title: Validation patient #49 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Validation IgG 1-50

tag: halabi predicted survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score


title: Validation patient #46 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

status: Public on Aug 26 2015

type: protein

city: Frederick

first: Christopher

last: Campbell

state: MD

address: 376 Boyles Street

country: USA

institute: NCI

hyb_protocol: Arrays were blocked with BSA overnight, and serum samples (diluted 1:50) was incubated on the array for 3 hours at 37 C and gentle agitation (100 RPM).  Slides were then washed with PBS contain 0.05% Tween (PBST).  After washing, bound antibodies were detected with fluorescently labeled secondary antibodies.  Slides were then washed with PBST, spun dry in a centrifuge, and scanned.

scan_protocol: Slides were scanned with a Genepix 4000A fluorescence scanner at two gain settings (typically 430 and 520) in order to increase dynamic range.  Signal from ch1 (532 nm) was analyzed to determine the level of bound DyLight 549 conjugated secondary antibody specific for human IgG.  Signal from ch2 (635nm) was analyzed to determine the level of bound DyLight 649 secondary antibody specific for human IgM.  Scanned images were analyzed with Genepix Pro (v6.0) to determine the fluorescence and background signal for each array component.

data_processing: First, median pixel intensity of each feature was background subtracted.  Second, signals for features that were saturated at the high photomultipler tube (PMT) setting were calculated by proportionally scaling the value from the low PMT setting according to a correction factor, which was calculated based on mid-intensity signals measured at the high and low PMT settings.  To account for slide-to-slide variations in array processing, microarray data were normalized by median centering based on a reference serum sample analyzed on each slide.  Additionally, a minimum signal of 150 was set as the floor.  Since array features were printed in duplicate and all samples were analyzed on two slides, pre-processing averaged normalized data from 4 technical replicates.  Final data are reported on a log 2 scale.

label: DyLight 549

molecule: protein

organism: Homo sapiens

source_name: Serum

label_protocol: After serum was incubated on the array, bound anti-glycan antibodies were labeled for 2 hours with a combination of DyLight549 conjugated anti human IgG (Jackson 109-505-008) and DyLight 649 conjugated anti-human IgM  (Jackson Immuno, 109-495-043).

extract_protocol: Serum was obtained from peripheral blood samples

treatment_protocol: Diluted 1:50

tag: post-vaccination survival (months)

tag: treatment arm

value: PROSTVAC

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: on-study psa

tag: treatment

value: Vaccine

tag: timepoint

value: Pre-treatment

tag: molecule

value: IgG

label: DyLight 649

value: IgM


title: Validation patient #47 |  Vaccine Arm  | Post-treatment | Day 28 | Validation IgG 1-50


title: Training patient #15 |  Vaccine Arm  | Day 82 | Training IgM 1-50

tag: gleason #

tag: ellispot

tag: tregs

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox

value: Post-vaccination


title: Validation patient #44 |  Control Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: halabi predicted survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

value: Control

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score


title: Validation patient #43 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: post-vaccination survival (months)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: on-study psa


title: Validation patient #41 |  Control Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: treatment

tag: timepoint

tag: molecule


title: Training patient #7 |  Vaccine Arm  | Day 87 | Training IgM 1-50

tag: gleason #

tag: ellispot

tag: tregs

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)


title: Training patient #8 |  Vaccine Arm  | Day 86 | Training IgM 1-50

tag: halabi predicted survival (months)

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox


title: Validation patient #42 |  Control Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score


title: Validation patient #39 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: on-study psa

tag: treatment


title: Training patient #1 |  Vaccine Arm  | Day 85 | Training IgM 1-50

tag: gleason #

tag: ellispot

tag: tregs

tag: timepoint

tag: molecule


title: Validation patient #54 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Validation IgG 1-50

tag: halabi predicted survival (months)


title: Validation patient #40 |  Control Arm  | Post-treatment | Day 84 | Validation IgG 1-50


title: Validation patient #37 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgG 1-50


title: Training patient #21 |  Vaccine Arm  | Day 89 | Training IgM 1-50

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox


title: Validation patient #36 |  Vaccine Arm  | Post-treatment | Day 56 | Validation IgG 1-50

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score


title: Training patient #32 |  Vaccine Arm  | Day 85 | Training IgM 1-50

tag: on-study psa

tag: treatment


title: Training patient #22 |  Vaccine Arm  | Day 88 | Training IgM 1-50

tag: gleason #

tag: ellispot


title: Validation patient #45 |  Control Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: timepoint


title: Training patient #16 |  Vaccine Arm  | Day 26 | Training IgM 1-50

tag: halabi predicted survival (months)

tag: tregs

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)

tag: molecule


title: Validation patient #35 |  Control Arm  | Post-treatment | Day 56 | Validation IgG 1-50

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)


title: Training patient #9 |  Vaccine Arm  | Day 85 | Training IgM 1-50

tag: age at enrollment (years)

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox

tag: post-vaccination igg titer for fowlpox


title: Training patient #31 |  Vaccine Arm  | Day 82 | Training IgM 1-50

tag: on-study psa

tag: gleason #

tag: ellispot

tag: treatment


title: Validation patient #38 |  Control Arm  | Post-treatment | Day 28 | Validation IgG 1-50

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: gleason score

tag: timepoint


title: Validation patient #34 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgG 1-50

tag: halabi predicted survival (months)

tag: molecule


title: Training patient #28 |  Vaccine Arm  | Day 83 | Training IgM 1-50

tag: tregs

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)


title: Training patient #23 |  Vaccine Arm  | Day 83 | Training IgM 1-50

tag: age at enrollment (years)

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for vaccinia


title: Validation patient #43 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50

hyb_protocol: Arrays were blocked with BSA overnight, and serum (diluted 1:50) was incubated on the array for 3 hours at 37 C and gentle agitation (100 RPM).  Slides were then washed with PBS contain 0.05% Tween (PBST).  After washing, bound antibodies were detected with fluorescently labeled secondary antibodies.  Slides were then washed with PBST, spun dry in a centrifuge, and scanned.

scan_protocol: Slides were scanned with a Genepix 4000A fluorescence scanner at two gain settings (typically 430 and 520) in order to increase dynamic range.  Signal from ch1 (532 nm) was analyzed to determine the level of bound Cy3 conjugated secondary antibody specific for human total immunoglobulin.  Scanned images were analyzed with Genepix Pro (v6.0) to determine the fluorescence and background signal for each array component.

label_protocol: After serum was incubated on the array, bound anti-glycan antibodies were labeled for 2 hours with Cy3-conjugated anti-human total immunoglobulin (IgM+IgG+IgA) (Jackson Immuno, 109-165-064).

treatment_protocol: Diluted 1:200

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: post-vaccination igg titer for fowlpox

tag: on-study psa

value: Total Ig


title: Validation patient #31 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: treatment arm

tag: treatment


title: Training patient #20 |  Vaccine Arm  | Day 81 | Training IgM 1-50

tag: gleason #

tag: ellispot

tag: pre-vaccination igg titer for fowlpox


title: Validation patient #32 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: halabi predicted survival (months)

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: gleason score

tag: timepoint


title: Validation patient #30 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Validation IgG 1-50

tag: age at enrollment (years)

tag: molecule


title: Training patient #27 |  Vaccine Arm  | Day 85 | Training IgM 1-50

tag: tregs

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for vaccinia


title: Validation patient #29 |  Vaccine Arm  | Post-treatment | Day168/EARLY WD | Validation IgG 1-50

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: post-vaccination igg titer for fowlpox

tag: on-study psa


title: Training patient #14 |  Vaccine Arm  | Day 82 | Training IgM 1-50

tag: halabi predicted survival (months)

tag: gleason #

tag: ellispot

tag: pre-vaccination igg titer for fowlpox

tag: treatment


title: Validation patient #28 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: age at enrollment (years)

tag: gleason score

tag: timepoint


title: Validation patient #33 |  Vaccine Arm  | Post-treatment | Day 56 | Validation IgG 1-50

tag: molecule


title: WM266-4_replicate2

type: RNA

city: East Melbourne

first: Petranel

middle: T

last: Ferrao

address: St. Andrew's Place

department: Cancer Research

country: Australia

institute: Peter MacCallum Cancer Centre

description: gene expression data from melanoma cell line WM266-4

hyb_protocol: Hybridization was for 16hours andaccording to the standard Affymetrix protocol.

scan_protocol: GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450 using standard Fluidics Protocol (Fluidics protocol FS450_007). GeneChips were scanned using the Affymetrix 7G Scanner.

data_processing: The data was rma normalised using the R Bioconductor package affy.

label: biotin

molecule: total RNA

source_name: melanoma cell line WM266-4

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1mg total RNA.

growth_protocol: Cell lines were plated and harvested when 50-80% confluent.  RNA was extracted and hybridized on Affymetrix microarrays. At least 2 biological repeats were performed for each cell line.

extract_protocol: QIAGEN RNeasy kit

tag: cell type

value: melanoma cell line

tag: cell line

value: melanoma cell line WM266-4


title: Training patient #29 |  Vaccine Arm  | Day 83 | Training IgM 1-50

tag: tregs

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for vaccinia


title: Validation patient #27 |  Vaccine Arm  | Post-treatment | Day 112 | Validation IgG 1-50

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: post-vaccination igg titer for fowlpox

tag: on-study psa


title: Training patient #30 |  Vaccine Arm  | Day 34 | Training IgM 1-50

tag: age at enrollment (years)

tag: gleason #

tag: ellispot

tag: pre-vaccination igg titer for fowlpox

tag: treatment


title: SK-MEL28_replicate1

description: gene expression data from melanoma cell line SK-MEL28

source_name: melanoma cell line SK-MEL28

tag: cell type

tag: cell line

value: melanoma cell line SK-MEL28


title: WM266-4_replicate1


title: Validation patient #26 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgG 1-50

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: gleason score

tag: timepoint

tag: molecule


title: Training patient #12 |  Vaccine Arm  | Day 80 | Training IgM 1-50

tag: halabi predicted survival (months)

tag: tregs

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for vaccinia


title: SK-MEL1_replicate2

description: gene expression data from melanoma cell line SK-MEL1

source_name: melanoma cell line SK-MEL1

value: melanoma cell line SK-MEL1


title: SK-MEL28_replicate2


title: Validation patient #25 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgG 1-50

