title: KRas(G12D/+);CreT Mouse Mammary Tumor: Ras RNA 11

source_name: Mouse Mammary Tumor B3117 5R


title: AN3-CA at C2, biological rep1

status: Public on Sep 17 2015

type: RNA

city: Seoul

first: yeonui

last: Kwak

address: Room#2224,Building L2, Hwarangno 14-gil 5, Seongbuk-Gu

country: South Korea

institute: Korea Institute of Science and Technology

description:
AN3-CA_C2-1
gene expression data from the inactivated state by co-treatment of aFGF and AZD4547. i.e, after inhibition of Fibroblast growth factor receptors

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Robust Multi-array Analysis(RMA) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: AN3-CA cells after 18 hr treatment of AZD4547 in the presence of aFGF stimulus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: AN3-CA cells that were suspended in DMEM supplemented with 10% FBS, 100U/mL penicllin, and 100ug/mL streptomycin, were plated into six  60mm dishes, followed by 18-hr incubation with different conditions C0-C2

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

treatment_protocol: AN3-CA cells were cultured in 6mm dishes for 24hrs, and media was changed to serum-free media treated with DMSO control or cotreated with 300nM AZD4547(or 0.5% DMSO)  in the presence of aFGF(10ng/mL). After 18hr treatment, total RNA was extracted.

tag: tissue

value: endometrium

tag: cell line

value: endometrial cancer cell line AN3-CA

tag: treatment


title: 391 EXPT: A549 CONTROL_2

status: Public on Sep 16 2015

city: Houston

first: David

middle: S

last: Loose

state: TX

address: 6431 Fannin St, MSB 4.130

department: Integrative Biology & Pharm

country: USA

institute: University of Texas

hyb_protocol: Standard Illumina

scan_protocol: Standard Illumina

data_processing: Genome Studio v2011.1

label_protocol: Standard Illumina

growth_protocol: Cells were grown in serum or complete medium to ~ 80% confluency.

extract_protocol: RNA was isolated using TRI-Reagent.

treatment_protocol: Cells were serum-straved overnight (16-18 h) and then treated with medium alone or poultry dust. extract


title: AN3-CA at C2, biological rep2

description:
AN3-CA_C2-2
gene expression data from the inactivated state by co-treatment of aFGF and AZD4547. i.e, after inhibition of Fibroblast growth factor receptors

value: AZD4547 in the presence of aFGF stimulus


title: MMTV-Neu Mouse Mammary Tumor: Ras RNA 4

city: Toronto

first: Sean

middle: Eoin

last: Egan

state: Ontario

address: 686 Bay Street, Room 15-9704

department: Program in Developmental and Stem Cell Biology

country: Canada

institute: The Hosital for Sick Children

description: Gene expression data from MMTV-Neu Solid nodular carcinoma

hyb_protocol: Affymetrix Mouse Gene 2.0 st microarray experiment were performed by the Centre of Applied Genomics (HSC, Toronto)

data_processing: Microarray Data were normalized using RMA method via Partek software and absolute expression values were obtained

organism: Mus musculus

source_name: Mouse Mammary Tumor B3644 2R

growth_protocol: Samples from independent primary mammary tumors from KRas(G12D/+);CreT, R26(H1047R/+);KRas(G12D/+);CreT, and MMTV-Neu models were harvested into RNAlater and frozen at -80

extract_protocol: Total RNA was extracted with Qiagen RNAeasy kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Total RNA obtained from primary tumors were used for microarray analysis to determine differentially regulated genes among different mouse models.  Cluster analysis and pathway analysis based on gene expression were then performed to determine significant genes/pathways

value: Primary Mammary Tumor

tag: genotype

value: MMTV-Neu

tag: pathology

value: Solid nodular carcinoma


title: R26(H1047R/+);KRas(G12D/+);CreT Mouse Mammary Tumor: Ras RNA 22

description: Gene expression data from R26(H1047R/+);KRas(G12D/+);CreT Complex adenocarcinoma

scan_protocol: Affymetrix Mouse Gene 2.0 st microarray experiment were performed by the Centre of Applied Genomics (HSC, Toronto)

source_name: Mouse Mammary Tumor B3749 5R

value: Complex adenocarcinoma


title: MMTV-Neu Mouse Mammary Tumor: Ras RNA 5

source_name: Mouse Mammary Tumor 4234 2L

label_protocol: Affymetrix Mouse Gene 2.0 st microarray experiment were performed by the Centre of Applied Genomics (HSC, Toronto)


title: MMTV-Neu Mouse Mammary Tumor: Ras RNA 8

source_name: Mouse Mammary Tumor B2101 1R


title: CSM2

city: Edmonton

first: Stephen

last: Tsoi

state: Alberta

address: 4-32G Agriculture/Forestry Cen

department: AFNS

institute: University of Alberta

description: Biological replicate 2 of 3.

hyb_protocol: Hybridization mixture and washing procedure were prepared and performed according to Agilent Gene Expression Hybridization Kit 60-mer oligo microarray protocol version 4.0.

scan_protocol: Array slides were immediately scanned at 5 μm resolution using an Axon 4200AL scanner (635 nm for Cy5 and at 532 nm for Cy3) with the autoscan feature from the default setting. TIFF images were analysed by software  Gene Pix Pro 6.0.

data_processing: FlexArray software version 1.6.3 (http://genomequebec.mcgill.ca/) was used for data normalization following first with simple background subtraction, LOWESS normalization within and between arrays.

organism: Sus scrofa

label_protocol: 200ng of total RNA with adding of external RNA spike-in was used for aRNA synthesis according to the manual provided by Low Input Quick Amp Labeling Kit (Agilent Technologies, Inc., Santa Clara, CA, USA) for two-color processing. Antisense RNA (aRNA) labelling with Cy3 and Cy5 was performed according to the kit under ozone free environmental chamber.

extract_protocol: Direct-zol™ RNA MiniPrep kit (Zymo Research Corporation, Irvine, CA, USA) was used for RNA extraction with in-column DNase treatment to remove DNA.

treatment_protocol:
Sows were euthanized at day 30 of gestation and embryos were recovered for DNA and RNA extraction.
Embryos were collected at Day 30 post-ovulation from sows submitted to  three different treatment groups such as C group; n= 6,  FE group ; n=3 and SE group; n=3 group. Three males and three females D30E were pooled separately from each sow in each treatment group ending up with 24 distinct biological replicates.

tag: developmental stage

value: Day 30 embryo

tag: Sex

value: male

tag: treatment group

value: Control


title: KRas(G12D/+);CreT Mouse Mammary Tumor: Ras RNA 13

description: Gene expression data from KRas(G12D/+);CreT Complex adenocarcinoma

source_name: Mouse Mammary Tumor B4228 4L


title: SCM3

description: Dye-swap replicate of biological replicate 3


title: CSM3

description: Biological replicate 3 of 3.


title: KRas(G12D/+);CreT Mouse Mammary Tumor: Ras RNA 10

source_name: Mouse Mammary Tumor B3033 2L


title: 391 EXPT: BEAS2B DUST EXTRACT 0.25 1H_2

value: BEAS 2B


title: SCM1

description: Dye-swap replicate of biological replicate 1


title: FCM1


title: VMM17 plx rep 3

city: Charlottesville

first: Stefan

last: Bekiranov

state: VA

address: 1340 Jefferson Park Avenue

department: Biochemistry and Molecular Genetics

institute: University of Virginia

description: Replicate 3

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: VSN By R package lumi

source_name: VMM17 plx

label_protocol: Biotin labeled RNA was hybridized to Illumina 3′IVT human HT-12 BeadChip arrays.

growth_protocol: Cells are grown in RPMI + 5% FBS and passaged at intervals of 80% confluence.

extract_protocol: RNA was isolated using the Qiashredder (Qiagen) and RNeasy Mini Kit (Qiagen). RNA was quantified on the NanoDrop 2000 spectrophotometer (Thermo Scientific) and RNA quality was inspected on a 1% agarose gel.

treatment_protocol: Cells were plated in RPMI + 5% FBS and incubated overnight before being treated with 125 nM plx4720 in phenol red–free RPMI-1640 without FBS for 8 hours at 37°C.

tag: braf status


title: FCM3


title: A375 control rep 6

description: Replicate 6

source_name: A375 control

growth_protocol: Cells are grown in RPMI + 10% FBS and passaged at intervals of 80% confluence.

treatment_protocol: Cells were plated in RPMI + 5% FBS and incubated overnight before being treated with vehicle control in phenol red–free RPMI-1640 without FBS for 8 hours at 37°C.


title: Parasitized by Pales pavida vs control in silkgland

city: Tsukuba

first: Yuki

last: Nakamura

state: Ibaraki

address: 1-2 Owashi

country: Japan

institute: National Institute of Agrobiological Sciences

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent Gene Expression Hybridization Kit) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed with AgilentExpression Wash Buffer Kit.

scan_protocol: Scanned on an Agilent G2565BA scanner with 5 μm scan resolution.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 9.1)

organism: Bombyx mori

source_name: control

label_protocol: Total RNA (500 ng each for Cy3 and Cy5) was processed to cRNA using Agilent Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions.

extract_protocol: Total RNA was isolated from the tissues using TRIzol reagent (Invitrogen) following manufacturer’s protocol.

treatment_protocol: Day 0 of 5th instar silkworm larvae were offered to the tachnid flies (D. inconspicuoides, E. japonica) in transparent ventilated cages. Silkworm-fly interactions were monitored to ensure only 3 eggs were laid per host. Parasitization  by P. pavida was achieved by inoculating three eggs on to the silkworm’s artificial diet. Parasitized larvae were maintained at 25oC and after 5 days, hemocytes and fat body were collected for extracting RNA.

value: Day 0 of 5th instar silkworm larvae

value: silkgland

source_name: Parasitized by Pales pavida


title: CSM1

description: Biological replicate 1 of 3.


title: SCF1

value: female


title: CFM1

description: Biological replicate 1 of 3.


title: VMM15 control rep 3

description: Replicate 3

source_name: VMM15 control


title: VMM39 plx rep 3

description: Replicate 3

source_name: VMM39 plx

value: WT/WT


title: CFM2

description: Biological replicate 2 of 3.


title: CSF3

description: Biological replicate 3 of 3.


title: VMM12 plx rep 3

description: Replicate 3

source_name: VMM12 plx


title: CSF2

description: Biological replicate 2 of 3.


title: Dhh1-GFP_YPD_ip_rep1

city: Pittsburgh

first: Gregory

last: Cary

state: PA

address: 4400 Fifth Ave

department: Biological Sciences

institute: Carnegie Mellon University

description: Detection with S9.6 antibody & Cy3 secondary

hyb_protocol: 5ug of Total RNA or 200ng of IP RNA was fragmented and hybridized to the array according to manufactuers directions for 17h at 65ºC. Arrays were washed in 6x SSPE and 0.005% N-lauronylsarcosine for 1min at RT and then in 0.6x SSPE, 0.005% N-lauronylsarcosine for 1min at 30ºC. Arrays were then incubated in 3 ng/ml S9.6 antibody (ATCC clone HB-8730) for 1hr at 25ºC and washed 4x in SSPE, 0.01% Tween. Primary antibody was detected with a Cy3 conjugated anti-mouse secondary antibody incubated at 6 ng/ml for 1hr at 25ºC followed by 4 washes in SSPE, 0.01% Tween. Prior to scanning, slides were dried by centrifugation 5 minutes at 600 rpm.

