title: KT2440turBHis(pCAR1)

first: Hideaki

last: Nojiri

address: 1-1-1 Yayoi, Bunkyo-ku

department: Biotechnology Research Center

institute: The University of Tokyo

description: This is an Affymetrix custom-commercial tiling array that covers thePseudomonas putida KT2440 chromosome (RefSeq: NC_002947) at 11-bp density.  BPMAP files are provided as supplementary files. KT2440b520511FR-3.bpmap represents  the forward strand of KT2440 chromosome, and KT2440b520511FF-3.bpmap represents the reverse strand of KT2440 chromosome.

hyb_protocol: The labelled samples were hybridized individually with each chip using a GeneChip Hybridization Oven 640 (Affymetrix) at 60 rpm and 50°C for 16 h. The chips were then washed and stained using a Hybridization, Wash and Stain Kit (Affymetrix) according to a modified version of the FleX450-0005 protocol of the GeneChip Fluidics station 450 (Affymetrix)

scan_protocol: Signals were detected using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
The CEL files were generated using Affymetrix GCOS. Data was quantile normalized and analyzed with Affymetrix Tiling Analysis Software v1.1, which uses non-parametric quantile normalization and a Hodges-Lehmann estimator for fold enrichment.The intensities were linearly scaled so that the median was 100. Each CEL file was converted into the BAR files using KT2440b520511FR-3.bpmap for the forward strand and KT2440b520511FF-3.bpmap for the reverse strand; the BAR files with F indicate the forward strand and with R indicate the reverse strand of KT2440 chromosome. Bandwidth: 30, Threshold: 0, MaxGap: 30, MinRun, 30.
KT2440b520511FR-3.bpmap BPMAP for the forward strand of KT2440 chromosome
KT2440b520511FF-3.bpmap BPMAP for the reverse strand of KT2440 chromosome

organism: Pseudomonas putida

source_name: ChIPed DNA prepared from succinate culture of KT2440turBHis(pCAR1) in log phase

label_protocol: Labelling of the cDNA or DNA was achieved using a GeneChip WT Double-Stranded DNATerminal Labeling Kit (Affymetrix, Santa Clara, CA).

growth_protocol: An overnight culture of each strain in LB at 30°C was inoculated into 100 ml NMM-4 supplemented with 0.1% (wt/vol) succinate to obtain an initial turbidity at 600 nm of 0.05 and then incubated at 30°C in a rotating shaker at 120 rpm for 4 h (log phase, a turbidity at 600 nm of 0.15 to 0.25) or 8 h (early-stationary phase, a turbidity at 600 nm of 0.35 to 0.4).

extract_protocol: [Transcriptome analysis] Cells were treated with RNA Protect Bacteria reagent (Qiagen, CA, USA). Total RNA was extracted using NucleoSpin RNA II (Macherey-Nagel GmbH & Co. KG, Düren, Germany) and RNeasy Midi kit (Qiagen). The eluted RNA was treated with RQ1 RNase-free DNase (Promega, Madison, WI). After inactivation of DNase by the addition of the provided stop reagent and subsequent incubation, total RNA was repurified using NucleoSpin RNA Clean-up (Macherey-Nagel). cDNA was synthesized using SuperScript II (Invitrogen, Carlsbad, CA) in the presence of actinomycin D (Sigma, St.Louis, USA) to prevent generation of spurious second-strand cDNA. [ChIP-chip analysis] Cells were disrupted by sonication and His-tagged proteins were purified by QuickPick IMAC metal affinity kit (Bio-Nobile, Turku, Finland). Cross-links were dissociated by heating and the resulting DNA was purified using Qiaquick kit (Qiagen).

treatment_protocol: [ChIP-chip analysis] Cells were treated with formaldehyde to a final concentration of 1% to cross-link proteins and DNA.

tag: treatment


title: 5N

status: Public on Sep 03 2015

type: RNA

city: Cambridge

first: Muhammad

middle: Abdullah

last: Alvi

address: Addenbrooke's site

country: United Kingdom

institute: University of Cambridge

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol using iScan

data_processing: Non-normalized and average normalised (background subtracted) using GenomeStudio v2011.1 9

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Standard Illumina protocol

extract_protocol: RNA was extracted using RNeasy FFPE Kit (Qiagen, UK)

tag: source

value: FFPE tissue blocks

tag: pathology

value: Normal small bowel epithelium from a cancer patient


title: KT2440(pCAR1pmrHis)

type: genomic

city: Tokyo

country: Japan

molecule: genomic DNA

source_name: ChIPed DNA prepared from succinate culture of KT2440(pCAR1pmrHis) in log phase

tag: strain


title: 6N


title: KT2440turAHis(pCAR1)

source_name: ChIPed DNA prepared from succinate culture of KT2440turAHis(pCAR1) in log phase


title: KT2440DturB(pCAR1)_ES

source_name: cDNA prepared from succinate culture of KT2440DturB(pCAR1) in early-stationary phase


title: 8N


title: KT2440DturA(pCAR1)_ES

source_name: cDNA prepared from succinate culture of KT2440DturA(pCAR1) in early-stationary phase


title: KT2440DturB(pCAR1)_L

source_name: cDNA prepared from succinate culture of KT2440DturB(pCAR1) in log phase


title: 1N


title: 2N


title: KT2440(pCAR1Dpmr)_L

source_name: cDNA prepared from succinate culture of KT2440(pCAR1Dpmr) in log phase


title: KT2440DturA(pCAR1)_L

source_name: cDNA prepared from succinate culture of KT2440DturA(pCAR1) in log phase


title: KT2440(pCAR1Dpmr)_ES

source_name: cDNA prepared from succinate culture of KT2440(pCAR1Dpmr) in early-stationary phase


title: 19716824

city: Madrid

first: Nerea

last: Matamala

address: Calle de Pedro Rico, 6

country: Spain

institute: IDIPAZ

hyb_protocol: Total RNA was hybridized on LNA based miRNA microarrays 7th generation containing probes for 1926 human miRNAs in quadruplicate, including 1894 miRNAs from miRBase Release 18.0, 25 hsa-miRPlus not included in miRBase (Exiqon proprietary) and 7 negative controls. Labeled RNA was hybridized to miRCURY LNA™ microRNA Arrays over 16 hours at 56C using Agilent Hybridization chambers SureHyb and a rotating oven.

scan_protocol: Arrays were washed, dried and scanned with Agilent G2565AA Microarray Scanner System (Agilent Technologies). Fluorescence intensities on scanned images were measured with Agilent Feature Extraction software, version 10.7.3 (Agilent Technologies), using the modified Exiqon protocol.

data_processing: Microarray background subtraction was carried out using normexp method. To normalize the dataset, we performed quantiles between arrays normalization. Human miRNAs were filtered and replicate probes were merged by their mean profile.

source_name: normal breast tissue

label_protocol: 300 ng of RNA was CIP treated and Hy3-labeled using miRCURY LNA™ microRNA Hi-Power Labeling Kit (Exiqon)

extract_protocol: FFPE blocks were analyzed by a pathologist and the tumoral area was identified and macrodissected. Total RNA was extracted from 3 sections of 30 μm thicknesses using miRNeasy FFPE Kit (Qiagen). RNA quality and quantity was assessed by NanoDrop Spectophotometer (NanoDrop technologies).

tag: gender

value: female

tag: tissue

value: normal breast tissue

tag: dataset group

value: Training


title: 19716825

source_name: primary breast cancer_luminal A

value: primary breast cancer

tag: molecular subtype

value: luminal A

value: Test


title: MCF10A-ErbB2* cells repressing STAT3 by sh262105 vs. WT, replicate 2

city: Memphis

first: Jiyang

last: Yu

state: TN

address: 262 Danny Thomas Place, MS 1135

department: Computational Biology

country: USA

institute: St. Jude Children's Research Hospital

hyb_protocol: standard Agilent hybridization protocol

scan_protocol: standard Agilent scanning protocol

data_processing: R package "lumi", V2.8, background subtraction and LOWESS normalization

label_protocol: 100 ng of RNA were labelled using Low Input Quick Amp Labeling kit from Agilent Technologies

growth_protocol: MCF-10A cells were seeded in 6-well plates and let attach for 24 hours. Next day they were incubated with IL6 (50ug/ml) for 6 hours. MCF-10A/ErbB2* cells infectes with the inducible shRNA were incubated with Doxycycline (100ng/ml) for 5 days before RNA extraction.

extract_protocol: RNA was extracted with Rnaeasy following manufacturer instructions.

tag: cell line


title: MCF10A-ErbB2* cells repressing STAT3 by sh88502 vs. WT, replicate 2


title: MCF10A-ErbB2* cells repressing STAT3 by sh88502 vs. WT, replicate 1


title: 19716823


title: Nonunion

city: Kobe

first: Takahiro

last: Waki

state: Hyogo

address: 7-5-1, Kusunoki-cho, Chu0-ku

department: Orthopaedic Surgery

institute: Kobe University Graduate School of Medicine

description: Universal Reference means that the sample was mixed with a equal volumes of each samples.

hyb_protocol: Labeled RNA was hybridized to the microarray slide for 16-20 hr at 56 degrees C and washed with miRCURY LNA microRNA Power Labeling kit (Exiqon) according to manufacture's protocol.

scan_protocol: Hybridization signals were detected by DNA microarray scanner G2505C (Agilent Technologies) with resolution of 10 micrometres . The scanned images were analyzed using Agilent Feature Extraction ver.10.7.3.1

data_processing: At first Hy3 (samples) signal was normalized with division used Hy5 (Universal reference) signal. Then each signal value of unique probe ID was calculated from average of Hy3/Hy5 normalized signal intensities of replicated probes.

organism: Rattus norvegicus

source_name: fibrous tissue in nonunion model

label_protocol: 1000 ng of total RNA was labeled with miRCURY LNA microRNA Power Labeling kit (Exiqon) according to manufacture's protocol.

extract_protocol: On  post-fracture day 14, the newly generated specific tissues, that is, the fracture callus for the standard healing fracture and the fibrous tissue surrounding the fracture site for the nonunions, were harvested. All harvested tissues were stored in RNAlater (Ambion, Austin, TX) at 4℃ until used. The tissue specimens from 5 different animals in each group on post-fracture day 14 were pooled, and were submitted to Cosmo Bio (Tokyo, Japan) for RNA isolation and microarray analysis. Total cellular RNA including miRNA was extracted from the tissue specimens, using miRCURY RNA Isolation Kit (Exiqon, Vedbaek, Denmark) according to manufacture's protocol.

value: Sprague-Dawley

value: male

value: fibrous tissue in nonunion model

source_name: Universal Reference

tag: sample type

value: Universal Reference


title: Standard

source_name: callus in standard fracture healing model


title: 19716822


title: 4N


title: MCF10A cells exposed IL6 vs. WT, replicate 1


title: 3N


title: MCF10A cells exposed IL6 vs. WT, replicate 2


title: 19716821


title: KT2440turBHis(pCAR1)

description: This is an Affymetrix custom-commercial tiling array that covers the IncP-7 carbazole-degradative plasmid pCAR1  (RefSeq: NC_004444.1) at 9-bp density.