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: on-study psa


title: SK-MEL1_replicate1

tag: cell type

tag: cell line


title: Training patient #26 |  Vaccine Arm  | Day 57 | Training IgM 1-50

tag: gleason #

tag: ellispot

tag: pre-vaccination igg titer for fowlpox

tag: treatment


title: SK-MEL24_replicate1

description: gene expression data from melanoma cell line SK-MEL24

source_name: melanoma cell line SK-MEL24

value: melanoma cell line SK-MEL24


title: SK-MEL24_replicate3


title: RPMI-7951_replicate1

description: gene expression data from melanoma cell line RPMI-7951

source_name: melanoma cell line RPMI-7951

value: melanoma cell line RPMI-7951


title: MALME-3M_replicate1

description: gene expression data from melanoma cell line MALME-3M

source_name: melanoma cell line MALME-3M

value: melanoma cell line MALME-3M


title: RPMI-7951_replicate2


title: LOX-IMVI_replicate4

description: gene expression data from melanoma cell line LOX-IMVI

source_name: melanoma cell line LOX-IMVI

value: melanoma cell line LOX-IMVI


title: Training patient #5 |  Vaccine Arm  | Day 84 | Training IgM 1-50

tag: halabi predicted survival (months)

tag: tregs

tag: timepoint

tag: molecule


title: Validation patient #23 |  Vaccine Arm  | Post-treatment | Day 56 | Validation IgG 1-50

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: gleason score


title: Training patient #24 |  Vaccine Arm  | Day 95 | Training IgM 1-50

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for vaccinia


title: Validation patient #24 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: on-study psa


title: Training patient #3 |  Vaccine Arm  | Day 85 | Training IgM 1-50

tag: halabi predicted survival (months)

tag: gleason #

tag: ellispot

tag: pre-vaccination igg titer for fowlpox

tag: treatment


title: Training patient #2 |  Vaccine Arm  | Day 85 | Training IgM 1-50

tag: tregs

tag: timepoint

tag: molecule


title: Training patient #19 |  Vaccine Arm  | Day 83 | Training IgG 1-50

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)


title: Validation patient #20 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgG 1-50

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: gleason score


title: Validation patient #21 |  Control Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm


title: Training patient #10 |  Vaccine Arm  | Day 79 | Training IgG 1-50

tag: age at enrollment (years)

tag: on-study psa

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for fowlpox


title: Validation patient #22 |  Control Arm  | Post-treatment | Day168/EARLY WD | Validation IgG 1-50

tag: halabi predicted survival (months)

tag: treatment


title: Validation patient #19 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgG 1-50

tag: timepoint


title: Training patient #7 |  Vaccine Arm  | Day 87 | Training IgG 1-50

tag: gleason #

tag: ellispot

tag: tregs

tag: pre-vaccination igg titer for fowlpox

tag: molecule


title: Validation patient #18 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgG 1-50

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: gleason score


title: Validation patient #17 |  Control Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm


title: LOX-IMVI_replicate1

tag: cell type

tag: cell line


title: Training patient #4 |  Vaccine Arm  | Day 81 | Training IgG 1-50

tag: age at enrollment (years)

tag: on-study psa

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for fowlpox


title: Training patient #25 |  Vaccine Arm  | Day 90 | Training IgG 1-50

tag: halabi predicted survival (months)

tag: gleason #

tag: ellispot

tag: tregs

tag: pre-vaccination igg titer for fowlpox

tag: treatment

tag: timepoint


title: Validation patient #16 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Validation IgG 1-50

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: gleason score

tag: molecule


title: HT144_replicate2

description: gene expression data from melanoma cell line HT144

source_name: melanoma cell line HT144

tag: cell type

tag: cell line

value: melanoma cell line HT144


title: HT144_replicate1


title: HS294T_replicate4

description: gene expression data from melanoma cell line HS294T

source_name: melanoma cell line HS294T

value: melanoma cell line HS294T


title: Training patient #13 |  Vaccine Arm  | Day 82 | Training IgG 1-50

tag: age at enrollment (years)

tag: on-study psa

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for fowlpox

value: Vaccine


title: HS294T_replicate2


title: D41-M1_replicate2

description: gene expression data from melanoma cell line D41

source_name: melanoma cell line D41

value: melanoma cell line D41


title: Training patient #22 |  Vaccine Arm  | Day 88 | Training IgG 1-50

tag: halabi predicted survival (months)

tag: gleason #

tag: ellispot

tag: tregs

tag: pre-vaccination igg titer for fowlpox

tag: treatment

tag: timepoint

value: IgG


title: D28-M3_replicate3

description: gene expression data from melanoma cell line D28

source_name: melanoma cell line D28

value: melanoma cell line D28


title: Validation patient #14 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

value: PROSTVAC

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: gleason score

value: Pre-treatment

tag: molecule

value: IgM


title: Validation patient #15 |  Control Arm  | Post-treatment | Day 84 | Validation IgG 1-50

value: Control

tag: age at enrollment (years)

tag: on-study psa


title: Training patient #15 |  Vaccine Arm  | Day 82 | Training IgG 1-50

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for fowlpox

value: Post-vaccination


title: Training patient #8 |  Vaccine Arm  | Day 86 | Training IgG 1-50

tag: halabi predicted survival (months)

tag: gleason #

tag: ellispot

tag: tregs

tag: pre-vaccination igg titer for fowlpox


title: Training patient #9 |  Vaccine Arm  | Day 85 | Training IgG 1-50

tag: treatment

tag: timepoint


title: D17-M1_replicate2

description: gene expression data from melanoma cell line D17

source_name: melanoma cell line D17

tag: cell type

value: melanoma cell line

tag: cell line

value: melanoma cell line D17


title: MALME-3M_replicate2


title: D28-M3_replicate2


title: Training patient #1 |  Vaccine Arm  | Day 85 | Training IgG 1-50

tag: molecule


title: Validation patient #11 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: age at enrollment (years)

tag: gleason score


title: Validation patient #13 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: halabi predicted survival (months)

tag: post-vaccination igg titer for fowlpox

tag: on-study psa


title: Validation patient #10 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50


title: Validation patient #12 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Validation IgG 1-50


title: D17-M1_replicate1b


title: Validation patient #8 |  Vaccine Arm  | Post-treatment | Day 56 | Validation IgG 1-50


title: Validation patient #7 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgG 1-50


title: D17-M1_replicate1


title: COLO829_replicate3

description: gene expression data from melanoma cell line COLO829

source_name: melanoma cell line COLO829

value: melanoma cell line COLO829


title: Training patient #16 |  Vaccine Arm  | Day 26 | Training IgG 1-50

tag: gleason #

tag: ellispot

tag: tregs

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for vaccinia


title: Training patient #2 |  Vaccine Arm  | Day 85 | Training IgG 1-50

tag: pre-vaccination igg titer for fowlpox

tag: treatment

tag: timepoint

tag: molecule


title: Training patient #21 |  Vaccine Arm  | Day 89 | Training IgG 1-50


title: C091-M1_replicate4

description: gene expression data from melanoma cell line C091

source_name: melanoma cell line C091

tag: cell type

tag: cell line

value: melanoma cell line C091


title: D41-M1_replicate1


title: Validation patient #4 |  Control Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: age at enrollment (years)

tag: gleason score


title: Validation patient #6 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: halabi predicted survival (months)

tag: post-vaccination igg titer for fowlpox

tag: on-study psa


title: COLO829_replicate1


title: C091-M1_replicate3


title: Training patient #30 |  Vaccine Arm  | Day 34 | Training IgG 1-50

tag: gleason #

tag: ellispot

tag: tregs

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for vaccinia


title: C089-M1_replicate3

description: gene expression data from melanoma cell line C089

source_name: melanoma cell line C089

tag: cell type

tag: cell line

value: melanoma cell line C089


title: Validation patient #3 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: treatment

tag: timepoint

tag: molecule


title: Training patient #20 |  Vaccine Arm  | Day 81 | Training IgG 1-50

tag: age at enrollment (years)

tag: halabi predicted survival (months)

tag: pre-vaccination igg titer for fowlpox

tag: post-vaccination igg titer for fowlpox


title: C088-M1_replicate2

description: gene expression data from melanoma cell line C088

source_name: melanoma cell line C088

value: melanoma cell line C088


title: Training patient #28 |  Vaccine Arm  | Day 83 | Training IgG 1-50

source_name: Serum

tag: on-study psa

tag: gleason #

tag: ellispot

tag: tregs


title: C089-M1_replicate2


title: Training patient #23 |  Vaccine Arm  | Day 83 | Training IgG 1-50

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for vaccinia


title: Training patient #32 |  Vaccine Arm  | Day 85 | Training IgG 1-50


title: Prog_nodox_techrep3

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

description: without induction

hyb_protocol: Hybridisation samples were prepared using 600 ng cRNA each according to the hybridisation protocol from Agilent: One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling), loaded onto the array slide and hybridised at 65 °C overnight

scan_protocol: After washing the microarray was scanned on an Agilent C Scanner using the Profile AgilentG3_GX_1Color for 8x60K microarrays (Dye channel: Green; Scan region: Scan Area (61 x 21.6 mm); Scan resolution (μm): 3; Tiff: 20 bit). The microarrays used were Agilent SurePrint G3 Mouse 8X60K microarrays (catalogue number: G4852A-028005).

data_processing: The microarray gene expression scanned images were analysed with Feature Extraction Software 10.7.1.1 (Agilent) (protocol GE1_107_Sep09, Grid: 028005_D_F_20100614 and platform Agilent SurePrint G3 Mouse GE 8x60K). The raw data output by Feature Extraction Software was analysed using the LIMMA R package 37 with quantile normalisation and background correction by the using of  normexp method 38 and an offset value of 16. Contrast matrix, lmFit and eBays function were used and a p value cut-off <= 0.001 was applied. Only genes with a minimum log2 intensity value equal to or greater than 6.5 in at least one array were selected as expressed genes. Genes that changed expression at least two fold up or down with respect to -/+ Dox or genes that changed expression at least two fold up or down through differentiation from haemogenic endothelium (HE) cells progressing to progenitors cells were considered as differentially expressed.

organism: Mus musculus

source_name: progenitors cells, noDox replicate 3

label_protocol: RNA was labelled with Cyanine 3-CTP according to the sample preparation protocol from Agilent: One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling). The cells were vortexed and pelleted. The aqueous phase was collected and an equal volume of isopropanol was added and mixed. The mixture was loaded onto a RNeasy Minelute column (Qiagen, 74204) and purified as per manufacturer’s instructions. RNA concentration was determined by a nanodrop and its integrity was checked by Bioanalyzer.

