title: S. gordonii_∆ahrC_arg-_rep3

status: Public on Jul 18 2017

city: Newcastle upon Tyne

first: Nicholas

middle: S

last: Jakubovics

address: Framlington Place

department: School of Dental Sciences

institute: Newcastle University

description: Gene expression after 30 min in no arginine

hyb_protocol: Samples were prepared as per Agilent One-color v6.5 protocol, hybridisation oven GA2545A was used at 65 degree centigrade, with rotator rack G2530-60029.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x15k array slides (Scan resolution 5um, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 041846_D_F_20120627) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Streptococcus gordonii str. Challis

source_name: S. gordonii ∆ahrC, no arginine, 30 min

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50ng RNA using the One-Color Low RNA Input Quick Amplification kit (Agilent 5190-2305) 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: Cells were cultured statically at 37⁰C to mid-exponential phase (OD600=0.3-0.4) in chemically defined medium (FMC) containing 0.5 mM L-arginine (Jakubovics et al., 2015, Mol Microbiol 97:281-300). Cultures were split into two 4 ml portions, harvested at 3,800 g in a swing-out rotor and resuspended (see treatment protocol).

extract_protocol: Intracellular RNA was stabilised by addition of 2 volumes of RNA Protect (Qiagen), mixed and incubated at 20⁰C, 5 min. Cells were harvested by centrifugation and supernatants were discarded. Cells were stored at -80⁰C for up to 72 h. Cells were resuspended in spheroplasting buffer containing 500 U/mL mutanolysin, incubated at 37⁰C, 5 min, and 350 µL RNAWiz (Life Technologies was added). Cells were disrupted by bead beating in a TissueLyser (Qiagen) and RNA was extracted using the Ambion RiboPure Bacteria RNA Isolation Kit.

treatment_protocol: Cells were resuspended in fresh chemically defined medium containing either 0.5 mM L-arginine ('arg+') or no L-arginine ('arg-') and incubated statically at 37⁰C for 30 min.

tag: medium

value: Chemically defined medium

tag: arginine

value: 0 mM


title: iPSC-CM Line 2 Replicate 2

status: Public on Jul 19 2017

type: RNA

city: Stanford

first: Joseph

last: Wu

state: Carlifornia

address: Stanford University School of Medicine

country: USA

institute: Stanford University School of Medicine

description: LncRNA profiling of exosomes collected at 36 hours at normoxia

hyb_protocol: Hybridization was performed in Agilent SureHyb Hybridization Chambers

scan_protocol: Slides were scanned with Agilent DNA Microarray Scanner

data_processing: Data were extracted using Agilent Feature Extraction software

molecule: total RNA

organism: Homo sapiens

source_name: Exosome iPS2 R2

label_protocol: Arraystar Flash RNA Labeling Kit was used for sample labeling

growth_protocol: Day 30 ESC-CMs and iPSC-CMs were cultured routinely

extract_protocol: Total RNA was extracted using Exiqon miRCURY RNA Isolation Kit

treatment_protocol: CMs were grown in RPMI-1640 media supplemented with B27 supplement minus antioxidants for 36 hours, following which the supernatant was removed and collected for exosome isolation.

tag: source

value: Media supernatant


title: 5_NOD-2

type: genomic

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

hyb_protocol: DNA was hybridized to each array according to the manufacturer's instructions using Genome-Wide SNP 6.0 Assaykit.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: The array image was acquired using Affymetrix Genotyping Console (version 4.2.0.26). SNP calls were extracted and converted from CEL files into signal intensities using Genotyping Console (version 4.2.0.26) software and BRLMM algorithm.

label: Biotin

molecule: genomic DNA

organism: Mus musculus

source_name: male NOD mice 12 weeks old

label_protocol: DNA was restriction digested, PCR amplified, fragmented and labeled according to the manufacturer's instructions using Genome-Wide SNP6.0 Assay kit.

growth_protocol: All mice were maintained under specific pathogen-free conditions and experimental studies were performed in accordance with the Institutional Animal Care and Use Guidelines and accredited by the ethic committee under the number CEEA34.CB.024.11.

extract_protocol: DNA extraction were realized from tails by 20 mg/ml proteinase K (Invitrogen) degradation, saturated NaCl/propanol DNA precipitation and DNA re-suspension 2 hours in TE10-4 buffer at 42°C.

treatment_protocol: No treatment of mice before DNA extraction

tag: strain

value: NOD

tag: Sex

value: male

tag: age

value: 12 weeks old


title: iPSC-CM Line 2 Replicate 1

source_name: Exosome iPS2 R1


title: iPSC-CM Line 1 Replicate 1

source_name: Exosome iPS1 R1


title: H9 ESC-CM Replicate 1

source_name: Exosome H9 R1


title: S. gordonii_∆ahrC_arg-_rep1

country: United Kingdom


title: H7 ESC-CM Replicate 1

source_name: Exosome H7 R1


title: iPSC-CM Line 1 Replicate 2

source_name: Exosome iPS1 R2


title: S. gordonii_∆ahrC_arg+_rep3

description: Gene expression after 30 min in 0.5 mM arginine

source_name: S. gordonii ∆ahrC, high arginine, 30 min


title: S. gordonii_∆ahrC_arg-_rep2


title: S. gordonii_∆ahrC_arg+_rep4


title: S. gordonii_∆ahrC_arg-_rep4


title: H7 ESC-CM Replicate 2

source_name: Exosome H7 R2


title: 6_B6-2

source_name: male C57BL/6j mice 12 weeks old


title: 8_YES8775

source_name: male YES mice 12 weeks old

value: YES


title: case 5050568003_C

city: Delhi

first: Mohammed

last: Faruq

address: Mall Road

department: Genomics and Molecular Medicine

country: India

institute: CSIR-IGIB

description: case

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw intensity data was extracted without background correction and normalization using GenomeStudio Software Illumina Inc. We have only retained probes with detection p-value less than equal to 0.05 in atleast 3 samples out of 6 in a given array. Background correction and quantile normalization was performed using limma package in R. Additionally, we have also checked for any batch effect using various methods such as SNM (supervised normalization method) and ComBat (sva package).