hyb_protocol: The labelled samples were hybridized individually with each chip using a GeneChip Hybridization Oven 640 (Affymetrix) at 60 rpm and 45°C for 16 h. The chips were then washed and stained using a Hybridization, Wash and Stain Kit (Affymetrix) according to the FlexFS450-0002 protocol of the GeneChip Fluidics station 450 (Affymetrix)

data_processing:
The CEL files were generated using Affymetrix GCOS. Data was quantile normalized and analyzed with Affymetrix Tiling Analysis Software v1.1, which uses non-parametric quantile normalization and a Hodges-Lehmann estimator for fold enrichment.The intensities were linearly scaled so that the median was 100. The replications of CEL files were together converted into the BAR files using pCAR1_8b520435FR-3.bpmap for the forward strand and pCAR1_8b520435FF-3.bpmap for the reverse strand; the BAR files with F indicate the forward strand and with R indicate the reverse strand of pCAR1. Bandwidth: 30, Threshold: 0, MaxGap: 30, MinRun, 30.
pCAR1_8b520435FR-3.bpmap BPMAP for the forward strand of pCAR1
pCAR1_8b520435FF-3.bpmap BPMAP for the reverse strand of pCAR1

value: ChIPed DNA prepared from succinate culture of KT2440turBHis(pCAR1) in log phase


title: MCF10A-ErbB2* cells repressing STAT3 by sh262105 vs. WT, replicate 1


title: KT2440(pCAR1pmrHis)

value: ChIPed DNA prepared from succinate culture of KT2440(pCAR1pmrHis) in log phase


title: KT2440turAHis(pCAR1)

value: ChIPed DNA prepared from succinate culture of KT2440turAHis(pCAR1) in log phase


title: KT2440DturB(pCAR1)_ES

value: cDNA prepared from succinate culture of KT2440DturB(pCAR1) in early-stationary phase


title: KT2440DturA(pCAR1)_L

value: cDNA prepared from succinate culture of KT2440DturA(pCAR1) in log phase


title: KT2440DturB(pCAR1)_L

value: cDNA prepared from succinate culture of KT2440DturB(pCAR1) in log phase


title: 19716820


title: KT2440DturA(pCAR1)_ES

value: cDNA prepared from succinate culture of KT2440DturA(pCAR1) in early-stationary phase


title: KT2440(pCAR1Dpmr)_L

value: cDNA prepared from succinate culture of KT2440(pCAR1Dpmr) in log phase


title: 19715719

source_name: primary breast cancer_luminal B

value: female

value: luminal B


title: 19715718

source_name: primary breast cancer_triple negative

value: primary breast cancer

value: triple negative


title: KT2440(pCAR1Dpmr)_ES

value: cDNA prepared from succinate culture of KT2440(pCAR1Dpmr) in early-stationary phase


title: 19715717

value: Training


title: 19715716

value: Test


title: 19715714

value: luminal A


title: 19715713


title: 19715715


title: 19715712


title: 19715709


title: 19715711

source_name: primary breast cancer_her2


title: 19715710


title: 19715720


title: 19715705


title: 19715707


title: 19715704


title: 19715702


title: 19715698


title: 19715699


title: 19715700


title: 19715701


title: 19715697


title: 19715696


title: 19715695


title: 19715691


title: 19715693


title: 19715692


title: 19715690


title: 19715694


title: 19715706


title: 19715689


title: 19715687


title: 19715681


title: 19715685


title: 19715686


title: 19715676


title: 19715677


title: 19715678


title: 19715680


title: 19715671


title: 19709779

value: normal breast tissue


title: 19709777


title: 19709778


title: 19715688


title: 19709775


title: 19709776


title: 19709774


title: 19715683


title: 19709773


title: 19709772


title: 19715675


title: 19709769


title: 19709767


title: 19709770


title: 19709765


title: 19709762


title: 19709763


title: 19709760


title: 19709761


title: 19709757


title: 19709758


title: 19709756


title: 19709755


title: 19709622


title: 19709621


title: 19709768


title: 19709771


title: 19709618


title: 19709620


title: 19709766


title: 19709617


title: 19709764


title: post-vaccination PBMCs no stimulation  with EV71 antigen_19

city: Beijing

first: Jun

last: Zhang

address: No.2,Tiantan Xili

country: China

institute: National Institute for Food and Drug Control

hyb_protocol: Oligoarray control targets and hybridization buffer  were added, and samples were applied to microarrays enclosed in Capitalbio hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Arrays were scanned with a confocal LuxScanTM scanner and the images obtained were then analyzed using LuxScanTM 3.0 software (CapitalBio).

data_processing: After background subtracted in both channels (Cy3 and Cy5)，faint spots were extracted for which intensities were exceed 400 units. A space- and intensity-dependent normalization based on a LOWESS program was employed.After normalized, data was log2 transformed.

label_protocol: 1 ug total RNA was used for double-stranded cDNA (ds-cDNA) synthesis with the CbcScript reverse transcriptase kit (Capitalbio) with the T7 Oligo (dT). Klenow enzyme labeling strategy was adopted after reverse transcription using CbcScript Ⅱ reverse transcriptase. Labeled cDNA were hybridized performed in a CapitalBio BioMixerTM II Hybridization Station and washed in a Capitalbio SlideWasher TM (CapitalBio) with two consecutive solutions.

growth_protocol: PBMCs (10*10^6) were plated in each well of a 6-well plate (Costar) in RPMI 1640 medium supplemented with penicillin-streptomycin (100g/ml-100U/ml; Invitrogen), L-glutamine (2mM), HEPES buffer (10mM), and 10% heat-inactivated FCS (HyClone).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Cells were cultured for 24h at 37°C with EV71 Ag (200u/ml) or Media

tag: cell type

value: PBMCs

source_name: Agilent Universal Human  Reference RNA

tag: rna source

value: Comprised of 10 cell lines for human


title: post-vaccination PBMCs no stimulation  with EV71 antigen_18


title: 19709615


title: 5T

value: FFPE tissue blocks

value: Small bowel cancer tissue from surgical resection


title: 1T


title: 19709612


title: post-vaccination PBMCs no stimulation  with EV71 antigen_16


title: 19709611


title: 19709605


title: 19709606


title: 19709610


title: post-vaccination PBMCs no stimulation  with EV71 antigen_15


title: post-vaccination PBMCs no stimulation  with EV71 antigen_13


title: 19709604


title: 19709603


title: 19709598


title: 19709601


title: 19709599


title: post-vaccination PBMCs no stimulation  with EV71 antigen_11


title: 19709602


title: 19709596


title: post-vaccination PBMCs no stimulation  with EV71 antigen_10


title: post-vaccination PBMCs no stimulation  with EV71 antigen_8


title: post-vaccination PBMCs no stimulation  with EV71 antigen_12


title: post-vaccination PBMCs no stimulation  with EV71 antigen_14


title: 19709593


title: 19709595


title: 19709592


title: post-vaccination PBMCs no stimulation  with EV71 antigen_4


title: post-vaccination PBMCs stimulation  with EV71 antigen_16


title: post-vaccination PBMCs no stimulation  with EV71 antigen_9


title: post-vaccination PBMCs no stimulation  with EV71 antigen_3


title: post-vaccination PBMCs stimulation  with EV71 antigen_17


title: post-vaccination PBMCs no stimulation  with EV71 antigen_7


title: post-vaccination PBMCs stimulation  with EV71 antigen_19


title: post-vaccination PBMCs no stimulation  with EV71 antigen_1


title: 19701993


title: post-vaccination PBMCs no stimulation  with EV71 antigen_2


title: KY2_FLAGMyb_rep3

city: Saint Louis

first: Todd

middle: A

last: Fehniger

state: MO

address: 660 S. Euclid Ave Campus Box 8007

department: Internal Medicine / Oncology

institute: Washington University in St. Louis School of Medicine

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing: Analyzed in Partek, using RMA scaling and Quantile Normalization

label: Biotin

organism: Mus musculus

source_name: KY-2 NK Cell Line + GFP-P2A-FLAGMyb

label_protocol: Standard Affymetrix

growth_protocol: KY-1 and KY-2 cell lines, cultured in cRPMI + 200U/mL hIL-15.

extract_protocol: Cellular material was resuspended in Trizol (Invitrogen) and processed using Directzol columns (Zymo Research) according to the manufacturer's instructions.

treatment_protocol: Transduced with either GFP or GFP-P2A-FLAG-Myb in above media, GFP+ sorted

tag: overexpression

tag: genotype


title: post-vaccination PBMCs stimulation  with EV71 antigen_18


title: post-vaccination PBMCs stimulation  with EV71 antigen_15


title: 28T

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing: GenomeStudio v2011.1 9

label: Cy3, Cy5

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA extracted using Maxwell 16 FFPE Plus LEV DNA Purification Kit (Promega, UK)


title: 22T


title: post-vaccination PBMCs stimulation  with EV71 antigen_12


title: KY2_FLAGMyb_rep2


title: 27T


title: 19701992


title: 18T


title: post-vaccination PBMCs stimulation  with EV71 antigen_13


title: KY2_GFP_rep2

source_name: KY-2 NK Cell Line + GFP

value: GFP


title: 23T


title: KY2_FLAGMyb_rep1


title: 24T


title: 17T


title: 25T


title: 20T


title: 21T


title: 26T


title: KY2_GFP_rep1


title: 19T


title: 15T


title: 13T


title: 16T


title: post-vaccination PBMCs stimulation  with EV71 antigen_11


title: 19701989


title: 19701987


title: 19701988


title: 12T


title: post-vaccination PBMCs stimulation  with EV71 antigen_8


title: 19701986


title: 14T


title: post-vaccination PBMCs stimulation  with EV71 antigen_10


title: 19701990


title: 19701984


title: 19701983


title: KY1_FLAGMyb_rep4

source_name: KY-1 NK Cell Line + GFP-P2A-FLAGMyb


title: KY1_FLAGMyb_rep3


title: post-vaccination PBMCs stimulation  with EV71 antigen_7


title: post-vaccination PBMCs stimulation  with EV71 antigen_9


title: 19701982


title: post-vaccination PBMCs stimulation  with EV71 antigen_4


title: post-vaccination PBMCs stimulation  with EV71 antigen_5


title: 11T


title: 19701980


title: KY1_GFP_rep3

source_name: KY-1 NK Cell Line + GFP


title: KY1_FLAGMyb_rep2


title: 9T


title: KY1_GFP_rep2


title: NK_CD27+_Ctrl_rep3

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Analyzed with Partek Genomics Suite  v6.6, using RMA scaling

source_name: Ctrl YFP+CD27+NK1.1+CD3- NK cells

label_protocol: Standard Affymetrix protocol

growth_protocol: 8-12 week old mice

treatment_protocol: Sorted immediately after spleen harvest.

value: spleen

value: CD27+ NK cells

tag: genotype/variation

value: Ctrl


title: 7T


title: 10T


title: 8T


title: 6T


title: 19701978

value: female


title: 19701979


title: pre-vaccination PBMCs no stimulation  with EV71 antigen_15


title: KY1_FLAGMyb_rep1


title: 19701977


title: 19701976


title: 5T


title: pre-vaccination PBMCs no stimulation  with EV71 antigen_11


title: NK_CD27+_Ctrl_rep2


title: KY1_GFP_rep1


title: NK_CD27+_15a/16-1FKO_rep3

source_name: 15a/16-1FKO YFP+CD27+NK1.1+CD3- NK cells


title: pre-vaccination PBMCs no stimulation  with EV71 antigen_10


title: pre-vaccination PBMCs no stimulation  with EV71 antigen_13


title: pre-vaccination PBMCs no stimulation  with EV71 antigen_14


title: NK_CD27+_15a/16-1FKO_rep2


title: 19701974


title: pre-vaccination PBMCs no stimulation  with EV71 antigen_9


title: 3T


title: NK_CD27+_15a/16-1FKO_rep1


title: NK_CD27+_Ctrl_rep1


title: 28N

value: Normal small bowel epithelium from a cancer patient


title: 4T


title: 1T


title: 19701972

value: primary breast cancer


title: 27N


title: 19701969


title: 19701966


title: pre-vaccination PBMCs no stimulation  with EV71 antigen_5


title: ERRg KO P0 cortex rep2b

city: La Jolla

first: Ruth

middle: T

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

description: technical replicate 2

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization in Illumina GenomeStudio and also using the VAMPIRE Bayesian model with a 2-sided Bonferroni-corrected threshold of 0.05.

source_name: P0 cortex

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: age

value: postnatal Day 0

value: cerebral cortex

value: ERRγ-/-


title: 25N


title: pre-vaccination PBMCs no stimulation  with EV71 antigen_8


title: 26N


title: pre-vaccination PBMCs no stimulation  with EV71 antigen_6


title: ERRg KO P0 cortex rep1

description: biological replicate 1


title: pre-vaccination PBMCs no stimulation  with EV71 antigen_4


title: 19701857

value: triple negative

value: Test


title: ERRg KO P0 cortex rep1b

description: technical replicate 1


title: pre-vaccination PBMCs no stimulation  with EV71 antigen_7


title: pre-vaccination PBMCs no stimulation  with EV71 antigen_3


title: wild-type P0 cortex rep2b

description: technical replicate 2

value: wild type


title: post-vaccination PBMCs stimulation  with EV71 antigen_2

value: PBMCs


title: 19701971


title: 19701858

value: Training


title: wild-type P0 cortex rep2

description: biological replicate 2


title: ERRg KO P0 cortex rep2

description: biological replicate 2


title: 19701981

value: luminal A


title: 23N

value: FFPE tissue blocks


title: 19701850


title: post-vaccination PBMCs stimulation  with EV71 antigen_1

value: Comprised of 10 cell lines for human


title: 24N


title: 19701851


title: wild-type P0 cortex rep1b

description: technical replicate 1


title: pre-vaccination PBMCs no stimulation  with EV71 antigen_2


title: pre-vaccination PBMCs no stimulation  with EV71 antigen_1


title: 19701856


title: wild-type P0 cortex rep1

description: biological replicate 1


title: 19701848


title: pre-vaccination PBMCs stimulation  with EV71 antigen_19


title: 22N


title: 19701846


title: NOP204C2

city: Seattle

first: Chester

last: Ni

state: WA

address: 1201 Ninth Ave

department: Systems Immunology

institute: Benaroya Research Institute

description:
Healthy control
X8363869086_L

data_processing: The data were normalised using quantile normalisation with in house R codes.  ALO (Present in at least one sample) filter is applied.