extract_protocol: For RNA extraction the cell pellet was resuspended in 800 µl Trizol™ and stored at -80ºC freezer until used. Before isolation, Trizol was thawed and 200µl chloroform was added to the Trizol™. Complementary DNA (cDNA) was prepared from the mRNAs using MMLV-RT (Promega M170A) as per manufacturers’ recommendations. Real time PCR was performed with SYBR Green PCR master mix (Life technologies, 4309155) in a Stepone qPCR machine.

tag: strain

tag: cell type

value: progenitors cells

value: without induction


title: Prog_plusdox_biorep2

description: with RUNX1/ETO induction

source_name: progenitors cells, plusDox replicate 2

tag: treatment

value: with RUNX1/ETO induction


title: Validation patient #1 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: gleason score

value: Vaccine

tag: timepoint


title: Validation patient #5 |  Control Arm  | Post-treatment | Day 56 | Validation IgG 1-50

tag: halabi predicted survival (months)

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: on-study psa

tag: molecule

value: IgG


title: Training patient #31 |  Vaccine Arm  | Day 82 | Training IgG 1-50

tag: gleason #

tag: ellispot

tag: tregs

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)

tag: pre-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox


title: Validation patient #9 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Validation IgG 1-50

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: treatment


title: C088-M1_replicate1

tag: cell type

tag: cell line


title: C074-M1_replicate1

description: gene expression data from melanoma cell line C074

source_name: melanoma cell line C074

value: melanoma cell line C074


title: C074-M1_replicate3


title: C088-M1_replicate1b


title: Training patient #29 |  Vaccine Arm  | Day 83 | Training IgG 1-50

tag: halabi predicted survival (months)

tag: post-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for fowlpox

tag: timepoint


title: Training patient #12 |  Vaccine Arm  | Day 80 | Training IgG 1-50

tag: age at enrollment (years)

tag: on-study psa

tag: gleason #

tag: molecule


title: Validation patient #2 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Validation IgG 1-50

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: gleason score


title: Training patient #27 |  Vaccine Arm  | Day 85 | Training IgG 1-50

tag: ellispot

tag: tregs

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)

tag: pre-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox


title: C057-M1_replicate3

description: gene expression data from melanoma cell line C057

source_name: melanoma cell line C057

tag: cell type

tag: cell line

value: melanoma cell line C057


title: Training patient #14 |  Vaccine Arm  | Day 82 | Training IgG 1-50

tag: halabi predicted survival (months)

tag: post-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for fowlpox

tag: treatment


title: C057-M1_replicate2


title: Training patient #24 |  Vaccine Arm  | Day 95 | Training IgG 1-50

tag: age at enrollment (years)

tag: on-study psa

tag: gleason #

tag: timepoint


title: Training patient #26 |  Vaccine Arm  | Day 57 | Training IgG 1-50

tag: molecule


title: Training patient #5 |  Vaccine Arm  | Day 84 | Training IgG 1-50

tag: ellispot


title: Prog_nodox_biorep1

description: without induction

source_name: progenitors cells, noDox replicate 1

tag: strain


title: Prog_plusdox_biorep1

description: with RUNX1/ETO induction

source_name: progenitors cells, plusDox replicate 1


title: Prog_nodox_biorep2

description: without induction

source_name: progenitors cells, noDox replicate 2


title: myeloidProg_plusdox_biorep2

description: with RUNX1/ETO induction

source_name: myeloid cultured progenitors cells, plusDox replicate 2

value: myeloid cultured progenitors cells


title: Training patient #3 |  Vaccine Arm  | Day 85 | Training IgG 1-50

tag: tregs

tag: survival status at last follow-up (1 = alive, 0 = deceased)

value: IgM


title: C055-M1_replicate1

description: gene expression data from melanoma cell line C055

source_name: melanoma cell line C055

value: melanoma cell line C055


title: myeloidProg_plusdox_biorep1

description: with RUNX1/ETO induction

source_name: myeloid cultured progenitors cells, plusDox replicate 1


title: myeloidProg_nodox_biorep3

description: without induction

source_name: myeloid cultured progenitors cells, noDox replicate 3


title: myeloidProg_nodox_biorep2

description: without induction

source_name: myeloid cultured progenitors cells, noDox replicate 2


title: A375_replicate1

description: gene expression data from melanoma cell line A375

source_name: melanoma cell line A375

value: melanoma cell line A375


title: myeloidProg_plusdox_biorep3

description: with RUNX1/ETO induction

source_name: myeloid cultured progenitors cells, plusDox TechReplicate 3


title: A15-M1_replicate1

description: gene expression data from melanoma cell line A15

source_name: melanoma cell line A15

value: melanoma cell line

value: melanoma cell line A15


title: A15-M1_replicate2


title: A375_replicate2


title: HE2_plusdox_biorep2

description: with RUNX1/ETO induction

source_name: endothelial-haematopoietic transition (EHT), cells acquire the CD41 marker (referred to as HE2), plusDox replicate 2


title: HE2_plusdox_biorep3

description: with RUNX1/ETO induction

source_name: endothelial-haematopoietic transition (EHT), cells acquire the CD41 marker (referred to as HE2), plusDox replicate 3


title: HE2_plusdox_biorep1

description: with RUNX1/ETO induction

source_name: endothelial-haematopoietic transition (EHT), cells acquire the CD41 marker (referred to as HE2), plusDox replicate 1


title: A02-M1_replicate3

description: gene expression data from melanoma cell line A02

source_name: melanoma cell line A02

value: melanoma cell line A02


title: myeloidProg_nodox_biorep1

description: without induction

source_name: myeloid cultured progenitors cells, noDox replicate 1


title: C055-M1_replicate2


title: HE2_nodox_biorep3

description: without induction

source_name: endothelial-haematopoietic transition (EHT), cells acquire the CD41 marker (referred to as HE2), noDox replicate 3


title: TSP-null, AOM-DSS treated, biological rep2

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

description: gene expression data from colon of TSP-deficient mouse were treated with AOM and DSS

hyb_protocol: Hybridization cocktails for Mini Array (169 format) were heated to 99oC for 2 minutes then incubated for 45oC for 5 min followed by centrifugation at 13,000 RPM for 5 min. Entire volume, 110 µl, was loaded onto arrays and hybridized for 17 hrs at 45oC. Washing and staining were performed on a Affymetrix FS 450 station.

scan_protocol: GeneChips were scanned on a GeneChip 3000 7G scanner using GeneChip® Command Console Software (AGCC).

data_processing: Further statistical analysis of the CEL files was done using GeneSpring GX 11 software. Signals were quantile normalized using PLIER16 algorithm and base line transformed to the median of all samples. The log2 normalized signal values were then filtered to remove entities that show signal in the bottom 20th percentile across all samples. This list was further filtered to only include entities where at least 1 out of 4 conditions have CV < 25%. The list was then subjected to ANOVA with Benjamini-Hochberg False Discovery Rate correction (p <0 .05) applied. A 2-fold filter was applied to identify genes that are differentially expressed between any two specific conditions.

source_name: colon

label_protocol: Fragmentation and labeling of 20 ng total RNA per sample were performed using the Ovation EXON and Encore Biotin Module (NuGEN Technologies).

growth_protocol: Mice were bred at room temperature at a vivarium facility of Wilkes University. Drinking bottles of the same capacity (4 oz) and antidrip system were used for the DSS treatment.

extract_protocol: Total RNA extraction was performed using the RNAqueous®-4PCR kit (Applied Biosystems) according to the manufacturer's instructions.

treatment_protocol: Except for the controls, a final concentration of 1.5% DSS was added to the drinking water and a single injection of AOM was IP injected at day 1 of treatment with DSS.

tag: genotype

value: TSP-null


title: TSP-null, AOM-DSS treated, biological rep3


title: Wt,AOM-DSS treated, biological rep3

description: gene expression data from colon of WT mouse, AOM-DSS treated

value: Wild-type


title: HE2_nodox_biorep2

description: without induction

source_name: endothelial-haematopoietic transition (EHT), cells acquire the CD41 marker (referred to as HE2), noDox replicate 2


title: HE_plusdox_biorep3

description: with RUNX1/ETO induction

source_name: Hemogenic endothelium (HE) cells, plusDox replicate 3

value: Hemogenic endothelium (HE) cells


title: peripheral T cells-ice storm-56

type: genomic

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

country: Canada

institute: McGill University

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

scan_protocol: Arrays were scanned using the Illumina iScan Reader using standard recommended Illumina scanner settings.

data_processing: Extracted microarray intensities were preprocessed and normalized using the 'minfi' Bioconductor R package according to the Illumina Genome Studio protocol--background correction followed by normalization to control probes.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: peripheral T cells/ice storm/56

label_protocol: Standard Illumina Infinium Assay Protocol

extract_protocol: T cells were isolated from the PBMCs by immunomagnetic positive selection using CD3 dynabeads (Dynal). DNA was extracted with Wizard Genomic DNA Purification kit (Promega) following the manufacturers protocol.  Genomic DNA was quantified using Picogreen protocol (Quant-iT PicoGreen dsDNA Products, Invitrogen) and read on SpectraMAX GeminiXS Spectrophotometer. Bisulfite conversion was performed with 250 ng of genomic DNA using the EZ-96 DNA Methylation-Gold Kit (Zymo Research) according to the manufacturer's instructions.

tag: Sex

value: F

tag: tissue

value: T cell


title: HE2_nodox_biorep1

description: without induction

source_name: endothelial-haematopoietic transition (EHT), cells acquire the CD41 marker (referred to as HE2), noDox replicate 1

tag: cell type

value: without induction


title: HE_plusdox_biorep2

description: with RUNX1/ETO induction

source_name: Hemogenic endothelium (HE) cells, plusDox replicate 2

value: with RUNX1/ETO induction


title: A02-M1_replicate2

tag: cell line


title: HE_nodox_biorep3

description: without induction

source_name: Hemogenic endothelium (HE) cells, noDox replicate 3


title: HE_plusdox_biorep1

description: with RUNX1/ETO induction

source_name: Hemogenic endothelium (HE) cells, plusDox replicate 1


title: Wt,AOM-DSS treated, biological rep1


title: Wt,AOM-DSS treated, biological rep2


title: peripheral T cells-ice storm-1316

source_name: peripheral T cells/ice storm/1316


title: TSP-null, AOM-DSS treated, biological rep1


title: HE_nodox_biorep1

description: without induction

source_name: Hemogenic endothelium (HE) cells, noDox replicate 1


title: peripheral T cells-ice storm-287

source_name: peripheral T cells/ice storm/287

value: M


title: peripheral T cells-ice storm-449

source_name: peripheral T cells/ice storm/449


title: peripheral T cells-ice storm-827

source_name: peripheral T cells/ice storm/827


title: Liver from RG3487 treated rat 5

city: Basel

first: Laura

last: Badi

address: Grenzacherstrasse

country: Switzerland

institute: Hoffmann La Roche LTD

description: liver gene expression data from RG3487 (180mg/kg) treated rat (24h post p.o. treatment)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Affymetrix RatGenome 230-2 Array. GeneChips were washed and stained in a Affymetrix Fluidics Station.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. Probes above a detection threshold of 20 RFUwere considered expressed and used for further study data analysis

organism: Rattus norvegicus

source_name: Study 8038P08, animal 135

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

growth_protocol: standard regulatory compliant animal housing with enriched environment. Animals were housed in groups of five also dirung the experiment

extract_protocol: RNA extractin form RNA later sample was performed according to the Affymetrix recommended protocols.