label: biotin

source_name: case

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

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

tag: tissue

value: Peripheral whole blood

tag: disease state

value: SCA12 symptomatic individual


title: S. gordonii_∆argR_arg-_rep3

source_name: S. gordonii ∆argR, no arginine, 30 min


title: H9 ESC-CM Replicate 2

source_name: Exosome H9 R2


title: S. gordonii_∆ahrC_arg+_rep2


title: S. gordonii_∆argR_arg-_rep1


title: S. gordonii_∆ahrC_arg+_rep1


title: S. gordonii_∆argR_arg+_rep2

source_name: S. gordonii ∆argR, high arginine, 30 min


title: S. gordonii_∆argR_arg-_rep2


title: S. gordonii_∆argR_arg+_rep3


title: S. gordonii_∆argR_arg+_rep1


title: S. gordonii_∆argR_arg+_rep4


title: S. gordonii_∆arcR_arg-_rep4

source_name: S. gordonii ∆arcR, no arginine, 30 min


title: S. gordonii_∆arcR_arg-_rep3


title: S. gordonii_∆arcR_arg-_rep2


title: Neuroblastoma cell line NBL-S

city: Valencia

first: Jaime

last: Font de Mora

address: Avenida Fernando Abril Martorell, 106; Torre A,  5-07

country: Spain

institute: Instituto de Investigación Sanitaria La Fe

description: Hybridized to CytoScan HD

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

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

source_name: Neuroblastoma cell line NBL-S

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from cell lines and tumors using standard proteinase K and phenol-chloroform extraction protocol. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

value: Neuroblastoma cell line


title: Neuroblastoma cell line NLF

description: Hybridized to CytoScan HD

source_name: Neuroblastoma cell line NLF


title: Neuroblastoma cell line SK-N-AS

description: Hybridized to CytoScan HD

source_name: Neuroblastoma cell line SK-N-AS


title: 7_YES8702


title: Neuroblastoma cell line SH-SY5Y

description: Hybridized to CytoScan HD

source_name: Neuroblastoma cell line SH-SY5Y


title: Neuroblastoma cell line LA-N-1

description: Hybridized to CytoScan HD

source_name: Neuroblastoma cell line LA-N-1


title: S. gordonii_∆arcR_arg+_rep4

source_name: S. gordonii ∆arcR, high arginine, 30 min


title: Neuroblastoma cell line SK-N-BE(2)

description: Hybridized to CytoScan HD

source_name: Neuroblastoma cell line SK-N-BE(2)


title: S. gordonii_∆arcR_arg+_rep2


title: Neuroblastoma cell line IMR-32

description: Hybridized to CytoScan HD

source_name: Neuroblastoma cell line IMR-32


title: S. gordonii_∆arcR_arg-_rep1


title: Neuroblastoma tumor TI_809

description: Hybridized to CytoScan HD

source_name: Neuroblastoma tumor TI_809

value: Primary neroblastoma


title: Neuroblastoma tumor A786

description: Hybridized to CytoScan HD

source_name: Neuroblastoma tumor A786


title: Neuroblastoma tumor TI_773

description: Hybridized to CytoScan HD

source_name: Neuroblastoma tumor TI_773


title: Neuroblastoma tumor TI_672

description: Hybridized to CytoScan HD

source_name: Neuroblastoma tumor TI_672


title: Neuroblastoma tumor TI_494

description: Hybridized to CytoScan HD

source_name: Neuroblastoma tumor TI_494


title: Neuroblastoma tumor TI_501

description: Hybridized to CytoScan HD

source_name: Neuroblastoma tumor TI_501


title: S. gordonii_∆arcR_arg+_rep1


title: Neuroblastoma tumor NBX_56

description: Hybridized to CytoScan HD

source_name: Neuroblastoma tumor NBX_56


title: Neuroblastoma tumor NBX_6

description: Hybridized to CytoScan HD

source_name: Neuroblastoma tumor NBX_6


title: Neuroblastoma tumor TI_423

description: Hybridized to CytoScan HD

source_name: Neuroblastoma tumor TI_423


title: Neuroblastoma tumor TI_719

description: Hybridized to CytoScan HD

source_name: Neuroblastoma tumor TI_719


title: Neuroblastoma tumor NBX_34

description: Hybridized to CytoScan HD

source_name: Neuroblastoma tumor NBX_34


title: S. gordonii_∆arcR_arg+_rep3


title: Neuroblastoma tumor NBX_19

description: Hybridized to CytoScan HD

source_name: Neuroblastoma tumor NBX_19


title: Neuroblastoma tumor TI_122

description: Hybridized to CytoScan HD

source_name: Neuroblastoma tumor TI_122


title: Neuroblastoma tumor NBX_29

description: Hybridized to CytoScan HD

source_name: Neuroblastoma tumor NBX_29


title: Neuroblastoma tumor NBX_18

description: Hybridized to CytoScan HD

source_name: Neuroblastoma tumor NBX_18


title: Neuroblastoma tumor NBX_17

description: Hybridized to CytoScan HD

source_name: Neuroblastoma tumor NBX_17


title: Neuroblastoma tumor NBX_49

description: Hybridized to CytoScan HD

source_name: Neuroblastoma tumor NBX_49


title: Patient1 cancer tissue (C1A)

city: Haikou

first: Yousheng

last: Huang

state: Hainan

address: The 3rd Xueyuan Road

department: Department of pathology

country: China

institute: Hainan Medical university

description: The expression profiles of microRAN were compared between colon cancer and its adjacent normal tissues

hyb_protocol: After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual

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

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs between two groups were identified through Fold change and P-value. Differentially expressed miRNAs between two samples were filtered through Fold change.

source_name: Patient1 cancer tissue

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

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

tag: individual

value: primary colon cancer

tag: Stage

tag: status after 1 years

value: alive

value: cancer tissue


title: Y. pestis, Kim53∆nlpD 37°C vs.Kim53 28°C

city: Ness-Ziona

first: Avital

last: Tidhar

department: Biochemistry and molecular Genetics

country: Israel

institute: Israel Institute for Biological Research

hyb_protocol: A slide (containing 8 arrays) was hybridized with samples originating from 2 independent biological experiments representing the same time point, performed with Cy3-Cy5 dye swap. Each array represent hybridization of treated sample with its growth-control sample. Hybridization was done using the Agilent Gene Expression Hybridization Kit according to Agilent protocol for two-color Microarray-Based Gene Expression Analysis.

scan_protocol: Scanned on an Agilent DNA microarray G2505B scanner. Images were quantified using Agilent Feature Extraction (FE) Software (version 9.5.1.1), with linear and LOWESS normalization.

data_processing: Agilent FE Software (9.5.1.1) was used for background subtraction and LOWESS normalization. Statistical analysis was performed using the Limma (Linear Models for Microarray Data) package from the Bioconductor project (http://www.bioconductor.org). The processed signal from the FE was read into Limma using the “read.maimages” function. Background subtraction and LOWESS normalization were performed for each array. Quantile normalization was applied between arrays. The Benjamini-Hochberg false discovery rate (FDR) was used to correct for multiple comparisons.