scan_protocol: Agilent G2565CA Microarray Scanner and Feature Extraction software

data_processing: Background signal for each hybridization was measured based on the median intensity from 1,573 array features that do not hybridize to a yeast transcript and subtracted from all features. Signals were then log transformed and pairs of total RNA and IP RNA arrays were normalized by cyclic loess as implemented in the Limma Bioconductor package (. Normalized signals for transcript replicate probes were averaged and transcript levels were thresholded to remove low intensity, high variability signal or high intensity, near saturation signal.

label: No label

organism: Saccharomyces cerevisiae

source_name: Dhh1-GFP IP RNA, +Glucose

label_protocol: RNA was not labeled prior to hybridization. RNA:DNA hybrids were detected using the S9.6 monoclonal antibody (ATCC clone HB-8730)

growth_protocol: Cells were grown in 2L rich media (YPD) to log phase (OD600 = 1.0) at which point they were either quickly collected or changed to media without glucose (YEP) for 30 minutes at which point they were collected. Cells were collected by filtration, concentrated into conical tubes by a low speed, 500g centrifugation and flash frozen in liquid nitrogen.

extract_protocol: RNA was extracted from total and IP fractions in parallel. To each fraction an equal volume of 1% SDS, 10mM Tris (pH 7.5) and 1mM EDTA was added followed by a total equal volume of acid phenol (pH 4) and incubated at 65ºC for 60min. Phenol:chloroform extraction was performed on the acqueous phase followed by a precipitation in cold ethanol. Pellets were washed in 70% ethanol, resuspended in TE and stored at -80ºC.

treatment_protocol: Cell pellets were lysed by grinding in a Retsch PM-100 planetary ball mill and pellets and resultant pulvarized cell powder were maintained at -80ºC for the duration of lysis. Cell powder was resuspended in a buffer optimized to maintain RNP complexes and subjected to an anti-GFP immunoprecipitation (IP) protocol using anti-GFP conjugated to magnetic beads. RNA was eluted from a fraction of the beads after the IP by incubating the beads in 1% SDS, 30 mM Hepes (pH 7.4), with protease and RNase inhibitors for 30 minutes at room temperature. RNA was extracted from a small amount of the resuspended cell powder set aside prior to IP (Total RNA) as well as from the fraction eluted off the beads after the IP (IP RNA).

tag: strain

value: YAD49, Dhh1-GFP

tag: condition

value: +glucose

tag: molecule type

value: IP RNA


title: SLM2 plx rep 3

description: Replicate 3

source_name: SLM2 plx


title: CFM3

description: Biological replicate 3 of 3.


title: SCF2

description: Dye-swap replicate of biological replicate 2


title: DM122 control rep 3

description: Replicate 3

source_name: DM122 control


title: DM6 plx rep 2

description: Replicate 2

source_name: DM6 plx


title: DM6 plx rep 3

description: Replicate 3


title: 452 EXPT: BEAS2B DUST ETRACT 0.25 3H_2


title: VMM5A control rep 6

description: Replicate 6

source_name: VMM5A control


title: SCF3


title: CSF1

description: Biological replicate 1 of 3.


title: VMM18 control rep 6

description: Replicate 6

source_name: VMM18 control


title: STKHLM8462_tumor

type: genomic

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

country: United Kingdom

institute: Cancer Research UK Cambridge Institute

description: tumor robotic radical prostatectomy tissue from patient STKHLM8462

hyb_protocol: Standard Affymetrix SNP6 hyb protocol

scan_protocol: Standard Affymetrix SNP6 scan protocol

data_processing:
SNP6 data were analyzed in ASCAT (van Loo et al., 2010). Processed data file (reporting Log R Ratio and B Allele Freq) is linked as a supplementary file on the Series record.
SNP6 genotype array data for matched tumor and benign or matched tumor and blood samples.

molecule: genomic DNA

label_protocol: Standard Affymetrix SNP6 label protocol

growth_protocol: N/A - surgical tissue or whole blood samples

extract_protocol: Qiagen AllPrep, according to manufacturer's instructions

treatment_protocol: tumor tissues were identified and prepared from RP surgical tissue as described in Warren et al. (2013).  The Prostate.  73:  194-202.  Matched whole blood samples were obtained from selected samples at treatment clinics.

tag: patient

tag: sample type

value: tumor

value: tissue core

tag: tumor gleason

tag: tumor %

tag: (derived data) iclusterplus group

tag: extra-capsular extension (ece)

value: N

tag: positive surgical margins (psm)

tag: biochemical relapse (bcr)

tag: time to bcr (months)

tag: tmprss2/erg gene fusion status

value: unknown


title: SKMEL2 control rep 6

description: Replicate 6

source_name: SKMEL2 control

tag: cell line


title: FCF3

tag: developmental stage

tag: Sex


title: VMM15 plx rep 3

description: Replicate 3

source_name: VMM15 plx

tag: braf status


title: DM13 plx rep 3

description: Replicate 3

source_name: DM13 plx


title: CFF3

description: Biological replicate 3 of 3.

tag: treatment group


title: STKHLM8462_blood

description: whole blood sample from patient STKHLM8462

source_name: whole blood sample

value: STKHLM8462 blood

value: blood

tag: tissue

value: see matched tumor sample


title: CFF1

description: Biological replicate 1 of 3.

value: Day 30 embryo


title: Rat Control 2

city: San Francisco

first: Katerina

last: Akassoglou

state: CA

address: 1650 Owens St

institute: Gladstone Institutes

description:
Gene expression data from unstimulated microglia
Rat_06.A-1-unstimulated_vitro_II

hyb_protocol: GeneChip Expression Analysis Technical Manual 702232 Rev. 3

data_processing: Microarrays were normalized for array-specific effects using Affymetrix's Robust Multi-Array (RMA) normalization. Normalized arrays values were reported on a log2 scale. For statistical analyses, we removed all array probesets where no experimental groups had an average log2 intensity greater than 3.0. Linear models were fitted for each gene using the Bioconductor limma package in R. Moderated t-statistics, fold-change and the associated P-values were calculated for each gene. To account for the fact that thousands of genes were tested, we reported false discovery rate (FDR)-adjusted values, calculated using the Benjamini-Hochberg method.

organism: Rattus norvegicus

source_name: RNA prepared from unstimulated microglia

label_protocol: NuGEN Ovation Pico WTA System V2 and NuGEN Encore Biotin protocol

growth_protocol: Microglia were prepared from neonatal rat pups at postnatal day 2-3 and plated into PDL-coated flasks with DMEM containing 10% FBS. On day 4 in vitro, microglia were shaken off the cortical cell layer.

extract_protocol: RNA extraction from microglia was performed using RNeasy kit according to the manufacturer's instructions (Qiagen, Valencia, CA).  Genomic DNA was removed during the RNeasy cleanup using Rnase-Free Dnase set (Qiagen, Valencia, CA).

treatment_protocol: Rat microglia were stimulated with fibrin for 6 hr.

tag: cell type

value: Microglia

tag: protocol

value: unstimulated


title: STKHLM8453_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM8453

tag: patient

tag: sample type


title: Rat Fibrin 1

description:
Gene expression data from fibrin-stimulated microglia
Rat_07.B-fibrin_vitro_I

source_name: RNA prepared from microglia treated with fibrin for 6 hr

value: fibrin-stimulated


title: CFF2

description: Biological replicate 2 of 3.

value: Control


title: FCF1

value: female


title: VMM12 control rep 3

description: Replicate 3

source_name: VMM12 control


title: FCF2


title: FCM2

value: male


title: VMM17 plx rep 2

description: Replicate 2

source_name: VMM17 plx


title: VMM39 control rep 6

description: Replicate 6

source_name: VMM39 control

value: WT/WT


title: A375 control rep 5

description: Replicate 5

source_name: A375 control


title: VMM18 control rep 5

description: Replicate 5


title: SLM2 plx rep 2

description: Replicate 2


title: VMM5A control rep 5

description: Replicate 5


title: DM13 plx rep 2

description: Replicate 2


title: VMM39 control rep 5

description: Replicate 5


title: DM122 control rep 2

description: Replicate 2


title: STKHLM8393_blood

description: whole blood sample from patient STKHLM8393

value: STKHLM8393 blood

tag: tumor gleason

tag: tumor %


title: STKHLM7493_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM7493

tag: (derived data) iclusterplus group

tag: extra-capsular extension (ece)

value: Y


title: STKHLM8453_blood

description: whole blood sample from patient STKHLM8453

value: STKHLM8453 blood

tag: positive surgical margins (psm)

tag: biochemical relapse (bcr)


title: STKHLM7493_adjacent_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM7493

value: benign

value: tissue core

tag: time to bcr (months)

tag: tmprss2/erg gene fusion status


title: STKHLM8393_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM8393

value: tumor

value: N

value: unknown


title: STKHLM7472_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM7472


title: STKHLM7472_blood

description: whole blood sample from patient STKHLM7472

value: STKHLM7472 blood

value: blood

value: see matched tumor sample


title: 391 EXPT: A549 CONTROL_1

tag: cell line


title: SLM2 plx rep 1

description: Replicate 1


title: DM6 plx rep 1

description: Replicate 1


title: 252800511556-7_siRNAs TL RNYs Replicate 3

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: siRNAs TL RNYs Replicate 3

hyb_protocol: Agilent : 600.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: OneChannelGui analysis using custom R script with interslide quantile normalization.

source_name: BMDMs_TL RNYs_siRNA

label_protocol:
Agilent - Low RNA input QuickAmp
cRNA Agilent

extract_protocol: Qiagen

tag: strain

tag: gender

value: Bone marrow-derived macrophages (BMDMs)

tag: transfected with

value: siRNA against terminal loop of RNY

tag: amount (µg)

tag: rin number


title: 252800511556-4_siRNA Ct Replicate 1

description: siRNA Ct Replicate 1

source_name: BMDMs_cotnrol siRNA

tag: tissue

value: Control (Ct) siRNA


title: 252800511556-1_siRNAs TL RNYs Replicate 2

description: siRNAs TL RNYs Replicate 2


title: 252800511556-3_siRNAs TL RNYs Replicate 1

description: siRNAs TL RNYs Replicate 1


title: VMM17 plx rep 1

description: Replicate 1

tag: braf status


title: STKHLM7421_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM7421

tag: patient

tag: sample type


title: 252800511556-8_siRNA Ct Replicate 3

description: siRNA Ct Replicate 3


title: 252800511556-6_siRNA Ct Replicate 4

description: siRNA Ct Replicate 4


title: VMM15 plx rep 2

description: Replicate 2


title: VMM5A plx rep 3

description: Replicate 3

source_name: VMM5A plx


title: 252800511556-5_siRNAs TL RNYs Replicate 4

description: siRNAs TL RNYs Replicate 4


title: VMM18 control rep 4

description: Replicate 4


title: A375 control rep 4

description: Replicate 4


title: STKHLM7421_blood

description: whole blood sample from patient STKHLM7421

value: STKHLM7421 blood

tag: tumor gleason

tag: tumor %


title: STKHLM7312_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM7312

tag: (derived data) iclusterplus group

tag: extra-capsular extension (ece)


title: SKMEL2 plx rep 2

description: Replicate 2

source_name: SKMEL2 plx


title: VMM12 control rep 2

description: Replicate 2


title: RC4 PBMC for patient 11-0755

city: palo alto

first: weiqi

last: wang

state: ca

address: 1291 welch road

institute: stanford

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Agilent Feature Extraction Software (v 11.5) was used for background subtraction

source_name: PBMC, stim

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

treatment_protocol: Cryopreserved PBMC were thawed, rested for 1 h at 37C, then stimulated, or not, with a cocktail of LPS, IFNalpha,CD3+CD28 beads, and anti-IgM+IgG beads for 4 h. See Whiting et al., PLoS One 2015, 10: 30133627.

