title: HepG2_DMSO_with_cytokines_6h_exp3

description:
DMSO+_6h_exp3: Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone with cytokines
Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone with cytokines


title: HepG2_Nimesulide_200uM_with_cytokines_6h_exp1

status: Public on Jul 29 2017

type: RNA

city: Maastricht

first: Jian

last: Jiang

address: Maastricht University

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

hyb_protocol: Individual samples were hybridized on Agilent 4×44K Whole Human Genome microarrays (G4112F; design ID 014850)

scan_protocol: Microarrays were scanned immediately after washing on an Agilent Technologies G2505C DNA Microarray Scanner. Raw data on pixel intensities were extracted from the scanned images using Agilent Feature Extraction Software (version 10.7.3.1; Agilent Technologies, Amstelveen, Netherlands) with default parameters (Protocol: GE1_107_Sep09; Grid 014850_D_F_20110325)

data_processing: All arrays were checked for their quality using ArrayQC (https://github.com/BiGCAT-UM/arrayQC_Module/), a quality control pipeline in R (version 2.10.1; The R Foundation for Statistical Computing, Vienna, Austria). For each spot the following steps were taken: local background correction, flagging of bad spots, controls and spots with too low intensity, log2 transformation, and quantile normalization. Probes with less than 30% flagged bad spots were selected, missing values were imputed by k-nearest neighbors (k-NN; k-value 15) and repeated identifiers merged.

molecule: total RNA

organism: Homo sapiens

label_protocol: 0.5 ug RNA samples were labelled with Cyanine 3 (Cy3) following the Agilent one-color Quick-Amp labeling protocol (Agilent Technologies, Amstelveen, The Netherlands)

growth_protocol: HepG2 cells were cultured in T25 flasks in the presence of minimal essential medium supplemented with 1% nonessential amino acids, 1% sodium pyruvate, 2% penicillin/streptomycin, and 10% fetal bovine serum (all from Gibco BRL, Breda, The Netherlands) at 37°C in a humidified chamber with 95%/5% air/CO2 to reach ∼ 80% confluence.

extract_protocol: Total RNA was isolated from the cells using QIAzol reagent with the RNeasy kit according to the manufacturer’s protocol. RNA concentrations were measured on a nanodrop spectrophotometer and the quality of each RNA preparation was determined with a bio-analyzer (Agilent Technologies, The Netherlands). Only samples with a good quality (clear 18S and 28S peaks and RNA integrity number>6) were used for hybridization. Extracted RNA was stored at −80°C until it was used as the template for cDNA synthesis.

treatment_protocol: HepG2 cells were exposed to Nimesulide, Nefazodone, and Trovafloxacin (idiosyncratic compounds) and Aspirin, Buspirone, and Levofloxacin (non-idiosyncratic compounds) with or without the cytokine mix (TNF 100 ng/ml + IFNγ 100 ng/ml + IL-1α 20 ng/ml + IL-6 20 ng/ml + LPS 10 µg/ml) as described previously (Cosgrove et al., 2009) for 6, 12 or 24

tag: cell line


title: HepG2_DMSO_with_cytokines_6h_exp1

description:
DMSO+_6h_exp1: Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone with cytokines
Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone with cytokines


title: HepG2_DMSO_without_cytokines_6h_exp1

description:
DMSO-_6h_exp1: Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone without cytokines
Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone without cytokines


title: HepG2_DMSO_without_cytokines_12h_exp1

description:
DMSO-_12h_exp1: Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone without cytokines
Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone without cytokines


title: HepG2_Nimesulide_400uM_without_cytokines_12h_exp1


title: HepG2_DMSO_without_cytokines_24h_exp1

description:
DMSO-_24h_exp1: Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone without cytokines
Solvent control for Nimesulide, Nefazodone, Aspirin, Buspirone without cytokines


title: BMDM_Mock8h_LPS4h_R4

status: Public on Jul 28 2017

city: TOULOUSE

first: Gilles

last: Foucras

state: Haute Garonne

address: 23 chemin des capelles

department: JRU1225 IHAP

country: France

institute: ENVT-INRA

description:
BMDM, Mock 8h, LPS 4h, Replicate 4
Gene expression in BMDM pretreated 8h with Mock and re-stimulated 4 h with LPS

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer’s instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE microarray (8X60K, Design 028005) enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 028005_D_F_20120201). All subsequent data analyses were done using GeneSpring GX software (Agilent Technologies). Briefly, all validated and normalized transcripts expression data were filtered on detected flags. Of the 55821 probes initially-contained in raw data files, 43097 entities are displayed in the submitted data table.

organism: Mus musculus

source_name: BMDM, Mock 8h, LPS 4h

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts). Dye incorporation and cRNA yield were checked with the Biospec nano spectrophotometer (Shimadzu).

growth_protocol: Myeloid cells precursors from C57BL/6 mice bone marrow were matured for 7 days (37°C, 5% CO2) in complete RPMI (containing RPMI GlutaMAX™ supplemented with 10%, heat-inactivated FBS, 1% sodium pyruvate, 1% NEAA, 100 U/mL Pen-Strep) supplemented with 30% LADMAC cell-conditioned medium (LCM) as a source of M-CSF. After differentiation, BMDM were seeded in 96-well tissue culture plates for 16 h in complete RPMI until complete adherence (37°C, 5% CO2).

extract_protocol: BMDM were lysed in RLT buffer and was subjected to RNA extraction using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. RNA was quantified with a NanoDrop®1000 spectrophotometer and quality was assessed using the Agilent RNA 6000 Nano Kit on BioAnalyzer and 2100 Expert Software (Agilent Technologies, Santa Clara, USA).

treatment_protocol: BMDM from four individuals were pretreated with 100 µg/mL of Saccharomyces cerevisiae cell wall compounds – i.e. ScCW (A), BG65 (C) or BG75 (D) - containing growing concentration of beta-glucans or Mock for 8 h in triplicate. After incubation, supernatants were removed and cells were further stimulated with 100 ng/mL of ultraPure LPS for 4 or 8 h (37°C, 5% CO2).

tag: stain

tag: gender

value: female

tag: age

value: 8 weeks

tag: cell type

value: Bone Marrow-derived Marophages

tag: pre-treatment

value: Mock

tag: treatment

value: LPS

tag: time


title: BMDM_A8h_LPS4h_R4

description:
BMDM, A 8h, LPS 4h, Replicate 4
Gene expression in BMDM pretreated 8h with A and re-stimulated 4 h with LPS

source_name: BMDM, A 8h, LPS 4h

value: A


title: BMDM_A8h_LPS8h_R4

description:
BMDM, A 8h, LPS 8h, Replicate 4
Gene expression in BMDM pretreated 8h with A and re-stimulated 8 h with LPS

source_name: BMDM, A 8h, LPS 8h


title: BMDM_D8h_LPS4h_R4

description:
BMDM, D 8h, LPS 4h, Replicate 4
Gene expression in BMDM pretreated 8h with D and re-stimulated 4 h with LPS

source_name: BMDM, D 8h, LPS 4h

value: D


title: BMDM_Mock8h_LPS8h_R4

description:
BMDM, Mock 8h, LPS 8h, Replicate 4
Gene expression in BMDM pretreated 8h with Mock and re-stimulated 8 h with LPS

source_name: BMDM, Mock 8h, LPS 8h


title: BMDM_Mock8h_LPS4h_R3

description:
BMDM, Mock 8h, LPS 4h, Replicate 3
Gene expression in BMDM pretreated 8h with Mock and re-stimulated 4 h with LPS


title: BMDM_C8h_LPS4h_R4

description:
BMDM, C 8h, LPS 4h, Replicate 4
Gene expression in BMDM pretreated 8h with C and re-stimulated 4 h with LPS

source_name: BMDM, C 8h, LPS 4h

value: C


title: BMDM_C8h_LPS4h_R3

description:
BMDM, C 8h, LPS 4h, Replicate 3
Gene expression in BMDM pretreated 8h with C and re-stimulated 4 h with LPS


title: BMDM_Mock8h_LPS8h_R3

description:
BMDM, Mock 8h, LPS 8h, Replicate 3
Gene expression in BMDM pretreated 8h with Mock and re-stimulated 8 h with LPS


title: BMDM_A8h_LPS4h_R3

description:
BMDM, A 8h, LPS 4h, Replicate 3
Gene expression in BMDM pretreated 8h with A and re-stimulated 4 h with LPS


title: BMDM_C8h_LPS8h_R3

description:
BMDM, C 8h, LPS 8h, Replicate 3
Gene expression in BMDM pretreated 8h with C and re-stimulated 8 h with LPS

source_name: BMDM, C 8h, LPS 8h


title: BMDM_D8h_LPS8h_R2

description:
BMDM, D 8h, LPS 8h, Replicate 2
Gene expression in BMDM pretreated 8h with D and re-stimulated 8 h with LPS

source_name: BMDM, D 8h, LPS 8h


title: BMDM_C8h_LPS8h_R4

description:
BMDM, C 8h, LPS 8h, Replicate 4
Gene expression in BMDM pretreated 8h with C and re-stimulated 8 h with LPS


title: BMDM_A8h_LPS8h_R3

description:
BMDM, A 8h, LPS 8h, Replicate 3
Gene expression in BMDM pretreated 8h with A and re-stimulated 8 h with LPS


title: BMDM_D8h_LPS8h_R3

description:
BMDM, D 8h, LPS 8h, Replicate 3
Gene expression in BMDM pretreated 8h with D and re-stimulated 8 h with LPS


title: BMDM_D8h_LPS8h_R4

description:
BMDM, D 8h, LPS 8h, Replicate 4
Gene expression in BMDM pretreated 8h with D and re-stimulated 8 h with LPS


title: BMDM_A8h_LPS8h_R2

description:
BMDM, A 8h, LPS 8h, Replicate 2
Gene expression in BMDM pretreated 8h with A and re-stimulated 8 h with LPS


title: BMDM_D8h_LPS4h_R3

description:
BMDM, D 8h, LPS 4h, Replicate 3
Gene expression in BMDM pretreated 8h with D and re-stimulated 4 h with LPS


title: BMDM_Mock8h_LPS8h_R2

description:
BMDM, Mock 8h, LPS 8h, Replicate 2
Gene expression in BMDM pretreated 8h with Mock and re-stimulated 8 h with LPS


title: BMDM_Mock8h_LPS4h_R2

description:
BMDM, Mock 8h, LPS 4h, Replicate 2
Gene expression in BMDM pretreated 8h with Mock and re-stimulated 4 h with LPS


title: BMDM_A8h_LPS4h_R2

description:
BMDM, A 8h, LPS 4h, Replicate 2
Gene expression in BMDM pretreated 8h with A and re-stimulated 4 h with LPS


title: BMDM_D8h_LPS4h_R1

description:
BMDM, D 8h, LPS 4h, Replicate 1
Gene expression in BMDM pretreated 8h with D and re-stimulated 4 h with LPS


title: BMDM_A8h_LPS8h_R1

description:
BMDM, A 8h, LPS 8h, Replicate 1
Gene expression in BMDM pretreated 8h with A and re-stimulated 8 h with LPS


title: BMDM_Mock8h_LPS8h_R1

description:
BMDM, Mock 8h, LPS 8h, Replicate 1
Gene expression in BMDM pretreated 8h with Mock and re-stimulated 8 h with LPS


title: BMDM_C8h_LPS8h_R2

description:
BMDM, C 8h, LPS 8h, Replicate 2
Gene expression in BMDM pretreated 8h with C and re-stimulated 8 h with LPS


title: BMDM_C8h_LPS8h_R1

description:
BMDM, C 8h, LPS 8h, Replicate 1
Gene expression in BMDM pretreated 8h with C and re-stimulated 8 h with LPS


title: BMDM_D8h_LPS4h_R2

description:
BMDM, D 8h, LPS 4h, Replicate 2
Gene expression in BMDM pretreated 8h with D and re-stimulated 4 h with LPS


title: BMDM_A8h_LPS4h_R1

description:
BMDM, A 8h, LPS 4h, Replicate 1
Gene expression in BMDM pretreated 8h with A and re-stimulated 4 h with LPS


title: BMDM_C8h_LPS4h_R2

description:
BMDM, C 8h, LPS 4h, Replicate 2
Gene expression in BMDM pretreated 8h with C and re-stimulated 4 h with LPS


title: BMDM_C8h_LPS4h_R1

description:
BMDM, C 8h, LPS 4h, Replicate 1
Gene expression in BMDM pretreated 8h with C and re-stimulated 4 h with LPS


title: BMDM_D8h_LPS8h_R1

description:
BMDM, D 8h, LPS 8h, Replicate 1
Gene expression in BMDM pretreated 8h with D and re-stimulated 8 h with LPS


title: non-small cell lung cancer patient 18408T

city: Rockville

first: Khadijah

middle: A

last: Mitchell

state: MD

address: 37 Convent Drive, Building 37, Room 3060

department: Laboratory of Human Carcinogenesis

country: USA

institute: National Cancer Institute

description: Gene expression data from fresh frozen lung tissues

hyb_protocol: Hybridization cocktails were prepared, including each fragmented target, and probe array controls. They were then hybridized to Affymetrix HG-U133 2.0 plus arrays during a 16-hour incubation (GeneChip Expression Analysis Technical Manual).

