title: MCF10AshDicer exosomes_2

city: Houston

first: RAGHU

last: KALLURI

address: 1881 East Rd.

department: CANCER BIOLOGY

institute: MDACC

description:
Biotinylated sense-strand DNA for hybridization to Affymetrix exon arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854).
T372 MCF10AshDicer exos

hyb_protocol: The standard Affymetrix hybridization protocol was used - P-AFFY3

scan_protocol: Standard Affy scanning protoco - array assay. Quantified using GenePix Pro-6.0.

data_processing: The raw intensity for each probe is the median feature pixel intensity with the median background subtracted.  Setting an offset one ensures that there will be no negative values after log-transforming data.  Data was quantile normalized followed by log2 transformation. Signals from probes measuring the same miRNA were averaged.

label: streptavidin-Alexa647 conjugate

source_name: breast epithelial exosomes

extract_protocol: Exosomes used for RNA extraction were resuspended in 500ul of Trizol and protocol as detailed by manufacturer. Cells were resuspended in 1000ul of Trizol and protocol as detailed by manufacturer.Cells were grown for RNA as well as for extraction of exosomes for posterior RNA extraction in media with FBS depleted of exosomes.

treatment_protocol: Exosomes were extracted from cancer cells and added to the culture media of non-tumorigenic cells.

tag: cell line source

tag: cell/tissue type

value: breast epithelial exosomes


title: MCF10A exosomes_1

status: Public on Aug 27 2014

type: RNA

country: USA

description:
Biotinylated sense-strand DNA for hybridization to Affymetrix exon arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854).
T369  MCF10Aexos

molecule: total RNA

organism: Homo sapiens

growth_protocol: Cells were grown for RNA as well as for extraction of exosomes for posterior RNA extraction in media with FBS depleted of exosomes.


title: MCF10A exosomes_2

description:
Biotinylated sense-strand DNA for hybridization to Affymetrix exon arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854).
T370  MCF10A exos


title: MDA-MB-231 exosomes Dicer antibody_2

description:
Biotinylated sense-strand DNA for hybridization to Affymetrix exon arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854).
T384 231 Exosomes Dicer Antibody

source_name: breast carcinoma exosomes

value: breast carcinoma exosomes


title: MCF10AshDicer exosomes_1

description:
Biotinylated sense-strand DNA for hybridization to Affymetrix exon arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854).
T371 MCF10AshDicer exos


title: MDA-MB-231 exosomes_1

description:
Biotinylated sense-strand DNA for hybridization to Affymetrix exon arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854).
T375 231 Exosomes


title: MDA-MB-231 exosomes Dicer antibody_1

description:
Biotinylated sense-strand DNA for hybridization to Affymetrix exon arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854).
T383 231 Exosomes Dicer Antibody


title: MDA-MB-231shDicer exosomes_1

description:
Biotinylated sense-strand DNA for hybridization to Affymetrix exon arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854).
T379 231shDicer exos


title: MDA-MB-231 exosomes_2

description:
Biotinylated sense-strand DNA for hybridization to Affymetrix exon arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854).
T376 231 Exosomes


title: MDA-MB-231shDicer exosomes_2

description:
Biotinylated sense-strand DNA for hybridization to Affymetrix exon arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854).
T380 231shDicer exos


title: MCF10A cells + MDA-MB-231 exosomes_2

description:
Biotinylated sense-strand DNA for hybridization to Affymetrix exon arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854).
T366  MCF10A cells 231 exos

source_name: breast epithelial cells

value: breast epithelial cells


title: MDA-MB-231 cells_2

description:
Biotinylated sense-strand DNA for hybridization to Affymetrix exon arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854).
T358  231 cells

source_name: breast carcinoma cells

value: breast carcinoma cells


title: MCF10A cells + MDA-MB-231 exosomes_1

description:
Biotinylated sense-strand DNA for hybridization to Affymetrix exon arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854).
T365  MCF10A cells 231 exos


title: Dicer KO Alone_mRNA_2

city: London

first: Mark

middle: Stephen

last: Wilson

address: The Ridgeway

department: Molecular Immunology

country: United Kingdom

institute: MR, NIMR

description: Dicer KO cells cultured alone-mRNA_2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on either mouse whoel genome array or miRNA3  Arraya. 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 RMA normalised using Agilent GeneSpring 12.6 GX.

label: Biotin

organism: Mus musculus

source_name: Dicer KO cells

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: complete IMDM media was used for all T cell culturs

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

treatment_protocol: T cells were isolated and stimulated with anti-CD3 (1ug/ml) and anti-CD28 (10ug/ml) for exosome release. Purified exosomes, as described, were harvested and RNA extracted.

tag: strain background

tag: cell type

value: Dicer KO cells


title: MCF10A cells_2

description:
Biotinylated sense-strand DNA for hybridization to Affymetrix exon arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854).
T352 MCF10A cells


title: MDA-MB-231 cells_1

description:
Biotinylated sense-strand DNA for hybridization to Affymetrix exon arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854).
T357  231 cells


title: MCF10A cells_1

description:
Biotinylated sense-strand DNA for hybridization to Affymetrix exon arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854).
T351 MCF10A cells


title: Treg_Exo_mRNA_3

description: Treg-Exo_3- mRNA

source_name: Exosome

value: Exosome


title: Treg_Exo_mRNA_2

description: Treg-Exo_2- mRNA


title: Treg_Exo_mRNA_1

description: Treg-Exo_1- mRNA


title: Treg_mRNA_3

description: Treg_3- mRNA

source_name: Regulatory T cells (Treg)

value: Regulatory T cells (CD4+CD25hiFoxp3rfp+, Treg)


title: Treg_mRNA_1

description: Treg_1- mRNA


title: BP-8-2 vs. BP-14-pool

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Tecan HS4800 hybridization

scan_protocol: Scanning of slides using the Agilent G2565BA scanner. Features were extracted using Imagene software from Biodiscovery.

data_processing: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), by estimating the LOESS curve for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from a set of wild-type wild-type hybridizations, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009.

organism: Saccharomyces cerevisiae BY4741

label_protocol: robot amplification and labeling v1.0

growth_protocol: Evolved yeast-lines were generated by growing strains for 400 doublings during 104 days on YPD medium in 96 wells plates. 0.5% sample volume was transferred to fresh medium every 48 hours during this period. 8 evolved lines were selected for microarray analysis. Two independent colonies of the wild type control, evolved and corresponding ancestor knock-out strains were inoculated into 15 ml YPD and grown overnight at 30 °C. The saturated populations were diluted to an OD600 of 0.15 in 60 ml YPD and grown to early mid-log phase (OD600 0.6 ± 0.05) in 250 ml Erlenmeyer flasks with 220 rpm shaking at 30 °C. Cells were harvested by centrifugation (4000 rpm, 3 min, 30 °C) and immediately frozen in liquid nitrogen after removal of supernatant. Total RNA was prepared by hot acidic phenol extraction and cleaned up using a robotic protocol with magnetic beads.

extract_protocol: yeast HTP RNA isolation for robot v2.0


title: CD4 T cells (C8166 cells) SIV acute infection rep

city: Esch-sur-Alzette

first: Feng

middle: Q.

last: Hefeng

address: 29, rue Henri Koch

department: Department of Infection and Immunity

country: Luxembourg

institute: Luxembourg Institute of Health

description: gene expression data from CD4 T cell line with acute SIV infection

hyb_protocol: Following fragmentation, 12.5ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

label: biotin

source_name: CD4 T cells 24h post SIVmac infection

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA.

growth_protocol: Human CD4 T cells (C8166 cells) were grown in RPMI 1640 medium supplemented by 10 % fetal bovine serum and antibiotics (R-10 medium).

extract_protocol: Total RNA was isolated using PeqGold TriFast FL RNA isolation kit (PeqLab) and quality was checked by formaldehyde gel electrophoresis. Prior to microarray analysis, a second RNA quality check was performed by Agilent Bioanalyzer.

treatment_protocol: For each type of infection 3 x107 cells were harvested by centrifugation (10 min, 600g). The mock-infected and permanently SIVmac251/32H producing C8166 were re-suspended in 20 ml old medium and 10 ml fresh R-10 medium. The newly-infected cells were re-suspended 20 ml stock solution of SIVmac251/32H grown on C8166 cell in R-10 medium and 10 ml fresh R-10 medium. These cells were infected at a multiplicity of infection of 0.2. However, as determined by Real-Time PCR, the virus stock solution contained about 4000fold more virus particles, so that each cell was theoretically in contact with about 800 particles. This number reflects the number of virus particles present in the supernatant of the permanently SIV producing cell line. After 24 h cells were harvested and processed for immediate RNA isolation.

tag: disease state

value: SIV acute infection

tag: cd4 t cell line


title: BP-9-2 vs. BP-14-pool


title: CD4 T cells (C8166 cells) SIV mock control infection rep

description: gene expression data from CD4 T cell line with mock infection (control)

source_name: CD4 T cells with mock infection

value: mock infected


title: Treg_mRNA_2

description: Treg_2- mRNA


title: CD4 T cells (C8166 cells) SIV chronic infection rep

description: gene expression data from CD4 T cell line with chronic SIV infection (ie., permanently releasing SIV)

source_name: CD4 T cells with permanent SIVmac infection

value: SIV chronic infection


title: BP-6-2 vs. BP-14-pool


title: BP-7-2 vs. BP-14-pool


title: mix-4

city: Harbin

first: Hongbao

last: Wang

address: No. 59 Mucai Street, Xiangfang District

country: China

institute: Northeast Agricultural University

description: Gene expression data from chicken adipose tissue at 7-week of age

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Gallus gallus

source_name: chicken mixed tissue 4 at 7-week of age

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

growth_protocol: All birds were kept in similar environmental conditions and had access to feed and water ad libitum, and were fed with a commercial corn-soybean-based diet that met all NRC requirements (National Research Council, 1994). From hatching to 3 weeks the birds received a starter feed (3,100 kcal ME/kg and 210 g/kg CP), and from 4 weeks to slaughter they were fed a grower diet (3,000 kcal ME/kg and 190 g/kg CP).

treatment_protocol: Birds were slaughtered at 7 weeks and total 21 tissues was isolated, immediately frozen in liquid nitrogen and stored at -80oC.

tag: tissue

value: mix

tag: breed

value: Arbor Acres

tag: gender

value: male

tag: age

value: 49 day after birth


title: Sham_1d_rep2

city: Tuxedo

first: Lisa

last: Passantino

state: New York

address: 57 Old Forge Road

department: School of Medicine

institute: New York University

description: sham irradiated

hyb_protocol: Samples were hybridized with Affymetrix Human Gene 1.0 ST Arrays and scanned at the NYU Cancer Institute Genomics Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Gene expression changes between sham and 12 J/cm2 irradiated cells at each of the recovery time points was conducted. Then the lists of differentially expressed genes at 1 day and 5 days were compared. Gene expression was analyzed using GeneSpring GX software (Agilent Technologies, Santa Clara, CA). Cells that recovered for 1 day were analyzed separately from the cells that recovered for 5 days. Significant genes were determined by a moderated T-test with p-values < 0.05.

