1_NonPregnant_GranulosaCells

tag: reference


title: colonic mucosal biopsy from pancolitis 7


title: C_1_NonPregnant_GranulosaCells


title: colonic mucosal biopsy from pancolitis 4


title: H_1_Unfertilized_GranulosaCells


title: Z_0_NonPregnant_GranulosaCells


title: colonic mucosal biopsy from pancolitis 5


title: colonic mucosal biopsy from pancolitis 6


title: U_1_Pregnant_CumulusCells


title: colonic mucosal biopsy from pancolitis 2


title: Prostate Tumor 34

description: Prostate tumor sample

tag: sample type

value: yes


title: sample836


title: sample837

value: others


title: Prostate Tumor 32

description: Prostate tumor sample

tag: disease state


title: Prostate Tumor 35

description: Prostate tumor sample

tag: total gleason score


title: Prostate Tumor 33

description: Prostate tumor sample

tag: t clinical stage


title: sample838


title: sample839


title: sample860


title: sample834


title: sample835

value: colon cancer


title: colonic mucosal biopsy from pancolitis 3


title: colonic mucosal biopsy from pancolitis 1


title: sample833


title: Prostate Tumor 30

description: Prostate tumor sample

tag: ki-67 index (%)


title: Prostate Tumor 31

description: Prostate tumor sample


title: colonic mucosal biopsy from left-sided colitis 19

source_name: Colonic mucosal biopsy from patient with left-sided coltis

tag: tissue

value: left-sided coltis


title: AG_3_Pregnant_CumulusCells

value: Pregnant


title: Prostate Tumor 29

description: Prostate tumor sample

tag: radical prostatectomy


title: colonic mucosal biopsy from left-sided colitis 17


title: H_1_Unfertilized_CumulusCells

value: Unfertilized

value: Cumulus cells


title: AE_2_Unfertilized_GranulosaCells


title: colonic mucosal biopsy from left-sided colitis 20


title: AN_2_NonPregnant_CumulusCells

value: NonPregnant


title: AJ_2_NonPregnant_CumulusCells


title: Prostate Tumor 27

description: Prostate tumor sample

tag: biochemical progression (bp)


title: Prostate Tumor 28

description: Prostate tumor sample

tag: bp free interval (months)


title: sample832

value: Wilms Tumor


title: AA_4_NonPregnant_CumulusCells


title: sample831

value: Renal cancer


title: colonic mucosal biopsy from left-sided colitis 16

value: Colonic mucosal biopsy from the left side of the colon


title: sample830


title: M_2_NonPregnant_CumulusCells

value: Agilent Universal Human Reference RNA


title: Prostate Tumor 26

description: Prostate tumor sample

tag: death of prostate cancer


title: Prostate Tumor 25

description: Prostate tumor sample

tag: follow-up (months)


