title: CEXO-41

description: re-analysis of GSM732049


title: CEXO-45

status: Public on Jun 04 2015

type: RNA

city: MEXICO CITY

first: INGRID

last: MEDINA MARTINEZ

state: CUAUHTEMOC

address: DR. BALMIS 148

department: MEDICINA GENOMICA

country: Mexico

institute: HOSPITAL GENERAL DE MEXICO OD

description: re-analysis of GSM732051

hyb_protocol: Following fragmentation, ssDNA were hybridized for 16 hr at 45C and 60 rpm on Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 protocol FS450_0007

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix) with GeneChip Scanner 3000

data_processing: Microarrays were normalized using the RMA algorithm (Robust Multichip Average) in the Affymetrix Expression Console. The analysis was done at Gene Level Default: RMA-Sketch

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Healthy female exocervix

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA (Expression Analysis Technical Manual, Affymetrix).

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

tag: clinic

value: Control


title: CEXO-38

description: re-analysis of GSM732046


title: CEXO-24

description: re-analysis of GSM732042


title: CEXO-13

description: re-analysis of GSM732038


title: Uninfected 3

city: Bronx

first: Gregoire

middle: S

last: Lauvau

state: NY

address: 1301 Morris park

department: M&I

country: USA

institute: Albert Einstein College of Medicine

description: Uninfected mouse

hyb_protocol: Hybridizations performed using Affymetrix MoGene 1.0 arrays. The hybridization, washing, staining and scanning of the genechips will be performed as described in current Affymetrix protocols.

scan_protocol: Initial quality control will be performed with Expression Console Software (Affymetrix) following the guidelines set forth in the Affymetrix Quality Assessment of Exon and Gene Arrays White Paper.

data_processing: For expression array analysis, probe intensities were extracted from Affymetrix CEL files, normalized and summarized at the transcript cluster level using the Robust Multiarray Average  method from the R/Bioconductor (http://bioconductor.org) oligo package (Carvalho and Irizarry, 2010). Expression values were analyzed on the log base 2 scales. Control probes were removed before normalization as recommended by bioconductor package limma user guide. There are 28944 data rows in total after removing control probes. Significance testing was  performed by fitting gene-wise linear models using the limma Bioconductor package, and genes were ranked for differential expression using Benjamini & Hochberg adjusted p-values and logposterior odds of differential expression (log probability of differential expression versus probability of no differential expression) (Smyth, 2004). Analysis for changes in gene expression of Gene Ontology (GO) categories was performed using the GOstats Bioconductor package to calculate Hypergeomtric p-values for over or under-representation of each GO term (Falcon and Gentleman, 2007). Significant GO terms were selected at p <0.01 levels.

label: biotin

organism: Mus musculus

source_name: Ly6C+ monocytes isolated from mouse spleen

label_protocol: For an accurate view of total transcription activity at each genomic locus we will use the GeneST Array System of Affymetrix. This comprises of a complete reagent kit with a random priming strategy, in combination with in vitro transcription-based linear amplification and novel end-point fragmentation and labeling. This Whole Transcriptome (WT) assay uses 100ng of Total RNA from each sample.  Each RNA sample will be run on a Bioanalyzer 2100 Nano Chip (Agilent) to determine its quality score (RNA Integrity Number.)  Samples with a score of 7.0 or greater will be used in the assay.  In the event of low RNA yield (< 100ng) from the Human samples an alternative amplification method will be used for the whole set of Human samples.  This method, WT-Ovation Pico System, will use 1ng to 50ng of Total RNA and is capable of amplifying partially degraded RNA.  It uses a random priming strategy for cDNA synthesis.  Second strand cDNA synthesis will be done incorporating a unique DNA/RNA heteroduplex at the 5’ end of each fragment.  This is used in a linear, isothermal DNA amplification process (SPIA) to prime repeated DNA replication and strand displacement that will produce sufficient cDNA for hybridization to the Gene ST 1.0 Genechip.

growth_protocol: CCR2-DTR-CFP+/- mice (C57BL/6 genetic background) from which monocytes were isolated were maintained and bred in our SPF animal facility. Between 6-8 weeks of age, mice were either immunized with WT Listeria monocytogenes (10e4) i.v. or left unimmunized. 4-6 weeks later, mice were challenged with 10e6 wt Listeria monocytogenes. 8 hours later, spleens were harvested for cell purification and RNA extraction.

extract_protocol: Purification of Ly6C+ monocytes for microarray analysis: Spleens were dissociated on a sterile nylon mesh and incubated at 37°C for 20 min in HBSS  medium (Gibco) containing 4,000 U/ml of collagenase I (Gibco) and 0.1 mg/ml of DNase I (Roche) and red blood cells (RBC) lysed with NH4Cl buffer (0.83% vol/vol). Spleens were from primary or secondary challenged CCR2-CFP+/- aged and sex-matched female B6 mice (all Ly6C+ monocytes express CFP). Myeloid cells were enriched by positive selection of cells expressing CD11b MACS beads (Miltenyi). Cells were further stained with B220, CD3, NK1.1, Ly6G to exclude lineage+ T, B, NK cells and neutrophils, flow-sorted (Aria III, BD) based on expression of CFP+ NK1.1-Ly6GB220- CD3- markers. 10,000 Cells were collected into 150 microL of lysis buffer from the RNAqueous micro kit (Ambion).

treatment_protocol: Inflammatory monocytes were purified from 4 groups of 3 individual CCR2-DTR+/- mice each (triplicate): (i) uninfected mice, (ii) primary infected with 10e6 WT Listeria, (iii) primary infected with 10e4 WT Listeria and secondary infected 4-6 weeks later with 10e6 WT Listeria, (iv) primary infected with 10e4 WT Listeria and secondary infected 4-6 weeks later with 10e6 WT Listeria, T-cell depleted 1 day before.

tag: tissue

value: spleen

tag: background strain

value: CCR2-DTR+/- C57BL/6 mouse

tag: cell subset

value: inflammatory Ly6C+ monocyte

tag: stimulation

value: No


title: Secondary infected 2

description: Primary immunized mouse with WT Listeria, secondary challenged 5 weeks later with WT Listeria

value: 10e6 Wild type Listeria monocytogenes i.v., 8 hrs (Secondary/recall)


title: CEXO-21

description: re-analysis of GSM732041


title: Uninfected 2

description: Uninfected mouse


title: CEXO-20

description: re-analysis of GSM732040


title: CEXO-36

description: re-analysis of GSM732045


title: Primary infected 3

description: Unimmunized mouse, primary infected with WT Listeria

value: 10e6 Wild type Listeria monocytogenes i.v., 8 hrs (Primary)


title: CEXO-39

description: re-analysis of GSM732047


title: CEXO-33

description: re-analysis of GSM732044


title: Secondary infected 1


title: CEXO-12

description: re-analysis of GSM732037


title: Primary infected 2


title: Secondary infected T depleted 2

description: Primary immunized mouse with WT Listeria, 5 weeks later T cell-depleted and secondary challenged with WT Listeria

value: T-cell depleted day -1, 10e6 Wild type Listeria monocytogenes i.v., 8 hrs (Secondary/recall)


title: CEXO-11

description: re-analysis of GSM732035


title: CEXO-10

description: re-analysis of GSM732034


title: CEXO-19

description: re-analysis of GSM732039


title: pIC_18h_2

city: DEBRECEN

first: LAJOS

last: SZELES

address: Egyetem tér

country: Hungary

institute: UNIVERSITY OF DEBRECEN

description: Gene expression data of CD8 DC

hyb_protocol: Samples were hybridized at 45 degrees Celsius for 16 hours and then standard washing protocol was performed using GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned on GeneChip Scanner 7G (Affymetrix), Affymetrix GeneChip Command Console (AGCC) was used to obtain image files.

data_processing: cel files were imported to GeneSpring  GX 12

source_name: CD8 positive dendritic cell line

label_protocol: Ambion WT Expression Kit (Applied Biosystems) and GeneChip WT Terminal Labeling and Control Kit (Affymetrix) were used for amplifying and labeling 150 ng of RNA samples.

growth_protocol: CD8+ DC lines were established from transgenic mice expressing SV40 large T Ag under the control of a CD11c promoter

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

treatment_protocol: 5 ug/ml final conc. polyI:C was added to the cultures , 6-well tissue culture plates

tag: cell type

value: CD8 positive dendritic cell line

tag: treatment

value: polyI:C for 18h

tag: genetic background


title: pIC_18h_3

description: Gene expression data of CD8 DC


title: Secondary infected T depleted 3


title: Secondary infected 3


title: Uninfected 1

description: Uninfected mouse


title: pIC_18h_1

description: Gene expression data of CD8 DC


title: pIC_6h_3

description: Gene expression data of CD8 DC

value: polyI:C for 6h


title: Primary infected 1


title: pIC_6h_2

description: Gene expression data of CD8 DC


title: R191LSTY

type: genomic

description: Copy Number data reference

hyb_protocol: Following fragmentation, ssDNA were hybridized for 18 hr at 49C and 60 rpm on Cytoscan HD Array. GeneChips were washed and stained in the Affymetrix Mapping500Kv1_450 protocol

data_processing: Microarrays were normalized with the Genotyping Console Software version 4.1.4.

molecule: genomic DNA

source_name: peripheral blood lymphocytes

label_protocol: Biotinylated DNA were prepared according to the standard Affymetrix protocol from 500 ng total DNA (Mapping 250K Nsp/Sty, Affymetrix).

extract_protocol: DNA extraction was performed according to the manufacturer's instructions.

tag: sample group

value: Control Reference


title: R170LSTY

description: Copy Number data reference


title: R161LSTY

description: Copy Number data reference


title: R221LSTY

description: Copy Number data reference


title: R219LSTY

description: Copy Number data reference


title: R156LSTY

description: Copy Number data reference


title: R120LSTY

description: Copy Number data reference


title: R248LSTY

description: Copy Number data reference


title: R075LSTY

description: Copy Number data reference


title: R065LSTY

description: Copy Number data reference


title: R064LSTY

description: Copy Number data reference


title: R119LSTY

description: Copy Number data reference


title: R052LSTY

description: Copy Number data reference


title: R036LSTY

description: Copy Number data reference


title: C284STY

description: Copy Number data reference


title: pIC_6h_1

description: Gene expression data of CD8 DC


title: R035LSTY

description: Copy Number data reference


title: pIC_2h_1

description: Gene expression data of CD8 DC

value: polyI:C for 2h


title: pIC_2h_3

description: Gene expression data of CD8 DC


title: C202STY

description: Copy Number data reference


title: ctrl_2

description: Gene expression data of CD8 DC

value: unstimulated


title: ctrl_3

description: Gene expression data of CD8 DC


title: pIC_2h_2

description: Gene expression data of CD8 DC


title: C174STY

description: Copy Number data reference


title: ctrl_1

description: Gene expression data of CD8 DC


title: C137STY

description: Copy Number data reference


title: C133STY

description: Copy Number data reference


title: C128STY

description: Copy Number data reference


title: R494STY

description:
Copy Number data from Cervical cancer biopsy
processed data file: R494_Tumor.500k-default-CN-20121109.CN4.cnchp

source_name: Cervical cancer biopsy

value: Case

tag: age (years)

tag: histology

value: SCC

tag: tumor stage

value: IIIB


title: C026STY

description: Copy Number data reference


title: R478STY

description:
Copy Number data from Cervical cancer biopsy
processed data file: R478_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R496STY

description:
Copy Number data from Cervical cancer biopsy
processed data file: R496_Tumor.500k-default-CN-20121109.CN4.cnchp


title: C025STY

description: Copy Number data reference


title: R483STY

description:
Copy Number data from Cervical cancer biopsy
processed data file: R483_Tumor.500k-default-CN-20121109.CN4.cnchp

value: IVB


title: C105STY

description: Copy Number data reference


title: R476STY

description:
Copy Number data from Cervical cancer biopsy
processed data file: R476_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R444STY

description:
Copy Number data from Cervical cancer biopsy
processed data file: R444_Tumor.500k-default-CN-20121109.CN4.cnchp

value: IIB


title: R386STY

description:
Copy Number data from Cervical cancer biopsy
processed data file: R386_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R392STY

description:
Copy Number data from Cervical cancer biopsy
processed data file: R392_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R380STY

description:
Copy Number data from Cervical cancer biopsy
processed data file: R380_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R057LSTY

description: Copy Number data reference


title: R369STY

description:
Copy Number data from Cervical cancer biopsy
processed data file: R369_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R365STY

description:
Copy Number data from Cervical cancer biopsy
processed data file: R365_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R260STY

