title: MSC_MIRNA_G2-3

city: Madrid

first: Manuel

middle: Angel

last: Gonzalez

address: Melchor Fernandez Almagro, 3

institute: CNIC

description: miRNA expression in GVHD clinical trial group 2 bone marrow-derived MSCs

hyb_protocol: 100 ng of Cy3 labelled RNA were hybridized for 20 hours at 55ºC in a hybridization oven  (G2545A, Agilent Technologies) set to 15 rpm in a final concentration of 1X GE Blocking Agent and 1X Hi-RPM Hybridization Buffer, according to manufacturer's instructions (miRNA Microarray System Protocol, Agilent Technologies). After hybridization, microarrays were washed according to manufacturer's instructions (miRNA Microarray System Protocol, Agilent Technologies). Arrays were dried out using a centrifuge at 1000 rpm for 2 min.

scan_protocol: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for miRNA Microarray v3 (miRNA Microarray System Protocol, Agilent Technologies).

data_processing: Images provided by the scanner were analyzed with Feature Extraction software V10 (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: bone marrow mesenquimal stem cells, GVHD clinical trial, group 2, replicate 3

label_protocol: miRNA Labeling Kit (Agilent Technologies) was used to label RNA. 100 ng of total RNA were dephosphorylated and Cyanine 3-pCp molecule was ligated to the 3´ end of each RNA molecule by using T4 RNA ligase.

growth_protocol: Human bone-marrow was obtained from healthy donors. Mesenchymal stem cells were isolated as described. All cells were cultured in expansion medium (Dulbecco’s modified Eagle’s medium (DMEM), with 4.5 g/l D-glucose supplemented with 10% heat-inactivated fetal calf serum (FCS), 2 mM L-glutamine, and 50 μg/ml gentamicin; all culture reagents from Invitrogen, Carlsbad, CA)

extract_protocol: Total RNA was isolated from cultured cells with a miRNeasy Mini Kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: untreated

value: cultured bone marrow-derived MSC


title: CECT11758-1

status: Public on Jun 01 2014

type: genomic

city: Montpellier cedex1

first: Jean-Luc

last: Legras

address: 2, place Viala

department: UMR1083, Science pour l'Oenologie

country: France

institute: INRA

description: analyzed strain (flor)

hyb_protocol: Winzeler2003 Genetics

scan_protocol: Affymetrix scanner

data_processing:
Background substraction with RMA and quantile normalisation and perfect match probe extraction with "apt-1-12-0" (241710 probes)
Then probes are filtered for having coordinates on S288C genome sequence  (Schizosacchaomyces pombe probes are removed), probes are scaled across all arrays.  Probes with signal values below 5 for one of S288C array or aberant values over 10000 3 probes on the whole dataset) are removed. 38864 probes are left.
From the filtered data, for each probe, after averaging the signal  from replicates , the log ratios  otained on are calculated using S288C as a reference . NA values are repalced by -2 hybridization on S288C genome and negative or null for other srains mean no hybridization of the probe)
The average of log ratios are calculated  for three adjacent positions in order to group them three by three in order to  reduce the number of probes (too many probes lead to a crash of DNAcopy). Log ratios are then centered  by substracting the median value.
Discontinuities in hybridization signal are detected with DNAcopy R package.
results file descriptions: RMA-bg quantile intensity file (RMAbackground quantile normalisation-probe intensity file)
results file descriptions: RMA-bgquantil+Saccerecoordinates (RMAbackground quantile normalisation-probe intensity file of Saccharomyces cerevisiae probes + coordinates)
results file descriptions: Log ratios for each probe (chromosome numbering changed from Sace A to 1 as requested by DNAcopy)
results file descriptions: Log ratios after averaging per three probes and centered
results file descriptions: Eg8segments (segments of hybridization found with DNAcopy for Eg8_
results file descriptions: CECT11758segments (segments of hybridization found with DNAcopy for CECT11758)
results file descriptions: Eg25segments (segments of hybridization found with DNAcopy for Eg25)
results file descriptions: FloraNerosegments (segments of hybridization found with DNAcopy for Flora Nero)
results file descriptions: LRJurasegments (segments of hybridization found with DNAcopy for LR Jura)
results file descriptions: MY138segments (segments of hybridization found with DNAcopy for My138)
results file descriptions: P3segments (segments of hybridization found with DNAcopy for P3)
results file descriptions: TA12CUBsegments (segments of hybridization found with DNAcopy for TA12CUB)
results file descriptions: U13segments (segments of hybridization found with DNAcopy for U13)
results file descriptions: V5segments (segments of hybridization found with DNAcopy for V5)

label: biotin

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: flor isolate, Spain

growth_protocol: overnight YPD shaken culture 28°

extract_protocol: DNA extraction according to legras et al. 2003 FEMS microbiol letters.

treatment_protocol: no treatment (CGH)

tag: strain


title: 7512560086_R04C02 (batch1)

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

country: USA

institute: UCLA

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

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

data_processing:
BeadStudio software
Raw data was processed using the Illumina GenomeStudio software (version 2010.3). Background correction and color normalization were performed using the R package minfi version 1.2.0 and normalization using Subset-quantile Within Array Normalization (SWAN). Probes were excluded from further analysis if >95% samples had detection p-value >0.01.
Raw data (Unmethylated and methylated signal intensities) linked as supplementary files on Series record.

label: Cy5 and Cy3

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified with standard methods

tag: diagnosis

value: FTD

tag: gender

value: UNKNOWN

tag: race

value: White

tag: age

tag: batch

tag: tissue

value: Peripheral Blood


title: S. mutans UA159 parent strain pH5 glucose replicate 3

type: RNA

city: Rochester

first: Roberta

middle: C

last: Faustoferri

state: NY

address: 601 Elmwood Ave. Box 611

department: Center for Oral Biology

institute: University of Rochester Medical Center

hyb_protocol: The slides were hybridized in a mixture containing equal amounts of labeled test and reference cDNA as described by the protocol from the Pathogen Functional Genomics Research Center (PFGRC) for 16 h at 42°C in a MAUI hybridization chamber (BioMicro Systems, Salt Lake City, UT).  Hybridized slides were washed and scanned using a GenePix 4000b scanner (Molecular Devices, Inc., Sunnyvale, CA).

scan_protocol: Hybridized slides were washed using the method described by the Pathogen Functional Genomics Research Center (PFGRC) and scanned using a GenePix 4000b scanner (Molecular Devices, Inc., Sunnyvale, CA).

data_processing: Data were analyzed using software available at the J. Craig Venter Institute PFGRC website.  Single-channel images of the slides were loaded into Spotfinder and overlaid.  MIDAS software was used to normalize the spot intensity data using LOWESS and iterative log mean centering with default setting, followed by in-slide replicate analysis.  Statistical analysis was carried out with BRB array tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) with a cutoff P-value of 0.01 and a ≥2-fold change of expression.

molecule: total RNA

organism: Streptococcus mutans UA159

source_name: RNA from parent strain, steady-state pH5, glucose

label_protocol: Once RNA was purified as described above, cDNA was generated from 2µg RNA per sample as described by the protocol available from the Pathogen Functional Genomics Research Center (PFGRC) using Invitrogen Superscript III Reverse Transcriptase (Life Technologies, Carlsbad, CA) to increase cDNA yields.  Purified cDNAs were coupled to Cy3 (experimental samples) or Cy5 (reference cDNA).

growth_protocol: S. mutans UA159 was grown in continuous culture to steady-state pH values of 7and 5 with either glucose or maltose  in a BioFlo2000 fermentor at a dilution rate of 0.144h-1 in non-limiting sugar concentrations.

extract_protocol: RNA was isolated from homogenized S. mutans cells grown in continuous culture in TY + 1% glucose or maltose medium to steady-state pH value of 7 or 5, by repeated hot acid-phenol: chloroform extractions, and the nucleic acid was precipitated with 1 volume ice-cold isopropanol and one-tenth volume 3M sodium acetate (pH 5) at –20°C overnight.  RNA pellets were resuspended in 80 mL nuclease-free H2O, and treated with DNase I (Ambion) at 37°C for 30 minutes.  RNA concentrations were determined using a Nanodrop ND-1000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA), and 1 µL samples were run on an agarose gel to verify RNA integrity.  The RNA was purified again using the RNeasy mini kit (Qiagen), including a second on-column DNase treatment that was performed as recommended by the supplier.  Final RNA concentrations were determined spectrophotometrically.

tag: genotype

value: parental

tag: ph

tag: sugar

value: glucose

source_name: RNA from parent strain, mid-log

tag: growth phase

value: mid-log


title: apomictic initial cell 1

city: Glarus

first: Marc

middle: William

last: Schmid

address: Hauptstrasse 34

country: Switzerland

institute: MWSchmid GmbH

description:
RNA amplification with Ambion Message AmpII Kit
apo_initial1

scan_protocol: GCOS

data_processing:
BgPANP algorith with R/Bioconductor
presence absence p-values with BgPANP

organism: Boechera gunnisoniana

source_name: pool of apomictic initial cells isolated by laser assisted microdissection

label_protocol: During the second round of amplification with the Message AmpII Kit (Ambion), biotin-11-UTP (ambion) was incorporated in th amplified aRNA for microarray analysis.

growth_protocol: Seeds were surface sterilized and grown on MS plates for 10-14 days before transfer to a mixture of soil (ED73, Universalerde, Germany) and sand (5:1) fertilized with Plantomaag (Syngenta, Switzerland) and Osmocote (Scotts, Marysville, USA). Plants were grown in a greenhouse chamber with 60% humidity and 16 h light/ 8 h darkness at 20 °C and 16 °C, respectively.

extract_protocol: For total RNA isolation from cells or tissues isolated by laser assisted microdissection, caps were covered with 10 ul extraction buffer from the PicoPure RNA isolation kit (Arcturus Engineering, Mountain View, USA), incubated at 42°C for 30 min before isolation according to manufacturers instructions. The DNAse treatment was performed on-column using the RNAse-free DNase set (QIAGEN, Hilden, Germany).

treatment_protocol: no treatment

value: female reproductive tissues, germline

tag: cell type

value: apomictic initial cell


title: S. mutans UA159 parent strain pH5 glucose replicate 2


title: S. mutans UA159 parent strain pH5 glucose replicate 1


title: 7512560082_R02C02 (batch1)

value: Control

value: MALE


title: S. mutans UA159 parent strain pH7 glucose replicate 4

source_name: RNA from parent strain, steady-state pH7, glucose


title: MSC_MIRNA_G2-1

country: Spain

source_name: bone marrow mesenquimal stem cells, GVHD clinical trial, group 2, replicate 1


title: U13-1  (reanalysis of GSM786818)

source_name: wine isolate Alsace , France


title: MSC_MIRNA_G1-5

description: miRNA expression in GVHD clinical trial group 1 bone marrow-derived MSCs

source_name: bone marrow mesenquimal stem cells, GVHD clinical trial, group 1, replicate 5


title: V5-2  (reanalysis of GSM786817)

source_name: spore of CIVC8130, wine isolate from Champagne, France


title: S. mutans UA159 parent strain pH7 glucose replicate 3


title: 7512560082_R03C02 (batch1)


title: MSC_MIRNA_G1-4

source_name: bone marrow mesenquimal stem cells, GVHD clinical trial, group 1, replicate 4


title: 7512560082_R01C02 (batch1)


title: V5-1  (reanalysis of GSM786816)


title: S. mutans UA159 parent strain pH7 glucose replicate 2


title: MSC_MIRNA_G1-3

source_name: bone marrow mesenquimal stem cells, GVHD clinical trial, group 1, replicate 3


title: 7512560082_R05C02 (batch1)


title: MSC_MIRNA_G1-2

source_name: bone marrow mesenquimal stem cells, GVHD clinical trial, group 1, replicate 2


title: Eg25-2  (reanalysis of GSM786815)


title: 7512560082_R03C01 (batch1)

value: FEMALE

value: Unknown


title: 7512560082_R01C01 (batch1)


title: Eg25-1  (reanalysis of GSM786814)


title: MSC_MIRNA_G1-1

source_name: bone marrow mesenquimal stem cells, GVHD clinical trial, group 1, replicate 1


title: Ca9-22_hypoxia_48h_rep1

city: Hiroshima

first: Keiji

last: Tanimoto

address: Kasumi 1-2-3, Minami-ku

country: Japan

institute: Research Institute for Radiation Biology and Medicine, Hiroshima University

hyb_protocol: Ten μg of fragmented cRNA was hybridized to commercially avairable CodeLinkTM Uniset Human 20 K I Bioarray (19,981 probes). After hybridization, the arrays were rinsed and labeled with streptavidin-Cy5.