title: sample829

tag: disease

value: lung cancer


title: sample828


title: Prostate Tumor 24

description: Prostate tumor sample

tag: gender

value: Male


title: U_7_NonPregnant_CumulusCells


title: colonic mucosal biopsy from left-sided colitis 15


title: Prostate Tumor 23

description: Prostate tumor sample

value: Prostate tissue

tag: age


title: sample827


title: colonic mucosal biopsy from left-sided colitis 13


title: colonic mucosal biopsy from left-sided colitis 14


title: colonic mucosal biopsy from left-sided colitis 10


title: AI_5_Pregnant_CumulusCells

tag: ivf outcome


title: AJ_3_Unfertilized_CumulusCells_replicate

tag: cell type


title: O_5_Unfertilized_GranulosaCells_replicate

value: Granulosa cells

tag: reference


title: colonic mucosal biopsy from left-sided colitis 18


title: colonic mucosal biopsy from left-sided colitis 11


title: colonic mucosal biopsy from left-sided colitis 12


title: V_5_Pregnant_CumulusCells_replicate


title: Z_2_Unfertilized_CumulusCells


title: colonic mucosal biopsy from left-sided colitis 9


title: sample826


title: Prostate Tumor 22

description: Prostate tumor sample

tag: sample type

value: Prostate tumor

value: no


title: sample825


title: Prostate Tumor 21

description: Prostate tumor sample

tag: disease state

value: yes


title: sample824


title: Prostate Tumor 20

description: Prostate tumor sample

tag: total gleason score


title: sample823


title: Prostate Tumor 19

description: Prostate tumor sample

tag: t clinical stage


title: AB_2_Unfertilized_GranulosaCells_replicate


title: colonic mucosal biopsy from left-sided colitis 8


title: Prostate Tumor 18

description: Prostate tumor sample

tag: ki-67 index (%)


title: sample822


title: colonic mucosal biopsy from left-sided colitis 6

tag: tissue


title: Prostate Tumor 17

description: Prostate tumor sample

tag: radical prostatectomy


title: Prostate Tumor 16

description: Prostate tumor sample

tag: biochemical progression (bp)


title: sample821

value: psoriasis


title: Z_2_Unfertilized_GranulosaCells


title: sample820


title: colonic mucosal biopsy from left-sided colitis 7

value: left-sided coltis


title: Prostate Tumor 15

description: Prostate tumor sample

tag: bp free interval (months)


title: sample819

value: others


title: P_4_Unfertilized_CumulusCells

value: Unfertilized


title: P_4_Unfertilized_GranulosaCells


title: Prostate Tumor 14

description: Prostate tumor sample

tag: death of prostate cancer


title: colonic mucosal biopsy from left-sided colitis 5


title: G_1_Unfertilized_CumulusCells

value: Cumulus cells


title: AM_1_Unfertilized_GranulosaCells


title: Prostate Tumor 13

description: Prostate tumor sample

tag: follow-up (months)


title: U_1_Pregnant_GranulosaCells

value: Pregnant


title: O_7_Pregnant_CumulusCells


title: colonic mucosal biopsy from left-sided colitis 4


title: sample817

tag: disease


title: G_1_Unfertilized_GranulosaCells


title: colonic mucosal biopsy from left-sided colitis 2


title: colonic mucosal biopsy from left-sided colitis 3


title: colonics mucosal biopsy from dysplasia 6

source_name: Colonic mucosal biopsy from patient with ulcerative colitis-associated dysplasia

value: ulcerative colitis-associated dysplasia


title: AN_2_NonPregnant_GranulosaCells

value: NonPregnant


title: Prostate Tumor 11

description: Prostate tumor sample

tag: gender


title: Prostate Tumor 12

description: Prostate tumor sample

tag: age


title: sample818

value: chronic obstructive pulmonary disease (COPD)


title: sample814

value: Wilms Tumor


title: sample815


title: sample816


title: Prostate Tumor 10

description: Prostate tumor sample


title: Prostate Tumor 9

description: Prostate tumor sample


title: sample813

value: lung cancer


title: Prostate Tumor 8

description: Prostate tumor sample

value: Male


title: sample811


title: sample812


title: Prostate Tumor 7

description: Prostate tumor sample

value: Prostate tissue


title: sample810

value: colon cancer


title: AR_4_NonPregnant_CumulusCells

tag: ivf outcome

value: Agilent Universal Human Reference RNA


title: J_1_NonPregnant_GranulosaCells

tag: cell type

value: Granulosa cells


title: colonic mucosal biopsy from left-sided colitis 1

value: Colonic mucosal biopsy from the left side of the colon


title: H_2_Pregnant_GranulosaCells

tag: reference


title: Z_3_NonPregnant_CumulusCells


title: AB_7_Unfertilized_CumulusCells


title: Prostate Tumor 6

description: Prostate tumor sample

tag: sample type

value: Prostate tumor

value: no

value: yes


title: AP_1_Pregnant_GranulosaCells


title: colonic mucosal biopsy from Control 15

source_name: Colonic mucosal biopsy from control individual

tag: disease state

value: control


title: colonic mucosal biopsy from Control 14


title: colonics mucosal biopsy from dysplasia 1


title: colonics mucosal biopsy from dysplasia 5


title: colonics mucosal biopsy from dysplasia 2


title: colonics mucosal biopsy from dysplasia 3


title: colonics mucosal biopsy from dysplasia 4


title: Prostate Tumor 4

description: Prostate tumor sample

tag: total gleason score


title: sample809


title: Prostate Tumor 3

description: Prostate tumor sample

tag: t clinical stage


title: Prostate Tumor 5

description: Prostate tumor sample

tag: ki-67 index (%)