description:
Copy Number data from Cervical cancer biopsy
processed data file: R260_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R248STY

description:
Copy Number data from Cervical cancer biopsy
processed data file: R248_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R322STY

description:
Copy Number data from Cervical cancer biopsy
processed data file: R322_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R221STY

description:
Copy Number data from Cervical cancer biopsy
processed data file: R221_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R240STY

description:
Copy Number data from Cervical cancer biopsy
processed data file: R240_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R298STY

description:
Copy Number data from Cervical cancer biopsy
processed data file: R298_Tumor.500k-default-CN-20121109.CN4.cnchp

value: ASCC


title: R282STY

description:
Copy Number data from Cervical cancer biopsy
processed data file: R282_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R208STY

description:
Copy Number data from Cervical cancer biopsy
processed data file: R208_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R198STY

description:
Copy Number data from Cervical cancer biopsy
processed data file: R198_Tumor.500k-default-CN-20121109.CN4.cnchp

value: IVA


title: R189STY

description:
Copy Number data from Cervical cancer biopsy
processed data file: R189_Tumor.500k-default-CN-20121109.CN4.cnchp

value: ACC


title: R183STY

description:
Copy Number data from Cervical cancer biopsy
processed data file: R183_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R194STY

description:
Copy Number data from Cervical cancer biopsy
processed data file: R194_Tumor.500k-default-CN-20121109.CN4.cnchp

value: IIA


title: R244STY

description:
Copy Number data from Cervical cancer biopsy
processed data file: R244_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R116STY

description:
Copy Number data from Cervical cancer biopsy
processed data file: R116_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R072STY

description:
Copy Number data from Cervical cancer biopsy
processed data file: R072_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R075STY

description:
Copy Number data from Cervical cancer biopsy
processed data file: R075_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R111STY

description:
Copy Number data from Cervical cancer biopsy
processed data file: R111_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R035STY

description:
Copy Number data from Cervical cancer biopsy
processed data file: R035_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R062STY

description:
Copy Number data from Cervical cancer biopsy
processed data file: R062_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R154STY

description:
Copy Number data from Cervical cancer biopsy
processed data file: R154_Tumor.500k-default-CN-20121109.CN4.cnchp


title: 8-761495

city: Valhalla

first: Sanghoon

last: Lee

address: 40 Sunshine Cottage Road, Vos 145

department: Pediatrics

institute: New York Medical College

hyb_protocol: Fifteen microgram fragmented cRNA was hybridieze to HG_U133 A2 Gene Chip arrays (Affymetrix)

scan_protocol: Scanning was performed by the Genechip scanner 3000 (Affymetrix)

data_processing: Signal intensities were calculated Affymetrix's Expression Console. Data were normalized by GeneSpring GX10 or Partek Genomics Suite and normalized

source_name: bone marrow, pleural fluid, peritoneal fluid and/or lymph node with tumor involvement

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol using 100ng total RNA

extract_protocol: Total RNA was isolated by Trizol and followed by affinity column purification

tag: diagnosis

value: Pediatric Burkitt lymphoma (PBS)

tag: age

tag: gender

value: Male

tag: status

value: CNS (-)


title: 10-762353


title: blood_HvHg_26 [7dpi]

city: East Lansing

first: juan

middle: p

last: steibel

state: MI

address: 1205 I Anthony Hall

institute: Michigan State University

hyb_protocol: Labeled aRNAs were purified and combined with 70 µl of Slide Hyb #1 solution (Ambion, Inc.) and denatured at 70C for 3 min. Hybridizations were performed in sealed hybridization cassettes (ArrayIt, TeleChem International, Inc., Sunnyvale, CA, USA) for 18 h at a humid 54C. Following hybridization, slides were washed in 2X SSC/0.5% SDS and 0.1X SSC/0.1% SDS solutions for 10 min each. The slides were rinsed in a 0.1X SSC solution and nuclease-free water and dried by centrifugation.

scan_protocol: Fluorescent images were detected by a GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA) and fluorescence intensity data were collected using GenePix software (Molecular Devices) after spot alignment. Median intensity values for each dye channel were stored as comma-separated values data files.

data_processing: Median intensities were extracted and normalized using a within print-tip loess location normalization implemented in LIMMA. Background was corrected following Ritchie et al. (2007) method using normexp() function of LIMMA with offset=50. The resulting normalized ratios were expressed in the log2 scale.

organism: Sus scrofa

source_name: HvHg_0 dpi

label_protocol: One µg of total RNA was reverse transcribed with a T7 oligo(dT) primer using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion Inc., Austin, TX, USA) according to the manufacturer’s instructions. Following first-strand and second-strand synthesis and purification, the cDNAs were in vitro transcribed to synthesize multiple copies of amino allyl-modified aRNAs. After purification, 10 ug of aRNA was labeled with N-hydroxysuccinate (NHS) ester Cy3 or Cy5 (GE Healthcare, UK).

growth_protocol: Crossbred commercial pigs from PPRS Host Genetics Consortium (PHGC) trial one were transported to a Kansas State University bio-secure testing facility at weaning (11 to 21 d. old) and allocated to pens (10 to 15 pigs/pen). Pigs came from PRRSV-, Influenza virus- and Mycoplasma hyopneumoniae-free farms.

extract_protocol: Tempus tube collected blood samples of PHGC pigs were stored at -20 until RNA was extracted

treatment_protocol: After a 7-day acclimation period and antibiotic treatments, pigs were intramuscularly and intranasally infected with a known isolate of the Porcine Reproductive and Respiratory Syndrome virus (PRRSV) (105 tissue culture infectious dose50 of NVSL 97-7985).Blood samples were collected in Tempus™ Blood RNA Tubes (Life Technologies, Carlsbad, CA) at several time-points post-infection, including 0, 4, 7, 11, 14, 21, 28 and 42 days post-infection (DPI). Individual animal weight was measured at weekly intervals. Serum viral level was quantified using a semi-quantitative TaqMan PCR assay.

tag: dpi

value: HvHg

value: AA

tag: auc

value: blood

source_name: HvHg_7 dpi


title: 11-756445


title: 7-779466


title: 4-758658


title: 3-757742

value: Female


title: 6-774772


title: blood_LvHg_24 [7dpi]

source_name: LvHg_0 dpi

value: LvHg

value: AB

tag: tissue

source_name: LvHg_7 dpi


title: blood_HvHg_25 [7dpi]


title: 5-763133


title: 2-758089


title: Secondary infected T depleted 1

description: Primary immunized mouse with WT Listeria, 5 weeks later T cell-depleted and secondary challenged with WT Listeria

value: spleen

tag: background strain

value: CCR2-DTR+/- C57BL/6 mouse

value: inflammatory Ly6C+ monocyte

value: T-cell depleted day -1, 10e6 Wild type Listeria monocytogenes i.v., 8 hrs (Secondary/recall)


title: 9-762912


title: blood_HvHg_27 [7dpi]


title: blood_HvLg_25 [7dpi]

source_name: HvLg_0 dpi

value: HvLg

source_name: HvLg_7 dpi


title: blood_HvLg_26 [7dpi]


title: blood_LvHg_23 [7dpi]


title: blood_LvLg_22 [7dpi]

source_name: LvLg_7 dpi

value: LvLg

source_name: LvLg_0 dpi


title: blood_HvLg_24 [7dpi]


title: blood_HvHg_24 [7dpi]


title: blood_LvLg_21 [7dpi]


title: 1-757487

value: CNS (+)


title: blood_HvLg_23 [7dpi]


title: blood_HvLg_22 [7dpi]


title: blood_HvHg_21 [7dpi]


title: blood_HvLg_21 [7dpi]


title: blood_HvHg_23 [7dpi]


title: blood_LvHg_25 [7dpi]


title: blood_HvHg_22 [7dpi]


title: blood_LvLg_20 [7dpi]


title: blood_LvLg_17 [7dpi]


title: blood_LvLg_16 [7dpi]


title: blood_LvLg_19 [7dpi]


title: blood_HvLg_20 [7dpi]


title: blood_LvHg_17 [7dpi]


title: blood_LvHg_22 [7dpi]


title: blood_LvHg_20 [7dpi]


title: SN10-0917

city: Seattle

first: Scott

last: Presnell

state: WA

address: 1201 Ninth Avenue

institute: Benaroya Research Institute

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Arrays were scanned using the Illumina HiScan and the standard Illumina scanning protocol.

data_processing: The data were preprocessed using R, which included the following steps: quantile normalization, flooring all intensities <10 to 10, and log2 transformation. PALO (Presence in At least One), which selects only transcripts with detection p-values < 0.01 in at least one sample, was performed to reduce background noise.

source_name: patients with sepsis caused by B. pseudomallei

label_protocol: Standard Illumina labeling protocol.

extract_protocol: Total RNA was isolated from whole blood lysate using the MagMAX™ for Stabilized Blood Tubes RNA Isolation Kit (Life Technologies, CA) according to the manufacturer’s instructions. Quality control was performed with the Agilent Bioanalyser.

tag: pathogens

value: Burkholderia pseudomallei

tag: study group

value: Septicemic melioidosis

value: Whole blood


title: SN10-0920

source_name: patients with sepsis caused by other pathogens

value: Viridans Streptococci

value: Other sepsis


title: blood_HvLg_17 [7dpi]


title: blood_LvLg_18 [7dpi]

value: AA


title: blood_HvLg_19 [7dpi]

value: blood


title: blood_LvLg_15 [7dpi]


title: SN10-0821

value: Staphylococcus aureus


title: blood_LvHg_21 [7dpi]

value: LvHg


title: blood_LvHg_18 [7dpi]

value: AB


title: blood_LvHg_19 [7dpi]


title: SN10-0790


title: blood_HvHg_20 [7dpi]

value: HvHg


title: SN10-0772

value: Micrococcus spp.


title: blood_HvHg_19 [7dpi]


title: SN10-0868


title: blood_HvHg_18 [7dpi]


title: blood_HvLg_16 [7dpi]


title: blood_LvHg_16 [7dpi]

value: BB


title: blood_HvLg_18 [7dpi]


title: SN10-0756


title: blood_LvLg_13 [7dpi]


title: SN10-0761

value: Salmonella


title: blood_LvHg_15 [7dpi]


title: SN10-0686

value: Acinetobacter baumannii


title: SN10-0747


title: blood_HvHg_17 [7dpi]


title: blood_HvLg_15 [7dpi]

value: HvLg


title: SN10-0675


title: SN10-0782


title: blood_HvLg_14 [7dpi]


title: blood_LvLg_14 [7dpi]

value: LvLg


title: blood_HvHg_14 [7dpi]


title: MK11-1659

value: Streptococcus pyogenes


title: MK11-1639


title: blood_LvLg_12 [7dpi]


title: blood_HvHg_16 [7dpi]


title: MK11-1662


title: blood_HvHg_15 [7dpi]


title: MK11-1642

value: Burkholderia pseudomallei

value: Septicemic melioidosis


title: MK11-1656

value: Eschericia coli

value: Whole blood


title: blood_LvHg_14 [7dpi]

value: AA


title: blood_LvLg_11 [7dpi]

value: blood


title: MK11-1649

value: Staphylococcus aureus

value: Other sepsis


title: blood_HvHg_13 [7dpi]

value: AB


title: MK11-1628


title: MK11-1661

value: Streptoccus suis


title: MK11-1657


title: blood_LvLg_10 [7dpi]


title: MK11-1626

value: Acinetobacter lwoffii


title: blood_HvHg_12 [7dpi]

value: HvHg


title: MK11-1610

value: Enterococcus spp.


title: MK11-1604


title: blood_LvHg_13 [7dpi]

value: LvHg


title: blood_HvLg_13 [7dpi]

value: HvLg


title: blood_HvLg_11 [7dpi]


title: blood_LvHg_11 [7dpi]


title: blood_HvHg_11 [7dpi]


title: MK11-1603


title: MK11-1574


title: blood_LvHg_12 [7dpi]


title: MK11-1573


title: DLEU1-2

description: Burkitt lymphoma

hyb_protocol: Fifteen microgram fragmented cRNA was hybridiezed to HG_U133_Plus Gene Chip arrays (Affymetrix)

scan_protocol: Scanning was performed by the Genechip scanner 3000 7G

data_processing: Signal intensities were processed by MAS5 Algorithm

source_name: Raji BL cell line

growth_protocol: Raji BL cells were maintained 10% FBS/RPMI medium

treatment_protocol: Raji BL cells were mediated DLEU1 targeting DLEU1-TALENs

tag: cell line

value: Burkitt lymphoma

tag: genotype/variation

value: DLEU1 downregulated


title: MK11-1577

value: Viridans Streptococci


title: Control 2

description: Burkitt lymphoma

value: control


title: blood_LvHg_10 [7dpi]


title: MK11-1553

value: Klebslella pneumoniae


title: MK11-1545

value: Bacillus spp., Micrococcus spp.

