title: RC2-SM vs all1 mutant_4

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

description:
samples in Minimal media
SM-A_vs_all1-A

hyb_protocol: Each sample pair (~20ul) is suspended in Formamide-based  hybridization buffer (vial 7-Genisphere) (26ul), Array 50dT blocker (Genisphere) (2ul), and Rnase/Dnase-free water (4ul).  Two hybridizations are carried out in a sequential manner. The primary hybridization is performed by adding 48ul of sample to the microarray under a supported glass coverslip (Erie Scientific) at 43C for 16-20 hours at high humidity.  Prior to the secondary hybridization, slides are gently submerged into 2X SSC, 0.2% SDS (at 43C) for 11 min., transferred to 2X SSC (at room temp.) for 11 min., transferred to 0.2X SSC (at room temp.) for 11 min., and then spun dry by centrifugation. Secondary hybridization is carried out using the complimentary capture reagents provided in the 3DNA Array 350 kit (Genisphere).  For each reaction, the following are added: 3DNA capture reagent with Cy3 (2.5ul), 3DNA capture reagent with Cy5 (2.5ul), SDS-based hybridization buffer (vial 6-Genisphere) (26ul), and Rnase/Dnase-free water (21ul).  The secondary hybridization solution is incubated in the dark at 80C for 10 min. then 50C for 15 min.  Hybridization is performed by adding 48ul secondary hybridization solution to the slide under a supported glass coverslip at 65C for 3 hr at high humidity in the dark. At hybridization termination, arrays are gently submerged into 2X SSC, 0.2% SDS (at 65C) for 11 min., transferred to 2X SSC (at room temp.) for 11 min., transferred to 0.2X SSC (at room temp.) for 11 min., and then spun dry by centrifugation.  To prevent fluorophore degredation, the arrays are treated with Dyesaver (Genisphere).

scan_protocol: Slides are scanned on a Molecular Devices Genepix 4000B microarray scanner to detect Cy3 fluorescence.  Laser power is kept constant and PMT voltage is established for all 12 arrays on the glass such that the each array has less than 1% signal saturation in either dye. Images were quantitated with Genepix Pro, v6.1 (Molecular Devices).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of test/reference.

organism: Cryptococcus neoformans

source_name: RC2  yeast cells,  growth at 37C in MM

label_protocol: First strand cDNA is generated by polyT primed reverse transcription (Superscript II; Invitrogen) utilizing the 3DNA Array350  kit (Genisphere).  For cDNA synthesis, 1ul of fluorophore specific oligo-dT primer is added to 8ug of total RNA and the solution is incubated at 80C for 10 minutes then cooled on ice for 2 minutes.  To each sample are added RNase inhibitor (Superase-In; Ambion) (1ul), 5X first strand buffer (4ul), dNTP mix (10mM each dATP, dCTP, dGTP, and dTTP) (1ul), 0.1M DTT (2ul), and Superscript II RNase H- Reverse Transcriptase (1ul).  Reverse transcription is carried out at 42C for 2 hours.  The reaction is terminated by adding 0.5M NaOH/ 50mM EDTA (3.5ul) and incubation at 65C for 15 minutes then neutralized with 1M Tris-HCL, pH 7.5 (5ul).  For RNA expression level comparison, samples are paired and concentrated using Microcon YM30 microconcentrators (Millipore) according to the manufacturer’s protocol.

growth_protocol: Yeast cells were grown on YPD or minimal medium for 16 hours at 37C prior with agitation at 150rpm

extract_protocol: RNA extraction using a QIAGEN RNeasy column

treatment_protocol: Not applicable

tag: strain

value: RC2-Serotype D

tag: genotype/variation

value: WT

tag: growth medium

value: Minimal media

source_name: all1 mutant yeast cells,  growth at 37C in MM

value: all1 mutant


title: Validation patient #28 | Vaccine Arm | Pre-treatment [IgG 1:50]

status: Public on Apr 01 2013

type: other

city: Frederick

first: Christopher

last: Campbell

state: MD

address: 376 Boyles Street

country: USA

institute: NCI

description: Sample name: 210

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.
The VALUEs represent the normalized ch1 signal for experiments that analyzed total Ig and IgG.  For the IgM experiments, the ch2 signal was normalized to determine levels of IgM antibodies.

label: DyLight 549

molecule: other

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: halabi predicted survival (months)

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: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score

tag: on-study psa

tag: treatment

value: Vaccine

tag: timepoint

value: Pre-treatment

tag: isotype-specific, secondary antibody [fluorescently labeled]

value: IgG

label: DyLight 649

value: IgM


title: Validation patient #29 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 218


title: Validation patient #25 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 192


title: Validation patient #24 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 184


title: Validation patient #26 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 197


title: Validation patient #23 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 177


title: Validation patient #20 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 157


title: Validation patient #22 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 170

value: Control


title: Validation patient #21 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 162


title: RC2-SM vs all1 mutant_1

type: RNA

description:
samples in YPD media
SM-1_vs_all1-1

molecule: total RNA

source_name: RC2  yeast cells,  growth at 37C in YPD

value: YPD

source_name: all1 mutant yeast cells,  growth at 37C in YPD


title: Validation patient #32 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 240


title: Validation patient #39 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 279


title: Validation patient #18 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 147


title: Validation patient #19 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 152


title: all1 mutant vs RC2-SM_5

description:
samples in Minimal media
all1-B_vs_SM-B


title: Validation patient #16 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 127


title: Validation patient #15 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 117


title: Validation patient #27 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 202


title: Validation patient #17 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 136


title: Validation patient #14 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 109


title: all1 mutant vs RC2-SM_2

description:
samples in YPD media
all1-2_vs_SM-2


title: Validation patient #9 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 65


title: Validation patient #10 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 74


title: Validation patient #8 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 46


title: Validation patient #12 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 89


title: Validation patient #7 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 41


title: Validation patient #5 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 29


title: Validation patient #6 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 33


title: Validation patient #13 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 101


title: PBMC_9-12

city: La Jolla

first: Sunil

last: Kurian

state: CA

address: 10550 N Torrey Pines Road

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

description: 1 Year_TOL

hyb_protocol: The Gene Titan Hybridization, Wash and Stain Kit for WT Array Plates (Affymetrix) is used to hybridize 3ug of the labeled cDNA to a multi peg Gene 1.1 ST Array Plate. The hybridization cocktail also contains Control Oligo B2 and 20X Eukaryotic Hybridization Controls as recommended by Affymetrix. Hybridization is carried out for 17 hours at 48C in the Gene Titan MC (Multichannel) Instrument ( Affymetrix). After hybridization the peg array plate is automatically washed and stained and moved to the scanner.

scan_protocol: The peg array plate is automatically moved to the Xenon laser scanner of the Titan MC instrument and scanned at default settings recommended for the peg array.

data_processing:
Probes to Import: Interrogating Probes and Control Probes, Probe filtering: skip, Algorithm: RMA, Background Correction: RMA Background Correction, Normalization: Quantile Normalization, Log Probes using Base: 2, Probeset Summarization: Median Polish
probe group file: HuGene-1_1-st-v1.r4.pgf
meta-probeset file: HuGene-1_1-st-v1.r4.mps

label: SAPE

source_name: Recipient 9; 1 Year; Tolerant

label_protocol: The cDNA generated from the WT Expression Kit is fragmented and biotin labeled with the Affymetrix GeneChip WT Terminal Labeling Kit ( Affymetrix). The cDNA is fragmented with a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonucleaseI (APE I). The fragmented cDNA is then labeled with terminal deoxynucleotidyl transferase (TdT) and a biotin reagent.

extract_protocol: RNA Extraction from PAXgene Blood Tubes: Total RNA including small and miRNA is extracted with the PreAnalytiX  PAXgene Blood miRNA kit ( QIAGEN). A semi automated method using the QIAcube (QIAGEN) is used following manufacturer’s instructions. The quantity and quality of the RNA is assessed on a nanodrop and Agilent Bioanalyzer. miRNAeasy kit PN 217004 (Qiagen)

tag: recipient

tag: tissue

value: Peripheral Blood

tag: time-point

value: 1 Year

tag: induction

value: Alemtuzumab

tag: tolerance

value: Tolerant


title: Validation patient #3 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 13

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)


title: Validation patient #11 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 82

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

tag: treatment arm


title: Validation patient #2 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 9

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia


title: PBMC_9-18

description: 2 Year_TOL

source_name: Recipient 9; 2 Year; Tolerant

value: 2 Year


title: Validation patient #1 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 1

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)


title: Training patient #10 | Vaccine Arm | Day 0 [IgM 1:50]

description: Sample name: X1

tag: on-study psa

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: Pre-vaccination


title: Training patient #13 | Vaccine Arm | Day 0 [IgM 1:50]

description: Sample name: Y1

tag: halabi predicted survival (months)

tag: treatment

tag: timepoint

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Training patient #19 | Vaccine Arm | Day 0 [IgM 1:50]

description: Sample name: Z1


title: Training patient #7 | Vaccine Arm | Day 0 [IgM 1:50]

description: Sample name: W1


title: Validation patient #4 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 21

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: gleason score


title: PBMC_8-18

description: 2 Year_TOL

source_name: Recipient 8; 2 Year; Tolerant

tag: recipient

tag: tissue

tag: time-point

tag: induction

tag: tolerance


title: PBMC_8-25

description: 2 Year_TOL


title: Training patient #4 | Vaccine Arm | Day 0 [IgM 1:50]

description: Sample name: V1

tag: age at enrollment (years)

tag: on-study psa

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 fowlpox


title: PBMC_8_39

description: 3 Year_TOL

source_name: Recipient 8; 3 Year; Tolerant

value: 3 Year


title: PBMC_8-0

source_name: Recipient 8; 0 Year; Tolerant

value: 0 Year


title: PBMC_7-25

description: 2 Year_nTOL

source_name: Recipient 7; 2 Year; Non-Tolerant

value: Non-Tolerant


title: PBMC_7_40

description: 3 Year_nTOL

source_name: Recipient 7; 3 Year; Non-Tolerant


title: PBMC_8-10

description: 1 Year_TOL

source_name: Recipient 8; 1 Year; Tolerant


title: RC2-SM vs all1 mutant_3

description:
samples in YPD media
SM-3_vs_all1-3

tag: strain

value: RC2-Serotype D

tag: genotype/variation

value: WT

tag: growth medium

value: all1 mutant


title: PBMC_7-13

description: 1 Year_nTOL

source_name: Recipient 7; 1 Year; Non-Tolerant

tag: recipient


title: PBMC_9-0

source_name: Recipient 9; 0 Year; Tolerant

tag: tissue


title: PBMC_6_36

description: 3 Year_TOL

source_name: Recipient 6; 3 Year; Tolerant

tag: time-point


title: PBMC_6_24

description: 2 Year_TOL

source_name: Recipient 6; 2 Year; Tolerant

tag: induction


title: PBMC_7-0

source_name: Recipient 7; 0 Year; Non-Tolerant

tag: tolerance


title: PBMC_6_49

description: 4 Year_TOL

source_name: Recipient 6; 4 Year; Tolerant

value: 4 Year


title: PBMC_6_10

description: 1 Year_TOL

source_name: Recipient 6; 1 Year; Tolerant


title: Training patient #9 | Vaccine Arm | Day 0 [IgM 1:50]

description: Sample name: Q2

source_name: Serum

tag: age at enrollment (years)

tag: halabi predicted survival (months)