organism: Yersinia pestis

source_name: grown at 37°C

label_protocol: Complementary RNA (cRNA) was produced from the total RNA samples and fluorescently labeled using the MessageAmpTM II-Bacteria kit (Ambion) according to the manufacturer’s instructions. Each experiment comprised of samples representing 4 different ciprofloxacin concentrations labeled with either Cy3-CTP or Cy5-CTP, which were co-hybridized with the growth control sample labeled with the 2nd dye (Cy5-CTP or Cy3-CTP, accordingly).

growth_protocol: For bacterial total RNA preparation, bacterial colonies were grown on BHIA plats for 48 h at 28°C , harvested and diluted in heart infusion broth (HIB) (BD, USA) supplemented with 0.2% xylose and 2.5 mM CaCl2 (Sigma-Aldrich, Israel) to an OD660 of 0.01 and grown over night (o.n.) at 28°C in a shaker (200 rpm). The resulting cultures were diluted in fresh broth to an OD660 of 0.05 and allowed to grow for 5 h at 37°C. Aliquots of ~5×108 cfu were collected by centrifugation and cells were immediately frozen at -70°C until use.

extract_protocol: Total RNA were extracted using RNeasy Mini kit (QIAGEN) according to the manufacturer’s instructions. Residual DNA was removed by 15 min on-column digestion using the RNase-free DNase kit (QIAGEN).

value: Kim53 ∆nlpD

source_name: grown at 28°C


title: Y. pestis, Kim53 37°C vs.Kim53∆nlpD 28°C


title: CMP derived cDC1_1

city: London

first: Julie

last: Helft

address: 44 Lincoln's Inn Fields

department: London Research Institute

institute: Cancer Research UK

description: CMP derived cDC1

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridised for 16hrs at 45c on Genechip Human Gene 2.0 ST arrays. Genechips were washed and stained in the Affymetrix Fludics station 450.

scan_protocol: Genechips were scanned using the Affymetrix Genechip Scanner 3000G

data_processing: Data were analyzed using Bioconductor 2.13 running on R 3.0.2. Probeset expression measures were calculated using the Affymetrix package’s Robust Multichip Average (RMA) default method.

source_name: Human hematopoietic progenitors culture

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

growth_protocol: Hematopoietic progenitors purified from umbilical cord blood were cultured for 12 days with recombinant GM-CSF (20ng/ml),  IL-4 (20ng/ml), FLT3L (100ng/ml) and SCF (20ng/ml).

extract_protocol: RLT buffer (+beta-ME) extraction of total RNA was performed and purified further with the Rneasy kit (Qiagen) according to the manufacturers instructions

value: umbilical cord blood

tag: cell type

value: CD141+DNGR-1+ dendritic cells (cDC1)

tag: cell origin

value: common myeloid progenitors (CMP)


title: CMP derived cDC1_3

description: CMP derived cDC1


title: Patient1 normal mucosa (C1B)

source_name: Patient1 adjacent normal mucosa

value: adjacent normal mucosa


title: CMP derived cDC1_2

description: CMP derived cDC1


title: MLP derived cDC1_4

description: MLP derived cDC1

value: multipotent lymphoid progenitors (MLP)


title: Patient2 cancer tissue (C2A)

source_name: Patient2 cancer tissue


title: Patient2 normal mucosa (C2B)

source_name: Patient2 adjacent normal mucosa


title: Patient3 cancer tissue (C3A)

source_name: Patient3 cancer tissue


title: Y. pestis, Kim53∆nlpD 28°C vs.Kim53∆nlpD 37°C


title: Patient3 normal mucosa (C3B)

source_name: Patient3 adjacent normal mucosa


title: MLP derived cDC1_3

description: MLP derived cDC1


title: GSK343_4h_HFF_rep3

status: Public on Jul 17 2017

city: Bethesda

first: Jesse

middle: H

last: Arbuckle

state: MD

address: 33 North Drive

department: Laboratory of Viral Diseases

institute: National Institute of Allergy and Infectious Diseases, NIH

description:
9965581135_H
Replicate 3

hyb_protocol: Biotinylated RNA was hybridized to Illumina Human HT-12 v4.0 Expression BeadChips (Gene Expression Omnibus accession no. GPL10558; >47,000 unique probes).

scan_protocol: Arrays were imaged with an Illumina HiScan-SQ.

data_processing: Signal data were extracted using the Gene Expression module (v. 1.9.0) of the GenomeStudio software (v. 2011.1, Illumina, Inc.).  Signal intensities were converted to log2 scale and p-values were determined as described in the GenomeStudio Gene Expression Module User Guide.  Data for array probes with insufficient signal were removed from the dataset (detection was defined as at least two arrays with detection p-value < 0.1) and quantile normalization was applied across all arrays.  ANOVA was performed on the normalized log2 expression values to test for mRNA expression differences by treatment.  A p-value of 0.05 was used for the statistical significance after adjusting for the familywise error rate (FWER) using the Benjamini–Hochberg method to account for multiple testing.  Statistical analysis was performed using JMP/Genomics software v. 7.0 (SAS Institute Inc.).

label_protocol: Amplification and labeling of the RNA samples were performed using the Illumina TotalPrep RNA Amplification (Applied Biosystems) and 500 ng of total RNA per sample.

growth_protocol: HFF cells were cultured in DMEM with 10% FBS.

extract_protocol: Total RNA was isolated with Isolate II RNA Kit (Bioline, Cat # BIO-52073).  RNA quality (RNA Integrity Number > 8.5) was verified by Bioanalyzer for all samples.

treatment_protocol: HFF cells seeded into a 6-well dish and grown for 3 days (37 degrees C, 5% CO2).  HFF cells were then treated with GSK126 (30 µM), GSK343 (35 µM), or vehicle (DMSO) for 4 hours.