title: sample807


title: 2G_2_Pregnant_GranulosaCells


title: sample806


title: Prostate Tumor 2

description: Prostate tumor sample


title: sample805


title: Prostate Tumor 1

description: Prostate tumor sample


title: sample804


title: M_1_Unfertilized_GranulosaCells

value: Unfertilized


title: sample803


title: colonic mucosal biopsy from Control 12

tag: tissue


title: U_7_NonPregnant_GranulosaCells


title: sample802

value: others


title: colonic mucosal biopsy from Control 11


title: AJ_3_Unfertilized_CumulusCells

value: Cumulus cells


title: sample801


title: colonic mucosal biopsy from Control 9


title: SZ95 cells 36 hours differentiated rep2

city: Munich

first: Maik

last: Dahlhoff

state: Bavaria

address: Feodor-Lynen-Str. 25

department: Gene Center

institute: LMU Munich

description: Gene expression after 36 hr in differentiated SZ95 cells

hyb_protocol: 600 ng of Cy3-labelled cRNA  was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x GEx Hybridization Buffer HI-RPM was added to stop the fragmentation. And then hybridized to Agilent G4851A surePrint G3vHmn GE 8*60K Microarrays  for 17 hours at 65 °C in a rotating Agilent hybridization oven with 10 rpm.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 31 °C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent).

source_name: differentiated 36 hours

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input QuickAmp Labeling kit (Agilent) according to the manufacturer's instructions, followed by Qiagens RNAeasy mini spin column purification.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: SZ95 sebocytes were cultured in Sebomed® medium (Biochrom, Berlin, Germany) supplemented with 10% fetal calf serum (PAA, Pasching, Austria) and 5 µg/l epidermal growth factor (EGF, Biochrom). The cells were incubated at 37°C in a humidified incubator at 5% CO2.

extract_protocol: RNA was isolated for cells yield in 1 ml Trizol. RNA was precipitated with chloroform and isopropanol and washed twice with ethanol. RNA was solved in water and then precipitated in NaAc-ethanol again. Finally the RNA was solved in water and quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: For differentiation, cells were cultured in the medium indicated above including linoleic acid (LA; 10-4 M, Merck, Darmstadt, Germany) for 6 hours, 18 hours and 36 hours and without EGF. Undifferentiated SZ95 Cells were cultured like indicated above.

tag: treatment

value: linoleic acid

tag: time

value: 36 hours

value: female

tag: cell line


title: rlma.D 2

city: Leiden

first: Benjamin

middle: M.

last: Nitsche

state: The Netherlands

address: Sylviusweg 72

department: Institute of Biology

country: Netherlands

institute: Leiden University

hyb_protocol: The GeneChip Hybridization, Wash and Stain Kit (#900720) is used for the for the hybridizations, washing, staining and scanning of the chips. The Affymetrixprotocols are strictly followed. The Affymetrix custom Aspergilus niger Genome Arrays are used for hybridization. To the 270 μl hybridization cocktail, 30 μl labeled material is added according the manual of the Affymetrix One Cycle Target Labeling Kit.

scan_protocol: Standard Affymetrix protocol

data_processing: RMA background correction, normalization and probe summarization steps were performed according to the default setting of the RMA package as implemented in Bioconductor.

organism: Aspergillus niger

source_name: whole fungal mycelium, A. niger strain MA47.1 ( rlmA deletion in AB4.1 background)

label_protocol: The Affymetrix One-Cycle Target Labeling Kit and Control Reagents (#900493) are used to synthesize Biotin-labeled cRNA. From each RNA sample 2 μg is used for the labeling experiments.