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox

tag: treatment

value: Vaccine

tag: timepoint

tag: isotype-specific, secondary antibody [fluorescently labeled]

value: IgG


title: Training patient #25 | Vaccine Arm | Day 0 [IgM 1:50]

description: Sample name: U2

tag: on-study psa

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

value: IgM


title: Training patient #15 | Vaccine Arm | Day 0 [IgM 1:50]

description: Sample name: R2

tag: post-vaccination igg titer for fowlpox


title: Training patient #22 | Vaccine Arm | Day 0 [IgM 1:50]

description: Sample name: T2


title: Training patient #8 | Vaccine Arm | Day 0 [IgM 1:50]

description: Sample name: P2


title: Training patient #1 | Vaccine Arm | Day 0 [IgM 1:50]

description: Sample name: O2


title: PBMC_5_40

description: 3 Year_TOL

source_name: Recipient 5; 3 Year; Tolerant

tag: recipient

tag: tissue

tag: time-point

tag: induction


title: Training patient #32 | Vaccine Arm | Day 0 [IgM 1:50]

description: Sample name: N1

tag: age at enrollment (years)

tag: halabi predicted survival (months)

tag: post-vaccination igg titer for vaccinia


title: Training patient #21 | Vaccine Arm | Day 0 [IgM 1:50]

description: Sample name: M1

tag: pre-vaccination igg titer for fowlpox

tag: treatment

tag: timepoint


title: PBMC_5_36

description: 3 Year_TOL

tag: tolerance


title: Training patient #16 | Vaccine Arm | Day 0 [IgM 1:50]

description: Sample name: K1

tag: on-study psa

tag: gleason #

tag: ellispot

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: PBMC_6_17

description: 2 Year_TOL


title: PBMC_4_34

description: 3 Year_nTOL

source_name: Recipient 4; 3 Year; Non-Tolerant


title: PBMC_6_0

source_name: Recipient 6; 0 Year; Tolerant


title: PBMC_5-0

source_name: Recipient 5; 0 Year; Tolerant


title: Training patient #2 | Vaccine Arm | Day 0 [IgM 1:50]

description: Sample name: I1

tag: tregs

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

tag: overall survival (mos)

tag: pre-vaccination igg titer for vaccinia


title: Training patient #30 | Vaccine Arm | Day 0 [IgM 1:50]

description: Sample name: Ee1

tag: post-vaccination igg titer for fowlpox


title: Training patient #23 | Vaccine Arm | Day 0 [IgM 1:50]

description: Sample name: F1


title: Training patient #20 | Vaccine Arm | Day 0 [IgM 1:50]

description: Sample name: E1


title: PBMC_5-24

description: 2 Year_TOL

source_name: Recipient 5; 2 Year; Tolerant

tag: recipient

tag: tissue

tag: time-point

tag: induction


title: Training patient #28 | Vaccine Arm | Day 0 [IgM 1:50]

description: Sample name: G1

tag: age at enrollment (years)

tag: halabi predicted survival (months)

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox


title: Training patient #31 | Vaccine Arm | Day 0 [IgM 1:50]

description: Sample name: H1

tag: on-study psa

tag: treatment

tag: timepoint


title: Training patient #14 | Vaccine Arm | Day 0 [IgM 1:50]

description: Sample name: D1

tag: gleason #

tag: ellispot

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Training patient #29 | Vaccine Arm | Day 0 [IgM 1:50]

description: Sample name: Cc1

tag: tregs

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

tag: overall survival (mos)


title: PBMC_5-11

description: 1 Year_TOL

source_name: Recipient 5; 1 Year; Tolerant

tag: recipient

tag: tolerance


title: PBMC_4_18

description: 2 Year_nTOL

source_name: Recipient 4; 2 Year; Non-Tolerant

tag: tissue

tag: time-point


title: PBMC_4_47

description: 4 Year_nTOL

source_name: Recipient 4; 4 Year; Non-Tolerant

tag: induction


title: PBMC_4_11

description: 1 Year_nTOL

source_name: Recipient 4; 1 Year; Non-Tolerant


title: PBMC_4_24

description: 2 Year_nTOL


title: Training patient #12 | Vaccine Arm | Day 0 [IgM 1:50]

description: Sample name: C1

tag: age at enrollment (years)

tag: halabi predicted survival (months)

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for fowlpox


title: PBMC_4_0

source_name: Recipient 4; 0 Year; Non-Tolerant


title: PBMC_3-0

source_name: Recipient 3; 0 Year; Non-Tolerant


title: PBMC_3-20

description: 2 Year_nTOL

source_name: Recipient 3; 2 Year; Non-Tolerant


title: PBMC_3-14

description: 1 Year_nTOL

source_name: Recipient 3; 1 Year; Non-Tolerant


title: PBMC_3-35

description: 3 Year_nTOL

source_name: Recipient 3; 3 Year; Non-Tolerant


title: PBMC_3_49

description: 4 Year_nTOL

source_name: Recipient 3; 4 Year; Non-Tolerant


title: Training patient #5 | Vaccine Arm | Day 0 [IgM 1:50]

description: Sample name: B1

tag: on-study psa

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox

tag: treatment


title: Training patient #26 | Vaccine Arm | Day 0 [IgM 1:50]

description: Sample name: Bb1

tag: gleason #

tag: ellispot

tag: timepoint

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Training patient #24 | Vaccine Arm | Day 0 [IgM 1:50]

description: Sample name: Aa1

tag: tregs

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

tag: overall survival (mos)


title: Training patient #27 | Vaccine Arm | Day 0 [IgM 1:50]

description: Sample name: Dd1


title: Training patient #3 | Vaccine Arm | Day 0 [IgM 1:50]

description: Sample name: A1


title: PBMC_2_53

description: 4 Year_TOL

source_name: Recipient 2; 4 Year; Tolerant

tag: recipient

tag: tissue

tag: time-point

tag: tolerance


title: Training patient #19 | Vaccine Arm | Day 0 [IgG 1:50]

description: Sample name: Z1

source_name: Serum

tag: age at enrollment (years)

tag: halabi predicted survival (months)

tag: pre-vaccination igg titer for vaccinia


title: Training patient #13 | Vaccine Arm | Day 0 [IgG 1:50]

description: Sample name: Y1

tag: on-study psa

tag: post-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for fowlpox


title: PBMC_2_48

description: 4 Year_TOL

tag: induction


title: PBMC_2_37

description: 3 Year_TOL

source_name: Recipient 2; 3 Year; Tolerant


title: PBMC_2_0

source_name: Recipient 2; 0 Year; Tolerant


title: Training patient #10 | Vaccine Arm | Day 0 [IgG 1:50]

description: Sample name: X1

tag: gleason #

tag: ellispot

tag: pre-vaccination igg titer for fowlpox

tag: treatment


title: PBMC_1_54

description: 4 Year_nTOL

source_name: Recipient 1; 4 Year; Non-Tolerant


title: PBMC_1_36

description: 3 Year_nTOL

source_name: Recipient 1; 3 Year; Non-Tolerant


title: PBMC_2_39

description: 3 Year_TOL


title: Training patient #7 | Vaccine Arm | Day 0 [IgG 1:50]

description: Sample name: W1

tag: tregs

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

tag: timepoint

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Training patient #25 | Vaccine Arm | Day 0 [IgG 1:50]

description: Sample name: U2

tag: overall survival (mos)


title: PBMC_1_24

description: 2 Year_nTOL

source_name: Recipient 1; 2 Year; Non-Tolerant

tag: recipient

tag: tissue

tag: time-point

tag: tolerance


title: Training patient #4 | Vaccine Arm | Day 0 [IgG 1:50]

description: Sample name: V1

tag: age at enrollment (years)

tag: halabi predicted survival (months)

tag: on-study psa

tag: pre-vaccination igg titer for vaccinia


title: Training patient #15 | Vaccine Arm | Day 0 [IgG 1:50]

description: Sample name: R2

tag: gleason #

tag: post-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for fowlpox


title: PBMC_1_12

description: 1 Year_nTOL

source_name: Recipient 1; 1 Year; Non-Tolerant

tag: induction


title: PBMC_1_0

source_name: Recipient 1; 0 Year; Non-Tolerant


title: Training patient #32 | Vaccine Arm | Day 0 [IgG 1:50]

description: Sample name: N1

tag: ellispot

tag: tregs

tag: pre-vaccination igg titer for fowlpox

tag: treatment


title: Training patient #1 | Vaccine Arm | Day 0 [IgG 1:50]

description: Sample name: O2

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

tag: overall survival (mos)

tag: timepoint

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Training patient #8 | Vaccine Arm | Day 0 [IgG 1:50]

description: Sample name: P2


title: Training patient #21 | Vaccine Arm | Day 0 [IgG 1:50]

description: Sample name: M1


title: Training patient #16 | Vaccine Arm | Day 0 [IgG 1:50]

description: Sample name: K1


title: Training patient #2 | Vaccine Arm | Day 0 [IgG 1:50]

description: Sample name: I1


title: Training patient #31 | Vaccine Arm | Day 0 [IgG 1:50]

description: Sample name: H1


title: Training patient #22 | Vaccine Arm | Day 0 [IgG 1:50]

description: Sample name: T2


title: Training patient #28 | Vaccine Arm | Day 0 [IgG 1:50]

description: Sample name: G1


title: Training patient #23 | Vaccine Arm | Day 0 [IgG 1:50]

description: Sample name: F1


title: Training patient #9 | Vaccine Arm | Day 0 [IgG 1:50]

description: Sample name: Q2


title: cartilage knee 10SE213

city: A Coruña

first: Juan

last: Fernandez Tajes

address: As Xubias

department: Genomics Area

country: Spain

institute: INIBIC

hyb_protocol: Washing and staining using kit for WT array plates, following Affymetrix protocol, Hybridization was carried out using GeneTitan Hybridization

scan_protocol: Scan was performed on GeneTitan instrument

data_processing:
CEL files were read with oligo package and subsequently analyzed with the same package. RMA algorithm was applied and a filter step based on annotation was also included in the analysis.
pd.hugene.1.1.st.v1
hugene11sttranscriptcluster.db

label: biotin

source_name: cartilage knee

label_protocol: Fragmented cDNA was labelled using the WT Terminal Labelling kit (Affymetrix)

extract_protocol: Total RNA was isolated from crushed tissue using the Rneasy Mini kit (Qiagen) following manufacturer instructions, with the addition of a DNAse digestion step.

