title: wildtype, control, biological rep3

city: Bangi

first: Lay Wen

last: Tan

state: Selangor

address: The National University of Malaysia

country: Malaysia

institute: Institute of Systems Biology

description: gene expression data from control group, wildtype rice cv. MR219

hyb_protocol: Following fragmentation, cRNA were hybridized GeneChip® Rice (Cn) Gene 1.0 ST Arrays for 16 hours at 45oC with rotation at 60 rpm. GeneChips were washed and stained using the FS450_0002 fluidics protocol.

scan_protocol: Genechips were scanned using an Affymetrix 3000 7G scanner (S/N 54716600).

data_processing: CEL. files generated were imported into expression console (EC) 1.4 software for array quality control. RMA normalisation was performed on the samples to generate the QC metrics. CHP. files generated were then imported into Affymetrix Transcriptome Analysis Console (TAC) software to identify differentially expressed genes. Significant expression fold-change was set at 2 with p-value 0.05.

organism: Oryza sativa Indica Group

source_name: wildtype

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Rice seeds were sterilised and grown on 1/2 MS medium under controlled temperature and light. Ten days old seedlings were harvested for experiment.

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

tag: cultivar

value: seedlings

tag: age

value: 10 days old

tag: genotype

value: wildtype


title: Overexpression, biological rep2

status: Public on Jun 01 2017

type: RNA

description: gene expression data from transgenic rice overexpressing Abp57

label: biotin

molecule: total RNA

source_name: transgenic rice overexpressing Abp57

tag: tissue

value: Abp57 overexpression


title: Gastric cancer tissues_rep5

status: Public on May 31 2017

city: Shenyang City

first: Zhenning

last: Wang

address: 155 North Nanjing Street

department: Department of Surgical Oncology and General Surgery

country: China

institute: The First Affiliated Hospital of China Medical University

description: miRNA expression in Case 5 gastric cancer tissues

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal. Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm.

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

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs were identified through Fold Change Filtering，and significant differentially expressed miRNAs were identified through Volcano Plot filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR).

organism: Homo sapiens

source_name: Gastric cancer tissues, rep5

label_protocol: After RNA isolation from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

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

tag: gender

value: Female

value: gastric cancer tissue


title: Overexpression, biological rep3


title: Gastric cancer tissues_rep1

description: miRNA expression in Case 1 gastric cancer tissues

source_name: Gastric cancer tissues, rep1

value: Male


title: non-tumorous adjacent tissues_rep3

description: miRNA expression in Case 3 non-tumorous adjacent tissues

source_name: non-tumorous adjacent tissues, rep3

value: non-tumorous adjacent tissues


title: THP-1 LPS 2 control

city: Nagasaki

first: Tomohiro

last: Koga

address: 1-7-1 Sakamoto

country: Japan

institute: Nagasaki University

description:
AR2377_05
Gene expression after 18hr LPS stimulation in macrophages derived from THP-1 cells.

hyb_protocol: 2.0ug of Cy3-labelled cDNA was filled up to 50 ul containing 1x Agilent blocking agent and 1x Agilent hybridization buffer, and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver2.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: macrophages derived from THP-1 cells

label_protocol: cDNA were amplified by Ovation® Pico WTA System V2（NuGEN Technologies) from 3ng total RNA according to the manufacturer's instructions. Amplified cDNA yield were checked with the NanoDrop ND-2000 Spectrophotometer. Cyanine-3 (Cy3) labeled cDNA was prepared with SureTag Complete DNA Labeling Kit (Agilent) according to the manufacturer's instructions, followed by Amicon Ultra-0.5 mL Centrifugal Filters for DNA Purification and Concentration (Merck Millipore). Dye incorporation and cDNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: The RNA was obtained from macrophages from THP-1 cells after LPS stimulation. Total cellular RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) following the manufacturer's recommendations. The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Macrophages derived from THP-1 cells were stimulated with 100ng/ml of LPS for 18 hours.

tag: cell line

value: THP-1 (ATCC TIB-202)

tag: cell type

value: macrophages

tag: treatment

value: LPS

tag: miRNA

value: control


title: non-tumorous adjacent tissues_rep4

description: miRNA expression in Case 4 non-tumorous adjacent tissues

source_name: non-tumorous adjacent tissues, rep4


title: non-tumorous adjacent tissues_rep5

description: miRNA expression in Case 5 non-tumorous adjacent tissues

source_name: non-tumorous adjacent tissues, rep5


title: THP-1 LPS 1 miR-204-3p

description:
AR2377_08
Gene expression after 18hr LPS stimulation in macrophages derived from THP-1 cells.


title: non-tumorous adjacent tissues_rep6

description: miRNA expression in Case 6 non-tumorous adjacent tissues

source_name: non-tumorous adjacent tissues, rep6


title: Gastric cancer tissues_rep2

description: miRNA expression in Case 2 gastric cancer tissues

source_name: Gastric cancer tissues, rep2


title: Overexpression, biological rep1


title: wildtype, control, biological rep2


title: Gastric cancer tissues_rep4

description: miRNA expression in Case 4 gastric cancer tissues

source_name: Gastric cancer tissues, rep4


title: non-tumorous adjacent tissues_rep2

description: miRNA expression in Case 2 non-tumorous adjacent tissues

source_name: non-tumorous adjacent tissues, rep2


title: wildtype, control, biological rep1


title: THP-1 LPS 1 control

description:
AR2377_02
Gene expression after 18hr LPS stimulation in macrophages derived from THP-1 cells.


title: Gastric cancer tissues_rep3

description: Gene and lncRNA expression in Case 3 gastric cancer tissues

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 4 out of 12 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs were identified through Fold Change filtering or Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: Gastric cancer tissues, rep3

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was extracted from the tissues using Trizol reagent (Invitrogen). RNA quantity and quality were measured by NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: gastric cancer tissues


title: Gastric cancer tissues_rep3

description: miRNA expression in Case 3 gastric cancer tissues


title: non-tumorous adjacent tissues_rep1

description: miRNA expression in Case 1 non-tumorous adjacent tissues

source_name: non-tumorous adjacent tissues, rep1


title: Gastric cancer tissues_rep6

description: Gene and lncRNA expression in Case 6 gastric cancer tissues

source_name: Gastric cancer tissues, rep6


title: Gastric cancer tissues_rep5

description: Gene and lncRNA expression in Case 5 gastric cancer tissues


title: Gastric cancer tissues_rep4

description: Gene and lncRNA expression in Case 4 gastric cancer tissues


title: Gastric cancer tissues_rep2

description: Gene and lncRNA expression in Case 2 gastric cancer tissues


title: non-tumorous adjacent tissues_rep5

description: Gene and lncRNA expression in Case 5 non-tumorous adjacent tissues


title: non-tumorous adjacent tissues_rep6

description: Gene and lncRNA expression in Case 6 non-tumorous adjacent tissues


title: non-tumorous adjacent tissues_rep4

description: Gene and lncRNA expression in Case 4 non-tumorous adjacent tissues


title: non-tumorous adjacent tissues_rep3

description: Gene and lncRNA expression in Case 3 non-tumorous adjacent tissues


title: Gastric cancer tissues_rep1

description: Gene and lncRNA expression in Case 1 gastric cancer tissues


title: Gastric cancer tissues_rep6

description: miRNA expression in Case 6 gastric cancer tissues


title: QM9414_LL_C_1 (cre)

city: Vienna

first: Monika

last: Schmoll

address: Djerassiplatz 1

department: Centre of Microbiology and Environmental Systems Science

country: Austria

institute: University of Vienna

description: one of two biological replicates

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Trichoderma reesei

source_name: QM9414 grown on cellulose in constant light

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Trichoderma reesei strains were grown in 1 l Erlenmeyer flasks on a rotary shaker (200 rpm) at 28°C in Mandels-Andreotti minimal medium with 1% microcrystalline cellulose as carbon source in constant light (LL) or constant darkness (DD) for 72 hours.

extract_protocol: Total RNA was extracted as described in Tisch et al., 2011 (New insights into the mechanism of light modulated signaling by heterotrimeric G-proteins: ENVOY acts on gna1 and gna3 and adjusts cAMP levels in Trichoderma reesei (Hypocrea jecorina). Fungal Genet Biol, 48 (6): 631 – 40) with supplies provided by the RNeasy Plant Mini Kit (QIAGEN, Hilden, Germany). The quality of the RNA was controlled with the Experion Automated Electrophoresis System (Bio-Rad, Hercules, USA). Total RNA was treated with DNase (Fermentas, Vilnius, Lithuania) and purified using the RNeasy Mini Kit (QIAGEN). cDNA synthesis was done with the RevertAid H- First Strand cDNA Synthesis Kit (Fermentas) and Oligo-d(T) Primer.

treatment_protocol: Mycelium was harvested under red-safety light when cultivated in darkness and frozen in liquid nitrogen.

tag: strain

value: parental strain


title: cre_DD_C_1

description: one of two biological replicates

source_name: delta-cre1 grown on cellulose in constant darkness


title: cre_LL_C_1

description: one of two biological replicates

source_name: delta-cre1 grown on cellulose in constant light


title: cre_DD_C_2

description: one of two biological replicates


title: cre_LL_C_2

description: one of two biological replicates


title: QM9414_LL_C_2 (cre)

description: one of two biological replicates


title: shLINC00173.2_batch3

city: Frankfurt

first: Jan-Henning

last: Klusmann

address: Theodor-Stern-Kai 7

department: Pediatric Hematology and Oncology

country: Germany

institute: Goehte University Frankfurt

description: Gene expression data from CD34+ HSPC in myeloid conditions transduced with linc00173 shRNA2 day 4

hyb_protocol: 0.6 ug of Cy3-labelled cRNA  was fragmented at 60°C for 30 minutes in 1x Agilent fragmentation buffer. After addition of  Agilent hybridization buffer the mixture was hybridized to Agilent-072363 SurePrint G3 Human GE v3 8x60K Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C)

data_processing: The scanned images were analyzed with Feature Extraction Software11.5. (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: CD34+ HSPC LINC00173 shRNA2 day 4_batch 3

label_protocol: 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, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: In three independent experiments (batches 1-3) human CD34+ HSPC from chord blood were transduced with VSV-G pseudotyped lentiviral constructs targeting LINC00173 or a control shRNA. Transduced cells were FACS sorted for EGFP expression and subjected to myeloid differentiation conditions. Total RNA was prepared 4 days after sorting.  We analyzed early gene expression changes using Agilent-072363 SurePrint G3 Human GE v3 8x60K Microarrays

extract_protocol: Zymo Research Quick RNA Miniprep Kit according to manufacturers instructions. RNA quality was assessed using the Agilent 2100 Bioanalyzer.