tag: treatment

tag: time

value: 4 h

tag: infection

value: Mock

tag: cell line

value: HFF


title: GSK126_4h_HFF_rep3

description:
9965581135_G
Replicate 3


title: Vehicle_4h_HFF_rep3

description:
9965581135_E
Replicate 3

value: Vehicle


title: Y. pestis, Kim53 28°C vs. Kim53 37°C


title: GSK343_4h_HFF_rep2

description:
9967453016_L
Replicate 2


title: Vehicle_4h_HFF_rep1

description:
9967453016_A
Replicate 1


title: Vehicle_4h_HFF_rep2

description:
9967453016_I
Replicate 2


title: ChIP-seq from GM12878 (ENCLB701POR)

status: Public on Jul 16 2017

type: SRA

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR849WCQ/
***************
biological replicate number: 3
technical replicate number: 2
description:
experiment encode accession: ENCSR849WCQ
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR142REC
encode release date: 2017-01-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB701POR
size range: 300-600

library_source: genomic

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens GM12878 immortalized cell line

tag: antibody

tag: line

value: immortalized cell line

tag: description

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

tag: biosample encode accession

tag: dev stage

value: adult

value: female

value: unknown

tag: health state

tag: lab

value: Bradley Bernstein, Broad

tag: link

value: ENCBS830CIQ at ENCODE; https://www.encodeproject.org/ENCBS830CIQ/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/

value: ENCODE dbxrefs Cellosaurus CVCL_7526; http://web.expasy.org/cellosaurus/CVCL_7526

value: ENCODE dbxrefs GM12878; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=GM12878

value: Coriell sample source; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878


title: Kras, muntant cell, biological rep1

city: Chiayi

first: Weng

middle: Ching

last: Chieh

address: No.168, Sec. 1, University Rd., Minhsiung

department: Department of Biomedical Sciences

country: Taiwan

institute: National Chung Cheng University

description: Kras mutantion and P53 deletion

hyb_protocol: Samples were hybridized to Mouse Gene ST 1.0 arrays using Affymetrix hybridization kit materials, according to the manufacturrer's instructions. Sample cocktails were heated at 99°C for 5 minutes, then 45°C for 5 minutes, centrifuged at max speed for 1 minute. Eighty ul of hyb solution was transferred to each array, and hybridized 17 hours at 45°C at 60rpm. Fluidics washing protocol used was FS450_0007.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data generated were analyzed using Affymetrix Transcriptome Analysis Console software with Gene Level Differential Expression Analysis.
MoGene-1_0-st-v1.na34.mm10.probeset.csv
MoGene-1_0-st-v1.na34.mm10.transcript.csv
Affymetrix Transcriptome Analysis Console 1.0.0.234

source_name: Pbsn-cre LSL- KrasG12D P53L/L

label_protocol: WT expression kit (Ambion), WT Terminal Labeling Kit (Affymetrix), according to the manufatcturer's instructions

growth_protocol: Mouse primary PCa cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum, nonessential amino acids, 100 units/ml penicillin and 100 μg/ml streptomycin at 37 °C in a 5% CO2 incubator.

extract_protocol: RNEasy Micro kit (Qiagen), following manufatcturer's instructions

tag: genotype

value: Pbsn-cre LSL- KrasG12D P53L/L


title: GSK343_4h_HFF_rep1

description:
9967453016_D
Replicate 1


title: MLP derived cDC1_2

description: MLP derived cDC1

tag: tissue

value: umbilical cord blood

value: CD141+DNGR-1+ dendritic cells (cDC1)

value: multipotent lymphoid progenitors (MLP)


title: GSK126_4h_HFF_rep1

description:
9967453016_C
Replicate 1

value: 4 h

value: Mock

value: HFF


title: MLP derived cDC1_1

description: MLP derived cDC1


title: Kras, muntant cell, biological rep2

description: Kras mutantion and P53 deletion


title: GSK126_4h_HFF_rep2

description:
9967453016_K
Replicate 2


title: Pbsn-cre p53L/L, normal cell, biological rep1

description: wild-type

source_name: Pbsn-cre p53L/L

value: Pbsn-cre p53L/L


title: Ebensen9032 y_48h_cdiAMP+Ag

status: Public on Jul 15 2017

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

hyb_protocol: Samples were hybridized to an identical lot of Affymetrix Gene ST 1.0 Array (169 Format) for 17 hours at 45°C.  Steps for washing and staining were processed on the fluidics station 450 using the GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix) and the FS450-0007  protocol (Affymetrix; Santa Clara, CA).

scan_protocol: Image Analysis was performed on GCOS3000 Scanner and GCOS1.2 Software Suite (Affymetrix; Santa Clara, CA).

data_processing: Signal intensities (raw data) were log2 transformed and normalized using RMA summarization method.

source_name: dendritic cells

label_protocol: 500 ng of total RNA were used for biotin labelling according the Ambion® WT Expression Kit (Ambion) and the GeneChip® WT Terminal Labeling and Hybridization Kit (Affymetrix). 5.5 µg of biotinylated cDNA were fragmented and placed in a hybridization cocktail containing four biotinylated hybridization controls (BioB, BioC, BioD, and Cre) as recommended by the manufacturer.

growth_protocol: BMDC were generated by incubating  1x10^6 bone marow cells in complete RPMI (10%FCS, 2mM L-Glu, pens/strept 50µg/ml)(Gibco, USA), with the addition of 20 ng/ml GM-CSF (BD, USA) for 6 days, cells were harvested and counted

extract_protocol: RNAeasy (Qiagen). Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany).

treatment_protocol: BMDC were re-stimulated for 30min, 2, 6, 24, and 48 h with Ovalbumin (Hyglos, Germany) alone or co administered with 10µg/ml CDA, or with CDA alone (Biolog, Bremen, Germany) to activate the cells.

value: Ovalbumin + 10µg/ml CDA

tag: time point


title: Braf, muntant cell, biological rep2

description: Braf mutantion and P53 deletion

source_name: Pbsn-cre LSL- BrafV600E P53L/L

value: Pbsn-cre LSL- BrafV600E P53L/L


title: Ebensen9037 y_24h_cdiAMPonly

value: 10µg/ml CDA


title: S. gordonii_∆argR_arg-_rep4

source_name: S. gordonii ∆argR, no arginine, 30 min

tag: medium

value: Chemically defined medium

tag: arginine

value: 0 mM


title: Braf, muntant cell, biological rep1

description: Braf mutantion and P53 deletion


title: Ebensen9034 y_24h_AgOnly

tag: treatment

value: Ovalbumin


title: ChIP-seq from GM12878 (ENCLB147VVR)

description:
https://www.encodeproject.org/experiments/ENCSR849WCQ/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR849WCQ
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR142REC
encode release date: 2017-01-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB147VVR
size range: 300-600

value: immortalized cell line

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: adult

tag: Sex

value: female

tag: age

value: unknown

value: Bradley Bernstein, Broad

value: ENCBS830CIQ at ENCODE; https://www.encodeproject.org/ENCBS830CIQ/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/