source_name: Sham 1 day

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Primary neonatal human dermal fibroblasts (Invitrogen, Carlsbad, CA) were grown in M106 media (Invitrogen) supplemented with Low Serum Growth Supplement (Invitrogen) and Gentamicin/Amphotericin (Invitrogen). They were cultured at 37oC with 5% CO2 and 100% humidity.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen). The isolated T.RNA was subjected to a colum purification using Rneasy Plus Micro Kit (Qiagen)

treatment_protocol: The cells were exposed to 12 J/cm2 ssUVR on a modified Hand Foot II phototherapy instrument (National Biological Corporation) that emits 95% UVA and 5% UVB. During irradiation, the medium was replaced with Hank's balanced salt solution and 4 mM glucose without phenol red. A sham exposure group (0 J/cm2 ssUVR) served as the negative control. The cells recovered in fresh medium for up to 5 days and then were collected.

value: Primary neonatal dermal fibroblasts

tag: recovery time

value: 1 day


title: mix-1

source_name: chicken mixed tissue 1 at 7-week of age


title: BP-5-2 vs. BP-14-pool


title: CD4 T cells (C8166 cells) SIV mock control infection


title: mix-2

source_name: chicken mixed tissue 2 at 7-week of age


title: CD4 T cells (C8166 cells) SIV chronic infection


title: 12J_1d recov_rep1

description: ssUVR irradiated

source_name: 12J 1 day recovery


title: Sham_1d_rep1

description: sham irradiated


title: Sham_5d_rep1

description: sham irradiated

source_name: Sham 5 days

value: 5 days


title: mix-3

source_name: chicken mixed tissue 3 at 7-week of age


title: Sham_5d_rep2

description: sham irradiated


title: 12J_1d recov_rep2

description: ssUVR irradiated


title: adipose tissue

source_name: chicken adipose tissue at 7-week of age

value: adipose


title: 12J_5d recov_rep2

description: ssUVR irradiated

source_name: 12J 5 days recovery


title: 12J_5d recov_rep1

description: ssUVR irradiated


title: BP-3-2 vs. BP-14-pool


title: CD4 T cells (C8166 cells) SIV acute infection


title: BP-24-2 vs. BP-14-pool


title: BP-25-2 vs. BP-14-pool


title: Dicer KO + Treg_miRNA_3

description: Dicer KO cells cultured with Treg cels-miRNA_3

source_name: co-cultured Dicer KO cells with Treg cells

growth_protocol: complete IMDM media was used for all T cell cultures


title: 4J_24h recov_rep1

description: ssUVR irradiated

data_processing: Gene expression changes for 4 J/cm2 and 12 J/cm2 ssUVR irradiated cells versus sham control cells (0 J/cm2 ssUVR) awere analyzed using GeneSpring GX software (Agilent Technologies, Santa Clara, CA). Cells that recovered for zero hours were analyzed separately from the cells that recovered for 24 hours. Significant genes were determined by a moderated T-test with p-values < 0.05.

source_name: 4J 24h recovery

treatment_protocol: The cells were exposed to 4 or 12 J/cm2 ssUVR on a modified Hand Foot II phototherapy instrument (National Biological Corporation) that emits 95% UVA and 5% UVB. During irradiation, the medium was replaced with Hank's balanced salt solution and 4 mM glucose without phenol red. A sham exposure group (0 J/cm2 ssUVR) served as the negative control. The cells recovered in fresh medium for up to 24 hours. Those that did not recover (zero hours) were collected immediately following treatment.

value: 24 hours


title: Sham_24h recov_rep2

description: Sham irradiated

source_name: Sham 24h recovery


title: liver

source_name: chicken liver tissue at 7-week of age

value: liver


title: 4J_24h recov_rep2

description: ssUVR irradiated


title: Sham_24h recov_rep1

description: Sham irradiated


title: 12J_24h recov_rep1

description: ssUVR irradiated

source_name: 12J 24h recovery


title: 12J_24h recov_rep2

description: ssUVR irradiated


title: BP-17-2 vs. BP-14-pool


title: 12J_0h recov_rep1

description: ssUVR irradiated

source_name: 12J 0h recovery

value: 0 hours


title: Dicer KO + Treg_miRNA_1

description: Dicer KO cells cultured with Treg cels-miRNA_1

value: co-cultured Dicer KO cells with Treg cells


title: BP-2-2 vs. BP-14-pool


title: Dicer KO Alone_miRNA_2

description: Dicer KO cells cultured alone-miRNA_2

source_name: Dicer KO cells

value: Dicer KO cells


title: MCF10A exos_2

description: Biotinylated sense-strand DNA for hybridization to Affymetrix exon arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854).

data_processing: The raw intensity for each probe is the median feature pixel intensity with the median background subtracted.  Setting an offset one ensures that there will be no negative values after log-transforming data.  Data was quantile normalized followed by log2 transformation (R computing environment  (version 3.0.1)). Signals from probes measuring the same miRNA were averaged.

source_name: breast epithelial cells

value: normosomes


title: BP-18-2 vs. BP-14-pool


title: BP-15-2 vs. BP-14-pool


title: BP-21-2 vs. BP-14-pool


title: MCF10A exos_1

label_protocol: Biotinylated sense-strand DNA for hybridization to Affymetrix exon arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854).


title: Treg_Exo_miRNA_3

description: Treg-Exo_3- miRNA

source_name: Exosome

value: Exosome


title: 4J_0h recov_rep2

description: ssUVR irradiated

source_name: 4J 0h recovery


title: Dicer KO Alone_miRNA_1

description: Dicer KO cells cultured alone-miRNA_1


title: Dicer KO Alone_miRNA_3

description: Dicer KO cells cultured alone-miRNA_3


title: 12J_0h recov_rep2

description: ssUVR irradiated


title: NMuMG exos_2


title: MDA-MB-231 exos_1

source_name: breast carcinoma cells

value: cancer exosomes


title: 4J_0h recov_rep1

description: ssUVR irradiated


title: Treg_Exo_miRNA_2

description: Treg-Exo_2- miRNA


title: BP-14-pool vs. BP-9-1


title: MDA-MB-231 exos_2


title: Treg_miRNA_3

description: Treg_3- miRNA

source_name: Regulatory T cells (Treg)

value: Regulatory T cells (CD4+CD25hiFoxp3rfp+, Treg)


title: Treg_Exo_miRNA_1

description: Treg-Exo_1- miRNA


title: 4T1 exos_2


title: Treg_miRNA_2

description: Treg_2 - miRNA


title: BP-14-pool vs. BP-8-1


title: Dicer mutant UB cells, biological rep 1

city: Charlottesville

first: Jing

last: Yu

state: VA

address: 1340 Jefferson Park Ave.

department: Cell Biology

institute: University of Virginia School of Medicine

hyb_protocol: Hybridization was performed following Affymetrix GeneChip WT terminal labeling and hybridization user manual

scan_protocol: Scan was performed following the Affymetrix GCOS user manual

data_processing: RMA algorithm was used for summarization, quantile normalization, and log2 transformation (RMA function from the Bioconductor 'affy' package in R). Only affymetrix probe IDs that match known genes are included.

source_name: E15.5 Dicer mutant mouse UB cells

label_protocol: labeling was performed following Affymetrix GeneChip WT terminal labeling and hybridization user manual

growth_protocol: Control and Dicer mutant kidneys were dissected at E15.5

extract_protocol: Total RNAs were purified with RNeasy plus microkit (Qiagen) following manufacturer protocol

treatment_protocol: Kidneys were trypsinized and YFP+ UB cells were FACS sorted

value: mixed

tag: genotype/variation

value: Dicerc/-; Hoxb7Cre; Rosa26YFP

value: kidney

value: FACS sorted ureteric bud (UB) cells


title: MCF7 exos_2


title: NMuMG exos_1


title: Sham_0h recov_rep2

description: Sham irradiated

source_name: Sham 0h recovery

value: Primary neonatal dermal fibroblasts


title: 4T1 exos_1


title: BP-14-pool vs. BP-3-1


title: BP-14-pool vs. BP-5-1


title: Dicer mutant UB cells, biological rep 2


title: BP-14-pool vs. BP-7-1


title: Dicer mutant UB cells, biological rep 3


title: Treg_miRNA_1

description: Treg_1- miRNA


title: BP-14-pool vs. BP-6-1


title: control UB cells, biological rep 3

source_name: E15.5 control mouse UB cells

value: wild type (control)


title: BP-14-pool vs. BP-22-1


title: control UB cells, biological rep 1


title: control UB cells, biological rep 2


title: BP-14-pool vs. BP-21-1


title: BP-14-pool vs. BP-25-1


title: KO-stimulated-6h

city: Shanghai

first: Yang

last: Sun

address: Yueyang Road 320

institute: Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences.

description: Gene expression after stimulation for 6hr

hyb_protocol: 1μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 4 out of 4 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes were identified through Fold Change filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: Knockout CD4 T cells, stimulated, 6h

label_protocol: 1 μg of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The Labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: RNA was prepared using TRIzol® Reagent (Invitrogen life technologies) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-ND1000 spectrophotometer and RNA integrity was assessed by standard denaturing agarose gel electrophoresis..

treatment_protocol: Freshly CD4 T cells from wildtype and Med23 knockout mice were left unstimulated or stimulated for 6 h.

value: lymph node

value: CD4 T

tag: genotype

value: Med23 knockout

value: male

value: 7 weeks


title: Sham_0h recov_rep1

description: Sham irradiated

value: 0 hours


title: BP-14-pool vs. BP-24-1


title: MCF7 exos_1


title: Adjacent_normal_PDAC_patient_8

city: Oslo

first: Vandana

last: Sandhu

state: oslo

address: Ullernchausseen 70

department: Department of Genetics

country: Norway

institute: Radiumhospitalet, Oslo

description: Gene expression of adjacent normal tissue from pancreatic ductal adenocarcinoma patient 8

hyb_protocol: For the expression arrays Cy-3-labeled cRNA was hybridized according to the manual One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling (version 6.5, May 2010) from Agilent Technologies.

scan_protocol: The slides were scanned immediately after washing on the Agilent Microarray Scanner G2565C using protocol GE1_107_Sep09 for the expression microarrays and protocol.

data_processing: The scanned images were analyzed using Feature Extraction Software 10.7.3.1 (Agilent Technologies) using default parameters.

source_name: Adjacent normal

label_protocol: mRNA was labeled with Cy-3 according to the manual One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling (version 6.5, May 2010) from Agilent Technologies, using 100 ng total RNA as input.

growth_protocol: Cell lines were cultured in Pancreatic Cell Culture Medium SCR016 (Millipore) with 5% Pancreatic Cell Culture Supplement SCR015 (Millipore). Conditioned culture medium was used, prepared by spinning the medium removed from the cell culture at 235 x g, 5 min., room temperature, then blending the supernatant with the same amount of freshly prepared medium. Cells were split using Trypsine (Gibco).

extract_protocol: Total RNA was isolated from cell pellets using mirVana kit (Ambion/Life Technologies) according to the manufacturer’s instructions. Total RNA was eluted in 100 µl H2O, concentration measured on NanoDrop ND-1000.