value: human CD34+ HSPC in myeloid differentiation medium


title: QM9414_DD_C_1 (cre)

description: one of two biological replicates

source_name: QM9414 grown on cellulose in constant darkness


title: non-tumorous adjacent tissues_rep1

description: Gene and lncRNA expression in Case 1 non-tumorous adjacent tissues


title: QM9414_DD_C_2 (cre)

description: one of two biological replicates


title: shRNA_ctr_batch3

description: Gene expression data from CD34+ HSPC in myeloid conditions transduced with ctrl shRNA day 4

source_name: CD34+ HSPC ctrl shRNA day 4_batch 3


title: shRNA_ctr_batch1

source_name: CD34+ HSPC ctrl shRNA day 4_batch 1


title: shLINC00173.1_batch3

description: Gene expression data from CD34+ HSPC in myeloid conditions transduced with linc00173 shRNA1 day 4

source_name: CD34+ HSPC LINC00173 shRNA1 day 4_batch 3


title: Intestinal epithelial cells_Xbp1sCreER CtnnbloxEx3/+ KrasG12D/+, biological replicate 4

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

hyb_protocol: Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Affimetrix GeneChip Scanner 3000 7G.

data_processing: Data were quantile normalized and log2 transformed using R/Bioconductor package limma

organism: Mus musculus

source_name: Epithelial cells, small intestine

label_protocol: GeneChip WT Terminal Labeling Kit.

growth_protocol: Mice heterozygous for the CtnnbloxEx3 and KrasG12D allels were crossed to VilCreER or Xbp1sCreER mice. Mice were maintained on a mixed background.

extract_protocol: Total RNA was isolated by Qiagen RNeasy Mini Kit according to the manufacturer's protocol.

treatment_protocol: To induce the expression of stabilized β-catenin and mutant Kras mice received 1 mg Tamoxifen on 5 consecutive days.

value: Xbp1sCreER CtnnbloxEx3/+ KrasG12D/+


title: shRNA_ctr_batch2

source_name: CD34+ HSPC ctrl shRNA day 4_batch 2


title: shLINC00173.2_batch2

source_name: CD34+ HSPC LINC00173 shRNA2 day 4_batch 2


title: Intestinal epithelial cells_Xbp1sCreER CtnnbloxEx3/+ KrasG12D/+, biological replicate 5


title: shLINC00173.1_batch1

source_name: CD34+ HSPC LINC00173 shRNA1 day 4_batch 1


title: Intestinal epithelial cells_Xbp1sCreER CtnnbloxEx3/+ KrasG12D/+, biological replicate 1


title: Intestinal epithelial cells_Xbp1sCreER CtnnbloxEx3/+ KrasG12D/+, biological replicate 3


title: Intestinal epithelial cells_VilCreER CtnnbloxEx3/+ KrasG12D/+, biological replicate 5

value: VilCreER CtnnbloxEx3/+ KrasG12D/+


title: shLINC00173.1_batch2

source_name: CD34+ HSPC LINC00173 shRNA1 day 4_batch 2


title: Intestinal epithelial cells_VilCreER CtnnbloxEx3/+ KrasG12D/+, biological replicate 4


title: Intestinal epithelial cells_VilCreER CtnnbloxEx3/+ KrasG12D/+, biological replicate 2


title: Intestinal epithelial cells_Xbp1sCreER CtnnbloxEx3/+ KrasG12D/+, biological replicate 2


title: Intestinal epithelial cells_VilCreER CtnnbloxEx3/+ KrasG12D/+, biological replicate 3


title: Intestinal epithelial cells_VilCreER CtnnbloxEx3/+ KrasG12D/+, biological replicate 1


title: CD8 T-cells_3

description: Gene expression data from CD8+ T-cells

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-021441 NCode Human Long Non-coding RNA microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2505B)

data_processing: The scanned images were analyzed with Feature Extraction Software10.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. For each sample the gProcessedSignal was extracted from the Agilent Feature Extraction Files and the log2 values were quantile normalized and averaged using the LIMMA package from R/Bioconductor.

source_name: CD8 T-cells purified from peripheral blood

growth_protocol: Human blood cells were FACS-purified from healthy donors after informed consent. Fetal liver CD34+ HSPCs were purchased from Novogenic Laboratories (LLC USA). Megakaryocytes and erythroblasts were obtained from CB CD34+ HSPCs through 7 days of in vitro differentiation followed by sorting for CD41+/CD42b+ (megakaryocytes) or CD36+/CD235a+ (erythroid cells). From purified cells total RNA was prepared using the Zymo Research Quick RNA Miniprep Kit and RNA quality was checked using the Agilent 2100 Bioanalyzer.

tag: facs

value: FSlowSSlow CD3+ CD4- CD8+

value: CD8+ T-cell


title: CD8 T-cells_4

description: Gene expression data from CD8+ T-cells


title: CD8 T-cells_2

description: Gene expression data from CD8+ T-cells


title: CD8 T-cells_1

description: Gene expression data from CD8+ T-cells


title: Nrdc-cKO

city: Kyoto

first: Kozo

last: Ikuta

address: 54 Shogoin-Kawahara-cho, Sakyo-ku

department: Department of Gastroenterology and Hepatology

institute: Kyoto University Graduate School of Medicine

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse Gene Expression v2 8x60K Microarray (Agilent technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent technologies).

scan_protocol: Microarray slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Nrdc-cKO pancreas, 5weeks

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA using the Low Input Quick Amp Labeling Kit (Agilent technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was prepared using RNAlater Solutions (ThermoFisher SCIENTIFIC, Waltham, MA) and RNeasy Mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.   RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: pancreas

value: male


title: CD4 T-cells_5

description: Gene expression data from CD4+ T-cells

source_name: CD4 T-cells purified from peripheral blood

value: FSlowSSlow CD3+ CD4+ CD8-

value: CD4+ T-cell


title: non-tumorous adjacent tissues_rep2

description: Gene and lncRNA expression in Case 2 non-tumorous adjacent tissues

source_name: non-tumorous adjacent tissues, rep2

value: Male


title: shLINC00173.2_batch1

source_name: CD34+ HSPC LINC00173 shRNA2 day 4_batch 1


title: CD4 T-cells_2

description: Gene expression data from CD4+ T-cells


title: CD8 T-cells_5

description: Gene expression data from CD8+ T-cells


title: CD4 T-cells_4

description: Gene expression data from CD4+ T-cells


title: NK-cells_5

description: Gene expression data from CD56+ natural killer cells

source_name: CD56+ NK-cells purified from peripheral blood

value: FSlowSSlow CD56+ CD3-

value: CD56+ natural killer cell


title: CD4 T-cells_3

description: Gene expression data from CD4+ T-cells


title: NK-cells_4


title: WT

source_name: WT pancreas, 5weeks


title: CD4 T-cells_1

description: Gene expression data from CD4+ T-cells


title: NK-cells_1


title: NK-cells_3


title: B-cells_6

description: Gene expression data from CD19+ B-cells

source_name: CD19+ Bcells purified from peripheral blood

value: FSlowSSlow CD19+ CD3-CD56-

value: CD19+ B-cell


title: MLL_T9-11_7

description: Gene expression data from AML t(10;11) M5

hyb_protocol: 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505B).

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images.For each sample the gProcessedSignal was extracted from the Agilent Feature Extraction Files and the log2 values were quantile normalized using the LIMMA package from R/Bioconductor

source_name: AML blasts purified from peripheral blood

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into Cy3-labeled fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was  fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA.

growth_protocol: Human AML blasts were FACS-purified from pediatric patients after informed consent. Total RNA was prepared from purified cells using the Zymo Research Quick RNA Miniprep Kit and RNA quality was checked using the Agilent 2100 Bioanalyzer.

value: AML blasts

tag: facs sorting gate

tag: aml subtype


title: MLL_T9-11_5


title: MLL_T9-11_6


title: MLL_T9-11_3


title: MLL_T9-11_4


title: B-cells_5

description: Gene expression data from CD19+ B-cells


title: MLL_T9-11_2


title: NK-cells_2


title: MLL_T10-11_8


title: B-cells_2

description: Gene expression data from CD19+ B-cells


title: B-cells_4

description: Gene expression data from CD19+ B-cells


title: MLL_T9-11_1


title: B-cells_1

description: Gene expression data from CD19+ B-cells


title: MLL_T10-11_7


title: MLL_T10-11_5


title: MLL_T10-11_4


title: Monocytes_6

description: Gene expression data from CD14+ monocytes

source_name: CD14+ Monocytes purified from peripheral blood

value: FShighSSlow-mid CD14+

value: CD14+ monocyte


title: Monocytes_4


title: MLL_T10-11_6


title: Monocytes_3


title: Monocytes_5


title: Monocytes_1


title: MLL_T10-11_3

value: CD117high+ CD33+ CD34-


title: Granulocytes_5

description: Gene expression data from mature granulocytes

source_name: mature Granulocytes purified from peripheral blood

value: FShighSShigh CD15+ CD66+

value: mature granulocyte


title: Monocytes_2


title: Granulocytes_4


title: MLL_T10-11_1


title: AML_t8-21_10

description: Gene expression data from AML t(8;21) M2


title: AML_t8-21_9


title: AML_t8-21_8


title: AML_t8-21_7


title: Granulocytes_3


title: Granulocytes_1


title: Megakaryocytes_5

description: Gene expression data from megakaryocytes in vitro derived from CD34+ HSPCs s

source_name: purified megakaryocytes in vitro derived

value: CD41a+ CD42b+


title: Granulocytes_2


title: Megakaryocytes_3

value: megakaryocytes in vitro derived from CD34+ HSPCs


title: AML_t8-21_6


title: AML_t8-21_5


title: AML_t8-21_4


title: AML_t8-21_1


title: AML_t8-21_3


title: Megakaryocytes_1


title: AML_t8-21_2


title: PML_4

description: Gene expression data from AML t(15;17) acute promyelocytic leukemia


title: Megakaryocytes_4


title: PML_3

value: AML t(15;17) acute promyelocytic leukemia


title: Erythroid cells_5

description: Gene expression data from erythroblasts in vitro derived from CD34+ HSPCs s

source_name: purified erythroblasts in vitro derived

value: CD36+ GlyA+


title: Erythroid cells_3

value: erythroblasts in vitro derived from CD34+ HSPCs


title: AML_inv16_9

description: Gene expression data from AML inv(16) M4eo

value: AML inv(16) M4eo


title: PML_2


title: Erythroid cells_2


title: Erythroid cells_1


title: Megakaryocytes_2


title: HSC_4

description: Gene expression data from CD34+ CD38- chord blood hematopoietic stem cells

source_name: CD34+ CD38- HSC purified from cord blood

value: FSlowSSlow CD34+ Lin-


title: Erythroid cells_4


title: HSC_5

value: CD34+ CD38- chord blood hematopoietic stem cell


title: AML_inv16_7


title: HSC_3


title: HSC_1


title: PML_1


title: AML_inv16_8


title: AML_inv16_2


title: AML_inv16_3


title: AML_inv16_5


title: MLL_T9-11_8


title: AMKL_4

description: Gene expression data from acute megakaryoblastic leukemia

value: acute megakaryoblastic leukemia


title: AML_inv16_6


title: AML_inv16_4


title: HSC_2


title: AMKL_6


title: DSAMKL_4

description: Gene expression data from Down-syndrome acute megakaryoblastic leukemia


title: AMKL_1

value: Down-syndrome acute megakaryoblastic leukemia


title: AMKL_2


title: DSAMKL_5


title: DSAMKL_2


title: AML_inv16_1


title: AMKL_3


title: DSAMKL_3


title: Megakaryocytes_2

description: Gene expression data from megakaryocytic progenitors in vitro derived from CD34+ HSPCs s

source_name: purified megakaryocytic progenitors in vitro derived

tag: subject status

value: healthy donor


title: Megakaryocytes_4

value: megakaryocytic progenitors in vitro derived from CD34+ HSPCs


title: DSAMKL_1

value: AML blasts


title: Erythroid cells_4


title: Megakaryocytes_1


title: Monocytes_4

value: peripheral blood

value: CD14+ monocyte

value: FShighSSlow-mid CD14+


title: BCBM biological rep2

city: Albuquerque

first: Dario

last: Marchetti

state: NM

address: 1 University of New Mexico

department: Internal Medicine

country: USA

institute: University of New Mexico

description: Gene expression data from breast cancer patient CTC

hyb_protocol: Affymetrix User Manual: GeneChip WT plus Reagent Kit for Whole Transcript Expression Assay, P/N 703174 Rev 1

source_name: BrPt7 blood

extract_protocol: Sorted cells were collected directly into a pre-chilled tube maintained at 4oC containing RNA lysis buffer and total RNA was collected according to the manufacturer’s protocol (Macherey-Nagel, Inc.).