treatment_protocol: test compound or vehicle (deionized water) applied orraly by gavage. Total volume of application 5 ml/kg. 24 hours after treatment animals were euthanized after sodium pentobarbiton (ip.) anesthesia. A piece of liver (from the bottm half or the left lateral lobe) was sampled and put and sotred in RNA later (Ambion)

value: CRL:WI (Han)

tag: animal age

value: 6-8 weeks

value: liver


title: Liver from RG3487 treated rat 3

source_name: Study 8038P08, animal 133


title: ANIT rat ID 159 sacrificed 120 h postdose, liver

city: Little Rock

first: Alison

middle: Hege

last: Harrill

state: AR

address: 4301 W Markham Street Slot 820-11

institute: University of Arkansas for Medical Sciences

hyb_protocol: The fragmented and labeled product was prepared for hybridization using the GeneChip Hybridization Control kit and then hybridized to an HT RG-230 PM Array Plate for 17h at 45⁰C (Affymetrix, Santa Clara, CA). The array was washed, stained with streptavidin R-phyoerythrin conjugate (Life Technologies).

scan_protocol: Arrays were scanned using a GeneTitan Multi-Channel Instrument (Affymetrix)

data_processing: Data were processed in Partek Genomics Suite using the default cel file importation settings. Data were normalized using RMA background correction. Data were then quantile normalized and the log(base2) was calculated. Probesets were summarized following median polish.

source_name: Sprague Dawley rat

label_protocol: Single stranded cDNA was reverse transcribed utilizing 50 ng of RNA on the Ovation RNA Amplification System v2 (NuGEN, San Carlos, CA). Following reverse transcription, 1.875 μg of cDNA was normalized to 150 ng/μl, then fragmented to <200bp products labeled with biotin using the Encore Biotin Module (NuGEN).

growth_protocol: 8 week old rats

extract_protocol: Between 100-500 mg of liver tissue was utilized for isolation of total RNA with the miRVana miRNA Isolation kit (Life Technologies) in accordance with the manufacturer’s specifications.

treatment_protocol: On the morning of dosing, all rats were weighed and received a single intragastric (i.g.) administration of either 50 mg/kg ANIT (Sigma-Aldrich, St Louis, MO) dissolved in corn oil (N=6/time point) or corn oil (N=6/time point) in a volume of 10 ml/kg. Groups of corn oil and ANIT-treated rats were euthanized 6, 24, 48, 72, 120, and 168h post dosing. With the exception of animals euthanized 6h following dosing, all animals were fasted overnight, for approximately 18h, on the night preceding necropsy. All animals received an intraperitoneal (i.p.) injection of 100 mg/kg of 5’-bromo-2’-deoxyuridine (BrdU; Sigma), approximately 2h prior to scheduled necropsy. Rats were euthanized by CO2 inhalation. Animal use was approved by the IACUC.

value: Sprague Dawley

tag: gender

value: male

tag: age

value: 8 weeks old

tag: agent

value: ANIT

tag: time

tag: condition

value: time of ANIT liver repair


title: ANIT rat ID 158 sacrificed 120 h postdose, liver


title: Liver from RG3487 treated rat 2

source_name: Study 8038P08, animal 132


title: peripheral T cells-ice storm-51

source_name: peripheral T cells/ice storm/51


title: ANIT rat ID 156 sacrificed 120 h postdose, liver


title: peripheral T cells-ice storm-1368

source_name: peripheral T cells/ice storm/1368


title: peripheral T cells-ice storm-1157

source_name: peripheral T cells/ice storm/1157


title: Liver from RG3487 treated rat 1

source_name: Study 8038P08, animal 131


title: peripheral T cells-ice storm-1427

source_name: peripheral T cells/ice storm/1427


title: peripheral T cells-ice storm-1191

source_name: peripheral T cells/ice storm/1191


title: Liver from RG3487 treated rat 4

source_name: Study 8038P08, animal 134


title: ANIT rat ID 155 sacrificed 120 h postdose, liver


title: peripheral T cells-ice storm-8

source_name: peripheral T cells/ice storm/8


title: ANIT rat ID 157 sacrificed 120 h postdose, liver


title: peripheral T cells-ice storm-826

source_name: peripheral T cells/ice storm/826


title: peripheral T cells-ice storm-105

source_name: peripheral T cells/ice storm/105


title: Liver from vehicle treated rat 4

description: liver gene expression data from vehicle (deionized water) treated rat (24h post p.o. treatment)

source_name: Study 8038P08, animal 4


title: Liver from vehicle treated rat 3

source_name: Study 8038P08, animal 3


title: Vehicle rat ID 154 sacrificed 120 h postdose, liver

value: vehicle

value: control for time of ANIT liver repair


title: Vehicle rat ID 153 sacrificed 120 h postdose, liver


title: HE_nodox_biorep2

description: without induction

source_name: Hemogenic endothelium (HE) cells, noDox replicate 2

tag: treatment


title: Vehicle rat ID 152 sacrificed 120 h postdose, liver


title: Liver from vehicle treated rat 5

source_name: Study 8038P08, animal 5


title: U3A Trophoblast CM

city: PITTSBURGH

first: Yoel

last: Sadovsky

state: Pennsylvania

address: 204 Craft Ave

department: Obstetrics and Gynecology

institute: MAGEE WOMENS RESEARCH INSTITUTE

description:
U3A cells and trophoblast medium
Gene expression after 24 h

hyb_protocol: The hybridization was performed using Gene Expression Hybridization Kit and Gene Expression Wash Buffer Kit from Agilent following the manufacturer's instructions

scan_protocol: Slides were scanned on Agilent Technologies Scanner G2600D using the protocol GE1_1100_July11

data_processing: The raw data were log2 transformed and normalized using the cyclic loess normalization algorithm. The values from duplicated probes were averaged

source_name: U3A and trophoblast medium

label_protocol: The labeling was performed using Low Input Quick Amp Labeling Kit, One-Color from Agilent following the manufacturer's instructions

growth_protocol: DMEM-H with 10% FBS and penicillin/streptomycin

extract_protocol: Total RNA were prepared using miRNeasy Mini Kit following the manufacturer's instructions

treatment_protocol: Additives to media for 24 h

value: fibrosarcoma

tag: genotype/variation

value: STAT -/-


title: Vehicle rat ID 151 sacrificed 120 h postdose, liver

source_name: Sprague Dawley rat


title: Liver from vehicle treated rat 2

source_name: Study 8038P08, animal 2


title: Vehicle rat ID 150 sacrificed 120 h postdose, liver


title: U3A INF-b

description:
U3A cells and IFN beta
Gene expression after 24 h

source_name: U3A and IFN beta (100u)


title: ANIT rat ID 184 sacrificed 24 h postdose, liver

value: time of peak ANIT liver injury


title: U3A NC2

description:
U3A cells and control medium 2
Gene expression after 24 h

source_name: U3A and control medium


title: peripheral T cells-ice storm-1030

source_name: peripheral T cells/ice storm/1030

value: T cell


title: ANIT rat ID 160 sacrificed 120 h postdose, liver


title: Liver from vehicle treated rat 1

source_name: Study 8038P08, animal 1


title: peripheral T cells-ice storm-1365

source_name: peripheral T cells/ice storm/1365

value: F


title: U3A NC1

description:
U3A cells and control medium 1
Gene expression after 24 h


title: Vehicle rat ID 149 sacrificed 120 h postdose, liver


title: peripheral T cells-ice storm-1248

source_name: peripheral T cells/ice storm/1248


title: ANIT rat ID 183 sacrificed 24 h postdose, liver


title: ANIT rat ID 182 sacrificed 24 h postdose, liver


title: peripheral T cells-ice storm-1036

source_name: peripheral T cells/ice storm/1036


title: peripheral T cells-ice storm-30

source_name: peripheral T cells/ice storm/30


title: peripheral T cells-ice storm-115

source_name: peripheral T cells/ice storm/115


title: TGH NC2

description:
HT1080 cells and control medium 2
Gene expression after 24 h

source_name: HT1080 and control medium

value: wild type


title: ANIT rat ID 180 sacrificed 24 h postdose, liver


title: CS3527 at 38 C 2nd

city: Kgs. Lyngby

first: Jun

last: Chen

state: Denmark

address: Søltofts Plads Building 221

department: Food

country: Denmark

institute: The Technical University of Denmark

description: Gene expression in strain CS3527 at growth temperature 38°C

hyb_protocol: For hybridization standard Agilent's kits, reagents and equipment were used according to manufacturers' specifications. See (http://www.chem.agilent.com/Library/usermanuals/Public/G4813-90000_OneColor_Prokaryote_Protocol_1.3.pdf)

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5 µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Lactococcus lactis

source_name: SA media, exponatial growth, OD600 = 0.3

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 5 ug total RNA using the FairPlay III Microarray Labeling Kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by purification procedure in the kit.  Dye incorporation and cDNA yield were checked with the NanoDrop ND-1000 Spectrophotometer  (Agilent Technologies, Santa Clara, CA).

growth_protocol: Growth temperature: 30 & 38°C. Growth media: SA media + 0.2% glucose with modifications ( extra addition of 200 mM uridine, cytidine, adenosine, guanosine, inosine and thymidine and 40mM MOPS; replacement of NaAC by 20 mM α-lipoic acid). SA media was described by Jensen, P. R. and K. Hammer (1993). Minimal Requirements for Exponential Growth of Lactococcus lactis. Appl. Environ. Microbial. 59(12): 4363-4366.