treatment_protocol: Cells were detached by Trypsine for approximately five minutes, spun at 235 x g, 5 min., room temperature.

tag: patient


title: BP-14-pool vs. BP-2-1


title: MCF7 cells_1

value: breast epithelial cells


title: KO-unstimulated

description: Gene expression without stimulation

source_name: Knockout CD4 T cells, unstimulated


title: BP-14-pool vs. BP-18-1


title: Adjacent_normal_PDAC_patient_6

description: Gene expression of adjacent normal tissue from pancreatic ductal adenocarcinoma patient 6


title: WT-unstimulated

description: Gene expression without stimulation

source_name: Wildtype CD4 T cells, unstimulated

value: wildtype


title: WT-stimulated-6h

source_name: Wildtype CD4 T cells, stimulated, 6h


title: Liver of S. aurata exposed to 16°C  [T4_CTRL_b]

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data were processed with FeatureExtraction v9.5 and filtering/cyclic lowess normalization were performednormalized using R2.6.1 statistical software.

label: Cyanine 3

organism: Sparus aurata

source_name: Liver of S. aurata exposed to 16°C

label_protocol: Amplified and labeled according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: Extracted according to QiAgen RNeasy MiniKit protocol for tissue samples

treatment_protocol: Sea breams (120±16 g body weight; 21±1 cm total length) caught in Valle Bonello were kept in 5 m3 circular recycling tanks an at 16 °C. F S.aurata were fasted during the trial.

tag: weight/length

tag: kept in

value: 5 m3 circular recycling tanks an at 16 °C (control)

value: liver


title: Cellline_PDAC_patient_8_replicate2

description: Gene expression of cell line from pancreatic ductal adenocarcinoma patient 8 (replicate 2)

source_name: Cell line

value: 8 (replicate 2)


title: Cellline_PDAC_patient_8_replicate4

description: Gene expression of cell line from pancreatic ductal adenocarcinoma patient 8 (replicate 4)

value: 8 (replicate 4)


title: Cellline_PDAC_patient_8_replicate3

description: Gene expression of cell line from pancreatic ductal adenocarcinoma patient 8 (replicate 3)

value: 8 (replicate 3)


title: Dicer KO + Treg_miRNA_2

description: Dicer KO cells cultured with Treg cels-miRNA_2

source_name: co-cultured Dicer KO cells with Treg cells


title: Liver of S. aurata exposed to 16°C  [T4_CTRL_a]

value: 120±16 g body weight; 21±1 cm total length


title: Vpara_37°C_rep3

city: Berlin

first: Stephan

last: Huehn

address: Koenigsweg 69

country: Germany

institute: Freie Universität Berlin

description:
Gene expression after incubation at 37°C for 30min.
Vp-37-w3

hyb_protocol: Finally 600 ng of the labelled and linear amplified cRNA (specific activity 9,0 pmol Cy3/µg cRNA) was fragmented, added to 25 µl Agilent-hybridization buffer resulting in 480 ng loaded on a microarray in a hybridization chamber (following manufacturers instructions). The hybridization was performed at 65°C for 17 hours and 10 rpm.  Washing of the slides was performed using preheated washing buffer (Gene expression wash buffer kit, Agilent). First the chamber was rinsed with washing buffer. Then the slides were washed once followed by a second wash using washing buffer containing 0.01% Triton X-102 (Agilent). The slides were dried using acetonitrile.

scan_protocol: Scanning was carried out immediately after washing using the Agilent G2565CA scanner with a resolution of 5 µm.

data_processing: After scanning, tiff-files were analysed and raw data was extracted using Feature Extraction Software (Agilent). Data processing was performed using Bioconductor V 2.12 package of the software R. At first, filtering of bad quality spots was performed and the data was background corrected with normexp method using offset = 50.

organism: Vibrio parahaemolyticus RIMD 2210633

source_name: bacterial cell culture incubated at 37°C

label_protocol: Reverse transcription of the RNA was performed. Briefly 200 ng of RNA were linear amplified using the full spectrum MultiStart primer (Biocat, Heidelberg, Germany) and Moloney murine leukemia virus (MMLV) reverse transcriptase (Agilent). The amplification was performed at 40°C for 2 hours followed by 65°C for 15 minutes and stored at 4°C. Labelling was performed using the Quick Amp Labeling Kit (Agilent). Briefly the amplified cDNA, the full spectrum MultiStart primer and T7 RNA polymerase were used along with Cyanine 3-CTP. Labeled cRNA was purified using the Qiagen RNeasy Mini Kit (Qiagen). A 3 µl-aliquot was used for quality control (NanoDrop 2000, Thermo Scientific).

growth_protocol: Prior use, the strain was stored in cryovials at -80°C (Cryobank; Mast Diagnostica, Bootle, England). For initial growth, cells were grown using a rotary shaker (Unimax 1010 and Incubator 1000; Heidolph, Schwabach, Germany) in alkaline peptone water (APW; 0.3% Yeast-Extract, 1% Peptone, 2% NaCl; pH 8.6) at 37°C overnight.

extract_protocol: Total RNA was isolated using the peqGold Bacterial RNA Kit (Peqlab, Erlangen, Germany). Obtained RNA was eluted into 43 µl of DEPC-treated, DNase- and RNase-free water (Carl Roth, Karlsruhe, Germany). Samples were then treated by DNase I along with an RNase-A, -B and -C inhibitor (Fermentas, Vilnius, Lithuania). RNA quantity was measured by spectrophotometry (NanoDrop 2000, Thermo Scientific). RNA quality of each sample was monitored via gel electrophoresis. Additionally, the RNA quality was assessed using the Agilent RNA 6000 Nano Kit on a 2100 Bioanalyzer (Agilent, Santa Clara, US).

treatment_protocol: The cultures were centrifuged (2 minutes, 8000 x g) and the supernatant was discarded. The pellet was immediately resuspended in 1.5 ml RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany) to minimize RNA degradation.

tag: temperature

value: whole cell

tag: growth phase

value: log-phase


title: BP-22-2 vs. BP-14-pool


title: MCF7 cells_2

tag: cell/tissue type


title: Liver of S. aurata exposed for 21 days to 6.8°C  [T4_CE_c]

treatment_protocol: Sea breams (120±16 g body weight; 21±1 cm total length) caught in Valle Bonello were kept in 5 m3 circular recycling tanks and acclimated over one month at 16 °C. Fish were then exposed for 21 days to 6.8 ± 0.3 °C (cold groups).  S.aurata were fasted during the trial.

tag: exposed to

value: 6.8 ± 0.3 °C (cold groups) for 21 days


title: Cellline_PDAC_patient_8_replicate1

description: Gene expression of cell line from pancreatic ductal adenocarcinoma patient 8 (replicate 1)

value: 8 (replicate 1)


title: Liver of S. aurata exposed to 16°C  [T4_CTRL_c]


title: Vpara_37°C_rep2

description:
Gene expression after incubation at 37°C for 30min.
Vp-37-w2

tag: cell type


title: Vpara_37°C_rep1

description:
Gene expression after incubation at 37°C for 30min.
Vp-37-w1


title: Vpara_42°C_rep3

description:
Gene expression after incubation at 42°C for 30min.
Vp-42-w3

source_name: bacterial cell culture incubated at 42°C


title: Liver of S. aurata exposed to 16°C  [T3_CTRL_b]


title: Liver of S. aurata exposed to 16°C  [T3_CTRL_c]


title: BP-14-pool vs. BP-1-1


title: BP-14-pool vs. BP-10-1


title: BP-14-pool vs. BP-14-1


title: BP-14-2 vs. BP-14-pool


title: BP-10-2 vs. BP-14-pool


title: Cellline_PDAC_patient_6_replicate2

description: Gene expression of cell line from pancreatic ductal adenocarcinoma patient 6 (replicate 2)

value: 6 (replicate 2)


title: Liver of S. aurata exposed for 21 days to 6.8°C  [T4_CE_b]


title: Liver of S. aurata exposed for 21 days to 6.8°C  [T4_CE_a]


title: Cellline_PDAC_patient_6_replicate3

description: Gene expression of cell line from pancreatic ductal adenocarcinoma patient 6 (replicate 3)

value: 6 (replicate 3)


title: BP-14-pool vs. BP-15-1


title: BP-14-pool vs. BP-17-1


title: Cellline_PDAC_patient_1_replicate3

description: Gene expression of cell line from pancreatic ductal adenocarcinoma patient 1 (replicate 3)

value: 1 (replicate 3)


title: Cellline_PDAC_patient_1_replicate2

description: Gene expression of cell line from pancreatic ductal adenocarcinoma patient 1 (replicate 2)

value: 1 (replicate 2)


title: BP-1-2 vs. BP-14-pool


title: Liver of S. aurata exposed for 24 hours to 6.8°C  [T3_CE_c]

treatment_protocol: Sea breams (120±16 g body weight; 21±1 cm total length) caught in Valle Bonello were kept in 5 m3 circular recycling tanks and acclimated over one month at 16 °C. Fish were then exposed for 24 hours to 6.8 ± 0.3 °C (cold groups).  S.aurata were fasted during the trial.

value: 6.8 ± 0.3 °C (cold groups) for 24hrs


title: Cellline_PDAC_patient_6_replicate1

description: Gene expression of cell line from pancreatic ductal adenocarcinoma patient 6 (replicate 1)

value: 6 (replicate 1)


title: Vpara_42°C_rep2

description:
Gene expression after incubation at 42°C for 30min.
Vp-42-w2


title: Vpara_37°C_rep4

description:
Gene expression after incubation at 37°C for 30min.
Vp-37-w4


title: Vpara_42°C_rep1

description:
Gene expression after incubation at 42°C for 30min.
Vp-42-w1


title: Cellline_PDAC_patient_1_replicate1

description: Gene expression of cell line from pancreatic ductal adenocarcinoma patient 1 (replicate 1)

value: 1 (replicate 1)


title: Human adult beta cells, shRNA β-catenin 45, donor S114, rep1

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

description: Gene expression data of de-differentiated cells.

hyb_protocol: According to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA).

data_processing: Gene-level analyses was performed. RMA normalization, summarization by mean and batch effect removal, all done by Partek Genomics Suite (version 6.6) Copyright ©.

source_name: Pancreatic islets from individual donor, shRNA β-catenin 45

growth_protocol: Growth protocol differentiation: Human islets were received 2-6 days following isolation. Islets from individual donors were dissociated into single cells and cultured in CMRL 1066 medium containing 5.6 mmol/liter glucose and supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin, 100 µg/ml streptomycin, 100 µg/ml gentamycin, and 5 µg/ml amphotericin B. The cultures were refed twice a week and split 1:2 once a week. Lineage tracing was performed using the RIP-Cre/ER and pTrip–loxP-NEO-STOP-loxP-eGFP lentiviral vectors. 4-hydroxytamoxifen (Sigma-Aldrich) was added to a final concentration of 1 µM 1 day post-infection. Following overnight incubation, the medium was changed to regular growth medium. Labeled cells were sorted using a FACS Aria sorter (BD Biosciences).