treatment_protocol: CTCs were isolated using a BD FACSAriaII (BD Biosciences) housed inside a BSL-2 facility allowing for collection of CTCs in sterile conditions. The flow cell was cleaned and sterilized before and after running each patient sample.

value: female

tag: primary tumor subtype


title: Monocytes_2


title: Megakaryocytes_3

value: CD41a+ CD42b+


title: Monocytes_1


title: Granulocytes_5

value: mature granulocyte

value: FShighSShigh CD15+ CD66+


title: BCBM biological rep1

scan_protocol: Affymetrix User Manual: GeneChip WT plus Reagent Kit for Whole Transcript Expression Assay, P/N 703174 Rev 1

source_name: BrPt6 blood


title: Erythroid cells_5

value: CD36+ GlyA+


title: CD8 T-cells_1

description: Gene expression data from CD8+ T-cells

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B)

data_processing: The scanned images were analyzed with Feature Extraction Software10.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: CD8 T-cells purified from peripheral blood

value: blood

value: FSlowSSlow CD3+ CD4- CD8+

value: CD8+ T-cell


title: No BCBM biological rep4

data_processing: Affymetrix User Manual: GeneChip WT plus Reagent Kit for Whole Transcript Expression Assay, P/N 703174 Rev 1

source_name: BrPt4 blood


title: BCBM biological rep3

source_name: BrPt8 blood

label_protocol: Affymetrix User Manual: GeneChip WT plus Reagent Kit for Whole Transcript Expression Assay, P/N 703174 Rev 1


title: Monocytes_3


title: Monocytes_5


title: CD8 T-cells_5

description: Gene expression data from CD8+ T-cells


title: Erythroid cells_3

value: erythroblasts in vitro derived from CD34+ HSPCs


title: CD4 T-cells_4

description: Gene expression data from CD4+ T-cells

source_name: CD4 T-cells purified from peripheral blood

value: FSlowSSlow CD3+ CD4+ CD8-

value: CD4+ T-cell


title: Granulocytes_4

value: healthy donor


title: Granulocytes_3


title: CD4 T-cells_3

description: Gene expression data from CD4+ T-cells


title: CD4 T-cells_2

description: Gene expression data from CD4+ T-cells


title: No BCBM biological rep3

source_name: BrPt3 blood

value: TNBC


title: No BCBM biological rep5

source_name: BrPt5 blood


title: CD8 T-cells_3

description: Gene expression data from CD8+ T-cells


title: BCBM biological rep5

source_name: BrPt10 blood


title: BCBM biological rep4

source_name: BrPt9 blood


title: Erythroid cells_1


title: CD8 T-cells_4

description: Gene expression data from CD8+ T-cells


title: Erythroid cells_2


title: Granulocytes_1


title: No BCBM biological rep2

source_name: BrPt2 blood


title: GMP_CB_1

description: Gene expression data from granulocyte-macrophage progenitors

source_name: GMP purified from cord blood

value: cord blood

value: granulocyte-macrophage progenitor


title: NK-cells_4

source_name: CD56+ NK-cells purified from peripheral blood

value: FSlowSSlow CD56+ CD3-

value: CD56+ natural killer cell


title: NK-cells_3


title: No BCBM biological rep1

source_name: BrPt1 blood

value: female


title: CD8 T-cells_2

description: Gene expression data from CD8+ T-cells


title: CMP_CB_1

description: Gene expression data from common myeloid progenitors

source_name: CMP purified from cord blood

value: common myeloid progenitor


title: GMP_CB_3


title: GMP_CB_2


title: B-cells_5

description: Gene expression data from CD19+ B-cells

source_name: CD19+ Bcells purified from peripheral blood

value: FSlowSSlow CD19+ CD3-CD56-

value: CD19+ B-cell


title: CD4 T-cells_1

description: Gene expression data from CD4+ T-cells


title: NK-cells_2


title: NK-cells_5


title: CMP_CB_3


title: CMP_CB_2


title: B-cells_6

description: Gene expression data from CD19+ B-cells


title: Monocytes_5

source_name: CD14+ Monocytes purified from peripheral blood

value: FShighSSlow-mid CD14+

value: CD14+ monocyte


title: B-cells_4

description: Gene expression data from CD19+ B-cells

value: blood


title: HSC_PB_2

description: Gene expression data from CD34+ CD38- peripheral blood hematopoietic stem cells

source_name: GCSF-mobilized CD34+ CD38-HSC purified from peripheral blood

value: peripheral blood

value: CD34+ Lin- CD38-


title: B-cells_2

description: Gene expression data from CD19+ B-cells


title: HSC_PB_1

value: CD34+ CD38- peripheral blood hematopoietic stem cell


title: Monocytes_6


title: Granulocytes_2

source_name: mature Granulocytes purified from peripheral blood

value: mature granulocyte

value: FShighSShigh CD15+ CD66+


title: B-cells_1

description: Gene expression data from CD19+ B-cells


title: NK-cells_1

description: Gene expression data from CD56+ natural killer cells


title: HSC_FL_3

description: Gene expression data from CD34+ CD38- fetal liver hematopoietic stem cells

source_name: CD34+ CD38- HSC purified from fetal liver

value: healthy donor

value: fetal liver


title: HSC_FL_1

value: CD34+ CD38- fetal liver hematopoietic stem cell


title: CD4 T-cells_5

description: Gene expression data from CD4+ T-cells

value: FSlowSSlow CD3+ CD4+ CD8-

value: CD4+ T-cell


title: HSC_FL_2


title: Granulocytes_5


title: Monocytes_2

description: Gene expression data from CD14+ monocytes


title: Monocytes_1


title: NK-cells_1

value: CD56+ natural killer cell

value: FSlowSSlow CD56+ CD3-


title: Granulocytes_4

description: Gene expression data from mature granulocytes


title: Granulocytes_2


title: Granulocytes_3


title: NK-cells_2


title: CD8 T-cells_5

description: Gene expression data from CD8+ T-cells

source_name: CD8 T-cells purified from peripheral blood

value: CD8+ T-cell

value: FSlowSSlow CD3+ CD4- CD8+


title: Granulocytes_1


title: Monocytes_4

value: FShighSSlow-mid CD14+


title: NK-cells_3


title: Megakaryocytes_5

source_name: purified megakaryocytes in vitro derived

value: CD41a+ CD42b+

value: megakaryocytes in vitro derived from CD34+ HSPCs


title: Erythroid cells_5

source_name: purified erythroblasts in vitro derived

value: blood

value: CD36+ GlyA+

value: erythroblasts in vitro derived from CD34+ HSPCs


title: CD8 T-cells_3

description: Gene expression data from CD8+ T-cells

value: peripheral blood


title: HSC_CB_1

source_name: CD34+ CD38- HSC purified from cord blood

value: cord blood

value: CD34+ CD38- chord blood hematopoietic stem cell

value: CD34+ Lin- CD38-


title: CD4 T-cells_2

description: Gene expression data from CD4+ T-cells

source_name: CD4 T-cells purified from peripheral blood

value: healthy donor


title: Megakaryocytes_4


title: CD8 T-cells_2

description: Gene expression data from CD8+ T-cells


title: Megakaryocytes_3


title: CD8 T-cells_4

description: Gene expression data from CD8+ T-cells


title: Megakaryocytes_1


title: CD8 T-cells_1

description: Gene expression data from CD8+ T-cells


title: HSC_CB_3


title: CD4 T-cells_4

description: Gene expression data from CD4+ T-cells

value: FSlowSSlow CD3+ CD4+ CD8-


title: Megakaryocytes_2


title: HSC_CB_2


title: CD4 T-cells_3

description: Gene expression data from CD4+ T-cells

value: CD4+ T-cell


title: Erythroid cells_2


title: CD4 T-cells_5

description: Gene expression data from CD4+ T-cells


title: B-cells_4

description: Gene expression data from CD19+ B-cells

value: CD19+ B-cell

value: FSlowSSlow CD19+ CD3-CD56-


title: HSC_3

value: FSlowSSlow CD34+ Lin-


title: Erythroid cells_4


title: B-cells_2

description: Gene expression data from CD19+ B-cells


title: OF84_neurons_CONTROL

status: Public on May 30 2017

type: genomic

city: Bronx

first: Stella

last: Dracheva

state: New York

address: James J. Peters VA Medical Center,130 W Kingsbridge Rd

department: Dept. of Psychiatry

institute: Icahn School of Medicine at Mount Sinai

description: FACS-isolated nuclei from postmortem human brain

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

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

data_processing:
Data processed with Minfi R package (Aryee et al, Bioinformatics 2014). Note that sample OF13 was excluded from the analysis due to ambiguous gender assignment.
Normalized average Beta. The data were pre-processed with stratified quantile normalization using the “minfi” R package. Detection P-values also provided, (as calculated with the detectionP() function.)
Unmethylated and methylated signal intensities (Raw data provided as idat files).