scan_protocol: The arrays were scanned using Agilent DNA Microarray ScannerTM (Agilent, Santa Clara, CA).

data_processing: The raw image data were analyzed with CodeLinkTM Expression Analysis ver.2.3 Software (GE Healthcare).

source_name: Cell line cultured in 1% pO2 for 48h

label_protocol: CodeLink Expression Bioarray System (GE Healthcare, Tokyo, Japan) was used. Briefly, from 1 μg of total RNA, double-strand cDNA and subsequent biotin-labeled cRNA were synthesized using CodeLinkTM Expression Assay Reagent Kit (GE Healthcare).

growth_protocol: Human oral squamous cell carcinoma cell lines, HSC-2 and Ca9-22, were cultured in DMEM  medium (Sigma-Aldrich Japan, Tokyo, Japan) supplemented with 10% fetal bovine serum (BioWhittaker, Verviers, Belgium) plus Kanamycin (100 mg/ml) with passage every 3 days.

extract_protocol: Total RNA was prepared from frozen cell pellets by using QIAGEN RNeasy® mini kit (QIAGEN) according to the manufacturer’s instruction.

treatment_protocol: Cells (4 x 10^5 cells) cultured in 10 cm diameter dish were incubated under normoxic (21% pO2) or hypoxic (1% pO2) conditions for 24 or 48hours.

tag: cell line

value: human oral squamous cell carcinoma cells

tag: cultured under

value: hypoxic conditions; 1% pO2 for 48h


title: Ca9-22_hypoxia_24h_rep1

source_name: Cell line cultured in 1% pO2 for 24h

value: hypoxic conditions; 1% pO2 for 24h


title: 7668610129_R06C02 (batch1)


title: 7668610129_R06C01 (batch1)

value: Filipino


title: MSC_MIRNA_SEN-4

description: miRNA expression in senescent bone marrow-derived MSCs

source_name: bone marrow mesenquimal stem cells, senescent, replicate 4

treatment_protocol: ionizing radiation (10 Gy) produced by a high-voltage X-ray-generator tube (Mark I-68, J.L. Shepherd & Associates, San Fernando, CA, USA)

value: cultured bone marrow-derived MSC


title: Eg8-3  (reanalysis of GSM786813)

organism: Saccharomyces cerevisiae x Saccharomyces kudriavzevii


title: Eg8-2 (reanalysis of GSM786812)


title: apomictic initial cell 2

description:
RNA amplification with Ambion Message AmpII Kit
apo_initial2


title: MSC_MIRNA_SEN-3

source_name: bone marrow mesenquimal stem cells, senescent, replicate 3


title: MSC_MIRNA_SEN-2

source_name: bone marrow mesenquimal stem cells, senescent, replicate 2


title: 7668610129_R05C02 (batch1)


title: 7512560082_R02C01 (batch1)


title: HSC2_hypoxia_48h_rep1


title: Ca9-22_normoxia_rep1

source_name: Cell line cultured in 21% pO2 for 24h

value: normoxic condition; 21% pO2


title: HSC2_hypoxia_24h_rep1


title: MSC_MIRNA_G2-2

source_name: bone marrow mesenquimal stem cells, GVHD clinical trial, group 2, replicate 2


title: MSC_MIRNA_SEN-1

source_name: bone marrow mesenquimal stem cells, senescent, replicate 1


title: U13-2  (reanalysis of GSM786819)


title: 7668610129_R03C02 (batch1)

value: White


title: HSC2_normoxia_rep1


title: 7668610129_R05C01 (batch1)

value: PSP

value: UNKNOWN

value: Peripheral Blood


title: MSC_MIRNA_WT-4

description: miRNA expression in untreated bone marrow-derived MSCs

source_name: bone marrow mesenquimal stem cells, untreated control, replicate 4


title: MSC_MIRNA_WT-3

source_name: bone marrow mesenquimal stem cells, untreated control, replicate 3


title: MSC_MIRNA_WT-2

source_name: bone marrow mesenquimal stem cells, untreated control, replicate 2


title: ko 13.5d replicate 11

city: South San Francisco

first: Li

last: Li

address: 1 DNA Way

institute: Genentech, Inc

hyb_protocol: Agilent In Situ Hybridization Kit Plus was used where Cy-dye labeled control and test samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, the arrays were washed twice, dried and then scanned.

scan_protocol: Scanned on an Agilent scanner, images were processed using Agilent Feature Extraction software version 9.5.

data_processing: Agilent Feature Extraction software version 9.5 was used for background subtraction and LOWESS normalization.

organism: Mus musculus

source_name: mouse embryo forelimbs

label_protocol: Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Agilent’s Low RNA Input Fluorescent Linear Amplification Kit. 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal mouse reference (Stratagene, La Jolla, CA).

growth_protocol: Mouse embryos were dissected and then forelimbs were collected for further gene expression analysis.

extract_protocol: Total RNA extracted using Qiagen Rneasy kit following manufacturer's instructions.

tag: genotype/variation

value: Chsy-1 knockout

source_name: Universal mouse reference

tag: reference

value: Universal mouse reference


title: 7668610129_R04C02 (batch1)


title: 7668610129_R03C01 (batch1)


title: S. mutans UA159 parent strain pH7 glucose replicate 1

source_name: RNA from parent strain, steady-state pH7, glucose

value: parental

value: glucose

source_name: RNA from parent strain, mid-log

value: mid-log


title: ko 13.5d replicate 10


title: 7668610129_R02C02 (batch1)

value: Control

value: FEMALE


title: PSA-NCAM_mas

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

institute: IDIBELL

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina custom golden gate DNA methylation array using standard Illumina protocol

scan_protocol: Standard Illumina Protocol

data_processing: R packages: lumi, genefilter, mpm, etc.

extract_protocol: genomic DNA was extracted and purified from brain samples using phenol-extraction standard protocol.

value: Brain


title: ko 13.5d replicate 12


title: ko 13.5d replicate 8


title: 7668610129_R02C01 (batch1)

value: MALE


title: ko 13.5d replicate 13


title: ko 13.5d replicate 6


title: ko 13.5d replicate 7


title: ko 13.5d replicate 9


title: Met_100

value: DNA


title: 7668610097_R06C01 (batch1)


title: 7668610129_R01C01 (batch1)


title: ko 13.5d replicate 5


title: 7668610129_R01C02 (batch1)


title: ko 13.5d replicate 4


title: Met_0


title: ko 13.5d replicate 3


title: 7668610097_R06C02 (batch1)


title: Met_25


title: A2B5_mas


title: ko 13.5d replicate 2


title: 7668610097_R03C02 (batch1)


title: 7668610097_R04C01 (batch1)

value: Other Race


title: 7668610097_R05C01 (batch1)


title: 7668610097_R04C02 (batch1)


title: wt 13.5d replicate 9

value: wild type


title: wt 13.5d replicate 8


title: ko 13.5d replicate 1


title: MSC_MIRNA_WT-1

source_name: bone marrow mesenquimal stem cells, untreated control, replicate 1

value: cultured bone marrow-derived MSC


title: Met_75


title: 7668610097_R02C01 (batch1)

value: White


title: 7668610097_R01C01 (batch1)

value: PSP


title: wt 13.5d replicate 7


title: 7668610097_R02C02 (batch1)


title: 6229050040_R06C01 (batch1)


title: 7668610097_R03C01 (batch1)


title: 7668610129_R04C01 (batch1)


title: wt 13.5d replicate 2


title: wt 13.5d replicate 3


title: wt 13.5d replicate 4


title: wt 13.5d replicate 1


title: Met_50


title: Sed 8

city: Rotterdam

first: Diederik

last: Kuster

address: Dr Molewaterplein 50

department: Experimental Cardiology

country: Netherlands

institute: Erasmus University Medical Center

hyb_protocol: Labeled cRNA was hybridized to according to the manufacturer’s instructions

scan_protocol: According to the  Affymetrix protocol

data_processing: Data was analyzed with R. To prevent batch effect, data was first rma per group and then all arrays were quantile normalized.

organism: Sus scrofa

source_name: Left ventricle, cardiac, sedentary

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: 2-3 months old swine

extract_protocol: Trizol followed by Qiagen's Rneasy clean-up kit

treatment_protocol: Frozen myocardium was crushed in liquid nitrogen.

value: F

value: 2-3 months


title: Sed 7

value: M


title: wt 13.5d replicate 6

value: Universal mouse reference


title: 6229050040_R06C02 (batch1)

value: FTD

value: Peripheral Blood


title: 6229050040_R05C01 (batch1)

value: UNKNOWN


title: Sed 6


title: 6229050040_R03C02 (batch1)

value: Control


title: Sed 4


title: 6229050040_R02C02 (batch1)

value: FEMALE


title: 7668610097_R05C02 (batch1)


title: Sed 5


title: 7668610097_R01C02 (batch1)


title: 6229050040_R04C02 (batch1)


title: Array-CGH analysis: FC16

city: Stockholm

first: Johanna

last: Winberg

address: CMM L8:02, Karolinska University Hospital

department: Molecular Medicine and Surgery

country: Sweden

institute: Karolinska Institutet

hyb_protocol: Corresponding labelled patient and reference samples were pooled and 5 µl CotDNA, 11 µl blocking buffer and 55 µl hybridization buffer from the Oligo aCGH/CHp-on chip hybridization kit (Agilent Technologies).Denaturation was performed at 95⁰ for 5 mins followed by pre-hybridization at 37⁰ for 45 min. 100 µl per sample were dispensed in each well on a 4x180K oligonucleotide array glass slide and a gasket slide added to close. The glass was hybridized for 24 hours in 65⁰ in a rotation oven. After 24 hours, each glass was put in wash solution B1 for 5 min followed by 1 min in 37⁰ wash solution B2 and subsequently air-dried and stored in a light-proof box.

scan_protocol: The glasses were scanned on a DNA Microarray Scanner from Agilent Technologies with 3 µm resolution.