growth_protocol: For treatment with FK506 and aureobasidin A, freshly harvested conidia (5x10^8) from strain N402 were used to inoculate 0.5 liters of FM. Cultivations were performed in BioFlo/CelliGen 115 bioreactors (New Brunswick Scientific). In brief, 250 rpm were used as agitation speed and aeration was performed via the headspace until the dissolved oxygen tension dropped to 40%. Thereafter, aeration was switched to sparger aeration. Temperature and pH were set to 30 °C and pH 3, respectively, and controlled on-line using the program NBS Biocommand. After 5 h of cultivation, AbaA (dissolved in 5 ml ethanol) or FK506 (dissolved in 5 ml DMSO) was added. 5 ml of ethanol or 5 ml of DMSO were added in the control runs. After an additional hour of cultivation, 500 ml of the culture broth were quickly harvested via filtration, and mycelial samples were immediately frozen using liquid nitrogen. In addition, samples were taken for microscopic analysis (see below) and calculation of the BI value. Cultivations of the strain lacking the rlmA gene were performed in a BioFlo3000 bioreactor (New Brunswick Scientific). Freshly harvested conidia (5× 10^9) were inoculated in 5 liters of FM medium and bioreactor runs were performed as described as described above. Each bioreactor run was performed twice (biological duplicate).

extract_protocol: Total RNA was isolated from homogenized mycelial samples using TRIzol reagent (Invitrogen) followed column purification including a DNAse I treatment.

treatment_protocol: See growth protocol

tag: genotype

value: rlmA deletion

tag: time point

value: germlings


title: rlma.D 1


title: NC3 2

source_name: whole fungal mycelium, wild type strain N402

value: wild type

value: DMSO (control for FK506)


title: SZ95 cells 36 hours undifferentiated rep2

description: Gene expression after 36 hr in undifferentiated SZ95 cells

source_name: undifferentiated 36 hours


title: colonic mucosal biopsy from Control 8


title: NC3 1


title: SZ95 cells 36 hours differentiated rep1


title: SZ95 cells 36 hours undifferentiated rep1


title: colonic mucosal biopsy from Control 10


title: colonic mucosal biopsy from Control 5


title: NC2 2

value: EtOH (control aureobasidin A control)


title: SZ95 cells 18 hours differentiated rep1

description: Gene expression after 18 hr in differentiated SZ95 cells

source_name: differentiated 18 hours

value: 18 hours


title: colonic mucosal biopsy from Control 3

value: Colonic mucosal biopsy from the left side of the colon


title: SZ95 cells 18 hours undifferentiated rep1

description: Gene expression after 18 hr in undifferentiated SZ95 cells

source_name: undifferentiated 18 hours


title: colonic mucosal biopsy from Control 7


title: SZ95 cells 18 hours differentiated rep2


title: colonic mucosal biopsy from Control 6


title: sample799

address: Building 60

hyb_protocol: according to manufacturers instruction (febit biomed)

scan_protocol: Wizard software on standard Microsoft Windows Workstation PC

source_name: RNA from blood

tag: disease


title: colonic mucosal biopsy from Control 4


title: SZ95 cells 18 hours undifferentiated rep2

tag: gender


title: NC2 1


title: sample800


title: sample797

value: chronic obstructive pulmonary disease (COPD)