value: Female

tag: age

tag: race

value: White

tag: fasting blood

value: yes

tag: individual

value: patient

tag: cell type

value: PBMC

tag: treatment

value: stimulated with a cocktail of IFNa, LPS, CD3+CD28 beads, and anti-IgM+IgG

source_name: PBMC, unstim

value: unstimulated


title: RC4 PBMC for patient 11-0753

tag: gender

value: Male


title: RC4 PBMC for patient 11-0737


title: SKMEL2 plx rep 3

description: Replicate 3

tag: cell line

value: WT/WT


title: RC4 PBMC for patient 11-0732

value: Asian


title: 252800511556-2_siRNA Ct Replicate 2

description: siRNA Ct Replicate 2

tag: strain

value: male

tag: transfected with

tag: amount (µg)

tag: rin number


title: RC4 PBMC for patient 11-0747

tag: tissue

value: blood


title: DM13 control rep 6

description: Replicate 6

source_name: DM13 control

tag: braf status


title: STKHLM7213_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM7213

tag: patient

tag: sample type

value: tumor

value: tissue core

tag: tumor gleason

tag: tumor %

value: Y

tag: positive surgical margins (psm)

tag: biochemical relapse (bcr)

tag: time to bcr (months)

tag: tmprss2/erg gene fusion status

value: unknown


title: STKHLM7213_blood

description: whole blood sample from patient STKHLM7213

value: STKHLM7213 blood

value: see matched tumor sample

tag: (derived data) iclusterplus group

tag: extra-capsular extension (ece)


title: RC4 PBMC for patient 11-0731

tag: gender

value: Female

tag: age

tag: race

value: Other

tag: fasting blood

tag: individual

tag: cell type

tag: treatment


title: DM122 control rep 1

description: Replicate 1

source_name: DM122 control

tag: cell line

tag: braf status


title: RC4 PBMC for patient 11-0707

value: White

value: yes

value: patient

tag: tissue


title: RC4 PBMC for patient 11-0713

value: PBMC

value: stimulated with a cocktail of IFNa, LPS, CD3+CD28 beads, and anti-IgM+IgG

value: unstimulated


title: STKHLM7179_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM7179

tag: patient

tag: sample type

tag: tumor gleason

tag: tumor %

value: N


title: VMM5A plx rep 2

description: Replicate 2


title: RC4 PBMC for patient 11-0729

value: Male

value: Asian


title: RC4 PBMC for patient 11-0635

value: blood


title: STKHLM7179_blood

description: whole blood sample from patient STKHLM7179

value: STKHLM7179 blood

tag: positive surgical margins (psm)

tag: biochemical relapse (bcr)

tag: time to bcr (months)

tag: tmprss2/erg gene fusion status


title: RC4 PBMC for patient 11-0702

tag: gender

tag: age


title: DM13 control rep 5

description: Replicate 5


title: RC4 PBMC for patient 11-0676

tag: race

tag: fasting blood


title: RC4 PBMC for patient 11-0613

tag: individual

tag: cell type


title: RC4 PBMC for patient 11-0688

tag: treatment


title: RC4 PBMC for patient 11-0649


title: STKHLM7106_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM7106

value: tumor

value: tissue core

tag: (derived data) iclusterplus group

tag: extra-capsular extension (ece)

value: Y


title: A375 plx rep 6

description: Replicate 6

source_name: A375 plx

tag: cell line

tag: braf status


title: STKHLM7106_blood

description: whole blood sample from patient STKHLM7106

tag: patient

value: STKHLM7106 blood

tag: sample type

tag: tissue

tag: tumor gleason

value: see matched tumor sample

value: unknown


title: VMM18 plx rep 3

description: Replicate 3

source_name: VMM18 plx


title: STKHLM6929_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM6929

tag: tumor %

tag: positive surgical margins (psm)

tag: biochemical relapse (bcr)

tag: time to bcr (months)


title: STKHLM6929_blood

description: whole blood sample from patient STKHLM6929

source_name: whole blood sample

value: STKHLM6929 blood

tag: tmprss2/erg gene fusion status


title: STKHLM7312_blood

description: whole blood sample from patient STKHLM7312

value: STKHLM7312 blood


title: STKHLM6631_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM6631


title: Rat Fibrin 2

description:
Gene expression data from fibrin-stimulated microglia
Rat_08.B-1_fibrin_vitro_II

value: Microglia

tag: protocol

value: fibrin-stimulated


title: RC4 PBMC for patient 11-0612

tag: gender

tag: age

tag: race

value: White

tag: fasting blood

value: yes

tag: individual

value: patient

value: PBMC

value: stimulated with a cocktail of IFNa, LPS, CD3+CD28 beads, and anti-IgM+IgG


title: RC4 PBMC for patient 11-0599

value: Female

value: blood

tag: cell type

tag: treatment

value: unstimulated


title: STKHLM6631_blood

description: whole blood sample from patient STKHLM6631

tag: patient

value: STKHLM6631 blood

tag: (derived data) iclusterplus group

tag: extra-capsular extension (ece)


title: RC4 PBMC for patient 11-0597

value: Asian

tag: tissue


title: RC4 PBMC for patient 11-0609

value: Male


title: VMM17 control rep 3

description: Replicate 3

source_name: VMM17 control

tag: cell line

tag: braf status


title: RC4 PBMC for patient 11-0590


title: RC4 PBMC for patient 11-0565


title: Rat Control 1

description:
Gene expression data from unstimulated microglia
Rat_05.A-unstimulated_vitro

source_name: RNA prepared from unstimulated microglia


title: RC4 PBMC for patient 11-0543

value: Black or African American


title: RC4 PBMC for patient 11-0603


title: RC4 PBMC for patient 11-0529


title: RC4 PBMC for patient 11-0581


title: DM122 plx rep 3

description: Replicate 3

source_name: DM122 plx

value: WT/WT


title: SLM2 control rep 6

description: Replicate 6

source_name: SLM2 control


title: STKHLM6159_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM6159

tag: sample type

value: tumor

value: tissue core

tag: tumor gleason

tag: tumor %

value: N

tag: positive surgical margins (psm)

tag: biochemical relapse (bcr)

value: unknown


title: RC4 PBMC for patient 11-0546

tag: gender

tag: age


title: RC4 PBMC for patient 11-0561

tag: race

tag: fasting blood


title: RC4 PBMC for patient 11-0578

value: White

tag: individual

tag: cell type


title: VMM15 control rep 2

description: Replicate 2

source_name: VMM15 control


title: VMM39 plx rep 2

description: Replicate 2

source_name: VMM39 plx


title: RC4 PBMC for patient 11-0574

value: yes

tag: treatment


title: VMM12 plx rep 2

description: Replicate 2

source_name: VMM12 plx


title: RC4 PBMC for patient 11-0508

value: patient


title: STKHLM6159_blood

description: whole blood sample from patient STKHLM6159

tag: patient

value: STKHLM6159 blood

value: see matched tumor sample

tag: (derived data) iclusterplus group

tag: time to bcr (months)

tag: tmprss2/erg gene fusion status


title: DM6 control rep 3

description: Replicate 3

source_name: DM6 control

tag: cell line

tag: braf status


title: SKMEL2 control rep 5

description: Replicate 5

source_name: SKMEL2 control


title: RC4 PBMC for patient 11-0497

value: Female

tag: tissue

value: PBMC

value: stimulated with a cocktail of IFNa, LPS, CD3+CD28 beads, and anti-IgM+IgG


title: STKHLM5967_blood

description: whole blood sample from patient STKHLM5967

value: STKHLM5967 blood

tag: sample type

value: blood

tag: tumor gleason

tag: tumor %

tag: extra-capsular extension (ece)


title: STKHLM5967_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM5967

tag: positive surgical margins (psm)

tag: biochemical relapse (bcr)


title: STKHLM5950_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM5950

value: Y


title: STKHLM5872_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM5872


title: STKHLM5872_blood

description: whole blood sample from patient STKHLM5872

value: STKHLM5872 blood


title: STKHLM5867_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM5867


title: STKHLM5950_blood

description: whole blood sample from patient STKHLM5950

value: STKHLM5950 blood


title: RC4 PBMC for patient 11-0461

tag: gender

value: Male

tag: age

tag: race

value: Native Hawaiian or Other Pacific Islander

tag: fasting blood

value: unstimulated


title: RC4 PBMC for patient 11-0482

tag: individual

tag: cell type

tag: treatment


title: RC4 PBMC for patient 11-0313


title: RC4 PBMC for patient 11-0514


title: RC4 PBMC for patient 11-0314


title: RC4 PBMC for patient 11-0462


title: RC4 PBMC for patient 11-0329

value: Asian


title: RC4 PBMC for patient 11-0311

value: White


title: RC4 PBMC for patient 11-0304

value: yes


title: VMM39 plx rep 1

description: Replicate 1

value: WT/WT


title: RC4 PBMC for patient 11-0338

value: patient


title: RC4 PBMC for patient 11-0345


title: STKHLM5867_blood

description: whole blood sample from patient STKHLM5867

tag: patient

value: STKHLM5867 blood

value: see matched tumor sample

tag: (derived data) iclusterplus group

tag: time to bcr (months)

tag: tmprss2/erg gene fusion status

value: unknown


title: RC4 PBMC for patient 11-0302

value: Female

tag: tissue

value: PBMC

value: stimulated with a cocktail of IFNa, LPS, CD3+CD28 beads, and anti-IgM+IgG


title: RC4 PBMC for patient 11-0328

value: blood


title: SLM2 control rep 5

description: Replicate 5

tag: cell line

tag: braf status


title: RC4 PBMC for patient 11-0352


title: RC4 PBMC for patient 11-0307


title: SKMEL2 control rep 4

description: Replicate 4


title: DM122 plx rep 2

description: Replicate 2


title: RC4 PBMC for patient 11-0315


title: DM6 control rep 2

description: Replicate 2


title: RC4 PBMC for patient 11-0445


title: RC4 PBMC for patient 11-0299


title: STKHLM9246_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM9246

tag: sample type

value: tumor

value: tissue core

tag: tumor gleason

tag: tumor %

tag: extra-capsular extension (ece)

value: Y


title: VMM17 control rep 2

description: Replicate 2


title: VMM18 plx rep 2

description: Replicate 2


title: STKHLM9246_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM9246

value: benign

tag: positive surgical margins (psm)

tag: biochemical relapse (bcr)


title: STKHLM9161_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM9161


title: VMM5A control rep 4

description: Replicate 4

source_name: VMM5A control


title: STKHLM9157_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM9157

value: N


title: STKHLM9161_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM9161


title: STKHLM9157_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM9157


title: STKHLM8659_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM8659


title: STKHLM8659_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM8659


title: STKHLM8341_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM8341


title: RC4 PBMC for patient 11-0298

source_name: PBMC, stim

tag: gender

tag: age

tag: race

tag: fasting blood

value: unstimulated


title: RC4 PBMC for patient 11-0287

value: Male

value: White

tag: individual

tag: cell type

tag: treatment

source_name: PBMC, unstim


title: RC4 PBMC for patient 11-0289

value: yes


title: A375 plx rep 5

description: Replicate 5


title: RC4 PBMC for patient 11-0282

value: patient


title: STKHLM8105_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM8105

tag: patient

tag: (derived data) iclusterplus group

tag: time to bcr (months)

tag: tmprss2/erg gene fusion status


title: STKHLM8341_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM8341

tag: sample type

tag: tissue


title: DM13 plx rep 1

description: Replicate 1

source_name: DM13 plx

tag: cell line

tag: braf status


title: VMM15 control rep 1

description: Replicate 1


title: RC4 PBMC for patient 11-0295


title: STKHLM8105_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM8105

tag: tumor gleason

tag: tumor %

tag: extra-capsular extension (ece)