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

source_name: genomic DNA from heart

label_protocol: 1.1 µg of genomic patient and control DNA (Promega) was diluted in water to a total volume of 19 µl. 20 µl of primer buffer (CGH labelling kit for oligo arrays, Enzo Life Sciences) was added on ice. The samples were incubated at 99⁰ for 10 min and then placed on ice for 5 mins. 10 µl of Cy3 or Cy5 were added to each sample and subsequently 1 µl of Klenow polymerase was added. The samples were incubated at 37⁰ for 12 hours and then heated to 65⁰ for 10 mins before cooling to 4⁰. Purification of labelled samples was performed by adding 250 µl of PB buffer to a spin column and adding 50 µl of labelled sample (the total volume). The samples were centrifuged at 14000 rpm for 1 min, and the flow-through discarded. 750 µl of PE wash buffer was added to each column, and the samples centrifuged at 14000 rpm for 1 min. The flow-through was discarded and the samples centrifuged once more at 14000 rpm for 1 min. DNA was eluated with 22 µl TE buffer and incubated at 2 min in room temperature before centrifugation at 14000 rpm for 1 min. Concentration of labelled DNA was measured using NanoDrop.

extract_protocol: Genomic DNA was isolated from either peripheral blood or tissue samples according to standard procedures. For fetal cases, DNA was isolated from routinely preserved fresh frozen heart, liver, lung, or spleen tissue using the Gentra Puregene Blood Kit (QIAGEN Sciences, Maryland, USA) in combination with Proteinase K (Finnzymes, Espoo, Finland) with slight modifications to the manufacturer’s protocol.

treatment_protocol: No cell culture was performed.

value: heart

source_name: DNA pooled from blood of 10 healthy individuals

value: Blood


title: 6229050032_R06C01 (batch1)

value: MALE


title: 6229050040_R03C01 (batch1)


title: 6229050040_R02C01 (batch1)


title: 6229050040_R01C02 (batch1)


title: 6229050040_R01C01 (batch1)


title: wt 13.5d replicate 5


title: E2A-/- hematopoietic progenitors cultured on TSt-4 cells

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: Lin- cells were MACS purified from E2A-/- bone marrow and cultured on TSt-4 in the presence of SCF, IL-7 and Flt3-L for at least 2 months.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: bone marrow

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: RPMI 1640 medium supplemented with 10% FCS, L-glutamine (2 mM), sodium pyruvate (1 mM), sodium bicarbonate (2 mg/ml), nonessential amino acid solution (0.1 mM), 2-ME (5 x 10-5 M), streptomycin (100 mg/ml), and penicillin (100 U/ml).

extract_protocol: Total RNA from each sample (1x10^5 - 1x10~6 cells) was purified by RNeasy mini Kit (Qiagen)

tag: genetic background


title: Control (Mock) Pro B cells cultured on TSt-4 cells

description: LKS cells were sorted from normal fetal livers, infected with Mock retrovirus. The hCD25+ cells were sorted after 2 days of infection and cultured on TSt-4 cells in the presence of SCF, IL-7 and Flt3-L for 30 days.

source_name: Fetal liver


title: 6229050032_R05C01 (batch1)


title: Sed 2


title: Array-CGH analysis: FC19


title: Array-CGH analysis: FC14

source_name: genomic DNA from spleen

value: spleen


title: Array-CGH analysis: FC15

source_name: genomic DNA from lung

value: lung


title: 6229050032_R06C02 (batch1)

value: Chinese


title: Ex 8

source_name: Left ventricle, cardiac, exercised


title: Sed 1


title: Ex 7


title: Array-CGH analysis: FC13


title: Ex 6


title: 6229050040_R05C02 (batch1)


title: Id3-transduced hematopoietic progenitors cultured on TSt-4 cells

description: LKS cells were sorted from normal fetal livers, infected with Id3 retrovirus. The hCD25+ cells were sorted after 2 days of infection and cultured on TSt-4 cells in the presence of SCF, IL-7 and Flt3-L for 30 days.


title: Array-CGH analysis: FC17

source_name: genomic DNA from liver

value: liver


title: 6229050032_R04C01 (batch1)

value: PSP

value: Other Race


title: Ex 4

value: F

value: 2-3 months


title: Hematopoietic stem/progenitor cells in mouse fetal liver

description: LKS cells were sorted from normal fetal livers


title: miR-17~92Hi

city: Louisville

first: Hong

last: Jiang

address: 505 S Hancock St

institute: University of Louisville

description:
cell line expressing  high levels of microRNA-17~92
[miR-17~92Hi](normalized)

hyb_protocol: The arrays are hybridized overnight at 45oC at 60rpm and then washed and stained using fluidics script FS450_0007.

scan_protocol: The arrays were scanned using the GeneArray Scanner 3000 7G and raw data analyzed using Expression Console in AGCC (Affymetrix GeneChip Command Console). .

data_processing: For data procesing we use Expression Console from Affymtrix running GCRMA.

source_name: CT26 cell line

label_protocol: Briefly, 100ng of total RNA from each sample is used to generate double strand cDNA by linear amplification using T7-linked random primers and reverse transcriptase.  Subsequently, cRNA is generated by standard methods (Affymetrix) followed by cRNA fragmentation, end label biotinylation and preparation of hybridization cocktail.

growth_protocol: cell lines were maintained in RPMI1640 (Invitrogen, Carlsbad, CA), supplemented with 10% fetal bovine serum (Invitrogen), penicillin, and streptomycin (Invitrogen).

extract_protocol: Total RNA was isolated fromr cell lines using RNeasy Mini Kit (Qiagen, Frederick, MD).

treatment_protocol: To generate cell lines stably expressing the miR-17~92 cluster, mouse cancer cell lines were seeded into a 6-well plate, cultured overnight and cells were then transfected with PIG-miR-Ctrl Vector or PIG-miR-17~92 WT (provided by Dr. Andrea Ventura 10). Six hours after transfection, cells were returned to regular culture media containing 7.5 g/mL puromycin (Sigma) (CT26 cell line). Two weeks after drug selection, GFP+ cells were sorted using a FACSAria™ III Flow Cytometer (BD Biosciences, San Jose, CA, USA) and were seeded into a 96-well plate for monoclonal selection by serial dilution.

value: CT-26 colon cancer cell line


title: 6229050040_R04C01 (batch1)

value: White


title: Ex 2


title: 6229050032_R05C02 (batch1)

value: Peripheral Blood


title: Ex 5

value: M


title: Ex 3


title: miR-17~92Med

description:
cell line expressing medium levels of microRNA-17~92
[miR-17~92Med](normalized)


title: Ex 1


title: Array-CGH analysis: FC5

source_name: genomic DNA from liver, lung

value: liver, lung


title: Array-CGH analysis: FC12


title: NB37

city: Cologne

first: Jessica

last: Theissen

state: NRW

address: Kerpener Straße 62

department: Department of Pediatric Oncology and Hematology

country: Germany

institute: University of Cologne

description: Agilent-013282 Human Genome CGH Microarray 44A (G4410B)

hyb_protocol: Labelled DNA were hybridized to oligonucleotide microarrays (Agilent Technologies) following the manufacture's instructions ("Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol”, v. 5.0 (Agilent Technologies). Briefly, fluorescent-labeled reference and tumor DNA (3 ug each) were mixed with 50 ug of human Cot-1 DNA (Invitrogen Life Technologies) and control targets (Agilent Technologies). Slides were hybridized in SureHyb gasket (Agilent Technologies) placed in rotisserie (20 RPM rotation speed) in hybridization oven at 65°C for 40 hrs. After hybridization, the slides were washed with Oligo aCGH Wash Buffer 1(Agilent Technologies) at room temperature for 5 min, with Oligo aCGH Wash Buffer 2 (Agilent Technologies) at 37°C for 1 min, with the Stabilization solution (Agilent) for 1 minute at room temperature, then dried immediately by rinsing slides into Drying solution (Agilent) for 30 seconds.

scan_protocol: Arrays were scanned by using an Agilent G2567AA Scanner follwowing the manufacturer's protocol (Agilent Technologies).

data_processing: The scanned TIFF images were loaded into the Feature Extraction (v9.5 Agilent technologies), Feature Extraction files were analyzed by CGH Analytics Software (v. 3.5.14 Agilent Technologies). The circular binary segmentation algorithm was applied. Ref: PMID:  17234643

source_name: Tumor DNA

label_protocol: We followed the "Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol”, v. 5.0 (Agilent Technologies). Briefly, 2 ug of sample and reference genomic DNAs (for reference were used Human Genomic DNA: male Cat G1471, female Cat G1521, Promega, Madison, WI) were separately digested with AluI/RsaI restriction enzyme mix (Promega). Fragmented DNA was labeled by direct enzymatic incorporation of fluorescent tags. Genomic DNA was labeled with Cy3-dUTP or Cy5-dUTP (Perkin Elmer) using the Random-Primed Bioprime DNA Labeling kit (Invitrogen Life Technologies). Briefly, 50 ul reaction mix containing dATP, dGTP and dTTP (120 ueach), dUTP (60 uM) and Cy3-dUTP (60 uM) or Cy5-dUTP (60 uM) was incubated with Klenow Fragment (40 units) at 37°C for 2 hrs. Unincorporated nucleotides were removed on Microcon YM-30 filters (Millipore) according to the manufacturer’s protocol. Dye incorporations of post-labeling products were measured by NanoDrop 1000 (ThermoScientific) and the parameters that predicted successful hybridization were a minimum Cy3 incorporation of 0.5 pmol/ul and Cy5 incorporation of 0.3 pmol/ul.

extract_protocol: Genomic DNA was isolated using the DNA-Isolation Kit (Gentra) according to the manufacturer's protocol. A pool of normal male or female DNA (Promega) was used as reference.

tag: Sex

value: male

tag: age at diagnosis (days)

tag: tumor stage

value: neuroblastoma

source_name: Promega Reference DNA


title: 6229050032_R02C01 (batch1)

tag: diagnosis

value: FTD

tag: gender

value: UNKNOWN

tag: race


title: 6229050032_R04C02 (batch1)

value: Control

value: FEMALE

value: Mexican

tag: age

tag: batch

tag: tissue


title: 6229050032_R02C02 (batch1)


title: miR-Ctrl

description:
cell line expressing control microRNA
[miR-Ctrl](normalized)

value: expressing control microRNA


title: Sed 3


title: 6229050032_R03C01 (batch1)

value: PSP

value: MALE

value: Somoan


title: 6229050032_R01C02 (batch1)

value: Refused to state/unknown


title: NB36


title: Array-CGH analysis: FC18

value: heart

value: Blood


title: NB35

value: female

value: F


title: NB34

value: M


title: sALS 193/90

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

country: United Kingdom

institute: University of Sheffield

description:
193_90
Lower motor neurons sALS.

hyb_protocol: Hybridized to GeneChip Human Exon 1.0 ST Arrays, washed and stained using the Affymetrix GeneChip Hybridization, Wash and Stain Kit and an Affymetrix Fluidics Station 450.

scan_protocol: Scanned on an Affymetrix® GeneChip Scanner 3000 according to manufacturer's protocols.

data_processing: The Partek Genomics Suite was used to normalize (by GC RMA) and then analyse the microarray data following Affymetrix guidelines. Core probesets only were used.

source_name: laser captured autopsy lower motor neurons, sporadic ALS

label_protocol: The Ambion WT Expression Kit was used to amplify the RNA and convert it to cDNA. The cDNA was then fragmented and biotin-labelled using the Affymetrix GeneChip WT Terminal Labelling Kit.

growth_protocol: Lower motor neurons were extracted from cervical spinal cord by laser capture microdissection.

extract_protocol: RNA was extracted from the motor neurons using the PicoPure RNA Isolation Kit (Life Technologies).

value: lower motor neurons

tag: patient group

value: sALS


title: 6229050023_R06C02 (batch1)

value: FTD

value: White

value: Peripheral Blood


title: Neurologically healthy control 129/94

description:
129_94
Lower motor neurons from non-disease individuals.

source_name: laser captured autopsy lower motor neurons, healthy control

value: control


title: Neurologically healthy control 114/93

description:
114_93
Lower motor neurons from non-disease individuals.


title: mtC9ORF72 155/96

description:
155_96
Lower motor neurons from C9ORF72-ALS.

source_name: laser captured autopsy lower motor neurons, C9ORF72-ALS

value: ALS due to mtC9ORF72


title: MSC-G2-2

description: Gene expression in GVHD clinical trial group 2 bone marrow-derived MSCs

hyb_protocol: Samples were hybridized to Whole Human Genome v2 Microarray 4x44K (G4845A, Agilent Technologies). 1.65 ug of Cy3 labelled aRNA were hybridized for 17 hours at 65ºC in a hybridization oven (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies). After hybridization, microarrays were washed according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies) and dried out using a centrifuge at 1000 rpm for 2 min.

scan_protocol: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for 4x44k format one-color arrays.

source_name: bone marrow mesenquimal stem cells, GVHD clinical trial, group 2, replicate 2

label_protocol: One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technologies, Palo Alto, CA, USA) was used to amplify and label RNA. 200 ng of total RNA was reverse transcribed using T7 promoter Primer and MMLV-RT. Then cDNA was converted to aRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3-labeled CTP.

value: cultured bone marrow-derived MSC


title: MSC-G2-3

source_name: bone marrow mesenquimal stem cells, GVHD clinical trial, group 2, replicate 3


title: sALS 088/96

description:
088_96
Lower motor neurons sALS.


