title: DMSO-treated sample 2

city: Baltimore

first: Yen-Ling

last: Chiu

address: 733 N. Broadway, BRB 615

institute: Johns Hopkins University

description: human T cell were stimulated in the presence of DMSO

hyb_protocol: Hybridization was performed according to the Agilent 60mer oligo microarray processing protocol

scan_protocol: Fluorescence was detected by the Agilent Scanner System

data_processing: The Agilent Feature Extraction Software was used to read out and process the image files. The software also determines the image intensity.

source_name: peripheral blood T cell cultured

label_protocol: RNA samples were amplified and labeled with Cy3 using Agilent Low Input Quick Amp Labeling Kit

growth_protocol: cells were sorted based on surface markers and cultured in RPMI media

extract_protocol: Trizol extraction was performed by Miltenyi Biotec

treatment_protocol: TWS119 3uM or DMSO equivalent amount

tag: treatment

value: DMSO

value: memory T cell


title: CD4+CD28+ T cells pool1

status: Public on Dec 15 2016

type: RNA

city: Oviedo

first: Beatriz

last: Suarez-Alvarez

state: Oviedo

address: Celestino Villamil s/n

country: Spain

institute: Hospital Universitario Central de Asturias

description: CD28+ #1

hyb_protocol: Whole-Genome Gene Expression Direct Hybridization Illumina Inc.'s protocol

scan_protocol: BeadScan Illumina Inc.

data_processing: Raw data was analyzed using the statistical computing framework R/Bioconductor lumi package (version 2.16.0). The background was substrated, the data were log2 transformed and quantile normalized using Bioconductor's "lumi-package". The normalized data matrix represents the probes that are detected in our samples. The exclusion criterion of the probes we use is the detection p-value as a threshold. That is, only probes with detection p-value smaller than 0.01 for any of the studied samples were chosen for the normalization.

molecule: total RNA

organism: Homo sapiens

source_name: CD4+CD28+ T cells pool

label_protocol: TargetAmp™ Nano-g™ Biotin-aRNA Labeling Kit for the Illumina® System, Epicentre (Cat.Num. TAN07924)

growth_protocol: CD4+CD28null and CD4+CD28+ T lymphocytes were isolated from peripheral blood of healthy donors by density gradient centrifugation and further total RNA was isolated.

extract_protocol: RNAqueous Micro kit (Ambion)

treatment_protocol: No treatments after purification from peripheral blood were performed

tag: sample type

value: pool from 12 healthy donors, male and female

tag: subject status

value: healthy donors

tag: tissue

value: Peripheral Blood

tag: cell type

value: CD4+CD28+ T lymphocytes


title: MCF-7_Rg-CNT conjugates (10ug/ml) rep.3

city: Little Rock

first: Mariya

last: Khodakovskaya

state: AR

address: 2801 S. University Avenue

department: Biology

country: USA

institute: University of Arkansas at Little Rock

description: Gene expression data from MCF_7 breast cancer cells (24 day incubation)

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® PrimeView™ Human . GeneChips were washed and stained in the Affymetrix Fluidics Station 400. Hybridization reactions to Affymetrix Maize GeneChip expression arrays were done using the services of Expression Analysis Inc. (http://www.expressionanalysis.com/).

scan_protocol: Scanning of the Affymetrix GeneChip® PrimeView™ Human  expression arrays were done using the services of Expression Analysis Inc. (http://www.expressionanalysis.com/).

data_processing: Data extraction was also performed by Expression Analysis Inc.  Expression values were calculated using the Affymetrix GeneChip Operating System (GCOS) and were based on the difference of the PM (Perfect Match) signal and MM (Mismatch) signal at each of the probe pairs.  The fluorescent signal values from each array were normalized to achieve similar overall intensity between arrays.  The fluorescent signal values of any hybridization reaction were then multiplied by a scaling factor to make their (trimmed) mean intensity equal to 500.  The scaling factor is unique to each hybridization reaction and is in general below 10

label: biotin

source_name: MCF-7 treated with Rg-CNTs conjugates (10ug/ml)

label_protocol: Complimentary RNA (cRNA) was produced according to Affymetrix geneChip® 3' IVT Express kit Technical Manual (http://media.affymetrix.com/support/downloads/manuals/3_ivt_express_kit_manual.pdf)

growth_protocol: Cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal calf serum, 2% glutamine, 1% penicillin and 1% streptomycin stock solutions. Cells were incubated at 37°C/ 95% air/ 5% CO2 and the media was changed every two days.

extract_protocol: Cells were washed 3 times using PBS  and total RNA was collected from adherent tissue culture cells using Trizol (Invitrogen) according to the manufacturer’s instructions. RNA was quantified (A260) using a Nanodrop-1000 spectrophotometer (Nanodrop Technologies).

treatment_protocol: No special treatments before harvesting were carried out.

tag: cell line

value: breast cancer

tag: gender

value: female


title: Patient_14390_CD8+TIM-3+T_cells_2

city: TOULOUSE

first: Pauline

last: Gravelle

address: 1 Avenue Irène Joliot Curie

department: Anatomy-Pathology

country: France

institute: IUCT-ONCOPOLE

description:
Gene expression data from CD3+CD8+TIM-3+ T cells sorted from patient n°14390
3-14390 TIM3+

hyb_protocol: Labeled complementary RNA (cRNA)  from these samples was then fragmented and hybridized to Affymetrix GeneChip® Human Gene 2.0 ST microarrays.

scan_protocol: The chips were then washed, scanned on the Affymetrix Fluidics Station 400, and controlled for quality, before analysis.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings, and then RMA normalized on Expression Console version 1.4.1 (Affymetrix).

source_name: Patient n°14390, fresh CD8+TIM-3+ T cells from FL lymph node

label_protocol: RNAs were amplified, prepared and labelled from 500 pg total RNA, with the Ovation Pico WTA system V2 (NUGEN, San Carlos, CA, USA).

growth_protocol: No culture was performed, cells were collected directly in RLT buffer after flow cytometry sorting, performed from freshly dissociated FL lymph nodes

extract_protocol: Samples were sorted directly in RLT buffer (QIAGEN, Hilden, Allemagne), and extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: No treatment

tag: individual

value: Patient n°14390

value: FL lymph node

value: CD8+TIM-3+ T cell


title: Bovine_Blasto_VERO_rep2

city: Jouy-en-Josas

first: Anaïs

last: Vitorino Carvalho

address: Domaine de Vilvert

department: BDR

institute: INRA

hyb_protocol: 600 ng of Cys-3 labeled cRNA were fragmented at 60°C for 30 minutes and then hybridized to the array for 17 hours at 65°C following the manufacturer’s instructions (Agilent Technologies).

scan_protocol: Slides were immediately scanned using G2565CA Scanner System (Agilent Technologies).

data_processing: The resulting images were analyzed with the Feature Extraction Software v10.7.3.1 (Agilent Technologies), using GE1_107_Sep09 protocol.

organism: Bos taurus

source_name: Bovine blastocysts (192 hpi), cultured in presence of VERO cells at 20% O2

label_protocol: Total of isolated RNA for microarray experiment were labeled into Cyanine-3 (Cys-3) labeled cRNA, using One-Color Low Input Quick Amp Labeling kit (Agilent Technologies, SantaClara, CA, USA) following the recommended protocol for 25 ng of RNA.

growth_protocol: In vitro produced putative zygotes were cultured in 500 µl weel (25 embryos per well) in control condition (5% O2, 5%), in high level of oxygen (20% O2, 20%), in presence of BOEC at 20%O2 (BOEC) or in presence of VERO (VERO). Embyos were sampled at blastocyst stage (192 hours post insemination).

extract_protocol: Total RNA was extracted from batches of embryos (n=10 of 16-cell embryos) using the PicoPure RNA extraction kit (Arcturus). A purification procedure using DNAse I (Qiagen) treatment at 25°C for 15 min was performed prior to elution.

value: embryo

tag: Stage

value: Blastocyst

tag: condition


title: Bovine_Blasto_BOEC_rep3

source_name: Bovine blastocysts (192 hpi), cultured in presence of BOEC at 20% O2

value: cultured in presence of BOEC at 20% O2


title: DMSO-treated sample 3

state: MD


title: Patient_14809_CD8+TIM-3+T_cells_3

description:
Gene expression data from CD3+CD8+TIM-3+ T cells sorted from patient n°14809
5-14809 TIM3+

source_name: Patient n°14809, fresh CD8+TIM-3+ T cells from FL lymph node

value: Patient n°14809


title: Bovine_Blasto_BOEC_rep4


title: Bovine_Blasto_20%_rep4

source_name: Bovine blastocysts (192 hpi), cultured without feeder at 20% O2


title: TWS-treated sample 3

description: human T cell were stimulated in the presence of TWS119


title: Patient_10190_CD8+TIM-3+T_cells_1

description:
Gene expression data from CD3+CD8+TIM-3+ T cells sorted from patient n°10190
1-10190 TIM3+

source_name: Patient n°10190, fresh CD8+TIM-3+ T cells from FL lymph node

value: Patient n°10190


title: Bovine_Blasto_20%_rep1


title: Bovine_Blasto_BOEC_rep2


title: Patient_10190_CD8+TIM-3-T_cells_1

description:
Gene expression data from CD3+CD8+TIM-3- T cells sorted from patient n°10190
2-10190 TIM3-

source_name: Patient n°10190, fresh CD8+TIM-3- T cells from FL lymph node

value: CD8+TIM-3- T cell


title: DMSO-treated sample 1

value: DMSO


title: Bovine_Blasto_5%_rep4

source_name: Bovine blastocysts (192 hpi), cultured without feeder at 5% O2


title: MCF-7_Rb-CNT conjugates (10ug/ml) rep.3

source_name: MCF-7 treated with Rb-CNTs conjugates (10ug/ml)


title: CD4+CD28null T cells pool2

description: CD28null #2

source_name: CD4+CD28null T cells pool

value: CD4+CD28null T lymphocytes


title: Bovine_Blasto_20%_rep3


title: Patient_14809_CD8+TIM-3-T_cells_3

description:
Gene expression data from CD3+CD8+TIM-3- T cells sorted from patient n°14809
6-14809 TIM3-

source_name: Patient n°14809, fresh CD8+TIM-3- T cells from FL lymph node


title: MCF-7_Rg-CNT conjugates (10ug/ml) rep.2


title: CD4+CD28null T cells pool1

description: CD28null #1

value: pool from 12 healthy donors, male and female


title: TWS-treated sample 2

value: memory T cell


title: Patient_14390_CD8+TIM-3-T_cells_2

description:
Gene expression data from CD3+CD8+TIM-3- T cells sorted from patient n°14390
4-14390 TIM3-

source_name: Patient n°14390, fresh CD8+TIM-3- T cells from FL lymph node


title: MCF-7_Rg-CNT conjugates (10ug/ml) rep.1


title: MCF-7_Rb-CNT conjugates (10ug/ml) rep.2


title: CD4+CD28null T cells pool1 [methylation]

type: genomic

description: CD28null #1

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Raw methylation and expression data were background corrected, log2-transformed and quantile-normalized using the R packages from the Bioconductor project and lumi package
Fluorescent siganls (from methylated and unmethylated beadtypes) were measured with the BeadStation GX scanner (Illumina) and ratio between the fluorescence intensities of the methylated probe and the sum of the intensities from the methylated and unmethylated probes were computed. The resulting beta-values (matrix processed) reflect a quantitative measure of the methylation level for each probe and range netween o (completely unmethylated) and 1 (completely methylated). The beta-values were processed with R/Bioconductor in oreder to detect differentially methylated genes between different groups to be copared.
The non_normalized_signal_intensities.txt contains unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

growth_protocol: CD4+CD28null and CD4+CD28+ T lymphocytes were isolated from peripheral blood of healthy donors by density gradient centrifugation and further genomic DNA was isolated.

extract_protocol: QiAmp DNA Micro Kit (Qiagen)

value: healthy donors

value: Peripheral Blood


title: Bovine_Blasto_5%_rep2


title: MCF-7_Rg1 ginsenoside (2ug/ml) rep.3

source_name: MCF-7 treated with Rg1 ginsenoside (2ug/ml)

value: breast cancer


title: CD4+CD28null T cells pool2 [methylation]

description: CD28null #2


title: MCF-7_Rg1 ginsenoside (2ug/ml) rep.2

value: female


title: CD4+CD28+ T cells pool2 [methylation]

description: CD28+ #2

value: CD4+CD28+ T lymphocytes


title: MCF-7_Rb1 ginsenoside (2ug/ml) rep.3

source_name: MCF-7 treated with Rb1 ginsenoside (2ug/ml)


title: S1_Lhx2_cKO_rep3

city: Taipei

first: Shen-Ju

last: Chou

address: 128 Sec. 2, Academia Rd, Nankang

department: Institute of Cellular and Organismic Biology

country: Taiwan

institute: Academia Sinica

description: Gene expression in Lhx2 cKO S1

hyb_protocol: 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent SurePrint G3 Mouse GE  8×60K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays were scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing: Scanned images were analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software was used to quantify signal and background intensity for each feature.