tag: disease state

value: osteoarthritis

tag: age

tag: Sex

value: Female

tag: haplogroup

value: T

tag: tissue

value: knee cartilage


title: cartilage knee 10SE214


title: cartilage knee 10SE215


title: cartilage knee 10SE222

value: U


title: cartilage knee 10SE212


title: cartilage knee 10SE360

value: J


title: cartilage knee 10SE223


title: cartilage knee 10SE211


title: cartilage knee 10SE210


title: cartilage knee 10SE209


title: cartilage knee 10SE207


title: cartilage knee 10SE357

value: Male


title: cartilage knee 10SE208


title: cartilage knee 10SE227

value: H


title: Training patient #30 | Vaccine Arm | Day 0 [IgG 1:50]

description: Sample name: Ee1

tag: age at enrollment (years)

tag: halabi predicted survival (months)

tag: on-study psa

tag: gleason #

tag: pre-vaccination igg titer for vaccinia

value: Pre-vaccination


title: cartilage knee 10SE226


title: Training patient #27 | Vaccine Arm | Day 0 [IgG 1:50]

description: Sample name: Dd1

tag: ellispot

tag: tregs

tag: post-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for fowlpox


title: Training patient #14 | Vaccine Arm | Day 0 [IgG 1:50]

description: Sample name: D1

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

tag: overall survival (mos)

tag: pre-vaccination igg titer for fowlpox

tag: treatment


title: cartilage knee 10SE229

tag: disease state

tag: age


title: cartilage knee 10SE220

tag: Sex

tag: haplogroup


title: Training patient #20 | Vaccine Arm | Day 0 [IgG 1:50]

description: Sample name: E1

tag: age at enrollment (years)

tag: timepoint

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Training patient #29 | Vaccine Arm | Day 0 [IgG 1:50]

description: Sample name: Cc1

tag: halabi predicted survival (months)

tag: on-study psa

tag: gleason #


title: Training patient #5 | Vaccine Arm | Day 0 [IgG 1:50]

description: Sample name: B1

tag: ellispot

tag: tregs

tag: pre-vaccination igg titer for vaccinia


title: Training patient #3 | Vaccine Arm | Day 0 [IgG 1:50]

description: Sample name: A1

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

tag: post-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for fowlpox


title: Training patient #26 | Vaccine Arm | Day 0 [IgG 1:50]

description: Sample name: Bb1

tag: overall survival (mos)

tag: pre-vaccination igg titer for fowlpox

tag: treatment


title: Training patient #24 | Vaccine Arm | Day 0 [IgG 1:50]

description: Sample name: Aa1


title: Training patient #12 | Vaccine Arm | Day 0 [IgG 1:50]

description: Sample name: C1


title: cartilage knee 10SE191_2

tag: disease state

tag: age

tag: Sex

tag: tissue


title: cartilage knee 10SE225

tag: haplogroup


title: cartilage knee 10SE216


title: cartilage knee 10SE218


title: cartilage knee 10SE219


title: NCI-H526 xenograft treated by IR 2 Gy (day7) rep2

status: Public on Mar 30 2013

city: Villejuif

first: Charles

last: Ferté

address: 114 rue Edouard Vaillant

department: Medical Oncology

country: France

institute: Gustave Roussy

hyb_protocol: The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip Human Genome U133 Plus 2.0 expression arrays (Affymetrix, Inc., Santa Clara, CA) according to the Affymetrix Expression Analysis Technical Manual.

scan_protocol: Chips were scanned using the GeneChip Scanner 3000

data_processing: Expression data were analyzed with R (v.2.15.3)/Bioconductor (v.2.12); RMA expression values were calculated using RMA as implemented in the affy package (v.1.38.0); probe sets were annotated using the hgu133plus2.db

label: Biotin

source_name: NCI-H526 xenograft_IR

label_protocol: Biotinylated cRNA were prepared using the Affymetrix 3’ IVT Express kit with 100 ng input total RNA, essentially according to the manufacturer's instructions.

growth_protocol: Mice were injected with 5.e+6 H526 cells into the flank. Animals were randomized to different treatment groups of 5-7 mice each when xenograft diameters attained 5mm.

extract_protocol: Extraction of total RNA was performed using RNAlater Tissue collection (Quiagen) according to the manufacturer's instructionsfrom homogenized tissue samples. Integrity was verified by capillary gel electrophoresis (Bio Analyzer, Agilent Technologies).

treatment_protocol: R1507 was administered via an intraperitoneal injection (IP) once weekly at a dose of 18 mg/kg and continued until the end of the experiment. Cisplatin was administered at a dose of 3 mg/kg IP at day 1, day 8 and day 15. IR was delivered in 4 fractions of 2 Gy on days 1 to 4 (A 200-kV X-ray irradiator, dose rate = 0.45 Gy min-1), using mouse jigs to exclusively expose the tumor beds.

tag: host strain

value: 7 wk-old female athymic Nude mice (Janvier, CERT, Le Genest St. Isle)

value: NCI-H526 SCLC (small-cell lung cancer) xenografts

value: IR 2 Gy

tag: treatment time


title: NCI-H526 xenograft treated by R1507 18mg/kg + IR 2 Gy (day7) rep6

source_name: NCI-H526 xenograft_R1507 + IR

value: R1507 18mg/kg + IR 2 Gy


title: NCI-H526 xenograft treated by CDDP 3mg/kg (day1) rep4

source_name: NCI-H526 xenograft_CDDP

value: CDDP 3mg/kg


title: NCI-H526 xenograft treated by IR 2 Gy (day7) rep1


title: NCI-H526 xenograft treated by R1507 18mg/kg (day1) rep2

source_name: NCI-H526 xenograft_R1507


title: NCI-H526 xenograft treated by IR 2 Gy (day1) rep4


title: NCI-H526 xenograft treated by R1507 18mg/kg (day7) rep4


title: NCI-H526 xenograft treated by R1507 18mg/kg + CDDP 3mg/kg (day7) rep3

source_name: NCI-H526 xenograft_R1507 + CDDP

value: R1507 18mg/kg + CDDP 3mg/kg


title: NCI-H526 xenograft treated by R1507 18mg/kg (day7) rep3


title: NCI-H526 xenograft treated by control (Vehicle) (day1)

source_name: NCI-H526 xenograft_control (Vehicle)

value: control (Vehicle)


title: NCI-H526 xenograft treated by CDDP 3mg/kg (day1) rep5


title: NCI-H526 xenograft treated by CDDP 3mg/kg (day1) rep3


title: NCI-H526 xenograft treated by control (Vehicle) (day7) rep1


title: NCI-H526 xenograft treated by R1507 18mg/kg + IR 2 Gy (day7) rep4


title: NCI-H526 xenograft treated by R1507 18mg/kg (day1) rep1


title: NCI-H526 xenograft treated by CDDP 3mg/kg (day1) rep2


title: NCI-H526 xenograft treated by R1507 18mg/kg + IR 2 Gy (day7) rep5


title: NCI-H526 xenograft treated by control (Vehicle) (day7) rep2


title: NCI-H526 xenograft treated by R1507 18mg/kg + CDDP 3mg/kg (day7) rep1


title: NCI-H526 xenograft treated by R1507 18mg/kg + CDDP 3mg/kg (day7) rep2


title: NCI-H526 xenograft treated by CDDP 3mg/kg (day1) rep6


title: NCI-H526 xenograft treated by R1507 18mg/kg + IR 2 Gy (day7) rep2


title: NCI-H526 xenograft treated by CDDP 3mg/kg (day1) rep1


title: NCI-H526 xenograft treated by R1507 18mg/kg (day7) rep2


title: NCI-H526 xenograft treated by R1507 18mg/kg + CDDP 3mg/kg (day1) rep2


title: NCI-H526 xenograft treated by IR 2 Gy (day1) rep3


title: NCI-H526 xenograft treated by R1507 18mg/kg + IR 2 Gy (day7) rep3


title: cartilage knee 10SE358


title: NCI-H526 xenograft treated by R1507 18mg/kg + CDDP 3mg/kg (day1) rep1


title: NCI-H526 xenograft treated by IR 2 Gy (day1) rep1


title: NCI-H526 xenograft treated by IR 2 Gy (day1) rep2


title: NCI-H526 xenograft treated by R1507 18mg/kg (day7) rep1


title: NCI-H526 xenograft treated by R1507 18mg/kg + IR 2 Gy (day7) rep1


title: WT 1

status: Public on Mar 28 2013

city: Bethesda

first: WeiPing

last: Chen

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

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

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

data_processing: RMA by software Partek 6.5

organism: Mus musculus

source_name: WT

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

growth_protocol: All animal studies were approved by the NIDDK/NIH Animal Care and Use Committee.

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

treatment_protocol: Mice were maintained in a pathogen-free facility, with 4–5 animals  per cage in a temperature-controlled room with a 12-h light/dark cycle and access to food  and water ad libitum. Age and sex matched littermate cohorts were used for all the  experiments to account for potential strain differences.

value: testes

tag: genotype

value: WT

tag: genetic background

value: mixed background of C57BL/6 x 129/SvEv x FVB/N


title: WT 3


title: WT 2


title: Ttll5/Stamp KO 3

source_name: Ttll5/Stamp KO

value: Ttll5/Stamp KO


title: NB56

status: Public on Mar 26 2013

type: genomic

city: Heidelberg

first: Thomas

last: Wolf

address: Im Neuenheimer Feld 580

country: Germany

institute: DKFZ

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

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

data_processing: The scanned TIFF images were loaded into the Feature Extraction (v9.5 Agilent technologies), Feature Extraction files (LogRatio column) were analyzed by CGH Analytics Software (v. 3.5.14 Agilent Technologies). The circular binary segmentation algorithm was applied. Ref: PMID:17234643.  See normalized.seg files linked as supplementary files on Series record.

molecule: genomic DNA

source_name: Tumor DNA

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

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

value: M

value: Neuroblastoma

tag: Stage

tag: age (1

value: <18 months, 2:>18 months):2

source_name: Promega Reference DNA


title: NCI-H526 xenograft treated by R1507 18mg/kg + CDDP 3mg/kg (day1) rep3


title: Ttll5/Stamp KO 1


title: NB60

value: F


title: Ttll5/Stamp KO 2


title: NB57


title: NB54

value: <18 months, 2:>18 months):1


title: NB61


title: NB55


title: NB58


title: NB53


title: NB49


title: NB51


title: NB48


title: NB52


title: NB59


title: NB46


title: NB47


title: NB50


title: NB43


title: NB62


title: NB44


title: NB45


title: NB39


title: NB41


title: NB40


title: NB42


title: NB36


title: NB37


title: NB33


title: NB38


title: NB32


title: NB27


title: NB22


title: NB21


title: NB31


title: NB25


title: NB28


title: NB30


title: NB35


title: NB23


title: NB20


title: NB19


title: NB15


title: NB29


title: NB24


title: NB16


title: NB209

data_processing:
The scanned TIFF images were loaded into the Feature Extraction (v9.5 Agilent technologies), Feature Extraction files (LogRatio column) were analyzed by CGH Analytics Software (v. 3.5.14 Agilent Technologies). The circular binary segmentation algorithm was applied. Ref: PMID:17234643
Because of technical reasons, 9 out of 209 aCGH profiles could not be visualized and therefore can not be uploaded as normalized files (normalized.seg) on GEO database.