title: vehicle rep3

city: Haifa

first: Ran

last: Rostoker

state: Israel

address: Efron st

department: faculty of medicne

country: Israel

institute: Technion

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The raw data obtained from a single microarray experiments and was imported into Illumina's GenomeStudio Software. The raw data was exported in xls format and was later used in EUREKA-DMA software for analysis

source_name: vehicle

label_protocol: RNA was amplified into cRNA, and biotinylated by in vitro transcription using the TargetAmp Nano-g Biotin-aRNA Labeling kit for the Illumina system (Epicentre Biotechnologies).

growth_protocol: Mvt-1 cells were grown in monolayer culture in DMEM  supplemented with 10% fetal bovine serum (Biological Industries) and antibiotics (penicillin:streptomycin; Biological Industries) at 37°C in a humidified atmosphere consisting of 5% CO2 and 95% air. Cells were serum-starved for 16 hours before insulin (10nM, 90 minutes) stimulation.

extract_protocol: RNA was extracted from treated Mvt-1cells with the Total RNA Purification Kit (NORGEN biotek corp)

tag: treatment

value: vehicle


title: insulin stimulation rep2

source_name: insulin stimulation

treatment_protocol: Cells were serum-starved for 16 hours before insulin (10nM, 90 minutes) stimulation.

value: insulin


title: 6229050023_R04C02 (batch1)

value: Control

value: FEMALE

value: Filipino


title: mtC9ORF72 LP081/09

description:
081_09
Lower motor neurons from C9ORF72-ALS.

tag: cell type


title: insulin stimulation rep1

tag: cell line


title: 6229050032_R03C02 (batch1)


title: 6229050023_R03C02 (batch1)

value: MALE


title: 6229050023_R06C01 (batch1)


title: MSC-G2-1

source_name: bone marrow mesenquimal stem cells, GVHD clinical trial, group 2, replicate 1


title: insulin stimulation rep3


title: sALS 088/89

description:
088_89
Lower motor neurons sALS.


title: 6229050032_R01C01 (batch1)

value: PSP


title: vehicle rep2


title: Neurologically healthy control 080/92

description:
080_92
Lower motor neurons from non-disease individuals.


title: 6229050023_R05C02 (batch1)


title: 6229050023_R05C01 (batch1)

value: UNKNOWN


title: 6229050023_R04C01 (batch1)


title: MSC_G1-3

description: Gene expression in GVHD clinical trial group 1 bone marrow-derived MSCs

source_name: bone marrow mesenquimal stem cells, GVHD clinical trial, group 1, replicate 3


title: Neurologically healthy control 056/90

description:
056_90
Lower motor neurons from non-disease individuals.


title: 6229050023_R01C02 (batch1)


title: Mice_mammary_Saureus_SA2_Rep1

city: Bangalore

first: Tapas

middle: Kumar

last: Kundu

state: Karnataka

address: Jakkur P.O.

department: Molecular Biology & Genetics Unit

country: India

institute: Jawaharlal Nehru Centre for Advanced Scientific Research

hyb_protocol: As per Illumina's recommended hybridization procedure

scan_protocol: As per Illumina's recommended scanning procedure

data_processing: Threshhold-1.0, logbase-2, Quantile Normalization, baseline correction-median of all samples

label: Biotin

source_name: Lactating mice mammary tissue for S. aureus-infected mouse

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure

extract_protocol: Total RNA was isolated with Trizol reagent following manufacturer's protocol.

treatment_protocol: Lactating mice mammary tissue was innoculated with S.aureus culture and incubated for 24 hr.

tag: strain

value: Swiss albino

value: mammary


title: MSC_G1-4

source_name: bone marrow mesenquimal stem cells, GVHD clinical trial, group 1, replicate 4


title: Mice_mammary_Saureus_SA2_Rep2


title: Mice_mammary_Saureus_SA1_Rep2


title: 6229050023_R03C01 (batch1)


title: MSC_G1-5

source_name: bone marrow mesenquimal stem cells, GVHD clinical trial, group 1, replicate 5


title: 6229050023_R02C02 (batch1)


title: 6229050023_R02C01 (batch1)


title: Mice_mammary_Saureus_SA1_Rep1


title: vehicle rep1


title: MSC_G1-2

source_name: bone marrow mesenquimal stem cells, GVHD clinical trial, group 1, replicate 2


title: Neurologically healthy control 039/07

description:
039_97
Lower motor neurons from non-disease individuals.

value: lower motor neurons


title: MSC_G1-1

source_name: bone marrow mesenquimal stem cells, GVHD clinical trial, group 1, replicate 1


title: 6229050007_R06C01 (batch1)


title: 6229050023_R01C01 (batch1)


title: 6229050007_R05C02 (batch1)


title: Sporadic ALS patient 31

description: Fibroblasts from individuals with sporadic ALS

hyb_protocol: hybridized to GeneChip Human Exon 1.0 ST Arrays, washed and stained using the Affymetrix GeneChip Hybridization, Wash and Stain Kit and an Affymetrix Fluidics Station 450

scan_protocol: scanned on an Affymetrix® GeneChip Scanner 3000 according to manufacturer's protocols

source_name: cultured fibroblasts

label_protocol: The Ambion WT Expression Kit was used to amplify the RNA and convert it to cDNA.  The cDNA was then fragmented and biotin-labelled using the Affymetrix GeneChip WT Terminal Labelling Kit

growth_protocol: Monolayers of fibroblasts were then grown in T75 flasks with 20mL of Ham’s F-10 Media (Gibco) with 10% Fetal Calf serum (Biosera), 1% Penicillin-streptomycin antibiotic solution, 0.25% Holo-transferrin (Sigma) and 2.5 ng epidermal growth factor (Sigma).

extract_protocol: RNA was extracted from the fibroblasts using the Qiagen RNeasy Mini Kit (Qiagen).

value: fibroblasts

value: sporadic ALS


title: Sporadic ALS patient 27


title: 6229050007_R05C01 (batch1)

value: Peripheral Blood


title: Mice_mammary_PBS_Rep2

source_name: Lactating mice mammary tissue


title: 6229050007_R06C02 (batch1)

value: White


title: MSC_SEN-2

description: Gene expression in senescent bone marrow-derived MSCs

source_name: bone marrow mesenquimal stem cells, senescent, replicate 2

extract_protocol: Total RNA was isolated from cultured cells with a miRNeasy Mini Kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).


title: testes_PWD_ST_rep2

city: Prague

first: Petr

last: Simecek

state: Not Applicable

address: Vídeňská 1083

department: Department of Mouse Molecular Genetics

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR, v. v. i.

description: SAMPLE 17

hyb_protocol: as per manufacturer's  recommended protocol

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

data_processing: The data were analyzed in R (v.2.6.0)/BioConductor (v.2.2) using affy package (v.1.16.0) and mirna10cdf annotation.

growth_protocol: The mice had ad libitum access to a standard rodent diet (VELAS, ST-1, 3.4% fat) and acidified water.

extract_protocol: Total RNA was isolated using Qiagen miRNeasy Mini kit following the manufacturer's instructions

treatment_protocol: Testes of 8-10 weeks old mice were dissected, testicular tunica was removed, spermatogenic populations were isolated using FACS and the cells were homogenized in QiAzol lysis reagent of the miRNeasy Mini isolation kit (QIAGEN) using syringe and needle.

value: PWD/Ph

value: 8-10 weeks

value: spermatids (ST)


title: MSC_SEN-4

city: Madrid

first: Manuel

last: Gonzalez

address: Melchor Fernandez Almagro, 3

institute: CNIC

data_processing: Images provided by the scanner were analyzed with Feature Extraction software V10 (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: bone marrow mesenquimal stem cells, senescent, replicate 4

value: cultured bone marrow-derived MSC


title: MSC_SEN-3

source_name: bone marrow mesenquimal stem cells, senescent, replicate 3


title: Mice_mammary_PBS_Rep1


title: Sporadic ALS patient 26


title: testes_B6_ST_rep3

description: SAMPLE 15

label_protocol: as per manufacturer's  recommended protocol


title: testes_PWD_ST_rep1

description: SAMPLE 16


title: 6229050007_R04C02 (batch1)

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

extract_protocol: genomic DNA was extracted and purified with standard methods

value: Control


title: testes_B6_ST_rep2

description: SAMPLE 14


title: MSC_SEN-1

source_name: bone marrow mesenquimal stem cells, senescent, replicate 1


title: Sporadic ALS patient 21


title: Sporadic ALS patient 23


title: MSC_WT-2

description: Gene expression in untreated bone marrow-derived MSCs

source_name: bone marrow mesenquimal stem cells, untreated control, replicate 2


title: Sporadic ALS patient 18


title: MSC_WT-4

source_name: bone marrow mesenquimal stem cells, untreated control, replicate 4


title: 6229050007_R03C02 (batch1)

value: FEMALE


title: ALS with TARDBP mutation patient 55

description: Fibroblasts from individuals with TDP43 mutations

value: ALS due to mtTARDBP


title: MSC_WT-3

source_name: bone marrow mesenquimal stem cells, untreated control, replicate 3


title: testes_PWD_ST_rep3

description: SAMPLE 18


title: Neurologically healthy control LP005/07

description:
005_07
Lower motor neurons from non-disease individuals.

source_name: laser captured autopsy lower motor neurons, healthy control

value: control


title: testes_PWD_RP_rep3

description: SAMPLE 12

value: pachytene spermatocytes (RP)


title: 6229050007_R03C01 (batch1)

value: PSP

value: MALE

value: Chinese


title: ALS with TARDBP mutation patient 51


title: ALS with TARDBP mutation patient 48


title: 6229050007_R02C02 (batch1)


title: MSC_WT-1

source_name: bone marrow mesenquimal stem cells, untreated control, replicate 1


title: testes_PWD_RP_rep2

description: SAMPLE 11


title: testes_B6_ST_rep1

description: SAMPLE 13


title: testes_PWD_RP_rep1

description: SAMPLE 10


title: P3HR1_miR28_B2_24h

city: New York

first: Riccardo

last: Dalla-Favera

address: 1130 St Nicholas Avenue

institute: Columbia University

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on the  HG-U133 Plus2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the  GeneChip Scanner 3000.

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

source_name: Burkitt lymphoma cell line stably expressing the doxycycline-inducible pRTS1-GFP vector carrying the miR-28 precursor (bulk population B) and induced by addition of 1ug/ml doxycycline for 24h.