value: Whole blood


title: MK11-1540

value: Burkholderia pseudomallei

value: Septicemic melioidosis


title: donor 182_treatment vehicle

description: gene expression data from differentiating dendritic cells stimulated with nuclear receptor ligands

data_processing: cel files were imported to and analysed by GeneSpring 12.5

source_name: donor 182_treatment vehicle

label_protocol: Affymetrix 3’IVT Expression Kit (Affymetrix) and GeneChip WT Terminal Labeling and Control Kit (Affymetrix) were used for amplifying and labeling 200 ng of RNA samples.

extract_protocol: Extraction of total RNA by RNeasy Mini Kit (Qiagen) was performed according to the manufacturer's instructions.

tag: cell type

value: dendritic cells

tag: experiment

value: samples from experiment 2

tag: donor


title: blood_HvLg_12 [7dpi]

value: AA

value: blood


title: blood_LvLg_9 [7dpi]

value: LvLg

value: AB


title: donor 183_treatment vehicle

source_name: donor 183_treatment vehicle


title: donor 182_treatment AM580

source_name: donor 182_treatment AM580


title: donor 183_treatment AM580

source_name: donor 183_treatment AM580


title: DLEU1-1

description: Burkitt lymphoma


title: blood_LvHg_9 [7dpi]

value: LvHg


title: donor 181_treatment AM580

source_name: donor 181_treatment AM580


title: Control 1

description: Burkitt lymphoma

hyb_protocol: Fifteen microgram fragmented cRNA was hybridiezed to HG_U133 Plus_2 Gene Chip arrays (Affymetrix)


title: MK11-1524


title: blood_LvHg_8 [7dpi]


title: MK11-1533

value: Other sepsis


title: blood_HvLg_10 [7dpi]

value: HvLg


title: blood_HvHg_10 [7dpi]

value: HvHg


title: MK11-1530

value: Klebseilla spp., Pseudomonas aeruginosa


title: donor 186_treatment GW1516

source_name: donor 186_treatment GW1516

value: samples from experiment 1


title: donor 186_treatment GW3965

source_name: donor 186_treatment GW3965


title: MK11-1514

value: Klebslella pneumoniae


title: MK11-1543

value: Eschericia coli


title: donor 181_treatment vehicle

source_name: donor 181_treatment vehicle


title: donor 186_treatment R-RA

source_name: donor 186_treatment R-RA


title: blood_HvLg_9 [7dpi]


title: MK11-1502

value: Cryptococcus neoformans

value: Whole blood


title: donor 186_treatment RSG

source_name: donor 186_treatment RSG


title: donor 186_treatment 9cis-RA

source_name: donor 186_treatment 9cis-RA


title: MK11-1496

value: Staphylococcus aureus


title: donor 186_treatment vehicle

source_name: donor 186_treatment vehicle

value: dendritic cells


title: MK11-1484


title: blood_HvHg_9 [7dpi]

source_name: HvHg_7 dpi

source_name: HvHg_0 dpi


title: donor 185_treatment RSG

source_name: donor 185_treatment RSG


title: donor 185_treatment S-RA

source_name: donor 185_treatment S-RA


title: donor 186_treatment S-RA

source_name: donor 186_treatment S-RA


title: blood_LvHg_7 [7dpi]

source_name: LvHg_0 dpi

source_name: LvHg_7 dpi


title: donor 185_treatment GW3965

source_name: donor 185_treatment GW3965


title: MK11-1482

source_name: patients with sepsis caused by other pathogens

value: Corynebacterium spp.


title: donor 186_treatment LG268

source_name: donor 186_treatment LG268


title: blood_LvLg_8 [7dpi]

source_name: LvLg_7 dpi

value: AA

source_name: LvLg_0 dpi


title: donor 185_treatment R-RA

source_name: donor 185_treatment R-RA


title: MK11-1480

value: Sphingobacterium spp.


title: MK11-1476


title: blood_HvLg_7 [7dpi]

source_name: HvLg_7 dpi

value: blood

source_name: HvLg_0 dpi


title: donor 184_treatment RSG

source_name: donor 184_treatment RSG


title: donor 184_treatment GW1516

source_name: donor 184_treatment GW1516


title: donor 185_treatment LG268

source_name: donor 185_treatment LG268


title: donor 185_treatment GW1516

source_name: donor 185_treatment GW1516


title: donor 185_treatment vehicle

source_name: donor 185_treatment vehicle


title: blood_HvLg_8 [7dpi]


title: blood_HvLg_6 [7dpi]


title: donor 184_treatment LG100

source_name: donor 184_treatment LG100


title: donor 184_treatment S-RA

source_name: donor 184_treatment S-RA


title: MK11-1467


title: MK11-1463


title: blood_HvLg_5 [7dpi]


title: donor 185_treatment 9cis-RA

source_name: donor 185_treatment 9cis-RA


title: blood_LvLg_7 [7dpi]

value: LvLg


title: donor 184_treatment R-RA

source_name: donor 184_treatment R-RA


title: MK11-1455

value: Acinetobacter Iwoffii


title: blood_LvHg_6 [7dpi]

source_name: LvHg_0 dpi

value: LvHg

value: AB

source_name: LvHg_7 dpi


title: donor 184_treatment 9cis-RA

source_name: donor 184_treatment 9cis-RA


title: MK11-1427

source_name: patients with sepsis caused by B. pseudomallei

value: Burkholderia pseudomallei

value: Septicemic melioidosis


title: blood_LvLg_6 [7dpi]

source_name: LvLg_7 dpi

source_name: LvLg_0 dpi


title: donor 184_treatment vehicle

source_name: donor 184_treatment vehicle

value: samples from experiment 1


title: blood_LvHg_5 [7dpi]


title: MK11-1373

source_name: patients with sepsis caused by other pathogens

value: Aeromonas spp.

value: Other sepsis


title: MK11-1392

value: Eschericia coli


title: blood_HvLg_4 [7dpi]

source_name: HvLg_0 dpi

value: HvLg

source_name: HvLg_7 dpi


title: MK11-1436

value: Eschericia coli, Viridans Streptococcus

value: Whole blood


title: donor 184_treatment GW3965

source_name: donor 184_treatment GW3965

value: dendritic cells


title: MK11-1411

value: Klebsiella pneumoniae


title: blood_HvHg_8 [7dpi]

source_name: HvHg_7 dpi

value: HvHg

source_name: HvHg_0 dpi


title: blood_LvHg_2 [7dpi]

value: blood


title: blood_LvLg_5 [7dpi]

value: LvLg

value: AA


title: MK11-1400


title: MK11-1348

value: Micrococcus spp.


title: blood_LvHg_4 [7dpi]

value: LvHg

value: AB


title: blood_HvLg_2 [7dpi]


title: blood_LvHg_3 [7dpi]


title: MK11-1370


title: blood_HvHg_7 [7dpi]


title: MK11-1310


title: blood_LvLg_4 [7dpi]


title: blood_HvLg_3 [7dpi]


title: MK11-1294.1

value: Viridans Streptococci


title: Ezh2Δ/Δ_MEP

city: Kumamoto

first: Goro

last: Sashida

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

department: IRCMS

country: Japan

institute: Kumamoto University

description: Gene expression in Ezh2Δ/Δ MEP cells at 2 months post transplantation

hyb_protocol: 600 ng of the labeled cRNA was hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarray. The process of hybridization and washing was performed using a Hi-RPM Gene Expression Hybridization Kit (Large) (Agilent) and a Gene Expression Wash Pack (Agilent), respectively.

scan_protocol: GeneChips were scanned using a DNA microarray scanner and Feature Extraction ver 10.7.1.1 (Agilent Technologies)

data_processing: Standard Agilent protocol using GeneSpringGX12.0 (Agilent Technologies): Threshold raw signals to 1.0. Normalizsation algorithm, Pertentile Shift. Shift to percentile, 75.

source_name: Bone marrow MEP cells, Ezh2Δ/Δ, replicate 1

label_protocol: 20 ng of total RNA was mixed with spike-in controls using an Agilent One Color Spike Mix Kit (Agilent), amplified and labeled with Cyanine 3 using a Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, which generated single-color labeled cRNA.

extract_protocol: RNeasy Plus Mini Kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Freshly isolated bone marrow cells were stained by appropriate antibodies, and then sorted on FACSAriaII (BD).

tag: strain

tag: genotype

value: MEP


title: Post DMSO_MEP

description: Gene expression in JAK2V617F/Ezh2Δ/Δ MEP cells post the treatment of DMSO

source_name: Bone marrow MEP cells, JAK2V617F/Ezh2Δ/Δ , DMSO, replicate 1

tag: treatment

value: DMSO


title: blood_LvLg_3 [7dpi]


title: blood_HvHg_6 [7dpi]


title: Post JQ1_MEP

description: Gene expression in JAK2V617F/Ezh2Δ/Δ MEP cells post the treatment of JQ1

source_name: Bone marrow MEP cells, JAK2V617F/Ezh2Δ/Δ , JQ1, replicate 1


title: MK11-1342

value: Other sepsis


title: Post JQ1_LSK

description: Gene expression in JAK2V617F/Ezh2Δ/Δ LSK cells post the treatment of JQ1

source_name: Bone marrow LSK cells, JAK2V617F/Ezh2Δ/Δ , JQ1, replicate 1

value: LSK


title: MK11-1272


title: Post DMSO_LSK

description: Gene expression in JAK2V617F/Ezh2Δ/Δ LSK cells post the treatment of DMSO

source_name: Bone marrow LSK cells, JAK2V617F/Ezh2Δ/Δ , DMSO, replicate 1


title: blood_LvHg_1 [7dpi]

source_name: LvHg_7 dpi

source_name: LvHg_0 dpi


title: MK11-1303

value: Streptococcus pyogenes


title: JAK2V617F/Ezh2Δ/Δ_MEP

description: Gene expression in JAK2V617F/Ezh2Δ/Δ MEP cells at 2 months post transplantation

source_name: Bone marrow MEP cells, JAK2V617F/Ezh2Δ/Δ, replicate 1


title: MK11-1346

value: Citrobacter freundii


title: MK11-1299

value: Corynebacterium spp.

value: Whole blood


title: blood_LvLg_1 [7dpi]

source_name: LvLg_7 dpi


title: MK11-1289


title: JAK2V617F_MEP

description: Gene expression in JAK2V617F MEP cells at 2 months post transplantation

source_name: Bone marrow MEP cells, JAK2V617F, replicate 1


title: blood_HvHg_5 [7dpi]


title: blood_LvLg_2 [7dpi]

source_name: LvLg_0 dpi


title: blood_HvLg_1 [7dpi]

value: HvLg


title: MK11-1267

source_name: patients with sepsis caused by B. pseudomallei

value: Burkholderia pseudomallei

value: Septicemic melioidosis


title: WT_MEP

description: Gene expression in WT MEP cells at 2 months post transplantation

source_name: Bone marrow MEP cells, WT, replicate 1

value: WT


title: JAK2V617F/Ezh2Δ/Δ_LSK

description: Gene expression in JAK2V617F/Ezh2Δ/Δ LSK cells at 2 months post transplantation

source_name: Bone marrow LSK cells, JAK2V617F/Ezh2Δ/Δ, replicate 1


title: Ezh2Δ/Δ_LSK

description: Gene expression in Ezh2Δ/Δ LSK cells at 2 months post transplantation

source_name: Bone marrow LSK cells, Ezh2Δ/Δ, replicate 1


title: WT_LSK

description: Gene expression in WT LSK cells at 2 months post transplantation

source_name: Bone marrow LSK cells, WT, replicate 1


title: MK10-812

source_name: patients with sepsis caused by other pathogens

value: Klebsiella pneumoniae


title: JAK2V617F_LSK

description: Gene expression in JAK2V617F LSK cells at 2 months post transplantation

source_name: Bone marrow LSK cells, JAK2V617F, replicate 1


title: blood_HvHg_1 [7dpi]

source_name: HvHg_7 dpi

value: HvHg

value: AA

value: blood

source_name: HvHg_0 dpi


title: MK10-854

value: Enterococcus spp.


title: MK10-811

value: Sphingomanas spp.