title: NB26


title: NB14


title: NB12


title: NB13


title: NB201


title: NB9


title: NB203


title: NB11


title: NB5


title: NB7


title: NB199


title: NB196


title: NB6


title: NB202


title: NB8


title: NB197


title: NB198


title: NB193


title: NB208


title: NB200


title: NB205


title: NB207


title: NB18


title: NB17


title: NB204


title: NB190


title: NB191


title: NB192


title: NB195


title: NB185


title: NB184


title: NB188


title: NB189


title: NB179


title: NB182


title: NB174


title: NB172


title: NB177


title: NB173


title: NB171


title: NB183


title: NB175


title: NB186


title: NB181


title: NB178


title: NB206


title: NB176


title: NB180


title: NB165


title: NB164


title: NB169


title: NB166

value: multilok.


title: NB168


title: NB167


title: NB170


title: NB159


title: NB162


title: NB161


title: NB158


title: NB157


title: NB156


title: NB163


title: NB155


title: NB160


title: NB146


title: NB194


title: NB149


title: NB143


title: NB151


title: NB147


title: NB144


title: NB152


title: NB148


title: NB140


title: NB150


title: NB153


title: NB154


title: NB145


title: NB187


title: NB137


title: NB141


title: NB136


title: NB139


title: NB142


title: NB130


title: NB129


title: NB133


title: NB131


title: NB134


title: NB128


title: NB121


title: NB119


title: NB138


title: NB132


title: NB135


title: NB127


title: NB126


title: NB122


title: NB124


title: NB117


title: NB123


title: NB125


title: NB116


title: NB118


title: NB120


title: NB114


title: NB113


title: NB108


title: NB111


title: NB109


title: NB115


title: NB112


title: NB107


title: NB110


title: NB104


title: NB102


title: NB106


title: NB99


title: NB100


title: NB101


title: NB96


title: NB94


title: NB95


title: NB86


title: NB91


title: NB97


title: NB89


title: NB77


title: NB98


title: NB103


title: NB88


title: NB85


title: NB92


title: NB76


title: NB78


title: NB74


title: NB84


title: NB87


title: NB75


title: NB82


title: NB80


title: NB83


title: NB81


title: NB79


title: NB93


title: NB70


title: NB64


title: NB10


title: Normal mucosa, sample 6

status: Public on Mar 18 2013

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol

data_processing: Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix)

source_name: Normal colon mucosa

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.

tag: disease status

value: AJCC stage II CRC

value: normal colon mucosa

tag: matching tumor sample


title: NB69


title: NB65


title: NB71


title: NB68


title: Normal mucosa, sample 5


title: Normal mucosa, sample 2


title: NB72


title: NB73


title: NB67


title: NB4


title: NB90


title: Normal mucosa, sample 3


title: NB3


title: NB1


title: NB66


title: Normal mucosa, sample 1


title: NB63


title: NB105


title: NB2


title: E11.5 AA4.1/VEC+CD45+ Rep 2

status: Public on Mar 12 2013

city: Toronto

first: Bhaskar

last: Chanda

address: 101 College Street

country: Canada

institute: University of Toronto

description: Replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: AGM sorted population

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

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

value: embryo

tag: cell type


title: E11.5 AA4.1/VEC+CD45- Rep 2

description: Replicate 2


title: E11.5 AA4.1/VEC+CD45+ Rep 3

description: Replicate 3


title: E11.5 AA4.1/VEC+CD45- Rep 1

description: Replicate 1


title: E11.5 AA4.1/VEC+CD45+ Rep 1

description: Replicate 1


title: Normal mucosa, sample 4


title: E11.5 AA4.1/VEC+CD45- Rep 3

description: Replicate 3


title: R. sphaeroides WT 2.4.1_90 min singlet oxygen stress versus 0 min stress_translatome replicate A

status: Public on Nov 14 2012

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

institute: Justus-Liebig University Gießen

description: biological sample 1-3

hyb_protocol: RNA of three independent experiments of Rhodobacter sphaeroides WT 2.4.1 at 7/45/90 min and 0 min were pooled and hybridized to one array. Gene chip hybridization and scanning were performed according to the specifications from Agilent.

scan_protocol: Scanned on an Agilent High Resolution Microarray Scanner. Images were quantified using Agilent Feature Extraction Software.

data_processing: LOESS normalization (within- and between-arrays) with Limma package for Bioconductor in R was applied for dye-bias correction.

organism: Cereibacter sphaeroides 2.4.1

source_name: R. sphaeroides polysome fractions_90 min

label_protocol: The ULS Fluorescent Labeling Kit for Agilent arrays (Kreatech) was used for RNA labeling and fragmentation.

growth_protocol: R. sphaeroides WT 2.4.1 was grown under aerobic conditions (100% oxygen) to an OD660 of 0.4 and stressed with 0.2 µM methylene blue in the presence of 800 W m-2 high light

extract_protocol: Transcriptome: Total RNA was isolated by the hot phenol method (Janzon et al., 1986). After DNaseI treatment, RNA was purified by phenol-chloroform-isoamylalcohol and chloroform-isoamylacohol. RNA was further purified by RNeasy®MinElute™ spin columns (Qiagen). Translatome: Polysome fractions were collected by sucrose density gradient centrifugation and polysomal RNA isolated by the hot phenol method. RNA was further purified by RNeasy®MinElute™ spin columns (Qiagen).

tag: rna fraction

value: polysomal RNA isolates

tag: time point after stress

value: 90 min

source_name: R. sphaeroides polysome fractions_0 min

value: 0 min


title: R. sphaeroides WT 2.4.1_90 min singlet oxygen stress versus 0 min stress_transcriptome replicate A

description: biological sample 1-3

source_name: R. sphaeroides crude extracts_90 min

value: total RNA isolates

source_name: R. sphaeroides crude extracts_0 min


title: R. sphaeroides WT 2.4.1_90 min singlet oxygen stress versus 0 min stress_translatome replicate B

description: biological sample 4-6


title: U87 10 uM Y15 rep1

status: Public on Jan 12 2013

city: Buffalo

first: Qiang

last: Hu

state: NY

address: Elm & Carlton Streets

institute: Roswell Park Cancer Institute

hyb_protocol: 750ng of the biotin labeled cRNA probes were mixed with hybridization reagents and hybridized overnight to the HumanHT-12 v4 BeadChips.

scan_protocol: Following washing and staining, the BeadChips were imaged using the Illumina iScan Reader to measure fluorescence intensity at each probe.

data_processing: BeadChip data files were analyzed with Illumina’s GenomeStudio gene expression module (v1.8.0)

label_protocol: Initially, 500ng total RNA was converted to cDNA, followed by an in vitro transcription step to generate biotin labeled cRNA using the Ambion Illumina Total Prep RNA Amplification Kit (Ambion, Austin, TX) as per manufacturer’s instructions.

extract_protocol: Total RNA from 10-20 mg fresh frozen tissues were prepared using the RNeasy mini kits (Qiagen, Valencia, CA) following manufacturer’s instructions. After elution, RNA samples were concentrated by EtOH precipitation at –20oC overnight, and resuspended in nuclease-free water.  Before labeling, RNA samples were quantitated using a ND-1000 spectrophotometer (NanoDrop Wilmington, DE) and evaluated for degradation using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Samples were required to have a RIN >6.5, an OD 260:280 of 1.9-2.1, an OD 260/230 >1.5 and >1.5 28S:18S ratio of the ribosomal bands for gene expression array analysis.

tag: cell line

tag: treatment

value: glioblastoma cancer cell line


title: U87 20 uM Temozolomide + 10 uM Y15 rep1

source_name: U87 20 uM Temozolomide + 10 uM Y15

value: 20 uM Temozolomide + 10 uM Y15


title: U87 20 uM Temozolomide + 10 uM Y15 rep2


title: U87 20 uM Temozolomide rep2

source_name: U87 20 uM Temozolomide

value: 20 uM Temozolomide


title: U87 untreated rep1

source_name: U87 untreated

value: untreated


title: HCT116b primary colon tumor

status: Public on Feb 20 2013

city: Omaha

first: Sanjib

last: Chowdhury

state: Nebraska

address: 985950 Nebraska Medical Center

institute: University of Nebraska Medical Center

description:
HCT116b
male athymic BALB/c nude mice

hyb_protocol: Cy3 fluorescent PCR products were hybridized to Illumina Humanref-8 v3 beadchips using standard Illumina protocol

scan_protocol: Illumina beadchips were scanned with an Illumina S486 BeadArray reader using standard settings

data_processing: Signal intensity values for each bead type was extracted and resultant data quantile normalized using Illumina Genome Studio Gene Expression module (v1.0.6)

source_name: HCT116b human colon cancer cell line

label_protocol: Cy3 labeling of gene specific targets was performed by PCR using standard Illumina Whole-Genome DASL gene expression assay protocol

growth_protocol: HCT116 and HCT116b sublines were adapted to growth in serum-free medium consisting of McCoy’s 5A medium (Sigma) supplemented with amino acids, pyruvate, and antibiotics containing the growth factors transferrin (4 µg/ml; Sigma), insulin (20 µg/ml; Sigma) and EGF (5 ng/ml; Collaborative Research)

extract_protocol: RNA was prepared using Qiagen RNeasy kit

treatment_protocol: Exponentially growing GFP-labeled HCT116 and HCT116b cells (5X106 cells) were inoculated subcutaneously onto the dorsal surfaces of separate BALB/c nude male mice. Once the xenografts were established, measuring approximately 500 mm3, they were excised and minced into 1 mm3 pieces. Two of these pieces were then orthotopically implanted into the colons of other male BALB/c nude mice and weekly GFP fluorescence imaging was performed for up to 7 wk.