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

growth_protocol: cells were grown in IMDM medium supplemented with 10% FCS

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

value: P3HR1 Burkitt lymphoma cell line

tag: bulk population

value: B

value: Doxycycline [0.1ug/ml], 24h

tag: genotype/variation

tag: time


title: P3HR1_miR28_B1_24h


title: ALS with SOD1 mutation patient 99

description: Fibroblasts from individuals with SOD1 mutations

value: fibroblasts

value: ALS due to mtSOD1


title: 6229050007_R01C02 (batch1)

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

institute: UCLA

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

data_processing:
BeadStudio software
Raw data was processed using the Illumina GenomeStudio software (version 2010.3). Background correction and color normalization were performed using the R package minfi version 1.2.0 and normalization using Subset-quantile Within Array Normalization (SWAN). Probes were excluded from further analysis if >95% samples had detection p-value >0.01.
Raw data (Unmethylated and methylated signal intensities) linked as supplementary files on Series record.

label_protocol: Standard Illumina Protocol

value: White

value: Peripheral Blood


title: ALS with SOD1 mutation patient 32


title: P3HR1_miR28_B3_24h


title: P3HR1_miR28_A3_24h

source_name: Burkitt lymphoma cell line stably expressing the doxycycline-inducible pRTS1-GFP vector carrying the miR-28 precursor (bulk population A) and induced by addition of 1ug/ml doxycycline for 24h.

value: A


title: ALS with SOD1 mutation patient 59


title: testes_PWD_LP_rep2

description: SAMPLE 8

value: PWD/Ph

value: 8-10 weeks

value: pre-pachytene spermatocytes (LP)


title: 6229050007_R02C01 (batch1)

value: FEMALE


title: testes_PWD_LP_rep3

description: SAMPLE 9


title: 6229050004_R06C02 (batch1)

value: FTD

value: UNKNOWN


title: mtC9ORF72 LP045/06

description:
045_06
Lower motor neurons from C9ORF72-ALS.

source_name: laser captured autopsy lower motor neurons, C9ORF72-ALS

value: lower motor neurons

value: ALS due to mtC9ORF72


title: P3HR1_miR28_A2_24h


title: testes_B6_RP_rep3

description: SAMPLE 6

value: pachytene spermatocytes (RP)


title: testes_PWD_LP_rep1

description: SAMPLE 7


title: P3HR1_CTR_B3_24h

source_name: Burkitt lymphoma cell line stably expressing the doxycycline-inducible pRTS1-GFP vector (bulk population B) and induced by addition of 1ug/ml doxycycline for 24h.

value: P3HR1 Burkitt lymphoma cell line

value: control


title: testes_B6_RP_rep2

description: SAMPLE 5


title: 6229050004_R06C01 (batch1)

value: Control

value: MALE


title: P3HR1_miR28_A1_24h

value: Doxycycline [0.1ug/ml], 24h


title: testes_B6_RP_rep1

description: SAMPLE 4


title: 6229050007_R04C01 (batch1)

value: PSP

value: White


title: P3HR1_CTR_B2_24h

value: B


title: Neurologically healthy control 13

description: Fibroblasts from non disease individuals

value: fibroblasts


title: P3HR1_CTR_B1_24h


title: 6229050004_R05C02 (batch1)

value: Peripheral Blood


title: testes_B6_LP_rep3

description: SAMPLE 3

value: 8-10 weeks

value: pre-pachytene spermatocytes (LP)


title: Neurologically healthy control 14


title: 6229050004_R04C02 (batch1)

value: FEMALE


title: 6229050007_R01C01 (batch1)


title: Neurologically healthy control 03


title: 6229050004_R05C01 (batch1)

value: UNKNOWN


title: testes_B6_LP_rep2

description: SAMPLE 2


title: ALS with SOD1 mutation patient 28

value: ALS due to mtSOD1


title: Neurologically healthy control 02


title: P3HR1_CTR_A2_24h

source_name: Burkitt lymphoma cell line stably expressing the doxycycline-inducible pRTS1-GFP vector (bulk population A) and induced by addition of 1ug/ml doxycycline for 24h.

value: A


title: 6229050004_R03C01 (batch1)


title: 6229050004_R03C02 (batch1)


title: P3HR1_CTR_A1_24h


title: testes_DB_rep2

description: SAMPLE 6

hyb_protocol: as per manufacturer's recommended protocol

source_name: PWD/Ph x C57BL/6J juvenile testicular tissue

treatment_protocol: Testes of 14.5day old mice were dissected, testicular tunica was removed, spermatogenic populations were homogenized in QiAzol lysis reagent of the miRNeasy Mini isolation kit (QIAGEN) using syringe and needle.

value: PWD/Ph x C57BL/6J

tag: phenotype

value: sterile

value: 14.5day old

value: testes


title: RAW 264.7 STH1-infected-24h

city: Stanford

first: Anjali

last: Shastri

address: D305 Farichild Building; 299 Campus Drive

department: Microbiology & Biology

institute: Stanford University

description: Gene expression data from STH1-infected RAW 264.7 cells

hyb_protocol: The fragmented and labeled targets were hybridized to the arrays per standard Affymetrix protocol, which includes 16hr (overnight) hybridization at 45degC at 60rpm in an Affymetrix GeneChip Hybridization Oven 645. The arrays were then washed and stained in an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G and the .CEL files (raw scan files) were generated within the AGCC software

data_processing: The .CEL files were analyzed using R/Bioconductor and normalized via RMA

source_name: RAW 264.7 STH1-infected

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ug total RNA

growth_protocol: Cells were cultured in Dulbecco’s modiﬁed Eagle medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/ml penicillin, and 100 g/ml streptomycin.

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

treatment_protocol: Cells were plated in 6 well dishes and infected with Toxoplasma parasites at an MOI=3 for ~24hours

tag: toxoplasma parasite strain


title: RAW 264.7 STH10-infected-24h

description: Gene expression data from STH10-infected RAW 264.7 cells

source_name: RAW 264.7 STH10-infected


title: P3HR1_miR28_B3_12h

source_name: Burkitt lymphoma cell line stably expressing the doxycycline-inducible pRTS1-GFP vector carrying the miR-28 precursor (bulk population B) and induced by addition of 1ug/ml doxycycline for 12h.

value: P3HR1 Burkitt lymphoma cell line

value: Doxycycline [0.1ug/ml], 12h


title: 6229050004_R04C01 (batch1)

value: PSP


title: RAW 264.7 STG5-infected-24h

description: Gene expression data from STG5-infected RAW 264.7 cells

source_name: RAW 264.7 STG5-infected


title: testes_DB_rep1

description: SAMPLE 5

label_protocol: as per manufacturer's recommended protocol


title: 6229050004_R02C01 (batch1)

value: MALE

value: White


title: Neurologically healthy control 11

source_name: cultured fibroblasts

value: fibroblasts

value: control


title: 6229050004_R02C02 (batch1)

value: Control

value: Peripheral Blood


title: RAW 264.7 STG4-infected-24h

description: Gene expression data from STG4-infected RAW 264.7 cells

source_name: RAW 264.7 STG4-infected


title: testes_KB_rep1

description: SAMPLE 3

source_name: PWK/Ph x C57BL/6J juvenile testicular tissue

value: PWK/Ph x C57BL/6J


title: testes_KB_rep2

description: SAMPLE 4


title: testes_BD_rep2

description: SAMPLE 2

source_name: C57BL/6J x PWD/Ph juvenile testicular tissue

value: C57BL/6J x PWD/Ph

value: fertile


title: testes_B6_LP_rep1

description: SAMPLE 1

value: 8-10 weeks

value: pre-pachytene spermatocytes (LP)


title: RAW 264.7 STF3-infected-24h

description: Gene expression data from STF3-infected RAW 264.7 cells

source_name: RAW 264.7 STF3-infected


title: P3HR1_miR28_A2_12h

source_name: Burkitt lymphoma cell line stably expressing the doxycycline-inducible pRTS1-GFP vector carrying the miR-28 precursor (bulk population A) and induced by addition of 1ug/ml doxycycline for 12h.

value: A


title: RAW 264.7 STD10reallySTG10-infected-24h

description: Gene expression data from STG10-infected RAW 264.7 cells

source_name: RAW 264.7 STD10reallySTG10-infected


title: 6229050004_R01C02 (batch1)

value: FEMALE


title: testes_BD_rep1

description: SAMPLE 1

value: 14.5day old

value: testes


title: 6229050001_R06C02 (batch1)

value: FTD

value: UNKNOWN


title: 6229050001_R06C01 (batch1)

value: MALE


title: P3HR1_miR28_A3_12h

value: P3HR1 Burkitt lymphoma cell line

value: Doxycycline [0.1ug/ml], 12h


title: P3HR1_CTR_A3_24h

value: Doxycycline [0.1ug/ml], 24h

value: control


title: P3HR1_miR28_B2_12h

value: B


title: P3HR1_miR28_A1_12h


title: RAW 264.7 STD3-infected-24h

description: Gene expression data from STD3-infected RAW 264.7 cells

source_name: RAW 264.7 STD3-infected


title: 6229050004_R01C01 (batch1)

value: PSP

value: White

value: Peripheral Blood


title: RAW 264.7 STE10-infected-24h

description: Gene expression data from STE10-infected RAW 264.7 cells

source_name: RAW 264.7 STE10-infected


title: 6229050001_R05C01 (batch1)

value: Control


title: HUVECs_7days_with NPs_rep3

city: Philadelphia

first: Sezin

last: Aday

state: Pennsylvania

address: 210 South 33rd Street, Skirkanich Hall

institute: University of Pennsylvania

description: Gene expression after 7 days in human umbilical vein endothelial cells treated with nanoparticles

hyb_protocol: 1.65 µg Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/µg cRNA) was mixed with Agilent 10× blocking agent (11 µL) and Fragmentation Buffer (2.2 µL) and incubated at 60ºC for exactly 30 min to fragment RNA. To stop de fragmentation reaction, 2x GEx Hybridization Buffer (55 µL) was added. After a short spin-down, the labelled cRNA mixture was applied to a microarray slide, assembled in a SureHyb Hybridization Chamber fitted with a gasket slide (Agilent), and incubated for 18 h at 65ºC in a hybridization oven (G2545A, SHEL LAB - Agilent), with 10 rpm rotation speed. Slides were washed as described in the Agilent One-Color Microarray-Based Gene Expression Analysis protocol. Afterwards, the microarray and gasket slide were briefly disassembled inside a staining dish containing 250 mL of GE Wash Buffer 1 and the slides (up to 4 slides) were washed in fresh 250 mL of GE Wash Buffer 1 solution at room temperature, during 1 min, with gentle agitation from a magnetic stirrer. A second wash step was carried out by immersing the slides in GE Wash Buffer 2 solution, previously warmed to 37ºC, during 1 min, also with gentle magnetic stirring. Finally, slides were dried by centrifugation at 800 rpm for 3 min.

scan_protocol: Microarrays were scanned in the Agilent B Scanner (G2565BA) using specific scanning protocols for gene expression microarrays and the format 4×44K. Agilent Feature Extraction Image Analysis Sofware (Version 10.7.3.1) was used to obtain fluorescence intensities from raw microarray image files.

data_processing: Analysis of raw data was performed using BRB-ArrayTools v3.4.0 developed by Dr. Richard Simon and BRB-ArrayTools Development Team. BRB-Array Tools incorporates the Bioconductor R functions and the R programming language required for raw data normalization within arrays. Each gene’s measured intensity was median normalized to correct for differences in the labelling efficiency between samples. This analysis provided a median normalized dataset that was subjected to statistical analysis and clustering using MeV software.

source_name: Human umbilical vein endothelial cells, 7 days, with nanoparticles, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the One Color Low Input Quick Amp Labeling Kit (Agilent, Part Number 5190-2305) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen, Valencia, CA). The efficiency of cRNA synyhesis and dye incorporation was measured using NanoDrop ND1000 spectrophotometer and samples with neither a yield below 1.65 µg nor a specific activity (pmol Cy3 per µg cRNA) below 6 were considered for hybridization.

growth_protocol: Human umbilical vein endothelial cells were expanded in 1% (w/v) gelatin-coated T75 flask (BD Falcon) in EGM-2 medium (Lonza). The cultures were incubated for 3 days at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: HUVECs cultured in different conditions (with and without nanoparticles) and at different time points (24 hours and 7 days) were homogenized in Trizol reagent (Life Technologies, 15596-026) and total RNA was extracted using the RNeasy Mini Kit (Qiagen, 74104), according to manufacturer’s instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was assessed by an Agilent 2100 Bioanalyser (G2943CA), using an Agilent RNA 6000 Nano Kit (5067-1511).

treatment_protocol: After 3 days of expansion, human umbilical vein endothelial cells were trypsinized and seeded into 24-well plates (Costar). The cells were incubated with 500 μg/mL fluorescein isothiocyanate (FITC)-labelled nanoparticles (500 µg NPs for 4×105 HUVECs) for 4 hours in M200 medium (Invitrogen, USA) at 37 ºC in a humidified incubator with 5% CO2. HUVECs without particles were cultured in M200 medium for 4 hours at 37 ºC in a humidified incubator with 5% CO2 and used as control. After incubation, the cells were washed 3 times with M200 and the cells labelled with NPs were collected using a FACSAria II cell sorter. After cell sorting, labelled and unlabelled HUVECs were incubated in EGM-2 for 20 hours (total time: 24  hours) or 7 days. The cell culture medium was changed every 2 days.

value: Human umbilical vein endothelial cells

tag: passage number

value: Passage 5

tag: days in culture

value: 7 days

value: with nanoparticles


title: P3HR1_CTR_B3_12h

source_name: Burkitt lymphoma cell line stably expressing the doxycycline-inducible pRTS1-GFP vector (bulk population B) and induced by addition of 1ug/ml doxycycline for 12h.


