title: Patient 4, CD14+ cells, after 3 months of fingolimod treatment [exon-level]

tag: relapses during 3-year follow-up

tag: relapses during 4-year follow-up

tag: completed years of fingolimod therapy


title: dkfz_ATRT_170

status: Public on Mar 02 2016

type: RNA

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

country: Germany

institute: German Cancer Research Center DKFZ

description: Gene expression data from an ATRT tumor sample

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 = 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Primary ATRT tumor tissue

label_protocol: Affymetrix protocol

extract_protocol: Total RNA from biopsy samples was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using the TRIzol reagent (Invitrogen, Carlsbad, USA), and subsequently passed over a RNeasy Mini Spin Column (Qiagen, Hilden, Germany) for the removal of small fragments. Integrity control and sample quantitation of total extracted RNA was performed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).

tag: gender

value: M

tag: age (years)

tag: tumor location


title: Patient 9, CD14+ cells, before second dose of fingolimod [exon-level]

status: Public on May 20 2016

city: Rostock

first: Michael

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

institute: University of Rostock

description: Gene expression data from a multiple sclerosis patient treated with fingolimod

hyb_protocol: Labeled single-stranded DNA in the sense orientation was hybridized for 16 hours at 45 °C on Affymetrix HTA 2.0 microarrays. The microarrays were washed and stained with a streptavidin-phycoerythrin conjugate in an Affymetrix Fluidics Station 450. Signal amplification with antibodies was applied following the instructions provided by Affymetrix.

scan_protocol: The microarrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data preprocessing of the raw microarray scans was performed using the Affymetrix GeneChip Command Console (AGCC) software version 4.0. The data were then processed using Expression Console version 1.3.1. The robust multi-array average (RMA) algorithm was applied with the default configuration, which includes a log2 data transformation and quantile normalization. In this step, the measured signal intensities of >6 million probes were summarized into gene level probe sets (n=70523) and exon level probe sets (n=914585). The Transcriptome Analysis Console (TAC) software version 1.0 was utilized to analyze the RNA expression dynamics.

label: Biotin

source_name: Peripheral blood CD14+ cells

label_protocol: According to the Affymetrix Whole Transcript (WT) manual, cRNA was prepared from 200 ng total RNA. The cRNA was then used to generate single-stranded DNA, which was fragmented and biotinylated.

growth_protocol: Patient blood samples were taken immediately before the first dose of fingolimod as well as one day and three months post therapy initiation.

extract_protocol: Peripheral blood CD14+ cells were separated by magnetic-activated cell sorting using Whole Blood CD14 MicroBeads (Miltenyi Biotec) and total RNA was isolated using the mirVana isolation kit (Thermo Fisher Scientific) according to the manufacturers' protocols.

treatment_protocol: Patients were treated with fingolimod (Gilenya, Novartis) according to the approved label (0.5 mg orally once-daily) and the guidelines and recommendations of the German Society of Neurology.

tag: patient identifier

value: male

tag: age in years at baseline

tag: disease duration in years at baseline

tag: previous treatment

value: interferon-beta-1b subcutaneous

tag: treatment gap in months

tag: edss at baseline

tag: edss after 1 year

tag: edss after 2 years

tag: edss after 3 years

tag: edss after 4 years

tag: relapses during the year prior to fingolimod

tag: relapses during 1-year follow-up

tag: relapses during 2-year follow-up


title: RMC_ INI85

status: Public on Mar 08 2016

city: Paris

first: Wilfrid

last: Richer

address: 26 rue d'Ulm

country: France

institute: Institut Curie

hyb_protocol: Hybridization performed by Institut Curie Affymetrix Microarray Core Facility according to the manufacturer's instructions

scan_protocol: Scanning were performed by Institut Curie Affymetrix Microarray Core Facility according to the manufacturer's instructions

data_processing: Arrays were normalized by the GCRMA procedure using Brainarray annotations (V.16.0.0, ENTREZG)

source_name: Renal Medullary Carcinoma

label_protocol: According to the standard Affymetrix protocol

extract_protocol: Total RNAs were collected from samples using the miRNeasy kit (Qiagen) according to the manufacturer's instructions

tag: tissue

value: MRC


title: Patient 8, CD14+ cells, after 3 months of fingolimod treatment [exon-level]

tag: gender

value: interferon-beta-1a subcutaneous

tag: relapses during 3-year follow-up

tag: relapses during 4-year follow-up

tag: completed years of fingolimod therapy


title: Patient 4, CD14+ cells, before second dose of fingolimod [exon-level]

tag: patient identifier

value: female

tag: age in years at baseline

value: interferon-beta-1a intramuscular


title: dkfz_ATRT_166

tag: age (years)

tag: tumor location


title: dkfz_ATRT_169

value: F

value: Infratentorial


title: dkfz_ATRT_158


title: dkfz_ATRT_168


title: dkfz_ATRT_162

value: Supratentorial


title: dkfz_ATRT_155


title: Patient 1, CD14+ cells, before second dose of fingolimod [exon-level]

tag: disease duration in years at baseline

tag: previous treatment

tag: treatment gap in months

tag: edss at baseline


title: dkfz_ATRT_46


title: dkfz_ATRT_156


title: Patient 3, CD19+ cells, after 3 months of fingolimod treatment [exon-level]

source_name: Peripheral blood CD19+ cells

label_protocol: According to the Affymetrix Whole Transcript (WT) manual, cRNA was prepared from 70 ng total RNA. The cRNA was then used to generate single-stranded DNA, which was fragmented and biotinylated.

extract_protocol: Peripheral blood CD19+ cells were separated by magnetic-activated cell sorting using Whole Blood CD19 MicroBeads (Miltenyi Biotec) and total RNA was isolated using the mirVana isolation kit (Thermo Fisher Scientific) according to the manufacturers' protocols.

value: glatiramer acetate

tag: edss after 1 year

tag: edss after 2 years

tag: edss after 3 years

tag: edss after 4 years


title: dkfz_ATRT_157


title: dkfz_ATRT_88


title: dkfz_ATRT_49


title: Patient 9, CD19+ cells, before first dose of fingolimod [exon-level]

tag: relapses during the year prior to fingolimod

tag: relapses during 1-year follow-up

tag: relapses during 2-year follow-up


title: dkfz_ATRT_7

tag: gender


title: dkfz_ATRT_51


title: dkfz_ATRT_163


title: Patient 4, CD14+ cells, before first dose of fingolimod [exon-level]

tag: relapses during 3-year follow-up

tag: relapses during 4-year follow-up

tag: completed years of fingolimod therapy


title: Patient 3, CD14+ cells, before second dose of fingolimod [exon-level]

tag: patient identifier

tag: age in years at baseline


title: Patient 1, CD14+ cells, before first dose of fingolimod [exon-level]

tag: disease duration in years at baseline


title: dkfz_ATRT_16

tag: age (years)

tag: tumor location


title: dkfz_ATRT_6


title: dkfz_ATRT_11


title: dkfz_ATRT_36


title: dkfz_ATRT_154


title: dkfz_ATRT_30


title: dkfz_ATRT_160


title: dkfz_ATRT_12


title: dkfz_ATRT_164


title: dkfz_ATRT_10


title: dkfz_ATRT_86


title: Patient 3, CD14+ cells, before first dose of fingolimod [exon-level]