organism: Mus musculus

source_name: Lhx2 cKO S1 cortex

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

extract_protocol: RNA was extracted using TriPure Isolation Reagent (Roche) following the manufacture's insreuctions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Primary somatosensory cortices were dissected from P7 mice brains.

tag: strain

tag: age

value: primary somatosensory cortex


title: MCF-7_Rg1 ginsenoside (2ug/ml) rep.1


title: MCF-7_MWCNTs (8 ug/ml) rep.2

source_name: MCF-7 cells treated with MWCNTs (8 ug/ml)


title: Bovine_16-cell_VERO_rep3

source_name: Bovine 16-cell embryos (96 hpi), cultured in presence of VERO cells at 20% O2

growth_protocol: In vitro produced putative zygotes were cultured in 500 µl weel (25 embryos per well) in control condition (5% O2, 5%), in high level of oxygen (20% O2, 20%), in presence of BOEC at 20%O2 (BOEC) or in presence of VERO (VERO). Embyos were sampled at 16-cell stage (96 hours post insemination).

extract_protocol: Total RNA was extracted from batches of embryos (n=20 of 16-cell embryos) using the PicoPure RNA extraction kit (Arcturus). A purification procedure using DNAse I (Qiagen) treatment at 25°C for 15 min was performed prior to elution.

value: presence of VERO at 20%O2


title: MCF-7_Rb1 ginsenoside (2ug/ml) rep.2


title: Bovine_16-cell_20%_rep3

source_name: Bovine 16-cell embryos (96 hpi), cultured without feeder at 20% O2

value: embryo


title: MCF-7_MWCNTs (8 ug/ml) rep.3


title: TWS-treated sample 1

source_name: peripheral blood T cell cultured


title: MCF-7_Rb-CNT conjugates (10ug/ml) rep.1


title: CD4+CD28+ T cells pool1 [methylation]

description: CD28+ #1

source_name: CD4+CD28+ T cells pool


title: MCF-7_Rb1 ginsenoside (2ug/ml) rep.1


title: Bovine_16-cell_VERO_rep1


title: Bovine_16-cell_20%_rep2


title: Bovine_Blasto_5%_rep3

value: Blastocyst


title: Bovine_16-cell_VERO_rep4


title: Bovine_16-cell_BOEC_rep2

source_name: Bovine 16-cell embryos (96 hpi), cultured in presence of BOEC at 20% O2

value: presence of BOEC at 20%O2


title: Bovine_16-cell_20%_rep4


title: MCF-7_MWCNTs (8 ug/ml) rep.1


title: Bovine_16-cell_BOEC_rep1


title: Bovine_16-cell_BOEC_rep3


title: MCF-7_control rep.3

source_name: MCF-7 cells non treated control


title: MCF-7_control rep.2


title: Bovine_16-cell_5%_rep3

source_name: Bovine 16-cell embryos (96 hpi), cultured without feeder at 5% O2


title: Bovine_16-cell_5%_rep1


title: Bovine_16-cell_5%_rep2


title: LOUCY_1µMJQ1_48h_rep3

city: Gent

first: Sofie

last: Peirs

address: De Pintelaan 185

country: Belgium

institute: Ghent University

description: Gene expression after 48h treatment of LOUCY cells with 1µM JQ1

hyb_protocol: 600ng cy3-labeled, linearly amplified cRNA (specific activity > 6 pmol cy3 per µg cRNA) was hybridised with the Gene Expression Hybridization Kit (Cat nr. 5188-5242, Agilent Technologies) to the SurePrint G3 Human Gene Expression Microarray G4851A (design ID 028004). After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with GE Wash Buffer 2 (Agilent) at room temperature and 1 minute with GE Wash Buffer 3 (Agilent) at 37°C.

scan_protocol: Slides were scanned on the Agilent G2564CA Microarray Scanner. Data was extracted using Agilent Feature Extraction Software.

data_processing:
Normalization of microarray intensities was done using the variance stabilization and calibration (VSN, version 3.30.0) package in R (version 3.0.2).
Probes with low expression were filtered out.

source_name: LOUCY T-ALL cell line, 1µM JQ1 treated, 48h

label_protocol: For all samples, 100ng RNA as input was used. RNA was amplified and labeled using the Low Input Quick Amp Labeling Kit, One Color (Cat nr. 5190-2305, Agilent Technologies)., followed by purification with the RNeasy mini kit (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: LOUCY cells were seeded at 0.7 x 10^6 cells/ml. Cells were cultured in RPMI 1640 medium supplemented with 10% FBS, 100 U/ml penicillin, 100 µg/ml streptomycin, 100 µg/ml kanamycin sulfate and 2 mM L-glutamine at 37°C with 5% CO2.

extract_protocol: RNA was isolated using the miRNeasy mini kit (Qiagen) with on-column DNase digestion. The RNA quality was checked by the Experion RNA StdSens analysis kit (Bio-Rad).

treatment_protocol: Cells were treated with DMSO or 1µM  (+)-JQ1 for 48h

value: LOUCY

tag: cell line bought from

value: DSMZ

tag: type

value: T-ALL

tag: agent

tag: dose

tag: time


title: Bovine_16-cell_5%_rep4


title: MCF-7_control rep.1


title: S1_Lhx2_WT_rep3

description: Gene expression in wild-type S1

source_name: WT S1 cortex


title: LOUCY_1µMJQ1_48h_rep2


title: LOUCY_DMSO_48h_rep3

description: Gene expression after 48h treatment of LOUCY cells with DMSO

source_name: LOUCY T-ALL cell line, DMSO treated, 48h

value: DMSO


title: LOUCY_DMSO_48h_rep2


title: Bovine_16-cell_VERO_rep2


title: LOUCY_1µMJQ1_48h_rep1


title: LOUCY_250nMJQ1_4h_rep3

description: Gene expression after 4h treatment of LOUCY cells with 250nM JQ1

source_name: LOUCY T-ALL cell line, 250nM JQ1 treated, 4h

label_protocol: For all samples, 50ng RNA as input was used. RNA was amplified and labeled using the Low Input Quick Amp Labeling Kit, One Color (Cat nr. 5190-2305, Agilent Technologies)., followed by purification with the RNeasy mini kit (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

treatment_protocol: Cells were treated with DMSO or 250nM  (+)-JQ1 for 4h


title: 0GyS3/ reference male mouse4

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: OGURA

state: Aomori

address: Takahoko, Hacchasawa,

department: Department of Radiobiology

country: Japan

institute: Institute for Environmental Science

hyb_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing: Agilent Genomic Workbench Software (v 7.0.) was used.

extract_protocol: PI-50a (Kurabo Industries LTD.) tissue DNA extraction protocol.

value: tail

value: progeny

source_name: reference male mouse4

value: reference

value: male


title: LOUCY_DMSO_4h_rep3

description: Gene expression after 4h treatment of LOUCY cells with DMSO

source_name: LOUCY T-ALL cell line, DMSO treated, 4h


title: reference male mouse4/ 0GyS2

label_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8


title: reference male mouse4/ 0GyS3


title: 0GySF/ reference male mouse4

value: parent


title: 0GyS1/ reference male mouse4


title: 0GyS4/ reference male mouse4


title: reference male mouse4/ 0GyS4


title: reference male mouse4/ 0GyS5


title: 0GyS2/ reference male mouse4


title: 0GyS6/ reference male mouse4


title: reference male mouse5/ 0GyR5

source_name: reference male mouse5


title: 0GyR4/ reference male mouse5


title: 0GyR5/ reference male mouse5


title: reference male mouse4/ 0GyS1


title: 0GySM/ reference male mouse4


title: LOUCY_DMSO_4h_rep2


title: 0GyR6/ reference male mouse5


title: reference male mouse4/ 0GyS6


title: 0GyS5/ reference male mouse4


title: reference male mouse4/ 0GySF


title: reference male mouse5/ 0GyR6


title: LOUCY_DMSO_4h_rep1


title: reference male mouse5/ 0GyR3


title: reference male mouse4/ 0GySM


title: reference male mouse5/ 0GyR4


title: 0GyR2/ reference male mouse5


title: 0GyR1/ reference male mouse5


title: LOUCY_250nMJQ1_4h_rep1


title: LOUCY_DMSO_48h_rep1


title: primary_visual_cortex-lynx1ko-adult-3

city: New York

first: Milo

middle: Robert

last: Smith

state: NY

address: 1 Gustave L Levy Place

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: 4.5 μg of biotin-labeled cRNA was hybridized to Illumina WG-6 2.0 microarrays (750 ng per subarray)

scan_protocol: Standard scan

data_processing: Quantile normalized and background corrected using Illumina BeadStudio GX Project - GenomeStudio Gene Expression Analysis Module. 1.9.0

source_name: v1, lynx1ko, adult

label_protocol: Biotin

growth_protocol: Standard rearing

extract_protocol: Experiment-naive juvenile C57Bl6 at postnatal day 29 (P29), adult Lynx1-/- (> P60), and adult C57Bl6 (> P60) mice (n = 3 each group) were anesthetized with isoflurane, cervically dislocated, bilateral primary visual cortex (V1) was removed, immediately frozen on dry ice, and stored at -80°C until processed. Total RNA was extracted from V1 using RNeasy Lipid Tissue Mini kit (Qiagen) and stored at -80°C

treatment_protocol: Normal visual experience

tag: genotype

tag: Sex

value: Male

value: Adult (>P60)

tag: visual stimulation

value: normal vision

value: Bilateral primary visual cortex

tag: batch


title: primary_visual_cortex-lynx1ko-adult-1

tag: tissue


title: primary_visual_cortex-wt-adult-2

source_name: v1, wt, adult

value: WT


title: primary_visual_cortex-lynx1ko-adult-2


title: primary_visual_cortex-wt-adult-3


title: primary_visual_cortex-wt-adult-1


title: LOUCY_250nMJQ1_4h_rep2

value: female

tag: cell line


title: primary_visual_cortex-wt-juvenile-3

source_name: v1, wt, juvenile

value: Juvenile (P29)


title: primary_visual_cortex-wt-juvenile-2


title: primary_visual_cortex-wt-juvenile-1


title: 436 T

city: Nashville

first: Yan

last: Guo

state: TN

address: 639 Preston Research Bld

institute: Vanderbilt Cancer Center

hyb_protocol: The GeneFilters were prehybridized for 2 h at 51C with 0.5 mg/ml of poly-dA (Invitrogen) and 0.5 mg/ml Cot-1 DNA (Invitrogen) in 10 ml of AlkPhos DIRECT hybridization buffer (Amersham Bioscience) and then hybridized for 17 h at 51C with the denatured radi

scan_protocol: The arrays were then exposed for 2 hours to an Imaging Plate and scanned at 25-mm resolution with a BAS5000 phosphoimager (Fuji Photo Film), images of the hybridized arrays were processed with L Process (Fuji Photo Film) and signal intensities quantified

data_processing: Data was quality controled and processed using Affymetrix Gene Expression Console.

source_name: esophageal tumor

label_protocol: Five mg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 100 mCi of [33P]dCTP (Amersham Bioscience, Piscataway, NJ) according to the instructions for the Gene

extract_protocol: Qiagen RNeasy Tissue kit (Qiagen, Germantown, MD).