label: Cy5 and Cy3

molecule: genomic DNA

source_name: genomic DNA from neurons

label_protocol: Standard Illumina Protocol

extract_protocol:
Neuronal nuclei from human postmortem brain material were isolated by fluorescence-activated sorting, as described in Kozlenkov et.al., (2013), Nucleic Acids Research
Genomic DNA was isolated by proteinase K treatment, phenol extraction and ethanol precipitation

tag: cohort

value: CONTROL

tag: Cause of death

value: sudden death, natural

value: M

tag: race

value: W

tag: pmi (hr)

tag: etoh blood (g/l)

tag: etoh urine (g/l)

tag: blood -morphine

tag: blood 6-mam

tag: blood - codein

tag: liver  -morphine

tag: liver  6-mam

tag: liver - codein

tag: urine - morphine

tag: urine - 6-mam

tag: urine - codein


title: OF87_neurons_SUICIDE

value: SUICIDE

value: suicide hanging

tag: gender

tag: age


title: OF83_neurons_CONTROL

tag: cohort


title: OF78_neurons_SUICIDE

tag: Cause of death

value: suicide (hanging)


title: Erythroid cells_1

tag: tissue

value: blood

tag: facs

value: CD36+ GlyA+

tag: cell type

value: erythroblasts in vitro derived from CD34+ HSPCs


title: OF79_neurons_SUICIDE

value: F

tag: race

tag: pmi (hr)

tag: comments

value: suicidical attempts and statements

tag: etoh blood (g/l)

tag: etoh urine (g/l)


title: OF82_neurons_CONTROL

tag: blood -morphine

tag: blood 6-mam

tag: blood - codein

tag: liver  -morphine

tag: liver  6-mam


title: OF85_neurons_SUICIDE

tag: gender

value: post-partum depression

tag: liver - codein

tag: urine - morphine

tag: urine - 6-mam

tag: urine - codein

tag: substance

value: olanzapine clozapine

tag: concentration

tag: contribution to death

value: no contribution


title: OF80_neurons_SUICIDE

tag: cohort

tag: Cause of death

tag: age

tag: race

tag: pmi (hr)

value: compulsive gambler


title: OF81_neurons_CONTROL

value: sudden death

tag: etoh blood (g/l)

tag: etoh urine (g/l)

tag: blood -morphine

tag: blood 6-mam


title: Erythroid cells_3

tag: tissue

tag: facs

tag: cell type


title: OF76_neurons_SUICIDE

tag: gender

tag: blood - codein

tag: liver  -morphine

tag: liver  6-mam

tag: liver - codein

tag: urine - morphine

tag: urine - 6-mam


title: OF88_neurons_SUICIDE

tag: cohort

tag: Cause of death

tag: age

tag: comments

value: depression

tag: urine - codein


title: OF77_neurons_SUICIDE

tag: race

tag: pmi (hr)

tag: etoh blood (g/l)

tag: etoh urine (g/l)

tag: blood -morphine


title: OF75_neurons_CONTROL

value: CONTROL

value: cardiac failure

tag: gender

tag: blood 6-mam


title: OF74_neurons_SUICIDE

value: M

value: W

tag: blood - codein

tag: liver  -morphine


title: B-cells_5

description: Gene expression data from CD19+ B-cells

tag: subject status

value: healthy donor

tag: tissue

value: peripheral blood

tag: cell type

value: CD19+ B-cell

tag: facs

value: FSlowSSlow CD19+ CD3-CD56-


title: B-cells_1

description: Gene expression data from CD19+ B-cells


title: HSC_4

value: blood

value: FSlowSSlow CD34+ Lin-

value: CD34+ CD38- chord blood hematopoietic stem cell


title: HSC_1


title: HSC_2


title: OF73_neurons_HEROIN

tag: cohort

value: HEROIN

tag: Cause of death

value: heroin overdose

tag: liver  6-mam

tag: liver - codein

tag: urine - morphine

tag: urine - 6-mam


title: OF71_neurons_HEROIN

tag: age

tag: race

tag: pmi (hr)

tag: comments

value: 4-5 months abuse

tag: etoh blood (g/l)

tag: urine - codein


title: OF72_neurons_CONTROL

value: electric shock

tag: gender

tag: etoh urine (g/l)

tag: blood -morphine

tag: blood 6-mam

tag: blood - codein

tag: liver  -morphine


title: OF70_neurons_CONTROL

tag: cohort

tag: Cause of death

value: viral infection

value: F


title: OF69_neurons_CONTROL

value: CONTROL

tag: liver  6-mam

tag: liver - codein


title: OF67_neurons_HEROIN

value: 2 yrs use

tag: urine - morphine

tag: urine - 6-mam


title: OF68_neurons_CONTROL

value: cardiac failure

tag: age

tag: race


title: OF64_neurons_CONTROL

value: sudden death, natural

value: M

value: W

tag: pmi (hr)


title: OF65_neurons_HEROIN

tag: comments

value: 4 yrs heroin use

tag: etoh blood (g/l)


title: OF54_neurons_HEROIN

tag: gender

value: 3 yrs heroin use

tag: urine - codein


title: OF55_neurons_HEROIN

tag: etoh urine (g/l)

tag: blood -morphine


title: OF58_neurons_CONTROL

tag: blood 6-mam

tag: blood - codein


title: OF61_neurons_SUICIDE

tag: cohort

value: SUICIDE

value: suicide (hanging)

value: suicide attempts

tag: liver  -morphine


title: OF59_neurons_HEROIN

value: HEROIN

tag: Cause of death

value: 7 yrs heroin use

tag: liver  6-mam


title: OF53_neurons_SUICIDE

tag: liver - codein

tag: urine - morphine


title: OF60_neurons_HEROIN

value: heroin overdose

tag: age

tag: urine - 6-mam


title: OF56_neurons_HEROIN

tag: race

tag: pmi (hr)


title: OF62_neurons_SUICIDE

tag: etoh blood (g/l)


title: OF51_neurons_CONTROL

tag: gender


title: OF52_neurons_HEROIN

tag: comments

value: 2.5 yrs heroin use

tag: urine - codein


title: OF63_neurons_CONTROL

tag: etoh urine (g/l)

tag: blood -morphine


title: OF49_neurons_CONTROL

tag: blood 6-mam

tag: blood - codein


title: OF47_neurons_HEROIN

tag: cohort

tag: liver  -morphine


title: OF48_neurons_HEROIN

tag: Cause of death

tag: liver  6-mam


title: OF50_neurons_HEROIN

tag: liver - codein

tag: urine - morphine


title: OF57_neurons_HEROIN

tag: age

value: 0.5 yr heroin use

tag: urine - 6-mam


title: OF66_neurons_CONTROL

value: juvenile sudden death. viral infection

tag: race

tag: pmi (hr)


title: OF46_neurons_HEROIN

tag: gender

value: F

tag: etoh blood (g/l)


title: B.B10Q.veh.Sp#2

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

label: Biotin

source_name: Spleen

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

value: 7 Weeks Old

tag: genetic background

tag: Sex

value: Male

tag: cell family

value: B Cell

tag: phenotype markers

tag: exclusion markers

value: TCRB-

tag: source prep description

value: Sacrifice at 5hr after sc treatment with vehicle

tag: separation method

value: FACSAria

tag: amplification technique

value: Ambion WT Expression Kit


title: MF.B10Q.veh.Sp#2

source_name: Peritoneal Cavity

value: Macrophage


title: OF45_neurons_CONTROL

tag: cohort

value: CONTROL

tag: Cause of death

value: cardiac failure

value: M

value: W

tag: etoh urine (g/l)

tag: blood -morphine

tag: blood 6-mam

tag: blood - codein

tag: liver  -morphine

tag: liver  6-mam

tag: urine - codein


title: T4.B10Q.veh.Sp#2

tag: age

tag: genetic background

value: CD4+ T Cell

value: TCRB+ CD4+


title: OF44_neurons_HEROIN

value: HEROIN

value: heroin overdose

tag: gender

tag: race

tag: pmi (hr)

tag: etoh blood (g/l)

tag: liver - codein

tag: urine - morphine

tag: urine - 6-mam


title: OF42_neurons_HEROIN

tag: cohort

tag: Cause of death

tag: comments

value: 8 yrs heroin use


title: OF40_neurons_SUICIDE

value: SUICIDE

value: suicide (hanging)

tag: etoh urine (g/l)

tag: blood -morphine

tag: blood 6-mam


title: OF41_neurons_HEROIN

value: 5 yrs heroin use

tag: blood - codein

tag: liver  -morphine

tag: liver  6-mam


title: OF43_neurons_SUICIDE

tag: age

tag: urine - codein


title: OF36_neurons_CONTROL

tag: gender

tag: race


title: OF38_neurons_HEROIN

value: F

tag: pmi (hr)

tag: etoh blood (g/l)


title: OF37_neurons_HEROIN

value: 10 yrs heroin use

tag: liver - codein

tag: urine - morphine


title: MF.B10Q.IFNa.5hr.Sp#2

value: 7 Weeks Old

tag: genetic background

tag: Sex

value: Male

tag: cell family

tag: phenotype markers

tag: exclusion markers

tag: source prep description

value: Sacrifice at 5hr after sc treatment with 10000u IFNa

tag: separation method

value: FACSAria

tag: amplification technique


title: OF39_neurons_CONTROL

tag: cohort

value: CONTROL

tag: Cause of death

value: cardiac failure

tag: etoh urine (g/l)

tag: blood -morphine

tag: blood 6-mam

tag: blood - codein

tag: liver  -morphine

tag: liver  6-mam

tag: urine - 6-mam


title: OF34_neurons_CONTROL

tag: gender

value: M

tag: age

tag: race

value: W

tag: pmi (hr)

tag: etoh blood (g/l)

tag: liver - codein

tag: urine - morphine

tag: urine - codein


title: T4.B10Q.IFNa.5hr.Sp#2

tag: genetic background

tag: Sex

tag: cell family

value: CD4+ T Cell

tag: phenotype markers

value: TCRB+ CD4+

tag: exclusion markers

tag: source prep description

tag: separation method

tag: amplification technique

value: Ambion WT Expression Kit


title: OF33_neurons_HEROIN

tag: cohort

value: HEROIN

tag: Cause of death

value: heroin overdose

tag: comments

value: 3 yrs heroin iv

tag: etoh urine (g/l)

tag: blood -morphine

tag: blood 6-mam

tag: blood - codein

tag: liver  -morphine

tag: liver  6-mam

tag: urine - 6-mam


title: OF32_neurons_HEROIN

tag: gender

tag: age

tag: race

tag: pmi (hr)

tag: etoh blood (g/l)

tag: urine - morphine

tag: urine - codein


title: B.B10Q.IFNa.2hr.Sp#2

tag: genetic background

tag: Sex

tag: cell family

value: B Cell

tag: phenotype markers

tag: exclusion markers

value: TCRB-

tag: source prep description

value: Sacrifice at 2hr after sc treatment with 10000u IFNa

tag: separation method

tag: amplification technique


title: MF.B10Q.IFNa.2hr.Sp#2

value: 7 Weeks Old

value: Macrophage


title: MF.B10Q.veh2hr.Sp#1

value: Male

value: Sacrifice at 2hr after sc treatment with vehicle


title: B.B10Q.IFNa.5hr.Sp#1

value: Sacrifice at 5hr after sc treatment with 10000u IFNa

value: FACSAria


title: B.B10Q.veh.Sp#1


title: B.B10Q.IFNa.5hr.Sp#2


title: T4.B10Q.IFNa.5hr.Sp#1


title: B.B10Q.veh2hr.Sp#1


title: T4.B10Q.IFNa.2hr.Sp#2


title: T4.B10Q.IFNa.2hr.Sp#1


title: OF35_neurons_HEROIN

tag: cohort

tag: Cause of death

value: F

tag: etoh urine (g/l)