tag: previous treatment

tag: treatment gap in months

tag: edss at baseline


title: dkfz_ATRT_43


title: dkfz_ATRT_152


title: dkfz_ATRT_171


title: dkfz_ATRT_173


title: dkfz_ATRT_41


title: dkfz_ATRT_153


title: dkfz_ATRT_172


title: Patient 1, CD14+ cells, after 3 months of fingolimod treatment [exon-level]

tag: edss after 1 year

tag: edss after 2 years

tag: edss after 3 years


title: Patient 3, CD14+ cells, after 3 months of fingolimod treatment [exon-level]

tag: edss after 4 years

tag: relapses during the year prior to fingolimod

tag: relapses during 1-year follow-up


title: dkfz_ATRT_159

tag: gender


title: dkfz_ATRT_17


title: dkfz_ATRT_101


title: Hs_soft-tissue_MRT (hEC._.INI90)

status: Public on Jan 27 2016

source_name: Malignant Rhabdoid Tumor

tag: tissue

value: MRT


title: Hs_soft-tissue_MRT (hEC._.INI97)


title: Hs_soft-tissue_MRT (hEC._.INI38)


title: Hs_soft-tissue_MRT (hEC._.INI59)


title: Hs_soft-tissue_MRT (hEC._.INI50)


title: Hs_soft-tissue_MRT (hEC._.INI91)


title: Hs_soft-tissue_MRT (hEC._.INI53b)


title: Hs_soft-tissue_MRT (hEC._.INI25)


title: Hs_soft-tissue_MRT (hEC._.INI93)


title: Hs_soft-tissue_MRT (hEC._.INI119)


title: Hs_soft-tissue_MRT (hEC._.INI28)


title: Hs_soft-tissue_MRT (hEC._.INI56)


title: dkfz_ATRT_48


title: Hs_soft-tissue_MRT (hEC._.INI18)


title: Hs_soft-tissue_MRT (hEC._.INI19)


title: Hs_soft-tissue_MRT (hEC._.INI22)


title: Hs_soft-tissue_MRT (hEC._.INI24)


title: Hs_soft-tissue_MRT (hEC._.INI110)


title: Hs_soft-tissue_MRT (hEC._.INI116)


title: Hs_soft-tissue_MRT (hEC._.INI109)


title: Patient 9, CD8+ cells, after 3 months of fingolimod treatment [gene-level]

status: Public on Sep 19 2015

source_name: Peripheral blood CD8+ cells

extract_protocol: Peripheral blood CD8+ cells were separated by magnetic-activated cell sorting using Whole Blood CD8 MicroBeads (Miltenyi Biotec) and total RNA was isolated using the mirVana isolation kit (Thermo Fisher Scientific) according to the manufacturers' protocols.

tag: relapses during 2-year follow-up

tag: relapses during 3-year follow-up

tag: relapses during 4-year follow-up

tag: completed years of fingolimod therapy


title: Patient 10, CD8+ cells, after 3 months of fingolimod treatment [gene-level]

tag: patient identifier

tag: age in years at baseline

tag: disease duration in years at baseline


title: Patient 5, CD8+ cells, after 3 months of fingolimod treatment [gene-level]

tag: previous treatment

tag: treatment gap in months


title: Patient 3, CD8+ cells, before second dose of fingolimod [gene-level]

tag: edss at baseline

tag: edss after 1 year


title: Patient 8, CD8+ cells, before first dose of fingolimod [gene-level]

tag: edss after 2 years

tag: edss after 3 years


title: Patient 8, CD8+ cells, after 3 months of fingolimod treatment [gene-level]

tag: edss after 4 years

tag: relapses during the year prior to fingolimod


title: Patient 10, CD8+ cells, before second dose of fingolimod [gene-level]

tag: gender

tag: relapses during 1-year follow-up


title: Patient 8, CD8+ cells, before second dose of fingolimod [gene-level]

tag: relapses during 2-year follow-up


title: Patient 10, CD8+ cells, before first dose of fingolimod [gene-level]

tag: relapses during 3-year follow-up


title: Patient 3, CD8+ cells, after 3 months of fingolimod treatment [gene-level]

tag: relapses during 4-year follow-up


title: Patient 3, CD8+ cells, before first dose of fingolimod [gene-level]

tag: completed years of fingolimod therapy


title: Patient 9, CD8+ cells, before second dose of fingolimod [gene-level]

tag: patient identifier


title: Patient 6, CD8+ cells, before first dose of fingolimod [gene-level]

tag: age in years at baseline


title: Patient 9, CD8+ cells, before first dose of fingolimod [gene-level]

tag: disease duration in years at baseline


title: Patient 5, CD8+ cells, before first dose of fingolimod [gene-level]

tag: previous treatment


title: Patient 6, CD8+ cells, after 3 months of fingolimod treatment [gene-level]

tag: treatment gap in months


title: Patient 2, CD8+ cells, after 3 months of fingolimod treatment [gene-level]

tag: edss at baseline


title: Patient 1, CD8+ cells, before second dose of fingolimod [gene-level]

tag: edss after 1 year


title: Patient 2, CD8+ cells, before first dose of fingolimod [gene-level]

tag: edss after 2 years


title: Patient 1, CD8+ cells, before first dose of fingolimod [gene-level]

tag: edss after 3 years


title: Patient 1, CD8+ cells, after 3 months of fingolimod treatment [gene-level]

tag: edss after 4 years


title: Patient 2, CD8+ cells, before second dose of fingolimod [gene-level]

tag: relapses during the year prior to fingolimod


title: Patient 6, CD8+ cells, before second dose of fingolimod [gene-level]

tag: gender


title: dkfz_ATRT_47

tag: age (years)

tag: tumor location


title: Patient 5, CD8+ cells, before second dose of fingolimod [gene-level]

tag: relapses during 1-year follow-up

tag: relapses during 2-year follow-up

tag: relapses during 3-year follow-up


title: Patient 10, CD4+ cells, after 3 months of fingolimod treatment [gene-level]

source_name: Peripheral blood CD4+ cells

extract_protocol: Peripheral blood CD4+ cells were separated by magnetic-activated cell sorting using Whole Blood CD4 MicroBeads (Miltenyi Biotec) and total RNA was isolated using the mirVana isolation kit (Thermo Fisher Scientific) according to the manufacturers' protocols.

tag: patient identifier

tag: relapses during 4-year follow-up

tag: completed years of fingolimod therapy


title: Patient 10, CD4+ cells, before first dose of fingolimod [gene-level]

tag: age in years at baseline

tag: disease duration in years at baseline

tag: previous treatment


title: Patient 10, CD4+ cells, before second dose of fingolimod [gene-level]

tag: treatment gap in months

tag: edss at baseline

tag: edss after 1 year


title: Patient 9, CD4+ cells, before first dose of fingolimod [gene-level]

tag: edss after 2 years

tag: edss after 3 years

tag: edss after 4 years


title: dkfz_ATRT_25

tag: gender

tag: age (years)


title: Patient 9, CD4+ cells, before second dose of fingolimod [gene-level]

tag: relapses during the year prior to fingolimod

tag: relapses during 1-year follow-up


title: Patient 8, CD4+ cells, after 3 months of fingolimod treatment [gene-level]

tag: relapses during 2-year follow-up

tag: relapses during 3-year follow-up


title: Patient 4, CD4+ cells, before second dose of fingolimod [gene-level]

tag: patient identifier

tag: relapses during 4-year follow-up


title: dkfz_ATRT_151

tag: tumor location


title: Patient 8, CD4+ cells, before first dose of fingolimod [gene-level]