tag: xenograft recipient gender

value: male

tag: xenograft recipient strain

value: BALB/c


title: R. sphaeroides WT 2.4.1_7 min singlet oxygen stress versus 0 min stress_transcriptome replicate A

description: biological sample 1-3

source_name: R. sphaeroides crude extracts_7 min

value: 7 min


title: DBTRG 10 uM Y15 rep1

source_name: DBTRG 10 uM Y15

value: DBTRG


title: U87 20 uM Temozolomide rep1


title: U87 untreated rep2


title: DBTRG 10 uM Y15 rep2


title: DBTRG untreated rep1

source_name: DBTRG untreated


title: R. sphaeroides WT 2.4.1_45 min singlet oxygen stress versus 0 min stress_transcriptome replicate B

description: biological sample 4-6

source_name: R. sphaeroides crude extracts_45 min

value: 45 min


title: R. sphaeroides WT 2.4.1_90 min singlet oxygen stress versus 0 min stress_transcriptome replicate B

description: biological sample 4-6


title: R. sphaeroides WT 2.4.1_45 min singlet oxygen stress versus 0 min stress_transcriptome replicate A

description: biological sample 1-3


title: R. sphaeroides WT 2.4.1_7 min singlet oxygen stress versus 0 min stress_transcriptome replicate B

description: biological sample 4-6


title: U87 10 uM Y15 rep2


title: DBTRG untreated rep2


title: ESC UNDIFF LINE UC01 PASSAGE 60

status: Public on Oct 31 2012

first: Kory

middle: R

last: Johnson

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

description:
ESC UNDIFF LINE UC01 PASSAGE 60
Raw data file: SAMPLE 188.txt

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR high 100%, XDR low 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_91 and Grid: 014868_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: ESC UNDIFF LINE UC01 PASSAGE 60 (SAMPLE 188)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: All culture reagents were acquired from Invitrogen unless stated otherwise. Standard culture conditions of 37oC, 5% CO2 and 95% humidity were maintained for all cells.  Human ES cells (hESCs) were cultured on a feeder-layer of irradiated CF1 mouse embryonic fibroblasts (MEFs) in DMEM:F12 (Cat# 11330-032) containing 20% Knockout Serum Replacement (KSR)(Cat# 10828-028), 1mM glutamine (Cat# 25030-081), 0.1mM beta-mercaptoethanol (beta-ME; Sigma), 1x non-essential amino acids (NEAA; Cat# 11140-050) and 4ng/ml bFGF (R&D Systems)(Cat# 233-FB). Fibroblasts were cultured in DMEM (Cat# 11965-092) containing 10% fetal bovine serum (FBS) (Gemini Bio-products), 2mM glutamine and 1x NEAA. Fibroblasts were irradiated with ~6500 rads using a Faxitron RX650 X-irradiator. They were subsequently plated on Falcon 6-well tissue culture dishes, coated with 0.1% gelatin, at a density of 0.1875 x 106/well. hESCs were plated in small clumps the following day, medium was exchanged every day and colonies were passaged by collagenase treatment every 3-4 days.  Embryoid bodies were cultured in fibroblast medium (FBS; EB_mesend) or in hESC medium without bFGF (EB_ecto) in 60mm Corning Low Attachment dishes for a total of 8 days. Media were changed by sedimentation every 2 days. An important point to note is that the same lot number of FBS was used for all studies.

extract_protocol: RNA was extracted using a modification of the basic Trizol (Invitrogen) protocol. Briefly, 1ml of Trizol was added to sedimented colonies or EBs and triturated to dissociate the cells. At this point the lysates were stored at -80oC until all samples for that cell line were collected. Upon thaw, lysates were incubated at room temperature for 10 mins, mixed with 200ul chloroform and centrifuged in a Phase-Lock Gel (Heavy) Eppendorf tube (Qiagen). RNA was precipitated from the aqueous phase by the addition of 250ul of isopropanol and 250ul of a high salt buffer (0.8 M sodium citrate and 1.2 M NaCl) followed by centrifugation. The RNA pellet was washed twice with 75% ethanol, dried and resuspended in nuclease-free water. RNA was DNase treated for 20 mins and the DNAse removed using Ambion’s DNA-Free kit. Concentration was determined using a NanoDrop ND-1000 UV-VIS Spectrophotometer.

tag: class

value: ESC

tag: condition

value: UNDIFF

tag: line

tag: passage

tag: gender

value: MALE

tag: processing control

value: SAMPLE 138


title: dsHSF123-treated males rep3

status: Public on Feb 08 2013

city: Perugia

first: tania

last: dottorini

address: via del Giochetto

department: Dept. Exp.Medicine and Bichem. Sci.

country: Italy

institute: University of Perugia

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1)

data_processing: Data analysis was performed by OGT according to a standardized procedure, as implemented by the software applications Feature Extraction (version 9.5.3.1.), and Genespring GX (version 11.0). Expression data was first normalised using linear and loess normalization in Feature Extraction, then it was imported into Genespring where it was converted into normalised log ratios (log2 of cy3 divided by cy5) (signal divided by control).

organism: Anopheles gambiae

source_name: whole adult, dsHSF123

extract_protocol: Total RNA from 4-d-old dsLacZ-treated controls and HSF-silenced males was extracted using TRIzol reagent (Life Technologies), following protocols set according to manufacturer’s instructions. RNA preparation, labelling, hybridization and data analysis were performed by the Oxford Gene Technology (OGT) company. In particular, RNA was further cleaned up using the RNeasy Mini Kit (Qiagen) followed by ethanol precipitation. Sample passing the purity metrics (260/280 and 260/230 ratio) were considered for labeling and hybridization procedures. Labeling was done with cyanine 3 (dsHSF1 and dsHSF123) and cyanine 5 (control dsLacZ).

tag: genotype/variation

value: HSF123 knockdown

source_name: whole adult, dsLacZ

value: control (dsLacZ)


title: HCT116 primary colon tumor

description:
HCT116
male athymic BALB/c nude mice

source_name: HCT116 human colon cancer cell line


title: ESC KSR LINE UC01 PASSAGE 60

description:
ESC KSR LINE UC01 PASSAGE 60
Raw data file: SAMPLE 187.txt

source_name: ESC KSR LINE UC01 PASSAGE 60 (SAMPLE 187)

value: KSR


title: iPSC KSR LINE i13 PASSAGE 11

description:
iPSC KSR LINE i13 PASSAGE 11
Raw data file: SAMPLE 93.txt

source_name: iPSC KSR LINE i13 PASSAGE 11 (SAMPLE 93)

value: iPSC

value: FEMALE

value: SAMPLE 148


title: ESC FBS LINE UC01 PASSAGE 60

description:
ESC FBS LINE UC01 PASSAGE 60
Raw data file: SAMPLE 186.txt

source_name: ESC FBS LINE UC01 PASSAGE 60 (SAMPLE 186)

value: FBS


title: iPSC KSR LINE i13 PASSAGE 15

description:
iPSC KSR LINE i13 PASSAGE 15
Raw data file: SAMPLE 96.txt

source_name: iPSC KSR LINE i13 PASSAGE 15 (SAMPLE 96)


title: ESC UNDIFF LINE UC01 PASSAGE 56

description:
ESC UNDIFF LINE UC01 PASSAGE 56
Raw data file: SAMPLE 185.txt

source_name: ESC UNDIFF LINE UC01 PASSAGE 56 (SAMPLE 185)


title: ESC KSR LINE BG03 PASSAGE 54

description:
ESC KSR LINE BG03 PASSAGE 54
Raw data file: SAMPLE 17.txt

source_name: ESC KSR LINE BG03 PASSAGE 54 (SAMPLE 17)

value: SAMPLE 123


title: ESC KSR LINE UC01 PASSAGE 56

description:
ESC KSR LINE UC01 PASSAGE 56
Raw data file: SAMPLE 184.txt

source_name: ESC KSR LINE UC01 PASSAGE 56 (SAMPLE 184)


title: iPSC UNDIFF LINE i13 PASSAGE 15

description:
iPSC UNDIFF LINE i13 PASSAGE 15
Raw data file: SAMPLE 97.txt

source_name: iPSC UNDIFF LINE i13 PASSAGE 15 (SAMPLE 97)


title: iPSC FBS LINE i13 PASSAGE 11

description:
iPSC FBS LINE i13 PASSAGE 11
Raw data file: SAMPLE 92.txt

source_name: iPSC FBS LINE i13 PASSAGE 11 (SAMPLE 92)


title: ESC UNDIFF LINE BG03 PASSAGE 50

description:
ESC UNDIFF LINE BG03 PASSAGE 50
Raw data file: SAMPLE 15.txt

source_name: ESC UNDIFF LINE BG03 PASSAGE 50 (SAMPLE 15)


title: ESC KSR LINE BG03 PASSAGE 50

description:
ESC KSR LINE BG03 PASSAGE 50
Raw data file: SAMPLE 14.txt

source_name: ESC KSR LINE BG03 PASSAGE 50 (SAMPLE 14)


title: ESC UNDIFF LINE BG03 PASSAGE 54

description:
ESC UNDIFF LINE BG03 PASSAGE 54
Raw data file: SAMPLE 18.txt

source_name: ESC UNDIFF LINE BG03 PASSAGE 54 (SAMPLE 18)


title: iPSC FBS LINE i13 PASSAGE 15

description:
iPSC FBS LINE i13 PASSAGE 15
Raw data file: SAMPLE 95.txt

source_name: iPSC FBS LINE i13 PASSAGE 15 (SAMPLE 95)


title: ESC FBS LINE BG03 PASSAGE 54

description:
ESC FBS LINE BG03 PASSAGE 54
Raw data file: SAMPLE 16.txt

source_name: ESC FBS LINE BG03 PASSAGE 54 (SAMPLE 16)


title: RT_03_15d_128_Lung_CLPR03_RSTSRP805

status: Public on Oct 12 2012

city: RTP

first: Longlong

last: Yang

state: NC

address: 6 Davis Dr.

institute: CIIT Centers for Health Research

description: RT_03_15d_128_Lung_CLPR03_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing:
RMAExpress
Written by B. M. Bolstad <bmb@bmbolstad.com>
Version: 1.0.5 Release
http://rmaexpress.bmbolstad.com

source_name: Lung tissue

label_protocol: standard Affymetrix protocol

extract_protocol:
Extraction Method: Trizol
Additional Purification Method: Qiagen Rneasy

treatment_protocol: in vivo Treatment: Chloroprene, Treatment Repeat: 5, Units of Treatment Repeat: days/week, Treatment Duration: 15, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: 6 hr/day, Vehicle for Chemical: Air, Route of Exposure: inhalation, Dose or Concentration: 0.3, Units of Dose or Concentration: ppm

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

value: excellent

tag: sample preservation

value: RNAlater

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

value: adult

tag: sacrifice method

value: Pentobarbital (5.2 mg/kg) and exsanguination

tag: age

tag: units of age

value: Weeks at start of exposure

tag: tissue

value: Lung

tag: tissue harvest methods

value: Lung samples were obtained by placing a suture loosely around the left bronchus at the site where the bronchus enters the left lung lobe.  A second suture was placed around the right bronchus and pulled tightly to tie off the right lung lobes.  The right lung lobes were removed and placed in RNAlater, and the left lung infused under hydrostatic pressure (~30 cm) with neutral buffered formalin.   Samples placed in RNAlater were incubated overnight at 4°C and frozen the next day at < 70°C.