extract_protocol:
Preparation of islet cells: As described in: Ouziel-Yahalom L, Zalzman M, Anker-Kitai L, Knoller S, Bar Y, Glandt M, Herold K, Efrat S (2006) Expansion and redifferentiation of adult human pancreatic islet cells. Biochem Biophys Res Commun 341:291-298.
Quick-RNA MiniPrep kit (Zymo Research Co., 17062 Murphy Ave. Irvine, CA 92614, U.S.A.), according to manufacturer's protocol.

treatment_protocol: Growth protocol re-differentiation: Expanded human islet cells or sorted BCD cells in passages 5-7 were infected with β-catenin shRNA or nontarget shRNA viruses. Five to 6 days following infection, cells were trypsinized, pelleted, and seeded at 3.8X10^4 cells/cm2 in ultra-low attachment plates (Corning) in CMRL 1066 medium containing 5.6 mM glucose and supplemented with 100 U/ml penicillin, 100 µg/ml streptomycin, 100 µg/ml gentamycin sulphate (Biological Industries), 1% BSA fraction V (Sigma), 1X insulin/transferrin/selenium (ITS, Invitrogen), D-Glucose (final concentration 25 mM), 8 nM exendin-4 (Acris), 8 nM activin A (Cytolab/PreproTech), 1X B27 supplement (Stem Cell Technologies), and 10 mM nicotinamide (Sigma) (Redifferentiation Cocktail 1, RC1) for the indicated periods. Half-volume medium changes were performed every other day.

value: pancreatic islets

tag: treatment

value: shRNA β-catenin 45

tag: donor

tag: date


title: Vpara_20°C_rep3

description:
Gene expression after incubation at 20°C for 30min.
Vp-20-w3

source_name: bacterial cell culture incubated at 20°C


title: Liver of S. aurata exposed to 16°C  [T3_CTRL_a]

value: 5 m3 circular recycling tanks an at 16 °C (control)

tag: tissue

value: liver


title: Human adult beta cells, shRNA β-catenin 45, donor S114, rep2

scan_protocol: According to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA).


title: Liver of S. aurata exposed for 24 hours to 6.8°C  [T3_CE_b]


title: Vpara_20°C_rep2

description:
Gene expression after incubation at 20°C for 30min.
Vp-20-w2


title: Liver of S. aurata exposed to 16°C  [T2_CTRL_c]


title: Vpara_15°C_rep2

description:
Gene expression after incubation at 15°C for 30min.
Vp-15-w2

source_name: bacterial cell culture incubated at 15°C


title: Vpara_15°C_rep3

description:
Gene expression after incubation at 15°C for 30min.
Vp-15-w3


title: Human adult beta cells, shRNA β-catenin 9, donor S112

source_name: Pancreatic islets from individual donor, shRNA β-catenin 9

label_protocol: According to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA).

value: shRNA β-catenin 9


title: Liver of S. aurata exposed to 16°C  [T2_CTRL_b]

value: 120±16 g body weight; 21±1 cm total length


title: Vpara_20°C_rep1

description:
Gene expression after incubation at 20°C for 30min.
Vp-20-w1

value: whole cell


title: PDAC_patient_8

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 8

source_name: Fresh frozen tumor


title: Human adult beta cells, untreated, donor S112

description: Gene expression data of intact islet cells.

source_name: Pancreatic islets from individual donor, untreated


title: Human adult beta cells, shRNA β-catenin 9, donor S114


title: Vpara_15°C_rep1

description:
Gene expression after incubation at 15°C for 30min.
Vp-15-w1

value: log-phase


title: Liver of S. aurata exposed for 24 hours to 6.8°C  [T3_CE_a]


title: PDAC_patient_6

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 6


title: Human adult beta cells, shRNA β-catenin 45, donor S109


title: PDAC_patient_1

description: Gene expression of fresh frozen pancreatic ductal adenocarcinoma patient 1


title: Vpara_4°C_rep3

description:
Gene expression after incubation at 4°C for 30min.
Vp-4-w3

source_name: bacterial cell culture incubated at 4°C


title: Liver of S. aurata exposed for 6 hours to 6.8°C  [T2_CE_b]

treatment_protocol: Sea breams (120±16 g body weight; 21±1 cm total length) caught in Valle Bonello were kept in 5 m3 circular recycling tanks and acclimated over one month at 16 °C. Fish were then exposed for 6 hours to 6.8 ± 0.3 °C (cold groups).  S.aurata were fasted during the trial.

value: 6.8 ± 0.3 °C (cold groups) for 6hrs


title: Liver of S. aurata exposed for 6 hours to 6.8°C  [T2_CE_a]


title: Vpara_4°C_rep1

description:
Gene expression after incubation at 4°C for 30min.
Vp-4-w1


title: Liver of S. aurata exposed to 16°C  [T2_CTRL_a]


title: Vpara_4°C_rep2

description:
Gene expression after incubation at 4°C for 30min.
Vp-4-w2


title: SCTR-siRNA

city: Seoul

first: Sun Jung

last: Kim

address: Pil-dong 3-ga, Jung-gu

department: Life Science

country: South Korea

institute: Dongguk university

description: SAMPLE 2

hyb_protocol: Following fragmentation, 0.75ug of cRNA were hybridized to the Illumina HumanHT-12 Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Array data export processing and analysis was performed using Illumina Genomestudio v2011.1(Gene Expresion Module v1.9.0). The data are normalized after filtering detection p-value.

source_name: Mammary epithelial cell line

label_protocol: Biotinylated cRNA were prepared from 0.55ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX).

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

tag: cell line

value: MCF-10A Mammary epithelial cell line

value: SCTR siRNA


title: Liver of S. aurata exposed for 6 hours to 6.8°C  [T2_CE_c]


title: Liver of S. aurata exposed to 16°C  [T1_CTRL_c]


title: Human adult beta cells, untreated, donor S109


title: Human adult beta cells, shRNA β-catenin 9, donor S109


title: olfactory bulb_adult mice_rep3

city: Hangzhou

first: Ting

middle: ting

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Neuroscience and Anatomy

institute: Zhejiang University School of Medicine

description: Experimental animals were male and commercially-available C57BL/6 mice (SLAC, Shanghai, China).

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.16.0) (Exiqon) according to array manual

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs with statistical significance were identified through Volcano Plot filtering

source_name: Olfactory bulb

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling

growth_protocol: All mice were raised in Pathogen-free room and the room was maintained at a constant temperature of 23±1℃ with a 12 h light/dark cycle. Food and water were available ad libitum in the home cages.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

treatment_protocol: Mice were deeply anesthetized with pentobarbital sodium and then olfactory bulbs were rapidly dissected from the fresh brains.

tag: age

value: 8 weeks old

value: olfactory bulb

tag: strain


title: Human adult beta cells, shRNA nontarget, donor S114

source_name: Pancreatic islets from individual donor, shRNA nontarget

value: shRNA nontarget


title: olfactory bulb_adult mice_rep1


title: Human adult beta cells, untreated, donor S108


title: Liver of S. aurata exposed to 6.8°C  [T1_CE_b]

source_name: Liver of S. aurata exposed to 6.8°C

treatment_protocol: Sea breams (120±16 g body weight; 21±1 cm total length) caught in Valle Bonello were kept in 5 m3 circular recycling tanks and acclimated over one month at 16 °C. Fish were then exposed to 6.8 ± 0.3 °C (cold groups). Water was firstly gradually cooled from 16 °C to 12 °C at a rate of 1°C day -1 and then reduced from 12 °C to 6.8 °C within 24 h. S.aurata were fasted during the trial.

value: 6.8 ± 0.3 °C (cold groups)


title: olfactory bulb_adult mice_rep2


title: Human adult beta cells, shRNA β-catenin 45, donor S108


title: Human adult beta cells, shRNA β-catenin 9, donor S108


title: Liver of S. aurata exposed to 16°C  [T1_CTRL_a]


title: Gli1CreER/WT; Smoflox/flox BBN-treated bladder, biological rep 3

city: Stanford

first: Agnes

last: Lim

state: CA

address: 265 Campus Drive

department: Developmental Biology

institute: Stanford University

description: bladder from one mouse

hyb_protocol: The fragmented and labeled targets were hybridized to the arrays per standard Affymetrix protocol, which includes 16hr (overnight) hybridization at 45degC at 60rpm in an Affymetrix GeneChip Hybridization Oven 645. The arrays were then washed and stained in an Affymetrix GeneChip Fluidics Station 450.

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

data_processing:
Data were processed using the Partek Genomics Suite software and RMA normalized.
probe group file: MoEx-1_0-st-v1.r2.clf
MoEx10stv1_Mm_REFSEQ.cdf

source_name: Gli1CreER/WT; Smoflox/flox bladder

label_protocol: Ambion WT Expression kit was used to generate ssDNA targets. Fragmentation and biotin-labeling were performed using Afymetrix WT Terminal Labeling and Hybridization kit.

growth_protocol: Mice were injected with Tamoxifen daily for 3 days when they were 8 weeks old. BBN-containing water was provided to the mice ad libitum after the last tamoxifen injection, and the mice were sacrificed after 2 months.

extract_protocol: RNA was extracted using the Qiagen RNeasy Plus Mini kit

treatment_protocol: not applicable

value: 4 months

value: bladder

value: Gli1CreER/WT; Smoflox/flox


title: SCTR-Control

description: SAMPLE 1

value: Negative control siRNA


title: Liver of S. aurata exposed to 6.8°C  [T1_CE_c]


title: Liver of S. aurata exposed to 16°C  [T1_CTRL_b]

source_name: Liver of S. aurata exposed to 16°C

value: 5 m3 circular recycling tanks an at 16 °C (control)


title: Gli1CreER/WT; Smoflox/flox BBN-treated bladder, biological rep 2

description: bladder from one mouse


title: MCF10A cells treated with MDA-MB-231 exosomes that have a Dicer antibody inside

description: MCF10A cells plus MDA-MB-231 exosomes with Dicer antibody

hyb_protocol: Samples are then hybridized onto arrays for approximately 18 hours. The arrays are then washed and stained with strepatavidin-Cy3.

scan_protocol: Standard Illumina scan array protocol

data_processing: Data was normalized using the neqc routine offered by the R package limma . Gene abundances were determined by the median of the probes per gene.

source_name: Cell lines

label_protocol: Total RNA undergoes a reverse transcription reaction to generate double-stranded cDNA. The cDNA then undergoes an in-vitro transcription reaction in which biotin-labeled cRNA is created.

treatment_protocol: Exosomes were extracted from cancer cells and added to the culture media of non-tumorigenic cells.