tag: age in years at baseline

tag: disease duration in years at baseline

tag: completed years of fingolimod therapy


title: Patient 3, CD4+ cells, before second dose of fingolimod [gene-level]

tag: previous treatment

tag: treatment gap in months

tag: edss at baseline


title: Patient 1, CD4+ cells, after 3 months of fingolimod treatment [gene-level]

tag: edss after 1 year

tag: edss after 2 years

tag: edss after 3 years


title: Patient 3, CD4+ cells, after 3 months of fingolimod treatment [gene-level]

tag: gender

tag: edss after 4 years


title: Patient 4, CD4+ cells, before first dose of fingolimod [gene-level]

tag: relapses during the year prior to fingolimod

tag: relapses during 1-year follow-up


title: Patient 3, CD4+ cells, before first dose of fingolimod [gene-level]

tag: relapses during 2-year follow-up

tag: relapses during 3-year follow-up


title: Patient 9, CD4+ cells, after 3 months of fingolimod treatment [gene-level]

tag: patient identifier

tag: relapses during 4-year follow-up


title: Patient 6, CD4+ cells, before second dose of fingolimod [gene-level]

tag: age in years at baseline


title: Patient 4, CD4+ cells, after 3 months of fingolimod treatment [gene-level]

tag: disease duration in years at baseline


title: Patient 8, CD4+ cells, before second dose of fingolimod [gene-level]

tag: completed years of fingolimod therapy


title: Patient 6, CD4+ cells, after 3 months of fingolimod treatment [gene-level]

tag: previous treatment


title: Patient 1, CD4+ cells, before first dose of fingolimod [gene-level]

tag: treatment gap in months


title: Patient 6, CD4+ cells, before first dose of fingolimod [gene-level]

tag: edss at baseline


title: Patient 1, CD4+ cells, before second dose of fingolimod [gene-level]

tag: edss after 1 year


title: Patient 10, CD8+ cells, before first dose of fingolimod [exon-level]

tag: edss after 2 years


title: Patient 10, CD8+ cells, before second dose of fingolimod [exon-level]

tag: edss after 3 years


title: Patient 8, CD8+ cells, before first dose of fingolimod [exon-level]

tag: gender


title: Patient 9, CD8+ cells, before second dose of fingolimod [exon-level]

tag: edss after 4 years


title: Patient 8, CD8+ cells, after 3 months of fingolimod treatment [exon-level]

tag: relapses during the year prior to fingolimod


title: Patient 9, CD8+ cells, before first dose of fingolimod [exon-level]

tag: relapses during 1-year follow-up


title: Patient 8, CD8+ cells, before second dose of fingolimod [exon-level]

tag: relapses during 2-year follow-up


title: Patient 10, CD8+ cells, after 3 months of fingolimod treatment [exon-level]

tag: relapses during 3-year follow-up


title: Patient 6, CD8+ cells, before second dose of fingolimod [exon-level]

tag: patient identifier


title: Patient 5, CD8+ cells, after 3 months of fingolimod treatment [exon-level]

tag: relapses during 4-year follow-up


title: Patient 9, CD8+ cells, after 3 months of fingolimod treatment [exon-level]

tag: age in years at baseline


title: Patient 5, CD8+ cells, before first dose of fingolimod [exon-level]

tag: disease duration in years at baseline


title: Patient 6, CD8+ cells, before first dose of fingolimod [exon-level]

tag: completed years of fingolimod therapy


title: Patient 10, CD4+ cells, before first dose of fingolimod [exon-level]

tag: previous treatment


title: Patient 5, CD8+ cells, before second dose of fingolimod [exon-level]

tag: treatment gap in months


title: Patient 1, CD8+ cells, before second dose of fingolimod [exon-level]

tag: edss at baseline


title: Patient 9, CD4+ cells, after 3 months of fingolimod treatment [exon-level]

tag: edss after 1 year


title: Patient 1, CD8+ cells, after 3 months of fingolimod treatment [exon-level]

tag: edss after 2 years


title: Patient 10, CD4+ cells, after 3 months of fingolimod treatment [exon-level]

tag: edss after 3 years


title: Patient 9, CD4+ cells, before second dose of fingolimod [exon-level]

tag: gender


title: Patient 3, CD8+ cells, after 3 months of fingolimod treatment [exon-level]

tag: edss after 4 years


title: Patient 1, CD8+ cells, before first dose of fingolimod [exon-level]

tag: relapses during the year prior to fingolimod


title: Patient 9, CD4+ cells, before first dose of fingolimod [exon-level]

tag: relapses during 1-year follow-up


title: Patient 3, CD8+ cells, before first dose of fingolimod [exon-level]

tag: relapses during 2-year follow-up


title: Patient 2, CD8+ cells, after 3 months of fingolimod treatment [exon-level]

tag: relapses during 3-year follow-up


title: Patient 10, CD4+ cells, before second dose of fingolimod [exon-level]

tag: patient identifier


title: Patient 2, CD8+ cells, before first dose of fingolimod [exon-level]

tag: relapses during 4-year follow-up


title: Patient 6, CD8+ cells, after 3 months of fingolimod treatment [exon-level]

tag: age in years at baseline


title: CT18 Replicate 2

status: Public on Jan 01 2013

city: Philadelphia

first: Utham Kashyap

last: Valekunja

state: PA

address: 3400 Civic Center Boulevard,

department: Department of Systems Pharmacology & Therapeutics, Perelman School of Medicine,

country: USA

institute: University of Pennsylvania

description: Gene expression data from mouse liver cicadian time pointCT18 Replicate 2

hyb_protocol: Standard Affymetrix protocol

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

data_processing: The data were analyzed with Genespring GX 11.

organism: Mus musculus

source_name: Mus musculus Liver

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated from liver samples of C57/BL6 mice over a circadian time course, 3 biological replicate samples per time point were collected and processed individually. RNA from each individual biological replicate sample was extracted using RNeasy mini kit (Qiagen Cat# 74106) and hybridized on an Affymetrix mouse Gene ST1.0 microarray.

treatment_protocol: Liver tissue was harvested from 4 adult male C57Bl/6 mice (Harlan-Olac, UK) once every 3 hours on the second cycle after transfer from 12L:12DR (stably entrained for 4 weeks) to DR:DR (L, light [220 µW cm-2] and DR, dim red light [< 5 µW cm-2]) and immediately frozen and then stored at -80°C prior to use.