scan_protocol: Once the probe arrays were hybridized, washed, and stained, they were scanned using a GeneChip Scanner 3000 for High-Resolution Scanning (GeneChip Expression Analysis Technical Manual).

data_processing: The data were analyzed by using Affymetrix Gene Chip Operating Software using default settings.

label: biotin

source_name: fresh frozen lung tissues from non-small cell lung cancer patients

label_protocol: One microgram of total RNA was labeled for each sample according to Affymetrix protocols (GeneChip Expression Analysis Technical Manual).

extract_protocol: One microgram of total RNA  was extracted for each sample using TRIzol following the manufacturer’s protocol (Thermo Fisher Scientific, Waltham, MA). Isolated total RNA was quantified using a NanoDrop 1000 (NanoDrop Products, Wilmington, DE). RNA integrity was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: individual

value: patient 18408

tag: smoking pack years

tag: Stage

value: III

tag: race

value: AA

tag: tumor_normal status

value: T

tag: survival (days)

tag: survival (months)

tag: survival (years)

tag: death due to lung cancer (all years)

value: Dead


title: BMDM_Mock8h_LPS4h_R1

description:
BMDM, Mock 8h, LPS 4h, Replicate 1
Gene expression in BMDM pretreated 8h with Mock and re-stimulated 4 h with LPS


title: non-small cell lung cancer patient 18544N

value: patient 18544

value: I

value: N


title: non-small cell lung cancer patient 20504T

value: patient 20504

value: Alive


title: non-small cell lung cancer patient 20413N

value: patient 20413

value: female


title: non-small cell lung cancer patient 17763T

value: patient 17763

value: II


title: non-small cell lung cancer patient 18408N


title: non-small cell lung cancer patient 17225T

value: patient 17225

value: male


title: non-small cell lung cancer patient 20413T


title: non-small cell lung cancer patient 18023T

value: patient 18023


title: non-small cell lung cancer patient 17225N


title: non-small cell lung cancer patient 16437N

value: patient 16437

value: EA


title: non-small cell lung cancer patient 19931T

value: patient 19931

value: III

value: AA


title: non-small cell lung cancer patient 15784T

value: patient 15784

value: T


title: non-small cell lung cancer patient 17763N

value: N

value: Dead


title: non-small cell lung cancer patient 16052T

value: patient 16052

value: Alive


title: non-small cell lung cancer patient 16437T

value: female


title: non-small cell lung cancer patient 15784N

value: I


title: non-small cell lung cancer patient 16052N


title: CD8_WT_18h_1

city: Pittsburgh

first: Hatice

middle: Ulku

last: Osmanbeyoglu

state: PA

address: 5117 Centre Ave

institute: University of Pittsburgh

description: Gene expression data from GABPα-sufficient mice Naive CD8+ T cells

hyb_protocol: Following fragmentation, cRNA was hybridized to M430 2.0 chips (Affymetrix)

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

data_processing:
Gene-expression profiling analyses were done with R statistical environment. Affymetrix CEL files of microarray experiments were processed using the “affy” package and differential expression was assessed using “limma” package of the Bioconductor Suite.
A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression using limma package

source_name: Naive CD8+T cells Gabpaf/f (WT) at 18hr , biological rep1

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

growth_protocol: Naive (CD25-CD62LhiCD44lo) CD4+ and CD8+ T cells were purified from spleen and lymph nodes of Gabpaf/f (WT) and CD4CreGabpaf/f  (KO) mice by FACS sorting.

extract_protocol: cells were lysed using QIAZol reagent (Qiagen), followed by RNA extraction with the miRNeasy Mini Kit according to the manufacturer’s instructions (Qiagen).

treatment_protocol: Half of the sorted naive T cells was used for the 0-hour time point, whereas the other half of cells was subject to α-CD3/28 and IL-2 stimulation for 18 hours.

tag: genotype

value: Gabpaf/f (WT)

tag: tissue

value: Naive CD8+ T cells


title: CD8_KO_18h_1

description: Gene expression data from GABPα-deficient mice Naive CD8+ T cells

source_name: Naive CD8+T cells  CD4CreGabpaf/f  (KO) at 18hr , biological rep1

value: CD4CreGabpaf/f  (KO)


title: CD8_KO_18h_2

source_name: Naive CD8+T cells  CD4CreGabpaf/f  (KO) at 18hr , biological rep2


title: CD8_KO_0h_1

source_name: Naive CD8+T cells  CD4CreGabpaf/f  (KO) at 0hr , biological rep1


title: CD8_WT_0h_1

source_name: Naive CD8+T cells Gabpaf/f (WT) at 0hr , biological rep1


title: CD8_KO_0h_2

source_name: Naive CD8+T cells  CD4CreGabpaf/f  (KO) at 0hr , biological rep2


title: non-small cell lung cancer patient 14811T

value: patient 14811

tag: gender

value: male


title: non-small cell lung cancer patient 15595N

value: patient 15595

tag: age

value: II

value: EA


title: CD8_WT_0h_2

source_name: Naive CD8+T cells Gabpaf/f (WT) at 0hr, biological rep2


title: CD8_WT_18h_2

source_name: Naive CD8+T cells Gabpaf/f (WT) at 18hr, biological rep2


title: CD4_KO_18h_2

description: Gene expression data from GABPα--deficient mice Naive CD4+ T cells

source_name: Naive CD4+T cells  CD4CreGabpaf/f  (KO) at 18hr , biological rep2

value: Naive CD4+ T cells


title: non-small cell lung cancer patient 15595T


title: CD4_KO_0h_2

description: Gene expression data from GABPα-deficient  mice Naive CD4+ T cells

source_name: Naive CD4+T cells  CD4CreGabpaf/f  (KO) at 0hr , biological rep2


title: CD4_KO_0h_1

source_name: Naive CD4+T cells  CD4CreGabpaf/f  (KO) at 0hr , biological rep1


title: non-small cell lung cancer patient 14811N

value: AA


title: non-small cell lung cancer patient 13965T

value: patient 13965

value: T


title: CD4_KO_18h_1

description: Gene expression data from GABPα-deficient mice Naive CD4+ T cells

source_name: Naive CD4+T cells  CD4CreGabpaf/f  (KO) at 18hr , biological rep1


title: CD4_WT_18h_1

description: Gene expression data from GABPα-sufficient mice Naive CD4+ T cells

source_name: Naive CD4+T cells Gabpaf/f (WT) at 18hr , biological rep1


title: CD4_WT_18h_2

source_name: Naive CD4+T cells Gabpaf/f (WT) at 18hr, biological rep2


title: non-small cell lung cancer patient 14516N

value: patient 14516

value: N


title: CD4_WT_0h_2

source_name: Naive CD4+T cells Gabpaf/f (WT) at 0hr, biological rep2


title: non-small cell lung cancer patient 13932T

value: patient 13932

value: Dead


title: non-small cell lung cancer patient 13965N

value: female


title: CD4_WT_0h_1

source_name: Naive CD4+T cells Gabpaf/f (WT) at 0hr , biological rep1

value: Gabpaf/f (WT)


title: non-small cell lung cancer patient 13581N

source_name: fresh frozen lung tissues from non-small cell lung cancer patients

value: patient 13581

value: I

value: Alive


title: non-small cell lung cancer patient 13539T

value: patient 13539

value: male


title: non-small cell lung cancer patient 13581T


title: non-small cell lung cancer patient 13932N


title: non-small cell lung cancer patient 13490T

value: patient 13490


title: non-small cell lung cancer patient 13539N

value: II

value: EA


title: non-small cell lung cancer patient 13371T

value: patient 13371


title: genomic DNA from breast tissue 82

type: genomic

city: Columbus

first: Daniel

middle: Yui

last: Weng

state: OH

address: 420 W. 12th Ave. Room 390

department: Comprehensive Cancer Center

institute: The Ohio State University

description: normal breast

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchips using standard Illumina protocol

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

data_processing: Genome Studio 1.9.0 and Partek Genomics Suite 6.6 (Partek Inc., St. Louis, MO) and normalized using the Subset-quantile Within Array Normalization (SWAN)

label: Cy5 and Cy3

molecule: genomic DNA

source_name: breast tissue 82

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from dissected frozen fresh breast tissues using MasterPure DNA purificationKit according to standard instructions (Epicenter, Madison, WI)

value: white

tag: bmi


title: non-small cell lung cancer patient 13371N


title: genomic DNA from breast tissue 59

description: normal breast

source_name: breast tissue 59


title: genomic DNA from breast tissue 102

description: normal breast

source_name: breast tissue 102


title: genomic DNA from breast tissue 107

description: normal breast

source_name: breast tissue 107


title: non-small cell lung cancer patient 13490N


title: non-small cell lung cancer patient 13063N

value: patient 13063

value: AA


title: non-small cell lung cancer patient 13063T

value: T


title: non-small cell lung cancer patient 12913T

value: patient 12913


title: genomic DNA from breast tissue 13

description: normal breast

source_name: breast tissue 13


title: genomic DNA from breast tissue 74

description: normal breast

source_name: breast tissue 74


title: genomic DNA from breast tissue 30

description: normal breast

source_name: breast tissue 30


title: genomic DNA from breast tissue 10

description: normal breast

source_name: breast tissue 10

value: black


title: genomic DNA from breast tissue 109

description: normal breast

source_name: breast tissue 109


title: non-small cell lung cancer patient 12899N

value: patient 12899

value: female

value: N


title: genomic DNA from breast tissue 90

description: normal breast

source_name: breast tissue 90


title: genomic DNA from breast tissue 35

description: normal breast

source_name: breast tissue 35


title: genomic DNA from breast tissue 55

description: normal breast

source_name: breast tissue 55


title: non-small cell lung cancer patient 12913N

value: I

value: Dead


title: non-small cell lung cancer patient 12899T

value: Alive


title: genomic DNA from breast tissue 71

description: normal breast

source_name: breast tissue 71


title: genomic DNA from breast tissue 5

description: normal breast

source_name: breast tissue 5


title: genomic DNA from breast tissue 64

description: normal breast

source_name: breast tissue 64


title: genomic DNA from breast tissue 24

description: normal breast

source_name: breast tissue 24


title: genomic DNA from breast tissue 37

description: normal breast

source_name: breast tissue 37


title: genomic DNA from breast tissue 48

description: normal breast

source_name: breast tissue 48


title: genomic DNA from breast tissue 15

description: normal breast

source_name: breast tissue 15


title: genomic DNA from breast tissue 51

description: normal breast

source_name: breast tissue 51


title: genomic DNA from breast tissue 11

description: normal breast

source_name: breast tissue 11


title: non-small cell lung cancer patient 12822T

source_name: fresh frozen lung tissues from non-small cell lung cancer patients

value: patient 12822

value: male


title: genomic DNA from breast tissue 58

description: normal breast

source_name: breast tissue 58


title: genomic DNA from breast tissue 99

description: normal breast

source_name: breast tissue 99


title: non-small cell lung cancer patient 12822N


title: genomic DNA from breast tissue 28

description: normal breast

source_name: breast tissue 28


title: genomic DNA from breast tissue 38

description: normal breast

source_name: breast tissue 38


title: genomic DNA from breast tissue 32

description: normal breast

source_name: breast tissue 32


title: genomic DNA from breast tissue 121

description: normal breast

source_name: breast tissue 121


title: genomic DNA from breast tissue 105

description: normal breast

source_name: breast tissue 105


title: genomic DNA from breast tissue 97

description: normal breast

source_name: breast tissue 97


title: non-small cell lung cancer patient 12819T

value: patient 12819

value: II


title: genomic DNA from breast tissue 23

description: normal breast

source_name: breast tissue 23


title: non-small cell lung cancer patient 12688N

value: patient 12688

value: EA


title: genomic DNA from breast tissue 63

description: normal breast

source_name: breast tissue 63

value: white


title: non-small cell lung cancer patient 12606N

value: patient 12606


title: genomic DNA from breast tissue 45

description: normal breast

source_name: breast tissue 45


title: non-small cell lung cancer patient 12251T

value: patient 12251

value: T


title: non-small cell lung cancer patient 11697N

value: patient 11697

value: AA


title: genomic DNA from breast tissue 103

description: normal breast

source_name: breast tissue 103


title: genomic DNA from breast tissue 31

description: normal breast

source_name: breast tissue 31

value: black


title: genomic DNA from breast tissue 65

description: normal breast

source_name: breast tissue 65


title: GTC_144hr_LP106_rep1

city: Gatersleben

first: Andreas

last: Graner

address: Corrensstrasse 3

country: Germany

institute: Leibniz Institute of Plant Genetics and Crop Plant Research

description: Gene expression  144 hours after imbibition

hyb_protocol: 600ng of Cy3-labeled, amplified cRNA were hybridized, following the manufacturer's protocol, to a custom-synthesized 60k Barley Microarray (Agilent Technologies)