title: blood_HvHg_2 [7dpi]


title: blood_HvHg_4 [7dpi]

value: AB


title: MK10-897


title: blood_HvHg_3 [7dpi]


title: 60 days old SOD1G93A transgenic mice 3

city: Sao Paulo

first: Jessica

middle: Ruivo

last: Maximino

state: SP

address: Av. Dr. Arnaldo, 455

department: Neurology

country: Brazil

institute: University of Sao Paulo (FMUSP)

hyb_protocol: Hybridation following manufacturer's instructions (Agilent)

scan_protocol: Scanned on an Agilent scanner

data_processing: Agilent Feature Extraction Software (version 11.0.1.1). Raw signal intensities were normalized using the GeneSpring GX v12.6 software package (Agilent Technologies, USA).

source_name: Sciatic nerve

label_protocol: RNA amplification and labeling following manufacturer's instructions (Agilent)

extract_protocol: Total RNA extracted using Miniprep kit (Zymo, USA) following manufacturer's instructions

value: SOD1G93A transgenic

value: male

source_name: Pool of neonatal organs

value: pooled NonTg and SOD1G93A


title: 60 days old SOD1G93A transgenic mice 2


title: blood_HvLg_26

data_processing: Median intensities were extracted and normalized using a within print-tip loess location normalization implemented in NormalizeWithinArrays() in LIMMA. Background was corrected following Ritchie et al. (2007) method using normexp() function of LIMMA with offset=50. The resulting normalized ratios were expressed in the log2 scale.

source_name: HvLg_4 dpi

extract_protocol: empus tube collected blood samples of PHGC pigs were stored at -20 until RNA was extracted

treatment_protocol: After a 7-day acclimation period and antibiotic treatments, pigs were intramuscularly and intranasally infected with a known isolate of the Porcine Reproductive and Respiratory Syndrome virus (PRRSV) (105 tissue culture infectious dose50 of NVSL 97-7985). Blood samples were collected in Tempus™ Blood RNA Tubes (Life Technologies, Carlsbad, CA) at several time-points post-infection, including 0, 4, 7, 11, 14, 21, 28 and 42 days post-infection (DPI). Individual animal weight was measured at weekly intervals. Serum viral level was quantified using a semi-quantitative TaqMan PCR assay.

source_name: HvLg_0 dpi


title: MK10-904

value: Salmonella

value: Other sepsis


title: 60 days old SOD1G93A transgenic mice 4


title: 60 days old SOD1G93A transgenic mice 1


title: MK10-1220

value: Salmonella gr.C

value: Whole blood


title: blood_HvLg_25

value: HvLg


title: MK10-799

value: Burkholderia pseudomallei

value: Septicemic melioidosis


title: MK10-793

value: Klebseilla pneumoniae,  Viridans Streptococci


title: MK09-732


title: blood_HvHg_25

value: HvHg

source_name: HvHg_4 dpi


title: MK09-714


title: blood_HvLg_24

value: AA


title: blood_HvHg_26

value: blood


title: 60 days old wild-type mice 3

value: wild-type


title: 60 days old wild-type mice 4


title: blood_LvHg_25

source_name: LvHg_0 dpi

value: LvHg

source_name: LvHg_4 dpi


title: MK09-712


title: 60 days old wild-type mice 2


title: 60 days old wild-type mice 1


title: MK09-687


title: blood_LvLg_22

source_name: LvLg_4 dpi

value: LvLg

source_name: LvLg_0 dpi


title: MK09-686

source_name: patients with sepsis caused by B. pseudomallei


title: blood_HvLg_23


title: HT-1080_80%

city: Nagoya

first: Atsushi

last: Enomoto

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Department of Pathology

institute: Nagoya University Graduate School of Medicine

description: HT-1080 cells cultured to 80% confluency

hyb_protocol: Cy3-labelled cRNA fragmentation reaction ahd hybridization to Agilent Whole Human Genome Microarray 4 x 44K were performed by Dragon Genomics Center (Takara Bio, Yokkaichi, Japan).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with the Agilent Feature Extraction software ver. 9.5 (Agilent).

source_name: HT-1080 cells, 80% confluency

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng RNA using the Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions.

extract_protocol: RNA was prepared using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer's recommendations. RNA quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

value: HT-1080 fibrosarcoma cells

tag: confluency


title: blood_HvHg_27


title: MK09-683


title: HT-1080_overconfluent (100% + 2 days)

description: HT-1080 cells cultured to 100% confluency, followed by additional culture for 2 days

source_name: HT-1080 cells,100% confluency, followed by additional culture for 2 days

value: Overconfluent


title: bcCML stem cells, Msi2 mutant, biological rep3

city: La Jolla

first: Roman

last: Sasik

state: CA

address: 9500 Gilman Dr.

department: Center for Computational Biology and Bioinformatics

institute: UCSD

description: Gene expression data from bcCML stem cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: CEL files analyzed with gcrma (Bioconductor), normalized with multiple loess normalization

source_name: Lin- cells from bcCML

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: Hematopoietic stem/progenitors (KLS) were isolated from wild type or Msi2 Gt/Gt mice and infected either with BCR-ABL/NUP98-HOXA9 or MLL-AF9 and transplanted to generate bcCML and AML respectively. Following disease establishment, bcCML and de novo AML stem cells were sorted and total cellular RNA purified.

treatment_protocol: No treatment was done.

value: :Msi2 mutant

value: Leukemic stem cells


title: blood_LvLg_21


title: bcCML stem cells, Msi2 mutant, biological rep2


title: blood_LvHg_24

value: AB


title: MK09-663


title: blood_LvHg_23


title: MK09-664


title: MK09-672


title: blood_HvHg_24


title: blood_HvHg_23


title: MK11-1398


title: bcCML stem cells, wt, biological rep3

value: :wild-type


title: MK09-653

value: Whole blood


title: bcCML stem cells, Msi2 mutant, biological rep1


title: bcCML stem cells, wt, biological rep2


title: MK11-1412


title: MK09-652


title: blood_HvLg_22

value: HvLg


title: CIU12-0528

source_name: Uninfected type 2 diabetes mellitus

value: Control

value: Uninfected type 2 diabetes mellitus


title: CIU12-0531


title: blood_HvLg_21


title: bcCML stem cells, wt, biological rep1


title: CIU12-0526


title: MLL-AF9 stem cells, Msi2 mutant, biological rep2

description: Gene expression data from AML stem cells

source_name: Lin-Sca1-ckit+ cells from de novo AML


title: blood_HvHg_21


title: MLL-AF9 stem cells, Msi2 mutant, biological rep3


title: CIU12-0525


title: CIU12-0530


title: MLL-AF9 stem cells, Msi2 mutant, biological rep1


title: blood_HvHg_22


title: MLL-AF9 stem cells, wt, biological rep3


title: blood_LvLg_20


title: MLL-AF9 stem cells, wt, biological rep2


title: MLL-AF9 stem cells, wt, biological rep1


title: CIU12-0523


title: blood_LvHg_21


title: blood_LvLg_17


title: blood_LvLg_19


title: blood_LvHg_22


title: blood_LvLg_18


title: CIU12-0521

source_name: Uninfected healthy

value: Uninfected healthy


title: CTX_KO_6hrsKCl_Repeat2

city: Boston

first: Ivo

last: Spiegel

state: MA

address: 220 Longwood Ave

department: Department of Neurobiology

institute: Harvard Medical School

description: 100 ng total RNA amplifed with NuGEN Ovation V2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Expression Set 430 2.0 microarray. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000

data_processing: Arrays from all experimental conditions and all replicates of a given condition were normalized to one another using the robust multichip averaging method (RMA normalization) using the MATLAB bioinformatics toolbox (Bolstad et al., 2003).

source_name: CTX 10 DIV

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA

growth_protocol: Mouse E14 MGE- and CTX-derived neurons were cultured for 10 days

extract_protocol: Total RNA was extracted with Trizol and then purified with QIAgen RNEasy MinElute columns according to manufacturer's instructions

treatment_protocol: At DIV 9, the cells were quieted O.N. with TTX and AP-5 and membrane-depolarized on DIV 10 for 0, 1 and 6 hours with 55 mM extracellular KCl

value: CTX-derived neurons

value: Npas4 KO

tag: time

value: 6 h

value: KCL

tag: genetic background


title: CIU12-0524


title: CTX_KO_1hrsKCl_Repeat2

value: 1 h


title: CIU12-0520


title: CIU12-0518


title: CIU12-0522


title: CIU12-0519


title: CTX_WT_6hrsKCl_Repeat2

value: WT


title: blood_HvHg_20

tag: dpi

value: HvHg

value: AA

value: blood

source_name: HvHg_0 dpi


title: CTX_KO_0hrsKCl_Repeat2

value: 0 h


title: blood_LvHg_20

value: LvHg

value: AB

tag: auc


title: CTX_WT_1hrsKCl_Repeat2


title: CIU12-0515

tag: tissue

value: Whole blood


title: blood_LvLg_16

value: LvLg


title: CTX_WT_0hrsKCl_Repeat2


title: CTX_KO_0hrsKCl_Repeat1


title: blood_HvLg_20

value: HvLg


title: CIU12-0512

value: Control

value: Uninfected type 2 diabetes mellitus


title: CIU12-0517

value: Uninfected healthy


title: CTX_KO_1hrsKCl_Repeat1

value: CTX-derived neurons

value: Npas4 KO


title: CTX_KO_6hrsKCl_Repeat1

value: 6 h

value: KCL


title: blood_LvHg_19


title: CIU12-0511


title: blood_LvHg_18


title: CTX_WT_6hrsKCl_Repeat1

value: WT


title: blood_LvLg_15


title: blood_LvHg_17


title: CIU12-0510


title: CTX_WT_0hrsKCl_Repeat1


title: CIU12-0508


title: blood_HvHg_19

value: HvHg


title: CIU12-0507


title: CIU12-0506


title: CTX_WT_1hrsKCl_Repeat1

value: 1 h


title: blood_HvLg_19

value: AA

value: blood


title: blood_HvLg_18


title: blood_HvLg_17


title: CIU12-0505


title: MGE_KO_1hrsKCl_Repeat2

source_name: MGE 10 DIV

value: MGE-derived neurons


title: CIU12-0504


title: MGE_KO_6hrsKCl_Repeat2


title: MGE_KO_0hrsKCl_Repeat2

value: 0 h


title: blood_LvHg_16

value: LvHg

value: BB


title: blood_HvLg_16

value: HvLg

source_name: HvLg_4 dpi


title: blood_HvHg_18


title: CIU12-0503

value: Control

value: Whole blood


title: blood_HvLg_15

source_name: HvLg_0 dpi


title: MGE_KO_1hrsKCl_Repeat1


title: CIU12-0501

value: Uninfected type 2 diabetes mellitus


title: MGE_WT_1hrsKCl_Repeat2


title: MGE_KO_6hrsKCl_Repeat1


title: MGE_WT_0hrsKCl_Repeat2


title: CIU12-0499


title: MGE_WT_6hrsKCl_Repeat2


title: CIU12-0498


title: R248LNSP

description: Copy Number data reference

source_name: Peripheral blood lymphocytes

tag: sample group

value: Control Reference


title: R221LNSP

description: Copy Number data reference


title: blood_LvLg_14

value: LvLg

value: AB


title: blood_LvHg_15

source_name: LvHg_0 dpi


title: CIU12-0496

tag: pathogens


title: CIU12-0494

tag: study group

value: Uninfected healthy


title: CIU12-0490


title: blood_HvLg_14


title: CIU12-0497


title: MGE_KO_0hrsKCl_Repeat1

value: Npas4 KO

value: KCL


title: MGE_WT_0hrsKCl_Repeat1

value: WT


title: R219LNSP

description: Copy Number data reference


title: R191LNSP

description: Copy Number data reference


title: MGE_WT_1hrsKCl_Repeat1

value: 1 h


title: R161LNSP

description: Copy Number data reference


title: MGE_WT_6hrsKCl_Repeat1

value: 6 h


title: blood_LvLg_13

value: AA

value: blood


title: blood_HvHg_16

source_name: HvHg_4 dpi

value: HvHg


title: R156LNSP

description: Copy Number data reference


title: blood_LvLg_12

source_name: LvLg_4 dpi


title: blood_LvHg_14

value: LvHg

source_name: LvHg_4 dpi


title: blood_LvLg_11

source_name: LvLg_0 dpi


title: blood_HvHg_15


title: blood_HvHg_17


title: CIU11-368


title: CIU11-369


title: CIU12-0492


title: blood_HvHg_14


title: CIU11-367


title: R170LNSP

description: Copy Number data reference


title: R119LNSP

description: Copy Number data reference


title: R075LNSP

description: Copy Number data reference


title: R065LNSP

description: Copy Number data reference


title: CIU11-365


title: blood_HvHg_13


title: R064LNSP

description: Copy Number data reference


title: CIU12-0486


title: R057LNSP

description: Copy Number data reference


title: R120LNSP

description: Copy Number data reference


title: R036LNSP

description: Copy Number data reference


title: blood_HvLg_13

value: HvLg


title: blood_LvLg_10


title: CIU11-363

value: Control


title: CIU12-0489

value: Whole blood


title: R035LNSP

description: Copy Number data reference


title: CIU11-359


title: blood_HvLg_12


title: blood_HvHg_12


title: CIU11-360


title: C284NSP

description: Copy Number data reference


title: blood_LvHg_13


title: C202NSP

description: Copy Number data reference


title: CIU11-364

value: Uninfected type 2 diabetes mellitus


title: CIU11-353


title: blood_HvHg_11


title: R052LNSP

description: Copy Number data reference

value: Control Reference


title: CIU11-352


title: blood_HvLg_11


title: C137NSP

description: Copy Number data reference


title: C174NSP

description: Copy Number data reference


title: CIU11-346


title: CIU11-351


title: blood_LvHg_11


title: C133NSP

description: Copy Number data reference


title: CIU11-354


title: CIU11-347


title: blood_LvLg_9

value: LvLg


title: CIU11-339


title: C128NSP

description: Copy Number data reference


title: C105NSP

description: Copy Number data reference


title: blood_HvHg_10

value: AB


title: blood_LvHg_12


title: C026NSP

description: Copy Number data reference


title: CIU11-338


title: blood_LvHg_9


title: blood_HvLg_10


title: blood_LvHg_8


title: CIU11-336


title: CIU11-335


title: blood_HvLg_9


title: R496NSP

description:
Copy Number data from Cervical cancer biopsy
processed data file: R496_Tumor.500k-default-CN-20121109.CN4.cnchp