tag: tissue

value: Liver

tag: genotype

tag: time point


title: Patient 3, CD8+ cells, before second dose of fingolimod [exon-level]

tag: disease duration in years at baseline

tag: previous treatment

tag: treatment gap in months

tag: completed years of fingolimod therapy


title: CT21 Replicate 2

description: Gene expression data from mouse liver cicadian time pointCT21 Replicate 2


title: CT21 Replicate 1

description: Gene expression data from mouse liver cicadian time pointCT21 Replicate 1


title: CT15 Replicate 1

description: Gene expression data from mouse liver cicadian time pointCT15 Replicate 1


title: CT12 Replicate 3

description: Gene expression data from mouse liver cicadian time pointCT12 Replicate 3


title: CT12 Replicate 1

description: Gene expression data from mouse liver cicadian time pointCT12 Replicate 1


title: CT18 Replicate 1

description: Gene expression data from mouse liver cicadian time pointCT18 Replicate 1


title: CT09 Replicate 3

description: Gene expression data from mouse liver cicadian time pointCT09 Replicate 3


title: Patient 8, CD4+ cells, before second dose of fingolimod [exon-level]

tag: edss at baseline

tag: edss after 1 year

tag: edss after 2 years

tag: edss after 3 years


title: CT15 Replicate 3

description: Gene expression data from mouse liver cicadian time pointCT15 Replicate 3


title: CT21 Replicate 3

description: Gene expression data from mouse liver cicadian time pointCT21 Replicate 3


title: CT09 Replicate 1

description: Gene expression data from mouse liver cicadian time pointCT09 Replicate 1


title: CT06 Replicate 2

description: Gene expression data from mouse liver cicadian time pointCT06 Replicate 2


title: CT03 Replicate 3

description: Gene expression data from mouse liver cicadian time pointCT03 Replicate 3


title: Patient 6, CD4+ cells, after 3 months of fingolimod treatment [exon-level]

tag: gender

tag: edss after 4 years

tag: relapses during the year prior to fingolimod

tag: relapses during 1-year follow-up


title: CT06 Replicate 1

description: Gene expression data from mouse liver cicadian time pointCT06 Replicate 1


title: Patient 2, CD8+ cells, before second dose of fingolimod [exon-level]

tag: patient identifier

tag: relapses during 2-year follow-up

tag: relapses during 3-year follow-up

tag: relapses during 4-year follow-up


title: CT03 Replicate 1

description: Gene expression data from mouse liver cicadian time pointCT03 Replicate 1

tag: tissue

tag: genotype

tag: time point


title: CT00 Replicate 2

description: Gene expression data from mouse liver cicadian time pointCT00 Replicate 2


title: CT00 Replicate 3

description: Gene expression data from mouse liver cicadian time pointCT00 Replicate 3


title: Patient 8, CD4+ cells, after 3 months of fingolimod treatment [exon-level]

description: Gene expression data from a multiple sclerosis patient treated with fingolimod

tag: age in years at baseline

tag: disease duration in years at baseline

tag: previous treatment

tag: treatment gap in months


title: Patient 8, CD4+ cells, before first dose of fingolimod [exon-level]

tag: edss at baseline

tag: edss after 1 year

tag: edss after 2 years

tag: completed years of fingolimod therapy


title: CT12 Replicate 2

description: Gene expression data from mouse liver cicadian time pointCT12 Replicate 2


title: CT00 Replicate 1

description: Gene expression data from mouse liver cicadian time pointCT00 Replicate 1


title: Patient 6, CD4+ cells, before second dose of fingolimod [exon-level]

tag: gender

tag: edss after 3 years

tag: edss after 4 years

tag: relapses during the year prior to fingolimod


title: Patient 4, CD4+ cells, before second dose of fingolimod [exon-level]

tag: patient identifier

tag: relapses during 1-year follow-up

tag: relapses during 2-year follow-up

tag: relapses during 3-year follow-up


title: Control_R_+Dox_rep3

status: Public on May 30 2012

city: san francisco

first: Yen-Sin

last: Ang

state: CALIFORNIA

address: 1650 Owens Street

institute: Gladstone Institute, UCSF

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was VST transformed, RSN normalized in R using LUMI package

source_name: Embryonic Stem Cell

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

growth_protocol: rtTA-expressing ES cells Aniv15 were used for derivation of rescue clones and were maintained on primary mouse embryonic fibroblasts with DMEM media supplemented with 15% FBS, 100 mM MEM non-essential amino acids, 0.1 mM 2-mercaptoethanol, 1 mM l-glutamine and 103 U ml-1 of LIF (Chemicon) and doxycycline (1ug/ml)

extract_protocol: total 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.

treatment_protocol: Each rescue ES clone was grown in +Dox (1ug/ml) media; Dox withdrawal was performed for 5days

tag: cell line

tag: strain background

tag: genotype/variation

value: Control

tag: condition

value: +Dox


title: Patient 3, CD4+ cells, before first dose of fingolimod [exon-level]

tag: age in years at baseline

tag: disease duration in years at baseline

tag: previous treatment

tag: treatment gap in months

tag: relapses during 4-year follow-up


title: CT09 Replicate 2

description: Gene expression data from mouse liver cicadian time pointCT09 Replicate 2

tag: tissue

tag: genotype

tag: time point


title: Patient 3, CD4+ cells, before second dose of fingolimod [exon-level]

tag: gender

tag: edss at baseline

tag: edss after 1 year

tag: edss after 2 years

tag: edss after 3 years

tag: edss after 4 years

tag: relapses during the year prior to fingolimod

tag: completed years of fingolimod therapy


title: Control_R_-Dox_rep3

tag: cell line

tag: strain background

tag: genotype/variation

tag: condition

value: -Dox


title: Control_R_-Dox_rep1


title: CT15 Replicate 2

description: Gene expression data from mouse liver cicadian time pointCT15 Replicate 2


title: CT06 Replicate 3

description: Gene expression data from mouse liver cicadian time pointCT06 Replicate 3


title: Control_R_-Dox_rep2


title: CT03 Replicate 2

description: Gene expression data from mouse liver cicadian time pointCT03 Replicate 2


title: CT18 Replicate 3

description: Gene expression data from mouse liver cicadian time pointCT18 Replicate 3


title: Patient 4, CD4+ cells, before first dose of fingolimod [exon-level]

tag: patient identifier

tag: age in years at baseline

tag: disease duration in years at baseline

tag: previous treatment

tag: treatment gap in months

tag: relapses during 1-year follow-up

tag: relapses during 2-year follow-up

tag: relapses during 3-year follow-up


title: Patient 1, CD4+ cells, before first dose of fingolimod [exon-level]

tag: gender

tag: edss at baseline

tag: edss after 1 year

tag: edss after 2 years

tag: relapses during 4-year follow-up


title: Control_R_+Dox_rep1

tag: cell line


title: Patient 3, CD4+ cells, after 3 months of fingolimod treatment [exon-level]

tag: edss after 3 years

tag: edss after 4 years

tag: relapses during the year prior to fingolimod

tag: completed years of fingolimod therapy


title: G-401

status: Public on Mar 20 2012

city: Cambridge

first: Nicolas

last: Stransky

state: MA

address: 7 Cambridge center

department: Cancer Program

institute: Broad Institute

description: Gene expression data from the CCLE

hyb_protocol: Fragmentation of the biotin-labeled cRNA prepared the sample for hybridization on the GeneChip Human U133 2.0 (PN 900467). The washing and staining was performed on the GeneChip Fluidics station using standard Affymetrix protocols outlined in the Expression Analysis Technical Manual, 2001, Affymetrix.

scan_protocol: The GeneChip® Scanner 3000 was used for scanning the arrays.

data_processing: The data were analyzed with 2.14.0, using the packages affyio_1.22.0 and affy_1.32.0, and RMA as normalization method. rma() was used with default options (normalize=TRUE, background=TRUE) and with the package hgu133plus2hsentrezgcdf_15.0.0 from Brainarray for the CDF file.

source_name: ATCC

label_protocol: The Affymetrix One-Cycle Target labeling assay was used to synthesize hybridization target using 1 mg of total RNA. Labeled cRNA hybridization target was produced using a 3-day, semi-automated workflow

growth_protocol: Cells lines were cultured following growth recommendations from the cell line source vendors. Cells were incubated at 37 ºC at 5% CO2 until 70% confluency was reached.  Pellets were harvested 48 hours post media change, flash frozen, and stored at -80 ºC until nucleic acid extraction.