title: Neurologically healthy control 01

value: fibroblasts


title: HUVECs_7days_with NPs_rep2

source_name: Human umbilical vein endothelial cells, 7 days, with nanoparticles, replicate 2


title: RAW 264.7 STD10-infected-24h

description: Gene expression data from STD10-infected RAW 264.7 cells

source_name: RAW 264.7 STD10-infected


title: HUVECs_7days_with NPs_rep1

source_name: Human umbilical vein endothelial cells, 7 days, with nanoparticles, replicate 1


title: P3HR1_CTR_B1_12h


title: 6229050001_R04C02 (batch1)

tag: diagnosis

tag: gender

value: FEMALE

value: Mexican


title: RAW 264.7 STC7-infected-24h

description: Gene expression data from STC7-infected RAW 264.7 cells

source_name: RAW 264.7 STC7-infected


title: RAW 264.7 STC8-infected-24h

description: Gene expression data from STC8-infected RAW 264.7 cells

source_name: RAW 264.7 STC8-infected


title: P3HR1_CTR_A3_12h

source_name: Burkitt lymphoma cell line stably expressing the doxycycline-inducible pRTS1-GFP vector (bulk population A) and induced by addition of 1ug/ml doxycycline for 12h.

value: A


title: P3HR1_CTR_A2_12h

value: P3HR1 Burkitt lymphoma cell line


title: HUVECs_24hours_with NPs_rep3

description: Gene expression after 24 hours in human umbilical vein endothelial cells treated with nanoparticles

source_name: Human umbilical vein endothelial cells, 24 hours, with nanoparticles, replicate 3

value: 24 hours


title: RAW 264.7 S30-infected-24h

description: Gene expression data from S30-infected RAW 264.7 cells

source_name: RAW 264.7 S30-infected


title: RAW 264.7 S2T-infected-24h

description: Gene expression data from S2T-infected RAW 264.7 cells

source_name: RAW 264.7 S2T-infected


title: 6229050001_R05C02 (batch1)

tag: race

tag: age


title: HUVECs_24hours_with NPs_rep2

source_name: Human umbilical vein endothelial cells, 24 hours, with nanoparticles, replicate 2


title: P3HR1_miR28_B1_12h

source_name: Burkitt lymphoma cell line stably expressing the doxycycline-inducible pRTS1-GFP vector carrying the miR-28 precursor (bulk population B) and induced by addition of 1ug/ml doxycycline for 12h.

value: Doxycycline [0.1ug/ml], 12h


title: 6229050001_R04C01 (batch1)

value: UNKNOWN

tag: batch

tag: tissue


title: P3HR1_CTR_A1_12h

tag: treatment

value: control


title: RAW 264.7 STE7-infected-24h

description: Gene expression data from STE7-infected RAW 264.7 cells

source_name: RAW 264.7 STE7-infected


title: HUVECs_24hours_with NPs_rep1

source_name: Human umbilical vein endothelial cells, 24 hours, with nanoparticles, replicate 1

tag: cell type


title: 6229050001_R03C02 (batch1)


title: cells treated with Vamp7 siRNA, biological replicate 3

city: Houston

first: Mounia

last: Tannour-Louet

address: One Baylor Plaza

institute: Baylor College of Medicine

description: Gene expression data from NTERA2/D1 cells treated with Vamp7 siRNA, biological replicate 1

hyb_protocol: GeneChip Human Genome U133 Plus 2.0 Array

scan_protocol: GeneChip Scanner 3000

data_processing: Microarray results were normalized using Robust Multichip Average (RMA). Statistical analysis approach of SAM (Significance Analysis of Microarray) was applied using Multiple Experiment Viewer (MeV). We determined a list of about 600 genes that are significantly altered at a 20% False Discovery Rate (FDR) when VAMP7 was knocked down in NT2 cells.

source_name: NTERA2/D1 cells, Vamp7 knockdown siRNA

label_protocol: Affymetrix labelling

growth_protocol: NTERA2/D1 (ATCC CRL-1973) cells were grown in a modified Dulbecco's medium without phenol red supplemented with 10% fetal bovine serum and L-glutamine in an atmosphere of 5% CO2. Cells were plated at 70% confluency in 6-well plates (1 x 105 cells/well) for RNA

extract_protocol: Total RNA was purified using the RNeasy Kit including an optional DNase I treatment according to the manufacturer's instructions (Qiagen, Valencia, CA, USA). USA).

treatment_protocol: After 24 hours, cells were transfected for 72 hours with nonspecific (Scrambled) or siRNA for human VAMP7 (Dharmacon, Lafayette, CO, USA) according to the manufacturer’s procedure

value: Vamp7 knockdown siRNA

tag: cell line


title: HUVECs_24hours_without NPs_rep2

description: Gene expression after 24 hours in human umbilical vein endothelial cells

source_name: Human umbilical vein endothelial cells, 24 hours, without nanoparticles, replicate 2

value: without nanoparticles


title: 6229050001_R03C01 (batch1)

value: PSP

value: MALE

value: White

value: Peripheral Blood


title: 6229050001_R02C02 (batch1)

value: Control


title: cells treated with Vamp7 siRNA, biological replicate 2


title: RAW 264.7 S28-infected-24h

description: Gene expression data from S28-infected RAW 264.7 cells

source_name: RAW 264.7 S28-infected


title: RAW 264.7 S26-infected-24h

description: Gene expression data from S26-infected RAW 264.7 cells

source_name: RAW 264.7 S26-infected


title: 6229050001_R02C01 (batch1)


title: cells treated with Vamp7 siRNA, biological replicate 1


title: CD34+cells_7days_with NPs_rep2

description: Gene expression after 7 days in human umbilical cord blood CD34+ cells treated with nanoparticles

hyb_protocol: 1.65 µg Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/µg cRNA) was mixed with Agilent 10× blocking agent (11 µL) and Fragmentation Buffer (2.2 µL) and incubated at 60ºC for exactly 30 min to fragment RNA. To stop de fragmentation reaction, 2x GEx Hy

scan_protocol: Microarrays were scanned in the Agilent B Scanner (G2565BA) using specific scanning protocols for gene expression microarrays and the format 4×44K. Agilent Feature Extraction Image Analysis Sofware (Version 10.7.3.1) was used to obtain fluorescence intens

data_processing: Analysis of raw data was performed using BRB-ArrayTools v3.4.0 developed by Dr. Richard Simon and BRB-ArrayTools Development Team. BRB-Array Tools incorporates the Bioconductor R functions and the R programming language required for raw data normalization

source_name: Human umbilical cord blood CD34+ cells, 7 days, with nanoparticles, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the One Color Low Input Quick Amp Labeling Kit (Agilent, Part Number 5190-2305) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen, Valencia, CA). The efficiency of

growth_protocol: CD34+ cells were isolated from umbilical cord blood mononuclear cells after Ficoll (Histopaque-1077 Hybri Max; Sigma-Aldrich, USA) density gradient separation. CD34+ cells were positively selected (2 times) using the mini-MACS immunomagnetic separation sy

extract_protocol: CD34+ cells cultured in different conditions (with and without nanoparticles) and at different time points (24 hours and 7 days) were homogenized in Trizol reagent (Life Technologies, 15596-026) and total RNA was extracted using the RNeasy Mini Kit (Qiage

treatment_protocol: Freshly isolated CD34+ cells were incubated with 500 ?g/mL FITC-labelled NPs (500 µg NP for 1 million CD34+ cells) for 4 hours in QBSF-60 medium (Quality Biological Inc, USA) at 37 ºC in a humidified incubator with 5% CO2. CD34+ cells without particles we

value: Hematopoietic stem cells

value: Passage 0 (Freshly isolated)

value: 7 days


description: Gene expression data from NTERA2/D1 cells treated with Scrambled siRNA, biological replicate 1

source_name: NTERA2/D1 cells, control siRNA


title: RAW 264.7 S27-infected-24h

description: Gene expression data from S27-infected RAW 264.7 cells

source_name: RAW 264.7 S27-infected


description: Gene expression data from NTERA2/D1 cells treated with Scrambled siRNA, biological replicate 2


title: RAW 264.7 CL19-infected-24h

description: Gene expression data from CL19-infected RAW 264.7 cells

source_name: RAW 264.7 CL19-infected


title: RAW 264.7 S22-infected-24h

description: Gene expression data from S22-infected RAW 264.7 cells

source_name: RAW 264.7 S22-infected


title: HUVECs_24hours_without NPs_rep1

source_name: Human umbilical vein endothelial cells, 24 hours, without nanoparticles, replicate 1

value: Human umbilical vein endothelial cells

value: Passage 5


title: CD34+cells_7days_with NPs_rep3

source_name: Human umbilical cord blood CD34+ cells, 7 days, with nanoparticles, replicate 3


title: 6229050001_R01C01 (batch1)


title: CD34+cells_7days_without NPs_rep3

description: Gene expression after 7 days in human umbilical cord blood CD34+ cells

source_name: Human umbilical cord blood CD34+ cells, 7 days, without nanoparticles, replicate 3


title: HUVECs_24hours_without NPs_rep3

source_name: Human umbilical vein endothelial cells, 24 hours, without nanoparticles, replicate 3


title: CD34+cells_7days_without NPs_rep2

source_name: Human umbilical cord blood CD34+ cells, 7 days, without nanoparticles, replicate 2


title: RAW 264.7 CL29-infected-24h

description: Gene expression data from CL29-infected RAW 264.7 cells

source_name: RAW 264.7 CL29-infected


title: RAW 264.7 S23-infected-24h

description: Gene expression data from S23-infected RAW 264.7 cells

source_name: RAW 264.7 S23-infected


title: 6229050001_R01C02 (batch1)

value: FEMALE


description: Gene expression data from NTERA2/D1 cells treated with Scrambled siRNA, biological replicate 3


title: CD34+cells_7days_with NPs_rep1

source_name: Human umbilical cord blood CD34+ cells, 7 days, with nanoparticles, replicate 1


title: CD34+cells_24hours_with NPs_rep3

description: Gene expression after 24 hours in human umbilical cord blood CD34+ cells treated with nanoparticles

source_name: Human umbilical cord blood CD34+ cells, 24 hours, with nanoparticles, replicate 3

value: 24 hours


title: RAW 264.7 CL18-infected-24h

description: Gene expression data from CL18-infected RAW 264.7 cells

source_name: RAW 264.7 CL18-infected


title: CD34+cells_24hours_with NPs_rep2

source_name: Human umbilical cord blood CD34+ cells, 24 hours, with nanoparticles, replicate 2


title: Blood from Stage II (GP2477_WB_143221HP133A11)

city: Stevenage

first: steve

middle: matthew

last: fox

address: Gunnels Wood Road

department: Statistics

institute: GlaxoSmithKline

hyb_protocol: Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on GeneChip HG-U133_plus_2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A.

data_processing: The data was analysed with Rosetta Resolver version 5.0

source_name: blood

label_protocol: NuGEN Ovation FLv2 methodology using NuGEN Ovation RNA amplification v2 including C1 spike with Agencourt RNAClean SPIA clean up. FLv2 biotin fragmentation and labelling.

value: blood

value: M

tag: gold stage

value: Stage II

tag: plateid

tag: subject type

value: COPD Subjects


title: P3HR1_CTR_B2_12h

source_name: Burkitt lymphoma cell line stably expressing the doxycycline-inducible pRTS1-GFP vector (bulk population B) and induced by addition of 1ug/ml doxycycline for 12h.