value: ENCODE dbxrefs Cellosaurus CVCL_7526; http://web.expasy.org/cellosaurus/CVCL_7526


title: Ebensen9033 y_24h_Ctrl


title: Ebensen9021 y_48h_Ctrl


title: Pbsn-cre p53L/L, normal cell, biological rep2

description: wild-type


title: E-tail

city: Kunming

first: XiaoMing

last: Dai

state: Yunnan

address: 293#,Xichang road

department: The maxillofacial service of the department of plastic surgery,

institute: The first affiliated hospital of Kunming Medical University

description:
Gene expression at the 28 week after oral delivery of 4-nitroquinoline-1-oxide (4NQO) at a dose of 50mg/L
tail28

hyb_protocol: 1 μg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 100 ml containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers’ instructions. On completion of the fragmentation reaction, 100 ml hybridization solution was dispensed for hybridization to Agilent Mouse 4x44K Gene Expression Microarrays v2 (G4846A) 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) using one color scan setting for4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green and Green PMT is set as XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software (version 11.0.1.1). Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 6 out of 9 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.

source_name: lingual mucosa

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted and purified from lingual mucosa samples using TRIzol® Reagent (Invitrogen life technologies) according to standard instructions

treatment_protocol: 4-NQO was obtained from Sigma-Aldrich Co. LLC. (U.S.A), dissolved in propylene glycol to a concentration of 500mg/L for storage. 4NQO in drinking water at a dose of 50mg/L for was delivered for16weeks. Drink water was changed every week. The drinking water in all groups was then exchanged for distilled water from the 17th week to the cessation of experiment at the 28th week.

value: lingual mucosa

tag: gender

value: 32 week

tag: strain


title: Ebensen8049 y_24h_Ctrl


title: Ebensen9006 y_48h_cdiAMP+Ag

value: Ovalbumin + 10µg/ml CDA


title: Ebensen9002 y_48h_AgOnly


title: M-tail

description:
Gene expression at the 12 week after oral delivery of 4-nitroquinoline-1-oxide (4NQO) at a dose of 50mg/L
tail12

value: 16 week


title: Ebensen8050 y_24h_AgOnly


title: Ebensen9001 y_48h_Ctrl


title: Ebensen8030 y_24h_cdiAMP+Ag


title: Ebensen9038 y_24h_cdiAMP+Ag


title: Ebensen9005 y_48h_cdiAMPonly

value: 10µg/ml CDA


title: M-arm

description:
Gene expression at the 12 week after oral delivery of 4-nitroquinoline-1-oxide (4NQO) at a dose of 50mg/L
arm12


title: Ebensen8053 y_24h_cdiAMPonly


title: C-back

description:
Gene expression at the 0 after oral delivery of 4-nitroquinoline-1-oxide (4NQO) at a dose of 50mg/L
back0

value: 4 week


title: Ebensen8029 y_24h_cdiAMPonly


title: Ebensen8054 y_24h_cdiAMP+Ag


title: Ebensen8005 y_24h_cdiAMPonly


title: Ebensen8025 y_24h_Ctrl


title: E-back

description:
Gene expression at the 28 week after oral delivery of 4-nitroquinoline-1-oxide (4NQO) at a dose of 50mg/L
back28


title: E-head

description:
Gene expression at the 28 week after oral delivery of 4-nitroquinoline-1-oxide (4NQO) at a dose of 50mg/L
head28


title: Ebensen5026 y_48h_cdiAMP+Ag


title: M-head

description:
Gene expression at the 12 week after oral delivery of 4-nitroquinoline-1-oxide (4NQO) at a dose of 50mg/L
head12


title: C-head

description:
Gene expression at the 0 after oral delivery of 4-nitroquinoline-1-oxide (4NQO) at a dose of 50mg/L
head0


title: Ebensen5022 y_48h_AgOnly


title: C-tail

description:
Gene expression at the 0 after oral delivery of 4-nitroquinoline-1-oxide (4NQO) at a dose of 50mg/L
tail0


title: PP_pig d_day 2_infected

city: Cordoba

first: Juan

middle: J

last: Garrido

address: Campus de Rabanales, Gregor Mendel building (C5), 1st floor

department: Genetica

institute: Universidad de Cordoba

description: Gene expression data from ileal Peyer's Patches from piglets non-infected and infected with Salmonella Typhimurium

hyb_protocol: Expression Analysis Technical Manual, Affymetrix

scan_protocol: Scanner 3000 7G de Affymetrix®

data_processing: GeneChip Operating Software 1.4.0.036 (Affymetrix)

organism: Sus scrofa

source_name: Peyer's patches_pig d_day 2_infected

label_protocol: One-Cycle Eukaryotic Target Labeling Assay

extract_protocol: RNeasy Mini Kit (Qiagen)