value: esophageal tumor


title: 700 T


title: 700 N

source_name: normal esophageal tissue

value: normal esophageal tissue


title: reference male mouse5/ 0GyR1

tag: sample type

tag: gender


title: 611 T


title: 0GyR3/ reference male mouse5


title: 487 T


title: 0GyRF/ reference male mouse5


title: 87 N


title: 11 N


title: reference male mouse5/ 0GyRF


title: Pooled Normal

source_name: pooled normal esophageal tissue

value: pooled normal esophageal tissue


title: 469 T


title: 426 T


title: 60 N


title: reference male mouse3/ 0GyQ8

source_name: reference male mouse3


title: reference male mouse5/ 0GyR2


title: 460 T


title: reference male mouse5/ 0GyRM


title: 44 N


title: 0GyQ5/ reference male mouse3


title: 0GyQ6/ reference male mouse3


title: reference male mouse3/ 0GyQ6


title: 144 T


title: reference male mouse3/ 0GyQ7


title: 0GyQ7/ reference male mouse3


title: 0GyRM/ reference male mouse5


title: 0GyQ8/ reference male mouse3


title: 158 N


title: 0GyQ3/ reference male mouse3


title: reference male mouse3/ 0GyQ1


title: reference male mouse3/ 0GyQ4


title: 409 N


title: 195 N


title: reference male mouse3/ 0GyQ5


title: 158 T


title: 409 T


title: 0GyQ4/ reference male mouse3


title: 484 T


title: 0GyQ2/ reference male mouse3


title: reference male mouse3/ 0GyQF


title: 484 N


title: 0GyP6/ reference male mouse2

source_name: reference male mouse2


title: 195 T


title: reference male mouse3/ 0GyQ3


title: 0GyQF/ reference male mouse3


title: reference male mouse2/ 0GyP7


title: adrenocortical tumor, IPACTR patient 29

status: Public on Dec 14 2016

city: Memphis

first: Stanley

middle: B

last: Pounds

address: 262 Danny Thomas Place

department: Biostatistics

institute: St. Jude Children's Research Hospital

description: Gene expression data of an adrenocortical tumor at diagnosis

hyb_protocol: 20 ug of biotinylated cRNA were hybridized for 16 hr at 45C on the Affymetrix Human Genome HG-U133A GeneChip Array. HG-U133A arrays were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Normalized probe signals were computed using the RMA algorithm as implemented in the affy_1.46.1 Bioconductor package in R version 3.2.2 for the x86_64-w64-mingw32/x64 (64-bit) platform runnin under Windows 7 x64 (build 7601) Service Pack 1.

source_name: adrenocortical tumor

label_protocol: Biotinylated cRNA were prepared according to the standard one-cycle eukaryote target Affymetrix protocol using 5-10 ug total RNA as starting template (Expression Analysis Technical Manual, 2004, Affymetrix).

extract_protocol: Tumor specimens were harvested during surgery and snap frozen in liquid nitrogen to preserve tissue integrity. Tissue samples were classified according to established histopathologic criteria. Total RNA was isolated from 50 to 100 mg of pediatric ACT using the RNeasy RNA Midi-Prep kit (Qiagen, Valencia, CA). Tumors were prepared in a 4 degree centigrade cold room, sliced into fine pieces using a sterile scalpel, and homogenized with 18- and 19-gauge needles in lysis Buffer RLT (Qiagen) containing beta-mercaptoethanol.

tag: histology

value: UND

tag: Stage

value: I


title: 0GyQ1/ reference male mouse3

tag: strain

value: tail


title: adrenocortical tumor, IPACTR patient 28

value: ACC

value: III


title: adrenocortical tumor, IPACTR patient 26


title: adrenocortical tumor, IPACTR patient 27


title: reference male mouse3/ 0GyQ2

value: reference

value: male

value: progeny


title: 0GyQM/ reference male mouse3

value: parent


title: adrenocortical tumor, IPACTR patient 25

value: ACA


title: adrenocortical tumor, IPACTR patient 23


title: adrenocortical tumor, IPACTR patient 18


title: adrenocortical tumor, IPACTR patient 17

value: II


title: adrenocortical tumor, IPACTR patient 21

value: IV


title: adrenocortical tumor, IPACTR patient 16


title: 0GyP5/ reference male mouse2


title: reference male mouse2/ 0GyP5


title: reference male mouse2/ 0GyP6


title: adrenocortical tumor, IPACTR patient 13


title: adrenocortical tumor, IPACTR patient 22


title: adrenocortical tumor, IPACTR patient 24


title: adrenocortical tumor, IPACTR patient 14


title: adrenocortical tumor, IPACTR patient 12


title: reference male mouse2/ 0GyP4


title: 0GyP4/ reference male mouse2


title: adrenocortical tumor, IPACTR patient 19


title: adrenocortical tumor, IPACTR patient 11


title: adrenocortical tumor, IPACTR patient 20


title: adrenocortical tumor, IPACTR patient 10


title: reference male mouse3/ 0GyQM


title: adrenocortical tumor, IPACTR patient 7


title: adrenocortical tumor, IPACTR patient 15


title: adrenocortical tumor, IPACTR patient 6


title: adrenocortical tumor, IPACTR patient 9


title: adrenocortical tumor, IPACTR patient 8


title: 0GyPM/ reference male mouse2


title: 0GyP2/ reference male mouse2


title: reference male mouse2/ 0GyP3


title: 0GyP3/ reference male mouse2


title: 0GyP1/ reference male mouse2


title: adrenocortical tumor, IPACTR patient 1


title: adrenocortical tumor, IPACTR patient 2


title: adrenocortical tumor, IPACTR patient 3


title: reference male mouse2/ 0GyPM


title: 2-LNCaP-Si-NC-DHT

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

institute: Tokyo Metropolitan Institute of Gerontology

description: Gene expression data from LNCaP cells treated with DHT 10 nM after transfected with siControl

hyb_protocol: The samples were hybridized to Human Gene 1.0 ST microarrays according to standardized protocols from Affymetrix.

scan_protocol: The samples were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The microarray data were preprocessed with Affymetrix Expression Console software using Affymetrix default Robust Multichip Analysis (RMA) sketch algorithm workflow.

label_protocol: Total RNA was labeled employing the Affymetrix GeneChip Whole Transcript (WT) Terminal Labeling kit according to the manufacturer’s instructions

growth_protocol: LNCaP cells were cultures in RPMI 1640 containing 10% FBS.  Before hormone treatment, cells were incubated in Phenol red-free RPMI 1640 containing 2.5% charcoal/dextran treated FBS for three days.

extract_protocol: Total RNAs were extracted using ISOGEN (Nippon gene) according to the manufacturer's instructions.

treatment_protocol: Cells were transfected with each siRNA 48 h before hormone treatment. Cells were treated with vehicle or DHT (10 nM).

value: LNCaP

tag: cell type

value: prostate cancer

tag: knockdown

value: siControl

tag: treatment

value: DHT 10 nM


title: reference male mouse2/ 0GyP1


title: 4-LNCaP-SiPOTEF-AS-DHT_

description: Gene expression data from LNCaP cells  treated with DHT 10 nM after trasfected with siPOTEF-AS1


title: 0GyP7/ reference male mouse2


title: 0GyPF/ reference male mouse2


title: adrenocortical tumor, IPACTR patient 5


title: 3-LNCaP-SiPOTEF-AS-veh

description: Gene expression data from LNCaP cells treated with vehicle (ethanol) after trasfected with siPOTEF-AS1

value: Vehicle


title: Liver, mutant, rep 2

city: Munich

first: Vladimir

last: Chubanov

state: Non-US/Canada

address: Goethestraße 33

department: Walther-Straub-Institut

country: Germany

institute: Ludwig-Maximilians-Universität München

hyb_protocol: 2.5 µg of fragmented and labeled ssDNA were hybridized for 16-18h hr at 45°C on GeneChip Mouse Gene 1.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Affymetrix Expression Console (version 1.4.0) using Affymetrix default analysis settings and RMA as processing algorithm.

label: Biotin

source_name: Liver

label_protocol: Biotinylated single-stranded DNA were prepared according to the standard Affymetrix protocol (Whole Transcript Expression arrays) from 100 ng total RNA  using the WT terminal labeling kit

growth_protocol: Liver tissues were collected from 12-13 weeks old Trpm6 deficient and control male littermates.

extract_protocol: Total RNA was extracted using the GenElute mammalian total RNA purification kit (Sigma-Aldrich).

treatment_protocol: Left lobe liver fragments (~100 mg) were collected in 1.5 ml tubes, snap-frozen in liquid nitrogen and stored at -80°C.

tag: genetic background

value: Mutant

tag: age

value: 12 weeks


title: Liver, control, rep 4

value: Control

value: 13 weeks


title: iPSC-CM_donorD_rep1

city: Fujisawa

first: Tadahiro

last: Shinozawa

address: Muraokahigashi 2chome

institute: Takeda pharmaceuticals

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE v2 8x60K Microarray (G039494) 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), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 039494_D_F_20140813) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Quick Amplification Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was purified with an RNeasy Mini Kit (Qiagen) following the manufacturer's protocol.

value: iPSC-CM

tag: donor

value: D


title: Liver, control, rep 3

tag: genotype

value: male


title: Liver, control, rep 1


title: iPSC-CM_donorD_rep2


title: Liver, mutant, rep 3


title: iPSC-CM_donorD_rep3


title: Liver, mutant, rep 1


title: iPSC-CM_donorF_rep2

value: F


title: reference male mouse2/ 0GyP2

value: tail

value: reference

value: progeny


title: Liver, control, rep 2


title: iPSC-CM_donorF_rep1


title: Ventricular tissue_donor1_rep1

source_name: Ventricular tissue_donor1

value: adult ventricular tissue


title: Ventricular tissue_donor2_rep1

source_name: Ventricular tissue_donor2


title: adrenocortical tumor, IPACTR patient 4

value: ACA

value: I


title: PT45 co-cultured with Cancer-Associated Fibroblasts (CAF) 3D rep2

city: Candiolo

first: Davide

last: Cora'

state: TO

department: Dept. of Oncology

country: Italy

institute: Piemonte Orientale University and IRCCS Candiolo Cancer Institute

description: Sample name: P14

hyb_protocol: 750 ng of cRNA was hybridized on HumanHT-12_v.4 for 18 h. Array washes were performed using wash buffer.

scan_protocol: Hybridized BeadChips were scanned using Illumina Array reader.

data_processing: Cubic spline-normalized probe intensity data, together with detection p-values, were obtained using the GenomeStudio software v2011.01 (Illumina).

source_name: PT45 sorted from microtissues obtained co-culturing CAF and PT45 within biodegradable microcarriers in a spinner flask reactor for 12 days

label_protocol: Biotinylated cRNA were prepared with Illumina TotalPrep RNA Amplification kit (Life Technologies).

growth_protocol: Normal fibroblasts (NF), cancer-associated fibroblasts (CAF) and pancreatic adenocarcinoma cell line (PT45) cultured in 2D or 3D conditions for 12 days, in mono- or co-cultures.

extract_protocol: Total RNA was extracted from frozen tumors with miRNeasy mini kit (Qiagen) after a preincubation with RNAlater (Life Technologies).

value: pancreatic adenocarcinoma cell line

tag: culture type

value: co-culture with Cancer-Associated Fibroblasts (CAF)

tag: culture condition


title: PT45 co-cultured with Normal Fibroblasts (NF) 3D rep4

description: Sample name: P12

source_name: PT45 sorted from microtissues obtained co-culturing NF and PT45 within biodegradable microcarriers in a spinner flask reactor for 12 days

value: co-culture with Normal Fibroblasts (NF)


title: PT45 co-cultured with Cancer-Associated Fibroblasts (CAF) 3D rep3

description: Sample name: P15


title: iPSC-CM_donorC_rep3

value: C


title: PT45 co-cultured with Normal Fibroblasts (NF) 3D rep2

description: Sample name: P10


title: iPSC-CM_donorH_rep2

value: H


title: Ventricular tissue_donor3_rep1

source_name: Ventricular tissue_donor3


title: iPSC-CM_donorC_rep1


title: iPSC-CM_donorI_rep3


title: PT45 co-cultured with Normal Fibroblasts (NF) 3D rep1

description: Sample name: P9


title: iPSC-CM_donorE_rep3

value: E


title: PT45 3D rep2

description: Sample name: P7

source_name: Microtissues obtained culturing PT45 within biodegradable microcarriers in a spinner flask reactor for 12 days

value: monoculture


title: iPSC-CM_donorC_rep2

value: iPSC-CM


title: PT45 co-cultured with Cancer-Associated Fibroblasts (CAF) 3D rep1

description: Sample name: P13


title: iPSC-CM_donorH_rep1


title: PT45 3D rep3

description: Sample name: P8


title: PT45 3D rep1

description: Sample name: P6


title: iPSC-CM_donorI_rep2


title: PT45 co-cultured with Normal Fibroblasts (NF) 3D rep3

description: Sample name: P11


title: reference male mouse2/ 0GyPF

value: parent


title: PT45 co-cultured with Normal Fibroblasts (NF) 2D rep2

description: Sample name: P4

source_name: PT45 sorted from NF/PT45 2D co-culture


title: Cancer-Associated fibroblast co-cultured with PT45 3D rep2

description: Sample name: C8

source_name: CAF sorted from microtissues obtained co-culturing CAF and PT45 within biodegradable microcarriers in a spinner flask reactor for 12 days