extract_protocol: Cells mixed with 200 µl Solution I (0.3M sucrose; 0.01M NaAC, pH = 4.8) and Solution II (2% SDS; 0.01M NaAC, pH = 4.8) were disrupted by acid washed glass beads (106 microns; sigma) in 400 µl hot phenol (equilibrated with acetate; Sigma). After centrifuge at full speed for 5 mins at room temperature, supernatant was extracted with hot phenol twice and followed by a extraction with 400 µ hot phenol and chloroform (1:1). Then, RNA was precipitated and washed by ethanol. RNA was dissolved in 25 µl DEPC-treated water. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: temperature

tag: replication id


title: ANIT rat ID 181 sacrificed 24 h postdose, liver

tag: strain


title: CS3527 at 38 C 4th


title: ANIT rat ID 179 sacrificed 24 h postdose, liver


title: Vehicle rat ID 178 sacrificed 24 h postdose, liver

value: control for time of peak ANIT liver injury


title: peripheral T cells-ice storm-1206

source_name: peripheral T cells/ice storm/1206


title: peripheral T cells-ice storm-1210

source_name: peripheral T cells/ice storm/1210

value: M


title: peripheral T cells-ice storm-1391

source_name: peripheral T cells/ice storm/1391


title: peripheral T cells-ice storm-363

source_name: peripheral T cells/ice storm/363


title: CS3527 at 38 C 1st


title: Vehicle rat ID 176 sacrificed 24 h postdose, liver

source_name: Sprague Dawley rat


title: peripheral T cells-ice storm-1315

source_name: peripheral T cells/ice storm/1315


title: Vehicle rat ID 177 sacrificed 24 h postdose, liver


title: AC_wnt3a, chd and kctd15 injected_rep3

city: Bethesda

first: Igor

last: Dawid

address: 6 Center Drive

institute: NICHD, NIH

description:
Gene expression data from animal caps injected with wnt3a, chordin and kctd15 mRNAs
12_wnt3a_chd_kctd15

hyb_protocol: Following fragmentation, 10 μg of aRNA were hybridized for 16 hr at 45°C on GeneChip® Xenopus laevis 2.0 Genome Array (64 Format). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Partek Genomics Suite with default analysis settings and global scaling as normalization method.

organism: Xenopus laevis

label_protocol: Biotinylated aRNA was synthesized through in vitro transcription according to the standard Affymetrix protocol (GeneChip® 3' IVT Express Kit user manual).

growth_protocol: Xenopus embryos were incubated in 0.2×MMR at 16°C and staged according to Nieuwkoop and Faber. The dissected animal caps were cultured in L-15 medium (67% L-15, 7.5 mM Tris-HCl pH7.5, 1 mg/ml BSA).

extract_protocol: Total RNA was extracted using the TRIzol reagent according to the manufacturer's instructions.

treatment_protocol: Xenopus embryos were injected with mRNAs in the animal pole at two-cell stage. The animal caps were dissected at stage 9 using forceps in 1×MMR on 1% agar plate.

value: animal caps


title: TGH INF-b

description:
HT1080 cells and IFN beta
Gene expression after 24 h

source_name: HT1080 cells and IFN beta (100u)


title: AC_wnt3a and chd injected_rep3

description:
Gene expression data from animal caps injected with wnt3a and chordin mRNAs
11_wnt3a_chd

value: injected with wnt3a and chordin mRNAs


title: MG1363 at 38 C 3rd

description: Gene expression in strain MG1363 at growth temperature 38°C


title: peripheral T cells-ice storm-9

source_name: peripheral T cells/ice storm/9


title: peripheral T cells-ice storm-879

source_name: peripheral T cells/ice storm/879


title: TGH Trophoblast CM

description:
HT1080 cells and trophoblast medium
Gene expression after 24 h

source_name: HT1080 cells and trophoblast medium


title: peripheral T cells-ice storm-709

source_name: peripheral T cells/ice storm/709


title: MG1363 at 38 C 1st


title: AC_lacZ injected_rep3

description:
Gene expression data from lacZ injected animal caps
9_lacZ

source_name: animal caps injected with lacZ mRNA

value: injected with lacZ mRNA


title: CS3527 at 38 C 3rd


title: Vehicle rat ID 174 sacrificed 24 h postdose, liver

value: Sprague Dawley

value: male

value: liver


title: Vehicle rat ID 175 sacrificed 24 h postdose, liver

value: 8 weeks old


title: CS3527 at 30 C 4th

description: Gene expression in strain CS3527 at growth temperature 30°C


title: peripheral T cells-ice storm-948

source_name: peripheral T cells/ice storm/948


title: AC_wnt3a, chd and kctd15 injected_rep2

description:
Gene expression data from animal caps injected with wnt3a, chordin and kctd15 mRNAs
8_wnt3a_chd_kctd15


title: Vehicle rat ID 173 sacrificed 24 h postdose, liver

value: vehicle


title: AC_kctd15 injected_rep3

description:
Gene expression data from animal caps injected with kctd15 mRNA
10_kctd15

source_name: animal caps injected with kctd15 mRNA

value: injected with kctd15 mRNA


title: MG1363 at 30 C 4th

description: Gene expression in strain MG1363 at growth temperature 30°C


title: peripheral T cells-ice storm-405

source_name: peripheral T cells/ice storm/405


title: AC_kctd15 injected_rep2

description:
Gene expression data from animal caps injected with kctd15 mRNA
6_kctd15


title: AC_wnt3a and chd injected_rep2

description:
Gene expression data from animal caps injected with wnt3a and chordin mRNAs
7_wnt3a_chd


title: AC_lacZ injected_rep2

description:
Gene expression data from lacZ injected animal caps
5_lacZ


title: peripheral T cells-ice storm-135

source_name: peripheral T cells/ice storm/135


title: CS3527 at 30 C 1st

source_name: SA media, exponatial growth, OD600 = 0.3


title: peripheral T cells-ice storm-1060

source_name: peripheral T cells/ice storm/1060


title: peripheral T cells-ice storm-384

source_name: peripheral T cells/ice storm/384


title: AC_wnt3a and chd injected_rep1

description:
Gene expression data from animal caps injected with wnt3a and chordin mRNAs
3_wnt3a_chd


title: TGH NC1

description:
HT1080 cells and control medium 1
Gene expression after 24 h

source_name: HT1080 and control medium

value: fibrosarcoma


title: MG1363 at 38 C 2nd


title: CS3527 at 30 C 3rd


title: MG1363 at 30 C 3rd


title: CS3527 at 30 C 2nd


title: peripheral T cells-ice storm-39

source_name: peripheral T cells/ice storm/39


title: peripheral T cells-ice storm-204

source_name: peripheral T cells/ice storm/204


title: MG1363 at 30 C 2nd


title: AAV8-TTR-miHBV7 4

status: Public on Aug 25 2015

city: Munich

first: Thomas

last: Michler

address: Trogerstr. 30

country: Germany

institute: Virology of Technische Universitaet Muenchen

description:
m948
cDNA generated using Ambion WT Expression kit

hyb_protocol: Hybridization was performed using GeneChip Hybridization, Wash, and Stain Kit kit (Affymetrix) according to instructions

scan_protocol: Scan was performed on a GeneChip Scanner 3000 7G with GeneChip Command Console (AGCC) Software (both Affymetrix)

data_processing: Data was analyzed in the “R” software environment (http://cran.r-project.org) using the Limma  and the oligo package from Bioconductor (http://bioconductor.org). Raw expression measurements have been quantile-normalized and background-corrected using the RMA background correction. A fixed-effects linear model was fit for each individual gene to estimate pairwise expression differences. Empirical Bayes approach was used to moderate the standard errors of the normalized log2 fold changes. Using a Principal Component Analysis and pairwise Pearson correlation coefficients for quality control of overall performance of the arrays. The samples m886, m939, m955, and m948 show different expression levels than the remaining arrays, thus they have been excluded from further analysis

source_name: Mouse treated with AAV expressing miRNA mimic replicate 4

label_protocol: Samples were labeled using GeneChip WT Terminal Labeling Kit (Affymetrix) according to instructions

growth_protocol: 1x10e11 particles AAV serotype 8 were injected in tail vene of HBV-transgenic mice and livers harvested 15 days later

extract_protocol: Total RNA was extracted using the miRNeasy kit including on-column DNA digest with the RNase-FreeDNase set (both Qiagen) and cDNA generated using Ambion WT Expression kit

treatment_protocol: Isolated liver pieces were conserved in RNAlater (Qiagen) and then lyzed using TissueLyser LT (Qiagen)

tag: organ


title: AC_lacZ injected_rep1

description:
Gene expression data from lacZ injected animal caps
1_lacZ


title: AAV8-H1-shHBV7-TTR-Ago2 4

description:
m955
cDNA generated using Ambion WT Expression kit

source_name: Mouse treated with AAV co-expressing shRNA & Ago2 replicate 4


title: AAV8-H1-shHBV7-TTR-Ago2 2

description:
m939
cDNA generated using Ambion WT Expression kit

source_name: Mouse treated with AAV co-expressing shRNA & Ago2 replicate 2


title: MG1363 at 30 C 1st


title: AC_wnt3a, chd and kctd15 injected_rep1

description:
Gene expression data from animal caps injected with wnt3a, chordin and kctd15 mRNAs
4_wnt3a_chd_kctd15


title: AAV8-empty vector 1

description:
m886
cDNA generated using Ambion WT Expression kit

source_name: Mouse treated with AAV control vector replicate 1


title: CNS cells, control mice, EAE D18, rep2

city: Kodaira

first: Shinji

last: Oki

state: Tokyo

address: 4-1-1 Ogawa-Higashi

department: Department of Immunology

country: Japan

institute: National Institute of Neuroscience, NCNP

hyb_protocol: cRNA was hybridised to Mouse Genome 430 2.0 Arrays using a GeneChip Hybridization, Wash, and Stain Kit (Affymetrix) according to manufacturer's instructions