value: ileum

tag: tissue compartment

value: Laser-capture dissected Peyer's patches

tag: infection status

value: infected with Salmonella Typhimurium phagetype DT104

value: 4 weeks


title: Ebensen5002 y_24h_AgOnly

value: Ovalbumin


title: PP_pig a_day 2_infected

source_name: Peyer's patches_pig a_day 2_infected


title: Ebensen4023 y_48h_AgOnly


title: Ebensen8002 y_24h_AgOnly


title: Ebensen5025 y_48h_cdiAMPonly


title: Ebensen5005 y_24h_cdiAMPonly


title: Ebensen4021 y_48h_Ctrl


title: PP_pig d_day 0_control

source_name: Peyer's patches_pig d_day 0_control

value: not infected


title: Ebensen5006 y_24h_cdiAMP+Ag


title: PP_pig a_day 0_control

source_name: Peyer's patches_pig a_day 0_control


title: Ebensen5021 y_48h_Ctrl


title: Ebensen17001 y_0.5h_AgOnly


title: Ebensen8006 y_24h_cdiAMP+Ag


title: Ebensen4003 y_24h_AgOnly


title: Ebensen4001 y_24h_Ctrl


title: Ebensen14016 y_2h_cdiAMP+Ag


title: PP_pig b_day 2_infected

source_name: Peyer's patches_pig b_day 2_infected


title: Ebensen14027 y_6h_Ctrl


title: PP_pig c_day 2_infected

source_name: Peyer's patches_pig c_day 2_infected


title: Ebensen5001 y_24h_Ctrl


title: Ebensen14011 y_2h_Ctrl


title: Ebensen14031 y_6h_cdiAMPonly


title: Ebensen14012 y_2h_AgOnly


title: PP_pig b_day 0_control

source_name: Peyer's patches_pig b_day 0_control


title: PP_pig c_day 0_control

source_name: Peyer's patches_pig c_day 0_control


title: Ebensen14005 y_0.5h_cdiAMP+Ag


title: Ebensen16029 y_48h_cdiAMPonly


title: Ebensen12042 y_6h_AgOnly


title: Ebensen14004 y_0.5h_cdiAMPonly


title: Ebensen14001 y_0.5h_Ctrl


title: Ebensen12006 y_0.5h_cdiAMP+Ag


title: Ebensen11042 y_6h_AgOnly


title: Ebensen11022 y_2h_AgOnly


title: Ebensen11026 y_2h_cdiAMP+Ag


title: Ebensen12045 y_6h_cdiAMPonly


title: Ebensen11046 y_6h_cdiAMP+Ag


title: Ebensen12021 y_2h_Ctrl


title: Ebensen11006 y_0.5h_cdiAMP+Ag


title: Ebensen12046 y_6h_cdiAMP+Ag


title: Ebensen12025 y_2h_cdiAMPonly


title: Ebensen10042 y_6h_AgOnly


title: Ebensen11001 y_0.5h_Ctrl


title: Ebensen10046 y_6h_cdiAMP+Ag


title: Ebensen10026 y_2h_cdiAMP+Ag


title: Ebensen11025 y_2h_cdiAMPonly


title: Ebensen11005 y_0.5h_cdiAMPonly


title: Ebensen10006 y_0.5h_cdiAMP+Ag


title: Ebensen10025 y_2h_cdiAMPonly


title: Ebensen10022 y_2h_AgOnly


title: Ebensen11002 y_0.5h_AgOnly


title: Ebensen12001 y_0.5h_Ctrl


title: Ebensen10041 y_6h_Ctrl


title: Ebensen11045 y_6h_cdiAMPonly


title: Ebensen10045 y_6h_cdiAMPonly


title: Ebensen11041 y_6h_Ctrl


title: Ebensen10005 y_0.5h_cdiAMPonly


title: Ebensen10021 y_2h_Ctrl


title: Esophageal dysplasia tissue from case 314

city: Hong Kong

first: Xiaoyan

last: Ming

address: 21 sassoon road, pokfulam, hong kong

country: Hong Kong

institute: the university of hong kong

description: Gene expression data from esophageal dysplasia tissue #314

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Eukaryotic target hybridization system. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with GCOS software using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Patient with  Esophageal dysplasia

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (GeneChip IVT Labeling Kit, Affymetrix).

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

treatment_protocol: The patients had received no previous local or systemic treatment before operation.

value: Esophagus dysplasia


title: paracancerous tissue of  lung SCC_Patient57

city: Beijing

first: Li

last: Ping

address: 17# Panjiayuan Nanli, , Chaoyang District

institute: National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

description: Gene expression after surgical resection

hyb_protocol: 1650 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions.  On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE  8x60K Microarray (G4851B) for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent).

scan_protocol: The slides were scanned with an Agilent Microarray Scanner System (G2505B)

data_processing: The fluorescence intensities were extracted and preprocessed using Agilent Feature Extraction Software (v9.1). Data extraction and annotation were performed using GeneSpring GX v12.6.1 (Agilent).

source_name: lung SCC patinent

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (Qiagen, MD, United States).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: The total RNA from the paracancerous tissues was isolated with TRIzol reagent (Invitrogen, CA, USA) and was purified using an RNeasy kit (QIAGEN, MD, USA). The RNA was then quantified using an ND-1000UV-VIS Spectrophotometer (NanoDrop Technologies, DE, USA), and the RNA integrity was determined using a 2100 Bioanalyzer (Agilent Technologies, CA, USA)

value: normal lung tissue adjacent to tumor

value: M

tag: tumor stage


title: paracancerous tissue of  lung SCC_Patient60

value: F


title: Esophageal normal tissue from case 314

description: Gene expression data from esophageal dysplasia patients #314, adjacent normal tissue


title: paracancerous tissue of  lung SCC_Patient48


title: paracancerous tissue of  lung SCC_Patient54


title: paracancerous tissue of  lung SCC_Patient59


title: ESCC adjacent non-tumor tissue from case 363

description: Gene expression data from ESCC patients #363's adjacent non-tumor tissue

source_name: Patient with Esophageal squamous cell carcinoma

value: Esophagus non-tumor


title: paracancerous tissue of  lung SCC_Patient56


title: paracancerous tissue of  lung SCC_Patient52


title: paracancerous tissue of  lung SCC_Patient55


title: paracancerous tissue of  lung SCC_Patient46


title: ESCC adjacent non-tumor tissue from case 351

description: Gene expression data from ESCC patients #351's adjacent non-tumor tissue


title: paracancerous tissue of  lung SCC_Patient47


title: paracancerous tissue of  lung SCC_Patient43


title: paracancerous tissue of  lung SCC_Patient58


title: ESCC tumor tissue from case 301

description: Gene expression data from ESCC patients #301's tumor tissue

value: Esophagus tumor


title: ESCC tumor tissue from case 327

description: Gene expression data from ESCC patients #327's tumor tissue


title: paracancerous tissue of  lung SCC_Patient49


title: ESCC adjacent non-tumor tissue from case 327

description: Gene expression data from ESCC patients #327's adjacent non-tumor tissue


title: ESCC adjacent non-tumor tissue from case 301

description: Gene expression data from ESCC patients #301's adjacent non-tumor tissue


title: paracancerous tissue of  lung SCC_Patient51


title: ESCC tumor tissue from case 363

description: Gene expression data from ESCC patients #363's tumor tissue


title: MCF-7_MDA-MB-231_time 32h

city: Monterrey

first: Rafael

middle: Julián

last: Chacolla Huaringa

state: Nuevo León

address: 3000 Ignacio Morones Prieto ave., Col. Los Doctores

department: Medical School

country: Mexico

institute: Tec de Monterrey, campus Monterrey

description: The collected MCF-7 and MDA-MB-231 cells at 32h were fractionated in cytoplasmic and nuclei fractions (cultures and fractionations were made in differents days). Total RNA were isolated from cytoplasmic fractions of both cell lines. Cytoplasmic RNA from MCF-7 and MDA-MB-231 were labeled with Cy3 and Cy5, respectively.

hyb_protocol: Cytoplasmic RNA samples were used for hybridization with miRNA complete labeling and the Hyb Kit (Agilent Technologies) according to the manufacturer’s instructions. Next, standard washing procedures and hybridization with microarray slides were performed according to the manufacturer’s instructions.