source_name: Whole blood

label_protocol: Biotinylated cRNA were prepared with the Illumina totalPrep 96 RNA amplification kit for Illumina arrays

extract_protocol: RNA was extracted with PAXgene Blood RNA Kit from Qiagen #762164. Each PAXgene Blood RNA Tube was incubated at least 2 hours at room temperature after blood draw, then centrifuged for 10 minutes at 4000 g.  The supernatant was decanted, pellet resuspended in 4 ml RNase-free water, then centrifuged for 10 minutes at 4000 g.  The pellet was incubated in 350 μl Buffer BR1, 300 μl Buffer BR2 and 40 μl proteinase K for 10 minutes at 55°C using a shaker–incubator at 400–1400 rpm.  The lysate was transferred into a PAXgene Shredder spin column (lilac) placed in a 2 ml processing tube, and centrifuge for 3 minutes at 14,000-20,000g.  The flow-through fraction was mixed with 350 μl ethanol, and added to the PAXgene RNA spin column (red) 700 μl at a time, centrifuging for 1 minute at 8000–20,000 g after each addition, discarding the flow-through fractions.  The column was washed with 350 μl Buffer BR3.  10 μl DNase I stock solution in 70 μl Buffer RDD was added to the spin column and incubated 15-30 minutes at room temperature.  The column was washed with 350 μl Buffer BR3 followed by two washes with 500 μl Buffer BR4.  RNA was eluted with 50 μl Buffer BR5 by centrifugation for 1 minute at 8000–20,000.  Samples were stored at -80°C until analyzed

tag: disease

value: Healthy control

tag: Sex


title: 21N

tag: source


title: 2T

tag: pathology

value: Small bowel cancer tissue from surgical resection


title: pre-vaccination PBMCs stimulation  with EV71 antigen_16


title: 19701841


title: NOP503C1

description:
Healthy control
X8363869086_K


title: pre-vaccination PBMCs stimulation  with EV71 antigen_13


title: 20N


title: 19701840


title: pre-vaccination PBMCs stimulation  with EV71 antigen_18


title: 19701839


title: pre-vaccination PBMCs stimulation  with EV71 antigen_11


title: NOP203C2

description:
Healthy control
X8363869086_J


title: 17N


title: pre-vaccination PBMCs stimulation  with EV71 antigen_12


title: 19701838


title: SoJIA021

description:
Systemic juvenile idiopathic arthritis
X8363869086_I

value: Systemic juvenile idiopathic arthritis

value: F


title: SoJIA020

description:
Systemic juvenile idiopathic arthritis
X8363869086_H

value: M


title: 18N

value: Normal small bowel epithelium from a cancer patient


title: 19701837

value: female

value: primary breast cancer


title: pre-vaccination PBMCs stimulation  with EV71 antigen_10


title: SoJIA019

description:
Systemic juvenile idiopathic arthritis
X8363869086_G


title: FWS018

description:
Fever Without Source. FWS defined as daily temperature ≥ 38oC for ≥ 5 days in a previously healthy child or daily fever ≥ 38oC for ≥ 2 days in a child previously-diagnosed with SJIA. Known SJIA patients were required to have been on stable doses of medications during the four weeks prior to enrollment.
X8363869086_F

value: Fever Without Source.


title: pre-vaccination PBMCs stimulation  with EV71 antigen_9


title: 14N


title: 19701836

value: triple negative


title: Kawasaki017

description:
Kawasaki disease
X8363869086_E

value: Kawasaki disease


title: 19N


title: pre-vaccination PBMCs stimulation  with EV71 antigen_7


title: 19701835


title: 16N


title: pre-vaccination PBMCs stimulation  with EV71 antigen_5


title: 19701824


title: 19701825

value: Test


title: 12N


title: pre-vaccination PBMCs stimulation  with EV71 antigen_4

value: PBMCs


title: Kawasaki014

description:
Kawasaki disease
X8363869086_C


title: Kawasaki016

description:
Kawasaki disease
X8363869086_D


title: FWS011

description:
Fever Without Source. FWS defined as daily temperature ≥ 38oC for ≥ 5 days in a previously healthy child or daily fever ≥ 38oC for ≥ 2 days in a child previously-diagnosed with SJIA. Known SJIA patients were required to have been on stable doses of medications during the four weeks prior to enrollment.
X8363869086_B


title: 19701823


title: SoJIA006

description:
Systemic juvenile idiopathic arthritis
X8363869086_A


title: pre-vaccination PBMCs stimulation  with EV71 antigen_2


title: 10N


title: SoJIA005

description:
Systemic juvenile idiopathic arthritis
X8363869084_L


title: 13N


title: pre-vaccination PBMCs stimulation  with EV71 antigen_1


title: SoJIA003

description:
Systemic juvenile idiopathic arthritis
X8363869084_K


title: 11N


title: 19701821

value: luminal B

value: Training


title: 9N

value: FFPE tissue blocks


title: 7N


title: colon_female_pup_lfd_replicate6

status: Public on Sep 02 2015

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.26.6).

source_name: colon, female pup of 14 days of age, dam received a low-fat diet

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Female C57BL/6 mice (five weeks of age) were purchased from Harlan (Horst, The Netherlands) and housed individually in the light- and temperature-controlled facility of the University Medical Center Groningen (lights on 7:00 am-7:00 pm, 21°C). Mice had free access to drinking water and were fed a semi-synthetic, low-fat [control] diet (3.85 kcal/g; 10 E% fat, 20 E% protein, 70 E% carbohydrate; D12450B, Research Diets, New Brunswick, USA). After 6 weeks, mice were mated with males and in case conceiving failed, mice were allowed to re-mate. Mice were allowed to deliver spontaneously and were left undisturbed with their litters for 24 h. Litter sizes were standardized to 5-7 pups, to ensure no litter was nutritionally biased due to lower or higher litter size. By natural circumstances, the litter size of some dams was reduced further, but not changing the overall male/female ratio significantly. Throughout pregnancy and lactation, the dams were kept on the same low-fat diet.

extract_protocol: Total RNA was isolated using RNeasy micro kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 Bioanalyzer, Agilent Technologies, Amsterdam, The Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Two weeks into lactation, pups were sacrificed by heart puncture under isoflurane anaesthesia. Both males and females were included. Pups included were derived from 3 different litters. Small intestine and colon were excised from each pup, snap-frozen in liquid nitrogen, and stored at -80 C until further use.

tag: mouse id

tag: litter id

tag: diet group dam

value: low-fat (control) diet (3.85 kcal/g; 10 E% fat, 20 E% protein, 70 E% carbohydrate; D12450B, Research Diets, New Brunswick, USA).

value: colon

value: wildtype

tag: strain

value: C57BL/6 (Harlan; Horst, The Netherlands)

value: 14 days


title: colon_female_pup_lfd_replicate5

tag: tissue


title: 8N


title: SI_female_pup_lfd_replicate6

source_name: small intestine, female pup of 14 days of age, dam received a low-fat diet

value: small intestine


title: 19701822

tag: gender

tag: molecular subtype

tag: dataset group


title: SI_male_pup_lfd_replicate6

source_name: small intestine, male pup of 14 days of age, dam received a low-fat diet

value: male


title: SI_female_pup_lfd_replicate5

value: female


title: colon_male_pup_lfd_replicate6

source_name: colon, male pup of 14 days of age, dam received a low-fat diet


title: SI_female_pup_lfd_replicate3


title: pre-vaccination PBMCs stimulation  with EV71 antigen_3

tag: cell type

tag: rna source

value: Comprised of 10 cell lines for human


title: colon_female_pup_lfd_replicate3

tag: genotype


title: SI_female_pup_lfd_replicate4


title: 5N

value: Normal small bowel epithelium from a cancer patient


title: 15N


title: 6N


title: 2N


title: 3N


title: 4N


title: SI_male_pup_lfd_replicate4


title: colon_male_pup_lfd_replicate4


title: colon_female_pup_lfd_replicate2


title: colon_male_pup_lfd_replicate3


title: colon_female_pup_lfd_replicate4


title: SI_female_pup_lfd_replicate1


title: SI_female_pup_lfd_replicate2


title: SI_male_pup_lfd_replicate5


title: SI_male_pup_lfd_replicate3


title: SI_male_pup_lfd_replicate2


title: SI_male_pup_lfd_replicate1


title: 1N


title: colon_male_pup_lfd_replicate5


title: healthy (GIK12)

city: Oslo

first: Silje

last: Fjellgård Jørgensen

address: Postboks 4950 Nydalen

department: Research institute of internal medicine

country: Norway

institute: Oslo University Hospital

scan_protocol: Standard Illumina hybridization protocol

data_processing: The raw data was imported into GenomeStudio Data Analysis Software (Illumina, Inc.). Probe signal values from GenomeStudio was imported into J-Express 2012 (Dysvik B, Jonassen I. J-Express: exploring gene expression data using Java. Bioinformatics 2001;17:369-370.) for quantile normalization

source_name: duodenal biopsy

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification kit

extract_protocol: Total RNA was extracted from the tissues using TissueLyzer and QIAGEN RNeasy minikit

tag: disease state

value: healthy controls

value: duodenal biopsy


title: healthy (GIK14)


title: colon_male_pup_lfd_replicate2

tag: age


title: healthy (GIK17)


title: colon_female_pup_lfd_replicate1


title: healthy (GIK07)


title: healthy (GIK09)


title: healthy (GIK18)


title: healthy (GIK19)


title: healthy (GIK15)


title: colon_male_pup_lfd_replicate1


title: healthy (GIK13)


title: healthy (GIK04)


title: healthy (GIK01)


title: healthy (GIK20)


title: healthy (GIK21)


title: celiac_disease (GI_962)

value: celiac disease


title: celiac_disease (GI_947)


title: healthy (GIK05)


title: CVID_IEL (GI_1513)

value: CVID with increased intraepithelial lymphocytes


title: CVID_normal (GI_1486)

value: CVID without increased intraepithelial lymphocytes


title: celiac_disease (GI_1030)


title: celiac_disease (GI_1032)


title: healthy (GIK08)


title: CVID_normal (GI_1522)


title: healthy (GIK03)


title: CVID_IEL (GI_1525)


title: celiac_disease (GI_939)


title: CVID_IEL (GI_1482)


title: celiac_disease (GI_870)


title: CVID_normal (GI_1392)


title: CVID_normal (GI_1526)


title: CVID_normal (GI_1534)


title: celiac_disease (GI_930)


title: CVID_IEL (GI_1438)


title: CVID_IEL (GI_1541)


title: CVID_IEL (GI_1517)


title: CVID_IEL (GI_1509)


title: celiac_disease (GI_940)


title: CVID_IEL (GI_1469)


title: celiac_disease (GI_959)


title: celiac_disease (GI_924)


title: CVID_normal (GI_1498)


title: CVID_IEL (GI_1340)


title: CVID_IEL (GI_1391)


title: healthy (GIK16)


title: CVID_IEL (GI_1107)


title: CVID_IEL (GI_1203)


title: PMA10_2

city: Bonston

first: Bon

middle: Quy

last: Trinh

state: MA

address: 330 Brookline Ave

department: Medicine

institute: Beth Israel Deaconess Medical Center

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

hyb_protocol: Labeled cRNA (750 ng per array) was hybridized to the Illumina HumanHT-12 v4 expression beadchip according to the manufacturer's procedure (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned using an Illumina Bead array Reader (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) following the manufacturer's procedure.