scan_protocol: Scanning of the slides was performed at high resolution of 3 µm double pass using Agilent DNA Microarray Scanner G2565CA

data_processing: The scanned images were analyzed with GeneSpring 12.0 software. After doing quantile normalization and baseline transformation to median of all samples, the probe sets (genes) were filtered by Coefficient of Variation <50%, followed by Moderated T-Test and Bonferroni correction. The probe sets which passed the P value cut-off ≤0.01 with the fold change of ≥2.0 were considered for interpreting the data

organism: Hordeum vulgare

source_name: Germinating barley seeds, LP106, 144hr, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: grains were germinating for 0-144 hours in the dark at 14.5°C

extract_protocol: RNA was extracted from tissues using the Plant Mini RNA kit (Qiagen, Hilden, Germany) following the manufacturer's protocol

value: Germinating seeds

tag: line


title: genomic DNA from breast tissue 57

description: normal breast

source_name: breast tissue 57


title: GTC_144hr_LP106_rep2

source_name: Germinating barley seeds, LP106, 144hr, replicate 2


title: genomic DNA from breast tissue 43

description: normal breast

source_name: breast tissue 43


title: genomic DNA from breast tissue 60

description: normal breast

source_name: breast tissue 60


title: GTC_144hr_LP106_rep3

source_name: Germinating barley seeds, LP106, 144hr, replicate 3


title: non-small cell lung cancer patient 11344N

source_name: fresh frozen lung tissues from non-small cell lung cancer patients

value: patient 11344

value: I

value: N


title: GTC_144hr_LP104_rep2

source_name: Germinating barley seeds, LP104, 144hr, replicate 2


title: genomic DNA from breast tissue 50

description: normal breast

source_name: breast tissue 50


title: genomic DNA from breast tissue 7

description: normal breast

source_name: breast tissue 7


title: non-small cell lung cancer patient 11344T

value: Dead


title: GTC_144hr_LP104_rep3

source_name: Germinating barley seeds, LP104, 144hr, replicate 3


title: non-small cell lung cancer patient 11039T

value: patient 11039

value: male

value: III


title: genomic DNA from breast tissue 115

description: normal breast

source_name: breast tissue 115


title: non-small cell lung cancer patient 12690T

value: patient 12690

value: Alive


title: genomic DNA from breast tissue 46

description: normal breast

source_name: breast tissue 46

value: white


title: genomic DNA from breast tissue 98

description: normal breast

source_name: breast tissue 98


title: genomic DNA from breast tissue 89

description: normal breast

source_name: breast tissue 89


title: genomic DNA from breast tissue 17

description: normal breast

source_name: breast tissue 17


title: genomic DNA from breast tissue 52

description: normal breast

source_name: breast tissue 52


title: genomic DNA from breast tissue 49

description: normal breast

source_name: breast tissue 49


title: non-small cell lung cancer patient 11039N


title: GTC_120hr_LP106_rep3

description: Gene expression  120 hours after imbibition

source_name: Germinating barley seeds, LP106, 120hr, replicate 3


title: GTC_120hr_LP106_rep1

source_name: Germinating barley seeds, LP106, 120hr, replicate 1


title: genomic DNA from breast tissue 61

description: normal breast

source_name: breast tissue 61


title: non-small cell lung cancer patient 10590N

value: patient 10590


title: genomic DNA from breast tissue 8

description: normal breast

source_name: breast tissue 8


title: non-small cell lung cancer patient 10585N

value: patient 10585

value: II


title: GTC_120hr_LP104_rep3

source_name: Germinating barley seeds, LP104, 120hr, replicate 3


title: non-small cell lung cancer patient 10484N

source_name: fresh frozen lung tissues from non-small cell lung cancer patients

value: patient 10484


title: non-small cell lung cancer patient 10484T

value: AA

value: T


title: genomic DNA from breast tissue 66

description: normal breast

source_name: breast tissue 66

value: black


title: genomic DNA from breast tissue 12

description: normal breast

source_name: breast tissue 12


title: GTC_120hr_LP106_rep2

source_name: Germinating barley seeds, LP106, 120hr, replicate 2

value: Germinating seeds


title: GTC_120hr_LP104_rep2

source_name: Germinating barley seeds, LP104, 120hr, replicate 2


title: non-small cell lung cancer patient 10444N

value: patient 10444

value: female

value: I

value: EA


title: genomic DNA from breast tissue 42

description: normal breast

source_name: breast tissue 42


title: GTC_120hr_LP104_rep1

source_name: Germinating barley seeds, LP104, 120hr, replicate 1


title: genomic DNA from breast tissue 100

description: normal breast

source_name: breast tissue 100


title: genomic DNA from breast tissue 91

description: normal breast

source_name: breast tissue 91


title: genomic DNA from breast tissue 67

description: normal breast

source_name: breast tissue 67


title: GTC_96hr_LP106_rep3

description: Gene expression  96 hours after imbibition

source_name: Germinating barley seeds, LP106, 96hr, replicate 3


title: non-small cell lung cancer patient 10198T

value: patient 10198


title: GTC_96hr_LP106_rep2

source_name: Germinating barley seeds, LP106, 96hr, replicate 2


title: non-small cell lung cancer patient 10379T

value: patient 10379

value: male

value: Dead


title: genomic DNA from breast tissue 33

description: normal breast

source_name: breast tissue 33

value: white


title: genomic DNA from breast tissue 69

description: normal breast

source_name: breast tissue 69


title: genomic DNA from breast tissue 4

description: normal breast

source_name: breast tissue 4


title: GTC_96hr_LP106_rep1

source_name: Germinating barley seeds, LP106, 96hr, replicate 1


title: genomic DNA from breast tissue 56

description: normal breast

source_name: breast tissue 56


title: genomic DNA from breast tissue 40

description: normal breast

source_name: breast tissue 40


title: non-small cell lung cancer patient 10198N

source_name: fresh frozen lung tissues from non-small cell lung cancer patients

value: III

value: N

value: Alive


title: GTC_144hr_LP104_rep1

source_name: Germinating barley seeds, LP104, 144hr, replicate 1


title: genomic DNA from breast tissue 27

description: normal breast

source_name: breast tissue 27


title: genomic DNA from breast tissue 72

description: normal breast

source_name: breast tissue 72


title: genomic DNA from breast tissue 53

description: normal breast

source_name: breast tissue 53


title: non-small cell lung cancer patient 10174T

value: patient 10174


title: genomic DNA from breast tissue 25

description: normal breast

source_name: breast tissue 25


title: GTC_96hr_LP104_rep3

source_name: Germinating barley seeds, LP104, 96hr, replicate 3


title: non-small cell lung cancer patient 10174N


title: genomic DNA from breast tissue 62

description: normal breast

source_name: breast tissue 62


title: genomic DNA from breast tissue 118

description: normal breast

source_name: breast tissue 118


title: GTC_96hr_LP104_rep1

source_name: Germinating barley seeds, LP104, 96hr, replicate 1


title: genomic DNA from breast tissue 96

description: normal breast

source_name: breast tissue 96


title: non-small cell lung cancer patient 10444T


title: non-small cell lung cancer patient 10146N

value: patient 10146

value: y

value: AA


title: genomic DNA from breast tissue 68

description: normal breast

source_name: breast tissue 68

value: black


title: genomic DNA from breast tissue 47

description: normal breast

source_name: breast tissue 47


title: genomic DNA from breast tissue 120

description: normal breast

source_name: breast tissue 120


title: GTC_72hr_LP106_rep3

description: Gene expression  72 hours after imbibition

source_name: Germinating barley seeds, LP106, 72hr, replicate 3

value: Germinating seeds


title: non-small cell lung cancer patient 10111N

value: patient 10111

value: female

value: II


title: genomic DNA from breast tissue 26

description: normal breast

source_name: breast tissue 26


title: GTC_72hr_LP106_rep2

source_name: Germinating barley seeds, LP106, 72hr, replicate 2


title: genomic DNA from breast tissue 119

description: normal breast

source_name: breast tissue 119


title: genomic DNA from breast tissue 85

description: normal breast

source_name: breast tissue 85


title: genomic DNA from breast tissue 73

description: normal breast

source_name: breast tissue 73


title: genomic DNA from breast tissue 94

description: normal breast

source_name: breast tissue 94


title: GTC_72hr_LP106_rep1

source_name: Germinating barley seeds, LP106, 72hr, replicate 1


title: genomic DNA from breast tissue 92

description: normal breast

source_name: breast tissue 92


title: genomic DNA from breast tissue 16

description: normal breast

source_name: breast tissue 16


title: GTC_72hr_LP104_rep3

source_name: Germinating barley seeds, LP104, 72hr, replicate 3


title: GTC_72hr_LP104_rep2

source_name: Germinating barley seeds, LP104, 72hr, replicate 2


title: genomic DNA from breast tissue 29

description: normal breast

source_name: breast tissue 29


title: GTC_48hr_LP106_rep2

description: Gene expression  48 hours after imbibition

source_name: Germinating barley seeds, LP106, 48hr, replicate 2


title: GTC_72hr_LP104_rep1

source_name: Germinating barley seeds, LP104, 72hr, replicate 1


title: genomic DNA from breast tissue 34

description: normal breast

source_name: breast tissue 34


title: GTC_48hr_LP106_rep3

source_name: Germinating barley seeds, LP106, 48hr, replicate 3


title: MM18 rep - 5 hr - rep 3

city: Cambridge

first: Jason

middle: H

last: Yang

state: MA

address: 415 Main St, Rm 2017

department: Biological Engineering

institute: MIT / Broad Institute

description: Maltose - 5 hr  - rep 3

hyb_protocol: 10 μg of fragmented, biotinylated cDNAs were combined with hybridization cocktail and hybridized to Affymetrix E. coli 2.0 arrays for 16-18 hours at 45 ºC and 60 rpm. The microarrays were then washed and stained.

scan_protocol: Arrays were washed and stained on Affymetrix Fluidics Station 450s using the appropriate Affymetrix protocol. The stained arrays were scanned at 532 nm using an Affymetrix GeneChip Scanner 3000.

data_processing: CEL files for the resulting expression profiles were background adjusted and RMA normalized using RMAExpress. Statistical analysis was performed in MATLAB.

organism: Escherichia coli str. K-12 substr. MC4100

source_name: MM18 MAL - 5 hr - rep 3

label_protocol: cDNAs were prepared from 10 µg total RNA through a random primed reverse transcription using SuperScript II (Invitrogen, Carlsbad, CA). The RNAs were digested with the addition of 1M NaOH and incubation at 65ºC for 30 minutes. The mixtures were neutralized with the addition of 1M HCl. The cDNAs were purified using QIAquick MinElute PCR purification columns (Qiagen, Valencia, CA), following the manufacturer’s protocol. The cDNAs (3 – 5 μg) were fragmented to a size range of 50-200 bases with DNase I (0.6 U/ μg cDNA) at 37 ºC for 10 minutes followed by inactivation of the enzyme at 98 ºC for 10 minutes.