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

data_processing: Arrays were anyalysed using GCOS software (Affymetrix) using Affymetrix default analysis settings

source_name: CNS CD4+ T cells

label_protocol: Biotinlyated cRNA was prepared using a 3' IVT express kit (Affymetrix) according to manufacture's instructions

extract_protocol: RNA was extracted using a RNAeasy kit (Qiagen) according to manufacturer's instructions

tag: genotype

value: control

tag: eae day

value: CNS CD4+ T cells


title: CNS cells, NR4A2 mice, EAE D32, rep1

value: NR4A2 mutant

tag: tissue


title: CNS cells, control mice, EAE D32, rep2


title: CNS cells, control mice, EAE D18, rep1


title: AAV8-TTR-miHBV7 2

description:
m892
cDNA generated using Ambion WT Expression kit

source_name: Mouse treated with AAV expressing miRNA mimic replicate 2

tag: Sex


title: AAV8-H1-shHBV7-TTR-Ago2 1

description:
m912
cDNA generated using Ambion WT Expression kit

source_name: Mouse treated with AAV co-expressing shRNA & Ago2 replicate 1


title: AAV8-H1-shHBV7-U6-TuDHBV7 2

description:
m929
cDNA generated using Ambion WT Expression kit

source_name: Mouse treated with AAV co-expressing shRNA & sense strand TuD replicate 2


title: AAV8-H1-shHBV7-U6-TuDHBV7 4

description:
m940
cDNA generated using Ambion WT Expression kit

source_name: Mouse treated with AAV co-expressing shRNA & sense strand TuD replicate 4


title: AAV8-H1-shHBV7 1

description:
m956
cDNA generated using Ambion WT Expression kit

source_name: Mouse treated with AAV expressing shRNA only replicate 1


title: CNS cells, control mice, EAE D32, rep1


title: AAV8-H1-shHBV7-U6-TuDHBV7 3

description:
m934
cDNA generated using Ambion WT Expression kit

source_name: Mouse treated with AAV co-expressing shRNA & sense strand TuD replicate 3


title: CNS cells, NR4A2 mice, EAE D32, rep2


title: AAV8-TTR-miHBV7 1

description:
m880
cDNA generated using Ambion WT Expression kit

source_name: Mouse treated with AAV expressing miRNA mimic replicate 1


title: AAV8-H1-shHBV7 2

description:
m964
cDNA generated using Ambion WT Expression kit

source_name: Mouse treated with AAV expressing shRNA only replicate 2


title: AAV8-empty vector 2

description:
m893
cDNA generated using Ambion WT Expression kit

source_name: Mouse treated with AAV control vector replicate 2


title: transformed human embryonic neural precursors, biological replicate 1

city: Winnipeg

first: Tamra

last: Werbowetski-Ogilvie

state: Manitoba

address: 611-745 Bannatyne Avenue

department: Biochemistry & Medical Genetics

institute: University of Manitoba

description: Expression data comparing transformed or neoplastic human neural precursors following OTX2 knockdown to transformed human neural precursor cells

hyb_protocol: 5.5 ug of single stranded cDNA was hybridized for 16 hr at 45C on GeneChip Human Gene 2.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: An Affymetrix GeneChip Scanner 3000 7G  was used and data extraction was performed using Affymetrix AGCC software.

data_processing: The data were analyzed with Partek Genomics Suite using the RMA normalization method

source_name: transformed human embyonic neural precursors

label_protocol: Biotin end labeled single strand cDNA was prepared according to the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual

growth_protocol: trans-hEN OTX2 KD and control trans-hENs were grown as neurospheres in defined medium (DMEM/F12 supplemented with 1% N2, 1% B27, 20 ng/ml EGF, and 20 ng/ml bFGF) and collected at passage 1.

extract_protocol: Norgen All-in-One kit according to manufacturer's guidelines.

treatment_protocol: OTX2 was knocked down in trans-hENs using Silencer Select siRNAs (Life Technologies). A non-silencing scramble siRNA was used as a negative control.

tag: cell type

value: neural precursor cells

value: transformed by non-silencing scramble siRNA


title: AT61 TCP

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials: Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute; Transfer 80μl of hyb solution to each array, then tape holes; Hybridize 16 hours at 45° at 60rpm; Fluidics washing is FS450_00007

scan_protocol: Scanning was performed according to Affymetrix protocol - Affymetrix Gene ChIP Scanner 3000 7G.

data_processing: CEL files were processed using the Affymetrix Power Tools (APT) Software Package. Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).

source_name: Adipose tissue derived MSCs

label_protocol: Samples were amplified and labelled using the Ambion® WT Expression Kit, combined with the GeneChip® WT Terminal Labeling and Controls Kit according to the manufacturers instructions.

growth_protocol: MSCs were isolated from lipoaspirates after patient’s written consent using guidelines approved by the Ethic Committee of the University of Aachen (Permit number: EK163/07). Culture medium consisted of Dulbecco´s Modified Eagles Medium-Low Glucose (DMEM-Low Glucose; PAA, Pasching, Austria) with 2 mM L-glutamine (Gibco/Invitrogen, Eugene, OR, USA), 100 U/mL penicillin/streptomycin and 10% human platelet lysate (hPL) which was pooled from five platelet units of healthy donors. Cultures were maintained at 37 °C in a humidified atmosphere containing 5 % CO2 with medium changes twice per week.

extract_protocol: Total RNA was isolated with the NucleoSpin® RNA Isolation Kit (Macherey-Nagel, Düren, Germany).

treatment_protocol: MSCs were seeded on different substrates: tissue culture plastic (TCP), non-structured polyimide  (PI flat) and nanogrooved polyimide (PI 650). Genome wide gene expression profiles of MSCs were analyzed after five days under normal culture conditions.

tag: donor

value: donor 61

value: Mesenchymal stromal cells

tag: passage

value: passage 3

tag: substrate

value: tissue culture plastic


title: AAV8-H1-shHBV7 4

description:
m966
cDNA generated using Ambion WT Expression kit

source_name: Mouse treated with AAV expressing shRNA only replicate 4


title: AAV8-empty vector 3

description:
m919
cDNA generated using Ambion WT Expression kit

source_name: Mouse treated with AAV control vector replicate 3


title: AAV8-empty vector 4

description:
m976
cDNA generated using Ambion WT Expression kit

source_name: Mouse treated with AAV control vector replicate 4


title: Mock 4

description:
m935
cDNA generated using Ambion WT Expression kit

source_name: Mouse treated with mock as control replicate 4


title: OTX2 KD transformed human embryonic neural precursors, biological replicate 1

source_name: transformed human embyonic neural precursors with OTX2 KD

value: OTX2 knock down by siRNA


title: AAV8-H1-shHBV7-TTR-Ago2 3

description:
m946
cDNA generated using Ambion WT Expression kit

source_name: Mouse treated with AAV co-expressing shRNA & Ago2 replicate 3


title: OTX2-overexpressing human embryonic neural precursors, biological replicate 1

description: Expression data comparing OTX2-overexpressing human neural precursors to human neural precursor cells       Human Gene 2.0 ST

source_name: human embyonic neural precursors overexpressing OTX2

growth_protocol: OTX2-hENs and control hENs were grown as neurospheres in defined medium (DMEM/F12 supplemented with 1% N2, 1% B27, 20 ng/ml EGF, and 20 ng/ml bFGF) and collected at passage 2.

treatment_protocol: OTX2 was stably overexpressed in human embyonic neural precursors (hEN) by lentiviral transduction. LentiORF RFP-expressing viral particles from the same backbone pLOC construct were used as a control.

value: overexpressing OTX2


title: AT58 PI 650

value: donor 58

value: passage 2

value: nanogrooved polyimide


title: human embryonic neural precursors, biological replicate 2

source_name: human embyonic neural precursors


title: AAV8-H1-shHBV7 3

description:
m965
cDNA generated using Ambion WT Expression kit

source_name: Mouse treated with AAV expressing shRNA only replicate 3

value: male

value: liver


title: AAV8-TTR-miHBV7 3

description:
m941
cDNA generated using Ambion WT Expression kit

source_name: Mouse treated with AAV expressing miRNA mimic replicate 3


title: AAV8-H1-shHBV7-U6-TuDHBV7 1

description:
m928
cDNA generated using Ambion WT Expression kit

source_name: Mouse treated with AAV co-expressing shRNA & sense strand TuD replicate 1


title: Mock 2

description:
m904
cDNA generated using Ambion WT Expression kit

source_name: Mouse treated with mock as control replicate 2


title: human embryonic neural precursors, biological replicate 1


title: AC_kctd15 injected_rep1

description:
Gene expression data from animal caps injected with kctd15 mRNA
2_kctd15

source_name: animal caps injected with kctd15 mRNA

value: animal caps

value: injected with kctd15 mRNA


title: OTX2 KD transformed human embryonic neural precursors, biological replicate 2


title: Mock 3

description:
m918
cDNA generated using Ambion WT Expression kit

source_name: Mouse treated with mock as control replicate 3


title: human embryonic neural precursors, biological replicate 3


title: AT61 PI flat

value: non-structured polyimide


title: AT58 PI flat


title: OTX2-overexpressing human embryonic neural precursors, biological replicate 2


title: AT58 TCP


title: Mock 1

description:
m903
cDNA generated using Ambion WT Expression kit

source_name: Mouse treated with mock as control replicate 1


title: AT57 PI 650

value: donor 57

value: passage 4


title: AT61 PI 650


title: transformed human embryonic neural precursors, biological replicate 2

source_name: transformed human embyonic neural precursors

value: neural precursor cells

value: transformed by non-silencing scramble siRNA


title: AT57 PI flat

source_name: Adipose tissue derived MSCs

value: Mesenchymal stromal cells


title: M117 long

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

description: Gene expression data from diagnostic T-ALL sample

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip murine Gene from Affymetrix GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix)

data_processing: the data were RMA normalized  and  analysed with Partek Genomic Suit

source_name: Pediatric T-ALL cells

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Following the GeneChip whole transcript (WT) Sense Target labelling assay kit Affymetrix)

extract_protocol: RNA was isolated using MirVana™ miRNA isolation kit (Ambion® Inc, Austin, TX, USA) according to manufacturer instructions for total RNA extraction

value: blood

tag: engraftment kinetics

value: long


title: M118 short

value: short


title: M126 long


title: HBZ-Tg/IFNgKO

city: Kyoto

first: Yu

last: Mitagami

address: Sakyo-ku

institute: IVR

hyb_protocol: 600ng of Cy3 labeled cRNA was hybridized following the instruction of Agilent.

scan_protocol: Signals were scanned by Agilent microarray scanner (G2565CA).

data_processing: Spots were quantified by Feature Extraction Software (Agilent Technologies). After that, data was analyzed by Gene Spring GX (Agilent Technonlogies).

source_name: freshly isolated CD4+ T cells

label_protocol: 70ng of RNA samples were labeled with Cy3 by Low Input Quick Amp Labeling Kit (Agilent Technologies).