value: mammary cancer-associated fibroblasts (CAF)

value: co-culture with PT45


title: iPSC-CM_donorI_rep1


title: PT45 2D rep1

description: Sample name: P1

source_name: PT45 from 2D culture


title: iPSC-CM_donorA_rep2

value: A


title: iPSC-CM_donorE_rep2


title: iPSC-CM_donorJ_rep3

value: J


title: 1-LNCaP-Si-NC-veh

description: Gene expression data from LNCaP cells treated with vehicle (ethanol) after transfected with siControl

value: LNCaP

value: prostate cancer

value: siControl

value: Vehicle


title: iPSC-CM_donorG_rep2

value: G


title: PT45 co-cultured with Normal Fibroblasts (NF) 2D rep1

description: Sample name: P3

value: pancreatic adenocarcinoma cell line


title: PT45 co-cultured with Normal Fibroblasts (NF) 2D rep3

description: Sample name: P5

value: co-culture with Normal Fibroblasts (NF)


title: iPSC-CM_donorE_rep1


title: iPSC-CM_donorG_rep3


title: Cancer-Associated Fibroblasts (CAF) 3D rep2

description: Sample name: C5

source_name: Microtissues obtained culturing CAF within biodegradable microcarriers in a spinner flask reactor for 12 days


title: iPSC-CM_donorA_rep1


title: PT45 2D rep2

description: Sample name: P2


title: Cancer-Associated fibroblast co-cultured with PT45 3D rep3

description: Sample name: C9


title: iPSC-CM_donorH_rep3


title: iPSC-CM_donorJ_rep1


title: iPSC-CM_donorJ_rep2


title: iPSC-CM_donorG_rep1


title: Cancer-Associated Fibroblasts (CAF) 2D rep2

description: Sample name: C2

source_name: CAF from 2D culture


title: iPSC-CM_donorA_rep3


title: Cancer-Associated Fibroblasts (CAF) 2D rep1

description: Sample name: C1


title: Cancer-Associated Fibroblasts (CAF) 2D rep3

description: Sample name: C3


title: Cancer-Associated fibroblast co-cultured with PT45 3D rep1

description: Sample name: C7


title: Cancer-Associated Fibroblasts (CAF) 3D rep1

description: Sample name: C4


title: Normal Fibroblasts (NF) co-cultured with PT45 3D rep2

description: Sample name: N10

source_name: NF sorted from microtissues obtained co-culturing NF and PT45 within biodegradable microcarriers in a spinner flask reactor for 12 days

value: normal mammary fibroblasts (NF)


title: Cancer-Associated Fibroblasts (CAF) 3D rep3

description: Sample name: C6


title: Normal Fibroblasts (NF) co-cultured with PT45 3D rep4

description: Sample name: N12


title: Normal Fibroblasts (NF) 3D rep3

description: Sample name: N8

source_name: Microtissues obtained culturing NF within biodegradable microcarriers in a spinner flask reactor for 12 days


title: Normal Fibroblasts (NF) co-cultured with PT45 3D rep3

description: Sample name: N11


title: iPSC-CM_donorB_rep3

value: B


title: Normal Fibroblasts (NF) 2D rep1

description: Sample name: N1

source_name: NF from 2D culture


title: iPSC-CM_donorB_rep2


title: Normal Fibroblasts (NF) 3D rep2

description: Sample name: N7


title: iPSC-CM_donorB_rep1


title: Normal Fibroblasts (NF) 3D rep1

description: Sample name: N6


title: Normal Fibroblasts (NF) co-cultured with PT45 2D rep2

description: Sample name: N4

source_name: NF sorted from NF/PT45 2D co-culture


title: Normal Fibroblasts (NF) co-cultured with PT45 2D rep3

description: Sample name: N5


title: Normal Fibroblasts (NF) 2D rep2

description: Sample name: N2


title: 0GyO8/ reference male mouse2

value: tail

value: progeny

source_name: reference male mouse2

value: reference

value: male


title: Normal Fibroblasts (NF) co-cultured with PT45 2D rep1

description: Sample name: N3


title: Normal Fibroblasts (NF) co-cultured with PT45 3D rep1

description: Sample name: N9


title: reference male mouse2/ 0GyO7


title: 0GyO7/ reference male mouse2


title: reference male mouse2/ 0GyO8


title: 0GyO6/ reference male mouse2


title: iPSC-CM_donorF_rep3

value: iPSC-CM

value: F


title: reference male mouse2/ 0GyO6


title: BS_49-3

city: Quebec

first: Julien

last: Prunier

state: QC

address: 1030 av. de la medecine

department: Forestry

country: Canada

institute: Université Laval

hyb_protocol: Array CGH hybridizations were performed with the SureTag DNA Labeling Kit (Agilent, protocol version 7.2), following manufacturer’s instructions

scan_protocol: arrays were scanned using Tecan scanner station

data_processing:
The fluorescence intensities were analyzed using an in-house pipeline of R (v3.1.3) and Pyton (v2.7.9) scripts (available in https://bitbucket.org/jprunier/git-CNVgene-discovery) in order to correct for dye bias, take into account the GC content in the intensity variations and finally compare the 'test' genome (a descendant) to the 'reference' genome (a parent).
Please note that the left-most ID column in the raw data files does not contain the Feature Numbers found on the platform supplementary file 052809_D_GEO_20130704.txt (in 'ID' column).

organism: Picea mariana

label_protocol: 250 ng of DNA were labelled using the Agilent consumable and protocol

growth_protocol: Samples were obtained cutting branches in outdoor sites

extract_protocol: Total DNA extracted using DNeasy Plant Mini Kit (QIAgen, http://www.qiagen.com/)

tag: generation

value: descendant

value: needles

value: parent


title: BS_47-3

tag: tissue


title: BS_50-3


title: BS_49-4


title: 0GyO5/ reference male mouse2


title: 0GyO4/ reference male mouse2


title: 0GyO3/ reference male mouse2


title: BS_50-4


title: BS_47-4


title: reference male mouse2/ 0GyO5


title: reference male mouse2/ 0GyO4


title: 0GyO2/ reference male mouse2


title: reference male mouse2/ 0GyO2


title: BS_47-2


title: BS_45-3


title: reference male mouse2/ 0GyO3


title: BS_46-3


title: BS_46-2


title: BS_49-2


title: BS_44-3


title: BS_45-4


title: reference male mouse2/ 0GyO1


title: BS_44-4


title: 0GyOM/ reference male mouse2


title: 0GyOF/ reference male mouse2

value: female


title: BS_45-2


title: 0GyO1/ reference male mouse2


title: BS_44-2


title: IS_13-1

organism: Picea engelmannii x Picea glauca


title: BS_44-1


title: BS_46-4


title: reference male mouse2/ 0GyOM


title: reference male mouse2/ 0GyOF


title: IS_12-1


title: IS_08-3


title: IS_05-2


title: IS_05-4


title: IS_10-2


title: IS_06-2


title: IS_12-2


title: IS_05-1


title: IS_10-3


title: IS_02-4


title: IS_12-3


title: IS_02-2


title: IS_02-1


title: IS_02-3


title: WT_Erythroblast_LID_W_7w_3

city: Sendai

first: Kazuhiko

last: Igarashi

state: Miyagi

address: Seiryo 2-1

institute: Tohoku University

description: Subset II erythroblasts sorted from bone marrow of WT under low iron diet after weaning for seven weeks

hyb_protocol: A sureprint G3 mouse GE microarray slide was used for hybridization according to the manufacturer's instructions(Agilent)

scan_protocol: After hybridization, slides were washed adequately and scanned immediately by using the Agilent DNA Microarray Scanner using one color scan setting

data_processing: Obtained scan data were analysed by using GeneSpring software (Agilent)

source_name: Bone marrow, erythroblast, LID_W for 7weeks, replicate 3

label_protocol: Amplified samples were labeled with indocarbocyanine by using a Cy3 post-labeling reactive dye pack (Amersham)

extract_protocol: Total RNA was extracted from sorted erythroblasts distributed in subset II by using Rneasy Plus Micro Kit (QIAGEN) and was amplified with an Amino Allyl MessageAmpII aRNA Amplification Kit (Ambion)

value: Subset II erythroblasts


title: IS_01-2


title: WT_Erythroblast_LID_W_7w_2

source_name: Bone marrow, erythroblast, LID_W for 7weeks, replicate 2


title: IS_01-1


title: WT_Erythroblast_LID_W_7w_1

source_name: Bone marrow, erythroblast, LID_W for 7weeks, replicate 1


title: WT_Erythroblast_LID_W_3w_2

description: Subset II erythroblasts sorted from bone marrow of WT under low iron diet after weaning for three weeks

source_name: Bone marrow, erythroblast, LID_W for 3weeks, replicate 2


title: WT_Erythroblast_LID_W_3w_3

source_name: Bone marrow, erythroblast, LID_W for 3weeks, replicate 3


title: IS_01-3


title: WT_Erythroblast_LID_W_3w_1

source_name: Bone marrow, erythroblast, LID_W for 3weeks, replicate 1


title: 0GyN6/ reference male mouse2


title: WS2_15-4

organism: Picea glauca


title: WT_Erythroblast_ND_2

description: Subset II erythroblasts sorted from bone marrow of WT under normal diet

source_name: Bone marrow, erythroblast, ND, replicate 2


title: WT_Erythroblast_ND_3

source_name: Bone marrow, erythroblast, ND, replicate 3


title: WS2_15-1


title: 0GyN5/ reference male mouse2


title: 0GyN4/ reference male mouse2


title: reference male mouse2/ 0GyN3


title: 0GyN2/ reference male mouse2


title: reference male mouse2/ 0GyN4


title: WS2_14-3


title: WS2_14-2


title: reference male mouse2/ 0GyN5


title: reference male mouse2/ 0GyN6


title: 0GyN3/ reference male mouse2


title: WS2_13-4


title: adrenocortical tumor, COG patient 33

hyb_protocol: 6 micrograms of biotinylated cRNA were fragmented, then hybridized for 16 hr at 45C on each array using the GeneTitan system. Following hybridization, HT_HG-U133_Plus_PM arrays were washed and stained using the GeneTitan system.

scan_protocol: Array plates were scanned using the Affymetrix GeneTitan system.

source_name: adrenocortical tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3’IVT Express protocol using 100 ng of total RNA as starting template (GeneChip 3’ IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix)