tag: agent

value: Chloroprene

tag: treatment repeat

tag: units of treatment repeat

value: days/week

tag: treatment duration

value: 5, Units of Duration:days

tag: treatment time

tag: units of treatment time

value: 6 hr/day

tag: vehicle for chemical

value: Air

tag: route of exposure

value: inhalation

tag: dose or concentration


title: ESC FBS LINE UC01 PASSAGE 56

description:
ESC FBS LINE UC01 PASSAGE 56
Raw data file: SAMPLE 183.txt

source_name: ESC FBS LINE UC01 PASSAGE 56 (SAMPLE 183)

tag: class

value: ESC

tag: condition

tag: line

tag: passage

tag: gender

value: MALE

tag: processing control

value: SAMPLE 138


title: iPSC UNDIFF LINE i13 PASSAGE 11

description:
iPSC UNDIFF LINE i13 PASSAGE 11
Raw data file: SAMPLE 94.txt

source_name: iPSC UNDIFF LINE i13 PASSAGE 11 (SAMPLE 94)

value: iPSC

value: UNDIFF

value: FEMALE

value: SAMPLE 148


title: RT_03_15d_126A_Lung_CLPR03_RSTSRP805

description: RT_03_15d_126A_Lung_CLPR03_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

value: excellent

tag: sample preservation

value: RNAlater

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

value: adult

tag: sacrifice method

value: Pentobarbital (5.2 mg/kg) and exsanguination

tag: age

tag: units of age

tag: tissue


title: ESC FBS LINE BG03 PASSAGE 50

description:
ESC FBS LINE BG03 PASSAGE 50
Raw data file: SAMPLE 13.txt

source_name: ESC FBS LINE BG03 PASSAGE 50 (SAMPLE 13)

tag: class

tag: condition

value: FBS

tag: line

tag: passage

tag: gender

tag: processing control

value: SAMPLE 123


title: RT_03_15d_127A_Lung_CLPR03_RSTSRP805

description: RT_03_15d_127A_Lung_CLPR03_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

value: Weeks at start of exposure

value: Lung

tag: tissue harvest methods

value: Lung samples were obtained by placing a suture loosely around the left bronchus at the site where the bronchus enters the left lung lobe.  A second suture was placed around the right bronchus and pulled tightly to tie off the right lung lobes.  The right lung lobes were removed and placed in RNAlater, and the left lung infused under hydrostatic pressure (~30 cm) with neutral buffered formalin.   Samples placed in RNAlater were incubated overnight at 4°C and frozen the next day at < 70°C.

tag: agent

value: Chloroprene

tag: treatment repeat

tag: units of treatment repeat

value: days/week

tag: treatment duration

value: 5, Units of Duration:days

tag: treatment time

tag: units of treatment time

value: 6 hr/day

tag: vehicle for chemical

tag: route of exposure

tag: dose or concentration


title: RT_90_15d_181A_Lung_CLPR90_RSTSRP805

description: RT_90_15d_181A_Lung_CLPR90_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

treatment_protocol: in vivo Treatment: Chloroprene, Treatment Repeat: 5, Units of Treatment Repeat: days/week, Treatment Duration: 15, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: 6 hr/day, Vehicle for Chemical: Air, Route of Exposure: inhalation, Dose or Concentration: 90, Units of Dose or Concentration: ppm

tag: bioanalyzer results

tag: sample preservation

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: sacrifice method

tag: age

tag: units of age

tag: tissue

value: Air

value: inhalation


title: RT_90_15d_178A_Lung_CLPR90_RSTSRP805

description: RT_90_15d_178A_Lung_CLPR90_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

tag: dilution

tag: rna integrity number

tag: tissue harvest methods

tag: agent

tag: treatment repeat

tag: units of treatment repeat


title: RT_13_15d_157_Lung_CLPR13_RSTSRP805

description: RT_13_15d_157_Lung_CLPR13_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

treatment_protocol: in vivo Treatment: Chloroprene, Treatment Repeat: 5, Units of Treatment Repeat: days/week, Treatment Duration: 15, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: 6 hr/day, Vehicle for Chemical: Air, Route of Exposure: inhalation, Dose or Concentration: 13, Units of Dose or Concentration: ppm

tag: ratio

tag: bioanalyzer results

tag: sample preservation

tag: strain

tag: treatment duration

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical

tag: route of exposure

tag: dose or concentration


title: RT_2_15d_141_Lung_CLPR2_RSTSRP805

description: RT_2_15d_141_Lung_CLPR2_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

treatment_protocol: in vivo Treatment: Chloroprene, Treatment Repeat: 5, Units of Treatment Repeat: days/week, Treatment Duration: 15, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: 6 hr/day, Vehicle for Chemical: Air, Route of Exposure: inhalation, Dose or Concentration: 2, Units of Dose or Concentration: ppm

tag: array type

tag: amount to core

tag: units of amount

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: sacrifice method

tag: age

tag: units of age

tag: tissue


title: RT_0_15d_113r_Lung_ACO2_RSTSRP805

description: RT_0_15d_113r_Lung_ACO2_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

treatment_protocol: in vivo Treatment: Air Control, Treatment Repeat: 5, Units of Treatment Repeat: days/week, Treatment Duration: 15, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: 6 hr/day, Vehicle for Chemical: Air, Route of Exposure: inhalation, Dose or Concentration: 0, Units of Dose or Concentration: ppm

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: strain

tag: tissue harvest methods

tag: agent

value: Air Control

tag: treatment repeat

tag: units of treatment repeat


title: heart_CTL_patient33_T2

city: Edmonton

first: Eliana

last: Lucchinetti

address: HMRC 408

institute: University of Alberta

hyb_protocol: Samples were hybridized using Affymetrix reagents according to the protocols established at the Functional Genomics Center Zurich (http://www.fgcz.uzh.ch). Washing using the Affymetrix Fluidics Station FS450.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Microarray analysis was performed using customCDF from Brainarray (Brainarray Version 11.0.1, HuEx10stv2_Hs_ENSG). For more information, please see:  http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp . Background correction, normalization, and calculation of probe set summaries done with the Robust Multichip Average (RMA) method.
Results were matched/mapped to U133 Plus 2.0 using BioMart.  These results were further subjected to Gene Set Enrichment Analysis (GSEA) and are included in the Sample data tables.  Annotations are included as a supplementary file on the Series record.

source_name: heart (atrial sample)

label_protocol: The cDNA was prepared from total RNA using the WT Ovation Pico System (NuGEN Technologies, Inc., San Carlos, CA).  The FL-Ovation cDNA Biotin Module V2 (NuGEN) was used to generate biotin-labeled single-stranded cDNA samples, which were subsequently fragmented randomly to 35 to 200 bp at 94°C in Fragmentation Buffer (Affymetrix Inc., Santa Clara, CA) and used to hybridize onto Affymetrix Exon 1.0 ST arrays (Affymetrix Inc.).

extract_protocol: Total RNA was isolated using the Qiagen RNeasy MiniKit (QIAGEN Inc., Toronto, ON)

value: heart

value: 50-85 years

tag: treatment

value: placebo (=CTL; cuff mounted but not inflated)

tag: sample collection time

value: after cross-clamp release


title: RT_2_15d_143r_Lung_CLPR2_RSTSRP805

description: RT_2_15d_143r_Lung_CLPR2_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

value: ul

value: excellent

value: RNAlater

tag: ncbi taxonomy id

tag: individual

tag: developmental state

value: adult

value: Pentobarbital (5.2 mg/kg) and exsanguination

tag: treatment duration

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical

tag: route of exposure

tag: dose or concentration


title: RT_90_15d_179_Lung_CLPR90_RSTSRP805

description: RT_90_15d_179_Lung_CLPR90_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

value: good

tag: sample preservation

tag: strain

tag: sacrifice method

tag: age

tag: units of age

value: Weeks at start of exposure

tag: tissue

value: Lung

tag: tissue harvest methods

value: Lung samples were obtained by placing a suture loosely around the left bronchus at the site where the bronchus enters the left lung lobe.  A second suture was placed around the right bronchus and pulled tightly to tie off the right lung lobes.  The right lung lobes were removed and placed in RNAlater, and the left lung infused under hydrostatic pressure (~30 cm) with neutral buffered formalin.   Samples placed in RNAlater were incubated overnight at 4°C and frozen the next day at < 70°C.

tag: agent


title: heart_CTL_patient35_T2

tag: treatment

tag: sample collection time


title: heart_CTL_patient23_T2


title: RT_0_15d_111A_Lung_ACO2_RSTSRP805

description: RT_0_15d_111A_Lung_ACO2_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: treatment repeat

tag: units of treatment repeat

value: days/week

tag: treatment duration

value: 5, Units of Duration:days

tag: treatment time

tag: units of treatment time

value: 6 hr/day

tag: vehicle for chemical


title: RT_0_15d_112A_Lung_ACO2_RSTSRP805

description: RT_0_15d_112A_Lung_ACO2_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: strain

tag: sacrifice method

tag: age

tag: units of age

tag: tissue

value: Air Control

value: Air

tag: route of exposure

value: inhalation

tag: dose or concentration


title: heart_CTL_patient28_T2

value: heart

value: 50-85 years

tag: treatment

value: placebo (=CTL; cuff mounted but not inflated)

tag: sample collection time


title: RT_0_15d_109_Lung_ACO2_RSTSRP805

description: RT_0_15d_109_Lung_ACO2_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

value: ul

value: excellent

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: tissue harvest methods

tag: agent

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

tag: treatment time


title: heart_CTL_patient19_T2

tag: tissue

tag: age

value: after cross-clamp release


title: heart_CTL_patient27_T2


title: heart_CTL_patient32_T2


title: heart_CTL_patient24_T2


title: heart_CTL_patient35_T1

value: before cannulation


title: heart_CTL_patient34_T1


title: heart_CTL_patient34_T2


title: heart_CTL_patient28_T1


title: heart_CTL_patient30_T2


title: heart_CTL_patient13_T2


title: heart_CTL_patient32_T1


title: heart_CTL_patient30_T1


title: heart_CTL_patient33_T1


title: UW_AffyExonArray_H7-hESC_diffProtA_9d_1

status: Public on Nov 08 2012

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

tag: lab

value: UW

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

value: AffyExonArray

tag: datatype description

value: Affymetrix Exon Microarray

tag: cell

tag: cell organism

value: human

tag: cell description

value: undifferentiated embryonic stem cells

tag: cell lineage

value: inner cell mass

tag: cell sex

value: U

tag: treatment description

value: H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage:mesoderm

tag: labexpid

tag: replicate


title: heart_CTL_patient27_T1

tag: treatment

tag: sample collection time


title: heart_CTL_patient24_T1


title: heart_CTL_patient19_T1


title: heart_CTL_patient23_T1


title: heart_CTL_patient13_T1


title: heart_RIPC_patient31_T2

value: RIPC


title: heart_RIPC_patient22_T2

value: heart


title: heart_RIPC_patient38_T1

value: 50-85 years


title: heart_RIPC_patient25_T1


title: heart_RIPC_patient21_T2


title: heart_RIPC_patient37_T1


title: heart_RIPC_patient38_T2


title: heart_RIPC_patient31_T1


title: heart_RIPC_patient20_T2


title: UW_AffyExonArray_H7-hESC_diffProtA_14d_2

value: H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage:mesoderm


title: heart_RIPC_patient16_T2


title: UW_AffyExonArray_H7-hESC_diffProtA_5d_1

value: H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage:mesoderm


title: heart_RIPC_patient15_T2


title: heart_RIPC_patient37_T2


title: heart_RIPC_patient21_T1


title: heart_RIPC_patient36_T1


title: UW_AffyExonArray_H7-hESC_diffProtA_14d_1


title: UW_AffyExonArray_H7-hESC_diffProtA_5d_2


title: heart_RIPC_patient36_T2


title: heart_RIPC_patient22_T1


title: heart_RIPC_patient25_T2


title: heart_RIPC_patient26_T2


title: heart_RIPC_patient20_T1


title: heart_RIPC_patient26_T1


title: heart_RIPC_patient16_T1


title: Mouse Ovary sense 2 (gene)

status: Public on Oct 10 2012

city: Brookings

first: Maurice

last: Ling

department: Mathematics and Statistics

institute: South Dakota State University

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Array hybridization was performed according to the manufacturer's instruction (Affymetrix) at the UCLA Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix) at the UCLA Microarray Core Facility.