growth_protocol: Triplicate overnight E. coli MM18 cells were prepared in M63 minimal media at 37C with shaking.

extract_protocol: RNA was extracted using the Qiagen Rneasy Protect Bacteria Mini Kit and Dnase treated using the Life Technologies Turbo DNA-free kit.

treatment_protocol: Exponential phase MM18 cells at OD600 = 0.1 were treated with 0.2% maltose or 0% maltose control. Cells were incubated at 37C with shaking and sampled hourly for RNA extraction.

tag: strain

value: MC4100 pMalE-LacZ

tag: protocol

value: Maltose

tag: time point

value: 5 hr


title: MM18 rep - 5 hr - rep 2

description: Maltose - 5 hr  - rep 2

source_name: MM18 MAL - 5 hr - rep 2


title: genomic DNA from breast tissue 44

description: normal breast

source_name: breast tissue 44


title: GTC_96hr_LP104_rep2

source_name: Germinating barley seeds, LP104, 96hr, replicate 2


title: GTC_48hr_LP106_rep1

source_name: Germinating barley seeds, LP106, 48hr, replicate 1


title: GTC_48hr_LP104_rep3

source_name: Germinating barley seeds, LP104, 48hr, replicate 3


title: genomic DNA from breast tissue 3

description: normal breast

source_name: breast tissue 3


title: MM18 rep - 4 hr - rep 3

description: Maltose - 4 hr  - rep 3

source_name: MM18 MAL - 4 hr - rep 3

value: 4 hr


title: MM18 rep - 4 hr - rep 2

description: Maltose - 4 hr  - rep 2

source_name: MM18 MAL - 4 hr - rep 2


title: genomic DNA from breast tissue 1

description: normal breast

source_name: breast tissue 1


title: genomic DNA from breast tissue 18

description: normal breast

source_name: breast tissue 18


title: genomic DNA from breast tissue 113

description: normal breast

source_name: breast tissue 113


title: GTC_48hr_LP104_rep2

source_name: Germinating barley seeds, LP104, 48hr, replicate 2


title: MM18 rep - 3 hr - rep 3

description: Maltose - 3 hr  - rep 3

source_name: MM18 MAL - 3 hr - rep 3

value: 3 hr


title: MM18 rep - 4 hr - rep 1

description: Maltose - 4 hr  - rep 1

source_name: MM18 MAL - 4 hr - rep 1


title: genomic DNA from breast tissue 117

description: normal breast

source_name: breast tissue 117

value: white


title: MM18 rep - 5 hr - rep 1

description: Maltose - 5 hr  - rep 1

source_name: MM18 MAL - 5 hr - rep 1


title: genomic DNA from breast tissue 111

description: normal breast

source_name: breast tissue 111


title: GTC_24hr_LP106_rep3

description: Gene expression  24 hours after imbibition

source_name: Germinating barley seeds, LP106, 24hr, replicate 3


title: GTC_48hr_LP104_rep1

source_name: Germinating barley seeds, LP104, 48hr, replicate 1


title: genomic DNA from breast tissue 54

description: normal breast

source_name: breast tissue 54


title: genomic DNA from breast tissue 88

description: normal breast

source_name: breast tissue 88


title: MM18 rep - 3 hr - rep 2

description: Maltose - 3 hr  - rep 2

source_name: MM18 MAL - 3 hr - rep 2


title: genomic DNA from breast tissue 101

description: normal breast

source_name: breast tissue 101


title: genomic DNA from breast tissue 2

description: normal breast

source_name: breast tissue 2


title: genomic DNA from breast tissue 80

description: normal breast

source_name: breast tissue 80


title: genomic DNA from breast tissue 87

description: normal breast

source_name: breast tissue 87


title: MM18 rep - 3 hr - rep 1

description: Maltose - 3 hr  - rep 1

source_name: MM18 MAL - 3 hr - rep 1


title: MM18 rep - 2 hr - rep 3

description: Maltose - 2 hr  - rep 3

source_name: MM18 MAL - 2 hr - rep 3

value: 2 hr


title: GTC_24hr_LP106_rep2

source_name: Germinating barley seeds, LP106, 24hr, replicate 2


title: genomic DNA from breast tissue 39

description: normal breast

source_name: breast tissue 39


title: genomic DNA from breast tissue 79

description: normal breast

source_name: breast tissue 79


title: genomic DNA from breast tissue 78

description: normal breast

source_name: breast tissue 78


title: GTC_24hr_LP104_rep1

source_name: Germinating barley seeds, LP104, 24hr, replicate 1


title: genomic DNA from breast tissue 86

description: normal breast

source_name: breast tissue 86


title: MM18 rep - 2 hr - rep 1

description: Maltose - 2 hr  - rep 1

source_name: MM18 MAL - 2 hr - rep 1


title: GTC_24hr_LP106_rep1

source_name: Germinating barley seeds, LP106, 24hr, replicate 1


title: GTC_24hr_LP104_rep2

source_name: Germinating barley seeds, LP104, 24hr, replicate 2


title: MM18 rep - 2 hr - rep 2

description: Maltose - 2 hr  - rep 2

source_name: MM18 MAL - 2 hr - rep 2


title: GTC_2hr_LP106_rep2

description: Gene expression  2 hours after imbibition

source_name: Germinating barley seeds, LP106, 2hr, replicate 2


title: MM18 rep - 1 hr - rep 3

description: Maltose - 1 hr  - rep 3

source_name: MM18 MAL - 1 hr - rep 3

value: 1 hr


title: MM18 rep - 1 hr - rep 1

description: Maltose - 1 hr  - rep 1

source_name: MM18 MAL - 1 hr - rep 1


title: GTC_2hr_LP106_rep3

source_name: Germinating barley seeds, LP106, 2hr, replicate 3


title: MM18 rep - 1 hr - rep 2

description: Maltose - 1 hr  - rep 2

source_name: MM18 MAL - 1 hr - rep 2


title: GTC_24hr_LP104_rep3

source_name: Germinating barley seeds, LP104, 24hr, replicate 3


title: GTC_2hr_LP104_rep3

source_name: Germinating barley seeds, LP104, 2hr, replicate 3


title: MM18 rep - 0 hr - rep 3

description: Maltose - 0 hr  - rep 3

source_name: MM18 MAL - 0 hr - rep 3

value: 0 hr


title: GTC_2hr_LP106_rep1

source_name: Germinating barley seeds, LP106, 2hr, replicate 1


title: genomic DNA from breast tissue 84

description: normal breast

source_name: breast tissue 84


title: GTC_2hr_LP104_rep2

source_name: Germinating barley seeds, LP104, 2hr, replicate 2


title: genomic DNA from breast tissue 116

description: normal breast

source_name: breast tissue 116


title: genomic DNA from breast tissue 83

description: normal breast

source_name: breast tissue 83


title: MM18 rep - 0 hr - rep 2

description: Maltose - 0 hr  - rep 2

source_name: MM18 MAL - 0 hr - rep 2


title: genomic DNA from breast tissue 95

description: normal breast

source_name: breast tissue 95


title: GTC_0hr_LP106_rep1

description: Gene expression  0 hours after imbibition

source_name: Germinating barley seeds, LP106, 0hr, replicate 1


title: MM18 rep - 0 hr - rep 1

description: Maltose - 0 hr  - rep 1

source_name: MM18 MAL - 0 hr - rep 1


title: genomic DNA from breast tissue 114

description: normal breast

source_name: breast tissue 114


title: GTC_0hr_LP106_rep2

source_name: Germinating barley seeds, LP106, 0hr, replicate 2


title: GTC_0hr_LP104_rep2

source_name: Germinating barley seeds, LP104, 0hr, replicate 2


title: MM18 CTL - 5 hr - rep 2

description: Control - 5 hr  - rep 2

source_name: MM18 CTL - 5 hr - rep 2

value: Control


title: genomic DNA from breast tissue 112

description: normal breast

source_name: breast tissue 112


title: MM18 CTL - 5 hr - rep 3

description: Control - 5 hr  - rep 3

source_name: MM18 CTL - 5 hr - rep 3


title: genomic DNA from breast tissue 93

description: normal breast

source_name: breast tissue 93


title: genomic DNA from breast tissue 110

description: normal breast

source_name: breast tissue 110


title: MM18 CTL - 5 hr - rep 1

description: Control - 5 hr  - rep 1

source_name: MM18 CTL - 5 hr - rep 1


title: MM18 CTL - 4 hr - rep 3

description: Control - 4 hr  - rep 3

source_name: MM18 CTL - 4 hr - rep 3


title: MM18 CTL - 4 hr - rep 1

description: Control - 4 hr  - rep 1

source_name: MM18 CTL - 4 hr - rep 1


title: genomic DNA from breast tissue 81

description: normal breast

source_name: breast tissue 81


title: GTC_0hr_LP104_rep3


title: MM18 CTL - 4 hr - rep 2

description: Control - 4 hr  - rep 2

source_name: MM18 CTL - 4 hr - rep 2


title: GTC_2hr_LP104_rep1

source_name: Germinating barley seeds, LP104, 2hr, replicate 1


title: genomic DNA from breast tissue 106

description: normal breast

source_name: breast tissue 106


title: genomic DNA from breast tissue 77

description: normal breast

source_name: breast tissue 77


title: GTC_0hr_LP104_rep1

source_name: Germinating barley seeds, LP104, 0hr, replicate 1


title: MM18 CTL - 3 hr - rep 2

description: Control - 3 hr  - rep 2

source_name: MM18 CTL - 3 hr - rep 2


title: MM18 CTL - 2 hr - rep 2

description: Control - 2 hr  - rep 2

source_name: MM18 CTL - 2 hr - rep 2


title: MM18 CTL - 2 hr - rep 1

description: Control - 2 hr  - rep 1

source_name: MM18 CTL - 2 hr - rep 1


title: genomic DNA from breast tissue 76

description: normal breast

source_name: breast tissue 76


title: MM18 CTL - 2 hr - rep 3

description: Control - 2 hr  - rep 3

source_name: MM18 CTL - 2 hr - rep 3


title: MM18 CTL - 3 hr - rep 3

description: Control - 3 hr  - rep 3

source_name: MM18 CTL - 3 hr - rep 3


title: MM18 CTL - 3 hr - rep 1

description: Control - 3 hr  - rep 1

source_name: MM18 CTL - 3 hr - rep 1


title: genomic DNA from breast tissue 41

description: normal breast

source_name: breast tissue 41


title: MM18 CTL - 0 hr - rep 2

description: Control - 0 hr  - rep 2

source_name: MM18 CTL - 0 hr - rep 2


title: MM18 CTL - 1 hr - rep 1

description: Control - 1 hr  - rep 1

source_name: MM18 CTL - 1 hr - rep 1


title: MM18 CTL - 0 hr - rep 1

description: Control - 0 hr  - rep 1

source_name: MM18 CTL - 0 hr - rep 1


title: genomic DNA from breast tissue 36

description: normal breast

source_name: breast tissue 36


title: MM18 CTL - 1 hr - rep 3

description: Control - 1 hr  - rep 3

source_name: MM18 CTL - 1 hr - rep 3


title: MM18 CTL - 0 hr - rep 3

description: Control - 0 hr  - rep 3

source_name: MM18 CTL - 0 hr - rep 3


title: MM18 CTL - 1 hr - rep 2

description: Control - 1 hr  - rep 2

source_name: MM18 CTL - 1 hr - rep 2


title: genomic DNA from breast tissue 22

description: normal breast

source_name: breast tissue 22


title: genomic DNA from breast tissue 20

description: normal breast

source_name: breast tissue 20


title: genomic DNA from breast tissue 104

description: normal breast

source_name: breast tissue 104


title: Adult D.1. 2.5SY/2.5SY M4

status: Public on Jul 27 2017

city: Wageningen

first: Christina

last: May

state: Gelderland

address: Droevendaalsesteeg 1

institute: Wageningen University

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized to the Affymetrix Drosophila 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix  3000G  scanner.

data_processing: The data was processed using the robust multi-array average (RMA) algorithm to perform background adjustment, quantile normalization and summarization

organism: Drosophila melanogaster

source_name: Adult male collected at one day old, raised on the 2.5SY diet as a larvae and maintained on the 2.5SY diet as an adult

label_protocol: Biotinylated cRNA were prepared using the Affymetrix 3' IVT-Express Labeling Kit (#901229) according to the standard Affymetrix protocol from 100 ug total RNA per sample.