tag: blood -morphine

tag: blood 6-mam

tag: blood - codein

tag: liver  -morphine

tag: liver  6-mam

tag: liver - codein


title: OF29_neurons_HEROIN

tag: gender

value: M

tag: age

tag: race

value: W

tag: pmi (hr)

tag: etoh blood (g/l)

tag: urine - morphine

tag: urine - 6-mam

tag: urine - codein


title: MF.B10Q.IFNa.5hr.Sp#1

tag: genetic background

tag: Sex

tag: cell family

tag: phenotype markers

tag: exclusion markers

tag: source prep description

tag: separation method

tag: amplification technique


title: OF30_neurons_CONTROL

tag: cohort

value: CONTROL

tag: Cause of death

value: cardiac failure. pulm. embolus. pneumonia

tag: etoh urine (g/l)

tag: blood -morphine

tag: blood 6-mam

tag: blood - codein

tag: liver  -morphine

tag: liver  6-mam

tag: liver - codein


title: OF28_neurons_HEROIN

value: HEROIN

tag: gender

tag: age

tag: race

tag: pmi (hr)

tag: etoh blood (g/l)

tag: urine - morphine

tag: urine - 6-mam

tag: urine - codein


title: MF.B10Q.IFNa.2hr.PC#1

tag: genetic background

tag: Sex

tag: cell family

tag: phenotype markers

tag: exclusion markers

tag: source prep description

tag: separation method

tag: amplification technique

value: Ambion WT Expression Kit


title: B.B10Q.IFNa.2hr.Sp#1


title: OF23_neurons_HEROIN

tag: cohort

tag: Cause of death

value: heroin overdose

tag: comments

value: 5 yrs heroin use

tag: etoh urine (g/l)

tag: blood -morphine

tag: blood 6-mam

tag: blood - codein

tag: liver  -morphine

tag: liver  6-mam

tag: liver - codein


title: OF24_neurons_SUICIDE

value: SUICIDE

value: suicide (hanging)

tag: gender

tag: age

tag: race

tag: pmi (hr)

value: depression, suicide attempts

tag: etoh blood (g/l)

tag: urine - morphine

tag: urine - 6-mam

tag: urine - codein


title: OF31_neurons_HEROIN

tag: cohort

tag: Cause of death

value: 1 yr heroin use


title: OF21_neurons_SUICIDE

tag: etoh urine (g/l)


title: OF20_neurons_CONTROL

value: sudden death, natural

tag: blood -morphine

tag: substance

value: pyrazolon

tag: concentration

value: unspecified, little

tag: contribution to death

value: no contribution


title: OF22_neurons_SUICIDE

tag: blood 6-mam

tag: blood - codein

tag: liver  -morphine

tag: liver  6-mam


title: OF16_neurons_HEROIN

tag: gender

tag: age

tag: race

tag: liver - codein


title: OF26_neurons_CONTROL

value: cardiac failure

tag: pmi (hr)

tag: etoh blood (g/l)

tag: urine - morphine

tag: urine - 6-mam


title: OF18_neurons_HEROIN

tag: cohort

tag: Cause of death

value: M

tag: etoh urine (g/l)

tag: urine - codein


title: OF17_neurons_SUICIDE

value: W

tag: comments

tag: blood -morphine


title: OF25_neurons_HEROIN

value: 4 yrs heroin use

tag: blood 6-mam

tag: blood - codein


title: OF27_neurons_HEROIN

value: 3 yrs heroin use

tag: liver  -morphine

tag: liver  6-mam


title: OF10_neurons_HEROIN

value: HEROIN

tag: gender

tag: age

value: 2-4 years heroin use


title: OF14_neurons_HEROIN

value: heroin overdose

tag: race

value: 6 yrs heroin use

tag: liver - codein


title: OF09_neurons_CONTROL

value: CONTROL

tag: pmi (hr)

tag: etoh blood (g/l)


title: OF03_neurons_CONTROL

value: heart failure

tag: urine - morphine

tag: urine - 6-mam


title: OF02_neurons_HEROIN

tag: cohort

tag: Cause of death

value: F


title: OF04_neurons_CONTROL

value: sudden death,heart

tag: etoh urine (g/l)

tag: urine - codein


title: OF15_neurons_HEROIN

tag: blood -morphine


title: OF12_neurons_SUICIDE

value: SUICIDE

value: suicide (hanging)

tag: comments

value: depression, suicide attempts

tag: blood 6-mam


title: OF11_neurons_HEROIN

tag: blood - codein

tag: liver  -morphine


title: OF13_neurons_CONTROL

value: pulmonary embolus

tag: gender

value: M?

value: Ambiguous gender information. Excluded from the analyses.

tag: liver  6-mam


title: OF05_neurons_CONTROL

value: M

tag: age

tag: race

value: W


title: OF06_neurons_SUICIDE

tag: pmi (hr)

tag: liver - codein


title: OF08_neurons_CONTROL

value: sudden death, natural

tag: etoh blood (g/l)

tag: urine - morphine


title: OF01_neurons_SUICIDE

tag: cohort

tag: urine - 6-mam


title: OF86_neurons_SUICIDE

tag: Cause of death

value: suicide hanging

value: depression after divorce

tag: etoh urine (g/l)


title: OF07_neurons_CONTROL

value: cardiac failure

tag: blood -morphine

tag: urine - codein


title: HSC_5

tag: tissue

value: blood

tag: facs

value: FSlowSSlow CD34+ Lin-

tag: cell type

value: CD34+ CD38- chord blood hematopoietic stem cell


title: NS_378

status: Public on May 27 2017

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

hyb_protocol: Not provided

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

data_processing: Data were background corrected, log2 transformed, and quantile normalized with Robust Multi-array Average (RMA) method.

source_name: gliomasphere culture

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol,concentration and quality of RNA samples was examined using the NanoDrop ND-1000 spectrophotometer (NanoDrop Tech- nologies) and the Agilent 2100 Bioanalyzer (Agilent Technologies). RNA samples were reverse transcribed and labeled according to manufacturer’s instructions

growth_protocol: Cells were plated at 5000 cells/100mL/well of a 96-well plate and grown for 5-7 days. Cell number was assessed using Dojindo Cell Counting Kit-8 (Dojindo Molecular Technolo-gies Inc.)

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

treatment_protocol: RNA was isolated from gliomaspheres and tumors samples using the Qiagen RNA isolation kit (RNeasy Kit, Qiagen).

tag: diagnosis

value: GBM Recurrent

tag: days


title: NS_412

value: GBM Primary


title: NS_382

value: resistant


title: NS_408


title: OF19_neurons_HEROIN

value: HEROIN

value: heroin overdose

tag: gender

tag: age

tag: comments

value: 2 yrs heroin use

tag: blood 6-mam

tag: blood - codein

tag: liver  -morphine

tag: liver  6-mam


title: NS_393

value: GBM Gliosarcoma Secondary


title: NS_371


title: NS_385

value: sensitive


title: NS_372


title: NS_345

value: GBM recurrent (secondary same pt. as 339)


title: NS_381


title: NS_348

value: GBM Primary Gliosarcoma (genetic?)


title: NS_357


title: NS_361


title: NS_390


title: NS_347


title: NS_359


title: NS_317


title: NS_316


title: NS_417


title: NS_401

value: GBM Recurrent/(prior Gliosarcoma/concurrent meningioma)


title: NS_320

value: GBM Secondary Recurrent (prior grade 3 Oligo)


title: NS_399


title: NS_374


title: NS_411


title: NS_350


title: NS_330

value: GBM Secondary


title: NS_339

value: GBM Recurrent/Gliosarcoma (secondary recurrent; same as 345)


title: NS_309


title: NS_282


title: NS_250


title: NS_336


title: NS_242


title: NS_245


title: NS_233


title: NS_254


title: NS_246

value: GBM Recurrent (same patient as206)


title: NS_261


title: NS_229

value: GBM Recurrent Gliosarcoma


title: NS_227


title: NS_252

value: GBM Secondary Recurrrent


title: NS_312


title: NS_296

value: GBM Recurrent


title: NS_308


title: NS_244

value: GBM Primary


title: NS_280

value: GBM Primary (highly oligo)


title: NS_228


title: NS_277

value: GBM Secondary (may be recurrent)


title: NS_313


title: NS_301


title: NS_272


title: NS_305

value: GBM Secondary (malignant astrocytoma may be recurrent


title: NS_237

value: GBM Secondary (prior tumor grade II oligoastrocytoma)


title: NS_222


title: NS_221


title: NS_216

value: GBM Recurrent/Gliosarcoma

value: resistant


title: NS_248


title: NS_217


title: NS_208


title: NS_189


title: NS_167


title: Control Replicate 4

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

country: France

institute: INRA

hyb_protocol: The hybridization was performed on a rotative Agilent Hybridization Oven, 17h at 65°C, 10g. Afterwards, the slides were washed and scanned.

scan_protocol: Slides were scanned at 532/635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200. Feature Extraction software v11.5.1.1 was used to extract pair-data files from the scanned images.

data_processing: All statistical analyses on the gene expression data were performed using the R language, version 2.5.1 (R Development Core Team, 2011) and the package LIMMA (Smyth G.K., 2005) from the Bioconductor project. For the processing step, data were normalized by the lowess method in LIMMA.

organism: Phelipanche ramosa

label_protocol: 400ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 200U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1,5nmol of Cyanine-3 (Cy3)-dCTP or Cyanine-5 (Cy5)-dCTP (Interchim, France), then purified with NucleoSpin Gel and PCR Clean-up column kits (Macherey-Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND-1000 (Nanodrop Technologies, DE, USA). Labelled samples were combined as 30 pmol for each dye and co-hybridized to the Orobanche_v1.1_s-as 4x180k.

growth_protocol: P. ramosa seeds were suspended (10 mg/mL) in HEPES 1 mM, pH 7.5, PPM 0.1% (incubation medium) and placed at 21°C in the dark for 7 days (conditioning period, Lechat et al., 2015).

extract_protocol: RNA was extracted using a Nucleospin RNA Plant kit (Macherey Nagel) according to the manufacturer’s instruction. Genomic DNA was removed from RNA samples by treatment with 6.8 units of RNase-free DNase I (Qiagen, Cat. No 79254) followed by a cleanup step with a RNA clean up XS spin column (Macherey Nagel) according to the manufacturer’s instruction. RNA was quantified using a NanoDrop ND-1000 (NanoDrop Technologies) and RNA quality was assessed with an Agilent 2100 Bioanalyser.

treatment_protocol: P. ramosa seeds were suspended (2.5 mg/mL) in germination medium (HEPES 0.5 mM, pH 7.5, PPM 0.05%, rac-GR24 10-7M (synthetic germination stimulant, kindly provided by Dr. Binne Zwanenburg)). One hundred microliters of GR24 treated P. ramosa seeds (around 25 seeds) were then distributed in 96-well plates (Cell Culture Multiwell Plate Cellstar; Greiner Bio-One) and placed to germinate at 21°C in the dark for 4 days. The germination solution was then removed from the wells and seeds were suspended in 100µL of test solutions. Test solutions for haustorium induction assays contain HEPES 0.5 mM, pH 7.5, PPM 0.05% (final concentration) and root exudates from B. napus half diluted.