tag: positive surgical margins (psm)


title: RC4 PBMC for patient 11-0278

tag: gender

tag: age

tag: race


title: SKMEL2 plx rep 1

description: Replicate 1

source_name: SKMEL2 plx

value: WT/WT


title: RC4 PBMC for patient 11-0279

tag: fasting blood

tag: individual

tag: cell type


title: VMM18 plx rep 1

description: Replicate 1


title: SLM2 control rep 4

description: Replicate 4


title: DM13 control rep 4

description: Replicate 4

source_name: DM13 control


title: RC4 PBMC for patient 11-0275

tag: treatment


title: RC4 PBMC for patient 11-0271


title: RC4 PBMC for patient 11-0285


title: VMM15 plx rep 1

description: Replicate 1

source_name: VMM15 plx


title: STKHLM8035_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM8035

tag: patient

tag: (derived data) iclusterplus group

tag: biochemical relapse (bcr)

tag: time to bcr (months)


title: STKHLM8035_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM8035

tag: sample type

tag: tissue

value: see matched tumor sample

tag: tmprss2/erg gene fusion status


title: RC4 PBMC for patient 11-0274


title: VMM39 control rep 4

description: Replicate 4

source_name: VMM39 control

tag: cell line

tag: braf status


title: VMM5A plx rep 1

description: Replicate 1

source_name: VMM5A plx


title: A375 plx rep 4

description: Replicate 4

source_name: A375 plx


title: STKHLM7100_blood

description: whole blood sample from patient STKHLM7100

source_name: whole blood sample

tag: tumor gleason

tag: tumor %

tag: extra-capsular extension (ece)

tag: positive surgical margins (psm)

value: unknown


title: STKHLM7067_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM7067


title: DM122 plx rep 1

description: Replicate 1

source_name: DM122 plx


title: RC4 PBMC for patient 11-0270

tag: gender

value: Female

tag: age

tag: race

tag: fasting blood


title: RC4 PBMC for patient 11-0268

tag: individual

tag: cell type

value: PBMC

tag: treatment


title: RC4 PBMC for patient 11-0266

value: stimulated with a cocktail of IFNa, LPS, CD3+CD28 beads, and anti-IgM+IgG


title: RC4 PBMC for patient 11-0262

value: blood


title: STKHLM6836_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM6836

tag: patient

value: tumor

tag: (derived data) iclusterplus group

tag: biochemical relapse (bcr)

tag: time to bcr (months)


title: RC4 PBMC for patient 11-0253

tag: tissue


title: STKHLM7100_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM7100

tag: sample type

value: tissue core

tag: tmprss2/erg gene fusion status


title: VMM12 plx rep 1

description: Replicate 1

tag: cell line

tag: braf status


title: VMM17 control rep 1

description: Replicate 1

source_name: VMM17 control


title: STKHLM6439_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM6439

tag: tumor gleason

tag: tumor %

tag: extra-capsular extension (ece)

tag: positive surgical margins (psm)


title: STKHLM6439_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM6439


title: STKHLM7067_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM7067


title: STKHLM6370_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM6370


title: RC4 PBMC for patient 11-0240

tag: gender

tag: age

tag: race

tag: fasting blood


title: RC4 PBMC for patient 11-0242

tag: individual

tag: cell type

tag: treatment


title: SKMEL28 plx rep 3

description: Replicate 3

source_name: SKMEL28 plx


title: STKHLM6032_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM6032

tag: patient

tag: (derived data) iclusterplus group

tag: biochemical relapse (bcr)

tag: time to bcr (months)


title: RC4 PBMC for patient 11-0215

tag: tissue


title: SKMEL28 lapatinib rep 3

description: Replicate 3

source_name: SKMEL28 lapatinib

treatment_protocol: Cells were plated in RPMI + 5% FBS and incubated overnight before being treated with 2 µM lapatinib in phenol red–free RPMI-1640 without FBS for 8 hours at 37°C.

tag: cell line

tag: braf status


title: A375 control rep 3

description: Replicate 3

source_name: A375 control


title: RC4 PBMC for patient 11-0218


title: DM6 control rep 1

description: Replicate 1

source_name: DM6 control


title: RC4 PBMC for patient 11-0247


title: STKHLM6836_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM6836

tag: sample type

tag: tumor gleason

tag: tumor %

tag: tmprss2/erg gene fusion status


title: DM331 control rep 3

description: Replicate 3

source_name: DM331 control


title: RC4 PBMC for patient 11-0199

source_name: PBMC, stim

tag: gender

tag: age

value: Asian


title: STKHLM5964_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM5964

tag: extra-capsular extension (ece)

tag: positive surgical margins (psm)


title: DM331 control rep 2

description: Replicate 2


title: HT144 lapatinib rep 3

description: Replicate 3

source_name: HT144 lapatinib


title: HT144 plx_lap rep 3

description: Replicate 3

source_name: HT144 plx_lap

treatment_protocol: Cells were plated in RPMI + 5% FBS and incubated overnight before being treated with 125 nM plx4720 and 2 µM lapatinib concurrently in phenol red–free RPMI-1640 without FBS for 8 hours at 37°C.


title: SKMEL28 control rep 3

description: Replicate 3

source_name: SKMEL28 control


title: SKMEL24 plx rep 3

description: Replicate 3

source_name: SKMEL24 plx


title: STKHLM6370_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM6370

value: benign


title: STKHLM6032_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM6032


title: SKMEL28 plx_lap rep 3

description: Replicate 3

source_name: SKMEL28 plx_lap


title: STKHLM5964_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM5964


title: RC4 PBMC for patient 11-0210

tag: race

tag: fasting blood

tag: individual

tag: cell type

source_name: PBMC, unstim


title: STKHLM5574_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM5574

tag: patient

value: UNKNOWN

tag: (derived data) iclusterplus group

value: N

tag: biochemical relapse (bcr)


title: STKHLM5605_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM5605

tag: tissue

tag: time to bcr (months)


title: STKHLM5574_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM5574

tag: sample type


title: RC4 PBMC for patient 11-0196

tag: treatment

value: unstimulated


title: RC4 PBMC for patient 11-0185

value: Male

value: White


title: STKHLM5433_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM5433

tag: tumor gleason

tag: tumor %


title: RC4 PBMC for patient 11-0200

tag: gender

value: yes

value: patient


title: RC4 PBMC for patient 11-0195

tag: age


title: RC4 PBMC for patient 11-0183


title: VMM12 control rep 1

description: Replicate 1

source_name: VMM12 control

tag: cell line

tag: braf status


title: A375 plx_lap rep 3

description: Replicate 3

source_name: A375 plx_lap


title: DM331 plx_lap rep 3

description: Replicate 3

source_name: DM331 plx_lap


title: RC4 PBMC for patient 11-0184

tag: race


title: SKMEL24 plx_mas rep 3

description: Replicate 3

source_name: SKMEL24 plx_mas

treatment_protocol: Cells were plated in RPMI + 5% FBS and incubated overnight before being treated with 125 nM plx4720 and 10 µM masitinib concurrently in phenol red–free RPMI-1640 without FBS for 8 hours at 37°C.


title: RC4 PBMC for patient 11-0181

tag: fasting blood


title: STKHLM5388_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM5388

value: see matched tumor sample

tag: extra-capsular extension (ece)

tag: positive surgical margins (psm)

tag: tmprss2/erg gene fusion status


title: STKHLM5433_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM5433

tag: patient

tag: (derived data) iclusterplus group

value: unknown


title: RC4 PBMC for patient 11-0182

value: Female

tag: individual

tag: tissue

tag: cell type


title: RC4 PBMC for patient 11-0171

value: PBMC

tag: treatment


title: STKHLM5605_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM5605

tag: sample type

tag: tumor gleason

tag: biochemical relapse (bcr)

tag: time to bcr (months)


title: SKMEL2 control rep 3

description: Replicate 3

source_name: SKMEL2 control

tag: cell line

value: WT/WT


title: RC4 PBMC for patient 11-0179

tag: gender

tag: age

value: Other

value: blood

value: stimulated with a cocktail of IFNa, LPS, CD3+CD28 beads, and anti-IgM+IgG


title: STKHLM5279_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM5279

value: tumor

value: tissue core

tag: tumor %

value: Y


title: SKMEL28 mastinib rep 3

description: Replicate 3

source_name: SKMEL28 mastinib

treatment_protocol: Cells were plated in RPMI + 5% FBS and incubated overnight before being treated with 10 µM masitinib in phenol red–free RPMI-1640 without FBS for 8 hours at 37°C.

tag: braf status


title: VMM18 control rep 3

description: Replicate 3

source_name: VMM18 control


title: VMM5A control rep 3

description: Replicate 3

source_name: VMM5A control


title: STKHLM5279_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM5279

value: benign

tag: extra-capsular extension (ece)

tag: positive surgical margins (psm)


title: RC4 PBMC for patient 11-0170

tag: race

value: Asian

tag: fasting blood

value: unstimulated


title: HT144 plx_mas rep 3

description: Replicate 3

source_name: HT144 plx_mas


title: SKMEL28 plx_lap rep 2

description: Replicate 2


title: STKHLM5388_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM5388

tag: patient

tag: (derived data) iclusterplus group

value: N

tag: tmprss2/erg gene fusion status


title: STKHLM4988_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4988

tag: tissue


title: VMM39 control rep 3

description: Replicate 3

source_name: VMM39 control


title: SKMEL28 lapatinib rep 2

description: Replicate 2

source_name: SKMEL28 lapatinib


title: SKMEL28 mastinib rep 2

description: Replicate 2


title: STKHLM4988_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM4988

tag: sample type


title: STKHLM4940_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM4940

tag: tumor gleason


title: STKHLM4940_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4940

tag: biochemical relapse (bcr)


title: STKHLM4920_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4920

tag: time to bcr (months)


title: RC4 PBMC for patient 11-0165

source_name: PBMC, stim

value: White

value: yes

tag: individual

tag: cell type

tag: treatment


title: RC4 PBMC for patient 11-0178

tag: gender

tag: age

value: patient


title: RC4 PBMC for patient 11-0168


title: VMM5A control rep 2

description: Replicate 2

tag: cell line

tag: braf status


title: RC4 PBMC for patient 11-0156

tag: race


title: RC4 PBMC for patient 11-0161

value: Male

tag: fasting blood


title: RC4 PBMC for patient 11-0160

value: Female


title: RC4 PBMC for patient 11-0163

value: PBMC


title: RC4 PBMC for patient 11-0158


title: SKMEL24 lapatinib rep 3

description: Replicate 3

source_name: SKMEL24 lapatinib


title: RC4 PBMC for patient 11-0157


title: RC4 PBMC for patient 11-0145


title: SKMEL24 lapatinib rep 2

description: Replicate 2


title: STKHLM4920_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM4920

tag: patient

value: see matched tumor sample

tag: tumor %

tag: extra-capsular extension (ece)

tag: positive surgical margins (psm)

value: unknown


title: STKHLM4757_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM4757

tag: sample type

tag: tissue

tag: (derived data) iclusterplus group

tag: tmprss2/erg gene fusion status


title: VMM5A control rep 1

description: Replicate 1


title: A375 plx_lap rep 2

description: Replicate 2


title: SKMEL24 plx_lap rep 3

description: Replicate 3

source_name: SKMEL24 plx_lap


title: STKHLM4753_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4753

tag: tumor gleason

value: UNKNOWN

tag: biochemical relapse (bcr)

tag: time to bcr (months)