data_processing: Data processing of arrays were performed using Illumina BeadStudio software. Gene expression data was normalized using Quantile normalization and log2 transformation. Sample Gene Profile option of Illumina BeadStudio was used to export to a data matrix.

source_name: K562 VEC

label_protocol: Biotin-labeled cRNA samples were prepared for hybridization using TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX) following the sample labeling procedure: Total RNA (500 ng) was used for cDNA synthesis. Amplification/labeling step (in vitro transcription) was then performed to synthesize biotin-labeled cRNA. Concentration of cRNA was then measured by spectrophotometer (Nanodrop, ND-1000)

extract_protocol: Total RNA was extracted from cells using the PureLink™ RNA Mini kit (Ambion) following the manufacturer protocol.

tag: treatment

value: 10 nM PMA

tag: cell line

tag: transfection


title: CVID_normal (GI_1180)


title: ActA25_1

value: 25 ng/ml ActA


title: ActA25_3


title: PMA10_3


title: PMA25_3

value: 25 nM PMA


title: VEC_2


title: PMA0_1

value: DMSO


title: VEC_3


title: DLX4_1

source_name: K562 DLX4


title: PMA0_3


title: PMA25_1


title: PMA0_2


title: ActA10_3

value: 10 ng/ml ActA


title: DLX4_3


title: VEC_1


title: PMA10_1


title: ActA0_3


title: ActA25_2


title: ActA10_2


title: PMA25_2


title: ActA10_1


title: ActA0_1


title: ActA0_2


title: Spleen Infected Chronic rep 35

city: London

first: Krzysztof

last: Potempa

address: The Ridgeway

institute: National Institute for Medical Research (NIMR)

description:
8697771083_D
replicate 35

data_processing: The data were normalized using quantile normalization with GeneSpring GX12.1

source_name: Mouse Spleen

value: Female

value: Spleen

value: Infected

tag: infection type

value: Chronic

tag: lesion severity

value: Severe

tag: chronic infection type

value: Active


title: Spleen Infected Chronic rep 30

description:
7988314100_F
replicate 30


title: Spleen Infected Chronic rep 33

description:
8697771083_A
replicate 33


title: Spleen Infected Chronic rep 31

description:
8615616009_F
replicate 31


title: Spleen Infected Chronic rep 24

description:
7988314086_C
replicate 24


title: Spleen Infected Chronic rep 20

description:
8697771073_E
replicate 20

value: Moderate


title: Spleen Infected Chronic rep 28

description:
7988314097_F
replicate 28


title: Spleen Infected Chronic rep 15

description:
8650489020_F
replicate 15

value: Latent


title: Spleen Infected Chronic rep 26

description:
7988314087_C
replicate 26


title: Spleen Infected Chronic rep 16

description:
7988314086_F
replicate 16


title: Spleen Infected Chronic rep 18

description:
8615616009_B
replicate 18


title: Spleen Infected Chronic rep 29

description:
7988314100_E
replicate 29


title: Spleen Infected Chronic rep 17

description:
7988314087_E
replicate 17


title: Spleen Infected Chronic rep 25

description:
7988314087_B
replicate 25


title: Spleen Infected Chronic rep 13

description:
8650489002_E
replicate 13


title: Spleen Infected Chronic rep 14

description:
8650489020_B
replicate 14


title: Spleen Infected Chronic rep 12

description:
8784129067_F
replicate 12


title: Spleen Infected Chronic rep 23

description:
7988314086_A
replicate 23


title: Spleen Infected Chronic rep 34

description:
8697771083_C
replicate 34


title: Spleen Infected Chronic rep 19

description:
8697771053_E
replicate 19


title: Spleen Infected Chronic rep 22

description:
8650489020_A
replicate 22


title: Spleen Infected Chronic rep 21

description:
8650489002_F
replicate 21


title: Spleen Infected Chronic rep 32

description:
8697771073_C
replicate 32


title: Spleen Infected Chronic rep 27

description:
7988314087_F
replicate 27


title: Spleen Infected Chronic rep 10

description:
8784129067_D
replicate 10


title: Spleen Infected Chronic rep 11

description:
8784129067_E
replicate 11


title: Spleen Infected Chronic rep 9

description:
8784129067_C
replicate 9


title: Spleen Infected Chronic rep 8

description:
8697771083_B
replicate 8


title: Spleen Infected Chronic rep 7

description:
8697771073_B
replicate 7


title: Spleen Uninfected Chronic rep 14

description:
8650489002_A
replicate 14

value: Uninfected


title: Spleen Infected Chronic rep 4

description:
8615616009_C
replicate 4


title: Spleen Uninfected Chronic rep 15

description:
8650489002_C
replicate 15


title: Spleen Uninfected Chronic rep 8

description:
8697771053_C
replicate 8


title: Spleen Uninfected Chronic rep 6

description:
7988314100_A
replicate 6


title: Spleen Infected Chronic rep 1

description:
7988314097_A
replicate 1


title: Spleen Uninfected Chronic rep 4

description:
7988314087_D
replicate 4


title: Spleen Uninfected Chronic rep 11

description:
8697771083_F
replicate 11


title: Spleen Uninfected Chronic rep 5

description:
7988314097_E
replicate 5


title: DLX4_2


title: Spleen Uninfected Chronic rep 12

description:
8784129067_A
replicate 12


title: Spleen Uninfected Chronic rep 9

description:
8697771053_F
replicate 9


title: Spleen Uninfected Chronic rep 3

description:
7988314087_A
replicate 3


title: Spleen Uninfected Chronic rep 16

description:
8650489020_C
replicate 16


title: Spleen Uninfected Chronic rep 10

description:
8697771073_F
replicate 10


title: Lung Infected day 3 rep 8

description:
7800220076_D
replicate 8

source_name: Mouse Lung

value: Lung

value: Acute Day3


title: Spleen Uninfected Chronic rep 7

description:
7988314100_D
replicate 7


title: Lung Infected day 3 rep 6

description:
7800220070_C
replicate 6


title: Spleen Uninfected Chronic rep 17

description:
8650489020_E
replicate 17


title: Lung Infected day 3 rep 9

description:
7800220076_F
replicate 9


title: Spleen Uninfected Chronic rep 13

description:
8784129067_B
replicate 13


title: Spleen Uninfected Chronic rep 2

description:
7988314086_D
replicate 2


title: Lung Infected day 3 rep 5

description:
7800220062_D
replicate 5


title: Spleen Infected Chronic rep 5

description:
8697771053_A
replicate 5


title: Lung Infected day 3 rep 7

description:
7800220070_F
replicate 7


title: Spleen Uninfected Chronic rep 1

description:
7988314086_B
replicate 1


title: Spleen Infected Chronic rep 2

description:
7988314097_D
replicate 2


title: db/+ bone marrow-derived progenitor cells_C2

city: DETROIT

first: JIEMEI

last: WANG

state: MI

address: 540 E CANFIELD STREET

department: CENTER FOR MOLECULAR MEDICINE AND GENETICS

institute: WAYNE STATE UNIVERSITY

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.  Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].  A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.  t-Test is performed between “control” and “test” sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.  All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

source_name: bone marrow

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 1 µg total RNA sample, which was 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy5 dye staining.

growth_protocol: Bone marrow mononuclear cells were cultured in endothelial growth medim-2 (EGM-2, Lonza) for 4 days. Non-adherent cells were washed off and new EGM-2 media were added. The cells were cultured for another 3 days before RNA extraction.

extract_protocol: Total RNA was extracted using miRNeasy Mini Kit (Qigen) based on manufacturer’s protocol.

treatment_protocol: C group was the cells from db/+ mice. D group was the cells from db/db mice.

value: male

tag: developmental stage

value: adult

value: control

value: bone marrow-derived progenitor cell


title: db/+ bone marrow-derived progenitor cells_C3


title: db/+ bone marrow-derived progenitor cells_C1


title: db/db bone marrow-derived progenitor cells_D3

value: diabetic


title: db/db bone marrow-derived progenitor cells_D1


title: db/db bone marrow-derived progenitor cells_D2


title: Lung Uninfected day 3 rep 6

description:
7509459088_E
replicate 6

tag: strain


title: Lung Infected day 3 rep 3

description:
7509459075_E
replicate 3

tag: tissue


title: Lung Uninfected day 3 rep 7

description:
7800220052_E
replicate 7

tag: gender


title: Lung Uninfected day 3 rep 10

description:
7800220076_C
replicate 10


title: Lung Infected day 3 rep 4

description:
7800220062_A
replicate 4


title: Lung Uninfected day 3 rep 1

description:
7469653020_B
replicate 1


title: Lung Uninfected day 3 rep 8

description:
7800220052_F
replicate 8


title: Lung Uninfected day 3 rep 9

description:
7800220070_B
replicate 9


title: Lung Infected day 3 rep 2

description:
7469653004_D
replicate 2


title: Lung Infected day 3 rep 1

description:
7469653004_C
replicate 1


title: Lung Uninfected day 3 rep 2

description:
7469653020_E
replicate 2


title: Lung Infected day 1 rep 9

description:
7800220070_A
replicate 9

value: Acute Day1


title: Spleen Infected Chronic rep 6

description:
8697771053_B
replicate 6

value: Female


title: Lung Uninfected day 3 rep 3

description:
7509459075_A
replicate 3


title: Lung Infected day 1 rep 10

description:
7800220076_A
replicate 10


title: Lung Uninfected day 3 rep 5

description:
7509459088_D
replicate 5


title: Lung Infected day 1 rep 7

description:
7800220052_C
replicate 7


title: Lung Uninfected day 3 rep 4

description:
7509459088_B
replicate 4


title: Lung Infected day 1 rep 8

description:
7800220062_F
replicate 8


title: Lung Infected day 1 rep 6

description:
7800220052_B
replicate 6


title: Spleen Infected Chronic rep 3

description:
7988314100_C
replicate 3

value: Spleen


title: Lung Infected day 1 rep 2

description:
7469653020_A
replicate 2

value: Infected


title: Lung Uninfected day 1 rep 8

description:
7800220062_C
replicate 8


title: Lung Uninfected day 1 rep 6

description:
7509459075_F
replicate 6


title: Lung Infected day 1 rep 3

description:
7469653020_D
replicate 3


title: Lung Infected day 1 rep 5

description:
7800220052_A
replicate 5


title: Lung Uninfected day 1 rep 9

description:
7800220070_E
replicate 9


title: Lung Infected day 1 rep 1

description:
7469653004_F
replicate 1


title: Lung Uninfected day 1 rep 10

description:
7800220076_B
replicate 10


title: Lung Uninfected day 1 rep 5

description:
7509459075_D
replicate 5


title: Lung Uninfected day 1 rep 4

description:
7469653020_F
replicate 4


title: Lung Infected day 1 rep 4

description:
7509459075_B
replicate 4


title: Lung Uninfected day 1 rep 7

description:
7800220052_D
replicate 7


title: Lung Uninfected day 1 rep 3

description:
7469653020_C
replicate 3


title: OA_Hip 16

city: Newcastle upon Tyne

first: Andrew

middle: James

last: Skelton

state: Tyne and Wear

address: Framlington Place

department: Bioinformatics

institute: Newcastle University

hyb_protocol: Infinium HumanMethylatio450 BeadChip array

scan_protocol: standard illumina scanner

data_processing: Minfi Bioconductor Package

label: Cy5 and Cy3

source_name: human hip cartilage from hip osteoarthritis patients

label_protocol: 500ng of DNA was bisulphite converted using the EZ DNA methylation kit (Zymo Research)

extract_protocol: DNA was extracted from 250mg of ground cartilage using the EZNA DNA/RNA isolation kit (Omega Bio-Tek)

value: Male

tag: scan date

tag: kl score

tag: sentrixid


title: Blood Infected Chronic rep 26

description:
8615616071_F
replicate 26

source_name: Mouse Blood

value: Blood

value: Chronic

value: Severe


title: Lung Uninfected day 1 rep 1

description:
7469653004_A
replicate 1


title: Blood Infected Chronic rep 28

description:
8697771056_F
replicate 28

value: Active


title: OA_Knee 61

description: Mainly medial

source_name: human knee cartilage from knee osteoarthritis patients


title: OA_Knee 62

description: Mainly medial


title: OA_Hip 15


title: Blood Infected Chronic rep 25

description:
8615616067_C
replicate 25


title: Blood Infected Chronic rep 27

description:
8615616073_E
replicate 27


title: Blood Infected Chronic rep 24

description:
8615616061_D
replicate 24


title: Lung Uninfected day 1 rep 2

description:
7469653004_E
replicate 2

value: Uninfected


title: Blood Infected Chronic rep 23

description:
8697771089_E
replicate 23

value: Moderate


title: Healthy control

city: Hannnover

first: Shashi

middle: Kumar

last: Gupta

address: Carl-Neuberg Strasse 1

department: IMTTS

country: Germany

institute: Hannover Medical School

data_processing:
Global Normalization was performed.  There is no normalized data file because during fold change calculation, normalization factor was used so normalization and fold change was done together.
Fold Change shows values for PSC vs healthy controls and CC vs healthy controls. Calculation was done as follows =2^-(PSC-healthy)*Normalization factor

label: SYBR Green

source_name: serum

label_protocol: In brief, poly-A-tailing of miRNAs, annealing of an oligo dT adaptor and then universal reverse transcription was performed. SYBR-Green based Real-time-polymerase chain reaction (PCR) was done with a miRNA-specific and a universal primer

extract_protocol: RNA isolation was done using miRNeasy Mini Kit (Qiagen, #217004).