tag: genotype/variation

value: Wild-type

value: Germinated seed

tag: treatment

value: incubation medium during 12h

value: 4 days

tag: growth medium

value: incubation medium

tag: harvest date


title: Exudate treatment Replicate 3

value: root exudate during 12h


title: NS_177


title: NS_207


title: Exudate treatment Replicate 1


title: NS_218

value: Grade III Anaplastic Oligodendroglioma


title: NS_163


title: Exudate treatment Replicate 2


title: NS_205


title: Exudate treatment Replicate 4


title: Control Replicate 3


title: NS_039


title: NS_213

value: GBM Secondary


title: NS_211


title: NS_206


title: 13delChop-/-_LHZ_rep2

status: Public on May 26 2017

city: Hong Kong S.A.R.

first: Kathryn

last: Cheah

state: Hong Kong

address: 3/F, Laboratory Block, 21 Sassoon Road, Pokfulam, Hong Kong

department: School of Biomedical Sciences

institute: University of Hong Kong

description: Gene expression data of late hypertrophic chondrocytes from 13del:Chop-/- proximal tibia growth plate at P10 stage

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix GeneChip™ Mouse Genome 430 2.0 Array. GeneChips were washed and stained according to the  manufacturer's protocol (Affy GeneChip Expression Wash and Stain_Rev 3)

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000 7G.

data_processing: Gene expression data for each sample in triplicate were normalized using Robust Multi-chip Average (RMA) algorithm of R Bioconductor package. The k-Means Clustering algorithm was used to identify the distinct expression patterns of genes in WT and 13del growth plates. The Gene Ontology analysis was performed for each cluster of genes by using the Gene Ontology database and the David Web Tools.

source_name: Chondrocytes from 13del:Chop-/- proximal tibia growth plate at P10 stage

label_protocol: Biotinylated cRNA were prepared according to the  manufacturer's protocol (Affy GeneChip 3'IVT Expression_Rev 8)

growth_protocol: Proximal tibia growth plates were dissected from WT, 13del and 13del:Chop-/- mice at P10 stage and stored in liquid nitrogen for fractionation.

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

treatment_protocol: The proximal part of the tibia was embedded in O.C.T. compound in vertical direction for fractionation. The fractionated growth plates were lysed in 0.4ml Trizol reagent (Invitrogen) with 30-second full-power vortex.

tag: genotype

value: proximal tibia growth plate

value: female

tag: Stage

value: chondrocytes


title: 13delChop-/-_LHZ_rep1

tag: tissue


title: 13delChop-/-_pHZ_rep2

description: Gene expression data of pre-hypertrophic chondrocytes from 13del:Chop-/- proximal tibia growth plate at P10 stage

tag: cell type


title: 13delChop-/-_pHZ_rep1


title: NS_157

tag: diagnosis

value: GBM Primary

value: sensitive


title: Control Replicate 2


title: NS_146

value: GBM Recurrent

tag: days


title: Control Replicate 1


title: 13delChop-/-_MHZ_rep2

description: Gene expression data of middle hypertrophic chondrocytes from 13del:Chop-/- proximal tibia growth plate at P10 stage

tag: gender


title: 13delChop-/-_PZ_rep1

description: Gene expression data of proliferating chondrocytes from 13del:Chop-/- proximal tibia growth plate at P10 stage


title: 13delChop-/-_PZ_rep2


title: 13delChop-/-_UHZ_rep1

description: Gene expression data of early hypertrophic chondrocytes from 13del:Chop-/- proximal tibia growth plate at P10 stage


title: 13del_MHZ_rep3

description: Gene expression data of middle hypertrophic chondrocytes from 13del proximal tibia growth plate at P10 stage

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix GeneChip™ Mouse Genome 430 2.0 Array. GeneChips were washed and stained according to the  manufacturer's protocol (GeneChip® Expression Analysis 701021 Rev.5)

source_name: Chondrocytes from 13del proximal tibia growth plate at P10 stage

label_protocol: Biotinylated cRNA were prepared according to the  manufacturer's protocol (MessageAmp™ II-Biotin Enhanced (Cat #1791))

value: 13del transgenic


title: 13delChop-/-_UHZ_rep2


title: 13delChop-/-_MHZ_rep1


title: 13del_MHZ_rep2


title: 13del_LHZ_rep2

description: Gene expression data of late hypertrophic chondrocytes from 13del proximal tibia growth plate at P10 stage


title: 13del_pHZ_rep2

description: Gene expression data of pre-hypertrophic chondrocytes from 13del proximal tibia growth plate at P10 stage


title: 13del_LHZ_rep1


title: 13del_UHZ_rep2

description: Gene expression data of early hypertrophic chondrocytes from 13del proximal tibia growth plate at P10 stage


title: 13del_UHZ_rep3


title: 13del_LHZ_rep3


title: 13del_UHZ_rep1


title: 13del_pHZ_rep1


title: 13del_PZ_rep1

description: Gene expression data of proliferating chondrocytes from 13del proximal tibia growth plate at P10 stage


title: 13del_MHZ_rep1


title: 13del_PZ_rep3


title: 13del_PZ_rep2


title: 13del_pHZ_rep3


title: WT_LHZ_rep1

description: Gene expression data of late hypertrophic chondrocytes from WT proximal tibia growth plate at P10 stage

source_name: Chondrocytes from WT proximal tibia growth plate at P10 stage

value: wild type


title: WT_LHZ_rep2


title: WT_UHZ_rep2

description: Gene expression data of early hypertrophic chondrocytes from WT proximal tibia growth plate at P10 stage


title: WT_LHZ_rep3


title: WT_UHZ_rep3


title: WT_PZ_rep2

description: Gene expression data of proliferating chondrocytes from WT proximal tibia growth plate at P10 stage


title: WT_pHZ_rep1

description: Gene expression data of pre-hypertrophic chondrocytes from WT proximal tibia growth plate at P10 stage


title: WT_pHZ_rep2


title: WT_pHZ_rep3


title: WT_PZ_rep3


title: WT_UHZ_rep1


title: WT_PZ_rep1


title: AsPC1-AKT obese tumor replicate 2

first: Nada

middle: Y

last: Kalaany

address: 3 Blackfan Circle CLS 16067

institute: Boston Children's Hospital

hyb_protocol: Equal amounts of differentially labeled control AsPC1-CFP cells propagated in culture and sample cRNA were combined such that each sample contained at least 2.5 pmol dye. Samples were mixed with control targets, fragmented, combined with hybridization buffer, and hybridized to the SurePrint G3 Human Gene Expression 8x60K v2 Microarray consisting of 60mer probes for each human open reading frame (Agilent). Microarrays were rotated at 60°C for 17 hours in a hybridization oven (Agilent).

scan_protocol: Arrays were then washed according to the Agilent SSPE wash protocol, and scanned on an Agilent scanner. The image was processed using the default settings with Agilent Feature Extraction software.

data_processing: All data analysis was performed using the resulting log2 ratio data of tumor samples/AsPC1-CFP cell line control samples, and filtered for spots called as significantly over background in at least one channel.

source_name: AsPC1-AKT orthotopic tumor

label_protocol: RNA quality was checked using the Bioanalyzer RNA Nano kit, and 325 ng were used for microarray labeling with the Agilent Low Input QuickAmp Labeling Kit Two-Color. Dye incorporation and yield were measured with a Nanodrop spectrophotometer.

growth_protocol: 100000  AsPC1-CFP and AsPC1-AKT cells suspended in 25ul 33% Matrigel in HBSS were injected into the pancreas of lean and obese rag1-/- male mice after 8 weeks on special diet.  Tumors were collected and flash frozen in liquid nitrogen 5 weeks post injection.

extract_protocol: Tumor tissues were homogenized and control AsPC1-CFP cultured cells were lysed in QIAzol lysis reagent and total RNA was extracted using the RNeasy Microarray Tissue Mini Kit (Qiagen).

tag: cell line

tag: host

value: obese mouse for 5 weeks

source_name: AsPC1-CFP cell line control


title: AsPC1-AKT obese tumor replicate 3


title: AsPC1-AKT obese tumor replicate 7


title: AsPC1-AKT obese tumor replicate 5


title: AsPC1-AKT lean tumor replicate 7

value: lean mouse for 5 weeks


title: AsPC1-AKT lean tumor replicate 8


title: AsPC1-AKT obese tumor replicate 4


title: AsPC1-AKT obese tumor replicate 1


title: Control array 3

city: Toronto

first: Eric

middle: J

last: Chater-Diehl

state: ON

address: 686 Bay St.

country: Canada

institute: SickKids Research Institute

description: Gene expression data from three pooled mice each exposed to saline

hyb_protocol: One microgram of total RNA was labeled using the Flash Tag Biotin HSR kit from Genisphere (http://www.genisphere.com/array_detection_flashtag_biotin.html). Samples were then hybridized to Affymetrix 2.0 arrays for 16 hours at 48°C.Fluidics Station 400.

scan_protocol: All washing steps were performed by a GeneChip Fluidics Station 450 and GeneChips were scanned with the GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, CA) using Command Console v1.1.

data_processing: Probe level (.CEL file) data was generated using Affymetrix Command Console v1.1. Individual probes were matched to their chromosomal locations and gene feature by merging information from the Affymetrix mm10 library file with information from the mouse genome informatics (MGI)28 using R

source_name: Mouse hippocampal RNA after neonatal saline

label_protocol: All sample labeling and GeneChip processing was performed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca). RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Single stranded complimentary DNA (sscDNA) was prepared from 200 ng of total RNA as per the Ambion WT Expression Kit for Affymetrix GeneChip Whole Transcript WT Expression Arrays (http://www.ambion.com/techlib/prot/fm_4411973.pdf, Applied Biosystems, Carlsbad, CA) and the Affymetrix GeneChip WT Terminal Labeling kit and Hybridization User Manual (http://media.affymetrix.com/support/downloads/manuals/wt_term_label_ambion_user_manual.pdf, Affymetrix, Santa Clara, CA). Total RNA was first converted to cDNA, followed by in vitro transcription to make cRNA. 5.5 ug of single stranded cDNA was synthesized, end labeled

growth_protocol: Mice reared in standard shoebox cages with standard bedding and ad libitum access to food and water

extract_protocol: Qiagen Allprep DNA RNA kit was used according to Qiagen protocol

treatment_protocol: All protocols were approved by the Animal Use Subcommittee (AUS) at the University of Western Ontario, London, Ontario, Canada. C57BL/6J (B6) mice were obtained from Jackson Laboratories (Bar Harbor, MA) and a population was subsequently maintained at the Animal Care Facility at the University of Western Ontario. Female mice 12-18 weeks of age were separated into individual cages and mated with males of approximately the same age. The day of birth was termed post-natal day (PD) zero. Sex and weight-matched littermate pups were divided into two groups: ethanol-treated and saline control mice. Pups were given two subcutaneous dorsal injections at 9 am and 11 am on both PD4 and PD7. Ethanol-treated mice were injected with 2.5 g/kg of ethanol in 0.15 M NaCl. Pups were weaned on PD21 and housed in cages of two to four same-sex littermates. Male mice were used for all subsequent analyses (n=18). Mice were sacrificed on PD 70 via carbon dioxide asphyxiation. The hippocampus was dissected out, snap-frozen in liquid nitrogen, and stored at -80°C

value: whole hippocampus

tag: age

value: 21 day old


title: AsPC1-AKT obese tumor replicate 8


title: AsPC1-AKT lean tumor replicate 9


title: AsPC1-AKT obese tumor replicate 9


title: AsPC1-AKT obese tumor replicate 6


title: AsPC1-AKT lean tumor replicate 5


title: Control array 1


title: Control

city: Higashi-Hiroshima

first: Takuya

last: Suzuki

state: Hiroshima

address: 1-4-4 Kagamiyama

department: Graduate School of Biosphere Science

institute: Hiroshima University

hyb_protocol: We followed protocol of manual that is GeneChip® WT PLUS Reagent Kit User Manual.