value: ACC

value: III


title: 0GyN1/ reference male mouse2


title: reference male mouse2/ 0GyN1


title: WT_Erythroblast_ND_1

source_name: Bone marrow, erythroblast, ND, replicate 1


title: reference male mouse2/ 0GyN2


title: WS2_14-1


title: adrenocortical tumor, COG patient 34

value: II


title: WS2_11-4


title: WS2_13-3


title: WS2_11-1


title: 0GyNF/ reference male mouse2


title: adrenocortical tumor, COG patient 29


title: adrenocortical tumor, COG patient 31

value: I


title: adrenocortical tumor, COG patient 30


title: adrenocortical tumor, COG patient 28

value: IV


title: adrenocortical tumor, COG patient 32


title: WS2_10-1


title: adrenocortical tumor, COG patient 27


title: 0GyNM/ reference male mouse2


title: reference male mouse2/ 0GyNM


title: reference male mouse2/ 0GyNF


title: adrenocortical tumor, COG patient 22


title: WS2_06-3


title: adrenocortical tumor, COG patient 24


title: adrenocortical tumor, COG patient 25


title: 0GyM7/ reference male mouse2


title: adrenocortical tumor, COG patient 23


title: adrenocortical tumor, COG patient 21


title: WS2_04-4


title: adrenocortical tumor, COG patient 19


title: 0GyM4/ reference male mouse2


title: 0GyM6/ reference male mouse2


title: WS2_04-1


title: adrenocortical tumor, COG patient 20


title: WS2_06-1


title: reference male mouse2/ 0GyM5


title: reference male mouse2/ 0GyM7


title: 0GyM5/ reference male mouse2


title: reference male mouse2/ 0GyM4


title: adrenocortical tumor, COG patient 17


title: adrenocortical tumor, COG patient 26


title: WS2_04-2


title: WS2_03-3


title: reference male mouse2/ 0GyM6


title: WS2_03-4


title: adrenocortical tumor, COG patient 12


title: reference male mouse2/ 0GyM3


title: adrenocortical tumor, COG patient 14


title: adrenocortical tumor, COG patient 9


title: 0GyM3/ reference male mouse2


title: adrenocortical tumor, COG patient 11


title: adrenocortical tumor, COG patient 16


title: adrenocortical tumor, COG patient 8


title: 0GyM1/ reference male mouse2


title: reference male mouse2/ 0GyM2


title: adrenocortical tumor, COG patient 10


title: adrenocortical tumor, COG patient 7


title: WS1_15-3


title: adrenocortical tumor, COG patient 18


title: adrenocortical tumor, COG patient 13


title: reference male mouse2/ 0GyM1


title: adrenocortical tumor, COG patient 15


title: WS1_15-2


title: WS1_01-4


title: WS1_14-4


title: WS1_03-2


title: 0GyM2/ reference male mouse2


title: adrenocortical tumor, COG patient 6


title: WS1_12-4


title: 0GyMM/ reference male mouse2


title: adrenocortical tumor, COG patient 3


title: adrenocortical tumor, COG patient 4


title: adrenocortical tumor, COG patient 2


title: adrenocortical tumor, COG patient 1


title: WS1_09-3


title: WS1_09-2


title: WS1_09-1


title: reference male mouse2/ 0GyMF


title: WS1_08-4


title: adrenocortical tumor, COG patient 5


title: WS1_08-1


title: WS1_08-2


title: WS1_11-3


title: 0GyMF/ reference male mouse2


title: reference male mouse2/ 0GyMM


title: WS1_11-2


title: reference male mouse2/ 0GyL6


title: WS1_07-3


title: 0GyL6/ reference male mouse2


title: WS1_07-4


title: 0GyL5/ reference male mouse2


title: WS1_07-1


title: WS1_07-2


title: reference male mouse2/ 0GyL5


title: 4T1-HAIFNgTf in RAGKO+IFNgKO ACT #1

status: Public on Dec 13 2016

city: Bunkyo-ku

first: Kazuyoshi

last: Takeda

state: Tokyo

address: 2-1-1 Hongo

department: Biomedical Research Center

institute: Juntendo Univ.

description: 4T1-HAIFNgTf cells grown in RAG-/- mice treated with 4T1-HA-specific draining lymph node IFN-g-/- CTL #1

hyb_protocol: Labelled samples were hybridized on SurePrint G3 Mouse CGH Microarray 4x180K  (Agilent) according to the manufacturer's instructions.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution.

data_processing: Images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent Technologies), in accordance to the CGH_107_Sep09 protocol for background subtraction and normalization.

source_name: HA/IFN-gamma-transfected 4T1 tumor cells after the growth in RAG-/- mice treated with 4T1-HA-specific draining lymph node IFN-gammma-/- CTL #1

label_protocol: 500ng DNA was labelled using the SureTag DNA Labeling Kit coupling method (Agilent – 5190-3400).

growth_protocol: 4T1-HAIFNgTf cells kept in complete RPMI1640-10% FCS medium after the establishment by Interferon-g-gene transfection into HA-expressing 4T1 cell-derived clone cells, 4T1-HA cells, follwed by single cell cloning.

extract_protocol: Total DNA extracted using DNeasy Blood & Tissue Kit (QUIAGEN) following manufacturer's instructions

treatment_protocol: Tumor cells were isolated from the out-growing tumor mass in the indicated RAG-/- mice and the primarily inoculated tumor cells was used as reference. Some mice were treated with 4T1-HA-specific draining lymph node CTL of  WT or IFN-g-/- mice.

tag: cell line

value: mammary tumor cell line

value: BALB/c

source_name: HA/IFN-gamma-transfected 4T1 tumor cells that was primarily inoculated into the mice


title: 0GyL3/ reference male mouse2

value: tail

tag: sample type

value: progeny


title: WS1_04-3


title: 4T1-HAIFNgTf in RAGKO+WT ACT #2

description: 4T1-HAIFNgTf cells grown in RAG-/- mice treated with 4T1-HA-specific draining lymph node WT CTL #2

source_name: HA/IFN-gamma-transfected 4T1 tumor cells after the growth in RAG-/- mice treated with 4T1-HA-specific draining lymph node WT CTL #2


title: 0GyL4/ reference male mouse2

value: reference

tag: gender

value: male


title: WS1_03-1


title: 4T1-HAIFNgTf in RAGKO+IFNgKO ACT #2

description: 4T1-HAIFNgTf cells grown in RAG-/- mice treated with 4T1-HA-specific draining lymph node IFN-g-/- CTL #2

source_name: HA/IFN-gamma-transfected 4T1 tumor cells after the growth in RAG-/- mice treated with 4T1-HA-specific draining lymph node IFN-gammma-/- CTL #2


title: reference male mouse2/ 0GyL4


title: 0GyL1/ reference male mouse2


title: reference male mouse2/ 0GyLF


title: reference male mouse2/ 0GyL1


title: reference male mouse2/ 0GyL2


title: 4T1-HAIFNgTf in RAGKO+WT ACT #1

description: 4T1-HAIFNgTf cells grown in RAG-/- mice treated with 4T1-HA-specific draining lymph node WT CTL #1

source_name: HA/IFN-gamma-transfected 4T1 tumor cells after the growth in RAG-/- mice treated with 4T1-HA-specific draining lymph node WT CTL #1


title: Malignant glioma clone U3065MG-C106

city: Uppsala

first: Bo

last: Segerman

address: Dag Hammarskjolds v 20

country: Sweden

institute: Uppsala University

hyb_protocol: bisulphite converted DNA, by using the EZ-96 DNA Methylation Gold Kit from Zymo Research, was hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina Protocol

data_processing: Illumina GenomeStudio 2011.1

source_name: Malignant glioma clone U3065MG-C106

growth_protocol: adherent cultures on laminin-coated dishes using neural stem cell media

extract_protocol: Dneasy blood and tissue kit (Qiagen)

value: Malignant glioma clone


title: Malignant glioma clone U3065MG-C466

source_name: Malignant glioma clone U3065MG-C466


title: Malignant glioma clone U3065MG-C94

source_name: Malignant glioma clone U3065MG-C94


title: Malignant glioma clone U3065MG-C95

source_name: Malignant glioma clone U3065MG-C95


title: Malignant glioma clone U3065MG-C113

source_name: Malignant glioma clone U3065MG-C113


title: CMS5a1 in RAGKO+ACT+VE822 #4

description: CMS5a1 cells grown in RAG-/- mice treated with CMS5a1-specific draining lymp node CTL and ATR-inhibitor VE822 #4

source_name: CMS5a1 cells after the growth in WT mice treated with CMS5a1-specific draining lymp node CTL and ATR-inhibitor VE822 #4

growth_protocol: CMS5a1 cells kept in complete RPMI1640-10% FCS medium after the establishment from CMS5a1 cells by single cell cloning.

treatment_protocol: Tumor cells were isolated from the out-growing tumor mass in the indicated RAG-/- mice and the primarily inoculated tumor cells was used as reference. Some mice were treated with CMS5a1-specific draining lymph node CTL and/or ATR-inhibitor (VE822).

value: MCA-induced fibrosarcom

source_name: CMS5a1 cells that was primarily inoculated into the mice


title: 0GyLF/ reference male mouse2

source_name: reference male mouse2


title: 4T1-HAIFNgTf in RAGKO #1

description: 4T1-HAIFNgTf cells grown in RAG-/- mice #1

source_name: HA/IFN-gamma-transfected 4T1 tumor cells after the growth in RAG-/- mice #1


title: reference male mouse2/ 0GyL3


title: Malignant glioma clone U3065MG-C475

source_name: Malignant glioma clone U3065MG-C475


title: Malignant glioma clone U3065MG-C271

source_name: Malignant glioma clone U3065MG-C271


title: Bone marrow cells

city: Tianjin

first: Jiaxuan

last: Xin

address: weijin Road 94

department: Department of Immunology

country: China

institute: Nankai University

description: BMCs control

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila 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: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization

source_name: BMCs control

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: BMCs were obtained from the femurs of C57BL/6 mice and cultured in RPMI-1640 medium supplemented with 5% FBS.

extract_protocol: Total RNA was extracted by using TRIzol reagent and reverse transcribed to cDNA according to the manufacturer’s instructions.

treatment_protocol: To prepare the tumor cell supernatant-induced CD11b+Gr1+ MDSCs in vitro, 5×10^4 1D8 tumor cells (upper chamber) were co-cultured with 2×10^6 BMCs (lower chamber) in a 24-transwell plate for 4 days.

value: femurs

value: bone marrow cells (BMCs)

tag: phenotype

value: CD11b+Gr1+ cells


title: reference male mouse2/ 0GyLM

value: parent


title: ID8 supernant-induced MDSCs

description: ID8 MDSCs

source_name: BMCs induced with ID8 supernant

tag: cultured with

value: 1D8 tumor cells (upper chamber)


title: 0GyLM/ reference male mouse2

tag: strain


title: Malignant glioma clone U3065MG-C80

source_name: Malignant glioma clone U3065MG-C80

label_protocol: Standard Illumina Protocol

tag: cell type


title: CMS5a1 in RAGKO+ACT+VE822 #2

description: CMS5a1 cells grown in RAG-/- mice treated with CMS5a1-specific draining lymp node CTL and ATR-inhibitor VE822 #2

source_name: CMS5a1 cells after the growth in WT mice treated with CMS5a1-specific draining lymp node CTL and ATR-inhibitor VE822 #2


title: Malignant glioma clone U3065MG-C482

source_name: Malignant glioma clone U3065MG-C482


title: Malignant glioma clone U3065MG-C494

source_name: Malignant glioma clone U3065MG-C494


title: 4T1-HAIFNgTf in RAGKO #2

description: 4T1-HAIFNgTf cells grown in RAG-/- mice #2

source_name: HA/IFN-gamma-transfected 4T1 tumor cells after the growth in RAG-/- mice #2

source_name: HA/IFN-gamma-transfected 4T1 tumor cells that was primarily inoculated into the mice


title: 0GyL2/ reference male mouse2


title: CMS5a1 in RAGKO+ACT+VE822 #3

description: CMS5a1 cells grown in RAG-/- mice treated with CMS5a1-specific draining lymp node CTL and ATR-inhibitor VE822 #3

source_name: CMS5a1 cells after the growth in WT mice treated with CMS5a1-specific draining lymp node CTL and ATR-inhibitor VE822 #3


title: Malignant glioma clone U3065MG-C349

source_name: Malignant glioma clone U3065MG-C349


title: CMS5a1 in RAGKO+ACT+VE822 #1

description: CMS5a1 cells grown in RAG-/- mice treated with CMS5a1-specific draining lymp node CTL and ATR-inhibitor VE822 #1

source_name: CMS5a1 cells after the growth in WT mice treated with CMS5a1-specific draining lymp node CTL and ATR-inhibitor VE822 #1


title: DKO_replicate 2

city: San Diego

first: Xiaolin

last: Luo

address: 9500 Gilman Dr.

department: Pathology

institute: University of California San Diego

description:
replicate 2
8615501094_A

hyb_protocol: Standard illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Microarray data were collected and analyzed in three steps. First, we obtained the sample probe file of all samples using illumina’s GenomeStudio software after expression intensities were calculated and quality controlled with a detection p value set to < 0.05 for each gene probed on the array for all hybridizations. Second, we  used hierarchical clustering methods to detect outliers in all samples. From this analysis, no outliers were detected. Finally, we further analyzed the expression data for differentially expressed genes using Agilent’s GeneSpring GX 11.5 software with quantile normalization, log transformation, and statistical analysis.   Microarray data were collected and analyzed in three steps. First, we obtained the sample probe file of all samples using illumina’s GenomeStudio software after expression intensities were calculated and quality controlled with a detection p value set to < 0.05 for each gene probed on the array for all hybridizations. Second, we  used hierarchical clustering methods to detect outliers in all samples. From this analysis, no outliers were detected. Finally, we further analyzed the expression data for differentially expressed genes using Agilent’s GeneSpring GX 11.5 software with quantile normalization, log transformation, and statistical analysis.