data_processing:
probeset group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps
CEL files were processed using Affymetrix Expression Console

source_name: Mouse Ovary sense 2 (gene)

label_protocol: Sense transcript detection labeled using standard Affymetrix labeling protocol. Antisense transcript detection labeled using ATE protocol (Ge et al., 2008; PMID 18211689)

extract_protocol: Tissue total RNA purchased from Ambion

value: ovary

tag: transcript type

value: Sense transcript (gene)

tag: ambion catalog number


title: Mouse Heart sense 2 (gene)

source_name: Mouse Heart sense 2 (gene)

tag: tissue


title: heart_RIPC_patient15_T1

tag: age

value: before cannulation


title: Mouse Kidney sense 2 (gene)

source_name: Mouse Kidney sense 2 (gene)

value: kidney


title: Mouse Testes sense 2 (gene)

source_name: Mouse Testes sense 2 (gene)

value: testes


title: Mouse Ovary sense 1 (gene)

source_name: Mouse Ovary sense 1 (gene)


title: Mouse Thymus sense 1 (gene)

source_name: Mouse Thymus sense 1 (gene)

value: thymus


title: Mouse Testes sense 1 (gene)

source_name: Mouse Testes sense 1 (gene)


title: Mouse Brain sense 1 (gene)

source_name: Mouse Brain sense 1 (gene)

value: brain


title: Mouse Liver sense 1 (gene)

source_name: Mouse Liver sense 1 (gene)

value: liver


title: Mouse Lung sense 2 (gene)

source_name: Mouse Lung sense 2 (gene)

value: lung


title: Mouse Lung sense 1 (gene)

source_name: Mouse Lung sense 1 (gene)


title: Mouse Kidney sense 1 (gene)

source_name: Mouse Kidney sense 1 (gene)


title: Mouse Thymus sense 2 (gene)

source_name: Mouse Thymus sense 2 (gene)


title: Mouse Spleen sense 1 (gene)

source_name: Mouse Spleen sense 1 (gene)

value: spleen


title: Mouse Brain sense 2 (gene)

source_name: Mouse Brain sense 2 (gene)


title: Mouse Liver sense 2 (gene)

source_name: Mouse Liver sense 2 (gene)


title: Mouse Embryo sense 2 (gene)

source_name: Mouse Embryo sense 2 (gene)

value: embryo


title: Mouse Heart sense 1 (gene)

source_name: Mouse Heart sense 1 (gene)


title: Mouse Embryo sense 1 (gene)

source_name: Mouse Embryo sense 1 (gene)


title: UW_AffyExonArray_H7-hESC_diffProtA_2d_2

tag: lab

value: UW

tag: lab description

value: Stamatoyannopoulous - University of Washington

value: AffyExonArray

value: Affymetrix Exon Microarray

value: human

value: undifferentiated embryonic stem cells

value: inner cell mass

value: U

value: H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage:mesoderm


title: Mouse Thymus antisense 2 (gene)

source_name: Mouse Thymus antisense 2 (gene)

value: Antisense transcript (gene)


title: Mouse Spleen sense 2 (gene)

source_name: Mouse Spleen sense 2 (gene)

value: Sense transcript (gene)


title: Mouse Thymus antisense 1 (gene)

source_name: Mouse Thymus antisense 1 (gene)

value: thymus


title: Mouse Testes antisense 1 (gene)

source_name: Mouse Testes antisense 1 (gene)

value: testes


title: Mouse Spleen antisense 2 (gene)

source_name: Mouse Spleen antisense 2 (gene)


title: Mouse Testes antisense 2 (gene)

source_name: Mouse Testes antisense 2 (gene)


title: Mouse Spleen antisense 1 (gene)

source_name: Mouse Spleen antisense 1 (gene)


title: Mouse Ovary antisense 2 (gene)

source_name: Mouse Ovary antisense 2 (gene)

value: ovary


title: Mouse Ovary antisense 1 (gene)

source_name: Mouse Ovary antisense 1 (gene)


title: Mouse Lung antisense 2 (gene)

source_name: Mouse Lung antisense 2 (gene)

value: lung


title: Rat Spleen sense 1 (gene)

data_processing:
probeset group file: RaEx-1_0-st-v1.r2.pgf
meta-probeset file: RaEx-1_0-st-v1.r2.dt1.rn4.core.mps
CEL files were processed using Affymetrix Expression Console

organism: Rattus norvegicus

source_name: Rat Spleen sense 1 (gene)

value: spleen


title: Rat Thymus sense 1 (gene)

source_name: Rat Thymus sense 1 (gene)


title: Mouse Liver antisense 2 (gene)

source_name: Mouse Liver antisense 2 (gene)

value: liver


title: Rat Spleen sense 2 (gene)

source_name: Rat Spleen sense 2 (gene)


title: Rat Ovary sense 2 (gene)

source_name: Rat Ovary sense 2 (gene)


title: Mouse Kidney antisense 1 (gene)

source_name: Mouse Kidney antisense 1 (gene)

value: kidney


title: Mouse Kidney antisense 2 (gene)

source_name: Mouse Kidney antisense 2 (gene)


title: Rat Testes sense 1 (gene)

source_name: Rat Testes sense 1 (gene)


title: Mouse Embryo antisense 2 (gene)

source_name: Mouse Embryo antisense 2 (gene)

value: embryo


title: Rat Thymus sense 2 (gene)

source_name: Rat Thymus sense 2 (gene)


title: Mouse Heart antisense 2 (gene)

source_name: Mouse Heart antisense 2 (gene)

value: heart


title: Mouse Liver antisense 1 (gene)

source_name: Mouse Liver antisense 1 (gene)


title: Rat Lung sense 2 (gene)

source_name: Rat Lung sense 2 (gene)


title: Mouse Embryo antisense 1 (gene)

source_name: Mouse Embryo antisense 1 (gene)


title: Rat Testes sense 2 (gene)

source_name: Rat Testes sense 2 (gene)


title: Mouse Lung antisense 1 (gene)

source_name: Mouse Lung antisense 1 (gene)


title: Rat Lung sense 1 (gene)

source_name: Rat Lung sense 1 (gene)


title: Rat Liver sense 2 (gene)

source_name: Rat Liver sense 2 (gene)


title: Rat Liver sense 1 (gene)

source_name: Rat Liver sense 1 (gene)


title: Rat Ovary sense 1 (gene)

source_name: Rat Ovary sense 1 (gene)


title: Rat Kidney sense 1 (gene)

source_name: Rat Kidney sense 1 (gene)


title: Rat Kidney sense 2 (gene)

source_name: Rat Kidney sense 2 (gene)


title: Rat Heart sense 2 (gene)

source_name: Rat Heart sense 2 (gene)


title: Rat Embryo sense 1 (gene)

source_name: Rat Embryo sense 1 (gene)


title: Rat Embryo sense 2 (gene)

source_name: Rat Embryo sense 2 (gene)


title: Mouse Heart antisense 1 (gene)

source_name: Mouse Heart antisense 1 (gene)


title: Mouse Brain antisense 1 (gene)

source_name: Mouse Brain antisense 1 (gene)

value: brain


title: Mouse Brain antisense 2 (gene)

source_name: Mouse Brain antisense 2 (gene)


title: Rat Brain sense 2 (gene)

source_name: Rat Brain sense 2 (gene)


title: Rat Thymus antisense 2 (gene)

source_name: Rat Thymus antisense 2 (gene)


title: Rat Heart sense 1 (gene)

source_name: Rat Heart sense 1 (gene)


title: Rat Brain sense 1 (gene)

source_name: Rat Brain sense 1 (gene)


title: Rat Thymus antisense 1 (gene)

source_name: Rat Thymus antisense 1 (gene)


title: Rat Testes antisense 2 (gene)

source_name: Rat Testes antisense 2 (gene)


title: Rat Testes antisense 1 (gene)

source_name: Rat Testes antisense 1 (gene)


title: Rat Lung antisense 2 (gene)

source_name: Rat Lung antisense 2 (gene)


title: Rat Heart antisense 2 (gene)

source_name: Rat Heart antisense 2 (gene)


title: Rat Spleen antisense 1 (gene)

source_name: Rat Spleen antisense 1 (gene)


title: Rat Spleen antisense 2 (gene)

source_name: Rat Spleen antisense 2 (gene)


title: Rat Kidney antisense 1 (gene)

source_name: Rat Kidney antisense 1 (gene)


title: Rat Liver antisense 2 (gene)

source_name: Rat Liver antisense 2 (gene)


title: Rat Embryo antisense 2 (gene)

source_name: Rat Embryo antisense 2 (gene)


title: Rat Embryo antisense 1 (gene)

source_name: Rat Embryo antisense 1 (gene)


title: Rat Liver antisense 1 (gene)

source_name: Rat Liver antisense 1 (gene)


title: Rat Ovary antisense 1 (gene)

source_name: Rat Ovary antisense 1 (gene)


title: Rat Brain antisense 2 (gene)

source_name: Rat Brain antisense 2 (gene)


title: Rat Heart antisense 1 (gene)

source_name: Rat Heart antisense 1 (gene)


title: Rat Ovary antisense 2 (gene)

source_name: Rat Ovary antisense 2 (gene)


title: Rat Lung antisense 1 (gene)

source_name: Rat Lung antisense 1 (gene)


title: Rat Brain antisense 1 (gene)

source_name: Rat Brain antisense 1 (gene)


title: Rat Kidney antisense 2 (gene)

source_name: Rat Kidney antisense 2 (gene)