growth_protocol: Flies were raised on one of three diets as larvae (0.25SY, 1SY, or 2.5SY) These three diets differed only in the amount of sugar and yeast they contained. The 1SY diet was identical to the standard laboratory diet (70g yeast, 100g sugar, 20g agar, 15mL nipagine, and 3mL propionic acid per liter of water), while the 0.25SY and 2.5SY diets contained 25% and 250% as much sugar and yeast as the 1SY diet, respectively. Newly eclosed adults were split across these same three diets in a fully factorial design and maintained on their adult diet until their death. Samples were collected at 1 day post eclosion and at 10% and 90% cohort mortality.

extract_protocol: RNA extraction was performed using the Machery Nagel Nucleospin II kit (Machery and Nagel) following the manufacturers instructions. We extracted RNA from whole bodies of five flies per replicate, with four replicates per combination of sex, larval diet, adult diet and age (4 replicates x 2 sexes x 3 larval diets x 3 adult diets x 3 ages = 216 arrays)

treatment_protocol: Adults in each age-class were flash frozen in liquid nitrogen and transferred to the -80 to await RNA extraction.

tag: Sex

value: male

value: one day old

tag: larval diet

tag: adult diet

value: whole body


title: Adult D.1. 2.5SY/2.5SY F4

source_name: Adult female collected at one day old, raised on the 2.5SY diet as a larvae and maintained on the 2.5SY diet as an adult


title: Adult D.1. 2.5SY/2.5SY F1


title: genomic DNA from breast tissue 19

description: normal breast

source_name: breast tissue 19

tag: race


title: Adult D.1. 2.5SY/2.5SY M1


title: Adult D.1. 2.5SY/2.5SY F3


title: Adult D.1. 2.5SY/2.5SY F2


title: Adult D.1. 2.5SY/2.5SY M2


title: Adult D.1. 2.5SY/2.5SY M3


title: Adult D.1. 2.5SY/0.25SY F3

source_name: Adult female collected at one day old, raised on the 2.5SY diet as a larvae and maintained on the 0.25SY diet as an adult


title: Adult D.1. 2.5SY/0.25SY M1

source_name: Adult male collected at one day old, raised on the 2.5SY diet as a larvae and maintained on the 0.25SY diet as an adult


title: Adult D.1. 2.5SY/0.25SY M4


title: Adult D.1. 2.5SY/0.25SY F4


title: genomic DNA from breast tissue 14

description: normal breast

source_name: breast tissue 14


title: genomic DNA from breast tissue 70

description: normal breast

source_name: breast tissue 70

value: black


title: Adult D.1. 2.5SY/0.25SY M2


title: Adult D.1. 2.5SY/1SY M4

source_name: Adult male collected at one day old, raised on the 2.5SY diet as a larvae and maintained on the 1SY diet as an adult


title: Adult D.1. 2.5SY/0.25SY F2


title: Adult D.1. 2.5SY/0.25SY M3


title: genomic DNA from breast tissue 75

description: normal breast

source_name: breast tissue 75


title: Adult D.1. 2.5SY/1SY M2


title: genomic DNA from breast tissue 9

description: normal breast

source_name: breast tissue 9


title: genomic DNA from breast tissue 6

description: normal breast

source_name: breast tissue 6


title: Adult D.1. 2.5SY/1SY M1


title: Adult D.1. 2.5SY/1SY F1

source_name: Adult female collected at one day old, raised on the 2.5SY diet as a larvae and maintained on the 1SY diet as an adult


title: Control_1

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

description:
Biological replicats 1 of 4
The methylation analysis was performed using EmbryoGENE DNA methylation array (EDMA) platform. The methodology have been thoroughly describef in (Saadi et al., 2014). Briefly, 10ng of DNA sample and spike-in control were cut in ≈160bp fragment using MSEI restriction enzyme. MseLig 12 and MseLig 21 adapters were added to the fragmented gDNA sites. Sample were the digested using methyl sensitive restriction enzyme HpaII, HinP1I and AciI. Only unmethylated fragment have been targeted by those enzyme, leaving only one adapter on the cleaved fragment.     Efficiency of the digestion was confirmed by analyzing the spike-in control added prior to the DNA fragmentation step. For the step, qPCR was performed by preparing a separate mixes containing forward and reverse primer targeting HpaII, HinP1I and AciI site. Undigested spike-in (1/1000 dilution) was used as a positive control and non-template controls were also added as negatives control. The amplification plot and the dissociation curve were evaluated for each primer set separately. The DNA fragmentation was considered successful when the threshold cycle (ct) was greater than 5 when compared to the undigested control.Fragment selection by ligation-mediated PCR  After cleavage by methyl sensitive enzyme, the gDNA was purified by ethanol precipitation and dissolve in nuclease free water. Selective amplification of methylated fragments was performed using two rounds of ligation-mediated PCR (LM-PCR). The PCR products were resolved on 0.8% agarose gel to assess the quality. Then the previously added linker were removed.

hyb_protocol: Hybridizations were performed according to the microarray manufacturer’s instructions (Agilent Technologies). Briefly, 1.4 μg of labeled sample (in 40 μL) was mixed with 158 μL of hybridization master mix containing 25 μL of Bovine Hybloc competitor DNA (1 mg/ml) , Applied Genetics Laboratories), 2.6 μL of Agilent 100x Blocking Agent and 130 μL of Agilent 2× HI-RPM Hybridization Buffer (Agilent Technologies). Samples were held at 95°C for 3 min and at 37°C for 30 min followed by addition of 65 μL of Agilent-CGHBlock (final volume 260 μL). The samples were loaded onto the microarray and hybridization was carried out in a hybridization oven (Shel Lab) for 40 h at 65°C and 20 rpm. Washing was carried out according to the microarray manufacturer’s instructions

scan_protocol: Slides were scanned with the PowerScanner (Tecan) and analyzed with Array-Pro Analyzer 6.3 software (MediaCybernetics).

data_processing: The array data analysis methods and downstream analysis pipelines are described in detail in (Saadi et al., 2014). Briefly, after Loess normalization, quantile inter-array scale normalization was performed and fitted to a linear model and thus, Bayesian statistics of differential expression were obtained. Thus, differentially methylated probes were identified using linear models for microarray data (LIMMA).

organism: Bos taurus

source_name: animal #0032 sperm cells

label_protocol: For each sample, 2 μg of DNA was labeled using the Universal Linkage System (ULS) labeling kit (Kreatech Biotechnology) according to the manufacturer’s instructions with minor modifications: 1 μL of Cy-ULS dye was added per 1 μg of genomic DNA adjusted with 10× labeling buffer. The labelling mixture was then held for 30 min at 85°C in a thermocycler, followed by 3 min on ice. Non-reacted ULS-Cy3/5 was removed by purification using a QIAquick PCR Purification Kit and samples were eluted in 23.5 μL nuclease-free water. A 1.5 μL aliquot was used to determine DNA concentration and dye incorporation using the ND- 1000 NanoDrop.

extract_protocol: Blastocysts Genomic DNA was extracted using the All prep Dna/RNA kit from Qiagen, following the protcol recommendations.

treatment_protocol: The glucose dose response experiment was performed by adding different concentrations of glucose (0.2 uM for the control and 5 uM for the treatment) (Cagnone et al. 2012) in SOF 1 during the first three days of embryo development. After this period, all embryos were transferred to normal culture conditions until the blastocyst stage

tag: Stage

value: Day 7 blastocyst

tag: treatment

value: Control (0.2uM glucose)

tag: specie

value: Holstein-Friesian

tag: sample type

value: DNA methylation

value: Glucose (5uM glucose)


title: Adult D.1. 2.5SY/1SY M3


title: genomic DNA from breast tissue 21

description: normal breast

source_name: breast tissue 21


title: Adult D.1. 2.5SY/1SY F4

value: female


title: Glucose_2

description:
Biological replicats 4 of 4
The methylation analysis was performed using EmbryoGENE DNA methylation array (EDMA) platform. The methodology have been thoroughly describef in (Saadi et al., 2014). Briefly, 10ng of DNA sample and spike-in control were cut in ≈160bp fragment using MSEI restriction enzyme. MseLig 12 and MseLig 21 adapters were added to the fragmented gDNA sites. Sample were the digested using methyl sensitive restriction enzyme HpaII, HinP1I and AciI. Only unmethylated fragment have been targeted by those enzyme, leaving only one adapter on the cleaved fragment.     Efficiency of the digestion was confirmed by analyzing the spike-in control added prior to the DNA fragmentation step. For the step, qPCR was performed by preparing a separate mixes containing forward and reverse primer targeting HpaII, HinP1I and AciI site. Undigested spike-in (1/1000 dilution) was used as a positive control and non-template controls were also added as negatives control. The amplification plot and the dissociation curve were evaluated for each primer set separately. The DNA fragmentation was considered successful when the threshold cycle (ct) was greater than 5 when compared to the undigested control.Fragment selection by ligation-mediated PCR  After cleavage by methyl sensitive enzyme, the gDNA was purified by ethanol precipitation and dissolve in nuclease free water. Selective amplification of methylated fragments was performed using two rounds of ligation-mediated PCR (LM-PCR). The PCR products were resolved on 0.8% agarose gel to assess the quality. Then the previously added linker were removed.

source_name: animal #0051 sperm cells


title: genomic DNA from breast tissue 108

description: normal breast

source_name: breast tissue 108


title: Adult D.1. 2.5SY/1SY F2


title: Adult D.1. 2.5SY/1SY F3


title: Adult D.1. 0.25SY/2.5SY F4

source_name: Adult female collected at one day old, raised on the 0.25SY diet as a larvae and maintained on the 2.5SY diet as an adult


title: Adult D.1. 0.25SY/2.5SY M3

source_name: Adult male collected at one day old, raised on the 0.25SY diet as a larvae and maintained on the 2.5SY diet as an adult


title: Adult D.1. 0.25SY/2.5SY M4


title: Adult D.1. 0.25SY/2.5SY M1


title: Adult D.1. 0.25SY/2.5SY M2


title: Adult D.1. 2.5SY/0.25SY F1


title: Adult D.1. 0.25SY/2.5SY F2


title: Adult D.1. 0.25SY/0.25SY F4

source_name: Adult female collected at one day old, raised on the 0.25SY diet as a larvae and maintained on the 0.25SY diet as an adult


title: Adult D.1. 0.25SY/0.25SY F1


title: Adult D.1. 0.25SY/0.25SY M1

source_name: Adult male collected at one day old, raised on the 0.25SY diet as a larvae and maintained on the 0.25SY diet as an adult


title: Adult D.1. 0.25SY/0.25SY M2


title: Adult D.1. 0.25SY/0.25SY F3


title: Adult D.1. 0.25SY/2.5SY F1


title: Glucose_1

description:
Biological replicats 2 of 4
The methylation analysis was performed using EmbryoGENE DNA methylation array (EDMA) platform. The methodology have been thoroughly describef in (Saadi et al., 2014). Briefly, 10ng of DNA sample and spike-in control were cut in ≈160bp fragment using MSEI restriction enzyme. MseLig 12 and MseLig 21 adapters were added to the fragmented gDNA sites. Sample were the digested using methyl sensitive restriction enzyme HpaII, HinP1I and AciI. Only unmethylated fragment have been targeted by those enzyme, leaving only one adapter on the cleaved fragment.     Efficiency of the digestion was confirmed by analyzing the spike-in control added prior to the DNA fragmentation step. For the step, qPCR was performed by preparing a separate mixes containing forward and reverse primer targeting HpaII, HinP1I and AciI site. Undigested spike-in (1/1000 dilution) was used as a positive control and non-template controls were also added as negatives control. The amplification plot and the dissociation curve were evaluated for each primer set separately. The DNA fragmentation was considered successful when the threshold cycle (ct) was greater than 5 when compared to the undigested control.Fragment selection by ligation-mediated PCR  After cleavage by methyl sensitive enzyme, the gDNA was purified by ethanol precipitation and dissolve in nuclease free water. Selective amplification of methylated fragments was performed using two rounds of ligation-mediated PCR (LM-PCR). The PCR products were resolved on 0.8% agarose gel to assess the quality. Then the previously added linker were removed.