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

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: liver

tag: genotype/variation

value: DKO (Ptenfl/fl:Shp2fl/fl:Alb-Cre+)


title: CMS5a1 in RAGKO+VE822 #3

description: CMS5a1 cells grown in RAG-/- mice treated with ATR-inhibitor VE822 #3

source_name: CMS5a1 cells after the growth in RAG-/- mice treated withATR-inhibitor VE822 #3


title: CMS5a1 in RAGKO+VE822 #1

description: CMS5a1 cells grown in RAG-/- mice treated with ATR-inhibitor VE822 #1

source_name: CMS5a1 cells after the growth in RAG-/- mice treated withATR-inhibitor VE822 #1

source_name: CMS5a1 cells that was primarily inoculated into the mice


title: PKO_replicate 1

description:
replicate 1
8615501094_E

value: PKO (Ptenhep-/-, or Pten2fl/fl:Alb-Cre+)


title: PKO_replicate 2

description:
replicate 2
8615501094_F


title: WT_replicate 2

description:
replicate 2
8615501094_B

value: WT (Pten2fl/fl:Shp2fl/fl:Alb-Cre-)


title: SKO_replicate 1

description:
replicate 1
8615501094_C

value: SKO (Shp2hep-/-, or Shp2fl/fl:Alb-Cre+)


title: SKO_replicate 2

description:
replicate 2
8615501094_D


title: CMS5a1 in RAGKO+VE822 #2

description: CMS5a1 cells grown in RAG-/- mice treated with ATR-inhibitor VE822 #2

source_name: CMS5a1 cells after the growth in RAG-/- mice treated withATR-inhibitor VE822 #2

value: BALB/c


title: DKO_replicate 1

description:
replicate 1
8615501094_G


title: CMS5a1 in WT+ACT #4

description: CMS5a1 cells grown in WT mice treated with mutated ERK2 kinase protein-specific DUC17 splenic CTL #4

source_name: CMS5a1 cells after the growth in WT mice treated with mutated ERK2 kinase protein-specific DUC17 splenic CTL #4

growth_protocol: CMS5a1gRDN cells kept in complete RPMI1640-10% FCS medium after the establishment by dominant-negative form of IFN-gamma receptor alpha chain gene transfection into CMS5 tumor cell-derived single cell clone, CMS5a1 cells, follwed by single cell cloning.

treatment_protocol: Tumor cells were isolated from the out-growing tumor mass in the indicated WT mice and the primarily inoculated tumor cells was used as reference. Some mice were treated with mutated ERK2 kinase protein-specific DUC17 splenic CTL or  CMS5a1-specific draining lymph node CTL.


title: CMS5a1 in WT+ACT #6

description: CMS5a1 cells grown in WT mice treated with CMS5a1-specific draining lymph node CTL #6

source_name: CMS5a1 cells after the growth in WT mice treated with CMS5a1-specific draining lymph node CTL #6


title: CMS5a1 in RAGKO+ACT #3

description: CMS5a1 cells grown in RAG-/- mice treated with CMS5a1-specific draining lymph node CTL #3

source_name: CMS5a1 cells after the growth in RAG-/- mice treated with CMS5a1-specific draining lymph node CTL #3


title: Malignant glioma clone U3065MG-C78

source_name: Malignant glioma clone U3065MG-C78


title: Malignant glioma cell line U3065MG

source_name: Malignant glioma cell line U3065MG

value: Malignant glioma cell line


title: CMS5a1gRDN in WT+ACT #2

description: CMS5a1gRDN cells grown in WT mice treated with mutated ERK2 kinase protein-specific DUC17 splenic CTL #2

source_name: CMS5a1gRDN cells after the growth in WT mice treated with mutated ERK2 kinase protein-specific DUC17 splenic CTL #2

source_name: CMS5a1gRDN cells that was primarily inoculated into the mice


title: Malignant glioma clone U3065MG-C60

source_name: Malignant glioma clone U3065MG-C60


title: E14Ta_rep2

city: Baltimore

first: Yong

last: Qian

address: 251 Bayview Blvd, Suite 100

department: NIA

institute: NIH

description: Biological replicate 2 of 2, Cy3 is mouse RNA and Cy5 is mouse reference

hyb_protocol: Slides were hybridized to Agilent-015087 arrays according to the manufacturer's protocol (Two-Color Microarray-Based Gene Expression Analysis Protocol, Product # G4140-90050, Version 5.0.1)

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5um.

data_processing:
Data are extracted with Agilent Feature Extraction Software. The data were further processed with NIA ANOVA tool utilities. See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal, rDyeNormSignal in the raw files and log-transform them using: log10(max(x,10)). These values will be referenced below as Xgi and Xri, where i is array number.
(2) Take average of Xri's for the oligo among 12 arrays in the series: AverXr = average(Xri).
(3) For each array, estimate Yi = Xgi-Xri+AverXr (adjust to UMR).
The result is used as the normalized VALUE. More detailed information with error correction can be found at: http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

source_name: Ta eyelids E14.5

label_protocol: Total RNA was labeled using the Agilent Low RNA Input Fluorescent Linear Amplification kit according to the manufacturer's instructions.

extract_protocol: 1ml of TRIzol reagent was added to each sample, and homogenized immediately. They were then transferred to Phase Lock Gel Heavy tubes (eppendorf) and 0.2 volumes of chloroform (Sigma-Aldrich) was added to each sample. They were mixed by hand and allowed to stand for 2-5 min at room temperature. The samples were then separated by centrifugation for 5 minutes at 13,000 rpm on an eppendorf centrifuge at 4C. The aqeous phase was transferred to another eppendorf tube, and 0.8 volumes of ice-cold isopropanol was added. They were allowed to incubate for a minimum of 10 minutes at room temperature. If longer, they were placed at 4C. The sample was centrifuged again at the same conditions for 15 minutes. After centrifugation, the liquid was dumped out of the tubes and the pellet was washed with 1 mL of ice-cold 70% ethanol. The tube was spun for 5 minutes, then the ethanol was dumped out. Excess was removed with a pipette and the pellet was allowed to air dry until no liquid remained, but no longer. ddH2O was then added in the appropriate volume, the sample was allowed to dissolve for 5 minutes at 55C and then transferred to -80C for storage.

treatment_protocol: Footpad skin was taken from wild-type and Tabby mutant mice at E17.5, P1, P3, P5 and P56 (adult) under a dissection microscope, and frozen immediately on dry ice, and stored in -80C freezer.

value: eyelids

value: Tabby mutant

tag: developmental stage

source_name: Universal Mouse Reference

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts. The resulting UMR RNA was mixed with 129ES cell RNA (Lif+) at 2:1 ratio and 2.5ug of mixed RNA was used for labeling in each tube

value: Referecne


title: CMS5a1 in WT+ACT #5

description: CMS5a1 cells grown in WT mice treated with CMS5a1-specific draining lymph node CTL #5

source_name: CMS5a1 cells after the growth in WT mice treated with CMS5a1-specific draining lymph node CTL #5


title: WT_replicate 1

description:
replicate 1
8615501094_A

value: male


title: CMS5a1 in RAGKO+ACT #4

description: CMS5a1 cells grown in RAG-/- mice treated with CMS5a1-specific draining lymph node CTL #4

source_name: CMS5a1 cells after the growth in RAG-/- mice treated with CMS5a1-specific draining lymph node CTL #4

value: MCA-induced fibrosarcom


title: CMS5a1 in WT+ACT #3

description: CMS5a1 cells grown in WT mice treated with mutated ERK2 kinase protein-specific DUC17 splenic CTL #3

source_name: CMS5a1 cells after the growth in WT mice treated with mutated ERK2 kinase protein-specific DUC17 splenic CTL #3


title: Malignant glioma clone U3065MG-C28

source_name: Malignant glioma clone U3065MG-C28

value: Malignant glioma clone


title: Malignant glioma clone U3065MG-C34

source_name: Malignant glioma clone U3065MG-C34


title: CMS5a1 in WT+ACT #2

description: CMS5a1 cells grown in WT mice treated with mutated ERK2 kinase protein-specific DUC17 splenic CTL #2

source_name: CMS5a1 cells after the growth in WT mice treated with mutated ERK2 kinase protein-specific DUC17 splenic CTL #2

source_name: CMS5a1 cells that was primarily inoculated into the mice


title: E14Ta_rep1

description: Biological replicate 1 of 2, Cy3 is mouse RNA and Cy5 is mouse reference

source_name: Ta eyelids E145


title: CMS5a1gRDN in WT+ACT #1

description: CMS5a1gRDN cells grown in WT mice treated with mutated ERK2 kinase protein-specific DUC17 splenic CTL #1

source_name: CMS5a1gRDN cells after the growth in WT mice treated with mutated ERK2 kinase protein-specific DUC17 splenic CTL #1


title: CMS5a1 in WT+ACT #1

description: CMS5a1 cells grown in WT mice treated with mutated ERK2 kinase protein-specific DUC17 splenic CTL #1

source_name: CMS5a1 cells after the growth in WT mice treated with mutated ERK2 kinase protein-specific DUC17 splenic CTL #1


title: E15Ta_rep1

source_name: Ta eyelids E15.5


title: E14WT_rep2

source_name: WT eyelids E14.5

value: wild-type


title: E15Ta_rep2


title: EG7.1 in RAGKO #1

description: EG7.1 cells grown in RAG-/- mice #1

source_name: EG7.1 tumor cells after the growth in RAG-/- mice #1

growth_protocol: EG7.1gRDN cells kept in complete RPMI1640-10% FCS medium after the establishment by dominant-negative form of IFN-gamma receptor alpha chain gene transfection into EG7 tumor cell-derived single cell clone, EG7.1 cells, follwed by single cell cloning.

treatment_protocol: Tumor cells were isolated from the out-growing tumor mass in the indicated mice and the primarily inoculated tumor cells was used as reference. Some mice were treated with OVA-specific OT-1 CTL.

value: OVA-gene transfected EL4 (EG7)

value: T cell lympoma

source_name: EG7.1 tumor cells that was primarily inoculated into the mice


title: EG7.1gRDN in WT+OT1 #2

description: EG7.1gRDN cells grown in WT mice treated with OVA-specific OT-1 CTL #1

source_name: dominant-negative form of IFN-gamma receptor-transfected EG7.1 tumor cells after the growth in WT mice treated with OVA-specific OT-1 CTL #2

source_name: dominant-negative form of IFN-gamma receptor-transfected EG7.1 tumor cells that was primarily inoculated into the mice


title: EG7.1gRDN in WT+OT1 #1

source_name: dominant-negative form of IFN-gamma receptor-transfected EG7.1 tumor cells after the growth in WT mice treated with OVA-specific OT-1 CTL #1


title: E14WT_rep1

source_name: Universal Mouse Reference


title: E15WT_rep1

source_name: WT eyelids E15.5


title: E15WT_rep2


title: E16Ta_rep2

source_name: Ta eyelids E16.5


title: EG7.1 in RAGKO+OT1 #2

description: EG7.1 cells grown in RAG-/- mice treated with OVA-specific OT1 CTL #2

source_name: EG7.1 tumor cells after the growth in RAG-/- mice treated with OVA-specific OT-1 CTL  #2


title: EG7.1 in WT+OT1 #1

description: EG7.1 cells grown in WT mice treated with OVA-specific OT1 CTL #1

source_name: EG7.1 tumor cells after the growth in WT mice treated with OVA-specific OT-1 CTL #1


title: EG7.1 in WT+OT1 #2

description: EG7.1 cells grown in WT mice treated with OVA-specific OT1 CTL #2

source_name: EG7.1 tumor cells after the growth in WT mice treated with OVA-specific OT-1 CTL #2


title: E16Ta_rep1


title: EG7.1 in WT+OT1 #4

description: EG7.1 cells grown in WT mice treated with OVA-specific OT1 CTL #4

source_name: EG7.1 tumor cells after the growth in WT mice treated with OVA-specific OT-1 CTL #4


title: EG7.1 in WT #3

description: EG7.1 cells grown in WT mice #1

source_name: EG7.1 tumor cells after the growth in WT mice  #3


title: EG7.1 in WT+OT1 #6

description: EG7.1 cells grown in WT mice treated with OVA-specific OT1 CTL #6

source_name: EG7.1 tumor cells after the growth in WT mice treated with OVA-specific OT-1 CTL #6


title: 4T1-HA in WT #33 35d LN metastasis

description: 4T1-HA cells grown in WT mice #33 35 days (metastasis to lymph node)

source_name: HA-transfected 4T1 tumor cells derived from metastatic foci of draining lymph node after the 35 days growth in WT mice #33

growth_protocol: 4T1-HAS1DN cells kept in complete RPMI1640-10% FCS medium after the establishment by dominant-negative form of STAT1 gene transfection into HA-expressing 4T1 (4T1-HA) tumor cells follwed by single cell cloning.

treatment_protocol: Tumor cells were isolated from the out-growing tumor mass in the indicated mice and the primarily inoculated tumor cells was used as reference. Some mice were treated with IFN-g-/-, perforin-/- or WT CTL or IL-12. 4T1-HA cells cultured with IFN-g were also examined and the tumor cells at the starting point of culture was used as reference.