value: MCF10A cells

value: breast epithelial

tag: treated with


title: MCf10A cells treated with MDA-MB-231 exosomes

description: MCF10A cells plus MDA-MB-231 exosomes

value: MCf10A cells

value: MDA-MB-231 exosomes


title: MCF10A cells

description: MCF10A cells


title: Gli1CreER/WT; Smoflox/flox BBN-treated bladder, biological rep 1

description: bladder from one mouse

tag: genotype


title: MDA-MB-231 cells

description: MDA-MB-231 cells

value: Breast cancer


title: Gli1CreER/WT; Smoflox/WT BBN-treated bladder, biological rep 3

description: bladder from one mouse

source_name: Gli1CreER/WT; Smoflox/WT bladder

value: Gli1CreER/WT; Smoflox/WT


title: Liver of S. aurata exposed to 6.8°C  [T1_CE_a]

value: 120±16 g body weight; 21±1 cm total length

value: liver


title: Rx1Rx3WT 2.2Dec09.rma-gene-default-Signal

status: Public on Aug 26 2014

city: Singapore

first: Motomi

last: Osato

address: 14 Medical Drive  #12-01

department: Cancer Science Institute of Singapore

country: Singapore

institute: National University of Singapore

description: Biological replicate 2 of 3. Untreated KSL cells fromRunx1;Runx3 WT mouse

hyb_protocol: 25μl of each fragmented, biotin-labeled amplified cDNA sample is hybridised using the Affymetrix GeneChip® Hybridization Wash and Stain (HWS) Kit for ST arrays according to the manufacturer's instructions. The GeneChip® Mouse Gene 1.0 ST Array is then applied.

scan_protocol: Slides were scanned on an Affymetrix GeneChip Scanner 3000.

data_processing: Resulting data was processed using Affymetrix Expression Console software v1.0.

source_name: Rx1Rx3WT KSL cells

label_protocol: Samples were processed, labeled and fragmented using the NuGEN WT-Ovation™ Pico RNA Amplification System [Nugen, Catalog # 3300-12], WT-Ovation Exon Module [Nugen, Catalog # 2000-12] and FL-Ovation™ cDNA Biotin Module v2 [Nugen, Catalog # 4200-12] according to the manufacturer's instructions.

growth_protocol: Runx1fl/fl (ref 32), Runx3fl/fl and Mx1-Cre+ mice were backcrossed to mice in the C57BL/6 background for at least 3 generations before being used for subsequent crosses. Animals carrying both floxed Runx1 (Runx1fl/fl) and floxed Runx3 (Runx3fl/fl) allelles were crossed with a Mx1-Cre transgenic line to obtain Runx1fl/fl;Runx3fl/fl;Mx1-Cre+ mice and Runx1fl/fl;Runx3fl/fl;Mx1-Cre- littermate controls on the C57BL/6 background. To induce Cre expression in hematopoietic cells, 4-week-old mice were injected intraperitoneally with 600 µg of pIpC (Sigma-Aldrich) on 7 alternate days. Time points after pIpC induction are counted from the last day of injection. All mice were maintained in the Biological Resource Center (Biopolis, Singapore) or MD2 Vivarium (NUS, Singapore) and all animal experiments followed the guidelines set by the National Advisory Committee for Laboratory Animal Research (NACLAR).

extract_protocol: RNA was isolated using the RNeasy Micro Kit (QIAgen).

tag: strain background

tag: genotype/variation

value: wild type (littermate control); Runx1fl/fl;Runx3fl/fl;Mx1-Cre-

value: cKit+Sca1+Lin- hematopoietic stem/progenitor (KSL) cells


title: Rx1Rx3DKO 3.2Dec09.rma-gene-default-Signal

description: Biological replicate 3 of 3. Untreated KSL cells fromRunx1;Runx3 DKO mouse

source_name: Rx1Rx3DKO KSL cells

value: Runx1;Runx3 double knockout; Runx1fl/fl;Runx3fl/fl;Mx1-Cre+


title: Gli1CreER/WT; Smoflox/WT BBN-treated bladder, biological rep 2

description: bladder from one mouse


title: Rx1Rx3WT 1.2Dec09.rma-gene-default-Signal

description: Biological replicate 1 of 3. Untreated KSL cells fromRunx1;Runx3 WT mouse


title: NQO1 knockown vs control LNCaP cells Replicate 1

city: San Antonio

first: Rita

last: Ghosh

state: TX

address: 8403 Floyd Curl Drive

department: Urology

institute: University of Texas Health Science Center at San Antonio

description: Biological replicate experiment 1 of 3. NQO1 knockdwon LNCaP cells vs control LNCaP cells

hyb_protocol: 300 ng of the corresponding Cy3- and Cy5-labeled fragmented cRNA were combined and hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome Oligo Microarrays 8x60K using Agilent’s recommended hybridization chamber and oven.

scan_protocol: Fluorescence signals of the hybridized Agilent Oligo Microarrays were detected using Agilent’s DNA microarray scanner G2505C (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities and ratios (including background subtraction and normalization), rejects outliers and calculates statistical confidences (p-values).

source_name: LNCaP NQO1 knockdown cells

label_protocol: To produce Cy3- and Cy5-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: Human prostate cancer LNCaP cells were maintained in RPMI 1640 medium supplemented with 10% FBS.

extract_protocol: For the linear T7-based amplification step, 100 ng of each total RNA sample was used.

treatment_protocol: Total RNA extracted using standard RNA extraction protocols (NucleoSpin® RNA II, Macherey-Nagel).

value: LNCaP (CRL-1740)

tag: disease

value: carcinoma

value: Prostate

value: NQO1 knockown

source_name: LNCaP control cells

value: control


title: NQO1 knockown vs control LNCaP cells Replicate 2


title: Descending aorta, biological replicate 1

city: Nashville

first: David

last: Bader

address: Pierce

institute: Vanderbilt

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix mouse Gene 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using an Affymetrix high resolution GenePix 4000B scanner

data_processing: The data were analyzed with Partek Genomics Suite 6.6 software using gene expression analysis default analysis settings and RMA (Robust Multi-chip Average) as the normalization method.

source_name: Descending aorta

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: Primary tissues were obtained from wild-type mice

treatment_protocol: No treatment

value: wild-type

value: 13.5 days postcoitum

value: Descending aorta


title: Descending aorta, biological replicate 2


title: Superior Mesenteric Artery, biological rep3

source_name: Superior Mesenteric Artery

value: 8 wks old

value: Superior Mesenteric Artery


title: Gli1CreER/WT; Smoflox/WT BBN-treated bladder, biological rep 1

description: bladder from one mouse

value: 4 months

value: bladder


title: Superior Mesenteric Artery, biological rep2


title: Descending aorta, biological replicate 3


title: Ascending aorta, biological replicate 1

source_name: Ascending aorta

value: Ascending aorta


title: Coronary artery, biological rep3

source_name: Coronary artery

value: Coronary artery


title: Rx1Rx3DKO 1.2Dec09.rma-gene-default-Signal

description: Biological replicate 1 of 3. Untreated KSL cells fromRunx1;Runx3 DKO mouse


title: Ascending aorta, biological rep3


title: Rx1Rx3WT 3.2Dec09.rma-gene-default-Signal

description: Biological replicate 3 of 3. Untreated KSL cells fromRunx1;Runx3 WT mouse

value: wild type (littermate control); Runx1fl/fl;Runx3fl/fl;Mx1-Cre-


title: Descending aorta, biological rep2


title: Superior Mesenteric Artery, biological rep1


title: Coronary artery, biological rep2


title: Ascending aorta, biological replicate 3


title: Coronary artery, biological rep1


title: Descending aorta, biological rep1


title: NQO1 knockown vs control LNCaP cells Replicate 3


title: Descending aorta, biological rep3


title: Ascending aorta, biological rep1


title: Rx1Rx3DKO 2.2Dec09.rma-gene-default-Signal

description: Biological replicate 2 of 3. Untreated KSL cells fromRunx1;Runx3 DKO mouse

value: cKit+Sca1+Lin- hematopoietic stem/progenitor (KSL) cells


title: Ascending aorta, biological replicate 2


title: TSP-null-water, biological rep3

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

description: gene expression data from colon of TSP-deficient mouse that drank water only

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

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

data_processing: Further statistical analysis of the CEL files was done using GeneSpring GX 11 software. Signals were quantile normalized using PLIER16 algorithm and base line transformed to the median of all samples. The log2 normalized signal values were then filtered to remove entities that show signal in the bottom 20th percentile across all samples. This list was further filtered to only include entities where at least 1 out of 8 conditions have CV < 10%. The list was then subjected to ANOVA with Benjamini-Hochberg False Discovery Rate correction (p < .05) applied. A 1.5-fold filter was applied to identify genes that are differentially expressed between any two specific conditions.

source_name: TSP-null-water

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

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

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

treatment_protocol: Except for the controls, a final concentration of 2.5% DSS was added to the drinking water of all treatment groups for 7 consecutive days. TSP-1 peptides (3TSR, TSR2, TSR2+RFK) were injected subcutaneously in respective TSR-treated mice.

value: colon

value: TSP-null


title: Ascending aorta, biological rep2


title: Wt, DSS treated, biological rep3

description: gene expression data from colon of WT mouse treated with DSS only

source_name: Wt, DSS treated

value: Wild-type


title: Wt, DSS treated, biological rep1


title: DSS-treated TSP-null, biological rep2

description: gene expression data from colon of TSP-deficient mouse treated with DSS.

source_name: DSS-treated TSP-null


title: Wt, DSS-saline treated, biological rep3

description: gene expression data from colon of WT mouse treated with DSS and saline

source_name: Wt, DSS-saline treated


title: Wt, DSS-TSR+RFK treated, biological rep2

description: gene expression data from colon of WT mouse treated with DSS and TSR2+RFK

source_name: Wt, DSS-TSR+RFK treated


title: Wt, water control, biological rep3

description: gene expression data from colon of WT mouse, water control

source_name: Wt, water control


title: Wt, DSS-saline treated, biological rep1


title: Wt, water control, biological rep1


title: B 71N

city: Hyderabad

first: Lekha

middle: Dinesh

last: Kumar

state: Andhra Pradesh

address: Uppal road, habshiguda

department: Cancer biology

country: India

institute: Centre for cellular and molecular biology

description: Biological Replicate 3 of 3 Adjacent Normal (AN) Stage II Grade 2

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA array version 11.0 (Exiqon, Denmark) following manufacturer's instructions usign Tecan HS4800 hybridization station (Tecan, Austria). After hybridization the slides were scanned and stored in an ozone free environment (ozon level below 2.0 ppb) in order to prevent potential bleaching of the flourescent dyes.

scan_protocol: Scanned on an Agilent G2565BA Microarray scanner. Image analysis was carried out using the ImaGene 8.0 software (BioDiscovery,Inc.,USA).

data_processing: Background corrected (Normexp with offset value 10 – Ritchie et al.,2007) and normalized using Lowess regression algorithm.

source_name: AN stage II Grade 2

label_protocol: One µg total RNA from sample and reference was labelled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark).

extract_protocol: Total RNA was extracted using mirVana™ miRNA isolation kit following manufacturer's instructions.