title: STKHLM4870_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM4870


title: STKHLM4753_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM4753


title: STKHLM4757_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4757


title: STKHLM4596_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4596


title: STKHLM4870_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4870


title: RC4 PBMC for patient 11-0143

tag: gender

tag: individual

value: blood

tag: cell type

tag: treatment

value: stimulated with a cocktail of IFNa, LPS, CD3+CD28 beads, and anti-IgM+IgG


title: STKHLM4596_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM4596

value: tissue core


title: RC4 PBMC for patient 11-0139

tag: age

tag: race


title: DM331 plx rep 3

description: Replicate 3

source_name: DM331 plx

tag: cell line

tag: braf status


title: STKHLM4441_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4441

tag: patient

value: tumor

tag: tumor %

tag: extra-capsular extension (ece)

value: Y


title: DM331 mastinib rep 3

description: Replicate 3

source_name: DM331 mastinib


title: DM331 lapatinib rep 3

description: Replicate 3

source_name: DM331 lapatinib


title: RC4 PBMC for patient 11-0142

tag: fasting blood

tag: tissue

source_name: PBMC, unstim


title: DM331 mastinib rep 2

description: Replicate 2


title: STKHLM4441_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM4441

tag: sample type

value: benign

tag: (derived data) iclusterplus group

tag: positive surgical margins (psm)

tag: tmprss2/erg gene fusion status


title: SKMEL28 plx_lap rep 1

description: Replicate 1

source_name: SKMEL28 plx_lap


title: A375 lapatinib rep 3

description: Replicate 3

source_name: A375 lapatinib


title: HT144 control rep 3

description: Replicate 3

source_name: HT144 control


title: STKHLM12012_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM12012

tag: tumor gleason

tag: biochemical relapse (bcr)

tag: time to bcr (months)


title: DM331 lapatinib rep 2

description: Replicate 2


title: STKHLM11405_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM11405


title: RC4 PBMC for patient 11-0137

tag: gender

tag: individual

tag: cell type

tag: treatment

value: unstimulated


title: RC4 PBMC for patient 11-0130

tag: age

tag: race


title: STKHLM12012_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM12012

tag: patient

tag: tumor %


title: RC4 PBMC for patient 11-0136

tag: fasting blood


title: A375 plx_mas rep 3

description: Replicate 3

source_name: A375 plx_mas

tag: cell line

tag: braf status


title: HT144 mastinib rep 3

description: Replicate 3

source_name: HT144 mastinib


title: STKHLM11198_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM11198

tag: sample type

tag: tissue

tag: (derived data) iclusterplus group

tag: extra-capsular extension (ece)

value: N


title: RC4 PBMC for patient 11-0126

value: White


title: STKHLM11198_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM11198

tag: tumor gleason

tag: positive surgical margins (psm)

tag: biochemical relapse (bcr)

tag: tmprss2/erg gene fusion status


title: RC4 PBMC for patient 11-0125

tag: gender

value: yes

tag: individual

tag: cell type


title: A375 plx rep 3

description: Replicate 3

source_name: A375 plx


title: RC4 PBMC for patient 11-0127

tag: age

tag: race

value: Other

value: patient

tag: treatment


title: SKMEL24 control rep 3

description: Replicate 3

source_name: SKMEL24 control


title: RC4 PBMC for patient 11-0075

value: Female

tag: fasting blood


title: SKMEL24 mastinib rep 3

description: Replicate 3

source_name: SKMEL24 mastinib

tag: cell line


title: RC4 PBMC for patient 11-0122

value: Asian

value: PBMC


title: RC4 PBMC for patient 11-0123

value: Male


title: STKHLM5690_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM5690

tag: patient

tag: tumor %

tag: time to bcr (months)

value: unknown


title: STKHLM11405_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM11405

tag: sample type

tag: tissue

value: see matched tumor sample

tag: (derived data) iclusterplus group


title: STKHLM5690_blood

description: whole blood sample from patient STKHLM5690

source_name: whole blood sample

value: blood

tag: tumor gleason

tag: extra-capsular extension (ece)

tag: positive surgical margins (psm)


title: SKMEL24 lapatinib rep 1

description: Replicate 1

tag: braf status


title: RC4 PBMC for patient 11-0059

tag: gender

tag: individual

value: stimulated with a cocktail of IFNa, LPS, CD3+CD28 beads, and anti-IgM+IgG


title: RC4 PBMC for patient 11-0071

tag: age

tag: cell type


title: RC4 PBMC for patient 11-0060

tag: race

tag: treatment


title: SKMEL24 mastinib rep 2

description: Replicate 2

tag: cell line


title: HT144 plx_mas rep 2

description: Replicate 2

source_name: HT144 plx_mas


title: HT144 control rep 2

description: Replicate 2


title: STKHLM5650_blood

description: whole blood sample from patient STKHLM5650

tag: patient

tag: biochemical relapse (bcr)

tag: tmprss2/erg gene fusion status


title: HT144 mastinib rep 2

description: Replicate 2


title: STKHLM5627_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM5627

tag: sample type

value: tumor

value: tissue core

tag: tumor %

tag: time to bcr (months)


title: STKHLM5627_blood

description: whole blood sample from patient STKHLM5627

tag: tissue

tag: tumor gleason

tag: (derived data) iclusterplus group


title: STKHLM5612_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM5612

tag: extra-capsular extension (ece)

tag: positive surgical margins (psm)

value: Y


title: STKHLM5571_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM5571

value: UNKNOWN


title: STKHLM5612_adjacent_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM5612

value: benign


title: STKHLM5571_adjacent_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM5571


title: STKHLM5469_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM5469

value: N


title: A375 plx_lap rep 1

description: Replicate 1

source_name: A375 plx_lap

tag: braf status


title: RC4 PBMC for patient 11-0015

source_name: PBMC, stim

tag: gender

tag: age

value: White

tag: fasting blood

value: yes

tag: individual

value: unstimulated


title: STKHLM5469_blood

description: whole blood sample from patient STKHLM5469


title: RC4 PBMC for patient 11-0018

value: Female

tag: race

value: patient

tag: cell type

tag: treatment


title: RC4 PBMC for C-1213 rep1

value: control

value: PBMC


title: RC4 PBMC for ctl rep1

value: Male


title: RC4 PBMC for ctl rep2


title: STKHLM5465_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM5465

tag: patient

tag: biochemical relapse (bcr)

tag: tmprss2/erg gene fusion status

value: unknown


title: RC4 PBMC for 1213 rep5

value: blood


title: SKMEL24 plx_mas rep 2

description: Replicate 2

source_name: SKMEL24 plx_mas

tag: cell line


title: RC4 PBMC for 1213 rep1

tag: tissue

value: stimulated with a cocktail of IFNa, LPS, CD3+CD28 beads, and anti-IgM+IgG


title: RC4 PBMC for C-1213 rep2


title: DM13 control rep 3

description: Replicate 3

source_name: DM13 control


title: RC4 PBMC for 1213 rep3


title: RC4 PBMC for 1213 rep4


title: RC4 PBMC for 1213 rep6


title: A375 plx_mas rep 2

description: Replicate 2


title: HT144 control rep 1

description: Replicate 1


title: A375 mastinib rep 3

description: Replicate 3

source_name: A375 mastinib


title: RC4 PBMC for 1213 rep2


title: STKHLM5465_blood

description: whole blood sample from patient STKHLM5465

tag: sample type

tag: tumor gleason

value: see matched tumor sample

tag: tumor %

tag: time to bcr (months)


title: DM331 plx_mas rep 3

description: Replicate 3

source_name: DM331 plx_mas

tag: braf status


title: HT144 lapatinib rep 2

description: Replicate 2

source_name: HT144 lapatinib


title: SKMEL28 mastinib rep 1

description: Replicate 1

source_name: SKMEL28 mastinib


title: VMM18 control rep 2

description: Replicate 2

source_name: VMM18 control


title: SKMEL24 plx rep 2

description: Replicate 2

source_name: SKMEL24 plx


title: STKHLM5445_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM5445

value: tumor

value: tissue core

tag: (derived data) iclusterplus group

tag: extra-capsular extension (ece)

tag: positive surgical margins (psm)


title: SKMEL24 mastinib rep 1

description: Replicate 1


title: SLM2 control rep 3

description: Replicate 3

source_name: SLM2 control

value: WT/WT


title: STKHLM5445_adjacent_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM5445

value: benign


title: STKHLM5441_blood

description: whole blood sample from patient STKHLM5441


title: STKHLM5441_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM5441

value: N

value: Y


title: STKHLM5428_adjacent_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM5428


title: STKHLM5428_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM5428


title: STKHLM5248_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM5248


title: A375 plx rep 2

description: Replicate 2


title: SKMEL2 control rep 2

description: Replicate 2

source_name: SKMEL2 control


title: SKMEL28 plx_mas rep 3

description: Replicate 3

source_name: SKMEL28 plx_mas


title: STKHLM5248_adjacent_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM5248


title: STKHLM5176_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM5176


title: STKHLM5176_blood

description: whole blood sample from patient STKHLM5176


title: UG26-1B6 stromal cells after two (d2; 48h) day of culture co-culture with Lineage- Sca-1+ Kit+ (LSKs), biol rep2

city: Munich

first: Robert

last: Oostendorp

state: Bavaria

address: Trogerstrasse 32

department: Klinikum Rechts der Isar Technische Universität München

country: Germany

institute: III. Medizinische Klinik und Poliklinik

description: Gene expression data of UG26-1B6 stromal cells after two (d2; 48 h) day of culture co-culture with Lineage- Sca-1+ Kit+ (LSKs), biological rep2

hyb_protocol: Biotinylated and fragmented aRNA was hybridized to the GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix, Santa Clara, US) using the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix, Santa Clara, US)

scan_protocol: standard Affymetrix protocol

data_processing: Microarray data analysis was performed using R /Bioconductor packages. Pre-processing of the microarray chips, including background correction, quantile normalization and summarization of the probe set values into expression measure was carried out using the GeneChip RMA (gcRMA) algorithm, as implemented into the gcrma package. The log2 scale data from gcRMA was used in statistical testing.

label_protocol: Biotin-labeled aRNA was obtained using MessageAmp aRNA Amplification Kit (Ambion, Austin, TX, US) and fragmented in RNA fragmentation reagent (Ambion, Austin, TX, US) by heating to 94◦C for 35 minutes.

growth_protocol: The midgestation-embryo-derived stromal clone UG26-1B6 (urogenital ridge-derived) cells were cultured on 0.1% gelatin-coated tissue culture plates in stromal cell medium (80% α-minimal essential medium (αMEM), supplemented with 15% fetal calf serum (FCS), 5% horse serum (HS), antibiotics penicillin and streptomycin (PenStrep; Gibco, Germany), and 10 μM β-mercaptoethanol (Gibco, Germany)) with 30% conditioned medium

extract_protocol: Total RNA was isolated using RNeasy Micro Kit (Quiagen Inc, Hilden, Germany), according to the manufacturer’s recommendation

treatment_protocol: Before seeding with LSK cells, UG26-1B6 stromal cells were plated into 0.1% gelatin-coated 12-well cell culture plates, (2x105 cells per well), grown to 100% confluence and irradiated at 30 Gy using a Mevatron KD2 (Siemens, Munich, Germany). Lin-Sca-1+c-Kit+ cells (LSKs) cells (>95% pure) cells were resuspended in stromal cell culture medium and seeded with stromal cells, ∼105 cells per well. Plates were incubated at 33◦C, 5% CO2 in air and 95% humidity for one to three days (Day1-Day3), respectively. In addition, in order to obtain Day 0 (uncultured; Day0; d0; 0h) cells, ∼2x105 UG26-1B6 stromal cells collected by trypsinization and washed. As an additional control, UG26-1B6 cells 24 h after changing the cell culture medium were also used (Day1 medium control; C).