value: mammary tumor cell line

source_name: HA-transfected 4T1 tumor cells that was primarily inoculated into the mice


title: 4T1-HA in WT #33 35d Lateral Caudalis

description: 4T1-HA cells grown in WT mice #33 35 days (lateral caudalis site of tumor mass)

source_name: HA-transfected 4T1 tumor cells derived from lateral caudalis site of tumor mass after the 35 days growth in WT mice #33


title: DcKOE17.5 Replicate 2

first: Minoru

last: Ko

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

description:
Biological replicate 2 of 2, Cy3 is mouse RNA and Cy5 is mouse reference
DicerE17.5KO_rep2

hyb_protocol: standard Agilent protocol

data_processing:
Data are extracted with Agilent Feature Extraction Software. The data were further processed with NIA ANOVA tool utilities. See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal, rDyeNormSignal in the raw files and log-transform them using: log10(max(x,10)). These values will be referenced below as Xgi and Xri, where i is array number.
(2) Take average of Xri's for the oligo among 8 arrays in the series: AverXr = average(Xri).
(3) For each array, estimate Yi = Xgi-Xri+AverXr (adjust to UMR).
The result Yi is used as the normalized VALUE. More detailed information with error correction can be found at: http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

source_name: DcKOE17.5FP (mRNA)

extract_protocol: E16.5 and E17.5 mouse embryos from timed-mating were euthanized and footpad skin was dissected out under a dissection microscope and were frozen on dry ice immediately, and were kept in -80C until use. The frozen footpads were pooled (3-5 embryos for one replicate), and total RNAs were isolated with TRizol reagent (Invitrogen) according to manufacturer’s standard protocol. Isolated RNAs were precipitated with LiCl, and kept in -80C freezer until use.

tag: strain background

value: Dicer cKO

value: footpad skin

tag: individual identifier


title: DcWTE17.5 Replicate 2

description:
Biological replicate 4 of 2, Cy3 is mouse RNA and Cy5 is mouse reference
DicerE17.5WT_rep2

source_name: DcWTE17.5 FP (mRNA)

value: wild type


title: DcWTE17.5 Replicate 1

description:
Biological replicate 3 of 2, Cy3 is mouse RNA and Cy5 is mouse reference
DicerE17.5WT_rep1


title: E16WT_rep1

source_name: WT eyelids E16.5


title: Malignant glioma clone U3065MG-C46

source_name: Malignant glioma clone U3065MG-C46


title: E16WT_rep2

description: Biological replicate 2 of 2, Cy3 is mouse RNA and Cy5 is mouse reference


title: DcKOE17.5 Replicate 1

description:
Biological replicate 1 of 2, Cy3 is mouse RNA and Cy5 is mouse reference
DicerE17.5KO_rep1


title: 4T1-HA in WT #33 17d  Medial

description: 4T1-HA cells grown in WT mice #33 17 days (resected medial site of tumor mass)

source_name: HA-transfected 4T1 tumor cells derived from resected medial site of tumor mass after the 17 days growth in WT mice #33


title: 4T1-HA in WT #33 35d  Lateral Cranialis

description: 4T1-HA cells grown in WT mice #33 35 days (lateral cranialis site of tumor mass)

source_name: HA-transfected 4T1 tumor cells derived fromlateral cranialisl site of tumor mass after the 35 days growth in WT mice #33


title: 4T1-HA in RAGKO + WT CTL

description: 4T1-HA cells grown in RAG -/- mice treated with WT CTL

source_name: HA-transfected 4T1 tumor cells after the growth in RAG-/- treated with WT CTL


title: patient 3.059|Post 3 vaccinations IgM

type: protein

city: Frederick

first: Jeff

last: Gildersleeve

address: 376 Boyles St.

institute: National Cancer Institute

description:
3.059_V4
IgM

hyb_protocol: Arrays were blocked with 3% BSA in PBS buffer for overnight, and serum samples (diluted 1:50) was incubated on the array for 4 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 4000B fluorescence scanner at two gain settings (typically 430 and 520) in order to increase dynamic range.  Signal from ch1 (532 nm) was analyzed to determine the level of bound DyLight 549 conjugated secondary antibody specific for human IgG.  Signal from ch2 (635nm) was analyzed to determine the level of bound DyLight 649 secondary antibody specific for human IgM.  Scanned images were analyzed with Genepix Pro (v6.0) to determine the fluorescence and background signal for each array component.

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

label: DyLight 649

molecule: protein

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: time point

value: Post 3 vaccinations

tag: survival months

tag: event at time of survival analysis

value: Deceased


title: patient 3.060|Post 3 vaccinations IgM

description:
3.060_V4
IgM


title: patient 3.054|Post 3 vaccinations IgM

description:
3.054_V4
IgM


title: patient 3.051|Post 3 vaccinations IgM

description:
3.051_V4
IgM


title: patient 3.052|Post 3 vaccinations IgM

description:
3.052_V4
IgM

value: Alive


title: patient 3.053|Post 3 vaccinations IgM

description:
3.053_V4
IgM


title: DcWTE16.5 Replicate 2

description:
Biological replicate 4 of 2, Cy3 is mouse RNA and Cy5 is mouse reference
DicerE16.5WT_rep2

source_name: DcWTE16.5 FP (mRNA)

source_name: Universal Mouse Reference


title: 4T1-HAS1DN in RAGKO + WT CTL

description: 4T1-HAS1N cells grown in RAG -/- mice treated with WT CTL

source_name: HA/dominant-negaive form of STAT1-transfected 4T1 tumor cells after the growth in RAG-/- treated with WT CTL

value: BALB/c

source_name: HA/dominant-negaive form of STAT1-transfected 4T1 tumor cells that was primarily inoculated into the mice


title: patient 3.043|Post 3 vaccinations IgM

description:
3.043_V4
IgM


title: 4T1-HA in pfp/IFNgKO + IFN-gKO CTL #1

description: 4T1-HA cells grown in pfp/IFN-gammma -/- mice treated with IFN-gammma-/- CTL #1

source_name: HA-transfected 4T1 tumor cells after the grwoth in pfp/IFN-gammma -/- mice treated with IFN-gammma-/- CTL #1


title: patient 3.041|Post 3 vaccinations IgM

description:
3.041_V4
IgM


title: 4T1-HA in pfp/IFNgKO + pfpKO CTL #1

description: 4T1-HA cells grown in pfp/IFN-gammma -/- mice treated with pfp-/- CTL #1

source_name: HA-transfected 4T1 tumor cells after the grwoth in pfp/IFN-gammma -/- mice treated with pfp-/- CTL #1


title: patient 3.044|Post 3 vaccinations IgM

description:
3.044_V4
IgM


title: DcWTE16.5 Replicate 1

description:
Biological replicate 3 of 2, Cy3 is mouse RNA and Cy5 is mouse reference
DicerE16.5WT_rep1


title: DcKOE16.5 Replicate 2

description:
Biological replicate 2 of 2, Cy3 is mouse RNA and Cy5 is mouse reference
DicerE16.5KO_rep2

source_name: DcKOE16.5FP (mRNA)


title: DcKOE16.5 Replicate 1

description:
Biological replicate 1 of 2, Cy3 is mouse RNA and Cy5 is mouse reference
DicerE16.5KO_rep1


title: 4T1-HA in vitro + IFN-g #1

description: 4T1-HAgRDN cells grown in vitro cultured with IFN-gamma

source_name: HA-transfected 4T1 tumor cells after the in vitro culture with IFN-gamma

source_name: HA-transfected 4T1 tumor cells at the start point for culture


title: patient 3.039|Post 3 vaccinations IgM

description:
3.039_V4
IgM


title: patient 3.037|Post 3 vaccinations IgM

description:
3.037_V4
IgM


title: CMS5a1 in RAGKO+VE822 #4

description: CMS5a1 cells grown in RAG-/- mice treated with ATR-inhibitor VE822 #4

source_name: CMS5a1 cells after the growth in RAG-/- mice treated withATR-inhibitor VE822 #4

source_name: CMS5a1 cells that was primarily inoculated into the mice


title: 4T1-HAgRDN in RAG KO + ACT #2

description: 4T1-HAgRDN cells grown in RAG-/- mice treated with HA-specific WT CTL #2

source_name: HA/dominant-negative form of IFN-gamma receptor-transfected 4T1 tumor cells after the growth in RAG-/- mice treated with HA-specific WT CTL #2

growth_protocol: 4T1-HAgRDN cells kept in complete RPMI1640-10% FCS medium after the establishment by dominant-negative form of IFN-gamma receptor alpha chain gene transfection into HA-expressing 4T1 (4T1-HA) tumor cells follwed by single cell cloning.

treatment_protocol: Tumor cells were isolated from the out-growing tumor mass in the indicated mice and the primarily inoculated tumor cells was used as reference. Some mice were treated with HA-specific WT CTL.

source_name: HA/dominant-negative form of IFN-gamma receptor-transfected 4T1 tumor cells that was primarily inoculated into the mice


title: patient 3.033|Post 3 vaccinations IgM

description:
3.033_V4
IgM


title: 4T1-HAgRDN in RAG KO #1

description: 4T1-HAgRDN cells grown in Rag-/- mice

source_name: HA/dominant-negative form of IFN-gamma receptor-transfected 4T1 tumor cellss after the growth in RAG-/- mice


title: 4T1-HAgRDN in IFN-gamma KO #1

description: 4T1-HAgRDN cells grown in IFN-gamma-/- mice #1

source_name: HA/dominant-negative form of IFN-gamma receptor-transfected 4T1 tumor cells after the growth in IFN-gammma-/- mice #1


title: 4T1-HAgRDN in IFN-gamma KO + ACT #2

description: 4T1-HAgRDN cells grown in IFN-gamma-/- mice treated with HA-specific WT CTL #2

source_name: HA/dominant-negative form of IFN-gamma receptor-transfected 4T1 tumor cells after the growth in IFN-gamma-/- mice treated with HA-specific WT CTL #2


title: 4T1-HAgRDN in IFN-gamma KO + ACT #1

description: 4T1-HAgRDN cells grown in IFN-gamma-/- mice treated with HA-specific WT CTL #1

source_name: HA/dominant-negative form of IFN-gamma receptor-transfected 4T1 tumor cells after the growth in IFN-gamma-/- mice treated with HA-specific WT CTL #1


title: 4T1-HAgRDN in WT #1

description: 4T1-HAgRDN cells grown in WT mice #1

source_name: HA/dominant-negative form of IFN-gamma receptor-transfected 4T1 tumor cells after the growth in WT mice #1


title: 4T1-HA in RAGKO + IL-12 #1

description: 4T1-HA cells grown in RAG -/- mice treated with IL-12 #1

source_name: HA-transfected 4T1 tumor cells after the grwoth in RAG -/- mice treated with IL-12 #1

source_name: HA-transfected 4T1 tumor cells that was primarily inoculated into the mice


title: 4T1-HAgRDN in WT #3

description: 4T1-HAgRDN cells grown in WT mice #3

source_name: HA/dominant-negative form of IFN-gamma receptor-transfected 4T1 tumor cells after the growth in WT mice #3


title: 4T1-HAgRDN in RAG KO + ACT #1

description: 4T1-HAgRDN cells grown in RAG-/- mice treated with HA-specific WT CTL #1

source_name: HA/dominant-negative form of IFN-gamma receptor-transfected 4T1 tumor cells after the growth in RAG-/- mice treated with HA-specific WT CTL #1


title: 4T1-HAgRDN in WT #2

description: 4T1-HAgRDN cells grown in WT mice #2

source_name: HA/dominant-negative form of IFN-gamma receptor-transfected 4T1 tumor cells after the growth in WT mice #2


title: patient 3.047|Post 3 vaccinations IgM

description:
3.047_V4
IgM

source_name: Serum


title: patient 3.032|Post 3 vaccinations IgM

description:
3.032_V4
IgM


title: patient 3.031|Post 3 vaccinations IgM

description:
3.031_V4
IgM


title: patient 3.029|Post 3 vaccinations IgM

description:
3.029_V4
IgM


title: patient 3.028|Post 3 vaccinations IgM

description:
3.028_V4
IgM


title: 4T1-HAgRDN in vitro #1

description: 4T1-HAgRDN cells in vitro cultured

source_name: HA/dominant-negative form of IFN-gamma receptor-transfected 4T1 tumor cells after in vitro culture

source_name: HA/dominant-negative form of IFN-gamma receptor-transfected 4T1 tumor cells at the start point for culture


title: 4T1-HA in IFN-gamma KO + ACT #1

description: 4T1-HA grown in IFN-gamma-/- mice treated with HA-specific WT CTL #1

hyb_protocol: Labelled samples were hybridized on SurePrint G3 Human CGH Microarray 4x180K  (Agilent) according to the manufacturer's instructions.