value: adjacent normal

value: Epithelial Tissue

source_name: Common reference pool

tag: sample type

value: Reference RNA


title: Wt, DSS-TSR2 treated, biological rep4

description: gene expression data from colon of WT mouse treated with DSS and TSR2

source_name: Wt, DSS-TSR2 treated


title: Wt, DSS-TSR2 treated, biological rep1


title: DSS-treated TSP-null, biological rep1


title: Wt, DSS-saline treated, biological rep2


title: Wt, DSS treated, biological rep2


title: TSP-null-water, biological rep2


title: Wt, DSS-TSR+RFK treated, biological rep4


title: DSS-treated TSP-null, biological rep3


title: Wt, water control, biological rep2


title: Wt, DSS-TSR2 treated, biological rep3


title: Wt, DSS-TSR+RFK treated, biological rep3


title: Wt, DSS-TSR2 treated, biological rep2


title: Wt, DSS-3TSR treated, biological rep4

description: gene expression data from colon of WT mouse treated with DSS and 3TSR

source_name: Wt, DSS-3TSR treated


title: Wt, DSS-3TSR treated, biological rep3


title: Wt, DSS-3TSR treated, biological rep1


title: Wt, DSS-saline treated, biological rep4


title: TSP-null-water, biological rep1


title: Wt, DSS-3TSR treated, biological rep2


title: Wt, DSS-TSR+RFK treated, biological rep1


title: B 83N

description: Biological Replicate 1 of 3 Adjacent Normal (AN) Stage II Grade 2


title: B 146N

description: Biological Replicate 2 of 3 Adjacent Normal (AN) Stage III Grade 3

source_name: AN Stage III Grade 3


title: B 66N

description: Biological Replicate 1 of 3 Adjacent Normal (AN) Stage III Grade 3


title: B 55

description: Biological Replicate 5 of 5 Stage II Grade 2

source_name: stage II Grade 2

value: stage II Grade 2


title: B 83

description: Biological Replicate 4 of 5 Stage II Grade 2


title: B 63N

description: Biological Replicate 3 of 3 Adjacent Normal (AN) Stage III Grade 3


title: B 12

description: Biological Replicate 3 of 5 Stage II Grade 2


title: B 146

description: Biological Replicate 5 of 5 Stage III G 3

source_name: stage III Grade 3

value: stage III Grade 3


title: B 71

description: Biological Replicate 2 of 5 Stage II Grade 2


title: B 80

description: Biological Replicate 4 of 5 Stage III G 3


title: B 75

description: Biological Replicate 1 of 5 Stage II Grade 2


title: B 10

description: Biological Replicate 1 of 5 Stage III G 3


title: Case 3: lenalidomide resistant clinically (cultured with lenalidomide)

city: Be'er Yacob

first: Yossi

last: Cohen

state: Zerifin

address: Assaf Harofhe, Institute of Hematology

department: Hematology

institute: Asaf Harofhe Hospital

hyb_protocol: Biotin-labeled cRNA was hybridized onto 1.0 ST Expression Bead Chips

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner.

data_processing: The data were analyzed Affymetrix gene expression command console and normalized with RMA.

source_name: cultured bone marrow_lenalidomide resistant_lenalidomide

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Cultured bone marrow cells were grown in high cell density imposing cell-cell contact

extract_protocol: Frozen samples were lyzed by adding 300 µl lysis buffer to tubes. RNA was isolated by MagNA Pure LC RNA Isolation procedure using MagNA Pure instrument (Roche). Integrity of RNA was examined by Agilent 2100 Bioanalyzer.

treatment_protocol: Thalidomide (0.8 µg/ml), lenalidomide (0.5 µg/ml) or DMSO (control) was added to the cultured bone marrow samples for 24 hour incubation.

value: cultured bone marrow

tag: drug treatment

value: lenalidomide


title: B 63

description: Biological Replicate 2 of 5 Stage III G 3


title: Case 2: lenalidomide resistant clinically (cultured with DMSO)

source_name: cultured bone marrow_lenalidomide resistant_DMSO

value: control


title: Case 1: lenalidomide-responsive clinically (cultured with lenalidomide)


title: Ogg1-RNAi/8-oxoguanine challenge 2

city: Galveston

first: Istvan

last: Boldogh

state: Texas

address: 301 UNIVERSITY BLVD.

department: Microbiology & Immunology

institute: UNIVERSITY OF TEXAS MEDICAL BRANCH

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of five housekeeping genes: Gusb, Hprt, Hsp90ab1, Gapdh, Actb.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports test/control (i.e., Saline/Control-RNAi-Glucose oxidase challenge) ratios.

label: SYBR Green

source_name: Lung lysate

label_protocol: PCR assays were performed using the Mouse Inflammatory Cytokines & Receptors PCR array PAMM-011A (SA Biosciences, Frederick, MD) following the Manufacturer’s instructions. Reverse transcription was performed from 1µg total RNA using the Superscript® IIIFirst Strand Synthesis System (Invitrogen)

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

treatment_protocol: Control-RNAi and Ogg1-RNAi groups were challenged intranasally 2 times (0h and 24 h) with the corresponding RNAi prior to glucose oxidase or 8-oxoguanine challenge.

tag: gender

value: Female

value: 5-6 weeks old

value: Balbc J

value: RNAi to 8-oxoguanine DNA glycosylase (Ogg1) intranasally prior to the exposure for 1 h to OGG1-BER product 8-oxoguanine (1 uM)


title: Case 3: lenalidomide resistant clinically (cultured with DMSO)


title: B 66

description: Biological Replicate 3 of 5 Stage III G 3


title: Ulk1/2-/- + IFNβ 1

first: Pawel

last: Lisowski

address: Hannoversche Str. 28

institute: Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association

description:
SAMPLE 10
replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile method with the Illumina function provided by beadarray Bioconductor package

source_name: MEFs

label_protocol: Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Life Technologies) according to the manufacturer’s protocol and starting with 150 ng of total RNA

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (QIAGEN) per the manufacturer’s instructions. Quantity and quality of each RNA sample was assessed using Nanodrop and Bioanalyzer (Agilent)

treatment_protocol: 6 hours treatment with mouse IFNβ (2500 IU/ml)

value: embryonic fibroblasts

tag: agent

value: IFNβ


title: Ulk1/2-/- + IFNβ 3

description:
SAMPLE 12
replicate 3

tag: cell type


title: Case 2: lenalidomide resistant clinically (cultured with lenalidomide)


title: Ulk1/2-/- + IFNβ 2

description:
SAMPLE 11
replicate 2


title: Ulk1/2-/- (untreated) 2

description:
SAMPLE 8
replicate 2

value: untreated


title: Saline challenge 2

description: Control 2

tag: treatment

value: saline


title: Case 1: lenalidomide-responsive clinically (cultured with DMSO)


title: Ulk1/2-/- (untreated) 1

description:
SAMPLE 7
replicate 1


title: Ulk1/2+/+ + IFNβ 2

description:
SAMPLE 5
replicate 2


title: Ulk1/2+/+ + IFNβ 3

description:
SAMPLE 6
replicate 3


title: Case 1: lenalidomide-responsive clinically (cultured with thalidomide)

value: thalidomide


title: Control-RNAi/8-oxoguanine challenge 1

description: Test

value: control RNAi intranasally prior to the exposure for 1 h to OGG1-BER product 8-oxoguanine (1 uM)


title: Ulk1/2-/- (untreated) 3

description:
SAMPLE 9
replicate 3


title: Ulk1/2+/+ (untreated) 2

description:
SAMPLE 2
replicate 2


title: Control-RNAi/Glucose oxidase challenge 1

description: Test

value: control RNAi intranasally prior to the exposure for 1 h to glucose oxidase (1 mU)


title: Saline challenge 1

description: Control 1


title: Ulk1/2+/+ (untreated) 1

description:
SAMPLE 1
replicate 1


title: Ulk1/2+/+ + IFNβ 1

description:
SAMPLE 4
replicate 1


title: BMMCs from NTAL WT, pLKO.1 infected, 2 h activated, biological rep3

city: Prague

first: Iva

last: Polakovicova

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics ASCR

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneTitan HT_MG-430_PM 24-Array Plate. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 gene chip scanner with GCOS 1.4.

data_processing: The data were analyzed with Genomic Suite Software Partek version 6.4 (6.09.0602) using the RMA algorithm.

source_name: BMMC, WT pLKO.1, activated

label_protocol: Affymetrix standard methods were applied using the high throughput protocol for PM arrays.

growth_protocol: Bone marrow derived mast cells (BMMCs) were isolated from femurs and tibias of 8 weeks old KO or WT mice of the same littermate  on C57BL/6 background, cultured in mast cell growth media supplemented with IL-3 and SCF for 8 weeks to obtain fully differentiated mast cells.

extract_protocol: RNA was extracted using RNeasy kit (QIAGEN) according to a manufacturer’s protocol.

treatment_protocol: Cells with stable NTAL KD were prepared by lentiviral infection of  NTAL shRNA TRCN0000127243 in pLKO.1 vector into wild type BMMCs, followed by selection in puromycin. As a negative control to these KDs, wild type BMMCs infected with empty pLKO.1 vector and selected in puromycin were used.  All four types of cells were sensitized in the medium without IL-3 and SCF supplemeted with IgE (IGEL b4 1 mAB; 1 µg/ml) for 4 hours and then half of the cells was activated with antigen (100 ng/ml TNP-BSA) for 2 hours, the other part remained nonactivated.

value: bone marrow derived mast cells

value: NTAL wild type

tag: genetic background

value: lentiviral infection

tag: vector

tag: activation

value: 2 h 100 ng/ml TNP-BSA


title: BMMCs from NTAL WT, pLKO.1 infected, 2 h activated, biological rep2


title: Ogg1-RNAi/Glucose oxidase challenge 2

description: Test

value: RNAi to 8-oxoguanine DNA glycosylase (Ogg1) intranasally prior to the exposure for 1 h to glucose oxidase (1 mU)


title: BMMCs from NTAL WT, NTAL shRNA infected, 2 h activated, biological rep2

source_name: BMMC, NTAL KD, activated

value: lentiviral infection - NTAL knock down


title: Amycolatopsis_WT_T5A

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

description: Wild type A. mediterranei S699 (WT)

hyb_protocol: The labeled cDNAs were then hybridized for 16 h at 50°C on individual GeneChips. After hybridization, GeneChips were washed and stained with streptavidin-conjugated phycoerythrin by using the Fluidic Station FS450 (Affymetrix) following the FS450_0005 Protocol. Fluorescent images of the microarrays were acquired using a GeneChip Scanner 3000 (Affymetrix).

scan_protocol: Chips were scanned through GeneArray Scanner 3000 7G (Affymetrix) at an emission wavelenght of 560nm.

data_processing: The quality of the raw data obtained from microarray hybridization was assessed considering the MAS5.0 (Microarray Suite/Software, Affymetrix) control parameters after a global scaling at a target intensity of 100. Quality and control parameters as well as box plots of raw intensities indicated the overall high quality of the data set and the absence of any outlying sample. Probe level data was converted to expression values using the Robust Multi-array Average (RMA) procedure. Genes characterized by a statistically significant modulation of the expression level during the growth time course (within-class temporal differential expression) were identified using the EDGE software package, which is based on the Optimal Discovery Procedure and allows identifying genes that are differentially expressed between two or more different biological conditions or to perform significance analysis on time course experiments

organism: Amycolatopsis mediterranei S699

source_name: Wild type, 72h

label_protocol: The protocol consists in cDNA synthesis by reverse transcription (starting with 10 µg RNA), followed by cDNA fragmentation with DNase I and labeling with Terminal Deoxynucleotidyl Transferase.