scan_protocol: Slides were scanned using the GenePix® 4000B Microarray Scanner (Molecular Devices, city, PA, USA) with GenePix® Pro 6.0.1.25 Acquisition and Analysis Software (Molecular Devices). The GenePix® results (GPR) files were imported into the software R, version 2.12.2 (http://www.R-project.org) for further analyses.

data_processing:
Spot intensities were background subtracted using the Linear Models for Microarray Data package (Limma, version 3.20.5). The miRNA array contained an average of 30 replicates per probe sequence, with a total of 60,000 unique features and controls. The data were normalized between arrays by quantile normalization and log10 transformed, and the median was applied to the replicated probes.
Data were quantile normalization and log10 transformed, and the median was applied to the replicated probes.

molecule: cytoplasmic RNA

source_name: MCF-7 cells collected at 32-h after serum shock

label_protocol: Cytoplasmic RNA time samples from MCF-10A labeled with Cy3 fluorochrome, while cyRNA time samples from MCF-7 and MDA-MB-231 were labeled with Cy3 and pCp (Cytidine-5′-phosphate-3′-(6-aminohexyl)phosphate)-Cy5 (277 µM) fluorochromes, respectively, according to the manufacturer’s instructions.

growth_protocol: MCF-10A cells were grown in Mammary Epithelial Basal Medium® supplemented with SingleQuots® from the MEGM® BulletKit® (Lonza, MD, USA). The MCF-7 and MDA-MB-231 cell lines were grown in Gibco® Dulbecco’s Modified Eagle Medium, which features a nutrient mixture of D-MEM and F-12 (Thermo Fisher Scientific, NY, USA), supplemented with 10% heat-inactivated FBS. The cultured-cells for the three cell lines were supplemented with Gibco® Penicillin-Streptomycin antibiotics. Cell cultures were grown at 37 °C with 5% CO2 and 95% air in a humidified incubator.

extract_protocol: Total RNA was isolated from cytosolic time fractions using the MIRVANA miRNA Ambion® Kit (Thermo Fisher Scientific, NY, USA) according to the manufacturer’s instructions.

treatment_protocol: Cells were seeded in six-well plates and until they reached near-confluence. Then, cells were synchronized using the serum shock procedure [10]. One day before serum shock, the plates with confluent cells were washed and left overnight in serum-free basal medium (starvation). RPMI-1640 was the basal medium for the ZR-75-30 and HCC-1954 cells, while D-MEM/F-12 was used for the MCF-10A, MCF-7, and MDA-MB-231 cells. After overnight starvation, the medium was exchanged with the appropriate basal medium, which contained 50% horse serum (Biowest, Mountain View, CA, USA). After incubation for 2 h at 37 °C, the medium was replaced with a serum-free basal medium. At this time (time zero), we started to harvest cells every 4 h for 48 h.

tag: cell line

source_name: MDA-MB-231 cells collected at 32-h after serum shock

tag: collected time


title: paracancerous tissue of  lung SCC_Patient40


title: paracancerous tissue of  lung SCC_Patient45


title: paracancerous tissue of  lung SCC_Patient44


title: paracancerous tissue of  lung SCC_Patient42


title: ESCC tumor tissue from case 351

description: Gene expression data from ESCC patients #351's tumor tissue


title: paracancerous tissue of  lung SCC_Patient38


title: paracancerous tissue of  lung SCC_Patient53


title: paracancerous tissue of  lung SCC_Patient36


title: MCF-7_MDA-MB-231_time 36h

description: The collected MCF-7 and MDA-MB-231 cells at 36h were fractionated in cytoplasmic and nuclei fractions (cultures and fractionations were made in differents days). Total RNA were isolated from cytoplasmic fractions of both cell lines. Cytoplasmic RNA from MCF-7 and MDA-MB-231 were labeled with Cy3 and Cy5, respectively.

source_name: MCF-7 cells collected at 36-h after serum shock

source_name: MDA-MB-231 cells collected at 36-h after serum shock


title: MCF-7_MDA-MB-231_time 40h

description: The collected MCF-7 and MDA-MB-231 cells at 40h were fractionated in cytoplasmic and nuclei fractions (cultures and fractionations were made in differents days). Total RNA were isolated from cytoplasmic fractions of both cell lines. Cytoplasmic RNA from MCF-7 and MDA-MB-231 were labeled with Cy3 and Cy5, respectively.

source_name: MCF-7 cells collected at 40-h after serum shock

source_name: MDA-MB-231 cells collected at 40-h after serum shock


title: paracancerous tissue of  lung SCC_Patient41


title: paracancerous tissue of  lung SCC_Patient50


title: paracancerous tissue of  lung SCC_Patient37


title: MCF-7_MDA-MB-231_time 16h

description: The collected MCF-7 and MDA-MB-231 cells at 16h were fractionated in cytoplasmic and nuclei fractions (cultures and fractionations were made in differents days). Total RNA were isolated from cytoplasmic fractions of both cell lines. Cytoplasmic RNA from MCF-7 and MDA-MB-231 were labeled with Cy3 and Cy5, respectively.

source_name: MCF-7 cells collected at 16-h after serum shock

source_name: MDA-MB-231 cells collected at 16-h after serum shock


title: MCF-7_MDA-MB-231_time 28h

description: The collected MCF-7 and MDA-MB-231 cells at 28h were fractionated in cytoplasmic and nuclei fractions (cultures and fractionations were made in differents days). Total RNA were isolated from cytoplasmic fractions of both cell lines. Cytoplasmic RNA from MCF-7 and MDA-MB-231 were labeled with Cy3 and Cy5, respectively.

source_name: MCF-7 cells collected at 28-h after serum shock

source_name: MDA-MB-231 cells collected at 28-h after serum shock


title: paracancerous tissue of  lung SCC_Patient31


title: MCF-10A_Cytoplasm-Nuclei_time 40h

description: The collected MCF-10A cells at 40h were fractionated in cytoplasmic and nuclei fractions. Total RNA were isolated from each fraction. Cytoplasmic RNA and nuclei RNA were labeled with Cy3 and Cy5, respectively.

source_name: MCF-10A cells collected at 40-h after serum shock

molecule: nuclear RNA


title: MCF-7_MDA-MB-231_time 24h

description: The collected MCF-7 and MDA-MB-231 cells at 24h were fractionated in cytoplasmic and nuclei fractions (cultures and fractionations were made in differents days). Total RNA were isolated from cytoplasmic fractions of both cell lines. Cytoplasmic RNA from MCF-7 and MDA-MB-231 were labeled with Cy3 and Cy5, respectively.