source_name: HA-transfected 4T1 tumor cells after the growth in IFN-gamma-/- mice treated with HA-specific WT CTL #1

growth_protocol: 4T1-HA cells kept in complete RPMI1640-10% FCS medium after the establishment by HA-gene,dominant-negative form of IFN-gamma receptor alpha chain and/or IFN-gammma gene transfection into 4T1 tumor cells follwed by single cell cloning.

treatment_protocol: Aftre the out growth of respective 4T1-HA cells in the indicated mice, transcriptional profiling of out-growing tumor was compared with primarily inoculated 4T1-HA cells.

source_name: HA-transfected 4T1 cells that was primarily inoculated into the mice


title: 4T1-HA in IFN-gamma KO + ACT #2

description: 4T1-HA grown in IFN-gamma-/- mice treated with HA-specific WT CTL #2

source_name: HA-transfected 4T1 tumor cells after the growth in IFN-gamma-/- mice treated with HA-specific WT CTL #2


title: patient 3.027|Post 3 vaccinations IgM

description:
3.027_V4
IgM


title: patient 3.023|Post 3 vaccinations IgM

description:
3.023_V4
IgM


title: patient 3.025|Post 3 vaccinations IgM

description:
3.025_V4
IgM


title: patient 3.015|Post 3 vaccinations IgM

description:
3.015_V4
IgM


title: patient 3.012|Post 3 vaccinations IgM

description:
3.012_V4
IgM


title: patient 3.013|Post 3 vaccinations IgM

description:
3.013_V4
IgM


title: patient 3.016|Post 3 vaccinations IgM

description:
3.016_V4
IgM


title: patient 3.009|Post 3 vaccinations IgM

description:
3.009_V4
IgM


title: 24+ NT

city: Cleveland

first: Mark

last: Jackson

state: OH

address: 10900 Euclid Ave

institute: Case Western Reserve University

hyb_protocol: Standard Illumina Hybridization protocol

data_processing: The data were normalised and interrogated using quantile normalisation with Genome Studio

source_name: Mammary Epithelial Cells

growth_protocol: Cells were cultured as previously described (Junk et al. Neoplasia 2013, doi:10.1593/neo.131114)

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

treatment_protocol: Sorted CD24+ 48R-shp16-shp53-MYC-RAS were cultured under normal conditions (CD24+ NT) or in the presence of human recombinant OSM 10ng/mL (CD24+ OSM) or human recombinant TGF-b 10ng/mL (CD24+ TGF-b) for three weeks. Cells were treated at every medium change.

value: Mammary Epithelial Cells

value: Female

tag: culture

value: normal


title: 4T1-HA in RAG KO + ACT #2

description: 4T1-HA grown in RAG-/- mice treated with HA-specific WT CTL #2

source_name: HA-transfected 4T1 tumor cells after the growth in RAG-/- mice treated with HA-specific WT CTL #2


title: 4T1-HA in WT #2

description: 4T1-HA grown in WT mice #2

source_name: HA-transfected 4T1 tumor cells after the growth in WT mice #2


title: 4T1-HA in WT #1

description: 4T1-HA grown in WT mice #1

source_name: HA-transfected 4T1 tumor cells after the growth in WT mice #1


title: 4T1-HA in IFN-gamma KO #1

description: 4T1-HA grown in IFN-gamma-/- mice #1

source_name: HA-transfected 4T1 tumor cells after the growth in IFN-gammma-/- mice #1


title: patient 3.005|Post 3 vaccinations IgM

description:
3.005_V4
IgM


title: 24+ OSM

value: OSM 10ng/mL


title: 4T1-HA in WT #3

description: 4T1-HA grown in WT mice #3

source_name: HA-transfected 4T1 tumor cells after the growth in WT mice #3


title: patient 3.004|Post 3 vaccinations IgM

description:
3.004_V4
IgM


title: patient 3.059|Post 1 vaccination IgM

description:
3.059_V2
IgM

value: Post 1 vaccination


title: patient 3.060|Post 1 vaccination IgM

description:
3.060_V2
IgM


title: 4T1-HA in RAG KO + ACT #1

description: 4T1-HA grown in RAG-/- mice treated with HA-specific WT CTL #1

source_name: HA-transfected 4T1 tumor cells after the growth in RAG-/- mice treated with HA-specific WT CTL #1


title: 4T1-HA in RAG KO #1

description: 4T1-HA grown in Rag-/- mice

source_name: HA-transfected 4T1 tumor cells after the growth in RAG-/- mice


title: MCF-sh8-1

city: BUFFALO

first: Eduardo

last: Cortes

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

description:
MCF7 cells transduced with  shRNA to SSRP1
SAMPLE 11

hyb_protocol: 750ng of the labeled probes are then mixed with hybridization reagents and hybridized overnight at 58°C to the HT-12v4 BeadChips.

scan_protocol: Following washing and staining with Cy3-streptavidin conjugate, the BeadChips are imaged using the Illumina iScan Reader to measure fluorescence intensity at each probe.

data_processing:
Data was processed using quantile normalization and log2 transformed using lumi_2.26.3 and limma_3.30.6.
Normalization and data manipulation using R-3.3.1.

source_name: Breast

label_protocol: 500ng total RNA is converted to cDNA, followed by in vitro transcription to generate biotin labeled cRNA using the Ambion Illumina TotalPrep RNA Amplification Kit (Ambion, Inc.) as per manufacturer’s instructions.

growth_protocol: standard growth conditions in DMEM + 5% FBS + antibiotic solution

extract_protocol: Trizol reagent

treatment_protocol: lentiviral transduction with control shRNA (scrambled) or shRNAs to SSRP1. 72 hours after transduction.

tag: condition

value: Treatment


title: 4T1-HA in vitro #1

description: 4T1-HA in vitro cultured

source_name: HA-transfected 4T1 tumor cells after in vitro culture

tag: tissue

source_name: HA-transfected 4T1 cells at the start point for culture


title: MCF-control-2

description:
MCF7 cells transduced with control shRNA
SAMPLE 10

value: Control

tag: cell line


title: patient 3.054|Post 1 vaccination IgM

description:
3.054_V2
IgM

source_name: Serum


title: MCF-sh8-2

description:
MCF7 cells transduced with  shRNA to SSRP1
SAMPLE 12


title: patient 3.010|Post 3 vaccinations IgM

description:
3.010_V4
IgM


title: patient 3.052|Post 1 vaccination IgM

description:
3.052_V2
IgM


title: patient 3.053|Post 1 vaccination IgM

description:
3.053_V2
IgM


title: 24+ TGF-b

value: TGF-b 10ng/mL


title: patient 3.051|Post 1 vaccination IgM

description:
3.051_V2
IgM


title: patient 3.047|Post 1 vaccination IgM

description:
3.047_V2
IgM


title: patient 3.044|Post 1 vaccination IgM

description:
3.044_V2
IgM


title: patient 3.043|Post 1 vaccination IgM

description:
3.043_V2
IgM


title: patient 3.041|Post 1 vaccination IgM

description:
3.041_V2
IgM


title: patient 3.039|Post 1 vaccination IgM

description:
3.039_V2
IgM


title: patient 3.037|Post 1 vaccination IgM

description:
3.037_V2
IgM


title: Malignant glioma cell line U3167MG

hyb_protocol: GeneChip® Human Transcriptome Array 2.0 were hybridized for 16 hours in a 45°C incubator. According to the GeneChip® Expression Wash, Stain and Scan Manual (PN 702731 Rev. 3, Affymetrix Inc., Santa Clara, CA) the arrays were washed and stained using the Fluidics Station 450

scan_protocol: scanned using the GeneChip® Scanner 3000 7G

data_processing:
The data were analyzed with Affymetrix® Expression Console™ Software using Affymetrix default analysis settings with the Robust Multiarray Averaging (RMA) algorithm.
HTA-2_0.r3.pgf
HTA-2_0.r3.Psrs.mps

source_name: Malignant glioma cell line U3167MG

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using GeneChip® WT PLUS Reagent Kit

extract_protocol: RNeasy Plus Mini Kit, QIAGEN

value: Malignant glioma cell line


title: T-sh8-1

description:
T47D cells transduced with  shRNA to SSRP1
SAMPLE 7


title: MCF-control-1

description:
MCF7 cells transduced with control shRNA
SAMPLE 9


title: patient 3.033|Post 1 vaccination IgM

description:
3.033_V2
IgM


title: Malignant glioma clone U3167MG-C709

source_name: Malignant glioma clone U3167MG-C709

value: Malignant glioma clone


title: T-sh8-2

description:
T47D cells transduced with  shRNA to SSRP1
SAMPLE 8


title: Malignant glioma clone U3167MG-C500

source_name: Malignant glioma clone U3167MG-C500


title: Malignant glioma clone U3167MG-C778

source_name: Malignant glioma clone U3167MG-C778


title: Malignant glioma clone U3167MG-C398

source_name: Malignant glioma clone U3167MG-C398


title: Malignant glioma clone U3167MG-C723

source_name: Malignant glioma clone U3167MG-C723


title: T-control-1

description:
T47D cells transduced with control shRNA
SAMPLE 5


title: Malignant glioma clone U3167MG-C442

source_name: Malignant glioma clone U3167MG-C442


title: Malignant glioma clone U3167MG-C510

source_name: Malignant glioma clone U3167MG-C510


title: Mv1-control-1 #2

description:
MCF7v1 cells transduced with control shRNA
SAMPLE 1


title: Mv1-sh8-2

description:
MCF7v1 cells transduced with  shRNA to SSRP1
SAMPLE 4


title: patient 3.032|Post 1 vaccination IgM

description:
3.032_V2
IgM


title: Malignant glioma clone U3167MG-C390

source_name: Malignant glioma clone U3167MG-C390


title: Malignant glioma clone U3167MG-C827

source_name: Malignant glioma clone U3167MG-C827


title: Malignant glioma clone U3167MG-C157

source_name: Malignant glioma clone U3167MG-C157


title: Malignant glioma clone U3167MG-C836

source_name: Malignant glioma clone U3167MG-C836


title: Malignant glioma clone U3167MG-C141

source_name: Malignant glioma clone U3167MG-C141


title: Mv1-sh8-1

description:
MCF7v1 cells transduced with  shRNA to SSRP1
SAMPLE 3

source_name: Breast


title: Malignant glioma clone U3167MG-C670

source_name: Malignant glioma clone U3167MG-C670


title: Mv1-control-2

description:
MCF7v1 cells transduced with control shRNA
SAMPLE 2


title: T-control-2

description:
T47D cells transduced with control shRNA
SAMPLE 6


title: Malignant glioma clone U3167MG-C173

source_name: Malignant glioma clone U3167MG-C173


title: patient 3.029|Post 1 vaccination IgM

description:
3.029_V2
IgM

source_name: Serum


title: patient 3.027|Post 1 vaccination IgM

description:
3.027_V2
IgM


title: Malignant glioma clone U3167MG-C449

source_name: Malignant glioma clone U3167MG-C449


title: patient 3.031|Post 1 vaccination IgM

description:
3.031_V2
IgM


title: patient 3.025|Post 1 vaccination IgM

description:
3.025_V2
IgM


title: Malignant glioma clone U3167MG-C116

source_name: Malignant glioma clone U3167MG-C116


title: patient 3.015|Post 1 vaccination IgM

description:
3.015_V2
IgM


title: patient 3.016|Post 1 vaccination IgM

description:
3.016_V2
IgM


title: patient 3.028|Post 1 vaccination IgM

description:
3.028_V2
IgM


title: patient 3.013|Post 1 vaccination IgM

description:
3.013_V2
IgM


title: Malignant glioma clone U3117MG-C174-repl1

source_name: Malignant glioma clone U3117MG-C174


title: Malignant glioma clone U3117MG-C48-repl1

source_name: Malignant glioma clone U3117MG-C48


title: patient 3.023|Post 1 vaccination IgM

description:
3.023_V2
IgM


title: Malignant glioma clone U3117MG-C232-repl1

source_name: Malignant glioma clone U3117MG-C232


title: Malignant glioma clone U3117MG-C568

source_name: Malignant glioma clone U3117MG-C568


title: Malignant glioma clone U3117MG-C568-repl1


title: Malignant glioma cell line U3117MG

source_name: Malignant glioma cell line U3117MG


title: Malignant glioma clone U3117MG-C612

source_name: Malignant glioma clone U3117MG-C612