title: Adult D.1. 0.25SY/0.25SY M3


title: Adult D.1. 0.25SY/0.25SY M4


title: Adult D.1. 0.25SY/0.25SY F2


title: Adult D.1. 0.25SY/1SY M4

source_name: Adult male collected at one day old, raised on the 0.25SY diet as a larvae and maintained on the 1SY diet as an adult


title: Adult D.1. 0.25SY/1SY M3


title: Adult D.1. 0.25SY/1SY M1


title: Adult D.1. 1SY/2.5SY M4

source_name: Adult male collected at one day old, raised on the 1SY diet as a larvae and maintained on the 2.5SY diet as an adult


title: Adult D.1. 0.25SY/1SY F1

source_name: Adult female collected at one day old, raised on the 0.25SY diet as a larvae and maintained on the 1SY diet as an adult


title: Adult D.1. 0.25SY/2.5SY F3


title: Adult D.1. 1SY/0.25SY F3

source_name: Adult female collected at one day old, raised on the 1SY diet as a larvae and maintained on the 0.25SY diet as an adult


title: Adult D.1. 1SY/2.5SY F2

source_name: Adult female collected at one day old, raised on the 1SY diet as a larvae and maintained on the 2.5SY diet as an adult


title: Adult D.1. 0.25SY/1SY M2


title: Adult D.1. 0.25SY/1SY F2


title: Adult D.1. 1SY/2.5SY F3


title: Adult D.1. 1SY/0.25SY F4


title: Adult D.1. 0.25SY/1SY F3


title: Adult D.1. 1SY/0.25SY M4

source_name: Adult male collected at one day old, raised on the 1SY diet as a larvae and maintained on the 0.25SY diet as an adult


title: Adult D.1. 0.25SY/1SY F4


title: Adult D.1. 1SY/2.5SY M3


title: Adult D.1. 1SY/0.25SY F1


title: Adult D.1. 1SY/0.25SY M2


title: Adult D.1. 1SY/0.25SY M1


title: Adult D.1. 1SY/1SY M3

source_name: Adult male collected at one day old, raised on the 1SY diet as a larvae and maintained on the 1SY diet as an adult


title: Adult D.1. 1SY/1SY M4


title: Adult D.1. 1SY/0.25SY M3


title: Control_2

description:
Biological replicats 3 of 4
The methylation analysis was performed using EmbryoGENE DNA methylation array (EDMA) platform. The methodology have been thoroughly describef in (Saadi et al., 2014). Briefly, 10ng of DNA sample and spike-in control were cut in ≈160bp fragment using MSEI restriction enzyme. MseLig 12 and MseLig 21 adapters were added to the fragmented gDNA sites. Sample were the digested using methyl sensitive restriction enzyme HpaII, HinP1I and AciI. Only unmethylated fragment have been targeted by those enzyme, leaving only one adapter on the cleaved fragment.     Efficiency of the digestion was confirmed by analyzing the spike-in control added prior to the DNA fragmentation step. For the step, qPCR was performed by preparing a separate mixes containing forward and reverse primer targeting HpaII, HinP1I and AciI site. Undigested spike-in (1/1000 dilution) was used as a positive control and non-template controls were also added as negatives control. The amplification plot and the dissociation curve were evaluated for each primer set separately. The DNA fragmentation was considered successful when the threshold cycle (ct) was greater than 5 when compared to the undigested control.Fragment selection by ligation-mediated PCR  After cleavage by methyl sensitive enzyme, the gDNA was purified by ethanol precipitation and dissolve in nuclease free water. Selective amplification of methylated fragments was performed using two rounds of ligation-mediated PCR (LM-PCR). The PCR products were resolved on 0.8% agarose gel to assess the quality. Then the previously added linker were removed.


title: Adult D.1. 1SY/2.5SY M2


title: Adult D.1. 1SY/1SY F2

source_name: Adult female collected at one day old, raised on the 1SY diet as a larvae and maintained on the 1SY diet as an adult


title: Adult D.1. 1SY/0.25SY F2


title: Adult D.1. 1SY/1SY F4


title: Adult D.1. 1SY/1SY F3


title: Adult D.1. 1SY/2.5SY F1


title: Adult D.1. 1SY/1SY M1


title: Adult D.1. 1SY/1SY M2


title: Adult D.1. 1SY/1SY F1


title: Adult 90%D 2.5SY/2.5SY M3

source_name: Adult male collected at 90% cohort mortality, raised on the 2.5SY diet as a larvae and maintained on the 2.5SY diet as an adult

value: 90% cohort mortality


title: Adult 90%D 2.5SY/2.5SY M4


title: Adult D.1. 1SY/2.5SY F4


title: Adult 90%D 2.5SY/2.5SY M2


title: Adult 90%D 2.5SY/2.5SY M1


title: Adult 90%D 2.5SY/2.5SY F3

source_name: Adult female collected at 90% cohort mortality, raised on the 2.5SY diet as a larvae and maintained on the 2.5SY diet as an adult


title: Adult 90%D 2.5SY/2.5SY F1


title: Adult 90%D 2.5SY/0.25SY M3

source_name: Adult male collected at 90% cohort mortality, raised on the 2.5SY diet as a larvae and maintained on the 0.25SY diet as an adult


title: Adult 90%D 2.5SY/0.25SY F1

source_name: Adult female collected at 90% cohort mortality, raised on the 2.5SY diet as a larvae and maintained on the 0.25SY diet as an adult


title: Adult 90%D 2.5SY/0.25SY F4


title: Adult 90%D 2.5SY/0.25SY F2


title: Adult 90%D 2.5SY/0.25SY M2


title: Adult 90%D 2.5SY/0.25SY M1


title: Adult 90%D 2.5SY/0.25SY M4


title: Adult 90%D 2.5SY/0.25SY F3


title: NR_15A

city: Belgrade

first: Miljana

last: Tanic

address: Pasterova 14

department: Experimental Oncology

country: Serbia

institute: Institute for Oncology and Radiology of Serbia (IORS)

description: Gene expression

hyb_protocol: The puriﬁed, Cy3-labeled samples were combined with Agilent 10x Blocking Agent and Agilent 2x Hi-RPM Hybridization Solution. Agilent-CGHblock (a component of the Genomic DNA ULS Labeling Kit) was added and samples were denatured at 95˚C for 3 minutes prior to array hybridization on the SurePrint G3 Hmn GE v.2 8x60K microarray, for a period of 17h at 65ºC. Washing was performed according to the procedures outlined in the Agilent One-Color Microarray-Based Gene Expression Analysis manual (Version 5.7).

scan_protocol: Washed microarray slides were scanned using Agilent SureScan Microarray Scanner (Agilent Technologies, Santa Clara, CA, USA). Images were processed using Agilent Feature Extraction v.11 software using default settings.

data_processing: Raw data preprocessing and quality control of IORS LABC cohort was performed using R version 3.0.1  and R/Bioconductor packages 'limma', 'ffpe' and  'ArrayQualityMetrics'. We filtered raw data to remove control probes and low expressed probes. To get an idea of how bright expression probes should be, we computed the 95% percentile of the negative control probes on each array and kept probes that are at least 10% brighter than the negative controls, retaining 50751 probes. Filtered data were background subtracted using the normexp method with offset set to 50 and normalized for inter-array comparison by scaling to the median intensity, and log2 transformed.  Probes with over 70% of missing values were removed, otherwise, missing values were imputed using KNN=15. Quality assessment and control for FFPE microarray expression data was performed using 'arrayQualityMetrics' package. Ten samples didn't pass the cutoff (0.3 R2) and were excluded (flagged as rejectQC=TRUE) from further analysis.

source_name: breast carcinoma

label_protocol: In brief, 300 ng of total RNA was reverse transcribed to generate double-stranded cDNA library using Transplex Whole Transcriptome  Amplification (WTA) Kit (Sigma) and HotStarTaq Plus DNA Polymerase (QIAGEN), followed by purification using QIAquick PCR Purification Kit (QIAGEN). One microgram of the amplified WTA library was further labelled with ULS-Cy3 dye for 30 minutes at 85˚C using Genomic DNA ULS Lab Kit (Agilent) and Cy3-labeled samples were cleaned up using Agilent-KREApure columns

extract_protocol: Tumour tissue sections were stained with H&E and examined by a pathologist. Only blocks with more than 50% of tumour cells were used. Total RNA was extracted from two 10 μm thick FFPE tissue sections using RNeasy FFPE Kit (Qiagen) utilising an 18-hour Proteinase K treatment time. The RNA quantity and purity were assessed by BioSpec-nano (Shimadzu Scientific Instruments).

treatment_protocol: samples were obtained either before preoperative radiotherapy( A) or after radiotherapy (B)

value: breast carcinoma

tag: biopsy status radiotherapy

value: pre-radio

tag: clinical response to prt

value: no response

value: FALSE


title: CR_56A

description: Gene expression

tag: tissue

value: complete response

value: TRUE


title: Adult 90%D 2.5SY/1SY M4

source_name: Adult male collected at 90% cohort mortality, raised on the 2.5SY diet as a larvae and maintained on the 1SY diet as an adult

value: male

tag: age


title: CR_62A

description: Gene expression


title: Adult 90%D 2.5SY/2.5SY F2


title: R_9B

description: Gene expression

value: post-radio

value: partial response


title: CR_1A

description: Gene expression


title: Adult 90%D 2.5SY/1SY M3

value: whole body


title: CR_3A

description: Gene expression


title: NR_18A

description: Gene expression


title: Hela cell

description: Gene expression

source_name: cell line

value: Hela cell line


title: R_84A

description: Gene expression


title: CR_2A

description: Gene expression


title: NR_41A

description: Gene expression


title: Adult 90%D 2.5SY/2.5SY F4


title: R_11A

description: Gene expression


title: NR_19B

description: Gene expression


title: NR_19A

description: Gene expression


title: NR_20A

description: Gene expression


title: Adult 90%D 2.5SY/1SY M1


title: NR_16A

description: Gene expression


title: Adult 90%D 2.5SY/1SY M2


title: Adult 90%D 0.25SY/2.5SY F1

source_name: Adult female collected at 90% cohort mortality, raised on the 0.25SY diet as a larvae and maintained on the 2.5SY diet as an adult


title: Adult 90%D 0.25SY/2.5SY M3

source_name: Adult male collected at 90% cohort mortality, raised on the 0.25SY diet as a larvae and maintained on the 2.5SY diet as an adult


title: NR_16B

description: Gene expression


title: Adult 90%D 0.25SY/0.25SY M4

source_name: Adult male collected at 90% cohort mortality, raised on the 0.25SY diet as a larvae and maintained on the 0.25SY diet as an adult


title: Adult 90%D 0.25SY/2.5SY M4


title: Adult 90%D 0.25SY/2.5SY M2


title: Adult 90%D 2.5SY/1SY F2

source_name: Adult female collected at 90% cohort mortality, raised on the 2.5SY diet as a larvae and maintained on the 1SY diet as an adult


title: R_8A

description: Gene expression


title: R_6B

description: Gene expression


title: R_79A

description: Gene expression


title: R_6A

description: Gene expression


title: Adult 90%D 2.5SY/1SY F3


title: Adult 90%D 0.25SY/0.25SY F4

source_name: Adult female collected at 90% cohort mortality, raised on the 0.25SY diet as a larvae and maintained on the 0.25SY diet as an adult


title: R_8B

description: Gene expression


title: Adult 90%D 0.25SY/2.5SY F3


title: R_13A

description: Gene expression


title: Adult 90%D 0.25SY/0.25SY M3


title: R_9A

description: Gene expression


title: Adult 90%D 2.5SY/1SY F4


title: Adult 90%D 2.5SY/1SY F1


title: Adult 90%D 0.25SY/2.5SY M1


title: Adult 90%D 0.25SY/0.25SY M1


title: Adult 90%D 0.25SY/2.5SY F2


title: Adult 90%D 0.25SY/0.25SY M2


title: Adult 90%D 0.25SY/0.25SY F3


title: Adult 90%D 1SY/2.5SY F3

source_name: Adult female collected at 90% cohort mortality, raised on the 1SY diet as a larvae and maintained on the 2.5SY diet as an adult


title: Adult 90%D 0.25SY/1SY F2

source_name: Adult female collected at 90% cohort mortality, raised on the 0.25SY diet as a larvae and maintained on the 1SY diet as an adult


title: Adult 90%D 0.25SY/2.5SY F4


title: Adult 90%D 1SY/2.5SY M1

source_name: Adult male collected at 90% cohort mortality, raised on the 1SY diet as a larvae and maintained on the 2.5SY diet as an adult