source_name: Cervical cancer biopsy

value: Case

tag: age (years)

tag: histology

value: SCC

tag: tumor stage

value: IIIB


title: C025NSP

description: Copy Number data reference


title: CIU11-326


title: CIU11-323


title: R483NSP

description:
Copy Number data from Cervical cancer biopsy
processed data file: R483_Tumor.500k-default-CN-20121109.CN4.cnchp

value: IVB


title: R476NSP

description:
Copy Number data from Cervical cancer biopsy
processed data file: R476_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R392NSP

description:
Copy Number data from Cervical cancer biopsy
processed data file: R392_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R478NSP

description:
Copy Number data from Cervical cancer biopsy
processed data file: R478_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R444NSP

description:
Copy Number data from Cervical cancer biopsy
processed data file: R444_Tumor.500k-default-CN-20121109.CN4.cnchp

value: IIB


title: blood_HvHg_9


title: blood_HvLg_8


title: CIU11-322


title: CIU11-318

value: Uninfected healthy


title: blood_HvLg_6

value: AA


title: R386NSP

description:
Copy Number data from Cervical cancer biopsy
processed data file: R386_Tumor.500k-default-CN-20121109.CN4.cnchp


title: blood_HvLg_7

value: blood


title: blood_HvLg_5


title: blood_LvHg_7


title: R494NSP

description:
Copy Number data from Cervical cancer biopsy
processed data file: R494_Tumor.500k-default-CN-20121109.CN4.cnchp


title: blood_HvLg_4


title: R365NSP

description:
Copy Number data from Cervical cancer biopsy
processed data file: R365_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R369NSP

description:
Copy Number data from Cervical cancer biopsy
processed data file: R369_Tumor.500k-default-CN-20121109.CN4.cnchp


title: blood_LvLg_8


title: R298NSP

description:
Copy Number data from Cervical cancer biopsy
processed data file: R298_Tumor.500k-default-CN-20121109.CN4.cnchp

value: ASCC


title: R282NSP

description:
Copy Number data from Cervical cancer biopsy
processed data file: R282_Tumor.500k-default-CN-20121109.CN4.cnchp


title: blood_HvHg_8

value: HvHg


title: blood_LvLg_7


title: R260NSP

description:
Copy Number data from Cervical cancer biopsy
processed data file: R260_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R248NSP

description:
Copy Number data from Cervical cancer biopsy
processed data file: R248_Tumor.500k-default-CN-20121109.CN4.cnchp


title: blood_LvHg_4

value: LvHg


title: blood_LvLg_6


title: blood_LvHg_6


title: R244NSP

description:
Copy Number data from Cervical cancer biopsy
processed data file: R244_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R240NSP

description:
Copy Number data from Cervical cancer biopsy
processed data file: R240_Tumor.500k-default-CN-20121109.CN4.cnchp


title: blood_HvLg_3

value: HvLg


title: blood_LvHg_3


title: blood_LvHg_2


title: blood_LvLg_5


title: R221NSP

description:
Copy Number data from Cervical cancer biopsy
processed data file: R221_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R322NSP

description:
Copy Number data from Cervical cancer biopsy
processed data file: R322_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R208NSP

description:
Copy Number data from Cervical cancer biopsy
processed data file: R208_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R198NSP

description:
Copy Number data from Cervical cancer biopsy
processed data file: R198_Tumor.500k-default-CN-20121109.CN4.cnchp

value: IVA


title: blood_HvHg_7


title: blood_HvLg_2


title: R194NSP

description:
Copy Number data from Cervical cancer biopsy
processed data file: R194_Tumor.500k-default-CN-20121109.CN4.cnchp

value: IIA


title: blood_LvHg_5


title: blood_LvLg_4


title: R183NSP

description:
Copy Number data from Cervical cancer biopsy
processed data file: R183_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R189NSP

description:
Copy Number data from Cervical cancer biopsy
processed data file: R189_Tumor.500k-default-CN-20121109.CN4.cnchp

value: ACC


title: R116NSP

description:
Copy Number data from Cervical cancer biopsy
processed data file: R116_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R154NSP

description:
Copy Number data from Cervical cancer biopsy
processed data file: R154_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R111NSP

description:
Copy Number data from Cervical cancer biopsy
processed data file: R111_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R075NSP

description:
Copy Number data from Cervical cancer biopsy
processed data file: R075_Tumor.500k-default-CN-20121109.CN4.cnchp


title: R380NSP

description:
Copy Number data from Cervical cancer biopsy
processed data file: R380_Tumor.500k-default-CN-20121109.CN4.cnchp


title: blood_LvHg_1


title: blood_LvLg_1

value: LvLg


title: blood_HvHg_5

value: AB


title: blood_HvHg_4


title: blood_LvLg_2


title: R072NSP

description:
Copy Number data from Cervical cancer biopsy
processed data file: R072_Tumor.500k-default-CN-20121109.CN4.cnchp

value: Case


title: blood_LvLg_3


title: blood_LvHg_10


title: R062NSP

description:
Copy Number data from Cervical cancer biopsy
processed data file: R062_Tumor.500k-default-CN-20121109.CN4.cnchp

value: SCC


title: blood_HvLg_1


title: R035NSP

description:
Copy Number data from Cervical cancer biopsy
processed data file: R035_Tumor.500k-default-CN-20121109.CN4.cnchp


title: blood_HvHg_6


title: blood_HvHg_2


title: blood_HvHg_1


title: blood_HvHg_3


title: DLD1_Vehicle

status: Public on Jun 03 2015

city: Busan

first: Do Sik

last: Min

address: 30 Jangjeon-dong, Geumjeong-gu

department: Molecular Biology

country: South Korea

institute: Pusan National University

description: replicate 1

hyb_protocol: After purification, labeled samples were resuspended with Gene Expression blocking Reagent and Hi-RPM Hybridization buffer, followed by boiling for 5 min at 100 °C and 5 min chilled on ice. Finally, denatured labeled probes were pipetted onto assembled Agilent’s miRNA Microarray and hybridized for 20 hours at 55°C with 20 RPM rotating in Agilent Hybridization oven (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and further analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

label_protocol: For control and test RNAs, the synthesis of target miRNA probes and hybridization were performed using Agilent’s miRNA Labeling Reagent and Hybridization kit (Agilent Technology, USA) according to the manufacturer’s instructions. Briefly, each 100 ng of total RNA were dephosphorylated with ~15 Units of calf intestine alkaline phosphatase (CIP), followed by RNA denaturation with ~40% DMSO and 10 min incubation at 100 °C. Dephosphorylated RNA were ligated with pCp-Cy3 mononucleotide and purified with MicroBioSpin 6 columns (Bio-rad, USA).

growth_protocol: DLD1 cells were cultured with DMEM medium supplemented with 1% heat-inactivated fetal bovine serum. The cultures were incubated for 36 hr at 37 ºC in a humidified incubator with 5% CO2.

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

treatment_protocol: DLD1 cells were treated with or without PLD1-Inh (10 μM).

tag: cell line

tag: cell type

value: Colon cancer cells

tag: treated with

value: vehicle

tag: serum (%)

value: 1% FBS condition


title: 50d_summer_V_b

city: Tampere

first: Tiina

middle: Susanna

last: Salminen

address: Biokatu 6, Finn-Medi 1

department: BioMediTech

country: Finland

institute: University of Tampere

hyb_protocol: 600 ng of each cRNA sample was hybridized to Agilent’s 8x15K D. montana / D. virilis custom arrays at 65˚C. Hybridization was performed overnight using Agilent’s Gene Expression Hybridization Kit and the plates were washed with Agilent’s Gene Expression Wash Pack and Stabilization and Drying solution.

scan_protocol: Arrays were scanned with Agilent Technologies Scanner (model G2565CA) and numerical results were extracted with Feature Extraction software version 10.7.1 using 026691_D_F_20091221grid, GE1_107_Sep09 protocol and GE1_QCMT_Sep09 metric set.

data_processing: The downstream analysis of the microarray data was carried out using R (R Foundation for Statistical Computing) and Bioconductor software (Gentleman et al., 2004). Probe level quantile normalization method was used for between sample normalization, after which the signals were summarized for each probe type by taking a median value. The data was found to be of high quality and the Pearson's correlations between the samples were between 0.86 and 0.99 in the different sample groups indicating high reproducibility. The statistical analyses were carried out using Bioconductor's Limma package. For filtering out differentially expressed genes, the minimum fold change limit was set at 2 and false discovery rate (FDR) adjusted significance level at 0.05.

organism: Drosophila montana

source_name: whole tissue, 50-day-old non-diapausing female

label_protocol: 600 ng of total RNA from each replicate was amplified and Cy3-labeled with Agilent’s Quick Amp Labeling (One Color) Kit and processed together with Agilent’s One-Colour RNA Spike-in Kit.

extract_protocol: RNA was prepared with Ambion RNAqueous 96 well total RNA Isolation Kit with DNase treatment (Qiagen) and purified with MinElute kit (Qiagen). The purity of each RNA sample was measured with NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and the integrity of the samples was studied with Agilent’s Bioanalyzer (Agilent, Santa Clara, CA, USA).

tag: strain

tag: state

value: non-diapausing


title: 50d_summer_V_a


title: DLD1_PLD1_Inh

description: replicate 1

value: 10 μM PLD1-Inh


title: Cerebral tumor control (mouse 3)

city: LA TRONCHE

first: Michèle

last: EL ATIFI

address: Chemin fortuné ferrini

country: France

institute: INSERM

description: Mouse received only orange juice, 45 days after cells implantation, for 5 days.

hyb_protocol: After fragmentation, biotinylated cRNA were hybridized for 16h at 45 °C on GeneChip® Human Genome U133 Plus 2.0 Array. The arrays were then washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000.

data_processing: The data were normalized using RMA algorithm with the Affymetrix software Expression Console Suite. To flag the transcript as Present (P) or Absent (A), data were processed with MAS5 algorithm.

source_name: Cerebral tumor, control

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol from 200 ng of total RNA using the GeneChip® 3' IVT Express Kit  Labeling and Hybridization

growth_protocol: Cell growth: Human glioblastoma neurospheres were cultured in medium DMEM/F12 (1:1); 0.5 N2;0.5 B-27 supplements, 1 X glutamax; heparin 2μg/ml, 30ng/ml bFGF and 30ng/ml EGF.

extract_protocol: 75 days after cells implantation, brain tumors were resected and total RNA were extracted with the MirVana TM isolation kit (Applied Biosystems).

treatment_protocol: Animal treatment: Brain tumors were developed in female nude mice by injection of 500,000 cells through a burr hole into the right caudate nucleus. 45 days after tumor implantation, some of them were treated daily with TMZ in orange juice for 5 days by gavage at a dose of 262,5Kg/KG body weight per day.