value: P3HR1 Burkitt lymphoma cell line

tag: bulk population

value: B

value: Doxycycline [0.1ug/ml], 12h

tag: genotype/variation

value: control

tag: time


title: Blood from Stage I (GP2477_WB_143219HP133A11)

value: Stage I

value: Smoker Controls


title: mec1_100_35min_rep1

first: Jared

middle: M

last: Peace

state: CA - California

address: 1050 Childs Way RRI 203

department: Molecular and Computational Biology

institute: University of Southern California

description: SAMPLE 17

hyb_protocol: Standard Nimblegen Protocol

scan_protocol: Genepix Personal 4100A Scanner (Axon Instruments)

data_processing: HU array experiments (arrays 1-6) were within array normalized as in Knott et al. BMC Bioinformatics 2009. Within array normalization for time course experiments (arrays 7-18) was performed as previously described in Knott et al Cell 2012. Final data for all samples is normalized as indicated above and median smoothed over a 2500bp window.

source_name: BrdU IP DNA from S. cerevisiae

label_protocol: Standard Nimblegen Protocol

growth_protocol: Cells were grown in YEPD to OD ~0.5

extract_protocol: Genomic DNA was extracted from 25ml of culture using standard phenol chloroform extraction

treatment_protocol: cells were arrested for 4 hours at 23 degrees C with 7.5 nM alpha factor and then released into fresh media containing  200ug/ml Pronase, 400 ug/ml BrdU

tag: strain

tag: drug

value: no drug

tag: time point

value: 35 minutes

tag: antibody

value: BrdU antibody (Invitrogen, catalog#033900, lot#1462116A)

source_name: Total DNA from WT G1-arrested S. cerevisiae

value: WT

value: G1 arrest


title: mec1_100_25min_rep2

description: SAMPLE 16

value: 25 minutes

treatment_protocol: cells were arrested for 4 hours at 23 degrees C with 7.5 nM alpha factor


title: CD34+cells_7days_without NPs_rep1

source_name: Human umbilical cord blood CD34+ cells, 7 days, without nanoparticles, replicate 1

value: Hematopoietic stem cells

tag: passage number

value: Passage 0 (Freshly isolated)

tag: days in culture

value: 7 days


title: RAW 264.7 CL15-infected-24h

description: Gene expression data from CL15-infected RAW 264.7 cells

source_name: RAW 264.7 CL15-infected

tag: toxoplasma parasite strain


title: Blood from Stage III (GP2477_WB_143220HP133A11)

tag: tissue

value: blood

tag: age

tag: gender

value: M

value: Stage III


title: CD34+cells_24hours_with NPs_rep1

source_name: Human umbilical cord blood CD34+ cells, 24 hours, with nanoparticles, replicate 1

tag: cell type

value: 24 hours


title: CD34+cells_24hours_without NPs_rep3

description: Gene expression after 24 hours in human umbilical cord blood CD34+ cells

source_name: Human umbilical cord blood CD34+ cells, 24 hours, without nanoparticles, replicate 3


title: RAW 264.7 CL17-infected-24h

description: Gene expression data from CL17-infected RAW 264.7 cells

source_name: RAW 264.7 CL17-infected


title: RAW 264.7 CL16-infected-24h

description: Gene expression data from CL16-infected RAW 264.7 cells

source_name: RAW 264.7 CL16-infected


title: RAW 264.7 CL13-infected-24h

description: Gene expression data from CL13-infected RAW 264.7 cells

source_name: RAW 264.7 CL13-infected


title: Blood from Stage I (GP2477_WB_143217HP133A11)

tag: gold stage


title: Blood from Stage IV (GP2477_WB_143218HP133A11)

value: Stage IV

tag: plateid

value: COPD Subjects


title: RAW 264.7 CL12-infected-24h

description: Gene expression data from CL12-infected RAW 264.7 cells

source_name: RAW 264.7 CL12-infected


title: mec1_100_25min_rep1

description: SAMPLE 15


title: Blood from Stage II (GP2477_WB_143216HP133A11)

value: Stage II

tag: subject type


title: Blood from Stage III (GP2477_WB_143215HP133A11)

value: F


title: RAW 264.7 C96E7-infected-24h

description: Gene expression data from C96E7-infected RAW 264.7 cells

source_name: RAW 264.7 C96E7-infected


title: CD34+cells_24hours_without NPs_rep2

source_name: Human umbilical cord blood CD34+ cells, 24 hours, without nanoparticles, replicate 2


title: Blood from Stage I (GP2477_WB_143214HP133A11)

value: Stage I

value: Smoker Controls


title: rif1_delta_35min_rep2

description: SAMPLE 14

value: rif1 delta

value: no drug

value: 35 minutes

value: BrdU antibody (Invitrogen, catalog#033900, lot#1462116A)


title: rif1_delta_35min_rep1

description: SAMPLE 13

value: WT

value: G1 arrest


title: rif1_delta_25min_rep2

description: SAMPLE 12

value: 25 minutes


title: mec1_100_35min_rep2

description: SAMPLE 18


title: Normal NW_115

city: Jacksonville

first: Catherine

last: Dumur

state: FL

address: 5008 Mustang Rd

department: Anatomic Pathology

institute: Sonic Healthcare USA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133A 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GC3000 scanner.

data_processing: After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries was performed using the log-scale Robust Multiarray Analysis (RMA) method.

source_name: Normal allografts

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (GeneChip® Expression Analysis Technical Manual, Affymetrix).

value: kidney biopsy

tag: histological diagnosis

value: Normal allografts


title: Blood from Stage III (GP2477_WB_143213HP133A11)

value: blood

value: Stage III


title: RAW 264.7 C96A5-infected-24h

description: Gene expression data from C96A5-infected RAW 264.7 cells

source_name: RAW 264.7 C96A5-infected


title: Normal NW_106


title: Normal NW_91


title: Normal NW_76


title: Blood from Stage I (GP2477_WB_143210HP133A11)

value: M


title: RAW 264.7 C96C12-infected-24h

description: Gene expression data from C96C12-infected RAW 264.7 cells

source_name: RAW 264.7 C96C12-infected


title: RAW 264.7 C96B4-infected-24h

description: Gene expression data from C96B4-infected RAW 264.7 cells

source_name: RAW 264.7 C96B4-infected


title: rif1_delta_25min_rep1

description: SAMPLE 11

tag: genotype/variation


title: WT_35min_rep1

description: SAMPLE 9


title: WT_25min_rep2

description: SAMPLE 8


title: pancreas_30ug_exenatide_12wk_rep2

city: Silver Spring

first: Rodney

middle: Lamar

last: Rouse

state: MD

address: 10903 New Hampshire Ave

department: DARS

institute: U. S. FDA, CDER

description: Gene expression data from mouse pancreas

hyb_protocol: Target preparation was performed using 4 μg of amplified cDNA and the NuGEN FL-Ovation cDNA Biotin Module V2. Fragmented and biotin-labeled target was hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 microarrays.

scan_protocol: GeneChips were scanned using the GeneArray Scanner M10

data_processing: Raw gene expression data were first analyzed using ArrayTrack bioinformatics tool with robust multichip average algorithm and quantile normalization.  Differentially expressed genes were defined by p < 0.05 and fold change > 1.3 in Welch t-test comparing treatment and control groups. Expression data were then imported to Ingenuity Pathway Analysis (IPA) tool for further analyses of pathway, biofunction, and toxicity using general and pancreas-specific knowledge bases.

source_name: Mouse Pancreas

label_protocol: The isolated RNA was labeled and gene expression analysis performed by Expression Analysis, Inc. (Durham, NC). The 3 samples with the highest RIN from each treatment group were used to probe treatment effect on gene expression.  Total RNA samples (100 ng) were converted into cDNA using Ovation WGA FFPE System (NuGEN, Part No. 6200). The second strand cDNA is then purified with Agencourt RNAClean beads and followed by SPIA amplification. Amplified SPIA cDNA product is purified using Agencourt RNAClean beads and quantitated using a NanoDrop ND-8000 spectrophotometer.

growth_protocol: Male C57BL/6 mice 6 to 8 weeks of age were purchased from Harlan Laboratories (Frederick, MD). Mice were housed individually in an environmentally controlled room (18°C–21°C, 40%–70% relative humidity) with a twelve-hour light/dark cycle.  Mice were initially fed Certified Purina Rodent Chow #5002 (Ralston Purina Co., St. Louis, MO) providing 63% of calories through carbohydrates, 24% from protein, and 13% from fat.  Per the experimental design, mice were subsequently placed on a Teklad Custom Research Diet, TD.06415 (Harlan, Frederick, MD), providing 45% of calories through fats (36% saturated, 47% monounsaturated, 17% polyunsaturated), 36% from carbohydrates, and 19% from protein.  Water and food were available ad libitum.

extract_protocol: Pancreas tissue was resected, preserved in RNALater, and stored at -80 C.  After thawing, 2.5 mg of each sample were processed using  miRNeasy Mini Kits  (Cat # 217004) (Qiagen, Valencia, CA).  Samples were homogenized in 700 uL of Qiazol Lysis Reagent (Qiagen), for 5 minutes at 50 hz in a TissueLyser LT (Qiagen), and processed using the automated purification of  total RNA on a Qiacube (Qiagen), using the “Purification of total RNA, including small RNAs, from animal tissues & cells (aqueous phase), version 2 (April 2010)” standard protocol, as described in the miRNeasy Mini Handbook (1073008 07/2012) & http://www.qiagen.com/QIAcube/Standard/ProtocolView.aspx?StandardProtocolID=847.Mean yield per 2.5 mg of pancreas tissue was approximately 35 ug, determined by NanoDrop spectrophotometer (Thermo Scientific, Wilmington, DE).   Average RIN values were approximately  5.4 +/- 1.4, as assayed by a 2100 Bioanalyzer Instrument (Agilent Technologies, Santa Clara, CA), using an Agilent RNA 6000 Nano Kit (cat # 5067-1511).  This RIN mean was consistent with our previous experiences in RNA extraction from murine pancreatic tissue.

treatment_protocol: Thorough out the experiment all mice were weighed weekly and dosing adjusted accordingly for each mouse.  A cohort of eighty 6 to 8 week-old male C57BL6 mice were received from Harlan Laboratories.  The cohort represented a  12 week experimental time point.  Cohort was further divided into 4 exenatide (EXE) treatment groups (0, 3, 10, or 30 μg/kg) of 20 mice each.  Initially, all mice were placed on HFD for six weeks without additional treatment and were then maintained on HFD for an additional 12 weeks while receiving daily subcutaneous injections of saline or EXE (Creative Peptides, Shirley, NY; 3, 10, or 30μg/kg).  At 12 week timepoint, twenty-four hours following their final dose, the mice from the treatment cohort were anesthetized with isoflurane and euthanized by exsanguination with collection of blood for serum harvest.  The pancreas from 12 mice in each cohort was preserved in 10% formalin for histology processing.  The pancreas from 5 mice in each cohort was placed in RNAlater (Life Technologies, Grand Island, NY) for subsequent RNA extraction and the pancreas from 3 mice in each cohort was immediately frozen in liquid nitrogen and then stored at -80°C.