title: Adult 90%D 0.25SY/0.25SY F1


title: Adult 90%D 0.25SY/1SY F3


title: Adult 90%D 1SY/2.5SY F4


title: Adult 90%D 0.25SY/1SY M4

source_name: Adult male collected at 90% cohort mortality, raised on the 0.25SY diet as a larvae and maintained on the 1SY diet as an adult


title: Adult 90%D 1SY/2.5SY M2


title: Adult 90%D 0.25SY/0.25SY F2


title: Adult 90%D 0.25SY/1SY M1


title: Adult 90%D 1SY/2.5SY M3


title: Adult 90%D 1SY/2.5SY F1


title: Adult 90%D 0.25SY/1SY M3


title: Adult 90%D 0.25SY/1SY M2


title: Adult D.1. 1SY/2.5SY M1

source_name: Adult male collected at one day old, raised on the 1SY diet as a larvae and maintained on the 2.5SY diet as an adult

value: one day old


title: Adult 90%D 1SY/0.25SY M2

source_name: Adult male collected at 90% cohort mortality, raised on the 1SY diet as a larvae and maintained on the 0.25SY diet as an adult


title: Adult 90%D 1SY/0.25SY M3


title: Adult 90%D 1SY/2.5SY F2


title: Adult 90%D 0.25SY/1SY F1


title: Adult 90%D 0.25SY/1SY F4


title: Adult 90%D 1SY/0.25SY M4


title: Adult 90%D 1SY/2.5SY M4


title: Adult 90%D 1SY/0.25SY M1


title: Adult 90%D 1SY/0.25SY F3

source_name: Adult female collected at 90% cohort mortality, raised on the 1SY diet as a larvae and maintained on the 0.25SY diet as an adult


title: Adult 90%D 1SY/1SY M4

source_name: Adult male collected at 90% cohort mortality, raised on the 1SY diet as a larvae and maintained on the 1SY diet as an adult


title: Adult 90%D 1SY/0.25SY F1


title: Adult 90%D 1SY/0.25SY F2


title: Adult 90%D 1SY/0.25SY F4


title: Adult 90%D 1SY/1SY F4

source_name: Adult female collected at 90% cohort mortality, raised on the 1SY diet as a larvae and maintained on the 1SY diet as an adult


title: Adult 90%D 1SY/1SY M1


title: Adult 10% cohort mortality 2.5SY/2.5SY M3

source_name: Adult male collected at 10% cohort mortality, raised on the 2.5SY diet as a larvae and maintained on the 2.5SY diet as an adult

value: 10% cohort mortality


title: Adult 90%D 1SY/1SY F3


title: Adult 90%D 1SY/1SY M2


title: Adult 90%D 1SY/1SY F2


title: Adult 10% cohort mortality 2.5SY/0.25SY F3

source_name: Adult female collected at 10% cohort mortality, raised on the 2.5SY diet as a larvae and maintained on the 0.25SY diet as an adult


title: Adult 10% cohort mortality 2.5SY/2.5SY F2

source_name: Adult female collected at 10% cohort mortality, raised on the 2.5SY diet as a larvae and maintained on the 2.5SY diet as an adult


title: Adult 10% cohort mortality 2.5SY/1SY F3

source_name: Adult female collected at 10% cohort mortality, raised on the 2.5SY diet as a larvae and maintained on the 1SY diet as an adult


title: Adult 10% cohort mortality 2.5SY/1SY F4


title: Adult 10% cohort mortality 2.5SY/1SY M4

source_name: Adult male collected at 10% cohort mortality, raised on the 2.5SY diet as a larvae and maintained on the 1SY diet as an adult


title: Adult 90%D 1SY/1SY M3


title: Adult 10% cohort mortality 2.5SY/1SY M1


title: Adult 10% cohort mortality 2.5SY/0.25SY F4


title: Adult 10% cohort mortality 2.5SY/1SY F2


title: Adult 10% cohort mortality 2.5SY/2.5SY F3


title: Adult 10% cohort mortality 2.5SY/2.5SY M1


title: Adult 10% cohort mortality 2.5SY/1SY M2


title: Adult 10% cohort mortality 2.5SY/0.25SY M2

source_name: Adult male collected at 10% cohort mortality, raised on the 2.5SY diet as a larvae and maintained on the 0.25SY diet as an adult


title: Adult 10% cohort mortality 2.5SY/2.5SY F4


title: Adult 10% cohort mortality 2.5SY/2.5SY M4


title: Adult 10% cohort mortality 2.5SY/0.25SY M4


title: Adult 10% cohort mortality 2.5SY/1SY M3


title: Adult 10% cohort mortality 0.25SY/2.5SY M4

source_name: Adult male collected at 10% cohort mortality, raised on the 0.25SY diet as a larvae and maintained on the 2.5SY diet as an adult


title: Adult 10% cohort mortality 2.5SY/2.5SY F1


title: Adult 10% cohort mortality 2.5SY/0.25SY M3


title: Adult 10% cohort mortality 2.5SY/0.25SY F1


title: Adult 10% cohort mortality 2.5SY/1SY F1


title: Adult 10% cohort mortality 0.25SY/2.5SY M3


title: Adult 10% cohort mortality 2.5SY/0.25SY M1


title: Adult 90%D 1SY/1SY F1


title: Adult 10% cohort mortality 0.25SY/2.5SY M1


title: Adult 10% cohort mortality 0.25SY/2.5SY M2


title: Adult 10% cohort mortality 2.5SY/2.5SY M2


title: Adult 10% cohort mortality 0.25SY/0.25SY F1

source_name: Adult female collected at 10% cohort mortality, raised on the 0.25SY diet as a larvae and maintained on the 0.25SY diet as an adult


title: Adult 10% cohort mortality 0.25SY/1SY M3

source_name: Adult male collected at 10% cohort mortality, raised on the 0.25SY diet as a larvae and maintained on the 1SY diet as an adult


title: Adult 10% cohort mortality 0.25SY/0.25SY M3

source_name: Adult male collected at 10% cohort mortality, raised on the 0.25SY diet as a larvae and maintained on the 0.25SY diet as an adult


title: Adult 10% cohort mortality 0.25SY/0.25SY F3


title: Adult 10% cohort mortality 0.25SY/1SY M2


title: Adult 10% cohort mortality 0.25SY/1SY F4

source_name: Adult female collected at 10% cohort mortality, raised on the 0.25SY diet as a larvae and maintained on the 1SY diet as an adult


title: Adult 10% cohort mortality 0.25SY/2.5SY F3

source_name: Adult female collected at 10% cohort mortality, raised on the 0.25SY diet as a larvae and maintained on the 2.5SY diet as an adult


title: Adult 10% cohort mortality 0.25SY/2.5SY F4


title: Adult 10% cohort mortality 0.25SY/0.25SY F2


title: Adult 10% cohort mortality 1SY/2.5SY M2

source_name: Adult male collected at 10% cohort mortality, raised on the 1SY diet as a larvae and maintained on the 2.5SY diet as an adult


title: Adult 10% cohort mortality 0.25SY/2.5SY F2


title: Adult 10% cohort mortality 0.25SY/1SY M1


title: Adult 10% cohort mortality 0.25SY/2.5SY F1


title: Adult 10% cohort mortality 0.25SY/0.25SY M2


title: Adult 10% cohort mortality 1SY/2.5SY F3

source_name: Adult female collected at 10% cohort mortality, raised on the 1SY diet as a larvae and maintained on the 2.5SY diet as an adult


title: Adult 10% cohort mortality 0.25SY/0.25SY M1


title: Adult 10% cohort mortality 1SY/2.5SY F2


title: Adult 10% cohort mortality 1SY/2.5SY F1


title: Adult 10% cohort mortality 0.25SY/1SY M4


title: Adult 10% cohort mortality 0.25SY/1SY F2


title: Adult 10% cohort mortality 1SY/2.5SY M3


title: Adult 10% cohort mortality 0.25SY/1SY F3


title: Adult 10% cohort mortality 1SY/2.5SY M1


title: Adult 10% cohort mortality 0.25SY/1SY F1


title: Adult 10% cohort mortality 2.5SY/0.25SY F2


title: HCT116 Kras+/- cells ECT2 siRNA replicate 2

city: Glasgow

first: W. Nicol

last: Keith

address: Wolfson Wohl Translational Cancer Research Centre

department: Institute of Cancer Science

country: United Kingdom

institute: University of Glasgow

hyb_protocol: 100 μl of purified labelled total RNA was hybridised to Agilent 4x44K whole human genome arrays for 17 hours at 65 °C rotating at 10 rpm and washed as as per manufacturers instructions for one colour arrays (Agilent Technologies)

scan_protocol: Slides were scanned using DNA microarray scanner model G2539A (Agilent Technologies) and Agilent Scan Control Software. Spot intensity and identity information was extracted using Agilent Feature Extraction Software.

data_processing:
Normalisation performed in GeneSpring GX (Agilent Technologies).  Feature extraction data normalised to the 75th percentile
Log transformed values normalised to the 75th percentile

source_name: HCT116 Kras+/- colorectal cancer cells transfected with ECT2 siRNA replicate 2

label_protocol: 800 ng of total RNA was labelled with Cy3 using the Low RNA Input Linear Amplification Kit (Agilent technologies) following manufacturers instructions

growth_protocol: HCT116 human colorectal cancer cells were cultured in phenol-red free DMEM containing 10% feotal bovine serum under 5% oxygen

extract_protocol: Total RNA was extracted from trypsinised cell pellets using the Nucleospin II kit (Macherey-Nagel) following manufacturers instructions

treatment_protocol: 3000 cells were transfected with 50nM ECT2 or scrambled siRNA using lipofectamine reagent. On day 5 post-transfection cells were harvested for RNA extraction.

tag: cell line


title: Adult 10% cohort mortality 1SY/2.5SY M4


title: Adult 10% cohort mortality 0.25SY/0.25SY M4


title: HCT116 Kras+/- cells scrambled siRNA replicate 1

source_name: HCT116 Kras+/- colorectal cancer cells transfected with scrambled siRNA replicate 1


title: Adult 10% cohort mortality 0.25SY/0.25SY F4


title: Adult 10% cohort mortality 1SY/0.25SY M2

source_name: Adult male collected at 10% cohort mortality, raised on the 1SY diet as a larvae and maintained on the 0.25SY diet as an adult


title: HCT116 cells ECT2 siRNA replicate 3

source_name: HCT116 colorectal cancer cells transfected with ECT2 siRNA replicate 3


title: Adult 10% cohort mortality 1SY/0.25SY M3


title: HCT116 Kras+/- cells ECT2 siRNA replicate 3

source_name: HCT116 Kras+/- colorectal cancer cells transfected with ECT2 siRNA replicate 3


title: Adult 10% cohort mortality 1SY/0.25SY F3

source_name: Adult female collected at 10% cohort mortality, raised on the 1SY diet as a larvae and maintained on the 0.25SY diet as an adult


title: HCT116 cells ECT2 siRNA replicate 1

source_name: HCT116 colorectal cancer cells transfected with ECT2 siRNA replicate 1


title: HCT116 Kras+/- cells ECT2 siRNA replicate 1

source_name: HCT116 Kras+/- colorectal cancer cells transfected with ECT2 siRNA replicate 1


title: Adult 10% cohort mortality 1SY/2.5SY F4


title: Adult 10% cohort mortality 1SY/0.25SY M1


title: Adult 10% cohort mortality 1SY/0.25SY M4


title: HCT116 cells scrambled siRNA replicate 4

source_name: HCT116 colorectal cancer cells transfected with scrambled siRNA replicate 4


title: Adult 10% cohort mortality 1SY/0.25SY F1


title: HCT116 Kras+/- cells scrambled siRNA replicate 2

source_name: HCT116 Kras+/- colorectal cancer cells transfected with scrambled siRNA replicate 2


title: HCT116 cells scrambled siRNA replicate 3

source_name: HCT116 colorectal cancer cells transfected with scrambled siRNA replicate 3


title: HCT116 cells scrambled siRNA replicate 1

source_name: HCT116 colorectal cancer cells transfected with scrambled siRNA replicate 1


title: Adult 10% cohort mortality 1SY/1SY M3

source_name: Adult male collected at 10% cohort mortality, raised on the 1SY diet as a larvae and maintained on the 1SY diet as an adult


title: HCT116 cells ECT2 siRNA replicate 2

source_name: HCT116 colorectal cancer cells transfected with ECT2 siRNA replicate 2


title: HCT116 cells scrambled siRNA replicate 5

source_name: HCT116 colorectal cancer cells transfected with scrambled siRNA replicate 5


title: Adult 10% cohort mortality 1SY/1SY F2

source_name: Adult female collected at 10% cohort mortality, raised on the 1SY diet as a larvae and maintained on the 1SY diet as an adult


title: Adult 10% cohort mortality 1SY/1SY M4


title: HCT116 cells scrambled siRNA replicate 2

source_name: HCT116 colorectal cancer cells transfected with scrambled siRNA replicate 2


title: Adult 10% cohort mortality 1SY/1SY M2


title: Adult 10% cohort mortality 1SY/0.25SY F2


title: Adult 10% cohort mortality 1SY/1SY F4


title: 42Y-2

city: Taichung

first: Yng-Tay

last: Chen

address: No 2 Yude road

department: Department of medical research

country: Taiwan

institute: China Medical University Hospital

description: fraction: promoter

hyb_protocol: Hybridization was performed with an Affymetrix Mouse Gene 1.0 ST Array.