tag: animal treatment

value: orange juice

value: brain tumor

tag: cell type implantation

value: glioblastoma neurospheres (Glio6)


title: Cerebral tumor control (mouse 2)


title: Temodal-treated cerebral tumor (mouse 5)

description: Mouse received Temodal (TMZ) in orange juice, 45 days after cells implantation, for 5 days by gavage at a dose of 262,5Kg/KG body weight per day.

source_name: Cerebral tumor, TMZ treated

value: Temodal (TMZ) in orange juice


title: Temodal-treated cerebral tumor (mouse 6)


title: Temodal-treated cerebral tumor (mouse 4)


title: Temodal-treated cerebral tumor (mouse 7)


title: 7d_autumn_D_c

source_name: whole tissue, 7-day-old diapausing female

value: diapausing


title: Cerebral tumor control (mouse 1)


title: 7d_autumn_D_a


title: 7d_summer_V_a

source_name: whole tissue, 7-day-old non-diapausing female


title: 7d_autumn_D_b


title: 250d_spring_OFF30_c

source_name: whole tissue, 250-day-old female, after the offset of diapause


title: 7d_summer_V_c


title: 250d_spring_OFF30_a


title: 250d_spring_OFF30_b


title: 220d_spring_OFF10_b

source_name: whole tissue, 220-day-old female, beginning of the offset of diapause


title: 220d_spring_OFF10_c


title: 220d_spring_OFF10_a


title: 150d_winter_D_c

source_name: whole tissue, 150-day-old diapausing female


title: 150d_winter_V_c

source_name: whole tissue, 150-day-old non-diapausing female


title: 150d_winter_V_b


title: 50d_summer_V_c


title: 150d_winter_D_b


title: 150d_winter_D_a


title: 50d_autumn_D_a

source_name: whole tissue, 50-day-old diapausing female


title: 50d_autumn_D_c


title: Basal Ganglia_E12.5_Otx2cKO_Rep3

city: San Francisco

first: John

last: Rubenstein

address: 1550 4th Street

department: Psychiatry

institute: UCSF

description:
RxCre cKO
Otx2_ cKO_litter2.4

hyb_protocol: Hybridization were performed for 14 hrs, according to the Agilent protocol.

scan_protocol: Arrays were scanned using the Agilent microarray scanner.

data_processing:
Raw signal intensities were extracted with Agilent Feature Extraction v10.5 software.
Significant changes in gene expression were defined as B value greater than zero. B = log 10 posterior odds ratio, ratio between the probability that a given gene is differentially expressed (DE)over the probability that a given gene is not differentially expressed.B≥0 means equal or greaterprobability that a gene is DE than non-DE

source_name: Otx2cKO, ganglionic eminences and septum

label_protocol: RNA was amplified (labeled with Cy3-CTP)withAgilent low RNA input fluorescent linear amplification kits, and cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE). Equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays, by theUCSF Genomics Core.

growth_protocol: Subpallial (ganglionic eminences and septum) tissue wasmicrodissected from E12.5 female brains (n=4 control, n=3 CKO), snap frozen, and stored at -80oC

extract_protocol: Total RNA was isolated using the Qiagen RNAeasy kit.

tag: genotype

value: Otx2 cKO

tag: litter

tag: gender

value: Female

tag: developmental stage

value: ganglionic eminences and septum


title: Basal Ganglia_E12.5_Control_Rep4

description:
Control
Control_litter4.4

source_name: control, ganglionic eminences and septum

value: Control

tag: tissue


title: Basal Ganglia_E12.5_Otx2cKO_Rep1

description:
RxCre cKO
Otx2_ cKO_litter2.1


title: Basal Ganglia_E12.5_Control_Rep1

description:
Control
Control_litter3.1


title: Basal Ganglia_E12.5_Control_Rep3

description:
Control
Control_litter2.3


title: roots Carrizo citrange vulcanic rep3

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

hyb_protocol: Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt's solution, 100 ng/ul Salmon Sperm DNA, 0.05% SDS) for 60 minutes at 45 °C. 5 ug of Labeled aRNA were fragmented by incubation with Fragmentation Solution (40mM Tris Acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc) for 20' at 95 °C. Hybridization was performed at 45°C for 16 hours in hybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 25% DiFormamide, 100 ng/ul Salmon Sperm DNA, 0.04% SDS).  Hybridization washings were performed as following:  - wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20).  - wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20).  - wash with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20).  - wash with PBST was solution (2X PBS, 0.1% Tween-20).  - 2 washes with 2X PBS. All the procedures provided were performed as indicated by Combimatrix protocols available at Combimatrix website (www.combimatrix.com)

scan_protocol: Scanning was performed on a Axon GenePix 4000A scanner. Laser was set at 33% power.

data_processing: Data extraction was carried out using the GenePix Pro 7 software. The normalization between arrays was performed using the quantile method.

organism: Citrus sinensis x Citrus trifoliata

source_name: citrus roots

label_protocol: Six µg of total RNA were labeled using RNA Ampulse amplification and labeling kit with Cy5 for Combimatrix arrays (Kreatech Diagnostics, The Netherlands) according to manufacturer instructions

extract_protocol: Extraction of total RNA was performed using root tips from a pool of 3 plants for each biological replicate. The RNA was extracted using the SpectrumTM Plant Total RNA Kit (Sigma).The RNA quantity was evaluated using a NanoDrop 1000 spectrophotometer and RNA integrity by an Agilent 2100 Bioanalyzer.

value: citrus root tips

tag: cultivar

value: Carrizo citrange (C. sinensis × P. trifoliata) rootstock, grafted with Tarocco Scirè [C. sinensis (L.) Osbeck], grown in vulcanic soil.

tag: treatment

value: volcanic soil


title: roots Carrizo Citrange calcareous rep1

value: Carrizo citrange (C. sinensis × P. trifoliata) rootstock, grafted with Tarocco Scirè [C. sinensis (L.) Osbeck], grown in a calcareous soil, containing 10% of active lime.

value: chlorotic soil


title: roots Carrizo Citrange calcareous rep2


title: roots Carrizo citrange vulcanic rep2


title: Basal Ganglia_E12.5_Otx2cKO_Rep2

description:
RxCre cKO
KO_litter1.3


title: Basal Ganglia_E12.5_Control_Rep2

description:
Control
Control_litter2.2


title: 50d_autumn_D_b


title: roots Carrizo Citrange calcareous rep3


title: roots Swingle citrumelo calcareous rep3

organism: Citrus x paradisi x Citrus trifoliata

value: Swingle citrumelo (C. paradisi × Poncirus trifoliata) rootstock, grafted with Tarocco Scirè [C. sinensis (L.) Osbeck], grown in a calcareous soil, containing 10% of active lime.


title: R496(CytoScanHD_Array)

description: Copy Number data from Cervical cancer biopsy

hyb_protocol: Following fragmentation, ssDNA were hybridized for 18 hr at 50C and 60 rpm on Cytoscan HD Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 protocol

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix) with GeneChip Scanner 3000

data_processing: Microarrays were normalized with the Chromosome Analysis Suite (ChAS) Software version 2.0 and compared with the Reference data set included in ChAS.

label_protocol: Biotinylated DNA were prepared according to the standard Affymetrix protocol from 500 ng total DNA (Cytoscan HD Technical Manual, Affymetrix).

tag: sample group

value: Case

tag: age (years)

tag: histology

value: SCC

value: IIIB


title: roots Swingle citrumelo calcareous rep1


title: 150d_winter_V_a

value: non-diapausing


title: roots Swingle citrumelo vulcanic rep1

value: Swingle citrumelo (C. paradisi × Poncirus trifoliata) rootstock, grafted with Tarocco Scirè [C. sinensis (L.) Osbeck], grown in vulcanic soil.


title: roots Swingle citrumelo calcareous rep2


title: roots Swingle citrumelo vulcanic rep3


title: R322(CytoScanHD_Array)

tag: tumor stage


title: roots Carrizo citrange vulcanic rep1


title: R397(CytoScanHD_Array)

description:
Copy Number data from Cervical cancer biopsy
This sample correponds to the sample 'R392' in the other subseries.


title: roots Swingle citrumelo vulcanic rep2


title: R386(CytoScanHD_Array)


title: R208(CytoScanHD_Array)


title: R260(CytoScanHD_Array)


title: R444(CytoScanHD_Array)

value: IIB


title: R154(CytoScanHD_Array)


title: R476(CytoScanHD_Array)


title: R198(CytoScanHD_Array)

value: IVA


title: R483(CytoScanHD_Array)

value: IVB


title: Parietal of subject 393 (Sample259)

city: Los Angeles

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

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 v3.2.
Unmethylated and methylated signal intensities and detection p values included in Series supplementary file

label: Cy3 and Cy5

source_name: Brain Parietal

label_protocol: Standard Illumina Protocol

growth_protocol: DNA extracted from fresh frozen tissue

extract_protocol: genomic DNA was extracted and purified from fresh frozen tissue using the AllPrep DNA/RNA mini kit according to standard instructions.

value: Brain Parietal

tag: subject id

tag: Sex

value: M

tag: predicted gender

value: male

tag: age

tag: dna methylation age

tag: age acceleration with respect to noncerebellar samples

tag: cor sample vs gold standard

tag: mean abs difference sample vs gold standard

tag: postmortem interval


title: R244(CytoScanHD_Array)

city: MEXICO CITY

first: INGRID

last: MEDINA MARTINEZ

address: DR. BALMIS 148

institute: HOSPITAL GENERAL DE MEXICO OD


title: Motor Cortex of subject 421 (Sample260)

source_name: Brain Motor Cortex

value: Brain Motor Cortex


title: R369(CytoScanHD_Array)


title: Frontal of subject 283 (Sample254)

source_name: Brain Frontal

value: Brain Frontal


title: Hippocampus of subject 149 (Sample257)

source_name: Brain Hippocampus

value: Brain Hippocampus


title: genomic DNA from Bladder Cancer Cell RT112 with knock-down for SCR RNA rep1

city: Honolulu

first: Rafael

last: Peres

state: HI

address: 701 Ilalo Street, #354

department: Clinical and Translational Research

institute: University Of Hawaii Cancer Center

description: genomic DNA from Bladder Cancer Cell RT112 with knock-down for SCR RNA, 2 replicates

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to  Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol

scan_protocol: The image intensities were extracted using Illumina's Bead Scan software (Illumina iScan scanner).

data_processing:
Illumina GenomeStudio v2011.1 (Methylatioin Module v1.9.0) and the statistical computing package R 3.0.2 (http://www.r-project.org).
The bisulfite treatment, microarray service and analysis of the array were provided by Macrogen Inc. (Seoul, South Korea).

label: Cy5 and Cy3

source_name: RT112 bladder cancer cell line

extract_protocol: genomic DNA was extracted and purified from Bladder Cancer Cells samples using Ultra Clean Tissue & Cells DNA Isolation Kit, Mo Bio Laboratories

value: SCR knockdown

tag: cell line

tag: tumor grade


title: genomic DNA from Bladder Cell UROtsa with knock-in for Angiogenin rep1

description: genomic DNA from Bladder Cell UROtsa with knock-in for Angiogenin, 2 replicates

source_name: UROtsa bladder cell line

value: angiogenin knock-in

value: UROtsa

value: Benign


title: genomic DNA from Bladder Cell UROtsa with knock-in for Angiogenin rep2


title: genomic DNA from Bladder Cancer Cell RT112 with knock-down for SCR RNA rep2


title: Motor Cortex of subject 71 (Sample256)

tag: tissue


title: Visual Cortex of subject 315 (Sample253)

source_name: Brain Visual Cortex

value: Brain Visual Cortex

value: F

value: female


title: Sensory Cortex of subject 71 (Sample258)

source_name: Brain Sensory Cortex

value: Brain Sensory Cortex


title: genomic DNA from Bladder Cancer Cell RT112 with knock-down for Angiogenin rep2

description: genomic DNA from Bladder Cancer Cell RT112 with knock-down for Angiogenin, 2 replicates

tag: treatment

value: angiogenin knock down


title: R035(CytoScanHD_Array)

source_name: Cervical cancer biopsy

extract_protocol: DNA extraction was performed according to the manufacturer's instructions.