title: sample798


title: colonic mucosal biopsy from Control 2


title: SZ95 cells 6 hours differentiated rep2

description: Gene expression after 6 hr in differentiated SZ95 cells

source_name: differentiated 6 hours

value: 6 hours


title: sample796


title: NC1 1

growth_protocol: For treatment with FK506 and aureobasidin A, freshly harvested conidia (5x10^8) from strain N402 were used to inoculate 0.5 liters of FM. Cultivations were performed in BioFlo/CelliGen 115 bioreactors (New Brunswick Scientific). In brief, 250 rpm were used as agitation speed and aeration was performed via the headspace until the dissolved oxygen tension dropped to 40%. Thereafter, aeration was switched to sparger aeration. Temperature and pH were set to 30 °C and pH 3, respectively, and controlled on-line using the program NBS Biocommand. After 5 h of cultivation, AbaA (dissolved in 5 ml ethanol) or FK506 (dissolved in 5 ml DMSO) was added. 5 ml of ethanol or 5 ml of DMSO were added in the control runs. After an additional hour of cultivation, 500 ml of the culture broth were quickly harvested via filtration, and mycelial samples were immediately frozen using liquid nitrogen. In addition, samples were taken for microscopic analysis (see below) and calculation of the BI value. Cultivations of the strain lacking the rlmA gene as well as caspofungin and fempropimorph treatments of the wild-type and the corresponding control were performed in BioFlo3000 bioreactors (New Brunswick Scientific). Freshly harvested conidia (5× 10^9) were inoculated in 5 liters of FM medium and bioreactor runs were performed as described as described above. Each bioreactor run was performed twice (biological duplicate).

value: water (control for rlmA deletion and treatment with  caspofungin/fenpropimorph treatment)


title: NC1 2


title: SZ95 cells 6 hours differentiated rep1


title: colonic mucosal biopsy from Control 1

value: control


title: sample795

value: colon cancer


title: sample794


title: SZ95 cells 6 hours undifferentiated rep2

description: Gene expression after 6 hr in undifferentiated SZ95 cells

source_name: undifferentiated 6 hours


title: FP 2

value: fenpropimorph


title: FP 1


title: R1 ES cells rep3

first: jiayu

last: chen

address: No1239, Siping Road

institute: Tongji University

description: R1 ES cells repeat_3

hyb_protocol: Hybridization, wash and Stain Kit (Affymetrix, Inc.)

scan_protocol: GeneChip® Scanner 3000 7G 3000 (Affymetrix, Inc.)

data_processing: The raw image files were processed by Bioconductor “Affy” and “vsn” package, the intensity of probes in arrays passed quality control were calculated and normalized for expression value.

source_name: mouse embryonic stem cells

label_protocol: WT Terminal Labeling Kit (Affymetrix, Inc.)

growth_protocol: The iPS cells and R1 ES cells were cultured on mitomycin C treated MEFs in ES medium containing DMEM medium (Gibco Invitrogen, Carlsbad, CA) supplemented with 15% (v/v) fetal bovine serum (FBS), 1 mM L-glutamine, 0.1 mM mercaptoethanol, 1% nonessential amino acid stock, and 1000 U/ml LIF. The OT secondary induction cells were derived from OT-iPSC mice and cultured with Feeder Medium for 3 passages. On passage 3, the culture were changed to ES Medium with doxycycline for 1 day.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Invitrogen).

treatment_protocol: The cells were cultured until the appropriate stage. The culture medium were though out and washed with PBS. The cells were centrifuge dissociated by 0.05% trypsin EDTA. The ESCs were added 2-folds-volume ESM and dissociated to single cells. The cell suspension were plated in new dishes for 0.5hr(37℃) to clear away the feeder cells. The supernatant supension were further collected carefully and centrifuged for RNA extraction. The fibroblasts were centrifuged to collect the cells and treated with Trizol (Invitrogen).

value: embryonic stem cells

tag: stage of passages

tag: strain/background


title: sample808


title: sample793


title: R1 ES cells rep2

description: R1 ES cells repeat_2

tag: cell type


title: AML_paired_case_3_DMSO

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: The data were analyzed with BRB ArrayTools using RMA. Intensity values were log2 transformed

source_name: mononuclear cells from bone marrow

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using the 3' IVT Express Kit from Affymetrix according to the manufacturer's recommendations.

extract_protocol: The total RNA was purified with a TRIzol-based protocol.