value: healthy

tag: biomaterial

value: serum


title: OA_Hip 13

description: Erosive OA


title: OA_Knee 57

description: All compartments


title: CC

value: cholangiocarcinoma (CC)

tag: n

value: 6 patients

tag: alt

tag: ast

tag: ap

tag: ggt

tag: bilirubin


title: OA_Knee 55

description: Mainly medial

tag: age


title: Hip_Control 19

source_name: human hip cartilage from neck-of-femur fracture patients


title: Hip_Control 17


title: PSC

tag: disease state

value: primary sclerosing cholangitis (PSC)


title: CC pool 2

description: CC

data_processing:
Normalization was performed on filtered data set as doing normalization on complete dataset which have very high and irelevant Ct Value will have very high effect on normlaiztaion factor and thus would not be appropriate.
Global Normalization was performed. Normalized data presented is the average value of 3 pools for PSC and 2 pools for CC.
Fold-Change is PSC/CC.

label: SYBR Green PCR

source_name: bile

extract_protocol: Bile was aspirated by placing a single-use (5 French), standard ERC catheter (without flushing or guidewire cannulation) into the bile duct. RNA isolation was done using miRNeasy Mini Kit (Qiagen, #217004).

value: 4 patients

value: bile


title: Blood Infected Chronic rep 22

description:
8697771063_D
replicate 22

value: Female

tag: treatment

tag: infection type

tag: lesion severity

tag: chronic infection type


title: OA_Knee 58

description: Mainly medial

tag: gender


title: OA_Hip 14

tag: scan date


title: OA_Knee 59

description: Mainly lateral

tag: kl score


title: OA_Knee 60

description: Mainly medial

tag: sentrixid


title: Hip_Control 18


title: OA_Hip 12


title: OA_Hip 11


title: CC pool 1

description: CC

tag: biomaterial


title: Blood Infected Chronic rep 21

description:
8650489035_F
replicate 21

tag: strain

tag: tissue


title: OA_Knee 56

description: Mainly lateral


title: PSC pool 3

description: PSC

tag: n

value: 5 patients

tag: alt

tag: ast


title: Hip_Control 16


title: Blood Infected Chronic rep 20

description:
8615616073_C
replicate 20

value: Infected


title: PSC pool 2

description: PSC

tag: ap

tag: ggt

tag: bilirubin


title: PSC pool 1

description: PSC

tag: disease state

tag: age


title: OA_Hip 10


title: Blood Infected Chronic rep 18

description:
8615616067_A
replicate 18

tag: treatment

tag: infection type

tag: lesion severity


title: Blood Infected Chronic rep 17

description:
8615616061_F
replicate 17

tag: gender

tag: chronic infection type


title: OA_Knee 53

description: Mainly medial

tag: scan date

tag: kl score

tag: sentrixid


title: Blood Infected Chronic rep 16

description:
8697771089_B
replicate 16

tag: strain

tag: tissue

value: Latent


title: Hip_Control 14


title: OA_Knee 54

description: Mainly medial

value: Male


title: Hip_Control 13


title: Blood Infected Chronic rep 19

description:
8615616071_E
replicate 19

value: Blood

value: Chronic


title: Blood Infected Chronic rep 13

description:
8697771063_B
replicate 13


title: OA_Knee 52

description: Medial and patellofemoral


title: Blood Infected Chronic rep 15

description:
8697771089_A
replicate 15


title: Blood Infected Chronic rep 14

description:
8697771063_E
replicate 14


title: Blood Infected Chronic rep 11

description:
8650489044_E
replicate 11


title: Blood Infected Chronic rep 12

description:
8697771056_A
replicate 12


title: OA_Knee 51

description: Mainly medial


title: Blood Infected Chronic rep 10

description:
8650489044_C
replicate 10

value: Active


title: Hip_Control 15


title: GC sensitive 697/EU cell line

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

description: Gene expression profile of GC sensitive preB 697/EU cell line

hyb_protocol: Target samples were hybridized to Human Exon 1.0 ST v2 microarrays according to the manufacturer's protocols in a Affymetrix hybridization oven.

scan_protocol: Microarrays were scanned in an Affymetrix 3000 scanner.

data_processing: Raw data was preprocessed using the GCRMA method (option GSB.adjust set to FALSE). For transcript probe set definition a custom CDF package was used, that was based on a complete re-alignment of the Exon microarray oligo-probes and annotation to Ensembl version 57.

source_name: pre-B-ALL 697 cell line

label_protocol: Target RNA was labeled by addition of biotin-linked deoxynucleotides with terminal deoxynucleotidyl transferase according to the manufacturer's (Affymetrix) protocols. Washing and staining was performed in an Affymetrix 450S fluidics station.

growth_protocol: Cells were cultured in RPMI 1640 supplemented with 10% fetal calf serum and 2mM L-glutamine at 37C, 5% carbon-dioxide and saturated humidity.

extract_protocol: Total RNA was extracted usinf the Qiagen Rneasy Mini kit.

tag: gc sensitivity

value: sensitive


title: GC resistent R3G7 697 subclone

description: Gene expression profile of GC resistent subclone R3G7 of GC sensitive preB 697/EU cell line

source_name: R3G7 subclone of pre-B-ALL 697/EU cell line

value: resistent


title: Blood Infected Chronic rep 8

description:
8650489038_C
replicate 8


title: OA_Hip 9


title: Hip_Control 11


title: OA_Knee 48

description: Mainly medial


title: GC resistent R4C10 697 subclone

description: Gene expression profile of GC resistent subclone R4C10 of GC sensitive preB 697/EU cell line

source_name: R4C10 subclone of pre-B-ALL 697 cell line


title: Hip_Control 12


title: GC resistent R3F9 697 subclone

description: Gene expression profile of GC resistent subclone R3F9 of GC sensitive preB 697/EU cell line

source_name: R3F9 subclone of pre-B-ALL 697 cell line


title: Blood Infected Chronic rep 7

description:
8650489038_A
replicate 7


title: OA_Knee 49

description: Mainly patellofemoral


title: OA_Knee 50

description: Mainly medial


title: Blood Infected Chronic rep 6

description:
8650489035_D
replicate 6


title: Blood Infected Chronic rep 4

description:
8650489010_D
replicate 4


title: Blood Infected Chronic rep 9

description:
8650489038_E
replicate 9


title: GC resistent R3C3 697 subclone

description: Gene expression profile of GC resistent subclone R3C3 of GC sensitive preB 697/EU cell line

source_name: R3C3 subclone of pre-B-ALL 697/EU cell line


title: OA_Hip 8


title: Blood Infected Chronic rep 3

description:
8650489010_A
replicate 3


title: Blood Infected Chronic rep 5

description:
8650489010_E
replicate 5


title: OA_Knee 47

description: Medial and patellofemoral


title: Blood Infected Chronic rep 2

description:
8615616073_D
replicate 2


title: OA_Knee 45

description: Mainly patellofemoral


title: Blood Infected Chronic rep 1

description:
8615616061_C
replicate 1


title: EPT91.Primary-Spinal

city: Houston

first: Stephen

middle: Mack

last: Christopher

state: TX

address: 1102 Bates Avenue C1030.02

department: Pediatrics

institute: Baylor College of Medicine

description: GeneArray1-1_EPT91.rma-gene-default-Signal

hyb_protocol: According to manufacturers recommendations

data_processing:
Data was processed using Affymetrix Expression Console further analysis was performed in R(v.3.0)/Bioconductor(v.2.14)  [PMID:21840481]
Data in the processed matrix has been processed using the RMA algorithm according to methods published previously [PMID:21840481]

source_name: Primary Spinal Ependymoma

extract_protocol: RNA was extracted using the Trizol Method  [PMID:21840481]

value: male

tag: age (yrs)