extract_protocol: RNA was isolated from frozen cell pellets, containing an average cell count of 4.5 million cells, via Trizol (Invitrogen) extraction following the manufacturers instructions. Samples were quantified using both the Nanodrop 8000 spectrophotometer (ThermoScientific) and via Agilent 2100 Bioanalyzer.

tag: primary site

tag: histology


title: G-402

description: Gene expression data from the CCLE


title: Patient 4, CD4+ cells, after 3 months of fingolimod treatment [exon-level]

tag: patient identifier

tag: age in years at baseline

tag: disease duration in years at baseline

tag: previous treatment


title: Control_R_+Dox_rep2

tag: strain background

tag: genotype/variation

tag: condition


title: A-204

description: Gene expression data from the CCLE

value: rhabdomyosarcoma


title: MyD88-/-_Spleen_control NON-INFECTED_rep 3

status: Public on Jan 13 2012

city: Worcester

first: Ricardo

middle: Tostes

last: Gazzinelli

state: Massachusetts

address: 364 Plantation Street

department: Medicine

institute: University of Massachusetts Medical School

description: Gene expression data from splenocytes obtained from non-infected mice

hyb_protocol: Chips were hybridized at 45-C for 16 h and washed with fluidics protocol EukGE-WS2v5 according to Affymetrix’s recommendation

scan_protocol: The arrays were scanned at an emission wavelength of 570 nm at 2.5-mm resolution in the GCS3000 laser scanner (Affymetrix). The intensity of the hybridization for each probe pair was computed by GCOS 1.1 software

data_processing: The expression value (average difference) for each gene was determined by calculating the average of differences in intensity (perfect match intensity – mismatch intensity) between its probe pairs. The expression analysis file created from each sample (chip) was imported into GeneSpring 7.2 (Agilent Technologies, Inc., Palo Alto, CA) for further data characterization. A new experiment was generated after importing data from the same organ in which data were normalized by the array to the 50th percentile of all measurements on that array. Lists of genes that were either induced or suppressed more that two fold between samples from non-infected vs. 6 days infected mice of same genotype were created by filtration-on-fold function within the presented list. The differential expression was evaluated in grouped samples from each mouse genotype (Wt or Knockout mice) and time point (non-infected vs 6 days post infection) using ANOVA. Values correspond to fold increase or suppression (threshold of two fold) of genes between infected Vs non-infected groups of same genotype.

source_name: spleen from MyD88-/- non-infected mice

label_protocol: Double-stranded cDNA was synthesized from total RNA and labeled using the ENZO BioArray RNA transcript labeling kit (Enzo Life Sciences, Inc., Farmingdale, NY, USA) to generate biotinylated cRNA. Biotin-labeled cRNA was purified and fragmented randomly according to Affymetrix’s protocol. A total of 200 µL of sample cocktail containing 15 µg of fragmented and biotin-labeled cRNA was loaded onto each chip

extract_protocol: Spleen from C57BL/6 or knockout mice non-infected or after 6 days post infection with 10E5 P. chabaudi infected red blood cells were harvested and immediately transferred into tubes containing TRIzol® reagent (Invitrogen, Carlsbad CA) and freeze in liquid nitrogen. Sample homogeinization and total RNA isolation were subsequently processed according to the manufacturer’s protocol (Invitrogen). RNA pellets were resuspended in nuclease-free water (Invitrogen) and quantified by ultraviolet spectroscopy for purity and concentration (NanoDrop, Wilmington, DE). Integrity of RNA samples was evaluated by electrophoresis in 1% agarose gel and were assessed further for RNA integrity on the Agilent Bioanalyzer (Santa Clara, CA).  Equivalent aliquots of 2.5 µg of total RNA from 12 independent samples (3 non-infected C57BL/6, or MyD88-/- and 3 P. chabaudi infected C57BL/6, or MyD88-/- mice) were assessed using the Affymetrix MOE 430 2.0 GeneChip array GeneChips.

treatment_protocol: Spleen from C57BL/6 or MyD88 knockout mice non-infected or after 6 days post infection with 10E5 P. chabaudi infected red blood

tag: gender

tag: strain/genotype

tag: age

value: 8 weeks

tag: tissue

value: spleen


title: MyD88-/-_Spleen  INFECTED at 6th P.chabaudi_rep 1

description: Gene expression data from splenocytes obtained from infected mice at 6th of P.chabaudi infection

source_name: spleen from MyD88-/- mice at 6th of P.chabaudi infection


title: MyD88-/-_Spleen  INFECTED at 6th P.chabaudi_rep 2


title: MyD88-/-_Spleen  INFECTED at 6th P.chabaudi_rep 3


title: C57BL/6_Spleen  INFECTED at 6th P.chabaudi_rep 1

source_name: spleen from C57BL/6 mice at 6th of P.chabaudi infection


title: C57BL/6_Spleen  INFECTED at 6th P.chabaudi_rep 3


title: C57BL/6_Spleen_control NON-INFECTED_rep 1

source_name: spleen from C57BL/6 non-infected mice


title: MyD88-/-_Spleen_control NON-INFECTED_rep 2


title: C57BL/6_Spleen_control NON-INFECTED_rep 3


title: KYM-1

description: Gene expression data from the CCLE

source_name: HSRRB


title: MyD88-/-_Spleen_control NON-INFECTED_rep 1


title: C57BL/6_Spleen_control NON-INFECTED_rep 2


title: C57BL/6_Spleen  INFECTED at 6th P.chabaudi_rep 2


title: Patient 6, CD4+ cells, before first dose of fingolimod [exon-level]

tag: treatment gap in months

tag: edss at baseline

tag: edss after 1 year

tag: edss after 2 years

tag: edss after 3 years

tag: relapses during 1-year follow-up

tag: relapses during 2-year follow-up

tag: relapses during 3-year follow-up

tag: relapses during 4-year follow-up


title: Patient 1, CD4+ cells, before second dose of fingolimod [exon-level]

tag: patient identifier

tag: age in years at baseline

tag: disease duration in years at baseline

tag: previous treatment

tag: edss after 4 years

tag: relapses during the year prior to fingolimod

tag: completed years of fingolimod therapy


title: Patient 1, CD4+ cells, after 3 months of fingolimod treatment [exon-level]

tag: gender


title: spinal_cord_anterior_rep2

status: Public on Aug 12 2011

city: Kobe, Hyogo

first: Hiroki

middle: R

last: Ueda

address: 2-2-3, Minatojima-minamimachi, Chuo-ku

department: Center for Developmental Biology

country: Japan

institute: RIKEN

description: Pooled samples collected at every 4 hours over 1 day

hyb_protocol: cRNA was subsequently fragmented and hybridized to the GeneChip according to manufacturer’s instructions. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix).

data_processing: The raw data were summarized with the RMA algorithm.

source_name: spinal cord anterior

label_protocol: cDNA samples were subjected to the one-cycle target labeling procedure for biotin labeling by in vitro transcription (Affymetrix)

growth_protocol: Balb/c mice (male) purchased 5 weeks postpartum, were adapted under standard 12 h light/dark cycles (LD) for 2 weeks, before samples were obtained under LD or constant darkness (DD) conditions, every 4 h over 1 day, starting at ZT0.