extract_protocol: RNA was extracted by TRIzol (Life Technologies) and Direct-zol RNA MiniPrep (ZYMO RESEARCH) according to manufacturer's instructions.

treatment_protocol: CD4+ T cells were isolated from splenocytes of each mice.

tag: strain background

value: HBZ-Tg/IFNgKO

value: CD4+ T cells


title: M113 short


title: M106 short


title: M120 long


title: HBZ-Tg

value: HBZ-Tg


title: IFNgKO

value: IFNgKO


title: WT

value: WT


title: M101 long


title: OTX2-overexpressing human embryonic neural precursors, biological replicate 3

value: overexpressing OTX2


title: M114 short


title: M109 long


title: AT57 TCP

value: tissue culture plastic


title: M105 short


title: M144 short


title: M111 long


title: DA4

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description:
raw data file: DA3_4-US83300186_252665223519_S01_GE2_1105_Oct12_1_1.txt
Gene expression in 5nM Capridine treated DU145 cell culture
Capridine-treated DU145 cells_Replicate 4

hyb_protocol: 825 ng from each of the Cy3 or Cy5 labeled samples from two cell dishes were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) rat (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing:
The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction 11.5.1 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.
Normalized log2 ratio of the background subtracted signal of that feature and the median of the background subtracted signals of all valid features in the green or red channel of the array. A NULL indicates that the feature was not considered because is a control fetarure, OR is locally corrupted, OR has saturated pixels, OR the median of the foreground signal is less than 2x median of the background signal

source_name: Capridine-treated DU145 cells

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

growth_protocol: DU145 cell culture

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE) Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: untreated or treated with 5nM Capridine

tag: cell line

tag: status

value: metastasis

value: brain

tag: developmental stage

value: prostate adenocarcinoma metastatic to the brain

value: 90 times in vitro passed epithelial cell culture

tag: treated with

value: 5nM Capridine


title: M80 long


title: M110 long


title: M69 short


title: M108 short


title: DA1

description:
raw data file: DA1_2-US83300186_252665223519_S01_GE2_1105_Oct12_1_2.txt
Gene expression in 5nM Capridine treated DU145 cell culture
Capridine-treated DU145 cells_Replicate 1


title: DA3

description:
raw data file: DA3_4-US83300186_252665223519_S01_GE2_1105_Oct12_1_1.txt
Gene expression in 5nM Capridine treated DU145 cell culture
Capridine-treated DU145 cells_Replicate 3


title: R910_BrdU_ChIP-chip

city: Milan

first: Madhusoodanan

last: Urulangodi

state: Milan

address: Via Adamello 16

country: Italy

institute: IFOM

description: FY1110 cells were arrested in G1 with alfa-factor (2μg/ml) and then released in media containing HU 0.2M for 90 minutes

hyb_protocol: Labelled probes were hybridized to Affymetrix S.cerevisiae whole genome tiling R arrays

scan_protocol: Arrays were scanned on an Affymetrix Scanner

data_processing: BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

organism: Saccharomyces cerevisiae

label_protocol: Synthesis of cDNA, IVT amplification, and labeling were carried out following the Affymetrix GeneChip Expression Anaysis protocol.

growth_protocol: Cells were grown in 200 ml of YPD media at 25°C in 1L falsk for a density of 1.2×10^7 cells/ml

extract_protocol: Extraction was performed as described in Bermejo et al., 2009 (Bermejo R, Katou YM, Shirahige K, Foiani M. ChIP-on-chip analysis of DNA topoisomerases. Methods Mol Biol. 2009;582:103-18).

treatment_protocol: G1 synchronization was performed by α−factor treatment (2 μg/ml) for 150 minutes. Cells were pelleted and released in media containing 0.2 M HU at 25°C for 60 min or 90 min (as indicated) and fixed with 1% formaldehyde for 30 min or 120 (as indicated) min at room temperature. Pelleted cells were washed twice with ice-cold PBS buffer and resespended in 0.8 ml of lysis buffer (50 mM HEPES, pH-7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton-X100,and 0.1%  Na-deoxycholate) supplemented wth 1X complete proteease inhibitor cocktail (Roche) and glass beads. Cells  were broken with multibeads shocker, 60 min total time with 1 min shaking and 1 min pause at 2500 rpm at 4°C. Recovered cell lysate was centrifuged and the pellete was then resuspended in 0.45 ml of protease inhibitor supplemented lysis buffer. Chromatin was sheared by applying 5 sonication cycles of 15 seconds at 1.5 tune while keeping the sample on ice. The supernatant recovered after centrifugation was then incubated with Myc antibody bound magnetic beads overnight at 4°C. Washing and the recovery of immunoprecipitated DNA  was performed as described in Bermejo et al., 2009 (Bermejo R, Katou YM, Shirahige K, Foiani M. ChIP-on-chip analysis of DNA topoisomerases. Methods Mol Biol. 2009;582:103-18).

tag: genotype/variation

tag: chip antibody

value: anti-BrdU (MBL, MI-11-3)


title: DA2

description:
raw data file: DA1_2-US83300186_252665223519_S01_GE2_1105_Oct12_1_2.txt
Gene expression in 5nM Capridine treated DU145 cell culture
Capridine-treated DU145 cells_Replicate 2


title: R1026_Pol3_Myc_ChIP-chip

description: Pol3-9Myc (FY1624) cells were arrested in G1 with alfa-factor (2μg/ml) and then released in media containing HU 0.2M for 90 minutes

tag: strain

value: Anti-Myc antibody [C-Myc (9E10, SC-40) Santa cruiz]


title: DO2

description:
raw data file: DO1_2-US83300186_252665223519_S01_GE2_1105_Oct12_1_4.txt
Gene expression in untreated DU145 cell culture
not treated DU145 cells_Replicate 2

source_name: not treated DU145 cells

value: none (untreated)


title: DO3

description:
raw data file: DO3_4-US83300186_252665223519_S01_GE2_1105_Oct12_1_3.txt
Gene expression in untreated DU145 cell culture
not treated DU145 cells_Replicate 3


title: High grade tumor sample [CVA_Ast_23072014_(HTA-2_0)] gene-level

city: México.

first: Ruth

last: Ruiz-Esparza

address: Centro Médico Nacional Siglo XXI, IMSS, México,

department: Pediatría

country: Mexico

institute: Instituto Mexicano del Seguro Social

description: Gene expression data from pediatric brain tumor grade V

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HTA 2.0 Array. Chips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneArray Scanner G2500A.

data_processing:
For data analysis two softwares were used: Expression Console and Transcript Analysis Console. The first software allows us to perform a gene and exon-level normalization, and signaling summarization by evaluating QC values for the array. The second software allows evaluating gene and exon expiration between samples. Parameters used for the analysis were: One-Way Between-Subject ANOVA (Unpaired); Fold Change (linear) < -2 or Fold Change (linear) > 2; and ANOVA p-value (Condition pair) < 0.05.
Fold Change (linear) < -2 or Fold Change (linear) > 2; and ANOVA p-value (Condition pair) < 0.05.

source_name: Tumor sample

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

extract_protocol: RNA was extracted from tissue samples using TRIzol (Ambion life technologies, Thermo Scientific Inc.) following the methodology described by Hongbao et al. 2008 and with certain modifications described by Vujovic et al. 2013. Briefly, tumor samples were homogenized in 1 ml of TRIZOL® Reagent (1ml per 50 mg of tissue), and incubated at room temperature (25°C) for 5 min. After that, we added 200 µl of chloroform (per ml TRIzol) and shake vigorously the samples for 15 sec. Then, samples were incubating at 4°C for 15 min and they were centrifuged at 12,000xg for 15 min (4°C). The aqueous phase, which corresponds to RNA was transferred to a new 1.5 ml tube and RNA was precipitated adding 500 µl isopropanol (per ml TRIzol) and incubating for 30 min at room temperature. After that, samples were centrifuged at 12,000xg (10 min) at 4°C, the supernatant was removed and pellet was washed once with 75% ethanol (1 ml/ml TRIzol), vortexed and centrifuged at 7,500xg for 5 min at 4°C. The final pellet was dissolved in 300-600 µl of RNase-free water and it was stored at -80 °C until use.

treatment_protocol: A total of eight astrocytic tumors and two control tissues were collected during the period of 2012–2014: four low-grade Ast (three pilocytic Ast (PAst) and one diffuse Ast (DAst)) and four high-grade Ast (four glioblastoma multiforme (GBM)). Brain tumor samples were collected at surgery, snap frozen in liquid nitrogen and stored at −80 °C until use.  All tumors were collected from children – one through 15 years of age – refer from the Children´s hospital, National Medical Center Century XXI, Mexican Institute of Social Security. All patients were from families with no history of cancer (de novo tumors)Control samples were obtained from pediatric patients (one boy and one girl) who had submitted to temporal lobe resection for epilepsy. Tumors were histopathologically classified by two pathologists according to a criteria established by the WHO.

value: glia tissue

tag: tumor grade

value: GBM


title: Low grade tumor sample [CAR_Ast_23072014_(HTA-2_0)] gene-level

description: Gene expression data from pediatric brain tumor grade I

value: Pilocitic astrocitoma


title: High grade tumor sample [Ast_15agosto2014_6_(HTA-2_0)] gene-level


title: Low grade tumor sample [Ast_15Agosto2014_4_(HTA-2_0)] gene-level


title: Control sample from pediatric patient with epilepsy [Ast_15Agosto2014_2_(HTA-2_0)] gene-level

description: Gene expression data frompediatric control tissue (epilepsy sample)

source_name: Control sample

value: Control Tissue


title: DO1

description:
raw data file: DO1_2-US83300186_252665223519_S01_GE2_1105_Oct12_1_4.txt
Gene expression in untreated DU145 cell culture
not treated DU145 cells_Replicate 1


title: DO4

description:
raw data file: DO3_4-US83300186_252665223519_S01_GE2_1105_Oct12_1_3.txt
Gene expression in untreated DU145 cell culture
not treated DU145 cells_Replicate 4


title: High grade tumor sample [Ast_15Agosto2014_3_(HTA-2_0)] gene-level


title: R1221_Esc2_154 198_Myc_ChIP-chip

description: W303 Esc2Δ154-198-13Myc (HY5923) cells were arrested in G1 with alfa-factor (2μg/ml) and then released in media containing HU 0.2M for 60 minutes

source_name: Esc2_154 198_Myc_SUP (INPUT)


title: Esco1 siRNA biological rep1

city: New York

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description: replicate 1

hyb_protocol: Following fragmentation, cRNA were hybridized for Illumina GX HT12 Array. Slides were washed and stained in the Illumina instrument.