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

data_processing: Data acquisition and normalization (RMA) were used Affymetrix® Expression Console™ Software.

source_name: Colons of mice fed the control diet.

growth_protocol: Mice were housed under conditions with controlled temperatures (22 ± 2°C), relative humidity (40-60%), and lighting (light: 0800-2000 hours).

extract_protocol: Total RNA was extracted from mouse colons using Nucleospin RNA (Takara) according to the manufacture's protocol.

treatment_protocol: Mice were fed the diets without and with psyllium fiber (10%) for 5 days.

value: male

value: 7wk old

value: colon

tag: disease state

value: healthy

tag: strain

value: ICR


title: AsPC1-AKT lean tumor replicate 4


title: AsPC1-AKT lean tumor replicate 6


title: Ethanol-exposed array 1

description: Gene expression data from three pooled mice each exposed to ethanol

source_name: Mouse hippocampal RNA after neonatal ethanol exposure


title: Ethanol-exposed array 2


title: Psyllium

source_name: Colons of mice fed the pysllium fiber-containing diet

label_protocol: We followed protocol of manual that is GeneChip® WT PLUS Reagent Kit User Manual.


title: Control array 2


title: AsPC1-AKT lean tumor replicate 2


title: AsPC1-AKT lean tumor replicate 3


title: AsPC1-AKT lean tumor replicate 1


title: AsPC1-CFP obese tumor replicate 6

source_name: AsPC1-CFP orthotopic tumor


title: AsPC1-CFP obese tumor replicate 7


title: AsPC1-CFP obese tumor replicate 5


title: AsPC1-CFP obese tumor replicate 4


title: AsPC1-CFP obese tumor replicate 3


title: AsPC1-CFP obese tumor replicate 8


title: AsPC1-CFP obese tumor replicate 9


title: AsPC1-CFP lean tumor replicate 6


title: AsPC1-CFP lean tumor replicate 8


title: AsPC1-CFP obese tumor replicate 2


title: AsPC1-CFP lean tumor replicate 5


title: AsPC1-CFP lean tumor replicate 7


title: AsPC1-CFP lean tumor replicate 4


title: AsPC1-CFP lean tumor replicate 9


title: AsPC1-CFP lean tumor replicate 3


title: AsPC1-CFP obese tumor replicate 1


title: AsPC1-CFP lean tumor replicate 2


title: fast growing Ruditapes decussatus [FG_FA534]

status: Public on May 25 2017

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

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

country: Italy

institute: University of Padova

description: Ruditapes decussatus

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

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

data_processing: Data processed with FeatureExtraction v9.5 and quantile normalized using R2.6.1 statistical software

label: Cyanine 3

organism: Ruditapes decussatus

source_name: gills of Ruditapes decussatus

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

extract_protocol: RNA was extracted with Trizol following the protocol suggested by the manufacturer. An aliquot of RNA from each sample was run in an agarose gel to check for RNA quality and integrity. Concentration was measured with NanoDrop. The RNA was further purified with a QiaQuick RNA Mini spin column and stored in TE buffer (10 mM Tris, 0.1 mM EDTA).

tag: condition

value: fast growing  Ruditapes decussatus


title: slow growing Ruditapes decussatus [SG_FA523]

description: Ruditapes decussatus

value: slow growing  Ruditapes decussatus


title: slow growing Ruditapes decussatus [SG_FA522]

description: Ruditapes decussatus


title: slow growing Ruditapes decussatus [SG_FA540]

description: Ruditapes decussatus


title: fast growing Ruditapes decussatus [FG_FA_512_DG]

description: Ruditapes decussatus

source_name: digestive gland of Ruditapes decussatus


title: slow growing Ruditapes decussatus [SG_FA555]

description: Ruditapes decussatus


title: fast growing Ruditapes decussatus [FG_FA552]

description: Ruditapes decussatus


title: fast growing Ruditapes decussatus [FG_FA512]

description: Ruditapes decussatus


title: slow growing Ruditapes decussatus [SG_FA_DG_554]

description: Ruditapes decussatus


title: slow growing Ruditapes decussatus [SG_FA_523_DG]

description: Ruditapes decussatus


title: fast growing Ruditapes decussatus [FG_FA_552_DG]

description: Ruditapes decussatus


title: fast growing Ruditapes decussatus [FG_FA_DG_544]

description: Ruditapes decussatus


title: fast growing Ruditapes decussatus [FG_FA_534_DG]

description: Ruditapes decussatus


title: AsPC1-CFP lean tumor replicate 1


title: fast growing Ruditapes decussatus [FG_FA_532_DG]

description: Ruditapes decussatus


title: slow growing Ruditapes decussatus [SG_FA_522_DG]

description: Ruditapes decussatus


title: slow growing Ruditapes decussatus [SG_FA_540_DG]

description: Ruditapes decussatus


title: slow growing Ruditapes decussatus [SG_FA_555_DG]

description: Ruditapes decussatus


title: P7 day-old mouse lens

status: Public on May 24 2017

city: Durham

first: Rupalatha

last: Maddala

state: NC

address: 2351 Erwin Road, AERI 4th floor

department: Ophthalmology

institute: Duke University Medical center

hyb_protocol: Hybridization targets were prepared from total RNA using a MessageAmp Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX, USA), hybridized to GeneChip™ Mouse Genome 430 2.0 Array (Affymetrix, Santa Clara, CA, USA) in an Affymetrix GeneChip hybridization Oven 645, washed in Affymetrix GeneChip Fluidics Station 450, and scanned with Affymetrix GeneChip Scanner 7G according to standard Affymetrix GeneChip hybridization, wash, and stain protocols.

scan_protocol: Affymetrix scanning protocol according to manufacturer.

data_processing: Raw data were normalized and analyzed using GeneSpring 10 (Silicon Genetics, Wilmington, DE, USA) with MAS5.0

source_name: 7 day-old Mouse lens

label_protocol: Ambion MessageAmp Premier labeling

extract_protocol: Mouse lenses (pooled) from respective ages were homogenized and passed through QiaShredder column (Qiagen) and treated with DNAse-I to eliminate genomic DNA contamination. Total RNA then was then extracted using the RNeasy Mini kit (Qiagen) according to the manufacturer’s instructions. RNAs, quality and quality was assessed using an Agilent 2100 Bioanalyzer G2939A (Agilent Technologies, SantaClara, CA, USA) and Nanodrop 8000 Spectrophotometer.

treatment_protocol: Wild type Blk6 mouse lenses were used

value: lens


title: ExVivoLV_DM_rep2

city: Sapporo

first: Masaya

last: Tanno

department: Department of Cardiovascular, Renal and Metabolic Medicine

institute: Sapporo Medical University

description: Gene expression in left ventricle of diabetic rat

hyb_protocol: 1.65 μg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Rat GE 4x44K v3 (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan resolution 5μm).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Rattus norvegicus

source_name: Left ventricular tissue of DM rat, replicate 2

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, Valencia, CA).

extract_protocol: Total RNA was isolated from rat LV tissues by using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Valencia, CA) by using the RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.  First-strand cDNA was synthesized using a SuperScript VILOTM cDNA Synthesis Kit (Invitrogen, Carlsbad, CA).  One-color microarray analysis for global gene expression was performed using Rat GE 4x44K v3 (Agilent Technologies) by Hokkaido System Science, according to the manufacturer's protocol.

value: OLETF

value: type 2 diabetes

value: heart

tag: tissue compartment

value: left ventricle


title: Il-4 stimulated microglia 2

city: Shanghai City

first: li

last: cao

address: 800 Xiangyin Road

department: Department of neurobiology

institute: second military medical university

description:
M2-2
Gene expression after 24hr with IL-4 stimulation

hyb_protocol: The labeled samples were hybridized onto Arraystar Mouse LncRNA Array V2.0 in Agilent’s SureHyb Hybridization Chambers according to the manufacturer’s standard protocols (Agilent Technologies).

scan_protocol: The arrays were scanned by the Agilent Scanner G2505C.

data_processing: Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). Only lncRNA probes were included, excluding the mRNAs in the array.

source_name: Il-4 stimulated microglia

label_protocol: Total RNA from each sample was amplified and transcribed into cyanine-3 (Cy3) labeled cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: P0 C57BL/6 mice were sacrificed to acquire mixed cerebrum glial cell cultures containing microglia. After 10-14 days of growth in DMEM/F12 medium (Invitrogen) containing 10% fetal bovine serum (FBS, GBICO), the cultures were shaken for 6 h at 180 rpm at 37°C to collect the microglia.

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

treatment_protocol: For M2 polarization, the microglia were stimulated with IL-4 (10 ng/ml, R&D).

value: primary cultured microglia

tag: treated with

value: 10 ng/ml IL-4


title: Wild type 2

city: Philadelphia

first: Patrick

last: Viatour

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

description:
gene expression from flow isolated HSC
WT2-3

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

scan_protocol: Genechips were scanned according to the manufacturer protocol

data_processing: Data were analyzed using R (cran.r-project.org) and Bioconductor (www.bioconductor.org) software. Background correction, normalization and calculation of gene expression values by model-fitting was performed using the Robust Multiarray Average procedure. Differential expression was called using the limma package.

source_name: Wild Type Cd48- Cd150+ HSCs

label_protocol: biotynilated cRNA were prepared according to the standard Affymetrix protocol from total RNA

growth_protocol: recombination was activated by Tamoxifen injection in adult mice. HSC were flow isolated two weeks post recombination

extract_protocol: Trizol extraction on total RNA was performed according to the manufacturer instructions

value: HSC


title: Rb family deficient HSC 1

description:
gene expression from flow isolated HSC
TKO1

source_name: Rb family deficient Cd48- Cd150+ HSCs


title: ExVivoLV_DM_rep3

source_name: Left ventricular tissue of DM rat, replicate 3


title: ExVivoLV_nonDM_rep2

description: Gene expression in left ventricle of non-diabetic rat

source_name: Left ventricular tissue of non-DM rat, replicate 1

value: LETO

value: healthy control


title: ExVivoLV_DM_rep1

source_name: Left ventricular tissue of DM rat, replicate 1

value: male


title: Resting microglia 3

description:
M0-3
Gene expression after 24hr without stimulation

source_name: Resting microglia

value: none (resting)


title: Wild type 1

description:
gene expression from flow isolated HSC
WT1


title: Il-4 stimulated microglia 3

description:
M2-3
Gene expression after 24hr with IL-4 stimulation


title: Rb family deficient HSC 2

description:
gene expression from flow isolated HSC
TKO2-5


title: Il-4 stimulated microglia 1

description:
M2-1
Gene expression after 24hr with IL-4 stimulation


title: Activated gametocyte TSA-treated 6hr

city: University Park

first: Manuel

last: Llinas

state: Pennsylvania

address: Millennium Science Complex, Pollock Rd

department: Biochemistry and Molecular Biology

institute: Penn State University

hyb_protocol: Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).