treatment_protocol: Primary AML samples were cultivated using RPMI 1640 (Biochrom AG, Berlin, Germany), supplemented with 20% FCS (Sigma-Aldrich, St. Louis, MO, USA), 2 mM L-Glutamin (Biochrom AG), and Penicillin/Streptomycin (GIBCO, Invitrogen Corporation, Grand Island, NY, USA). Prior to treatment, cells were stained with trypan blue (Sigma-Aldrich), counted, and diluted to a density of 1.0x106 cells/ml. Thawing of viably frozen samples followed the DSMZ (German Collection of microorganisms and cell lines, Braunschweig) guideline. Agents used to treat primary AML sample for 24 hours in vitro were DMSO (control/carrier; dimethyl sulfoxide; Sigma-Aldrich) and BV6 was synthesized at Genentech, Inc. (South San Francisco, CA, USA).

tag: age (years)

value: m

tag: sample source

value: BM

tag: karyotype

value: WT

tag: cebpa

tag: bv6 response

value: resistant

value: DMSO


title: sample792


title: FK506 2

value: wild type

value: germlings


title: R1 ES cells rep1

description: R1 ES cells repeat_1


title: FK506 1


title: AML_paired_case_2_DMSO

source_name: mononuclear cells from peripheral blood

value: PB


title: SZ95 cells 6 hours undifferentiated rep1

value: female


title: AML_paired_case_3_BV6


title: colonic mucosal biopsy from Control 13

value: Colonic mucosal biopsy from the left side of the colon

tag: disease state


title: AML_paired_case_1_DMSO

value: MUT


title: AML_paired_case_2_BV6


title: sample791


title: sample789


title: sample790


title: CA 2

value: caspofungin


title: Fibroblast cell line rep2

description: Fibroblast cells repeat 2

source_name: mouse fibroblast cells

value: fibroblast cells


title: sample785

value: Renal cancer


title: Fibroblast cell line rep3

description: Fibroblast cells repeat 3


title: AbA 2

value: aureobasidin A


title: sample788


title: CA 1


title: Fibroblast cell line rep1

description: Fibroblast cells repeat 1


title: sample786


title: AML_paired_case_5_BV6

value: sensitive


title: iPS cell line rep3

description: OT#b iPSC_repeat 3

source_name: mouse pluripotent iPS cells

value: Oct4 and Tet1 induced iPS cells


title: AbA 1


title: iPS cell line rep2

description: OT#b iPSC_repeat 2


title: iPS cell line rep1

description: OT#b iPSC_repeat 1


title: OT-1D cells (intermediate stage) rep1

description: Oct4+Tet1-mediated reprogrammed Day1 cells_repeat 1

source_name: mouse fibroblast cell under reprogramming

value: OT-iPSC derived fibroblast cells

value: supply with doxycycline for 1 day


title: AML_paired_case_6_DMSO

value: f

value: WT


title: AML_paired_case_5_DMSO

value: m

value: DMSO


title: AML_paired_case_1_BV6

value: resistant


title: AML_30

value: BM

value: untreated


title: AML_paired_case_4_DMSO


title: AML_paired_case_6_BV6

value: PB


title: AML_3

value: MUT


title: OT-1D cells (intermediate stage) rep3

description: Oct4+Tet1-mediated reprogrammed Day1 cells_repeat 3


title: sample784


title: sample781


title: OT-1D cells (intermediate stage) rep2

description: Oct4+Tet1-mediated reprogrammed Day1 cells_repeat 2


title: sample787


title: sample783


title: sample780


title: T4.WSB#2

city: Boston

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

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: Spleen

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

tag: age

value: 6 weeks

tag: exclusion markers

tag: genetic background

value: WSB/EiJ

tag: phenotype markers

tag: separation method

value: FACs Aria

tag: Sex

value: Male


title: sample779

tag: disease

value: Renal cancer


title: sample778

value: Wilms Tumor


title: sample782


title: AML_paired_case_4_BV6

tag: gender

value: sensitive

tag: treatment


title: AML_25


title: P6_Rep3

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

description: Replicate 3 of 3. Differentiating neuroblastoma #2.

hyb_protocol: Hybridization was performed according to the Agilent 60-mer oligo microarray processing protocol v2.1 with the following modifications: 2 microgram labeled DNA per channel were mixed; no fractionation; probes were denatured for 3 min at 98 degree celcius; hybridization at 65 degree celcius; SSPE washes as recommended; slides were dipped in acetonitril (10 s) then dried.

scan_protocol: Scanned with a G2505B Microarray Scanner (Agilent Technologies). Quantification software: Feature Extraction 9 (Agilent Technologies).