scan_protocol: Array was scanned on an Affymetrix GeneChip Scanner 3000.

data_processing: Expression Console affymetrix-algorithm-name = rma-gene-default

label_protocol: Then, 3.5 mg (7 mL) of MBD-Biotin Protein was added to 10 mL Dynabeads M-280 Streptavidin according to the manufacturer’s instructions.

growth_protocol: Peripheral blood leukocytes was collected from T2D mice and control mice.

extract_protocol: One microgram of cDNA was sonicated to produce fragments ranging from 100 to 500 bp.

treatment_protocol: Message RNA was extracted from peripheral blood leukocytes by using the Total RNA extraction kit (Qiagen, Valencia, CA, USA), according to the manufacturer’s instructions.

tag: genotype/variation

value: control

value: Blood


title: 10 uM UT-69+0.1 nM R1881

city: Memphis

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

description: gene expression data human tissue

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Clariom®D Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with affmetrix expression console default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

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

extract_protocol: Total RNA was extracted from LNCaP cells using the qiagen RNA isolation kit and its quality was verified using the Agilent 2100 Bioanalyzer (Agilent Technologies).

value: LNCaP

tag: agent


title: 10 uM Enzalutamide+0.1 nM R1881

description: gene expression data human tissue

source_name: 10 uM Enzalutamide+0.1 nM R1881

value: 10 uM Enzalutamide+0.1 nM R1881


title: Adult 10% cohort mortality 1SY/1SY F1

value: female


title: Adult 10% cohort mortality 1SY/1SY M1


title: Adult 10% cohort mortality 1SY/0.25SY F4


title: PD 9

city: Hirosaki

first: Shuji

last: Shimoyama

state: Aomori

address: 5 Zaifu-cho

department: Department of Neurophysiology

country: Japan

institute: Hirosaki University Graduate School of Medicine

hyb_protocol: 5.5 μg of fragmented and biotin-labeled single-strand cDNA were hybridized on ClariomTM D array (human) for 16 h at 45°C with rotation at 60 rpm using GeneChip® Hybridization Oven 645.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: The data were analyzed with Expression Console version 1.4.1 (Affymetrix) using default settings.

source_name: peripheral blood mononuclear cells

label_protocol: Fragmented single-strand cDNA were subjected to 3' terminal labeling with biotin using GeneChip® WT PLUS Reagent Kit in accordance with manufacturer's protocol.

extract_protocol: Total RNA was isolated from PBMC using an illustra RNAspin mini RNA isolation kit (GE Healthcare) according to the manufacturer's protocol. 100 ng of total RNA was carried out to First-strand cDNA synthesis using GeneChip® WT PLUS Reagent Kit (Affymetrix).

value: peripheral blood

tag: cell type

value: mononuclear cells

tag: gender

value: 69 years old

tag: diagnosis

value: Parkinson's disease


title: 42Y-1

description: fraction: promoter


title: Adult 10% cohort mortality 1SY/1SY F3

tag: Sex

tag: larval diet


title: 10 uM R-UT-155+0.1 nM R1881

description: gene expression data human tissue


title: PD 8

value: 53 years old


title: PD 6

value: male

value: 80 years old


title: PD 5

value: 58 years old


title: 16Y-1

description: fraction: promoter


title: PD 10

value: 73 years old


title: 16Y-2

description: fraction: promoter


title: 42WKKA

description: fraction: promoter


title: 42WKKB

description: fraction: promoter


title: PD 7

value: 70 years old


title: 6Y-1

description: fraction: promoter


title: 6Y-2

description: fraction: promoter


title: 10 uM UT-155+0.1 nM R1881

description: gene expression data human tissue


title: PD 1

value: 67 years old


title: PD 2

value: 75 years old


title: 1-5

description: fraction: promoter

value: control


title: 1-3

description: fraction: promoter

value: Blood


title: control 9

value: 78 years old

value: healthy control


title: 6K-1

description: fraction: promoter


title: PD 4

value: female


title: PD 3

value: peripheral blood

value: 55 years old


title: 0.1 nM R1881

description: gene expression data human tissue

value: LNCaP


title: 6K-2

description: fraction: promoter


title: control 1

value: mononuclear cells


title: control 5

value: 60 years old


title: control 8

value: 64 years old


title: control 4

value: 65 years old


title: control 3

value: 53 years old


title: control 7

value: male


title: control 6


title: DNA6050-053(2)_16zero

status: Public on Jul 26 2017

city: Gosselies

first: Baharak

last: Hooshiar Kashani

state: Charleroi

address: Rue Adrienne Bolland 8

department: Institute for Medical Immunology

country: Belgium

institute: Université Libre de Bruxelles

description: Mock infected_16 hours

hyb_protocol: About 10 mg from each experimental sample along with Affymetrix eukaryotic hybridization controls were hybridized for 16 h to Human U 133 Plus 2.0 genome arrays, containing 54 676 transcripts.

scan_protocol: Arrays were scanned with an Affymetrix GeneChips Scanner 3000 at 570nm.

data_processing:
Simpleaffy package was used to pre-process the raw data for background correction, normalization and probe summarization by the RMA method
Differentially expressed genes were defined using a statistical tool called LIMMA package, which is part of the Bioconductor statistical analysis software.

source_name: Adult

label_protocol: Probes were generated using the Affymetrix GeneChip Expression 3’ Amplification Two-cycle Target Labeling and Controls Reagents kit

growth_protocol: Dendritic cells derived from cord or adult blood monocytes

extract_protocol: Total RNA was isolated using TRIzol reagent and RNeasy Micro kit

treatment_protocol: HCMV or Mock infection for 6 and 16 hours

value: Dendritic cells

value: Mock

tag: time point

value: 16 hours


title: DNA6050-019(2)_16zero

description: Mock infected_16 hours


title: DNA6050-030(2)_6ten

description: HCMV infected_6 hours

source_name: Neonate

value: HCMV

value: 6 hours


title: DNA6050-020(2)_16ten

description: HCMV infected_16 hours


title: DNA6050-024(2)_6ten

description: HCMV infected_6 hours


title: DNA6050-026(2)_16ten

description: HCMV infected_16 hours


title: DNA6050-007(2)_16zero

description: Mock infected_16 hours


title: control 2

value: 54 years old


title: DNA6050-008(2)_16ten

description: HCMV infected_16 hours


title: DNA6050-025(2)_16zero

description: Mock infected_16 hours


title: DNA6050-054(2)_6ten

description: HCMV infected_6 hours


title: DNA6050-018(2)_16ten

description: HCMV infected_16 hours


title: CL1-0 shKSRP-2 biological rep1

city: Taipei

first: Kuo-Tai

last: Hua

address: No. 1, Sec. 1, Jen-Ai Rd.

institute: National Taiwan University

description: Gene expression data from CL1-0 cells with KSRP shRNA

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 PLUS 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

source_name: CL1-0 shKSRP-2

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: Cells were cultured in 5% CO2 incubator at 37℃.

extract_protocol: Qiagene RNeasy mini kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cell were selected with puromycin for two weeks.  Stably transduced cells were use for this experiment.

tag: tissue type

value: lung cancer

tag: genotype

value: KSRP shRNA


title: DNA6050-022(2)_6ten

description: HCMV infected_6 hours


title: DNA6050-006(2)_16ten

description: HCMV infected_16 hours


title: DNA6050-002(2)_6ten

description: HCMV infected_6 hours


title: DNA6050-004(2)_6ten

description: HCMV infected_6 hours


title: CL1-0 shKSRP-1 biological rep2

source_name: CL1-0 shKSRP-1


title: CL1-0 shKSRP-2 biological rep2


title: DNA6050-017(2)_16zero

description: Mock infected_16 hours


title: CL1-0 shKSRP-1 biological rep3


title: DNA6050-005(2)_16zero

description: Mock infected_16 hours


title: CL1-0 shscramble biological rep3

description: Gene expression data from CL1-0 cells with scramble shRNA

source_name: CL1-0 shscramble

value: scramble shRNA


title: CL1-0 shKSRP-2 biological rep3


title: CL1-0 shscramble biological rep2


title: CL1-0 shKSRP-1 biological rep1


title: CL1-0 shscramble biological rep1


title: overexpression of the empty lentiviral vector_rep1

city: Fuzhou

first: Yang

last: wenjing

address: 156 Xierhuan Road

country: China

institute: Fuzhou General Hospital

description: overexpression of the empty lentiviral vector in HEK293T cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000.

data_processing: The data were analyzed using Affymetrix GeneChip Command Console Software.

growth_protocol: cell lines were grown at 37C with 5% CO2

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

treatment_protocol: DMEM medium with 10% FBS and 1% penicillin/streptomycin

value: human emborynic kidney 293 cells


title: overexpression of the empty lentiviral vector_rep2

source_name: overexpression of the empty lentiviral vector in HEK293T cells


title: KO_16m_9970_2_4

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

description:
2KO#4
KO_16m_9970_2_4

hyb_protocol: Standard agilent protocol

scan_protocol: Standard agilent protocol

data_processing: Agilent Feature Extraction software with default parameters was used for data processing. Expression levels were extracted from Agilent microarray image files, then normalized and log2-transformed, with software R (version 2.15.3) and Bioconductor (version 2.11) packages.

source_name: KO_16 month_microglia

label_protocol: Standard agilent protocol

growth_protocol: Animals were generated on C57B/6J background as previously described (Martins et al 2012, PMID 23041626)

extract_protocol: we isolated microglia from 4 and 16 month old Grn+/+ and Grn−/− mice using Percoll gradients and fluorescence-activated cell sorting (FACS) with microglia/macrophage/neutrophil markers, CD11b PE, CD45 APC and anti-Ly6G PE-Cy7

tag: strain background

value: KO

value: 16 month

value: microglia


title: KO_16m_9970_2_1

description:
2KO#1
KO_16m_9970_2_1


title: KO_16m_9970_2_3

description:
2KO#3
KO_16m_9970_2_3


title: WT_16m_9970_1_4

description:
1WT#4
WT_16m_9970_1_4

source_name: WT_16 month_microglia

value: WT


title: WT_16m_9970_1_3

description:
1WT#3
WT_16m_9970_1_3


title: KO_16m_9970_2_2

description:
2KO#2
KO_16m_9970_2_2


title: SPC_A-1sci_rep2

city: Shanghai

first: Shengli

last: Li

address: 650 Xinsongjiang Road

institute: Shanghai Jiao Tong University School of Medicine

description: lncRNA expression in SPC-A-1sci cell line

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: SPC-A-1sci cell line

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

extract_protocol: RNA was prepared using the TRIzol reagent (Invitrogen, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000 spectrophotometer (Thermo, Japan) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: SPC-A-1 and SPC-A-1sci cell lines were routinely cultured at 37°C in a humidified air atmosphere containing 5% carbon dioxide in Dulbecco’s Modified Eagle Media supplemented with 10% fetal bovine serum (FBS) (Biowest, South America origin), 100u/ml penicillin (Sigma-Aldrich), and 100ug/ml streptomycin (Sigma-Aldrich).

value: non-small cell lung cancer (NSCLC) cell line

tag: cell phenotype

value: highly metastatic