tag: molecular subgroup

value: Grade II

tag: histological grade

value: Spinal Cord

tag: tissue subtype

value: Primary Spinal Ependymoma


title: EPT285.Primary-Spinal

description: GeneArray1-1_EPT285.rma-gene-default-Signal

scan_protocol: According to manufacturers recommendations


title: Blood Uninfected Chronic rep 18

description:
8697771089_D
replicate 18

value: Uninfected


title: Hip_Control 9


title: Hip_Control 10


title: Blood Uninfected Chronic rep 17

description:
8697771063_C
replicate 17


title: VCU-EP25.Primary-Spinal

description: GeneArray1-1_VCU-EP25.rma-gene-default-Signal

label_protocol: According to manufacturers recommendations


title: OA_Knee 44

description: Mainly medial


title: HAMS6-81906.Primary-Spinal

description: GeneArray1-1_HAMS6-81906.rma-gene-default-Signal

value: female

value: MPE


title: Blood Uninfected Chronic rep 16

description:
8697771063_A
replicate 16

value: Female


title: Blood Uninfected Chronic rep 15

description:
8697771056_E
replicate 15


title: GER-2E34.Primary-Spinal

description: GeneArray1-1_GER-2E34.rma-gene-default-Signal


title: GER-2E11.Primary-Spinal

description: GeneArray1-1_GER-2E11.rma-gene-default-Signal


title: GER-2E14.Primary-Spinal

description: GeneArray1-1_GER-2E14.rma-gene-default-Signal


title: Hip_Control 8


title: OA_Hip 7


title: Blood Uninfected Chronic rep 14

description:
8697771056_C
replicate 14


title: Blood Uninfected Chronic rep 13

description:
8650489038_F
replicate 13


title: OA_Knee 43

description: Mainly medial


title: GER-2E35.Primary-Spinal

description: GeneArray1-1_GER-2E35.rma-gene-default-Signal


title: Blood Uninfected Chronic rep 12

description:
8650489038_D
replicate 12


title: GER-2E9.Primary-Spinal

description: GeneArray1-1_GER-2E9.rma-gene-default-Signal


title: Blood Uninfected Chronic rep 10

description:
8650489035_B
replicate 10


title: OA_Knee 40

description: Mainly medial


title: GER-1E22.Primary-Spinal

description: GeneArray1-1_GER-1E22.rma-gene-default-Signal


title: OA_Knee 46

description: mainly medial


title: OA_Knee 41

description: Medial and patellofemoral


title: Blood Uninfected Chronic rep 11

description:
8650489035_E
replicate 11


title: OA_Knee 37

description: Mainly medial


title: OA_Knee 38


title: Blood Uninfected Chronic rep 9

description:
8650489010_C
replicate 9


title: GER-1E9.Primary-Spinal

description: GeneArray1-1_GER-1E9.rma-gene-default-Signal


title: GER-1E2.Primary-Spinal

description: GeneArray1-1_GER-1E2.rma-gene-default-Signal


title: OA_Knee 36

description: Medial and patellofemoral


title: Blood Uninfected Chronic rep 7

description:
8615616073_F
replicate 7


title: OA_Knee 35

description: Mainly medial


title: Blood Uninfected Chronic rep 6

description:
8615616073_A
replicate 6


title: OA_Knee 39

description: Mainly medial


title: OA_Knee 33

description: Mainly lateral


title: OA_Knee 34

description: All compartments


title: GER-1E10.Primary-Spinal

description: GeneArray1-1_GER-1E10.rma-gene-default-Signal


title: Blood Uninfected Chronic rep 5

description:
8615616071_C
replicate 5


title: VCU-EP13.Primary-Spinal

description: GeneArray1-1_VCU-EP13.rma-gene-default-Signal


title: VCU-EP19.Primary-Spinal

description: GeneArray1-1_VCU-EP19.rma-gene-default-Signal


title: CVTB2562.Primary-Spinal

description: GeneArray1-1_CVTB2562.rma-gene-default-Signal


title: OA_Knee 32

description: Mainly medial


title: Blood Uninfected Chronic rep 3

description:
8615616067_B
replicate 3


title: Blood Uninfected Chronic rep 8

description:
8650489010_B
replicate 8


title: CVTB2665.Primary-Spinal

description: GeneArray1-1_CVTB2665.rma-gene-default-Signal


title: CVTB2452.Primary-Spinal

description: GeneArray1-1_CVTB2452.rma-gene-default-Signal


title: Blood Uninfected Chronic rep 2

description:
8615616061_B
replicate 2


title: OA_Hip 6


title: OA_Knee 31


title: Blood Uninfected Chronic rep 1

description:
8615616061_A
replicate 1


title: OA_Knee 30

description: Mainly medial


title: OA_Knee 42

description: Medial and patellofemoral


title: Blood Uninfected Chronic rep 4

description:
8615616071_B
replicate 4


title: CVTB2656.Primary-Spinal

description: GeneArray1-1_CVTB2656.rma-gene-default-Signal


title: MDT-EP40.Primary-Spinal

description: GeneArray1-1_MDT-EP40.rma-gene-default-Signal


title: Blood Infected day 3 rep 7

description:
8697771081_D
replicate 7

value: Acute Day3


title: OA_Knee 28


title: 37A55.Primary-Spinal

description: GeneArray1-1_37A55.rma-gene-default-Signal


title: CVTB2412.Primary-Spinal

description: GeneArray1-1_CVTB2412.rma-gene-default-Signal


title: OA_Knee 26

description: Mainly medial


title: Blood Infected day 3 rep 9

description:
8784129070_B
replicate 9

value: Infected


title: POL5_15357.Primary-Spinal

description: GeneArray1-1_POL5_15357.rma-gene-default-Signal


title: OA_Knee 29

description: Mainly medial


title: Blood Infected day 3 rep 8

description:
8697771097_D
replicate 8


title: OA_Knee 25

description: All compartments


title: Blood Infected day 3 rep 4

description:
8697771067_A
replicate 4


title: OA_Knee 27

description: Medial and patellofemoral


title: BTTB1074.Primary-Spinal

description: GeneArray1-1_BTTB1074.rma-gene-default-Signal


title: Blood Infected day 3 rep 6

description:
8697771071_D
replicate 6


title: Blood Infected day 3 rep 3

description:
8615616102_F
replicate 3


title: CVTB2065.Primary-Spinal

description: GeneArray1-1_CVTB2065.rma-gene-default-Signal


title: OA_Knee 24

description: Obese, erosive OA, mainly medial


title: 93A26.Primary-Spinal

description: GeneArray1-1_93A26.rma-gene-default-Signal


title: Blood Infected day 3 rep 1

description:
7988314090_B
replicate 1


title: CVTB39.Primary-Spinal

description: GeneArray1-1_CVTB39.rma-gene-default-Signal


title: Blood Uninfected day 3 rep 11

description:
8784129070_F
replicate 11


title: CVTB2541.Primary-Spinal

description: GeneArray1-1_CVTB2541.rma-gene-default-Signal


title: Blood Infected day 3 rep 2

description:
8615616101_A
replicate 2


title: CVTB2524.Primary-Spinal

description: GeneArray1-1_CVTB2524.rma-gene-default-Signal


title: OA_Knee 20

description: All compartments


title: CVTB2394.Primary-Spinal

description: GeneArray1-1_CVTB2394.rma-gene-default-Signal


title: Blood Uninfected day 3 rep 10

description:
8784129070_D
replicate 10


title: CVTB2518.Primary-Spinal

description: GeneArray1-1_CVTB2518.rma-gene-default-Signal


title: OA_Knee 21

description: Mainly medial


title: Blood Uninfected day 3 rep 9

description:
8697771097_E
replicate 9


title: OA_Knee 23

description: Mainly medial


title: Blood Uninfected day 3 rep 8

description:
8697771097_B
replicate 8


title: OA_Knee 19

description: Mainly medial


title: OA_Knee 18

description: All compartments


title: OA_Knee 17

description: Mainly medial


title: CVTB2369.Primary-Spinal

description: GeneArray1-1_CVTB2369.rma-gene-default-Signal


title: OA_Knee 22

description: Mainly lateral - erosive OA


title: OA_Knee 16

description: Mainly patellofemoral


title: OA_Knee 15

description: Mainly lateral


title: HoxA9-Meis1 AML cells treated with Pyrydopyrazine A2

city: Dijon

first: ronan

last: quere

address: 7 bd Jeanne d'Arc

country: France

institute: Inserm U866

hyb_protocol: Mouse Gene Expression Microarray 8x60K (Agilent), hybridization during 17h

scan_protocol: Scanner Agilent version C

data_processing: Feature Extraction version 11.5.1.1

source_name: Bone marrow

label_protocol: 50 ng total RNA using the « Low Input Amplification » Kit

growth_protocol: HoxA9-Meis1 AML cells isolated from bone marrow were maintained in SFEM medium during 24 hours

extract_protocol: Total RNA were extracted using Qiagen Mini Elute columns and DNA was removed with Dnase

treatment_protocol: HoxA9-Meis1 AML cells were either untreated or treated 24h with Pyrydopyrazine A2 or a combinaison of Retinoic Acid and D3 Vitamin

value: whole bone marrow

tag: cell line

value: HoxA9-Meis1 AML cells

value: Pyrydopyrazine A2


title: Blood Uninfected day 3 rep 6

description:
8697771071_A
replicate 6

value: Blood


title: HoxA9-Meis1 AML cells treated with Retinoic Acid plus D3 Vitamin

value: Retinoic Acid plus D3 Vitamin


title: Blood Infected day 3 rep 5

description:
8697771071_B
replicate 5


title: CVTB2384.Primary-Spinal

description: GeneArray1-1_CVTB2384.rma-gene-default-Signal


title: Blood Uninfected day 3 rep 5

description:
8697771067_C
replicate 5


title: Blood Uninfected day 3 rep 7

description:
8697771081_B
replicate 7


title: HoxA9-Meis1 AML cells untreated

description: AML-Control

value: Control


title: CVTB2549.Primary-Spinal

description: GeneArray1-1_CVTB2549.rma-gene-default-Signal


title: OA_Knee 14

description: Mainly medial

value: Male

tag: age


title: OA_Knee 10

description: Mainly medial


title: Blood Uninfected day 3 rep 2

description:
7988314090_E
replicate 2

tag: treatment


title: OA_Knee 9

description: Medial and patellofemoral


title: CVTB2116.Primary-Spinal

description: GeneArray1-1_CVTB2116.rma-gene-default-Signal


title: Blood Uninfected day 3 rep 4

description:
8615616102_B
replicate 4

tag: infection type


title: Blood Uninfected day 3 rep 1

description:
7988314090_D
replicate 1

tag: lesion severity


title: Blood Infected day 1 rep 5

description:
8697771081_A
replicate 5

tag: gender

value: Acute Day1


title: Blood Infected day 1 rep 4

description:
8697771071_F
replicate 4

tag: chronic infection type


title: Blood Uninfected day 3 rep 3

description:
8615616101_C
replicate 3


title: OA_Knee 11

description: Medial and patellofemoral

tag: scan date


title: Blood Infected day 1 rep 3

description:
8697771067_F
replicate 3


title: OA_Knee 13

description: Mainly lateral

tag: kl score


title: Blood Infected day 1 rep 2

description:
8615616102_E
replicate 2


title: Blood Uninfected day 1 rep 8

description:
8784129070_C
replicate 8


title: Blood Infected day 1 rep 1

description:
8615616101_D
replicate 1


title: OA_Knee 12

description: Mainly medial

tag: sentrixid


title: OA_Knee 5

description: Medial and patellofemoral


title: Blood Uninfected day 1 rep 7

description:
8697771097_A
replicate 7

tag: strain


title: Blood Uninfected day 1 rep 6

description:
8697771081_F
replicate 6

tag: tissue


title: OA_Knee 6

description: Mainly medial


title: OA_Knee 7

description: Medial and patellofemoral


title: OA_Knee 4

description: Mainly medial


title: Blood Uninfected day 1 rep 5

description:
8697771071_E
replicate 5


title: OA_Knee 8

description: All compartments


title: Blood Uninfected day 1 rep 4

description:
8697771067_D
replicate 4


title: Macrophages treated with ManLAM + GW9662 (replicate)   vs. untreated 2

city: Kolkata

first: Joyoti

last: Basu

address: A.P.C. Road

department: Chemistry

country: India

institute: Bose Institute

description: J774.1 cell treated with ManLAM + GW9662

hyb_protocol: Agilent's In situ Microarray Hybridization Chamber Kit (G2534A)

scan_protocol: Microarray slides were scanned using an Agilent microarray scanner at 3 micron resolution.

data_processing: Microarray data was normalized and analysed using using GeneSpring GX version 11.5 and Microsoft Excel.

label_protocol: T7 RNA polymerase amplification to generate labeled complementary RNA. Treated: Cy5; Untreated: Cy3

growth_protocol: J774A.1  cells were grown in DMEM supplemented with 10% FBS at 37 degrees C in 5% CO2.

extract_protocol: RNA was isolated using the Ambion miRVana RNA isolation kit.

treatment_protocol: Cells were treated with ManLAM (5 ug/ml) either in the absence or in the presence of GW9662 for 6 h, washed and RNA was isolated.

value: ManLAM + GW9662

source_name: Untreated J774A.1 cells


title: OA_Knee 1

description: Mainly patellofemoral


title: Blood Uninfected day 1 rep 2

description:
8615616101_B
replicate 2

hyb_protocol: Standard Illumina hybridization protocol


title: Vo + 10nM PTX_rep3

city: Melbourne

first: Daniel

middle: Glyn

last: Hurley

address: Level 4, Bldg 193, EEE

department: Systems Biology Laboratory

country: Australia

institute: The University of Melbourne

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

scan_protocol: GeneChips were scanned using the Affymetrix Command Console software v3.2

data_processing: Data was RMA-normalised following background correction and log-transformation.  The ‘limma’ package in the statistical language R was used to assess the evidence for differential abundance of RNA transcripts between each of the three cell types (EVT, CTP and SP).   A blocked analysis was performed to correct for within-patient variance.  Benjamini-Hochberg false-discovery rate control (FDR) was used to adjust p-values for differential expression.

source_name: Vo + 10nM PTX_rep3

label_protocol: Purified cDNA was biotin-labelled and hybridised to Affymetrix PrimeView microarrays (Affymetrix, California) according to the manufacturer's instructions

extract_protocol: RNA was extracted using the Invitrogen PureLink mini-kit (Life Technologies, California) according to the manufacturer's instructions.  RNA quality was assessed using Experion RNA HighSens chips (Biorad, Auckland) according to the manufacturer’s instructions. RNA was converted to cDNA and amplified using a NuGEN Ovation Pico WTA system V2 kit according to the manufacturer’s instructions.

tag: vector

value: empty

value: paclitaxel


title: Blood Uninfected day 1 rep 3

description:
8615616102_C
replicate 3

value: Uninfected


title: Macrophages treated with ManLAM + GW9662 (replicate)   vs. untreated 1


title: Macrophages treated with ManLAM + GW9662   vs. untreated 1


title: OA_Hip 3


title: Vo + 10nM PTX_rep2

source_name: Vo + 10nM PTX_rep2


title: OA_Knee 3

description: Mainly lateral


title: OA_Hip 1


title: Blood Uninfected day 1 rep 1

description:
7988314090_A
replicate 1


title: Vo + 10nM PTX_rep1

source_name: Vo + 10nM PTX_rep1


title: Macrophages treated with ManLAM (replicate)  vs. untreated 2

description: J774.1 cell treated with ManLAM

source_name: Macrophages treated with ManLAM

value: ManLAM


title: WT_P40_2

city: Paris

first: Guillaume

last: soubigou

address: 25 rue du Docteur Roux

institute: Institut Pasteur

description: Gene expression data from MDR2+/+ MEFs Passage 40, replicate 2

hyb_protocol: Following fragmentation, 2,5 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: The data were summarized with Affymetrix Expression Console software using Affymetrix default analysis settings for Mouse Gene 1.0 ST array

source_name: MDR2+/+ MEFs Passage 40, replicate 2

label_protocol: Biotinylated cDNA were prepared according to the standard Nugen protocol from 50 ng total RNA (Ovation Pico WTA System v2, Nugen Technologies Inc.  #3302-12 ; fragmented and biotin labeled using the Encore Biotin Module, (Nugen Technologies, Inc. #4200-12).