tag: sample group

value: Case

value: SCC


title: R075(CytoScanHD_Array)

tag: age (years)

value: ACC


title: genomic DNA from Bladder Cell UROtsa with knock-in for empty plasmid (control) rep2

description: genomic DNA from Bladder Cell UROtsa with knock-in for empty plasmid (control), 2 replicates

value: empty plasmid knock-in control


title: genomic DNA from Bladder Cancer Cell RT112 with knock-down for Angiogenin rep1


title: Caudate Nucleus of subject 315 (Sample251)

source_name: Brain Caudate Nucleus

value: Brain Caudate Nucleus


title: Frontal of subject 34 (Sample252)


title: genomic DNA from Bladder Cell UROtsa with knock-in for empty plasmid (control) rep1


title: Frontal of subject 487 (Sample246)


title: Mid of subject 7 (Sample248)

source_name: Brain MidBrain

value: Brain MidBrain

value: M

value: male


title: Frontal of subject 239 (Sample244)

value: Brain Frontal


title: Temporal of subject 328 (Sample250)

source_name: Brain Temporal

value: Brain Temporal


title: Occipital of subject 225 (Sample245)

source_name: Brain Occipital

value: Brain Occipital


title: Sensory Cortex of subject 513 (Sample240)


title: Frontal of subject 351 (Sample255)


title: Caudate Nucleus of subject 513 (Sample247)


title: Temporal of subject 131 (Sample242)


title: Occipital of subject 17 (Sample243)


title: Occipital of subject 239 (Sample237)


title: Visual Cortex of subject 513 (Sample233)


title: Cingulate Gyrus of subject 467 (Sample239)

source_name: Brain Cingulate Gyrus

value: Brain Cingulate Gyrus


title: Temporal of subject 149 (Sample229)


title: Motor Cortex of subject 393 (Sample236)

value: Brain Motor Cortex


title: Parietal of subject 421 (Sample249)

value: Brain Parietal


title: Parietal of subject 467 (Sample235)


title: Visual Cortex of subject 393 (Sample231)

value: Brain Visual Cortex


title: Temporal of subject 299 (Sample232)

value: F

value: female


title: Caudate Nucleus of subject 87 (Sample230)


title: CRBM of subject 379 (Sample226)

source_name: Brain CRBM

value: Brain CRBM


title: Caudate Nucleus of subject 71 (Sample228)


title: Frontal of subject 57 (Sample224)


title: Caudate Nucleus of subject 365 (Sample227)


title: CRBM of subject 502 (Sample225)


title: Sensory Cortex of subject 393 (Sample241)

value: Brain Sensory Cortex


title: Frontal of subject 204 (Sample222)


title: Frontal of subject 215 (Sample238)


title: Temporal of subject 487 (Sample220)


title: Hippocampus of subject 107 (Sample217)

value: Brain Hippocampus


title: Temporal of subject 107 (Sample213)


title: CRBM of subject 178 (Sample221)


title: Temporal of subject 131 (Sample216)


title: Occipital of subject 487 (Sample223)


title: CRBM of subject 107 (Sample215)


title: Occipital of subject 351 (Sample214)


title: Temporal of subject 34 (Sample207)


title: Frontal of subject 107 (Sample211)


title: Occipital of subject 107 (Sample212)


title: Temporal of subject 194 (Sample196)


title: Mid of subject 487 (Sample203)


title: Occipital of subject 131 (Sample219)


title: Occipital of subject 194 (Sample204)


title: Occipital of subject 299 (Sample206)


title: CRBM of subject 239 (Sample218)


title: Frontal of subject 131 (Sample210)


title: CRBM of subject 487 (Sample200)


title: Sensory Cortex of subject 315 (Sample234)


title: Temporal of subject 25 (Sample205)


title: CRBM of subject 34 (Sample195)


title: Frontal of subject 7 (Sample209)


title: Temporal of subject 299 (Sample193)


title: CRBM of subject 131 (Sample194)


title: Hippocampus of subject 487 (Sample202)


title: Occipital of subject 204 (Sample192)


title: Occipital of subject 185 (Sample208)

value: Unsure


title: CRBM of subject 17 (Sample191)


title: Occipital of subject 328 (Sample201)


title: Hippocampus of subject 131 (Sample199)


title: Caudate Nucleus of subject 437 (Sample184)

value: Brain Caudate Nucleus


title: Sensory Cortex of subject 267 (Sample189)


title: Parietal of subject 87 (Sample187)


title: Frontal of subject 194 (Sample190)


title: Frontal of subject 165 (Sample186)


title: Frontal of subject 107 (Sample177)


title: Frontal of subject 267 (Sample179)


title: Parietal of subject 421 (Sample188)


title: Temporal of subject 165 (Sample180)


title: CRBM of subject 57 (Sample172)


title: Hippocampus of subject 107 (Sample181)


title: CRBM of subject 194 (Sample171)


title: Occipital of subject 254 (Sample176)


title: Temporal of subject 254 (Sample178)


title: Temporal of subject 487 (Sample173)


title: Motor Cortex of subject 267 (Sample174)


title: Frontal of subject 315 (Sample164)


title: CRBM of subject 165 (Sample175)


title: CRBM of subject 225 (Sample169)


title: Sensory Cortex of subject 283 (Sample165)


title: Frontal of subject 421 (Sample167)


title: Mid of subject 487 (Sample160)

value: Brain MidBrain


title: CRBM of subject 7 (Sample197)

value: M


title: Frontal of subject 487 (Sample170)


title: Occipital of subject 455 (Sample162)


title: CRBM of subject 131 (Sample159)


title: Cingulate Gyrus of subject 283 (Sample163)

value: male


title: Occipital of subject 7 (Sample161)


title: Hippocampus of subject 487 (Sample158)


title: CRBM of subject 487 (Sample157)


title: Parietal of subject 71 (Sample185)


title: Frontal of subject 87 (Sample148)

value: Brain Frontal


title: Motor Cortex of subject 87 (Sample155)


title: CRBM of subject 299 (Sample149)


title: Frontal of subject 71 (Sample153)


title: Occipital of subject 165 (Sample154)


title: Hippocampus of subject 379 (Sample183)


title: Parietal of subject 467 (Sample166)


title: Temporal of subject 455 (Sample168)

value: Brain Temporal


title: Occipital of subject 57 (Sample198)

value: Brain Occipital


title: Parietal of subject 71 (Sample147)


title: Sensory Cortex of subject 437 (Sample152)


title: Frontal of subject 467 (Sample131)


title: Temporal of subject 379 (Sample151)


title: Parietal of subject 283 (Sample146)


title: Occipital of subject 379 (Sample145)


title: CRBM of subject 448 (Sample128)


title: Occipital of subject 299 (Sample140)


title: Parietal of subject 87 (Sample143)


title: Occipital of subject 165 (Sample139)


title: CRBM of subject 165 (Sample144)


title: Temporal of subject 339 (Sample141)


title: Visual Cortex of subject 87 (Sample134)


title: Frontal of subject 502 (Sample150)


title: Visual Cortex of subject 421 (Sample156)


title: Occipital of subject 215 (Sample136)


title: CRBM of subject 351 (Sample126)


title: Hippocampus of subject 204 (Sample129)


title: Visual Cortex of subject 283 (Sample137)


title: Frontal of subject 339 (Sample133)


title: Caudate Nucleus of subject 393 (Sample138)


title: Hippocampus of subject 165 (Sample135)


title: CRBM of subject 45 (Sample130)


title: CRBM of subject 299 (Sample122)


title: CRBM of subject 328 (Sample123)


title: Occipital of subject 178 (Sample125)


title: CRBM of subject 204 (Sample121)


title: Frontal of subject 328 (Sample127)


title: Occipital of subject 131 (Sample124)


title: Hippocampus of subject 239 (Sample120)


title: Hippocampus of subject 45 (Sample119)


title: Parietal of subject 437 (Sample118)


title: Mid of subject 299 (Sample114)


title: Parietal of subject 315 (Sample113)


title: Temporal of subject 165 (Sample142)


title: Caudate Nucleus of subject 407 (Sample107)


title: Hippocampus of subject 57 (Sample116)


title: Visual Cortex of subject 267 (Sample111)


title: Occipital of subject 502 (Sample182)


title: Motor Cortex of subject 513 (Sample109)


title: Hippocampus of subject 185 (Sample117)


title: Hippocampus of subject 339 (Sample115)


title: Occipital of subject 45 (Sample108)


title: Mid of subject 225 (Sample105)


title: Frontal of subject 254 (Sample100)


title: Frontal of subject 131 (Sample106)


title: Frontal of subject 393 (Sample132)


title: Mid of subject 45 (Sample97)


title: Caudate Nucleus of subject 467 (Sample96)


title: Mid of subject 254 (Sample94)


title: Mid of subject 379 (Sample93)


title: Hippocampus of subject 7 (Sample103)


title: Motor Cortex of subject 467 (Sample99)


title: Mid of subject 57 (Sample110)


title: Caudate Nucleus of subject 267 (Sample112)


title: Cingulate Gyrus of subject 421 (Sample95)

value: Brain Cingulate Gyrus


title: Hippocampus of subject 455 (Sample98)


title: Hippocampus of subject 34 (Sample91)


title: Sensory Cortex of subject 421 (Sample104)


title: Sensory Cortex of subject 467 (Sample101)


title: Mid of subject 339 (Sample89)


title: Cingulate Gyrus of subject 407 (Sample88)


title: Occipital of subject 339 (Sample86)


title: Cingulate Gyrus of subject 71 (Sample87)


title: Hippocampus of subject 194 (Sample78)


title: Mid of subject 149 (Sample79)


title: Hippocampus of subject 215 (Sample81)


title: Frontal of subject 45 (Sample68)


title: Visual Cortex of subject 467 (Sample84)


title: Frontal of subject 165 (Sample82)


title: Parietal of subject 267 (Sample72)


title: Parietal of subject 393 (Sample85)


title: Frontal of subject 25 (Sample71)


title: Hippocampus of subject 328 (Sample90)


title: Mid of subject 131 (Sample64)


title: Parietal of subject 513 (Sample102)


title: Temporal of subject 225 (Sample77)


title: Motor Cortex of subject 437 (Sample70)

value: Brain Motor Cortex


title: Occipital of subject 34 (Sample65)


title: Mid of subject 107 (Sample66)


title: CRBM of subject 149 (Sample83)


title: Caudate Nucleus of subject 421 (Sample74)


title: Mid of subject 131 (Sample76)


title: Mid of subject 215 (Sample73)


title: Parietal of subject 407 (Sample75)

value: Brain Parietal


title: Sensory Cortex of subject 365 (Sample80)


title: Mid of subject 107 (Sample92)


title: Hippocampus of subject 239 (Sample63)


title: Cingulate Gyrus of subject 393 (Sample69)


title: Hippocampus of subject 351 (Sample61)


title: Parietal of subject 315 (Sample60)


title: Temporal of subject 17 (Sample59)


title: Frontal of subject 407 (Sample50)


title: Caudate Nucleus of subject 283 (Sample62)


title: Motor Cortex of subject 407 (Sample56)


title: Visual Cortex of subject 365 (Sample55)

value: Brain Visual Cortex


title: Frontal of subject 239 (Sample52)

value: F


title: Frontal of subject 455 (Sample58)

value: female


title: Cingulate Gyrus of subject 437 (Sample51)


title: Hippocampus of subject 178 (Sample53)


title: Mid of subject 299 (Sample42)


title: Occipital of subject 239 (Sample34)


title: Sensory Cortex of subject 407 (Sample40)


title: Cingulate Gyrus of subject 87 (Sample45)


title: Cingulate Gyrus of subject 365 (Sample67)


title: Frontal of subject 185 (Sample36)


title: Cingulate Gyrus of subject 513 (Sample46)


title: Parietal of subject 513 (Sample47)


title: Cingulate Gyrus of subject 267 (Sample38)


title: Parietal of subject 365 (Sample48)


title: Frontal of subject 379 (Sample44)


title: Parietal of subject 365 (Sample32)


title: Temporal of subject 45 (Sample37)


title: Frontal of subject 448 (Sample35)


title: Frontal of subject 17 (Sample41)


title: Cingulate Gyrus of subject 315 (Sample33)


title: CRBM of subject 25 (Sample57)

value: Brain CRBM


title: Motor Cortex of subject 283 (Sample49)


title: Frontal of subject 365 (Sample30)


title: Visual Cortex of subject 437 (Sample31)


title: Temporal of subject 215 (Sample25)


title: Mid of subject 351 (Sample27)


title: Temporal of subject 239 (Sample28)


title: Parietal of subject 437 (Sample54)


title: Temporal of subject 351 (Sample39)


title: Frontal of subject 437 (Sample26)


title: Frontal of subject 513 (Sample21)


title: Temporal of subject 239 (Sample24)


title: Motor Cortex of subject 365 (Sample29)


title: Temporal of subject 204 (Sample43)