title: UG26-1B6 stromal cells after two (d2; 48h) day of culture co-culture with Lineage- Sca-1+ Kit+ (LSKs), biol rep1

description: Gene expression data of UG26-1B6 stromal cells after two (d2; 48 h) day of culture co-culture with Lineage- Sca-1+ Kit+ (LSKs), biological rep1


title: UG26-1B6 stromal cells after one (d1; 24h) day of culture co-culture with Lineage- Sca-1+ Kit+ (LSKs), biol rep3

description: Gene expression data of UG26-1B6 stromal cells after one (d1; 24 h) day of culture co-culture with Lineage- Sca-1+ Kit+ (LSKs), biological rep3


title: UG26-1B6 stromal cells after three (d3; 72h) day of culture co-culture with Lineage- Sca-1+ Kit+ (LSKs), biol rep2

description: Gene expression data of UG26-1B6 stromal cells after three (d3; 72 h) day of culture co-culture with Lineage- Sca-1+ Kit+ (LSKs), biological rep2


title: UG26-1B6 stromal cells after one (d1; 24h) day of culture medium change (control), biol rep2

description: Gene expression data of UG26-1B6 stromal cells after one (d1; 24 h) day of culture medium change (control), biological rep2


title: UG26-1B6 stromal cells after one (d1; 24h) day of culture co-culture with Lineage- Sca-1+ Kit+ (LSKs), biol rep2

description: Gene expression data of UG26-1B6 stromal cells after one (d1; 24 h) day of culture co-culture with Lineage- Sca-1+ Kit+ (LSKs), biological rep2


title: UG26-1B6 stromal cells after three (d3; 72h) day of culture co-culture with Lineage- Sca-1+ Kit+ (LSKs), biol rep1

description: Gene expression data of UG26-1B6 stromal cells after three (d3; 72 h) day of culture co-culture with Lineage- Sca-1+ Kit+ (LSKs), biological rep1


title: UG26-1B6 stromal cells after one (d1; 24h) day of culture co-culture with Lineage- Sca-1+ Kit+ (LSKs), biol rep1

description: Gene expression data of UG26-1B6 stromal cells after one (d1; 24 h) day of culture co-culture with Lineage- Sca-1+ Kit+ (LSKs), biological rep1


title: UG26-1B6 stromal cells after two (d2; 48h) day of culture co-culture with Lineage- Sca-1+ Kit+ (LSKs), biol rep3

description: Gene expression data of UG26-1B6 stromal cells after two (d2; 48 h) day of culture co-culture with Lineage- Sca-1+ Kit+ (LSKs), biological rep3


title: VMM39 control rep 2

description: Replicate 2

source_name: VMM39 control


title: A375 plx_mas rep 1

description: Replicate 1

source_name: A375 plx_mas


title: STKHLM4972_blood

description: whole blood sample from patient STKHLM4972

source_name: whole blood sample


title: UG26-1B6 stromal cells before co-culture (d0), biol rep2

description: Gene expression data of UG26-1B6 stromal cells before co-culture (d0), biological rep2


title: UG26-1B6 stromal cells before co-culture (d0), biol rep3

description: Gene expression data of UG26-1B6 stromal cells before co-culture (d0), biological rep3


title: UG26-1B6 stromal cells after one (d1; 24h) day of culture medium change (control), biol rep1

description: Gene expression data of UG26-1B6 stromal cells after one (d1; 24 h) day of culture medium change (control), biological rep1


title: SKMEL2 control rep 1

description: Replicate 1


title: STKHLM4966_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4966


title: DM331 plx_mas rep 2

description: Replicate 2


title: UG26-1B6 stromal cells before co-culture (d0), biol rep1

description: Gene expression data of UG26-1B6 stromal cells before co-culture (d0), biological rep1


title: SKMEL28 lapatinib rep 1

description: Replicate 1

source_name: SKMEL28 lapatinib


title: STKHLM4966_blood

description: whole blood sample from patient STKHLM4966


title: SKMEL24 control rep 2

description: Replicate 2

source_name: SKMEL24 control


title: DM331 plx_lap rep 2

description: Replicate 2

source_name: DM331 plx_lap


title: STKHLM4956_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4956


title: STKHLM4956_adjacent_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM4956


title: STKHLM4925_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4925


title: VMM18 control rep 1

description: Replicate 1


title: STKHLM4972_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4972


title: STKHLM5650_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM5650


title: STKHLM4917_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4917


title: HT144 plx_lap rep 2

description: Replicate 2

source_name: HT144 plx_lap


title: DM331 plx_mas rep 1

description: Replicate 1


title: STKHLM4925_blood

description: whole blood sample from patient STKHLM4925


title: STKHLM4891_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4891


title: STKHLM4917_blood

description: whole blood sample from patient STKHLM4917


title: STKHLM5445_blood

description: whole blood sample from patient STKHLM5445


title: STKHLM4890_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4890


title: A375 mastinib rep 2

description: Replicate 2


title: SKMEL28 plx rep 2

description: Replicate 2

source_name: SKMEL28 plx


title: STKHLM4875_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4875


title: STKHLM4891_blood

description: whole blood sample from patient STKHLM4891


title: STKHLM4856_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4856


title: STKHLM4890_blood

description: whole blood sample from patient STKHLM4890


title: STKHLM4875_blood

description: whole blood sample from patient STKHLM4875


title: STKHLM4856_blood

description: whole blood sample from patient STKHLM4856


title: A375 control rep 2

description: Replicate 2

source_name: A375 control


title: STKHLM4847_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4847


title: STKHLM4847_blood

description: whole blood sample from patient STKHLM4847


title: STKHLM4841_blood

description: whole blood sample from patient STKHLM4841


title: HT144 plx rep 3

description: Replicate 3

source_name: HT144 plx


title: SKMEL28 control rep 2

description: Replicate 2

source_name: SKMEL28 control


title: HT144 plx rep 2

description: Replicate 2


title: STKHLM4787_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4787


title: STKHLM4787_blood

description: whole blood sample from patient STKHLM4787


title: STKHLM4755_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4755


title: A375 mastinib rep 1

description: Replicate 1

source_name: A375 mastinib


title: SKMEL28 plx_mas rep 2

description: Replicate 2


title: HT144 plx_lap rep 1

description: Replicate 1


title: STKHLM4750_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4750


title: HT144 plx_mas rep 1

description: Replicate 1

source_name: HT144 plx_mas


title: HT144 plx rep 1

description: Replicate 1


title: DM13 control rep 2

description: Replicate 2

source_name: DM13 control


title: DM331 control rep 1

description: Replicate 1

source_name: DM331 control


title: STKHLM4841_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4841


title: A375 lapatinib rep 1

description: Replicate 1

source_name: A375 lapatinib


title: SKMEL24 control rep 1

description: Replicate 1


title: SKMEL28 plx_mas rep 1

description: Replicate 1

source_name: SKMEL28 plx_mas


title: STKHLM4750_blood

description: whole blood sample from patient STKHLM4750


title: VMM39 control rep 1

description: Replicate 1

source_name: VMM39 control


title: STKHLM4666_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4666


title: A375 lapatinib rep 2

description: Replicate 2


title: SKMEL28 control rep 1

description: Replicate 1


title: STKHLM4666_blood

description: whole blood sample from patient STKHLM4666


title: SKMEL24 plx_mas rep 1

description: Replicate 1

source_name: SKMEL24 plx_mas


title: DM331 plx rep 2

description: Replicate 2

source_name: DM331 plx


title: STKHLM4661_blood

description: whole blood sample from patient STKHLM4661

source_name: whole blood sample


title: DM331 mastinib rep 1

description: Replicate 1

source_name: DM331 mastinib


title: STKHLM4659_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4659


title: STKHLM4661_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4661


title: STKHLM4755_adjacent_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM4755


title: STKHLM4650_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4650


title: SKMEL28 plx rep 1

description: Replicate 1


title: STKHLM4650_blood

description: whole blood sample from patient STKHLM4650


title: STKHLM4659_blood

description: whole blood sample from patient STKHLM4659


title: STKHLM4605_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4605


title: STKHLM4605_blood

description: whole blood sample from patient STKHLM4605


title: STKHLM4659_adjacent_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM4659


title: STKHLM4487_blood

description: whole blood sample from patient STKHLM4487


title: STKHLM4608_adjacent_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM4608


title: SKMEL24 plx rep 1

description: Replicate 1

source_name: SKMEL24 plx


title: STKHLM4487_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4487


title: Mock-treated 12mM nitrate R3

city: Santiago

first: Andrea

last: Vega

address: Vicuña Mackenna 4860

department: Ciencias Vegetales

country: Chile

institute: Pontificia Universidad Catolica de Chile

hyb_protocol: The fragmented aRNA (7.5 μg) was hybridized on a GeneChip Tomato genome array (containing 10,038 tomato probe sets for more than 9,200 tomato genes) using standard procedures (45°C for 16 h).

scan_protocol: Array scanning was carried out with the GeneChip scanner 300 and image analysis was performed using the GeneChip Operating Software.

data_processing: GeneChip array data were quality assessed using a set of standard quality control steps described in the Affymetrix manual ‘‘GeneChip Expression Analysis: Data Analysis Fundamentals’’. Array data were processed and normalized with RMA (Robust Multi-Array Average) (Irizarry et al., 2003) using the affy R package (Gautier et al., 2004).

organism: Solanum lycopersicum

source_name: Mock leaves grown under 12mM nitrate

label_protocol: Five hundred ng of total RNA was processed for microarray hybridization using the GeneChip one-cycle target-labeling kit (Affymetrix), according to the manufacturer’s instructions.

growth_protocol: Solanum lycopersicum cv. MicroTom plants were cultivated under different N growth conditions employing 16:8 h light:dark cycles (150 micromoles/m2/s) at 20 ºC.

extract_protocol: Total RNA was extracted from both mock-treated and fungus-infected tomato leaves and fruits, following CTAB-spermidine extraction protocol.

treatment_protocol: four week-old tomato plants grown under different nitrate conditions were inoculated in several leaves in planta. Conidia were suspended in Gamborg B5-2% glucose medium and adjusted to a final concentration of 5×105 conidia/ml in the same medium supplemented with 10 mM KH2PO4/K2HPO4, pH 6.4. Conidial suspensions (10 μl) were used to inoculate leaves of six tomato plants obtained from each N condition analyzed. All plants were incubated inside plastic boxes at 20 °C employing the growth conditions mentioned above, under humid environment for 3 days post-inoculation

value: leaves

tag: disease state

value: mock infected

tag: growth condition

value: 12mM nitrate


title: Mock-treated 12mM nitrate R2


title: SKMEL24 plx_lap rep 1

description: Replicate 1

source_name: SKMEL24 plx_lap


title: HT144 lapatinib rep 1

description: Replicate 1

source_name: HT144 lapatinib


title: SKMEL24 plx_lap rep 2

description: Replicate 2


title: SLM2 control rep 2

description: Replicate 2

source_name: SLM2 control


title: DM331 plx rep 1

description: Replicate 1


title: STKHLM4433_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4433


title: STKHLM4433_blood

description: whole blood sample from patient STKHLM4433


title: STKHLM4608_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4608


title: A375 plx rep 1

description: Replicate 1

source_name: A375 plx


title: STKHLM4421_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4421


title: DM13 control rep 1

description: Replicate 1


title: Mock-treated 12mM nitrate R1


title: DM331 lapatinib rep 1

description: Replicate 1

source_name: DM331 lapatinib


title: DM331 plx_lap rep 1

description: Replicate 1

source_name: DM331 plx_lap


title: HT144 mastinib rep 1

description: Replicate 1

source_name: HT144 mastinib


title: STKHLM4322_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4322


title: SLM2 control rep 1

description: Replicate 1


title: A375 control rep 1

description: Replicate 1

source_name: A375 control


title: STKHLM4421_adjacent_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM4421


title: STKHLM4165_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM4165


title: STKHLM4165_blood

description: whole blood sample from patient STKHLM4165


title: STKHLM4322_blood

description: whole blood sample from patient STKHLM4322


title: Mock-treated 6mM nitrate R1

source_name: Mock leaves grown under 6mM nitrate

value: 6mM nitrate


title: Mock-treated 6mM nitrate R3


title: Mock-treated 6mM nitrate R2


title: Mock-treated 2mM nitrate R3

source_name: Mock leaves grown under 2mM nitrate

value: 2mM nitrate


title: STKHLM3953_blood

description: whole blood sample from patient STKHLM3953


title: Mock-treated 2mM nitrate R2


title: B. cinerea infection 12mM nitrate R3

source_name: Infected leaves grown under 12mM nitrate

value: Botrytis cinerea infected


title: STKHLM3878_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM3878


title: STKHLM3878_blood

description: whole blood sample from patient STKHLM3878


title: Mock-treated 2mM nitrate R1


title: Primary mouse astrocytes, TNF, 24H, rep3

city: Belvaux

first: Enrico

last: Glaab

state: Capellen

address: 6, avenue du Swing

country: Luxembourg

institute: University of Luxembourg

hyb_protocol: The cDNA was hybridized onto Affymetrix GeneChip Mouse Gene 1.0 ST Arrays according to the GeneChip WT Terminal Labeling and Hybridization User Manual for use with the Ambion Whole Transcript Expression kit (P/N 702808 Rev.6)

scan_protocol: Arrays were scanned with a GCS3000 Scanner (Affymetrix) for images and intensities.