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

tag: cell type

value: MEFs

tag: genotype


title: Macrophages treated with ManLAM + GW9662   vs. untreated 2


title: OA_Hip 2

source_name: human hip cartilage from hip osteoarthritis patients

value: Female


title: WT_P40_3

description: Gene expression data from MDR2+/+ MEFs Passage 40, replicate 3

source_name: MDR2+/+ MEFs Passage 40, replicate 3


title: Macrophages treated with ManLAM vs. untreated 2

description: J774.1 cell treated with ManLAM


title: Vo + media control_rep3

source_name: Vo + media control_rep3

value: control


title: Vo + media control_rep2

source_name: Vo + media control_rep2


title: OA_Hip 5


title: OA_Knee 2

description: Mainly medial

source_name: human knee cartilage from knee osteoarthritis patients


title: Macrophages treated with ManLAM (replicate)  vs. untreated 1

description: J774.1 cell treated with ManLAM


title: KO_P40_3

description: Gene expression data from MDR2-/- MEFs Passage 40, replicate 3

source_name: MDR2-/- MEFs Passage 40, replicate 3


title: YB-1_o/e + siYB-1+10nM PTX_rep3

source_name: YB-1_o/e + siYB-1+10nM PTX_rep3

value: siRNA+paclitaxel


title: KO_P40_2

description: Gene expression data from MDR2-/- MEFs Passage 40, replicate 2

source_name: MDR2-/- MEFs Passage 40, replicate 2


title: Macrophages treated with ManLAM vs. untreated 1

description: J774.1 cell treated with ManLAM


title: Hip_Control 3

source_name: human hip cartilage from neck-of-femur fracture patients


title: YB-1_o/e + siYB-1+10nM PTX_rep2

source_name: YB-1_o/e + siYB-1+10nM PTX_rep2


title: YB-1_o/e + 10nM PTX_rep3

source_name: YB-1_o/e + 10nM PTX_rep3


title: Hip_Control 6


title: Hip_Control 2


title: Hip_Control 1


title: Vo + media control_rep1

source_name: Vo + media control_rep1


title: YB-1_o/e + 10nM PTX_rep1

source_name: YB-1_o/e + 10nM PTX_rep1


title: KO_P40_1

description: Gene expression data from MDR2-/- MEFs Passage 40, replicate 1

source_name: MDR2-/- MEFs Passage 40, replicate 1


title: YB-1_o/e + siYB-1+10nM PTX_rep1

source_name: YB-1_o/e + siYB-1+10nM PTX_rep1


title: OA_Hip 4


title: Hip_Control 7


title: S50_Tumor

city: Barcelona

first: Jordi

last: Camps

state: Catalonia

address: c/Rosselló 149-153 4th floor, Center Esther Koplowitz

department: Gastroenterology

institute: IDIBAPS / Hospital Clinic

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

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

data_processing: BeadStudio software v3.2 and beta-value correction using metillumi R package

label: Cy3 and Cy5

source_name: Tumor colorectal tissue

value: male

tag: age of surgery

value: Tumor colorectal tissue

tag: tumor stage

value: IIA


title: YB-1_o/e + 10nM PTX_rep2

source_name: YB-1_o/e + 10nM PTX_rep2


title: YB-1_o/e + media control_rep3

source_name: YB-1_o/e + media control_rep3


title: S49_Tumor


title: S48_Tumor

hyb_protocol: Standard Affymetrix Protocol. DNA digestion was done by using Sty I restriction enzyme.

scan_protocol: The chips were processed using fluidics station 450, high-resolution microarray scanner 3000, and GCOS workstation version 1,2

data_processing:
Allele call and signal intensity generated
Data were processed using Affymetrix Genotyping Console 3.0.2 software from CEL data. Genotype calling with BRLMM was performed on the Genotyping Console using default settings. Derived signal is computed using the two alleles using the formula (log2(A) +log2(B))/2.
Series-level supplementary file includes processed CNV and LOH calls.

source_name: Tumor colorectal tissue (Crc48T)

label_protocol: Standard Affymetrix Protocol

value: female

value: IIIB


title: YB-1_o/e + media control_rep2

source_name: YB-1_o/e + media control_rep2


title: Hip_Control 5


title: S45_Tumor

label_protocol: Standard Illumina Protocol

value: I


title: S49_Tumor

source_name: Tumor colorectal tissue (Crc49T)


title: S48_Tumor


title: S50_Tumor

source_name: Tumor colorectal tissue (Crc50T)


title: S44_Tumor


title: S46_Tumor

value: IV


title: Hip_Control 4


title: S43_Tumor


title: S46_Tumor

source_name: Tumor colorectal tissue (Crc46T)


title: S42_Tumor


title: S47_Tumor

source_name: Tumor colorectal tissue (Crc47T)


title: S45_Tumor

source_name: Tumor colorectal tissue (Crc45T)


title: YB-1_o/e + media control_rep1

source_name: YB-1_o/e + media control_rep1


title: S41_Tumor


title: S50

hyb_protocol: Oligo aCGH/ChIP-on-Chip Hybridization kit (Agilent Technologies). Hybridizations were performed on SureHyb chambers on a rotator oven at 65C for 20 hours.

scan_protocol: Agilent G2565BA scanner was used for scanning and the Feature Extraction sotftware V9.1 (Agilent Technologies) was used to performed data extraction.

data_processing: Raw files were uploaded to the software Nexus Copy Number (BioDiscovery). Rank segmentation was applied and analysis was done based on log2 ratio intensities.

source_name: Tumor colorectal DNA

label_protocol: BioPrime Array CGH Genomic Labeling Module (Life Technologies)

tag: tumor grade

source_name: Normal adjacent mucosa DNA

value: Normal adjacent mucosa


title: S49

tag: age


title: S43_Tumor

source_name: Tumor colorectal tissue (Crc43T)


title: S42_Tumor

source_name: Tumor colorectal tissue (Crc42T)


title: S48


title: S40_Tumor


title: S38_Tumor


title: S39_Tumor


title: S45


title: S36_Tumor

value: IIB


title: S47


title: S37_Tumor


title: S41_Tumor

source_name: Tumor colorectal tissue (Crc41T)


title: S34_Tumor


title: S46


title: S35_Tumor


title: S38_Tumor

source_name: Tumor colorectal tissue (Crc38T)


title: S39_Tumor

source_name: Tumor colorectal tissue (Crc39T)


title: S42


title: S40_Tumor

source_name: Tumor colorectal tissue (Crc40T)


title: S44


title: S37_Tumor

source_name: Tumor colorectal tissue (Crc37T)


title: S43


title: S33_Tumor

source_name: Tumor colorectal tissue


title: S36_Tumor

source_name: Tumor colorectal tissue (Crc36T)


title: S41


title: S34_Tumor

source_name: Tumor colorectal tissue (Crc34T)


title: S13_Tumor


title: S32_Tumor


title: S12_Tumor


title: S32_Tumor

source_name: Tumor colorectal tissue (Crc32T)


title: S11_Tumor


title: S38


title: S13_Tumor

source_name: Tumor colorectal tissue (Crc13T)


title: S39


title: S33_Tumor

source_name: Tumor colorectal tissue (Crc33T)


title: S37


title: S40


title: S35_Tumor

source_name: Tumor colorectal tissue (Crc35T)


title: S44_Tumor

source_name: Tumor colorectal tissue (Crc44T)


title: S10_Tumor


title: S8_Tumor


title: S9_Tumor


title: S10_Tumor

source_name: Tumor colorectal tissue (Crc10T)


title: S12_Tumor

source_name: Tumor colorectal tissue (Crc12T)


title: S7_Tumor


title: S8_Tumor

source_name: Tumor colorectal tissue (Crc8T)


title: S9_Tumor

source_name: Tumor colorectal tissue (Crc9T)


title: S6_Tumor


title: S7_Tumor

source_name: Tumor colorectal tissue (Crc7T)


title: S5_Tumor


title: S34

source_name: Tumor colorectal DNA

source_name: Normal adjacent mucosa DNA


title: S33


title: S11_Tumor

source_name: Tumor colorectal tissue (Crc11T)


title: S6_Tumor

source_name: Tumor colorectal tissue (Crc6T)


title: S32


title: S2_Tumor

source_name: Tumor colorectal tissue


title: S1_Tumor


title: S5_Tumor

source_name: Tumor colorectal tissue (Crc5T)


title: S2_Tumor

source_name: Tumor colorectal tissue (Crc2T)


title: S12


title: S50_Normal

source_name: Normal adjacent mucosa


title: S8


title: S49_Normal


title: S49_Normal

source_name: Normal adjacent mucosa (Crc49N)


title: S11


title: S48_Normal

source_name: Normal adjacent mucosa (Crc48N)


title: S13


title: S50_Normal

source_name: Normal adjacent mucosa (Crc50N)


title: S46_Normal


title: 3-BI-II

description: Expression profile of HeLa cells synchronized in mitosis transfected with Beclin 1-II siRNA, experiment 3

hyb_protocol: Resulting targets, fragmented and labeled RNA, were hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 in an Affymetrix fluidic station 450

scan_protocol: GeneChips were scanned using the Affymetrix scanner 3000

data_processing: Quality assessment and preprocessing of the microarrays was done in R version 3.0.2 by utilizing the Bioconductor packages affyPLM version 1.38.0 and GCRMA version 2.34.0 respectively

label_protocol: 500 ng of RNA per sample were processed to generate biotinylated hybridization targets using the Affymetrix GeneChip 3′ IVT Express kit and the Affymetrix GeneChip hybridization, wash, and stain kit

growth_protocol: The cervix carcinoma cell line HeLaS3 was a gift of E. Nigg (University of Basel) and was cultured in DMEM (PAA laboratories, E15-009 or Sigma-Aldrich, D5671) supplemented with 10% fetal bovine serum (FBS, PAA laboratories, A15-151), 1% L-glutamine (PAA laboratories, M11-004), 100 U/ml penicillin and 100 ug/ml streptomycin (PAA laboratories, P11-010). Cells were incubated at 37 °C with 5% CO2.

extract_protocol: Total RNA was extracted using the standard TRIZOL protocol.

treatment_protocol: Cells were transfected with 40 nM siRNA pre-mixed with Oligofectamine (Life Technologies, 12252-011) in Optimem (Life Technologies 31985-054) with the following siRNA sequences: Becn1-II: CAGUUUGGCACAAUCAAUAdTdT, Becn1-ER: GCUCAGUAUCAGAGAGAAUdTdT for a total of 48 h. 12 h following the siRNA transfection cells have been arrested for 24h by a single 2 mM thymidine (Sigma-Aldrich, T1895) arrest, followed by release in the presence of 1 uM Nocodazole (Sigma-Aldrich, M1404). 12 h later mitotic cells were harvested by selective shake off.

tag: cell line

tag: sirna

value: II


title: S10


title: S9


title: S6


title: S7


title: S48_Normal


title: S45_Normal


title: 3-BI-ER

description: Expression profile of HeLa cells synchronized in mitosis transfected with Beclin 1-ER siRNA, experiment 3

value: ER


title: S44_Normal


title: S2


title: S46_Normal

source_name: Normal adjacent mucosa (Crc46N)


title: S1_Tumor

source_name: Tumor colorectal tissue (Crc1T)


title: S47_Normal

source_name: Normal adjacent mucosa (Crc47N)


title: S5


title: KO_6 Biological Rep 3

city: Umea

last: Hanson

address: KBC

department: Plant Physiology, Umeå University

country: Sweden

institute: Umeå Plant Science Centre

hyb_protocol: Affymetrix OneCycle Lab protocols

scan_protocol: Affymetrix OneCycle Lab protocols

data_processing: Data were analysed statistically using the R language environment for statistical computing (http://www.r-project.org) version 2.9 and Bioconductor release 2.4 (Gentleman et al., 2004). Data were normalized using the Robust Multichip Average (RMA) expression measure in the Affy package (Gautier et al., 2004). Differentially expressed genes were identified using the LIMMA package. The obtained p-values were corrected for multiple testing errors using the BH procedure (Benjamini and Hochberg, 1995) and transferred to Microsoft Excel™. The probe set sequences were aligned to the TAIR9 gene model database of transcripts (www.arabidopsis.org).