title: Motor Cortex of subject 315 (Sample23)


title: Temporal of subject 107 (Sample18)


title: Hippocampus of subject 165 (Sample17)


title: Sensory Cortex of subject 87 (Sample16)

value: Brain Sensory Cortex


title: Occipital of subject 149 (Sample22)


title: Parietal of subject 283 (Sample12)


title: CRBM of subject 339 (Sample14)


title: Temporal of subject 7 (Sample8)


title: CRBM of subject 239 (Sample6)


title: Hippocampus of subject 131 (Sample15)

value: Brain Hippocampus


title: CRBM of subject 254 (Sample9)


title: CRBM of subject 185 (Sample7)


title: CRBM of subject 107 (Sample10)


title: Occipital of subject 25 (Sample20)


title: Visual Cortex of subject 71 (Sample13)


title: Occipital of subject 107 (Sample2)


title: genomic DNA from BoneMarrow of a 112 year old female subject (Sample63)

source_name: BoneMarrow

value: Bone Marrow


title: Temporal of subject 57 (Sample5)


title: Occipital of subject 448 (Sample3)


title: CRBM of subject 215 (Sample11)


title: genomic DNA from Cartilage of a 112 year old female subject (Sample57)

source_name: Cartilage

value: Cartilage


title: genomic DNA from Muscle of a 112 year old female subject (Sample64)

source_name: Muscle

value: Muscle


title: Occipital of subject 487 (Sample4)


title: Parietal of subject 267 (Sample1)

source_name: Brain Parietal

value: M


title: genomic DNA from Esophagus of a 112 year old female subject (Sample58)

source_name: Esophagus

value: Esophagus


title: genomic DNA from Lung of a 112 year old female subject (Sample60)

source_name: Lung

value: Lung


title: genomic DNA from Thyroid of a 112 year old female subject (Sample56)

source_name: Thyroid

value: Thyroid


title: genomic DNA from Pericardium of a 112 year old female subject (Sample52)

source_name: Pericardium

value: Pericardium


title: genomic DNA from BrainFrontal of a 112 year old female subject (Sample59)

source_name: BrainFrontal

value: Brain Frontal


title: genomic DNA from Bone of a 112 year old female subject (Sample62)

source_name: Bone

value: Bone


title: Frontal of subject 149 (Sample19)

source_name: Brain Frontal

value: male


title: genomic DNA from BrainOccipital of a 112 year old female subject (Sample51)

source_name: BrainOccipital

value: Brain Occipital


title: genomic DNA from Aorta of a 112 year old female subject (Sample53)

source_name: Aorta

value: Aorta


title: genomic DNA from Pancreas of a 112 year old female subject (Sample44)

source_name: Pancreas

value: Pancreas

value: female


title: genomic DNA from Buccal of a 112 year old female subject (Sample55)

source_name: Buccal

value: Buccal


title: genomic DNA from Skin of a 112 year old female subject (Sample54)

source_name: Skin

value: Skin


title: 2614, 4 d after Fg inoculation, rep 2

city: Ottawa

first: Thérèse

last: Ouellet

state: ON

address: 960 Carling Ave, room 2091

department: Eastern Cereal and Oilseed Research Centre

country: Canada

institute: Agriculture and Agri-Food Canada

description:
2614 +2DL+3BS+5A Fg rep2
Gene expression data from Fg-inoculated 2614 spikelets

hyb_protocol: According to Affymetrix instructions for the GeneChip® HT One-Cycle Target Labeling and Controls Kit. All samples were processed in one experimental batch.

scan_protocol: According to Affymetrix instructions for the GeneChip® HT One-Cycle Target Labeling and Controls Kit, using the Affymetrix GeneChip® 3000 Scanner.

data_processing: The probe-level data for the whole profiling experiment were assembled into one dataset using the Robust Multichip Analysis (Irizarry et al, 2002) implemented in the software Acuity 4.0 (Molecular Devices, CA, USA), with quantile normalization and summarization by median polish.

organism: Triticum aestivum

source_name: Fusarium graminearum-inoculated 2614 spikelets_4 d

growth_protocol: Plants were grown in growth cabinets at 20 C/16 hrs daylight; 16 C/8 hrs night until heads reach mid anthesis; then they were moved to the misting room.

extract_protocol: Total RNA from each sample was isolated using a modified form of the guanidine isothiocyanate-cesium chloride method of Chirgwin et al (Biochem. 18: 5294-5299, 1979), as outlined in Ohan and Heikkila (Dev. Genet. 17: 176-184, 1995).  The RNA samples were treated with an RNase-free DNase (Qiagen, Mississauga, Canada) and cleaned up using the RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: Wheat heads at mid-anthesis were inoculated using the point inoculation method: 10 µl of a 100,000 spores/ml suspension of the isolate Fusarium graminearum strain DAOM 180378 was point-inoculated into each of two basal florets of each developed spikelet of the wheat heads.  Water was used as a mock-inoculation treatment.  The inoculated plants were mist-irrigated for 10 second intervals every 15 minutes for 48 hours to maintain high humidity at a temperature of 25 oC. Five treated heads were used for each biological replicate, and inoculated spikelets were sampled at 4 days after inoculation.  The sampled tissues were immediately frozen in liquid nitrogen and stored at -80 C until used.

tag: wheat line

value: near isogenic spring wheat line 2614

value: inoculated spikelets

tag: tissue age

value: heads after mid-anthesis

tag: inoculated with

value: Fusarium graminearum


title: 2614, 4 d after Fg inoculation, rep 3

description:
2614 +2DL+3BS+5A Fg rep3
Gene expression data from Fg-inoculated 2614 spikelets

label_protocol: According to Affymetrix instructions for the GeneChip® HT One-Cycle Target Labeling and Controls Kit. All samples were processed in one experimental batch.


title: genomic DNA from Diaphragm of a 112 year old female subject (Sample49)

source_name: Diaphragm

value: Diaphragm

tag: subject id

tag: Sex


title: genomic DNA from BrainTemporal of a 112 year old female subject (Sample46)

source_name: BrainTemporal

value: Brain Temporal

tag: predicted gender

tag: age


title: genomic DNA from Spleen of a 112 year old female subject (Sample40)

source_name: Spleen

value: Spleen

tag: dna methylation age


title: genomic DNA from Breast of a 112 year old female subject (Sample47)

source_name: Breast

value: Breast

tag: cor sample vs gold standard


title: genomic DNA from Adrenal of a 112 year old female subject (Sample45)

source_name: Adrenal

value: Adrenal

tag: mean abs difference sample vs gold standard


title: 2557, 4 d after Fg inoculation, rep 2

description:
2557 +2DL+5A Fg rep2
Gene expression data from Fg-inoculated 2557 spikelets

source_name: Fusarium graminearum-inoculated 2557 spikelets_4 d

value: near isogenic spring wheat line 2557


title: 2557, 4 d after Fg inoculation, rep 3

description:
2557 +2DL+5A Fg rep3
Gene expression data from Fg-inoculated 2557 spikelets


title: genomic DNA from LymphNodes of a 112 year old female subject (Sample43)

source_name: LymphNodes

value: LymphNodes


title: genomic DNA from Kidney of a 112 year old female subject (Sample50)

source_name: Kidney

value: Kidney


title: 2557, 4 d after Fg inoculation, rep 1

description:
2557 +2DL+5A Fg rep1
Gene expression data from Fg-inoculated 2557 spikelets


title: genomic DNA from Heart of a 112 year old female subject (Sample42)

source_name: Heart

value: Heart


title: genomic DNA from Bone of a 112 year old female subject (Sample38)

source_name: Bone

value: Bone


title: 2614, 4 d after Fg inoculation, rep 1

description:
2614 +2DL+3BS+5A Fg rep1
Gene expression data from Fg-inoculated 2614 spikelets


title: 2543, 4 d after Fg inoculation, rep 3

description:
2543 +2DL+3BS Fg rep3
Gene expression data from Fg-inoculated 2543 spikelets

source_name: Fusarium graminearum-inoculated 2543 spikelets_4 d

value: near isogenic spring wheat line 2543


title: genomic DNA from BrainMidbrain of a 112 year old female subject (Sample36)

source_name: BrainMidbrain

value: Brain MidBrain

value: female


title: genomic DNA from Adipose of a 112 year old female subject (Sample37)

source_name: Adipose

value: Adipose


title: genomic DNA from Blood of a 112 year old female subject (Sample61)

source_name: Blood

value: Blood


title: genomic DNA from Stomach of a 112 year old female subject (Sample48)

source_name: Stomach

value: Stomach


title: genomic DNA from Liver of a 112 year old female subject (Sample35)

source_name: Liver

value: Liver


title: genomic DNA from Stomach of a 112 year old female subject (Sample32)


title: genomic DNA from Colon of a 112 year old female subject (Sample41)

source_name: Colon

value: Colon


title: 2543, 4 d after Fg inoculation, rep 2

description:
2543 +2DL+3BS Fg rep2
Gene expression data from Fg-inoculated 2543 spikelets

value: inoculated spikelets

value: heads after mid-anthesis

value: Fusarium graminearum


title: genomic DNA from Breast of a 112 year old female subject (Sample31)

value: Breast


title: 2543, 4 d after Fg inoculation, rep 1

description:
2543 +2DL+3BS Fg rep1
Gene expression data from Fg-inoculated 2543 spikelets


title: 2598, 4 d after Fg inoculation, rep 3

description:
2598 +3BS Fg rep3
Gene expression data from Fg-inoculated 2598 spikelets

source_name: Fusarium graminearum-inoculated 2598 spikelets_4 d

value: near isogenic spring wheat line 2598


title: genomic DNA from BoneMarrow of a 112 year old female subject (Sample39)

source_name: BoneMarrow

value: Bone Marrow


title: genomic DNA from LymphNodes of a 112 year old female subject (Sample27)

value: LymphNodes


title: genomic DNA from BrainCRBM of a 112 year old female subject (Sample33)

source_name: BrainCRBM

value: Brain CRBM


title: 2598, 4 d after Fg inoculation, rep 1

description:
2598 +3BS Fg rep1
Gene expression data from Fg-inoculated 2598 spikelets


title: genomic DNA from BrainHippocampus of a 112 year old female subject (Sample34)

source_name: BrainHippocampus

value: Brain Hippocampus


title: genomic DNA from Heart of a 112 year old female subject (Sample26)

value: Heart


title: genomic DNA from Pancreas of a 112 year old female subject (Sample28)

source_name: Pancreas

value: Pancreas


title: genomic DNA from Adrenal of a 112 year old female subject (Sample29)

source_name: Adrenal

value: Adrenal

value: female


title: 2890, 4 d after Fg inoculation, rep 3

description:
2890 null Fg rep3
Gene expression data from Fg-inoculated 2890-spikelets

source_name: Fusarium graminearum-inoculated 2890 spikelets_4 d

value: near isogenic spring wheat line 2890


title: 72h_BM-9

city: Houston

first: Wencai

last: Ma

address: 7455 Fannin st

institute: MD Anderson Cancer Center

hyb_protocol: As per Illumina instructions, with detection by Streptavidin-Cy3 conjugate.

scan_protocol: As per instructions for Illumina BeadArray Reader

data_processing: The non-normalized data were generated by GenomeStudio. The normalized data were generated from bead-level data by methods previously described (PMID: 20805315). In brief, bead-level values were quantile-normalized, adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, and then averaged to give a single probe-level value.

source_name: Human AML cell line OCI-AML3

label_protocol: 100 ng of total RNA was first reverse-transcribed and amplified with unlabeled ribonucleotides, using the MessageAmp™ II aRNA Amplification Kit (Ambion). 1000 ng of aRNA was then amplified and biotin-labeled using an Illumina TotalPrep RNA Amplification kit (Ambion).

extract_protocol: Total RNA was extracted using the RNAqueous kit (Ambion, Austin, TX).

treatment_protocol: LY2510924 treatment was 2.5 mg/kg subcutaneously, daily

tag: strain

value: NOD/SCID/IL-2rγnull (NSG)

value: 72 hours with daily injections of LY2510294

tag: cell source

value: bone marrow


title: 2598, 4 d after Fg inoculation, rep 2

description:
2598 +3BS Fg rep2
Gene expression data from Fg-inoculated 2598 spikelets

value: inoculated spikelets


title: genomic DNA from Muscle of a 112 year old female subject (Sample24)

source_name: Muscle

value: Muscle


title: genomic DNA from Colon of a 112 year old female subject (Sample25)

value: Colon


title: genomic DNA from Blood of a 112 year old female subject (Sample21)

value: Blood