data_processing: The data was processed using R/bioconductor and RMA with default parameters. The programming language R in version 2.15.2 was used for data   processing in combination with the Bioconductor package 'limma' in version 3.14.4.

label: phycoerythrin

source_name: Primary mouse astrocytes_TNF_24H

label_protocol: The cDNA was labeled according to the GeneChip WT Terminal Labeling and Hybridization User Manual for use with the Ambion Whole Transcript Expression kit (P/N 702808 Rev.6)

extract_protocol: Total RNA was extracted according to RNA NOW (OZYME) manufacturer's recommendations with -20°C overnight incubation for small RNA precipitation.

treatment_protocol: Cultures of primary mouse astrocytes were treated with TNF (50 ng/mL) for 24 hours.

tag: strain

value: C57BL/6J (Harlan, The Netherlands)

tag: cell type

value: primary mouse astrocytes

tag: treated with

value: TNF (50 ng/mL)

tag: time after treatment


title: Primary mouse astrocytes, control, 24H, rep3

source_name: Primary mouse astrocytes_control_24H

value: control


title: STKHLM3821_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM3821

tag: patient

tag: biochemical relapse (bcr)

tag: tmprss2/erg gene fusion status

value: unknown


title: Primary mouse astrocytes, TNF, 24H, rep2


title: STKHLM3821_blood

description: whole blood sample from patient STKHLM3821

source_name: whole blood sample

tag: sample type

value: blood

tag: tissue

value: see matched tumor sample


title: B. cinerea infection 12mM nitrate R1


title: Primary mouse astrocytes, control, 24H, rep2


title: B. cinerea infection 6mM nitrate R2

source_name: Infected leaves grown under 6mM nitrate


title: Primary mouse astrocytes, TNF, 24H, rep1


title: B. cinerea infection 6mM nitrate R3


title: Primary mouse astrocytes, control, 24H, rep1


title: STKHLM3953_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM3953

value: tumor

value: tissue core

tag: tumor gleason

tag: tumor %

value: UNKNOWN


title: B. cinerea infection 6mM nitrate R1


title: B. cinerea infection 12mM nitrate R2


title: Mouse Fibrinogen 1

description:
Gene expression data from fibrinogen-injected corpus callosum at 12 hr
Mouse_02.2-In_Vivo_fibrinogen_2

source_name: corpus callosum

extract_protocol: RNA extraction from  tissues was performed using RNeasy Lipid Tissue kits according to the manufacturer's instructions (Qiagen, Valencia, CA).  Genomic DNA was removed during the RNeasy cleanup using Rnase-Free Dnase set (Qiagen, Valencia, CA).

treatment_protocol: Fibrinogen was stereotactically injected into the corpus callosum.

value: brain

tag: tissue region

value: corpus callosum

tag: protocol

value: fibrinogen-injected


title: STKHLM3805_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM3805

tag: (derived data) iclusterplus group

tag: extra-capsular extension (ece)

value: Y

tag: time to bcr (months)


title: B. cinerea infection 2mM nitrate R3

source_name: Infected leaves grown under 2mM nitrate

value: leaves

tag: disease state

tag: growth condition


title: STKHLM3805_blood

description: whole blood sample from patient STKHLM3805

tag: positive surgical margins (psm)


title: STKHLM3759_tumor

description: tumor robotic radical prostatectomy tissue from patient STKHLM3759

value: N


title: STKHLM3759_adjacent_normal

description: benign robotic radical prostatectomy tissue from patient STKHLM3759

value: benign


title: Mouse Fibrinogen 2

description:
Gene expression data from fibrinogen-injected corpus callosum at 12 hr
Mouse_04.4-In_Vivo_fibrinogen_II

tag: strain


title: Mouse Control 1

description:
Gene expression data from acsf-injected corpus callosum at 12 hr
Mouse_01.1-In_Vivo_acsf

value: acsf-injected


title: Mouse Control 2

description:
Gene expression data from acsf-injected corpus callosum at 12 hr
Mouse_03.3-In_Vivo_acsf_II_2


title: B. cinerea infection 2mM nitrate R1

value: Botrytis cinerea infected

value: 2mM nitrate


title: NeuroD treated sample 3

city: Suzhou

first: Ming

last: Li

address: No. 199 Ren'ai Road

country: China

institute: Soochow University

description: NeuroD 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: mouse jejunum

label_protocol: Cy3 labeled cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

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

tag: gender

value: male

value: jejunum


title: NeuroD treated sample 1

description: NeuroD 1


title: B. cinerea infection 2mM nitrate R2


title: 1221-OR1 replicate 2

status: Public on Sep 15 2015

city: Leicestershire

first: Amy

last: John

address: Loughborough

institute: University of Nottingham

description: Biological replicate 2of 3. Control 1221 to OR1

hyb_protocol: The slides used for the genome analysis were γ APS coated, A+ bar-coded Schott nexterion slides. The slides were printed according to campy dense array gal by Microgrid II 600 robot using TAS software version V2.4.03. They had 12 pins with a 26 x 26 pin grid configuration. The spacing between the spots was 0.165mm and the slides were prepared at 60% humidity. Each slide was printed with duplicate sets of oligos for NCTC 11168, RM1221 and RM2228. A sample of each labelled probe (one cy3, one cy5) for each slide was taken to be hybridized which contained 500ng of labelled DNA and placed them together in a 0.5 ml tube.  The volume was adjusted to 4.5µl total volume by adding nuclease free water. To each tube 0.5 µl of Fragmentation Buffer was added before being incubated at 70OC (in Thermo Cycler) for 2 min followed by 0.5 µl of Stop Solution (Ambion Kit 8740).  This was followed by the addition of 2µl Lithium Heperin (to reduce non specific hybridization). Add 100 µl of Schott 1x Hybridization Buffer which was pre-warmed to 50OC and added to the probe carefully to avoid introducing any air bubbles.  The total volume was 107.5 µl.  The DNA microarray slides were blocked before hybridisation by using blocking solution (5xSSC, 0.2%SDS, 1%BSA). After blocking, the slides were washed in ultra pure water and then in 100% ethanol. The prepared slides were kept in the slide holder and were inserted into the TECAN HS 4800 chamber. Approximately 5 min before the probes were inserted they were heated to 95o C for 2 min and then spun at 15.000rpm for 5 minutes in a microcentrifuge to pellet up any impurities. The probe was injected into the hybridisation chamber. The hybridisation was done at 45º C for 16h with gentle agitation. After hybridisation the slides were washed in 1 X SSC buffer with 0.6% SDS for 2 min, followed by two washes in 0.06 X SSC buffer, each for 2 min. The slides are then dried at 23º C with nitrogen.

scan_protocol: Slides were scanned using Axon Genepix 4200AL scanner (Molecular Devices Corporation, Sunnyvale, CA ) at 532 (Cy3) and 635 (Cy5) excitation wavelengths with 5 µm resolution. The slides were scanned using the Auto PMT function with the threshold for saturation set at 0.05%.  Fluorescent spot intensities were quantified using Genepix Pro 6.0 software. Spots were excluded from further analysis if they contain anomalous spot morphology or were within regions of non-specific fluorescence.

data_processing: The data was analysed by Genespring GX 7.3  and the oligos which have more than 2 fold change and p<0.05 were selected for further studies.

organism: Campylobacter jejuni RM1221

source_name: Lab Stock

label_protocol: 1. Set up a labelling reaction by mixing.   9 µg Random primers (Promega, UK).  3 µg Template genome.  Make the volume to 41.5 µl by adding nuclease free water.  2. Heat at 95° C for 5 min and snap cool.  3. Add final reaction elements.  41.5 µl heated template.  1.5 µl dye-dCTP  1 µl dNTP mix (5mM dA, dT, dG, 2mM dC)  5 µl Klenow Reaction mix. (Fermentas, UK)  1 µl Klenow @ 10 U/ µl (Fermentas, UK)   4. Heat at 37° C for 1.5 hrs.   5. Min elute reaction clean up kit was used to clean up the reaction mix according to the manufacturer’s instructions (Qiagen, UK)

growth_protocol: The control and the sample strains were grown in blood agar plates {Blood Agar Base no: 2 (CM271, Oxoid, UK) supplemented with 5% defibrinated horse blood (TCS, UK)} overnight at 42ºC in an anaerobic jar (Oxoid, UK) vacuumed to - 22 psi and  atmospheric pressure was restored with a gas mixture consisting of 85 % v / v nitrogen, 10 % v / v carbon dioxide and 5 % v / v hydrogen (Air Products, Crewe, UK).

extract_protocol: Genomic DNA was isolated using Qiagen genomic extraction kit (using genomic DNA buffer set Cat no: 19060 and Genomic tip20/G Cat No: 10223) according to the manufacturer’s instructions.

treatment_protocol: Not applicable

value: control (representing 5 independent DNA preps of C. jejuni RM1221)

organism: Campylobacter jejuni

source_name: Campylobacter cells isolated from chicken cells

value: test


title: Brain, 7weeks, GSC272, Control

first: Soon Young

last: Park

address: 6767 Bertner Ave BSRB S5.8224

department: Neuro-oncology

institute: UT MD Anderson Cancer Center

hyb_protocol: Samples (12 ug of amplified, biotinylated cRNA) were hybridized onto Affymetrix GeneChip Human Genome U133 Plus 2.0 cartridge arrays and incubated in an Affymetrix GeneChip Hybridization Oven 450 using reagents from Affymetrix GeneChip Hybridization, Wash and Stain kit following manufacturer’s instructions. Arrays were washed and stained using Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000 with 7G upgrade.

data_processing: The initial raw data analysis and quality checks performed using Affymetrix GeneChip Command Console-Expression Console software.

source_name: Brain tissue from mouse

label_protocol: samples (100 ng total RNA with Poly-A Spike-in controls) were amplified and labeled using Affymetrix’s (Santa Clara, CA) GeneChip®3’ IVT Express Kit following manufacturer’s instructions (see Assay Overview on page 6 of the attached 3’IVT Express Kit manual) .