value: male

tag: agent

value: exenatide

tag: dose

value: 30 ug

value: pancreas


title: pancreas_30ug_exenatide_12wk_rep3

tag: strain


title: RAW 264.7 S21-infected-24h

description: Gene expression data from S21-infected RAW 264.7 cells

source_name: RAW 264.7 S21-infected


title: WT_25min_rep1

description: SAMPLE 7

source_name: BrdU IP DNA from S. cerevisiae

tag: drug

tag: time point

source_name: Total DNA from WT G1-arrested S. cerevisiae


title: Blood from Stage I (GP2477_WB_143211HP133A11)

source_name: blood

value: F

value: Stage I

value: Smoker Controls


title: Blood from Stage III (GP2477_WB_143209HP133A11)

value: COPD Subjects


title: Normal NW_93


title: Blood from Stage II (GP2477_WB_143222HP133A11)

value: Stage II


title: WT_35min_rep2

description: SAMPLE 10

value: WT

value: no drug

value: 35 minutes

tag: antibody

value: BrdU antibody (Invitrogen, catalog#033900, lot#1462116A)


title: Blood from Stage III (GP2477_WB_143212HP133A11)


title: Normal NW_51

value: kidney biopsy

value: Normal allografts


title: Blood from Stage I (GP2477_WB_143208HP133A11)

value: blood


title: Normal NW_75


title: pfa4_delta_HU_rep2

description: SAMPLE 6

treatment_protocol: cells were arrested for 4 hours at 23 degrees C with 7.5 nM alpha factor and then released into fresh media containing 0.2 Hydroxyurea, 200ug/ml Pronase, 400 ug/ml BrdU

value: pfa4 delta

value: HU

value: 45 minutes

value: G1 arrest


title: Normal NW_48


title: Normal NW_45


title: pancreas_30ug_exenatide_12wk_rep1

value: male

value: exenatide

value: 30 ug

value: pancreas


title: pancreas_10ug_exenatide_12wk_rep2

value: 10 ug


title: Normal NW_42


title: pancreas_3ug_exenatide_12wk_rep3

value: 3 ug


title: Blood from Stage I (GP2477_WB_143207HP133A11)

value: M

value: Stage I

value: Smoker Controls


title: pfa4_delta_HU_rep1

description: SAMPLE 5

value: BrdU antibody (Invitrogen, catalog#033900, lot#1462116A)

value: WT


title: Normal NW_21

value: kidney biopsy

value: Normal allografts


title: pancreas_10ug_exenatide_12wk_rep3


title: Blood from Stage III (GP2477_WB_143203HP133A11)

value: blood

value: Stage III

value: COPD Subjects


title: Blood from Stage I (GP2477_WB_143204HP133A11)

value: F


title: Blood from Stage III (GP2477_WB_143206HP133A11)


title: Normal 145K9


title: WT_HU_rep2

description: SAMPLE 2

value: HU

value: 45 minutes

value: G1 arrest


title: rif1_delta_HU_rep2

description: SAMPLE 4

value: rif1 delta


title: pancreas_3ug_exenatide_12wk_rep2

value: male

value: exenatide

value: pancreas


title: Blood from Stage II (GP2477_WB_143205HP133A11)

value: M

value: Stage II


title: Blood from Stage II (GP2477_WB_143202HP133A11)


title: pancreas_3ug_exenatide_12wk_rep1

value: 3 ug


title: rif1_delta_HU_rep1

description: SAMPLE 3

value: BrdU antibody (Invitrogen, catalog#033900, lot#1462116A)

value: WT


title: pancreas_10ug_exenatide_12wk_rep1

value: 10 ug


title: Uninfected Control_5

city: San Antonio

first: Mahesh

last: Mohan

state: Texas

address: 8715 West Military Road

department: Host Pathogen Interaction Program

institute: Southwest National Primate Research Center

description:
FK25
Control

data_processing:
TLDA-SDS run files from ten SIV-infected and five uninfected control macaques were loaded onto Applied Biosystems Relative Quantification (RQ) Manager Software v1.2.2 and analyzed using automatic baseline settings and a manual threshold of 0.2.
The results from the RQ manager analysis containing five columns (well, sample, detector, task and CT values) were saved as a tab-delimited text file which was later imported and analyzed using the DataAssist version 3.01 software (Lifetech Corp), a data analysis tool designed to compare samples using the deltadelta CT method for relative quantification of gene expression.
MiRNA expression data was analyzed using global normalization method.
In all experiments, the CT upper limit was set to 33 meaning that all miRNA detectors with a CT value greater than or equal to 33 were excluded.
Multiple comparisons correction using Benjamini-Hochberg method for false discovery rate was simultaneously applied to all 768 miRNA target probes (card A and B combined).
DataAssist software automatically performs global normalization including all deltadeltaCT based fold-change calculations from the uploaded raw threshold cycle values.
Fold Change worksheet reports test/control (i.e., Acute SIV infected/uninfected control) ratios.

label: FAM

organism: Macaca mulatta

source_name: Intact Colon_Uninfected_Control

label_protocol: microRNA profiling was performed using the TaqMan® Array Human MicroRNA A+B Cards Set v3.0 (Life Tech) following the manufacturer’s instructions. Reverse transcription was first performed from 350 ng of total RNA using the microRNA reverse transcription kit. 2.5 µL of cDNA was preamplified using the TaqMan® PreAmp Master Mix kit. Preamplified products were first diluted and then loaded onto to TLDA plates. TLDA plates were run on the ABI 7900 HT Fast PCR system following the manufacturer’s recommended thermal cycling conditions.

extract_protocol: Total RNA (small and large) was extracted using the miRNeasy Mini kit (Qiagen). On-column DNase digestion was also performed to eliminate contaminating genomic DNA.

treatment_protocol: 10 animals were infected intravenously with 100 TCID50 SIVmac251 and 5 remained uninfected

tag: days post siv infection (dpi)

value: Uninfected

value: colon


title: Uninfected Control_4

description:
GI92
Control


title: Normal 146K9

value: kidney biopsy

value: Normal allografts


title: Uninfected Control_3

description:
EH80
Control


title: Normal 37K9mo


title: Blood from Stage I (GP2477_WB_143201HP133A11)

value: blood

value: Stage I

value: Smoker Controls


title: Uninfected Control_2

description:
EH70
Control


title: Pancreas_Vehicle_12wk_rep3

value: Vehicle

value: control


title: Blood from Stage II (GP2477_WB_143200HP133A11)

value: F

value: COPD Subjects


title: Pancreas_Vehicle_12wk_rep2

value: male

value: pancreas


title: Uninfected Control_1

description:
EL66
Control


title: Blood from Stage II (GP2477_WB_143199HP133A11)

value: M

value: Stage II


title: Acute SIV_10

description:
CT16
Test

source_name: Intact Colon_Acute_SIV

value: 29 DPI


title: Normal 93K12


title: Blood from Stage II (GP2477_WB_143223HP133A11)


title: Normal 31K9mo


title: Pancreas_Vehicle_12wk_rep1


title: Normal 109K12


title: Blood from Stage I (GP2477_WB_143197HP133A11)


title: WT_HU_rep1

description: SAMPLE 1

value: WT

value: HU

value: 45 minutes

value: BrdU antibody (Invitrogen, catalog#033900, lot#1462116A)

value: G1 arrest


title: CNIT BxBC 16K_3mo

source_name: Kidney biopsies from transplant recipients with histological diagnosis of calcineurin inhibitor toxicity (CNIT)

value: kidney biopsy

value: calcineurin inhibitor toxicity (CNIT)


title: Blood from Stage II (GP2477_WB_143198HP133A11)

value: blood


title: Acute SIV_8

description:
HB31
Test

value: 21 DPI

value: colon


title: Normal 27K9mo

value: Normal allografts


title: Blood from Stage I (GP2477_WB_143196HP133A11)

value: Stage I

value: Smoker Controls


title: Acute SIV_7

description:
HC36
Test


title: CNIT BxBC 11K_32mo


title: 4T1.2-Bmp4 tumor2

city: East Melbourne

first: Cameron

middle: N

last: Johnstone

state: Vic

address: 2 St. Andrew's Place

department: Research Division

country: Australia

institute: Peter MacCallum Cancer Centre

hyb_protocol: Hybridization was performed using the GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix) in accordance with the manufacturer's instructions. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
Data were processed using Partek Genomics Suite v6.6. Robust Multiarray Averaging (RMA) background correction were applied to probe intensities, gene level expression were quantile normalized.
Ratio and fold-change differences between average gene signal intensities from 4T1.2 tumours and average gene signal intensities from 4T1.2-Bmp4 tumours are provided.  P values were determined by one-way ANOVA using Partek Genomics Suite v6.6.

source_name: pBabepuro murine Bmp4

label_protocol: Total RNA was labeled using the 3' IVT Express Kit (Affymetrix) in accordance with the manufacturer's instructions.

growth_protocol: 6-8 week old female Balb/c mice were obtained from the Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia abnd housed at the Peter MacCallum Cancer Centre, East Melbourne, Australia, in a standard mouse barrier facility (SPF). 4T1.2 cells were inoculated into the 4th inguinal mammary fat pad. 100,000 cells in a 20mL volume of HBSS were inoculated.

extract_protocol: RNeasy mini kits (Qiagen) were used to isolated total RNA from each sample in accordance with the manufacturer's instructions.

treatment_protocol: Primary mammary tumours were excised at a size of approximately 0.3g and total RNA isolated.

value: female

tag: background strain

value: Balb/c

tag: tissue type

value: mammary tumour


title: 4T1.2-Bmp4 tumor1


title: Acute SIV_9

description:
GA19
Test

tag: tissue


title: 4T1.2-Bmp4 tumor3

tag: gender


title: Blood from Stage II (GP2477_WB_143195HP133A11)

tag: age

value: M

value: Stage II

value: COPD Subjects


title: Acute SIV_6

description:
HI58
Test

value: 13 DPI


title: CNIT BxBC 9K_81mo


title: Blood from Stage II (GP2477_WB_143194HP133A11)

tag: gold stage


title: 4T1.2 tumor2

source_name: pBabepuro vector control

tag: cell type


title: Blood from Stage II (GP2477_WB_143193HP133A11)

tag: plateid

tag: subject type


title: Acute SIV_5

description:
HI63
Test


title: 4T1.2 tumor1


title: CNIT 106K_1mo

tag: histological diagnosis


title: Acute SIV_4

description:
M992
Test


title: 4T1.2 tumor3


title: Blood from Stage III (GP2477_WB_143192HP133A11)

value: Stage III


title: testes_PWD_LP_rep2

description: SAMPLE 12

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with Bioconductor 1.9 and R statistics (version 2.3) using the gcRMA method with default settings and custom chip description file (probes were annotated to Ensembl).

label_protocol: Between 15 to 40 ng of total RNA were used to prepare biotinylated cRNA according to the standard Affymetrix Two-Cycle protocol (Expression Analysis Technical Manual, 701021 Rev. 5, Affymetrix).

extract_protocol: Total RNA was isolated Using Qiagen RNeasy Micro kit according to manufacturer's instructionsl

treatment_protocol: Testes of 8-10 weeks old mice were dissected, testicular tunica was removed, spermatogenic populations were isolated using FACS and the cells were placed into RLT buffer of the RNeasy Micro isolation kit (QIAGEN) and homogenized using syringe and needle.

value: PWD/Ph

value: 8-10 weeks

value: prepachytene spermatocytes (LP)


title: testes_PWD_LP_rep1

description: SAMPLE 11


title: Acute SIV_3

description:
AV91
Test

value: 10 DPI


title: Acute SIV_2

description:
HI52
Test

value: 8 DPI


title: Acute SIV_1

description:
IA85
Test

value: 7 DPI

value: colon


title: CNIT 110K_1mo

value: kidney biopsy

value: calcineurin inhibitor toxicity (CNIT)


title: 1833-Treatment-3

city: Chicago

first: Miao

last: Sun

institute: University of Chicago

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA Array version 5th Generation (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 15.0 at the Sanger Institute.

scan_protocol: After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System and the image analysis was carried out using the ImaGene 9.0 software (BioDiscovery, Inc., USA).

data_processing: Background correction was conducted to remove non-biological contributions.  The quantified signals were normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

source_name: 1833 cells with depleted HMGA2 expression

label_protocol: The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile. 500 ng total RNA from sample and reference was labelled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer.

growth_protocol: Cells were cultured in a complete medium consisting of DMEM supplemented with 10% FBS, 50 U/ml penicillin and 50 μg/ml streptomycin.

extract_protocol: Total RNA was isolated from cells using miRNeasy Mini Kit following the manufacturer’s instructions.

treatment_protocol: HMGA2 depletion (shHMGA2) and control (SCR sh) were achieved by transducing the cells with HMGA2 shRNA or scrambled control in a pLKO.1 lentiviral vector.  After 48 h transduction, cells were selected and maintained in 0.5 μg/ml puromycin.

tag: cell line

value: breast cancer cells

tag: transduced with

value: HMGA2 shRNA in a pLKO.1 lentiviral vector

tag: treated with

value: breast cancer cells expressing shHMGA2

source_name: Common reference for ms1-ms6

tag: sample type

value: all 6 samples pooled (reference)


title: Blood from Stage II (GP2477_WB_143191HP133A11)

value: blood

value: F

value: Stage II


title: CNIT 87K6


title: CNIT 98K1mo