title: Rat Thymus sense 1 (exon)

source_name: Rat Thymus sense 1 (exon)

value: Sense transcript (exon)


title: Rat Testes sense 1 (exon)

source_name: Rat Testes sense 1 (exon)


title: Rat Spleen sense 1 (exon)

source_name: Rat Spleen sense 1 (exon)


title: Rat Ovary sense 1 (exon)

source_name: Rat Ovary sense 1 (exon)


title: Rat Testes sense 2 (exon)

source_name: Rat Testes sense 2 (exon)


title: Rat Lung sense 2 (exon)

source_name: Rat Lung sense 2 (exon)


title: Rat Liver sense 1 (exon)

source_name: Rat Liver sense 1 (exon)


title: Rat Lung sense 1 (exon)

source_name: Rat Lung sense 1 (exon)


title: Rat Thymus sense 2 (exon)

source_name: Rat Thymus sense 2 (exon)


title: Rat Kidney sense 1 (exon)

source_name: Rat Kidney sense 1 (exon)


title: Rat Ovary sense 2 (exon)

source_name: Rat Ovary sense 2 (exon)


title: Rat Heart sense 1 (exon)

source_name: Rat Heart sense 1 (exon)


title: Mouse Testes sense 1 (exon)

source_name: Mouse Testes sense 1 (exon)


title: Rat Kidney sense 2 (exon)

source_name: Rat Kidney sense 2 (exon)


title: Mouse Lung sense 1 (exon)

source_name: Mouse Lung sense 1 (exon)


title: Mouse Testes sense 2 (exon)

source_name: Mouse Testes sense 2 (exon)


title: Rat Liver sense 2 (exon)

source_name: Rat Liver sense 2 (exon)


title: Rat Embryo sense 2 (exon)

source_name: Rat Embryo sense 2 (exon)


title: Rat Brain sense 1 (exon)

source_name: Rat Brain sense 1 (exon)


title: Mouse Ovary sense 1 (exon)

source_name: Mouse Ovary sense 1 (exon)


title: Rat Brain sense 2 (exon)

source_name: Rat Brain sense 2 (exon)


title: Mouse Spleen sense 1 (exon)

source_name: Mouse Spleen sense 1 (exon)


title: Mouse Lung sense 2 (exon)

source_name: Mouse Lung sense 2 (exon)


title: Rat Heart sense 2 (exon)

source_name: Rat Heart sense 2 (exon)


title: Rat Embryo sense 1 (exon)

source_name: Rat Embryo sense 1 (exon)


title: Mouse Liver sense 1 (exon)

source_name: Mouse Liver sense 1 (exon)


title: Mouse Ovary sense 2 (exon)

source_name: Mouse Ovary sense 2 (exon)


title: Mouse Liver sense 2 (exon)

source_name: Mouse Liver sense 2 (exon)


title: Mouse Thymus sense 1 (exon)

source_name: Mouse Thymus sense 1 (exon)


title: Rat Thymus antisense 2 (exon)

source_name: Rat Thymus antisense 2 (exon)

value: Antisense transcript (exon)


title: Mouse Spleen sense 2 (exon)

source_name: Mouse Spleen sense 2 (exon)


title: Mouse Heart sense 2 (exon)

source_name: Mouse Heart sense 2 (exon)


title: Mouse Thymus sense 2 (exon)

source_name: Mouse Thymus sense 2 (exon)


title: Mouse Kidney sense 1 (exon)

source_name: Mouse Kidney sense 1 (exon)


title: Mouse Embryo sense 2 (exon)

source_name: Mouse Embryo sense 2 (exon)


title: Mouse Heart sense 1 (exon)

source_name: Mouse Heart sense 1 (exon)


title: Mouse Kidney sense 2 (exon)

source_name: Mouse Kidney sense 2 (exon)


title: Rat Thymus antisense 1 (exon)

source_name: Rat Thymus antisense 1 (exon)


title: Rat Testes antisense 2 (exon)

source_name: Rat Testes antisense 2 (exon)


title: Human Thymus sense 2 (exon)

data_processing:
probeset group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps
CEL files were processed using Affymetrix Expression Console

source_name: Human Thymus sense 2 (exon)


title: Rat Testes antisense 1 (exon)

source_name: Rat Testes antisense 1 (exon)


title: Human Thymus sense 1 (exon)

source_name: Human Thymus sense 1 (exon)


title: Rat Spleen antisense 1 (exon)

source_name: Rat Spleen antisense 1 (exon)


title: Rat Spleen antisense 2 (exon)

source_name: Rat Spleen antisense 2 (exon)


title: Rat Spleen sense 2 (exon)

source_name: Rat Spleen sense 2 (exon)


title: Mouse Brain sense 2 (exon)

source_name: Mouse Brain sense 2 (exon)


title: Human Testes sense 2 (exon)

source_name: Human Testes sense 2 (exon)


title: Human Testes sense 1 (exon)

source_name: Human Testes sense 1 (exon)


title: Rat Ovary antisense 1 (exon)

source_name: Rat Ovary antisense 1 (exon)


title: Rat Lung antisense 2 (exon)

source_name: Rat Lung antisense 2 (exon)


title: Rat Lung antisense 1 (exon)

source_name: Rat Lung antisense 1 (exon)


title: Mouse Thymus antisense 2 (exon)

source_name: Mouse Thymus antisense 2 (exon)


title: Rat Ovary antisense 2 (exon)

source_name: Rat Ovary antisense 2 (exon)


title: Human Spleen sense 2 (exon)

source_name: Human Spleen sense 2 (exon)


title: Mouse Thymus antisense 1 (exon)

source_name: Mouse Thymus antisense 1 (exon)


title: Mouse Brain sense 1 (exon)

source_name: Mouse Brain sense 1 (exon)


title: Mouse Embryo sense 1 (exon)

source_name: Mouse Embryo sense 1 (exon)


title: Human Ovary sense 2 (exon)

source_name: Human Ovary sense 2 (exon)


title: Human Lung sense 2 (exon)

source_name: Human Lung sense 2 (exon)


title: Mouse Testes antisense 1 (exon)

source_name: Mouse Testes antisense 1 (exon)


title: Mouse Testes antisense 2 (exon)

source_name: Mouse Testes antisense 2 (exon)


title: Mouse Spleen antisense 2 (exon)

source_name: Mouse Spleen antisense 2 (exon)


title: Rat Liver antisense 2 (exon)

source_name: Rat Liver antisense 2 (exon)


title: Mouse Spleen antisense 1 (exon)

source_name: Mouse Spleen antisense 1 (exon)


title: Human Ovary sense 1 (exon)

source_name: Human Ovary sense 1 (exon)


title: Human Spleen sense 1 (exon)

source_name: Human Spleen sense 1 (exon)


title: Human Lung sense 1 (exon)

source_name: Human Lung sense 1 (exon)


title: Human Liver sense 2 (exon)

source_name: Human Liver sense 2 (exon)


title: Rat Liver antisense 1 (exon)

source_name: Rat Liver antisense 1 (exon)


title: Mouse Lung antisense 2 (exon)

source_name: Mouse Lung antisense 2 (exon)


title: Rat Kidney antisense 2 (exon)

source_name: Rat Kidney antisense 2 (exon)


title: Human Liver sense 1 (exon)

source_name: Human Liver sense 1 (exon)


title: Rat Heart antisense 2 (exon)

source_name: Rat Heart antisense 2 (exon)


title: Mouse Lung antisense 1 (exon)

source_name: Mouse Lung antisense 1 (exon)


title: Rat Embryo antisense 1 (exon)

source_name: Rat Embryo antisense 1 (exon)


title: Rat Heart antisense 1 (exon)

source_name: Rat Heart antisense 1 (exon)


title: Mouse Liver antisense 2 (exon)

source_name: Mouse Liver antisense 2 (exon)


title: Rat Kidney antisense 1 (exon)

source_name: Rat Kidney antisense 1 (exon)


title: Rat Embryo antisense 2 (exon)

source_name: Rat Embryo antisense 2 (exon)


title: Mouse Ovary antisense 1 (exon)

source_name: Mouse Ovary antisense 1 (exon)


title: Human Kidney sense 1 (exon)

source_name: Human Kidney sense 1 (exon)


title: Mouse Ovary antisense 2 (exon)

source_name: Mouse Ovary antisense 2 (exon)


title: Rat Brain antisense 2 (exon)

source_name: Rat Brain antisense 2 (exon)


title: Mouse Kidney antisense 2 (exon)

source_name: Mouse Kidney antisense 2 (exon)


title: Human Heart sense 1 (exon)

source_name: Human Heart sense 1 (exon)


title: Rat Brain antisense 1 (exon)

source_name: Rat Brain antisense 1 (exon)


title: Human Colon sense 2 (exon)

source_name: Human Colon sense 2 (exon)

value: colon


title: Mouse Liver antisense 1 (exon)

source_name: Mouse Liver antisense 1 (exon)


title: Human Heart sense 2 (exon)

source_name: Human Heart sense 2 (exon)


title: Mouse Heart antisense 2 (exon)

source_name: Mouse Heart antisense 2 (exon)


title: Human Kidney sense 2 (exon)

source_name: Human Kidney sense 2 (exon)


title: Mouse Kidney antisense 1 (exon)

source_name: Mouse Kidney antisense 1 (exon)


title: Human Colon sense 1 (exon)

source_name: Human Colon sense 1 (exon)


title: Human Thymus sense 2 (gene)

source_name: Human Thymus sense 2 (gene)


title: Mouse Embryo antisense 1 (exon)

source_name: Mouse Embryo antisense 1 (exon)


title: Human Brain sense 1 (exon)

source_name: Human Brain sense 1 (exon)


title: Human Thymus sense 1 (gene)

source_name: Human Thymus sense 1 (gene)


title: Mouse Heart antisense 1 (exon)

source_name: Mouse Heart antisense 1 (exon)


title: Human Testes sense 1 (gene)

source_name: Human Testes sense 1 (gene)


title: Human Testes sense 2 (gene)

source_name: Human Testes sense 2 (gene)


title: Human Brain sense 2 (exon)

source_name: Human Brain sense 2 (exon)


title: Mouse Embryo antisense 2 (exon)

source_name: Mouse Embryo antisense 2 (exon)


title: Human Ovary antisense 2 (exon)

source_name: Human Ovary antisense 2 (exon)


title: Human Spleen antisense 2 (exon)

source_name: Human Spleen antisense 2 (exon)


title: Human Thymus antisense 2 (exon)

source_name: Human Thymus antisense 2 (exon)


title: Human Testes antisense 2 (exon)

source_name: Human Testes antisense 2 (exon)


title: Human Thymus antisense 1 (exon)

source_name: Human Thymus antisense 1 (exon)


title: Mouse Brain antisense 2 (exon)

source_name: Mouse Brain antisense 2 (exon)


title: Human Testes antisense 1 (exon)

source_name: Human Testes antisense 1 (exon)