growth_protocol: GSC272 were cultured Dulbecco’s modified Eagle’s medium-F12 medium  (1:1) with B27, basic fibroblast growth factor, and epidermal growth factor at 37°C in a humidified atmosphere of   5% CO2 and 95% air.

extract_protocol: The mice were killed at indicated weeks, and their brains were removed and frozen in -70℃. Fresh frozen tumor tissue was collected total RNA extracted using standard methods (Qiagen).

treatment_protocol: GSC272 were infected virus soup (pGIPZ control or POSTN shRNA), selected with puromycin (1 μg/mL) and make permenant cells. Each of cells (5 x 105) were implanted intracranially into the 4- to 6-week-old   female nude mice and collect randemly mouse brain from each grops at 7 weeks after implantation.

tag: cell type

value: GSC272 glioma stem cells

tag: treatment

value: Control


title: 1221-OR12 replicate 3

description: Biological replicate 3 of 3. Control 1221 to OR12

organism: Campylobacter coli


title: 1221-OR1 replicate 3

description: Biological replicate 3 of 3. Control 1221 to OR1


title: 1221-OR12 replicate 1

description: Biological replicate 1 of 3. Control 1221 to OR12


title: 1221-OR12  replicate 2

description: Biological replicate 2 of 3. Control 1221 to OR12


title: EGFP treated control sample 2

description: EGFP 2


title: Brain, 7weeks, GSC272, POSTN knock down, 2

value: POSTN Knockdown


title: 1221-OR1 replicate 1

description: Biological replicate 1 of 3. Control 1221 to OR1


title: NeuroD treated sample 2

description: NeuroD 2


title: HPC5-HPC5 replicate 3_R20C

description: Biological replicate 3 of 3. Control HPC5 to HPC5 itself

source_name: Campylobacter cells isolated from Chicken

label_protocol: 1. Add 5 μl of nuclease free water and heat it to 42°C for 5 min.  2. Add 3 μl labelling buffer to it (25 mg/ ml sodium bicarbonate).  3. Dissolve 1 vial of AF555/645 (Fisher, UK) in 2 μl DMSO and vortex it for 10 sec and add it to 8 μl cDNA labelling buffer mix.  4. Incubate at room temperature for 1 hr in the dark.  5. Add 80 μl of water and 10 μl of sodium acetate (3M) and purify using QIA PCR purification kit but wash three times with 70% ethanol.  7. Precipitate DNA using 3M sodium acetate and 100% ethanol and resuspend it in nuclease free water.   8. Quantify and check label.

growth_protocol: C. jejuni HPC5 and its daughter strains were grown in Nutrient broth (NB No. 2, Oxoid, UK) until it reaches 107 – 108 cfu /ml (~ 9 hrs except for R20 which is grown for 12 h).

extract_protocol: The cells were collected by spinning it in pre chilled tubes @ 6000x g for 15 min in beckman centrifuge. Maximum Enhancement Reagent of 200 µl was preheated to 95ºC and was added to the tube. The cell mix was heated at 95 ºC for 4 min. To it 1ml of trizol was added and was mixed well. It was incubated at room temperature for 5 min. After incubation it was spun for 15 min at 12000 x g at 4 ºC. Approximately 400 µl of the top phase was transferred to a fresh eppendorf. To it 700 µl of 100% ethanol was added and mixed thoroughly. This was used in RNA clean up kit (Qiagen, UK) according to the manufacturer’s instructions. For the synthesis of cDNA, SuperscriptTM direct cDNA labelling system (Invitrogen, UK) was used according to manufacturer’s instructions.    QIA quick PCR Purification kit was used for purifying the product (Qiagen, UK).  The cDNA produced was ethanol precipitated by adding 0.1 v of sodium acetate (3M) and 2.5 v 100% ethanol.

value: control (representing 7 independent preps of C. jejuni HPC5)


title: HPC5-R20C replicate 1_R20C

description: Biological replicate 1 of 3. Control HPC5 to R20C


title: HPC5-R20C replicate 2_R20C

description: Biological replicate 2 of 3. Control HPC5 to R20C


title: HPC5-R20C replicate 3_R20C

description: Biological replicate 3 of 3. Control HPC5 to R20C


title: HPC5-HPC5 replicate 2_R20C

description: Biological replicate 2 of 3. Control HPC5 to HPC5 itself


title: Peritoneal macrophages treated with Tau 623-628

city: Stanford

first: Jonathan

last: Rothbard

state: California

address: 2230 CCSR

department: Medicine

institute: Stanford University School of Medicine

description:
MF Tau
Gene expression in peritoneal macrophages treated withTau 623-628

hyb_protocol: Hybridization was performed using the Agilent Gene Expression Hybridization Kit and the Agilent Microarray Hybridization Chamber as instructed by the manufacturer. Samples were hybridized for 17 h at 65ºC, and slides were washed with Gene Expression Wash Buffer (Agilent) according to maufacturer's instructions.

scan_protocol: Microarray chips were scanned using the DNA microarray scanner (Agilent Technologies) and data were extracted using Feature Extraction software.

data_processing: Data were processed using Genespring 12.6.  Samples were filtered for detected entities.

source_name: peritoneal macrophages

label_protocol: 1 ug of total RNA was labeled with Cy3 using the Agilent low RNA input fluorescence linear amplification kit (Agilent Technologies) according to manufacturer's instructions.

growth_protocol: not applicable

extract_protocol: Total RNA was extracted using Trizol Reagent combined with the Qiagen Rneasy Mini Kit.

treatment_protocol: Groups of three, 10 week old, female C57BL/6 mice treated with either 10ug of LPS, amylin 28-33, or Tau 623-628, or PBS alone. 30-40 minutes post injection, peritoneal cells were lavaged and the CD11b high (macrophages) and CD5+CD19+ (B1a cells) were isolated by flow cytometry.

value: female

tag: time

value: 30-40 minutes in vivo

value: peritoneal macrophages


title: Peritoneal macrophages treated with Amylin 28-33

description:
MF Amylin
Gene expression in peritoneal macrophages treated with Amylin 28-33

value: 10ug Amylin 28-33


title: untreated peritoneal macrophages

description:
MF untreated
Gene expression in untreated peritoneal macrophages

value: untreated


title: B1a lymphocytes treated with Tau 623-628

description:
B1a Tau
Gene expression in B1a lymphocytes treated withTau 623-628

source_name: B1a lymphocytes

value: B1a lymphocytes


title: Peritoneal macrophages treated with LPS

description:
MF LPS
Gene expression in peritoneal macrophages treated with LPS

value: 10ug LPS


title: EGFP treated control sample 3

description: EGFP 3


title: Barin, 7weeks, GSC272, POSTN knock down,1


title: HPC5-R20B replicate 3_R14BR20B

description: Biological replicate 3 of 3. Control HPC5 to R20B

tag: sample type


title: untreated B1a lymphocytes

description:
B1a untreated
Gene expression in untreated B1a lymphocytes


title: EGFP treated control sample 1

description: EGFP 1

tag: tissue


title: HPC5-R20B replicate 1_R14BR20B

description: Biological replicate 1 of 3. Control HPC5 to R20B


title: HPC5-HPC5 replicate 1_R20C

description: Biological replicate 1 of 3. Control HPC5 to HPC5 itself


description:
B1a Amylin
Gene expression in B1a lymphocytes treated with Amylin 28-33


title: HPC5-R14B replicate 1_R14BR20B

description: Biological replicate 1 of 3. Control HPC5 to R14B


title: HPC5-HPC5 replicate 1_R14BR20B


title: CD8_MP_Zeb2-KO_lumi.3

city: New Haven

first: Susan

middle: M

last: Kaech

state: CT

address: 300 Cedar St, TAC S640

department: Immunobiology

institute: Yale University

description:
Illumina Microarray of MP (KLRG1lo IL7Rhi) Zeb2-KO P14 CTLs isolated 8 d.p.i. with LCMV replicate 3
6096357002_C

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Utilized R::beadarray package with the readIdatFiles and normaliseIllumina functions to extract raw and normalised (neqc, log2 transformed) values.

molecule: polyA RNA

label_protocol: standard Illumina protocol

extract_protocol: Rneasy with on column digestion

tag: strain background

tag: genotype/variation

value: Zeb2-KO; GzmB-Cre Zeb2-fl/fl

tag: age

tag: time point

value: 8 d.p.i. with LCMV

value: cytotoxic T lymphocyte (CTL)

tag: cell subtype

value: MP (KLRG1lo IL7Rhi)


title: HPC5-R14B replicate 2_R14BR20B

description: Biological replicate 2 of 3. Control HPC5 to R14B


title: HPC5-R20B replicate 2_R14BR20B

description: Biological replicate 2 of 3. Control HPC5 to R20B


title: HPC5-R14B replicate 3_R14BR20B

description: Biological replicate 3 of 3. Control HPC5 to R14B


title: Developing seed at 72HAF control, biological rep2

city: Gainesville

last: Begcy

state: Florida

address: 1535 Fifield Hall

institute: University of Florida

description:
Gene expression of developing seeds
Endosperm - Whole seed
Wheat_72HAF_c2

hyb_protocol: Hybridization was done on a GeneChip Wheat Genome Array.

scan_protocol: GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA)

data_processing: Affymetrix GeneChip Operating Software generated the images and probe set signal values as CEL files, and the CEL files were processed with the affy package using the robust multiarray analysis (RMA) to generate normalized signal values. The RMA signal values were log2 transformed. To detect differentially expressed genes, the transformed RMA expression values were analyzed with an empirical Bayes linear model. A probeset was considered differentially expressed when it satisfied two conditions, up-regulation or down-regulation more than 2-fold after drought treatment; and a false discovery rate-adjusted P-value was less than <0.05.

label: Biotin

organism: Triticum aestivum

source_name: Wheat seeds 72 hours after fertilization - control

label_protocol: 15 µg of total RNA was used to synthesize cDNA using Affymetrix One-Cycle cDNA Synthesis Kit according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA).

growth_protocol: Winter wheat cultivar Redland, PI 502907 (Triticum aestivum L.) seedlings were vernalized at 4°C for 6 weeks and then transplanted to a one gallon pot of soil-sand mixture (3:1, v/v) and grown in a growth chamber under the following conditions: relative humidity, 50–70%; 16-h light/8-h dark photoperiod; 21°C daytime temperature and 18°C nights. Plants were watered regularly twice daily at the rate of 100ml/ per pot. Because, wheat has an asynchronous fertilization pattern for ovlues in the inflorescence, each floret needs to be specifically marked for timing the fertilization and stress induction. After spikes developed, unfertilized ovules were monitored and observed for the fertilization process. Closed wheat spikes with anthers outside were marked as fertilized. Drought stress was imposed 24h after the fertilization (HAF).

extract_protocol: Total RNA were isolated from seeds of drought-stressed and control plants at 24, 48 and 72 HAF from. Total RNA was isolated using a Trizol (Invitrogen, Carlsbad, CA) protocol and puriﬁed using an RNeasy MinElute Cleanup Kit (Qiagen, Hilden, Germany). Total RNA quality and concentration were determined on a 2100 Bioanalyzer (Agilent, Santa Clara, CA).

treatment_protocol: Drought stress treatment was initiated by discontinuing watering on the drought treatment plants while control plants were regularly watered twice daily. Stress treatment was applied at 48 HAF and relieved at 96 HAF (Fig. S1).

tag: stress

value: control

value: developing seed


title: B1a lymphocytes treated with LPS

description:
B1a LPS
Gene expression in B1a lymphocytes treated with LPS


title: HPC5-HPC5 replicate 3_R14BR20B

description: Biological replicate 3 of 3. Control HPC5 to HPC5 itself

value: test