scan_protocol: Slides were scanned using Illumina iScanner

data_processing: The data were analyzed with GenomeStudio using Illumina default analysis settings. No normalization and background correction are performed first, then quantile normalization and background correction are done.

source_name: HeLa, Esco1 siRNA

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA.

extract_protocol: Total RNA was isolated with an RNeasy Mini Kit (Qiagen).

value: HeLa


title: non-depleting Esco1 siRNA rep2

description: replicate 2

source_name: HeLa, non-depleting Esco1 siRNA rep2


title: High grade tumor sample [ARI_Ast_23072014_(HTA-2_0)] gene-level


title: non-depleting Esco1 siRNA rep1

description: replicate 1

source_name: HeLa, non-depleting Esco1 siRNA rep1


title: non-depleting Esco1 siRNA rep3

description: replicate 3

source_name: HeLa, non-depleting Esco1 siRNA rep3


title: Rad21 siRNA biological rep1

description: replicate 1

source_name: HeLa, Rad21 siRNA


title: Rad21 siRNA biological rep3

description: replicate 3


title: Rad21 siRNA biological rep2

description: replicate 2


title: Control no siRNA biological rep3

description: replicate 3

source_name: HeLa, Control no siRNA


title: Control sample from pediatric patient with epilepsy [Ast_15Agosto2014_1_(HTA-2_0)] gene-level

description: Gene expression data from pediatric control tissue (epilepsy sample)


title: Control no siRNA biological rep1

description: replicate 1


title: Esco1 siRNA biological rep3

description: replicate 3


title: Esco1 siRNA biological rep2

description: replicate 2


title: 143B-shIRX1 cells, biological rep3

city: Toronto

first: Jinchang

last: Lu

state: Ontario

address: 101 College Street

institute: Princess Margaret Cancer Centre, University of Toronto

description: This sample is 143B stable IRX1 knockdown cells. It is the third of three biological replicates used in this experiment, each from separate cultures.

hyb_protocol: The labeled cDNA was hybridized to NimbleGen Human Gene Expression 12×135K Array.

scan_protocol: The arrays were then scanned using MS200 scanner (NimbleGen).

data_processing: The expression data of probes were normalized using quantile normalization (Bolstad, et al. Bioinformatics. 2003,19(2):185-93)and expression data of genes were generated using the Robust Multichip Average (RMA) algorithm.

source_name: 143B stable IRX1 knockdown cell line

label_protocol: The cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction as previously described.(Guo,Y. et al, JVirol. 2005,79:14392-14403)

growth_protocol: 143B-shCtrl and 143B-shIRX1 cells are cultured in Dulbecco's modified Eagle's medium (Gibco) supplemented with 10% fetal bovine serum (Gibco) at 37°C and 5% CO2.

extract_protocol: Total RNA was extracted using Qiagen RNeasy Mini Kit according to the manufactures’ instructions. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantitated spectrophotometrically.

treatment_protocol: Cells are harvested at 80-90% confluency for RNA extraction.

tag: transfection

value: IRX1-targeting shRNA


title: Low grade tumor sample [Ast_15Agosto2014_5_(HTA-2_0)] gene-level

tag: tissue


title: Control no siRNA biological rep2

description: replicate 2


title: Gill-TankControl-na-recovery-Replicate1

city: Davis

first: Lisa

last: Komoroske

state: CA

address: One Shields Ave

department: Wildlife, fish and conservation biology

institute: University of California, Davis

hyb_protocol: Prior to hybridization, 1.65 µg of dye labeled complementary RNA (specific activity >16.0 pmol Cy3/ug cRNA) for each sample was combined with 2.2 µl of 25x fragmentation buffer, 11 µl of 10X Gene Expression Blocking Agent and nuclease-free water to bring the final volume to 55 µl. The fragmentation mix was incubated at 60°C for 30 min, cooled on ice for 1 min, and the fragmentation was stopped by adding 55 µl of 2X Hi-RPM Hybridization Buffer. Samples were centrifuged for 1 min, placed on ice and 100 µl of the mix was loaded onto arrays and each microarray slide was placed in a single hybridization chamber. Individuals from each treatment were randomized between slides and array position on the slide. All samples were hybridized to the arrays (custom designed Agilent 4x44K oligonucleotide microarrays) for 17 h at 65°C, followed by a wash with Gene Expression Wash Buffer 1 (Agilent) at room temperature and a wash with Gene Expression Wash Buffer 2 (Agilent) heated to 37ºC. Slides were scanned immediately after washing.

scan_protocol: Fluorescent images were scanned using an Axon GenePix 4000B Scanner and the analysis software GenePix Pro (Molecular Devices, LLC, Sunnyvale, CA). The images were quantified using Feature Extraction 11.5.1.1 (Agilent Technologies).

data_processing: Normalization of the microarray data and statistical analysis was performed in Genespring v12.6 (Agilent Technologies). Data was quantile normalized and Log2 transformed prior to statistical analysis. Probes that had a raw signal less than 100 (~2 times the intensity of the background) were filtered out of the statistical analysis to eliminate sources of background noise, but still retain probes with low intensity.

organism: Hypomesus transpacificus

source_name: Gill, TankControl

label_protocol: Two hundred ng of total RNA was amplified and labeled with Cy3 using the Low Input Quick Amp Labeling kit (Agilent Technologies). To minimize technical artefacts, labeling reactions were performed simultaneously.  Dye incorporation and cRNA yield were assessed with a NanoDrop Spectrometer.

growth_protocol: Delta smelt were allowed three weeks to acclimatize to holding conditions at 16°C at the Center for Aquatic Biology and Aquaculture at the University of California, Davis.

extract_protocol: At each time point, fish were sacrificed by a lethal dose of MS-222, gills dissected and immediately frozen in liquid nitrogen and stored at -80°C until RNA extraction. Gill samples were then homogenized using Qiagen's TissuelyserLT and Trizol reagent following manufacturer’s protocols. Samples purity was improved by using RNEasy columns and reagents prior to final elution in water. Concentration and purity (260/280, 260/230) were assessed using a Nanodrop spectrometer (Thermo Scientific) and RNA integrity was determined through electrophoresis.

treatment_protocol: Fish were placed in treatment vessels and given thirty minutes to acclimate, followed by ramping increases in temperatures (0.3°C/min) to treatments selected relative to acute thermal tolerance (CTmax-2°C, CTmax-4°C, CTmax-6°C). When each treatment temperature was reached, fish were removed and either immediately sacrificed and sampled (0 min recovery), or transferred into 9.5 L (larval fish) or 35.2 L (adult) black round recovery tanks at the original acclimation temperature and allowed to recover for 30 or 60 minutes prior to sampling. Handling control trials were conducted by subjecting fish to the same conditions except they were held at the acclimation temperature for the average time of the treatment trials, followed by subsequent transfer into appropriate recovery tanks

tag: treatment

value: TankControl

tag: recovery time

value: not applicable


title: 143B-shIRX1 cells, biological rep2

description: This sample is 143B stable IRX1 knockdown cells. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: Gill-26.4C-60min-recovery-Replicate3

source_name: Gill, 26.4C exposure, 60min recovery

value: 26.4C exposure

value: 60minutes recovery


title: Gill-26.4C-30min-recovery-Replicate4

source_name: Gill, 26.4C exposure, 30min recovery

value: 30minutes recovery


title: 143B-shIRX1 cells, biological rep1

description: This sample is 143B stable IRX1 knockdown cells. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: Gill-26.4C-30min-recovery-Replicate3


title: Gill-26.4C-60min-recovery-Replicate4


title: Gill-26.4C-30min-recovery-Replicate2


title: Gill-26.4C-0min-recovery-Replicate4

source_name: Gill, 26.4C exposure, 0min recovery

value: 0minutes recovery


title: Gill-TankControl-na-recovery-Replicate3


title: 143B-shCtrl cells, biological rep2

description: This sample is 143B stable control cells. It is the second of three biological replicates used in this experiment, each from separate cultures.

source_name: 143B stable control cell line

value: non-targeting shRNA


title: 143B-shCtrl cells, biological rep3

description: This sample is 143B stable control cells. It is the third of three biological replicates used in this experiment, each from separate cultures.


title: 143B-shCtrl cells, biological rep1

description: This sample is 143B stable control cells. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: Gill-26.4C-60min-recovery-Replicate5


title: Gill-TankControl-na-recovery-Replicate2


title: Gill-26.4C-30min-recovery-Replicate1


title: PC3M untreated for 8 hr, biological replicate 3

first: Donald

middle: P

last: Bottaro

address: Bldg 10 CRC Rm 2-3952, 10 Center Drive

department: Center for Cancer Research

institute: National Cancer Institute

description:
PC3M untreated for 8 hr
Untreated 8 hr_3

hyb_protocol: Labeled cDNAs were hybridized to HG U133A Plus 2.0 Affymetrix GeneChip™ arrays, stained with streptavidin phycoerythrin with antibody amplification.

scan_protocol: Scanning was performed following manufacturer’s instructions.

data_processing: Microarray data were analyzed using Partek Genomic Suite software v6.6.  Thirty-six CEL files were loaded into Partek and normalized by the RMA (robust multichip average) algorithm.

label_protocol: A total of 4 micrograms of the amplified cDNA was fragmented and biotin labeled using FL-Ovation™ cDNA Biotin Module V2 (NuGEN # 4200) according to the manufacturer’s instructions.

growth_protocol: PC3M cells were grown to 70% confluenc and serum deprived for 16 h (T0) prior to treatment for various intervals and sample processing.

extract_protocol:
At termination, total RNA was extracted using Qiagen’s All Prep DNA/RNA Kit™ (Qiagen) following the manufacturer’s instructions. Resulting RNA was quantitated by Nanodrop spectrophotometry and stored at -80oC until use.
Total RNA (50 ng) was amplified using the WT-Ovation FFPE System™ (NuGEN) according to the manufacturer’s instructions.  Quantity and quality of the resulting amplified cDNA were measured by Nanodrop spectrophotometry.

treatment_protocol: At T0, biological triplicate cell groups were left untreated or treated with hHGF (1 nM), hNK2 (30 nM) or mHGF (1 nM) for and additional 8, 16 or 32 hours (termination).  Dosing is based on known difference in ligand-receptor binding affinity and is designed to achieve equivalent receptor occupancy.

value: prostate adenocarcinoma cell line PC3M

tag: agent

value: untreated

tag: time

value: 8 hr