extract_protocol: The total RNA was prepared from the pooled samples for each region taken at all time points using Trizol reagent (GIBCO BRL).

treatment_protocol: Slices (0.5-mm thick) of mouse brain were cut on a Mouse Brain Matrix (Neuroscience, Tokyo), frozen, and the specific regions were punched out bilaterally with a microdissecting needle (gauge 0.5 mm) under a stereomicroscope.

value: male

tag: strain

value: Balb/c

tag: age

value: 7-8 weeks

tag: tissue

value: spinal cord anterior


title: Cb_nucleus_rep1

source_name: cerebellar nucleus

value: cerebellar nucleus


title: Retina_rep2

source_name: retina

value: retina


title: Tg_rep1

source_name: dorsal tegmental nucleus

value: dorsal tegmental nucleus


title: Cb_lobe_rep1

source_name: cerebellar cortex lobe

value: cerebellar cortex lobe


title: Pn_rep1

source_name: pontine nucleus

value: pontine nucleus


title: Cb_lobe_rep2


title: Cb_vermis_rep1

source_name: cerebellar cortex vermis

value: cerebellar cortex vermis


title: Cb_vermis_rep2


title: Pn_rep2


title: Tg_rep2


title: spinal_cord_posterior_rep2

source_name: spinal cord posterior

value: spinal cord posterior


title: SC_rep2

source_name: superior colliculus

value: superior colliculus


title: SN_rep1

source_name: substantia nigra

value: substantia nigra


title: spinal_cord_posterior_rep1


title: VTA_rep1

source_name: ventral tegmental area

value: ventral tegmental area


title: VTA_rep2


title: SN_rep2


title: MVe_rep2

source_name: medial vestibular nucleus

value: medial vestibular nucleus


title: PAG_rep2

source_name: periaqueductal gray

value: periaqueductal gray


title: Cb_nucleus_rep2


title: IC_rep2

source_name: inferior colliculus

value: inferior colliculus


title: IC_rep1

value: male


title: SC_rep1

value: Balb/c


title: LH_rep2

source_name: lateral hypothalamus

value: 7-8 weeks

value: lateral hypothalamus


title: PAG_rep1


title: LH_rep1


title: spinal_cord_anterior_rep1

value: spinal cord anterior


title: MVe_rep1


title: VMH_rep1

source_name: ventromedial hypothalamic nucleus

value: ventromedial hypothalamic nucleus


title: DM_rep2

source_name: dorsomedial hypothalamic nucleus

value: dorsomedial hypothalamic nucleus


title: Arc_rep1

source_name: arcuate hypothalamic nucleus

value: arcuate hypothalamic nucleus


title: Arc_rep2


title: Pa_rep2

source_name: paraventricular hypothalamic nucleus

value: paraventricular hypothalamic nucleus


title: SO_rep1

source_name: supraoptic nucleus

value: supraoptic nucleus


title: SO_rep2


title: SPa_dorsal_rep1

source_name: subparaventricular zone dorsal

value: subparaventricular zone dorsal


title: MPA_rep2

source_name: medial preoptic area

value: medial preoptic area


title: SCN_rep1

source_name: suprachiasmatic nucleus

value: suprachiasmatic nucleus


title: Pituitary_rep2

source_name: pituitary

value: pituitary


title: SPa_ventral_rep2

source_name: subparaventricular zone ventral

value: subparaventricular zone ventral


title: ME_rep1

source_name: median eminence

value: median eminence


title: Pa_rep1


title: ME_rep2


title: VMH_rep2


title: M_rep2

source_name: mammillary body

value: mammillary body


title: Pineal_rep2

source_name: corpus pineal

value: male

value: corpus pineal


title: MPA_rep1

value: Balb/c

value: 7-8 weeks


title: DM_rep1


title: SPa_ventral_rep1


title: SPa_dorsal_rep2


title: MG_rep2

source_name: medial geniculate nucleus

value: medial geniculate nucleus


title: M_rep1


title: SCN_rep2


title: Hb_rep1

source_name: habenular nucleus

value: habenular nucleus


title: Pituitary_rep1


title: Pineal_rep1


title: GP_rep1

source_name: globus pallidus

value: globus pallidus


title: MG_rep1


title: Retina_rep1

source_name: retina

value: retina


title: CPu_lateral_rep1

source_name: caudate putamen lateral

value: caudate putamen lateral


title: CPu_medial_rep1

source_name: caudate putamen medial

value: caudate putamen medial


title: A_posterior_rep2

source_name: amygdaloid complex (posterior)

value: amygdaloid complex (posterior)


title: LG_rep1

source_name: lateral geniculate body

value: lateral geniculate body


title: VPM_VPL_rep1

source_name: ventral posterolateral thalamic nucleus / ventral posteromedial thalamic nucleus


title: CPu_lateral_rep2


title: VPM_VPL_rep2

value: ventral posterolateral thalamic nucleus / ventral posteromedial thalamic nucleus


title: VA_VL_rep2

source_name: ventral anterior thalamic nucleus / ventrolateral thalamic nucleus


title: MD_rep1

source_name: mediodorsal thalamic nucleus

value: mediodorsal thalamic nucleus


title: Hb_rep2


title: LG_rep2


title: A_posterior_rep1


title: MD_rep2


title: A_anterior_rep1

source_name: amygdala anterior

value: amygdala anterior


title: GP_rep2


title: DG_rep2

source_name: dentate gyrus (hippocampus)

value: dentate gyrus (hippocampus)


title: A_anterior_rep2


title: DG_rep1


title: VA_VL_rep1

value: ventral anterior thalamic nucleus / ventrolateral thalamic nucleus


title: CA2_CA3_rep1

source_name: CA2 / CA3 (hippocampus)

value: male

value: CA2 / CA3 (hippocampus)


title: CA2_CA3_rep2

value: Balb/c


title: CA1_rep2

source_name: CA1 (hippocampus)

value: 7-8 weeks

value: CA1 (hippocampus)


title: ventral_S_rep2

source_name: ventral subiculum

value: ventral subiculum


title: CA1_rep1


title: Tu_rep2

source_name: olfactory tubercle

value: olfactory tubercle


title: ventral_S_rep1


title: Tu_rep1


title: Cx_cingulate_rep1

source_name: cerebral cortex cingulate

value: cerebral cortex cingulate


title: OB_anterior_rep1

source_name: olfactory bulb anterior

value: olfactory bulb anterior


title: Cx_cingulate_rep2


title: Pir_rep1

source_name: piriform cortex

value: piriform cortex


title: OB_posterior_rep1

source_name: olfactory bulb posterior

value: olfactory bulb posterior


title: Pir_rep2


title: Cx_motor_rep2

source_name: cerebral cortex motor

value: cerebral cortex motor


title: Cx_motor_rep1


title: LS_rep2

source_name: lateral septal nucleus

value: lateral septal nucleus


title: OB_posterior_rep2


title: RS_rep2

source_name: retrosplenial cortex

value: retrosplenial cortex


title: LS_rep1


title: OB_anterior_rep2


title: RS_rep1


title: Human synovial sarcoma SS111

status: Public on Sep 01 2010

city: Tokyo

first: Hitoshi

last: Ichikawa

address: 5-1-1 Tsukiji, Chuo-ku

institute: National Cancer Center Research Institute

hyb_protocol: Following fragmentation, 10 μg of cRNA were hybridized for 16 hr at 45˚C on GeneChip Human Genome U133 plus 2.0 array (Affymetrix). Arrays were washed and stained in Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data were analyzed with GeneChip Operating Softwere version 1.3 (GCOS1.3, Affymetrix) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Synovial sarcoma tumor tissue

label_protocol: Biotinylated cRNA was prepared from 1 μg of total RNA with a one-cycle cDNA synthesis kit and 3’-amplification reagents for in vitro transcription labeling (Affymetrix).