scan_protocol: Agilent G2600D Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version 11.5.1.1).

data_processing: Agilent Feature Extraction Software (v 11.5.1.1) was used for background subtraction.

organism: Plasmodium falciparum

source_name: Activated gametocyte RNA

extract_protocol: Gametocytes samples were purified from different cultures, treated as indicated and stored in Trizol at –80°C. Samples treated in the same way were then pooled together and total RNA extracted according to the manufacturer´s instructions (Invitrogen).

treatment_protocol: P. falciparum Percoll enriched immature (stages II-IV) gametocytes (imGC), mature (stage V) gametocytes (mGC) and gametocytes at 1 h post-activation with 100 µM Xanthurenic acid at RT (aGC) were obtained. Each enriched gametocyte sample was treated with TSA at IC90 concentrations (0.26 µM) or with 0.5% vol. ethanol (untreated control) for 1 h and 6 h.

value: NF54 Wildtype

value: Activated gametocyte

source_name: Mixed gametocyte and asexual blood stage reference pool

value: NF54 and 3D7


title: ExVivoLV_nonDM_rep3

source_name: Left ventricular tissue of non-DM rat, replicate 3


title: ExVivoLV_nonDM_rep1


title: Activated gametocyte untreated 1 h

label_protocol: Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).

value: Mixed gametocyte and asexual blood stage


title: P60 day-old mouse lens

source_name: 60 day-old Mouse lens


title: Mature gametocytes TSA-treated 1 h

source_name: Mature gametocyte RNA

value: Mature gametocyte


title: Resting microglia 2

description:
M0-2
Gene expression after 24hr without stimulation


title: Activated gametocyte TSA-treated 1 h


title: Mature gametocytes TSA-treated 6 h


title: Resting microglia 1

description:
M0-1
Gene expression after 24hr without stimulation


title: Activated gametocyte untreated 6 h


title: BreastCancerBiopsie_Sample2-Sensitive-Rep2

city: Guadalajara

first: Mariel

last: Garcia-Chagollan

state: Jalisco

address: Sierra Mojada 950

department: Departamento Fisiologia

country: Mexico

institute: Universidad de Guadalajara, Centro Universitario de Ciencias de la Salud

description:
Sample Sensitive to Taxane Treatment
Sensitive4

hyb_protocol: Labeled doble stranded cDNA was hybridized for 20h into HumanExpression 12x135K microarrays (Roche Applied Science)

scan_protocol: Microarrays were scanned on an MS200 Scanner (Roche Applied Science)

data_processing: Microarray images were processed using the DEVA 1.2 software (Roche Applied Science) and the fluorescence intensities were normalized using the RMA algorithm.

source_name: Breast Cancer Biopsie, Sensitive, Taxane Treatment

label_protocol: Doble stranded cDNA products were labeled with the NimbleGen One-Color DNA labeling kit (RocheAppliedScience)

extract_protocol: Biopsies stored at −80°C in RNAlater were used for the isolation of total RNA with the RNeasy Plus Mini kit (QIAGEN) according to the manufacturer’s instructions. RNA was quantified by absorbance at 260/280 nm and quality was evaluated using an Agilent 2100 Bioanalyzer and the RNA 6000 NanoChip kit (Agilent Technologies). Double stranded complementary DNA (ds-cDNA) was generated from 5 µg of RNA using the cDNA Synthesis Kit System (Roche Applied Science), and purified with the GenElute™ PCR Clean-up Kit (Sigma-Aldrich Quimica)

treatment_protocol: Small tumor explants (4–5 mm in diameter and 250–300 um in thickness) were prepared using the Krumdieck slicing system. Tumor explants were culture in DMEM/F12 medium supplemented with 10% fetal bovine serum, 5 ug/mL bovine insulin, 100 ug/mL gentamicin, insulin-transferrin-selenium, and 25 mM glucose. The treatment of tumor explants with 20 μg/mL paclitaxol was performed after 1 h of preincubation.

value: female

value: breast

value: Ductal Infiltrating


title: Mature gametocytes untreated 1 h


title: BreastCancerBiopsie_Sample2-Sensitive-Rep1

description:
Sample Sensitive to Taxane Treatment
Sensitive3


title: Immature gametocytes TSA-treated 1 h

source_name: Immature gametocyte RNA

value: Immature gametocyte


title: Mature gametocytes untreated 6 h


title: Immature gametocytes untreated 6 h


title: BreastCancerBiopsie_Sample2-Resistant-Rep1

description:
Sample Resitant to Taxane Treatment
Resistant3

source_name: Breast Cancer Biopsie, Resistant, Taxane Treatment

value: Canalicular Infiltrating

value: Basal like


title: 6_LmxFox_dblNEG

status: Public on May 23 2017

city: Cambridge

first: Alison

last: O'Neil

address: 7 Divinity Ave

department: Stem Cell and Regnerative Biology

institute: Harvard University

description: control

hyb_protocol: Followed Affy guidelines

scan_protocol: Followed Affy guidelines

data_processing:
Used the Affymetrix Transcriptome Analysis Console
Processed data supplementar file: Condition One = average double positive samples, Condition 2 = average of double negative samples

source_name: human iPS derived day 14 neural progenitor

label_protocol: Followed Affy guidelines

growth_protocol: iPSCs were dissociated with Accutase and resuspended in neural induction medium containing DMEM/F12, Neurobasal, N2, B27 without vitamin A, Dorsomorphin (1µM), Purmorphamine (1µM), SAG 1.3 (1µM), SB431542 (10µM), and CHIR99021 (0.5µM). Cells were then grown in suspension using ultra non-attachment plates for 14 days. To generate the double negative population, only Dorsomophrin and Purmorphamine were used.

extract_protocol: RNA was extracted with Trizol (chloroform and isopropanol)

tag: cell markers

value: FOXA2/LMX1 double negative


title: 5_LmxFox_dblNEG

description: control


title: Immature gametocytes untreated 1 h


title: BreastCancerBiopsie_Sample1-Sensitive-Rep1

description:
Sample Sensitive to Taxane Treatment
Sensitive1

value: Luminal B


title: N2_Fed_G

first: Brad

middle: T

last: Moore

address: Box 90338, Duke University

department: Biology

institute: Duke University

description: Gene expression data from larvae hatched in the presence or absence of food.

hyb_protocol: 12.5 micrograms of biotin-labeled cRNA was fragmented and hybridized according to the Affymetrix protocol.

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

data_processing: Data was processed in R using the LIMMA package.  GCRMA was used to normalize the entire array.  A single representative probeset per gene was chosen (Baugh 2009), and genes that weren't above detection (> 2.18 log2 GCRMA) in at least 3 replicates (across all conditions) were filtered.  GCRMA-normalized data passing the above filters were subjected to LIMMA's empirical Bayes test for several hypotheses.

organism: Caenorhabditis elegans

source_name: L1 larvae 3 hours after hatching

label_protocol: Biotinylated cRNA were prepared according to the standard protocol for MessageAmp II-Biotin Enhanced kit (Ambion) starting with 100 ng total RNA.

growth_protocol: C. elegans strains were grown in S-complete at a density of 1 worm/microliter with or without 25 mg/ml E. coli HB101 at 20C. Cultures were 10 ml volume (10,000 larvae).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions except 50 micrograms of linear polyacrylamide was added as a carrier (Sigma). After TRIzol extraction, the RNA pellet was dissolved in Rnase-free water and further purified using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol and eluted in 14 μl RNAse-free water.

treatment_protocol: Worms were briefly pelleted in a clinical centrifuge, fed samples were washed three times in S-complete. All but 100 microliters of buffer was removed, and the pelleted worms were frozen in liquid nitrogen.

value: whole larvae

tag: developmental stage

value: L1 larvae

value: Fed

value: 2-4 hours

value: wild-type


title: 2_LmxFox_dblPOS

description: sample

value: FOXA2/LMX1 double positive


title: BreastCancerBiopsie_Sample1-Sensitive-Rep2

description:
Sample Sensitive to Taxane Treatment
Sensitive2


title: GR1307_Fed_E

tag: genotype

value: daf-16 (mgDf50)


title: Immature gametocytes TSA-treated 6 h

value: NF54 Wildtype

value: NF54 and 3D7

value: Mixed gametocyte and asexual blood stage


title: N2_Starved_F

value: Starved


title: BreastCancerBiopsie_Sample2-Resistant-Rep2

description:
Sample Resitant to Taxane Treatment
Resistant4

value: female

value: breast


title: GR1307_Starved_G


title: GR1307_Starved_F


title: BreastCancerBiopsie_Sample1-Resistant-Rep1

description:
Sample Resitant to Taxane Treatment
Resistant1

value: lobulillar infiltrating

value: Luminal A


title: GR1307_Starved_E


title: N2_Starved_G


title: fast growing Ruditapes decussatus [FG_FA544]

description: Ruditapes decussatus

source_name: gills of Ruditapes decussatus

value: fast growing  Ruditapes decussatus


title: GR1307_Fed_G


title: 4_LmxFox_dblNEG

description: control

value: FOXA2/LMX1 double negative


title: BreastCancerBiopsie_Sample1-Resistant-Rep2

description:
Sample Resitant to Taxane Treatment
Resistant2


title: N2_Fed_F

value: whole larvae


title: 1_LmxFox_dblPOS

description: sample


title: N2_Starved_E

value: L1 larvae


title: N2_Fed_E

value: Fed


title: 3_LmxFox_dblPOS

description: sample


title: GR1307_Fed_F

value: 2-4 hours


title: Hepatitis C_HCC_05

city: Hamamatsu

first: Takanori

last: Sakaguchi

address: 1-20-1 Handayama Higashi-ku

department: Second Department of Surgery

institute: Hamamatsu University School of Medicine

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized on the GeneChip Human Gene 2.0 ST Array using  the GeneChip Hybridization Oven 645. GeneChips were washed and stained in the  GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with GeneSpring GX version12.6 (Agilent Technologies). RMA16 was used as summarization algorithm.

source_name: HCC arising from hepatitis C (HCV-HCC)

label_protocol: cDNA synthesis, amplification and labeling were performed with Ambion WT Expression Kit(Life Technologies) and WT Terminal Labeling Kit (Affymetrix).

extract_protocol: Total RNA was extracted from the frozen resected sample using an RNeasy Mini Kit (Quiagen, Valencia, CA, USA).

value: Hepatocellular carcinoma