organism: Arabidopsis thaliana

source_name: KO_seedling_NaCl_6 h

label_protocol: Affymetrix OneCycle Lab protocols

growth_protocol: Plants were cultured hydroponically (8/16 h day/night regime) according to (Gibeaut et al., 1997). Roots of 6-week-old plants were treated with 150 mM NaCl or equimolar concentrations of salts (KCl, MgSO4, Na2SO4) or mannitol, respectively (final osmolarity 0.25 mosM/l). To minimize the effect of circadian regulation, root material from salt-treated WT and mutant lines utilized for RT-qPCR and transcriptome studies was harvested simultaneously 1 h before the end of the light period.

extract_protocol: RNAeasy, quiagen kit

treatment_protocol: Transcriptome analysis was performed on root material from hydroponically grown Col-0 WT and bzip1/bzip53 plants 1 h, 3 h, and 6 h after treatment with 150 mM NaCl.

tag: ecotype background

tag: genotype/variation

value: bzip1/bzip53 knockout

tag: treated with

value: 150 mM NaCl for 6hrs

value: seedling roots


title: 2-BI-ER

description: Expression profile of HeLa cells synchronized in mitosis transfected with Beclin 1-ER siRNA, experiment 2


title: S45_Normal

source_name: Normal adjacent mucosa (Crc45N)

tag: gender


title: 2-BI-II

description: Expression profile of HeLa cells synchronized in mitosis transfected with Beclin 1-II siRNA, experiment 2


title: KO_6 Biological Rep 2


title: S35


title: 1-BI-ER

description: Expression profile of HeLa cells synchronized in mitosis transfected with Beclin 1-ER siRNA, experiment 1


title: S43_Normal


title: S42_Normal


title: S36


title: S43_Normal

source_name: Normal adjacent mucosa (Crc43N)


title: S40_Normal


title: S41_Normal


title: S1

source_name: Tumor colorectal DNA


title: S39_Normal


title: S38_Normal


title: S41_Normal

source_name: Normal adjacent mucosa (Crc41N)


title: S36_Normal


title: S37_Normal


title: KO_6 Biological Rep 1


title: S42_Normal

source_name: Normal adjacent mucosa (Crc42N)


title: S44_Normal

source_name: Normal adjacent mucosa (Crc44N)


title: KO_1 Biological Rep 2

source_name: KO_seedling_NaCl_1 h

value: 150 mM NaCl for 1hr


title: 1-BI-II

description: Expression profile of HeLa cells synchronized in mitosis transfected with Beclin 1-II siRNA, experiment 1


title: KO_3 Biological Rep 3

source_name: KO_seedling_NaCl_3 h

value: 150 mM NaCl for 3hrs


title: KO_3 Biological Rep 1


title: CON-iPSC-5_neural derivative_10 weeks

city: Taipei

first: Hung-Chih

last: Kuo

address: No.128, Sec. 2 Academia Rd

department: Institute of Cellular and Organismic Biology

country: Taiwan

institute: Academia Sinica

description:
GABAergic neural differentiation for 10 weeks
iPBMC-3_ND10W.CEL

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Raw data were normalized independently for each cell line using Robust Multichip Average.

source_name: CON-iPSC-5_neural derivative_10 weeks

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: CON-iPSC-1, CON-iPSC-5, HD-iPSC-A1, -A7 and -B16-derived neurons at 10 weeks into neural differentiation.

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

treatment_protocol: Striatal differentiation of neural progenitors was induced by replacing N2 media with N2/B27 media, and then changing to neural differentiation B27 medium.

tag: subject status/id

value: healthy control

value: iPSCs from human PBMC:reprogramming factors OSKM

value: con-iPSC neural derivatives


title: HD-iPSC-A1_neural derivative_10 weeks

description:
iHD-A1_ND10W.CEL
GABAergic neural differentation for 10 weeks

source_name: HD-iPSC neural derivatives_10wks

value: HD patient A

value: iPSCs from dermal fibroblast

value: HD-iPSC neural derivatives


title: S40_Normal

source_name: Normal adjacent mucosa (Crc40N)

value: male


title: KO_1 Biological Rep 1


title: 2D2-UV-2

city: Los Angeles

first: Andrea

middle: M

last: Kasko

address: 410 Westwood Plaza, 4121 Engineering V

department: Bioengineering

institute: University of California, Los Angeles

hyb_protocol: RNA integrity analysis was performed by the UCLA Clinical Microarray Core/JCCC Genomics Shared Resource located at UCLA. Analysis was performed using the Agilent 2100 bioanalyzer. The bioanlayzer generated electropherograms and RNA integrity number (RIN). Samples used for microarray experiments need to have  RIN > 7. All our samples had distinct 18s and 28s RNA subunit peaks and average RIN > 9.40.  The Core then also performed the labeling, hybdridization, and scanning.

data_processing: Gene array processing and post-processing of data were performed by the UCLA Clinical Microarray Core/JCCC Genomics Shared Resource. We used the Affymetrix human genome U133 Plus 2.0 array. The Core used Partek Genomics Suite to identify differentially expressed genes (> 2-fold change, p < 0.05, unless otherwise noted). Gene lists were exported for functional annotation clustering and pathway analysis in two different programs, the Database for Annotation, Visualization, and Integrated Discovery (DAVID v6.7)5, 6_and Ingenuity Pathway Analysis (IPA, build version 242990, content version 17199142). When using DAVID for functional annotation clustering, default selections and medium stringency for filtering were used unless otherwise noted, and Benjamini-Hochberg multiple comparison correction p-values were used to determine significance in functional annotation clustering in DAVID.

source_name: bone marrow stromal cell

growth_protocol: Human mesenchymal stem cells (hMSCs) were obtained from Texas A&M Health Science Centre College of Medicine through a grant obtained from NCRR of the NIH (P40RR017447). The frozen cells were recovered overnight and passaged (seeding density: 60 cells/cm2) the next day. The cell culture medium used was MEM Richter's Modification medium with 20% Fetal Bovine Serum, 1% L-Glutamine and 1% Penicillin-Streptomycin. Media was changed once every 3 days. Once the cells reached ~80% confluency, they were trypsinized, counted and used for sample preparation (passage 2 hMSCs). For the scope of this project, we were interested in only analyzing the initial effects of free-radicals, UV exposure, and culture systems. Therefore, we did not test the effect of cell age (by using cells in different passage numbers) on free-radical sensitivity, UV exposure, and culture systems. All our sample sets had hMSCs in passage 2.

extract_protocol: Total RNA was extracted using the commercially available TRIzol® guanidinium-phenol based reagent followed by spin column purification using Ambion PureLink kit. For homogenization of samples: Homogenization  2D Samples: Plated cells were trypsinized and centrifuged at 0.5 rcf for 10 minutes. 1000 µL TRIzol® was added to the pellet and was pipette homogenized.  3D Samples: Gels were removed from the medium and washed with PBS. They were coarsely homogenized using a plastic tissue homogenizer and then flash frozen in liquid nitrogen. Each sample was thawed in 1000 µL TRIzol®. Fine homogenization was performed on ice using an electric tissue homogenizer (Tissue Tearor , Biospec Products, Inc) for 1 minute at speed 35.

treatment_protocol: Cells were plated or encapsulated on day 0. On day 1 samples were either irradiated with UVA light for 25 mintues at 3.5mW/cm^2 or not irradiated. On day 2 all samples were collected for total RNA extraction

value: bone marrow

value: mesenchymal stem cells

tag: culture conditions

value: hmsc plated in T75 flask at 500,000 cells

tag: uva treatment at day 1

value: 5.25 J/cm^2 UVA radiation exposure at day 2


title: KO_3 Biological Rep 2

tag: tissue


title: HD-iPSC-A7_neural derivative_10 weeks

description:
iHD-A7_ND10W.CEL
GABAergic neural differentation for 10 weeks

value: female


title: S35_Normal

source_name: Normal adjacent mucosa

value: Normal adjacent mucosa


title: KO_C Biological Rep 2

value: bzip1/bzip53 knockout


title: CON-iPSC-1_neural derivative_10 weeks

description:
iCFB-50_ND10W.CEL
GABAergic neural differentation for 10 weeks

source_name: con-iPSC neural derivatives_10wks

value: iPSCs from human foreskin fibroblast


title: S34_Normal


title: KO_1 Biological Rep 3

value: 150 mM NaCl for 1hr

value: seedling roots


title: KO_C Biological Rep 3


title: S39_Normal

source_name: Normal adjacent mucosa (Crc39N)


title: 2D2-UV-1

scan_protocol: performed by the UCLA Clinical Microarray Core/JCCC Genomics Shared Resource

value: 5.25 J/cm^2 UVA radiation exposure at day 1


title: HD-iPSC-B4_neural derivative_10 weeks

description:
iHD-B4_ND10W.CEL
GABAergic neural differentation for 10 weeks

value: HD patient B


title: 2D2-UV-3

label_protocol: performed by the UCLA Clinical Microarray Core/JCCC Genomics Shared Resource

value: 5.25 J/cm^2 UVA radiation exposure at day 3


title: S33_Normal


title: WT_6 Biological Rep 3

source_name: WT_seedling_NaCl_6 h

value: wild type

value: 150 mM NaCl for 6hrs


title: S35_Normal

source_name: Normal adjacent mucosa (Crc35N)


title: S34_Normal

source_name: Normal adjacent mucosa (Crc34N)


title: 2D2-noUV-2


title: S38_Normal

source_name: Normal adjacent mucosa (Crc38N)


title: S32_Normal


title: S36_Normal

source_name: Normal adjacent mucosa (Crc36N)


title: S13_Normal


title: S33_Normal

source_name: Normal adjacent mucosa (Crc33N)


title: S37_Normal

source_name: Normal adjacent mucosa (Crc37N)


title: 2D2-noUV-3


title: KO_C Biological Rep 1


title: S11_Normal


title: WT_6 Biological Rep 1


title: S12_Normal


title: WT_3 Biological Rep 3

source_name: WT_seedling_NaCl_3 h

value: 150 mM NaCl for 3hrs


title: S13_Normal

source_name: Normal adjacent mucosa (Crc13N)


title: WT_6 Biological Rep 2


title: 2D2-noUV-1


title: S32_Normal

source_name: Normal adjacent mucosa (Crc32N)

value: male


title: 3DC-UV-3

value: bone marrow

value: hmsc encapsulated by conjugate addition at 3,000,000 cells/100uL


title: S10_Normal


title: S11_Normal

source_name: Normal adjacent mucosa (Crc11N)


title: WT_3 Biological Rep 1


title: 3DC-UV-2

value: mesenchymal stem cells


title: WT_3 Biological Rep 2


title: S8_Normal


title: S9_Normal


title: S10_Normal

source_name: Normal adjacent mucosa (Crc10N)


title: 3DC-UV-1


title: S12_Normal

source_name: Normal adjacent mucosa (Crc12N)


title: S7_Normal


title: 3DC-noUV-2

source_name: bone marrow stromal cell


title: S9_Normal

source_name: Normal adjacent mucosa (Crc9N)


title: S8_Normal

source_name: Normal adjacent mucosa (Crc8N)


title: S6_Normal

source_name: Normal adjacent mucosa


title: WT_1 Biological Rep 3

source_name: WT_seedling_NaCl_1 h


title: WT_1 Biological Rep 1


title: 3DC-noUV-3


title: 3DC-noUV-1


title: WT_1 Biological Rep 2


title: S2_Normal


title: S5_Normal

source_name: Normal adjacent mucosa (Crc5N)


title: WT_C Biological Rep 2


title: S1_Normal


title: WT_C Biological Rep 1


title: 3DR-UV-2

value: hmsc encapsulated by radical polymerization at 3,000,000 cells/100uL

value: 5.25 J/cm^2 UVA radiation exposure at day 2


title: S6_Normal

source_name: Normal adjacent mucosa (Crc6N)

value: Normal adjacent mucosa


title: WT_C Biological Rep 3


title: 3DR-noUV-3


title: 3DR-UV-1


title: 3DR-UV-3


title: S5_Normal