extract_protocol: Total RNA was isolated using an Isogen reagent (Nippon Gene) and purified using an RNeasy MinElute cleanup kit (Qiagen).

treatment_protocol: Tumor samples were collected from a region of macroscopically high tumor content immediately after surgical excision and cryopreserved.

value: Synovial sarcoma tumor tissue

tag: sex

value: Female

tag: histological subtype

value: MSS

tag: syt-ssx fusion type


title: Human synovial sarcoma SS101

value: Male


title: Human synovial sarcoma SS054

value: BSS


title: Human synovial sarcoma SS107


title: Human synovial sarcoma SS102

value: PDSS


title: Human synovial sarcoma SSR01


title: Human synovial sarcoma SS113


title: Human synovial sarcoma SS047


title: Human synovial sarcoma SS052


title: Human synovial sarcoma SS109


title: Human synovial sarcoma SS115


title: CPu_medial_rep2

source_name: caudate putamen medial

value: male

value: Balb/c

value: 7-8 weeks

value: caudate putamen medial


title: Human synovial sarcoma SS119


title: Human synovial sarcoma SS051


title: Human synovial sarcoma SS055


title: Human synovial sarcoma SS114


title: Human synovial sarcoma SS042


title: Human synovial sarcoma SS106


title: Human synovial sarcoma SS049


title: Human synovial sarcoma SS112


title: Human synovial sarcoma SS012


title: Human synovial sarcoma SS043


title: Human synovial sarcoma SS041


title: Human synovial sarcoma SS046


title: Human synovial sarcoma SS013


title: Human synovial sarcoma SS044


title: Human synovial sarcoma SS045


title: Human synovial sarcoma SS053

tag: reclassified histological subtype


title: Human synovial sarcoma SS050


title: Human synovial sarcoma SS008


title: Human synovial sarcoma SS006


title: Human synovial sarcoma SS007


title: Human synovial sarcoma SS005


title: C57BL/6_Tumor_MCA203_rep3

status: Public on Jun 03 2010

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

description: Gene expression profile of CD11b+ cells from tumor infiltarte of MCA203 tumor-bearing mice

hyb_protocol: Accordingly to Expression Analysis: Technical Manual. 701021 Rev. 5. Santa Clara, CA, Affymetrix; 2004

data_processing: RMA of .CEL files using Bioconductor affy library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization

extract_protocol: Trizol extraction of total RNA was performed accordingly to manifacturer guidelines, with minor modifications. Extraction was followed by Qiagen Rneasy column clean-up accordingly to manifacturer instructions.

value: Tumor infiltrate

tag: experimental condition

value: Tumor-bearing


title: BALB/c_Bone Marrow_Fresh_rep1

description: Gene expression profile of CD11b+ cells from ex-vivo BALB/c mice bone marrow

scan_protocol: Accordingly to Expression Analysis: Technical Manual. 701021 Rev. 5. Santa Clara, CA, Affymetrix; 2004

value: BALB/c

value: Bone marrow

value: Ex-vivo


title: BALB/c_Bone Marrow_GM-CSF+IL-6_rep3

description: Gene expression profile of CD11b+ cells from in-vitro GM-CSF+IL-6 treated BALB/c mice bone marrow

label_protocol: Accordingly to Expression Analysis: Technical Manual. 701021 Rev. 5. Santa Clara, CA, Affymetrix; 2004

value: In-vitro GM-CSF + IL-6


title: BALB/c_Bone Marrow_Fresh_rep2

source_name: CD11b+ cells from ex-vivo BALB/c mice bone marrow


title: Human synovial sarcoma SS004


title: Human synovial sarcoma SS001


title: C57BL/6_Tumor_EL-4_rep2

description: Gene expression profile of CD11b+ cells from tumor infiltarte of EL-4 tumor-bearing mice


title: BALB/c_Bone Marrow_GM-CSF+G-CSF_rep1

description: Gene expression profile of CD11b+ cells from in-vitro GM-CSF+G-CSF treated BALB/c mice bone marrow

value: In-vitro GM-CSF + G-CSF


title: BALB/c_Bone Marrow_Fresh_rep3


title: BALB/c_Bone Marrow_GM-CSF+G-CSF_rep3

source_name: CD11b+ cells from in-vitro GM-CSF+G-CSF treated BALB/c mice bone marrow


title: BALB/c_Bone Marrow_GM-CSF+IL-6_rep2

source_name: CD11b+ cells from in-vitro GM-CSF+IL-6 treated BALB/c mice bone marrow


title: BALB/c_Bone Marrow_GM-CSF+G-CSF_rep2


title: BALB/c_Tumor_C26-GM_rep3

description: Gene expression profile of CD11b+ cells from tumor infiltarte of GM-CSF tumor-bearing mice


title: BALB/c_Tumor_4T1_rep3

description: Gene expression profile of CD11b+ cells from tumor infiltarte of 4T1 tumor-bearing mice


title: BALB/c_Tumor_4T1_rep1

source_name: CD11b+ cells from tumor infiltarte of 4T1 tumor-bearing mice


title: BALB/c_Bone Marrow_GM-CSF+IL-6_rep1


title: C57BL/6_Tumor_EL-4_rep3

source_name: CD11b+ cells from tumor infiltarte of EL-4 tumor-bearing mice


title: C57BL/6_Tumor_EL-4_rep1


title: BALB/c_Spleen_C26-GM_rep1

description: Gene expression profile of CD11b+ cells from spleen of GM-CSF tumor-bearing mice

value: Spleen


title: BALB/c_Spleen_C26-GM_rep3

source_name: CD11b+ cells from spleen of GM-CSF tumor-bearing mice


title: BALB/c_Tumor_C26-GM_rep2

source_name: CD11b+ cells from tumor infiltarte of GM-CSF tumor-bearing mice


title: C57BL/6_Tumor_MCA203_rep1

source_name: CD11b+ cells from tumor infiltarte of MCA203 tumor-bearing mice


title: BALB/c_Tumor_4T1_rep2


title: BALB/c_Spleen_C26-GM_rep2


title: BALB/c_Tumor_C26-GM_rep1


title: C57BL/6_Tumor_MCA203_rep2


title: C57BL/6_Spleen_Healthy_rep2

description: Gene expression profile of CD11b+ cells from spleen of healthy BALB/c mice

value: Healthy


title: C57BL/6_Spleen_Healthy_rep3

source_name: CD11b+ cells from spleen of healthy BALB/c mice


title: BALB/c_Spleen_Healthy_rep1


title: C57BL/6_Spleen_Healthy_rep1


title: BALB/c_Spleen_Healthy_rep3


title: BALB/c_Spleen_Healthy_rep2


title: Aorta AAA 4

status: Public on Aug 26 2009

city: Townsville

first: Catherine

last: Rush

state: Queensland

address: Douglas Campus

country: Australia

institute: James Cook University

hyb_protocol: RNA hybridization was performed at the SRC Microarray Facility, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia using standard Illumina protocols (illumina.com) and using Illumina Sentrix Mouse WG-6 version 1.1 beadchips.