growth_protocol: For shake-flask experiments, vegetative mycelium was used to inoculate 500 ml baffled Erlenmeyer flask containing 50 ml of the modified RFB 2244 liquid media (50 g defatted soybean meal, 50 g D(+)-glucose monohydrate, 10 g propylene glycol, 5 g (NH4)2SO4, 1 g KH2PO4, 5 g CaCO3, 1 g MgSO4 • 7H2O, 0.01 g FeSO4 • 7H2O, 0.0033 g CuSO4 • 5H2O, 0.05 g ZnSO4 • 7H2O, 0.004 MnSO4 • 5H2O, CoCl2 • 6H2O, (NH4)6Mo7O24 • 4H2O, 4 ml silicon antifoam reagent). Cultures were incubated at 28°C with shaking at 250 rpm. For bioreactor experiments, culture were pre-inoculated in Erlenmeyer flasks and grown for 120 h; then they were inoculated into bioreactors at 10% inoculum density.

extract_protocol: For each time point, RNA was extracted from mycelium pellets deriving from 1-ml culture samples using the GeneElute™ total RNA Purification Kit (SIGMA), recovering it in 50 µl of Elution Solution. After extraction RNAs were quantified with a NanoDrop spectrophotometer (NanoDrop Technologies) and analyzed by capillary electrophoresis on a Agilent Bioanalyzer (Agilent). The RNA samples showing an RIN (RNA Integrity Number, a quality parameter calculated by the instrument software) value higher than 7 were processed for microarray hybridization,

tag: phenotype

value: wild type rifamycin B producer

tag: time


title: Amycolatopsis_WT_T5B

description: Wild type A. mediterranei S699 (WT)


title: Ulk1/2+/+ (untreated) 3

description:
SAMPLE 3
replicate 3

tag: strain


title: BMMCs from NTAL WT, NTAL shRNA infected, 2 h activated, biological rep3


title: BMMCs from NTAL KO, noninfected, 2 h activated, biological rep3

source_name: BMMC, NTAL KO, activated

value: NTAL knock out


title: Amycolatopsis_WT_T4A

description: Wild type A. mediterranei S699 (WT)

source_name: Wild type, 60h


title: Amycolatopsis_WT_T3B

description: Wild type A. mediterranei S699 (WT)

source_name: Wild type, 48h


title: Sf21_mock_rep4

city: 6th of october

first: Tamer

middle: Zaki

last: Salem

state: Giza

address: Shiekh Zayed

department: Biomedical sciences

country: Egypt

institute: Zewail city of science and technology

description:
Sf21_13
Gene expression of mock-infected cells.

hyb_protocol: The hybridization was performed at 65 for 19 hours. Then the slides were washed and handled according to the protocol (One-Color Microarray-based Gene Expression Analysis, Agilent).

scan_protocol: The microarray slides were scanned by Agilent scanner (Agilent’s G2505B Array Scanner).

data_processing: The data were extracted by Agilent Feature Extraction Software (v8.1). Quality Control (QC) reports were verified for all the arrays before the data analysis. Then GeneSpring GX11 software (Agilent) was used to analyze the data. The data was normalized by a shift to the 75th percentile followed by median baseline subtraction for each of the arrays. The level of gene expression was calculated as fold change and only genes whose level of expression changed with more than 1.2 fold and with a p<0.05 were considered for the analysis. This was performed by One-Way ANOVA (GeneSpring GX11software, Agilent).

organism: Spodoptera frugiperda

source_name: Sf21 cells, mock infection

label_protocol: One-Color Spike-in Mix was added to 500 ng of total RNA and the cRNAs were synthesized for mock infection and for three AcMNPV-infected samples (6, 12, 24 h.p.i.) following the recommended methods described in One-Color Microarray-Based Gene Expression Analysis manual (Agilent). Complementary RNAs were purified by RNeasy Mini Kits (Qiagen) and quantified by NanoDrop ND1000 (Thermo Scientific). Approximately, 1.65 µg of each of the Cy3-labeled linearly amplified cRNAs were fragmented by the fragmentation mix and applied to the microarrays for hybridization.

growth_protocol: Sf21 cells were maintained in TC-100 medium at 27 °C. Cells were split twice a week and cell viability was above 95%.

extract_protocol: Total RNA were purified by RNeasy Mini Kits (Qiagen) according to the manual. The quality of total RNA were assessed by Agilent 2100 Bioanalyzer using Agilent RNA 6000 Nano LabChip kit.

treatment_protocol: A total of 2 x 10^6 Sf21 cells were seeded into 60mm dish and infected with either TC-100 medium (Mock-infection) or wild-type AcMNPV strain L1 at MOI of 10. Cells were collected at 6 h, 12 h, and 24 h post-infection. Mock-infection cells were collected at 12 h. Four biological repeats were set up for each time point and mock-infection.

tag: cell line

value: ovary cell line

value: mock infection

tag: time point

value: 12 hpi

tag: replicate


title: Sf21_AcMNPV_24hpi_rep2

description:
Sf21_12
Gene expression of AcMNPV-infected cells at 24 hpi.

source_name: Sf21 cells, AcMNPV infection, 24hpi

value: Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) infection

value: 24 hpi


title: Amycolatopsis_WT_T4B

description: Wild type A. mediterranei S699 (WT)


title: Amycolatopsis_WT_T3A

description: Wild type A. mediterranei S699 (WT)


title: Sf21_AcMNPV_12hpi_rep4

description:
Sf21_11
Gene expression of AcMNPV-infected cells at 12 hpi.

source_name: Sf21 cells, AcMNPV infection, 12hpi


title: BMMCs from NTAL WT, pLKO.1 infected, 2 h activated, biological rep1

tag: genotype


title: Sf21_AcMNPV_12hpi_rep3

description:
Sf21_8
Gene expression of AcMNPV-infected cells at 12 hpi.


title: Sf21_mock_rep3

description:
Sf21_10
Gene expression of mock-infected cells.


title: BMMCs from NTAL WT, noninfected, 2 h activated, biological rep2

source_name: BMMC, WT, activated


title: BMMCs from NTAL WT, noninfected, 2 h activated, biological rep3


title: BMMCs from NTAL WT, NTAL shRNA infected, 2 h activated, biological rep1


title: Sf21_AcMNPV_6hpi_rep4

description:
Sf21_14
Gene expression of AcMNPV-infected cells at 6 hpi.

source_name: Sf21 cells, AcMNPV infection, 6hpi

value: 6 hpi


title: Sf21_AcMNPV_24hpi_rep1

description:
Sf21_9
Gene expression of AcMNPV-infected cells at 24 hpi.


title: BMMCs from NTAL KO, noninfected, 2 h activated, biological rep1


title: Amycolatopsis_WT_T2B

description: Wild type A. mediterranei S699 (WT)

source_name: Wild type, 36h


title: Amycolatopsis_WT_T1B

description: Wild type A. mediterranei S699 (WT)

source_name: Wild type, 24h


title: Amycolatopsis_HP-130_T5B

description: improved rifamycin B producer (HP-130)

source_name: improved rifamycin B producer, 72h

value: improved rifamycin B producer


title: BMMCs from NTAL WT, pLKO.1 infected, nonactivated, biological rep3

source_name: BMMC, WT pLKO.1, nonactivated


title: BMMCs from NTAL WT, pLKO.1 infected, nonactivated, biological rep2


title: BMMCs from NTAL WT, NTAL shRNA infected, nonactivated, biological rep2

source_name: BMMC, NTAL KD, nonactivated


title: Amycolatopsis_WT_T1A

description: Wild type A. mediterranei S699 (WT)


title: Sf21_AcMNPV_6hpi_rep2

description:
Sf21_5
Gene expression of AcMNPV-infected cells at 6 hpi.


title: BMMCs from NTAL WT, pLKO.1 infected, nonactivated, biological rep1


title: Sf21_AcMNPV_6hpi_rep3

description:
Sf21_7
Gene expression of AcMNPV-infected cells at 6 hpi.


title: Amycolatopsis_HP-130_T5A

description: improved rifamycin B producer (HP-130)


title: Amycolatopsis_WT_T2A

description: Wild type A. mediterranei S699 (WT)


title: Sf21_mock_rep2

description:
Sf21_4
Gene expression of mock-infected cells.


title: Sf21_AcMNPV_6hpi_rep1

description:
Sf21_2
Gene expression of AcMNPV-infected cells at 6 hpi.


title: Amycolatopsis_HP-130_T3A

description: improved rifamycin B producer (HP-130)

source_name: improved rifamycin B producer, 48h


title: Amycolatopsis_HP-130_T4B

description: improved rifamycin B producer (HP-130)

source_name: improved rifamycin B producer, 60h


title: B 75N

description: Biological Replicate 2 of 3 Adjacent Normal (AN) Stage II Grade 2

source_name: AN stage II Grade 2

value: adjacent normal

tag: tissue

value: Epithelial Tissue

source_name: Common reference pool

value: Reference RNA


title: Sf21_AcMNPV_12hpi_rep2

description:
Sf21_6
Gene expression of AcMNPV-infected cells at 12 hpi.


title: BMMCs from NTAL WT, NTAL shRNA infected, nonactivated, biological rep3

value: bone marrow derived mast cells

value: NTAL wild type


title: BMMCs from NTAL KO, noninfected, nonactivated, biological rep2

source_name: BMMC, NTAL KO, nonactivated


title: Amycolatopsis_HP-130_T4A

description: improved rifamycin B producer (HP-130)


title: BMMCs from NTAL KO, noninfected, nonactivated, biological rep3


title: Amycolatopsis_HP-130_T3B

description: improved rifamycin B producer (HP-130)


title: Sf21_AcMNPV_12hpi_rep1

description:
Sf21_3
Gene expression of AcMNPV-infected cells at 12 hpi.


title: BMMCs from NTAL WT, NTAL shRNA infected, nonactivated, biological rep1


title: BMMCs from NTAL WT, noninfected, nonactivated, biological rep3

source_name: BMMC, WT, nonactivated


title: BMMCs from NTAL WT, noninfected, nonactivated, biological rep2


title: BMMCs from NTAL KO, noninfected, nonactivated, biological rep1


title: Amycolatopsis_HP-130_T1A

description: improved rifamycin B producer (HP-130)

source_name: improved rifamycin B producer, 24h


title: Sf21_mock_rep1

description:
Sf21_1
Gene expression of mock-infected cells.

source_name: Sf21 cells, mock infection


title: Amycolatopsis_HP-130_T2B

description: improved rifamycin B producer (HP-130)

source_name: improved rifamycin B producer, 36h


title: Amycolatopsis_HP-130_T1B

description: improved rifamycin B producer (HP-130)


title: Amycolatopsis_HP-130_T2A

description: improved rifamycin B producer (HP-130)


title: f-MDSC, transwell replicate 7

description: Gene expression data of CD33+IL4Ra+ sorted cell after in vitro co-culture with autologus PHA activated CD3+ T cells in transwell condition

hyb_protocol: GeneChip® Hybridization, Wash, and Stain Kit - Following labeling, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 2.0 ST arrays. GeneChips were washed and stained (streptavidin,R-phycoerythrin conjugate and biotinylated anti-streptavidin) in the Affymetrix Fluidics Station 400.

scan_protocol: Standard Affymetrix scanning procedures on a GeneChip® Scanner 3000 7G . Affymetrix GeneChip® Command Console® Software (AGCC)- used to view CEL file images.