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOESS normalization.

source_name: neuroblastoma, patient 6

label_protocol: The samples for hybridization were prepared from total RNA according to the Atlas SMART Fluorescent Probe Amplification Kit protocol (Clontech-Takara Bio Europe), with minor modifications: The RNA template was hydrolyzed under alkaline conditions before cDNA purification, and the PCR amplification process was monitored and stopped in the exponential phase. Quantity and Cy-dye incorporation rates of the generated target material were assessed using a NanoDrop ND-100 spectrophotometer.

growth_protocol: NB cell line SH-EP was cultured at 37C, 5% CO2 and grown in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum (FBS). A total of six NB samples (P1-P6) were obtained prior to cytotoxic therapy from patients participating in the NB97 German Neuroblastoma Study Group following informed consent. Selected tumors were localized in the adrenal glands and contained at least 60% tumor cells.

extract_protocol: Total RNA was isolated from 30 to 60 mg of snap-frozen tissue or cell cultures using Qiagen’s RNeasy MiniKit.

treatment_protocol: Treatment with helminthosporium carbonum (HC)-toxin (15 nM) and valproic acid (VPA; 1 mM) was carried out as indicated. Dulbecco’s phosphate-buffered saline (DPBS) served as solvent for VPA, methanol for HC-toxin.

tag: tissue

value: neuroblastoma

tag: nb differentiation degree

value: differentiating neuroblastoma #2

source_name: Total RNA from pooled NB cells

tag: sample type

value: reference


title: AML_12

tag: age (years)

value: m

tag: sample source

value: WT


title: sample777


title: LX2 C 1

city: ShangHai

first: Yang

last: Bu

address: 180 Fenglin Road

institute: Liver Cancer Institute, Zhongshan Hospital, Fudan University

hyb_protocol: The pre-hybridization of HOAv6.1 arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled aaRNA was hybridize on HOA v6.1 in dulication (two arrays for each sample) at 50℃ for 16 hour in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Agilent G2505C scanner (635nm PMT 10 ; 532nm PMT 10) and quantify the fluoresence intensity.

data_processing:
The data processing was processed by Rosetta Resolver® System (Rosetta Biosoftware, USA). We filtered the spots in which flag=-50 within all arrays and control probes. Probes passed filter were normalized by median scaling to remove systemic effect, then combine the duplicate data by averaging their intensity value.
The pairwised comparison were performed by Rosetta Resolver® System error-weighted modeling to find significant diffrential expressed probes (log2 |Fold change| ≥ 1 and P < 0.05).

source_name: control, HSC

label_protocol: aaRNAs were amplified using Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion #AM1753, CA, USA) from 1μg total RNA and directed labeled by NHS-CyDye (Cy5, Amershan) to uridine (dUTP).

growth_protocol: Hepatic stellate cells(HSC) was selected and cultured for study.

extract_protocol: RNA extraction by Qiagen RNeasy Mini kit (Qiagen, Chatsworth, CA, USA) . RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧ 1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧7).

treatment_protocol: A  cell line of HSC was cultured according to standard protocol. Total RNA was isolated from this cell line using the Qiagen RNeasy Mini kit (Qiagen, Chatsworth, CA, USA) according to manufacture’s protocols.

tag: cell line

value: hepatic stellate cell line LX2

tag: agent

value: control


title: T4.SM#1

last: Yang

value: SM/J


title: T4.WSB#1


title: T4.SM#2


title: T4.SJL#2

value: SJL/J


title: LX2 C 3


title: LX2 C 2


title: LX2 Syy 2

source_name: Syy, HSC

value: Syy


title: LX2 Syy 1


title: sample776


title: T4.SJL#1

value: 6 weeks


title: sample774


title: LX2 Syy 3


title: T4.SWR#1

value: SWR/J