scan_protocol: Slide scanning on BeadArray Reader was performed at SRC Microarray Facility, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia using standard Illumina protocols (illumina.com)

data_processing: Raw data was extracted with BeadStudio V2 and imported into Genespring GX 7.3.1. Default GeneSpring normalisation was used i.e. Data transformation: values less than 0.01 were set to 0.01; Per Chip Normalisation: normalised to 50th percentile; Per Gene Normalisation: normalised to median. Normalised values= raw signal/control signal, where control signal for each gene is calculated by the default Genespring normalisations i.e. Per Chip normalised to 50th percentile and per gene normalised to median. The control value then corresponds roughly to the product of these two normalisation factors.  Normalized values are calculated by simply dividing the raw expression value by the control value. Dividing raw signal by control signal centres data around 1.

source_name: aorta

label_protocol: Performed at SRC Microarray Facility, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia using standard Illumina protocols (illumina.com). Expression protocols feature a first- and second-strand reverse transcription step, followed by a single in vitro transcription (IVT) amplification that incorporates biotin-labeled nucleotides. Subsequent steps include array hybridization, washing, blocking, and streptavadin-Cy3 staining. Fluorescence emission by Cy3 is quantitatively detected for downstream analysis.

growth_protocol: RNA extracted from aortas of mice at necroscopy

extract_protocol: Total RNA was extracted from homogenised aortas using TRI Reagent (Sigma) and  RNeasy Mini kit (Qiagen) and analysed on the HP 2100 Bioanalyzer (Agilent Technologies) for integrity. All samples had RNA integrity scores of between 7.5 and 8.1. RNA extracted from the whole aortas of 5 mice with aneurysms was compared with that extracted from the whole of aortas of 6 saline controls and 7 mice exposed to angiotensin II which did not develop aneurysms.

treatment_protocol: 13-14 week old male ApoE-/- mice were exposed to angiotensin II (1.44 µg/kg/min, via Alzet miniosmotic pump model 2004) or saline for 4 weeks. Mice exposed to AngII that develped AAA were included in AAA group, whilst those that did not were included in no AAA group. Saline infused mice were included in saline group

tag: ApoE-/-, male, 17 weeks


title: Aorta no AAA 7


title: Aorta AAA 3


title: Aorta no AAA 3


title: Aorta saline 4


title: Aorta no AAA 2


title: Aorta AAA 1


title: Aorta AAA 2


title: Aorta saline 3


title: Aorta saline 5


title: Aorta no AAA 1


title: Aorta AAA 5


title: Aorta saline 6


title: Aorta no AAA 4


title: Aorta saline 2


title: Aorta saline 1


title: Aorta no AAA 6


title: Aorta no AAA 5


title: DKF-2-GFP Rep2

status: Public on Jan 12 2009

city: Bronx

first: Charles

middle: S

last: Rubin

state: NY

address: 1300 Morris Park Avenue

department: Molecular Pharmacology

institute: Albert Einstein College of Medicine

description: Biological replicate 2 of 3.  dkf-2::DKF-2-GFP transgene versus wildtype (N2).

hyb_protocol: Microarray slides, containing 60-mer oligonucleotides representing transcripts encoded by ~22,000 C. elegans genes (whole genome), were obtained from the C. elegans Genome Project at Washington University, St. Louis, MO. Control and experimental cDNA samples (Cy3 and Cy5 labeled) were combined in 60 µl hybridization buffer (35% formamide, 0.5% SDS, 2.5X Denhardt’s solution and 4X SSPE) along with a blocking reagent (2µg polydA, 4µg tRNA) and pre-hybridized for 1 h at 50C. The microarray slide was rinsed with nuclease-free water and pre-incubated in hybridization buffer supplemented with salmon sperm DNA. Probe solution was dispensed over the array and covered with an M series Lifterslip (Erie Scientific). Hybridization was performed at 50C for 16 h in an Arrayit Hybridization Cassette (Telechem International). Water (10 µl) was placed in wells at the ends of the chamber to maintain 100% humidity within the sealed chamber. After hybridization, arrays were successively washed in 2XSSC + 0.1% SDS, 0.2XSSC + 0.1% SDS, and 0.2XSSC. Next, slides were placed in 50 ml tubes and centrifuged for 5 min at 1,000 rpm to remove the aqueous solution. Slides were shielded from light prior to scanning.

scan_protocol: Each array was scanned at 10 μm, using an AXON GenePix 4000A Microarray Scanner. The Cy3 and Cy5 channels were equilibrated during a pre-scan and brought within an equivalent range. Once the PMT and POW settings were adjusted, the array was scanned.

data_processing: Each array was quantified using Axon's GenePix 6.0 software and  gal file provided by Washington University. Both channels were loaded, inspected for defective spots and flagged accordingly. Then GenePix generated a gpr file that was used for downstream analysis. Locally weighted linear regression (LOWESS) normalization was used globally to reduce systematic errors in measured expression levels. The Red signal was adjusted by the computed LOWESS normalization factor while the Green signal was held constant. The ratio for each spot is computed as Ratio = Red.norm / Green.

organism: Caenorhabditis elegans

source_name: Cyanine-5 (red) labeled cDNA derived from transgenic C. elegans expressing DKF-2-GFP under regulation of the dkf-2 promoter (wild type background).

label_protocol: cDNA probes for DNA microarray hybridization were prepared with the SuperScript Plus cDNA Labeling System (Invitrogen). Samples of total RNA (20 μg) isolated from WT C. elegans and animals expressing a dkf-2::DKF-2-GFP transgene (WT background) were used as templates. MMLV reverse transcriptase catalyzed cDNA synthesis using dNTPs that contain Cy3 or Cy5 tagged dUTP. After completion of cDNA synthesis, template RNA was eliminated by digestion with RNAse. Cy3- and Cy5-labeled cDNA probes were concentrated by centrifugation at 3000 x g, using an Amicon YM-50 membrane.

growth_protocol: Synchronized animals were grown on NGM plates (20˚C).

extract_protocol: C. elegans was grown on agar plates seeded with E. coli OP50 at 20C. Animal development was synchronized by standard procedures. Young adult worms were harvested by washing plates with M9 buffer (20C) and transferring suspended animals to 50 ml conical centrifuge tubes. Nematodes were pelleted by centrifugation at 2000 x g for 10 min and washed three times with M9 buffer to remove bacteria. Next, pelleted worms were extracted with 10 vol of Trizol (Invitrogen) reagent and total RNA was isolated according to the manufacturer’s protocol. RNA was purified on an RNeasy column (Qiagen) as described by the manufacturer. Purified RNA was eluted with nuclease-free water. RNA concentration was determined by using a Nanodrop spectrophotometer. RNA quality was verified by electrophoresis in an Agilent Bioanalyzer.

treatment_protocol: Young adult animals were harvested 20 h after the L4 larval stage.

tag: Animals express a dkf-2::DKF-2-GFP transgene (N2 background).

source_name: Cyanine-3 (green) labeled cDNA derived from wild type (N2) C. elegans.

tag: wild type (N2)


title: DKF-2-GFP Rep1

description: Biological replicate 1 of 3.  dkf-2::DKF-2-GFP transgene versus wildtype (N2).


title: DKF-2-GFP Rep3

description: Biological replicate 3 of 3.  dkf-2::DKF-2-GFP transgene versus wildtype (N2).