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

source_name: UCB derived CD33+IL4Rα+ after 3 days with autologus PHA activated CD3+T cells in transwell condition

label_protocol: Affymetrix GeneChip WT Terminal Labeling Kit - sense-strand cDNA is fragmented with a combination of uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1 and its yield is further labeled by terminal deoxynucleotidyl transferase (TdT) with the Affymetrix® proprietary DNA Labeling Reagent that is covalently linked to biotin.

growth_protocol: Human Umbilical cord blood (UCB) samples underwent Ficoll-Paque gradient separation and ACK red cell lysis, and then were cultured for 4 days in the presence of GM-CSF and G-CSF (40ng/ml).  CD33 and IL-4Rα positive cells were sterilely sorted, part of the cells stored for RNA extraction, and part co-cultured for 3 days with autologous PHA activated CFSE labeled CD3+ T cells either in cell to cell contact (CONTACT) or using a transwell device to avoid cell contact (TRANSWELL). HEK-293 cells were maintained in complete RPMI-140 10% FBS.

extract_protocol: RNA was purified using the miRNA easy kit from Qiagen and following the manufacture instruction.

treatment_protocol: Sterilely sorted CD33 and IL-4Rα positive cells before and after been co-culture with autologous CD3+ T cells were lysed with TRIZOL and stored at -80◦C till RNA extraction was performed. TRIZOL samples preservation was also used for the control cells line HEK-293.

value: After co-culture in transwell

tag: cell state

value: No activated by T cells contact


title: f-MDSC, transwell replicate 6

value: UCB derived CD33+IL4Rα+ after 3 days with autologus PHA activated CD3+T cells in transwell condition


title: Gammadelta_LoIncidence_Unstim_rep4

city: San Francisco

first: Charlie

address: 1001 Potrero Ave

department: Medicine

institute: University of California, San Francisco

description: Gene expression in Vdelta2+ gammadelta T cells after incubation without stimulation

hyb_protocol: 1.5 ug of Cy3-labeled aRNA was fragmented and hybridized to Agilent 8x60k mouse gene expression microarrays as per manufacturer instructions.

scan_protocol: Arrays were scanned on an Agilent scanner at 3 um resolution as 20-bit TIFF images.

data_processing: Features were extracted using Agilent Feature Extraction software. Non-background subtracted raw Cy3 intensities were taken as gene expression values and quantile normalized.

source_name: Gammadelta T cells, low incidence, unstimulated, replicate 4

label_protocol: Aminoallyl-incorporated aRNA was conjugated to Cy3 dye (Life Technologies) for 1 h in sodium bicarbonate buffer and cleaned up on a spin column.

growth_protocol: PBMCs were isolated from Ugandan children over Ficoll-Histopaque and cryopreserved in liquid nitrogen.

extract_protocol: RNA was isolated with the RNAqueous Micro kit (Life Technologies).  Isolated RNA was amplified using the Aminoallyl MessageAmp II kit (Life Technologies).

treatment_protocol: PBMCs were thawed, rested overnight, and co-incubated with P. falciparum-infected red blood cells for 6 hours, followed by FACS isolation of the Vdelta2+ subset of gammadelta T cells.

tag: cells

value: Vdelta2+ gammadelta T cells

value: Unstimulated

tag: incidence

value: low


title: HEK-293 cell line, replicate 2

institute: University of Padova

description: Gene expression data of HEK-293 control cell line used as steric embrance in the suppressive assay

source_name: HEK-293 cell line ATCC # CRL-1573

value: Control cell line

value: untreated

value: HEK-293 cell line ATCC # CRL-1573


title: f-MDSC, transwell replicate 2


title: f-MDSC, transwell replicate 5


title: Irf8KO_cMoPs_exp2

city: Yokohama

first: Tomohiko

last: Tamura

address: 3-9 Fukuura, Kanazawa-ku

department: Department of Immunology

country: Japan

institute: Yokohama City University

hyb_protocol: Slides were hybridized according to the manufacturer's protocol (One-Color Microarray-Based Gene Expression Analysis Protocol, Product # G4140-90040, Version 6.5, May 2010).

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-60502) at 100% in Green channel, with a scan resolution of 3 um.

data_processing: Data are extracted with Agilent Feature Extraction Software and normalized.

source_name: Irf8KO cMoPs, isolated from bone marrow cells, experiment 2

label_protocol: Total RNA was labeled using the Agilent Low Input Quick Amp Labeling Kit according to the manufacturer's instructions.

growth_protocol: 32D.cl3 cells were cultured with WEHI3B conditioned medium.

extract_protocol: Total RNA was extracted using RNeasy Micro Kit (Qiagen) according to the manufacturers' instructions.

treatment_protocol: 32Dcl.3 cells were transduced with retroviral vectors by spinoculation.

value: Bone marrow derived cMoPs

value: Primary isolated cells

tag: plasmids used for transduction


title: Gammadelta_HiIncidence_Unstim_rep3

source_name: Gammadelta T cells, high incidence, unstimulated, replicate 3

value: high


title: Gammadelta_LoIncidence_Unstim_rep3

source_name: Gammadelta T cells, low incidence, unstimulated, replicate 3


title: Gammadelta_HiIncidence_Unstim_rep1

source_name: Gammadelta T cells, high incidence, unstimulated, replicate 1


title: f-MDSC, transwell replicate 3

tag: cell type


title: f-MDSC, transwell replicate 1

tag: treatment


title: WT_cMoPs_exp2

source_name: WT cMoPs, isolated from bone marrow cells, experiment 2


title: Gammadelta_HiIncidence_Unstim_rep2

source_name: Gammadelta T cells, high incidence, unstimulated, replicate 2


title: colon cancer 19

city: Guangzhou

first: Lekun

last: Fang

address: Yuancunerheng Road

institute: Sun Yat-sen University

description: Gene expression data from colon cancer 19 of resistance

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 NexusExp3 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: colon cancer patient 19-r

growth_protocol: snap-frozen tissue samples were obtained from 20 colorectal cancer (CRC) patients during the surgery

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

treatment_protocol: colon cancer samples were harvested and treated with Trizol

tag: group

value: RFS<3 years


title: colon cancer 16

description: Gene expression data from colon cancer 16 of resistance

source_name: colon cancer patient 16-r


title: Gammadelta_HiIncidence_Unstim_rep4

source_name: Gammadelta T cells, high incidence, unstimulated, replicate 4


title: BMMCs from NTAL WT, noninfected, nonactivated, biological rep1

tag: genetic background

tag: vector


title: colon cancer 20

description: Gene expression data from colon cancer 20 of resistance

source_name: colon cancer patient 20-r


title: Refractory anemia with excess of blasts type II (patient 1)

type: genomic

city: Perugia

first: Cristina

last: Mecucci

address: Santa Maria della Misericordia University Hospital

institute: University of Perugia

description: acute leukemia

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics station 450, and scanned using the Gene Chip Scanner 3000 7G.

data_processing: The array image was acquired using Affymetrix GeneChip® Command Consolle  (AGCC) Software. Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using Chromosome Analysis Suite Software (ChAS) 2.0 software.

molecule: genomic DNA

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Leukemic cells were not grown

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations of leukemic blasts obtained from peripheral blood or bone marrow at diagnosis using classical Salting out method

tag: phenotype


title: Irf8KO_cMoPs_exp1

source_name: Irf8KO cMoPs, isolated from bone marrow cells, experiment 1


title: Gammadelta_LoIncidence_Unstim_rep2

source_name: Gammadelta T cells, low incidence, unstimulated, replicate 2


title: colon cancer 15

description: Gene expression data from colon cancer 15 of resistance

source_name: colon cancer patient 15-r


title: colon cancer 17

description: Gene expression data from colon cancer 17 of resistance

source_name: colon cancer patient 17-r


title: HEK-293 cell line, replicate 1


title: colon cancer 18

description: Gene expression data from colon cancer 18 of resistance

source_name: colon cancer patient 18-r


title: 32Dcl3_cells_IRF8-CD8+CEBPalpha-puro_day3_exp2

source_name: 32Dcl.3 cells, MSCV-IRF8-CD8 and MSCV-C/EBPalpha-puro transduced, day 3, experiment 2

value: 32Dcl.3 cells

value: 3 days after transduction


title: colon cancer 14

description: Gene expression data from colon cancer 14 of resistance

source_name: colon cancer patient 14-r


title: 32Dcl3_cells_IRF8-CD8+CEBPalpha-puro_day3_exp1

source_name: 32Dcl.3 cells, MSCV-IRF8-CD8 and MSCV-C/EBPalpha-puro transduced, day 3, experiment 1


title: f-MDSC, contact, replicate 7

description: Gene expression data of CD33+IL4Rα+ sorted cell after contact with autologus PHA activated CFSE labeled CD3+ T cells

source_name: UCB derived CD33+IL4Rα+ after 3 days in contact with autologus PHA activated CD3+T cells

value: After co-culture in contact

value: Activated by T cells contact


title: BMMCs from NTAL WT, noninfected, 2 h activated, biological rep1

source_name: BMMC, WT, activated,

value: bone marrow derived mast cells

value: NTAL wild type

tag: activation

value: 2 h 100 ng/ml TNP-BSA


title: f-MDSC, contact, replicate 5

value: UCB derived CD33+IL4Rα+ after 3 days in contact with autologus PHA activated CD3+T cells


title: 32Dcl3_cells_IRF8-CD8+MSCV-puro_day3_exp2

source_name: 32Dcl.3 cells, MSCV-IRF8-CD8 and empty MSCV-puro transduced, day 3, experiment 2

value: MSCV-IRF8-IRES-hCD8t + Empty MSCV-IRES-puro


title: f-MDSC, contact, replicate 3


title: f-MDSC, contact, replicate 4


title: Gammadelta_LoIncidence_Stim_rep4

description: Gene expression in Vdelta2+ gammadelta T cells after Pf iRBC stimulation

source_name: Gammadelta T cells, low incidence, iRBCs, replicate 4

value: Vdelta2+ gammadelta T cells

value: P. falciparum-infected red blood cells

value: low


title: 32Dcl3_cells_MSCV-CD8+CEBPalpha-puro_day3_exp2

source_name: 32Dcl.3 cells, empty MSCV-CD8 and MSCV-C/EBPalpha-puro transduced, day 3, experiment 2

value: Empty MSCV-IRES-hCD8t + MSCV-C/EBPalpha-IRES-puro


title: 32Dcl3_cells_IRF8-CD8+MSCV-puro_day3_exp1

source_name: 32Dcl.3 cells, MSCV-IRF8-CD8 and empty MSCV-puro transduced, day 3, experiment 1


title: f-MDSC, contact, replicate 2


title: f-MDSC, contact, replicate 6


title: Gammadelta_HiIncidence_Stim_rep1

source_name: Gammadelta T cells, high incidence, iRBCs, replicate 1


title: colon cancer 12

description: Gene expression data from colon cancer 12 of sensitive

source_name: colon cancer patient 12

value: RFS>3 years


title: colon cancer 13

description: Gene expression data from colon cancer 13 of sensitive

source_name: colon cancer patient 13


title: colon cancer 11

description: Gene expression data from colon cancer 11 of sensitive

source_name: colon cancer patient 11