source_name: MCF-7 cells collected at 24-h after serum shock

source_name: MDA-MB-231 cells collected at 24-h after serum shock


title: MCF-7_MDA-MB-231_time 12h

description: The collected MCF-7 and MDA-MB-231 cells at 12h were fractionated in cytoplasmic and nuclei fractions (cultures and fractionations were made in differents days). Total RNA were isolated from cytoplasmic fractions of both cell lines. Cytoplasmic RNA from MCF-7 and MDA-MB-231 were labeled with Cy3 and Cy5, respectively.

source_name: MCF-7 cells collected at 12-h after serum shock

source_name: MDA-MB-231 cells collected at 12-h after serum shock


title: MCF-10A_Cytoplasm-Nuclei_time 32h

description: The collected MCF-10A cells at 32h were fractionated in cytoplasmic and nuclei fractions. Total RNA were isolated from each fraction. Cytoplasmic RNA and nuclei RNA were labeled with Cy3 and Cy5, respectively.

source_name: MCF-10A cells collected at 32-h after serum shock


title: MCF-7_MDA-MB-231_time 20h

description: The collected MCF-7 and MDA-MB-231 cells at 20h were fractionated in cytoplasmic and nuclei fractions (cultures and fractionations were made in differents days). Total RNA were isolated from cytoplasmic fractions of both cell lines. Cytoplasmic RNA from MCF-7 and MDA-MB-231 were labeled with Cy3 and Cy5, respectively.

source_name: MCF-7 cells collected at 20-h after serum shock

source_name: MDA-MB-231 cells collected at 20-h after serum shock


title: paracancerous tissue of  lung SCC_Patient33

description: Gene expression after surgical resection

source_name: lung SCC patinent


title: MCF-10A_Cytoplasm-Nuclei_time 36h

description: The collected MCF-10A cells at 36h were fractionated in cytoplasmic and nuclei fractions. Total RNA were isolated from each fraction. Cytoplasmic RNA and nuclei RNA were labeled with Cy3 and Cy5, respectively.

source_name: MCF-10A cells collected at 36-h after serum shock


title: paracancerous tissue of  lung SCC_Patient35


title: MCF-10A_Cytoplasm-Nuclei_time 28h

description: The collected MCF-10A cells at 28h were fractionated in cytoplasmic and nuclei fractions. Total RNA were isolated from each fraction. Cytoplasmic RNA and nuclei RNA were labeled with Cy3 and Cy5, respectively.

source_name: MCF-10A cells collected at 28-h after serum shock


title: MCF-10A_Cytoplasm-Nuclei_time 24h

description: The collected MCF-10A cells at 24h were fractionated in cytoplasmic and nuclei fractions. Total RNA were isolated from each fraction. Cytoplasmic RNA and nuclei RNA were labeled with Cy3 and Cy5, respectively.

source_name: MCF-10A cells collected at 24-h after serum shock


title: paracancerous tissue of  lung SCC_Patient32


title: DH1-log-tr

city: Suita

first: Kazufumi

last: Hosoda

state: Osaka

address: Yamadaoka 1-5

country: Japan

institute: Osaka university

description:
T-20
A technical replicate of DH1-log.
DH1 is a recombinant derivative of MM294.
Platform: EcFS_03

hyb_protocol: Samples (from 10ug total RNA) were prepared and hybridized to Affymetrix Escherichia coli full sequence array (EcFS) 03 according to the standard Affymetrix protocol (Expression Analysis Technical Manual).

scan_protocol: The arrays were scanned using an Affymetrix GeneChip Scanner 3000 according to manufacturer's instruction.

data_processing:
Microarray data were processed using a custom R software for the finite hybridisation (FH) model (Ono et al., 2008, Bioinformatics 24, p1278).
The processed gene expression data in log10 scale are provided in the supplementary file "Ecoli_co_results.xlsx".
Metabolome data for these cultures are also provided in the supplementary file "Ecoli_co_results.xlsx", just for information.

organism: Escherichia coli K-12

source_name: Original prototroph DH1 cells at log phase in monoculture, a technical replicate

growth_protocol: All cultures were grown at 37C in well-mixed minimal media modified with M63 (mM63: pH 7.0, 62 mM K2HPO4, 39 mM KH2PO4, 15 mM ammonium sulfate, 1.8 µM FeSO4-7H2O, 15 µM thiamine hydrochloride, 0.2 mM MgSO4-7H2O and 22 mM glucose). One amino acid, Ile or Leu, was added to the monoculture medium when appropriate. Prior to coculturing, at both the initial inoculation and transfer, we washed the E. coli cells with fresh mM63 without amino acids to exclude the carry-over of supplements from the pre-culture. For coculture samples, we used cell culture inserts with a pore size of 0.45 µm at a density of 10^8/cm^2, and used six-well cell culture companion plates for the inserts (BD Falcon, Franklin Lakes, NJ, USA), to separately harvest I– and L– populations from cocultures (Hosoda et al., "Transcriptome Analysis of a Microbial Coculture in which the Cell Populations Are Separated by a Membrane", in Engineering and Analyzing Multicellular Systems (Methods in Molecular Biology), vol 1151, p151, 2014). We inoculated I– and L– cells at the initial concentration of 3x10^7 cells/mL and 6x10^5 cells/mL for the cocultures of ancestral (IA and LA) and evolved (IE and LE) cells, respectively, to adjust the late growth phase in one day. We incubated the coculture for 26 hours and then harvested the cells separately from the above and below the membrane insert. For monoculture samples, the required amino acid was supplied at 1mM, and 0.01mM for log-phase and starvation cells, respectively.

extract_protocol: The total RNA was extracted using an RNeasy kit, Qiagen, in accordance with the manufacturer's instructions.

treatment_protocol: The cell cultures were interrupted by placing them directly into a cold phenol-ethanol solution (0.1g-phenol/mL-ethanol). The cells were collected using centrifugation at 12,000g for 5 min at 4C, and the pelleted cells were once stored at -80C prior to use.

tag: substrain

tag: genotype/variation

tag: cell type

value: Original prototroph DH1 cells

tag: culture type

value: monoculture

tag: growth type

value: log phase


title: LE-co2

description:
T-17
A biological replicate of LE-co1.
DH1 is a recombinant derivative of MM294.
Platform: EcFS_03

source_name: Evolved L- cells in coculture, a biological replicate

label_protocol: Samples (from 10ug total RNA) were prepared and hybridized to Affymetrix Escherichia coli full sequence array (EcFS) 03 according to the standard Affymetrix protocol (Expression Analysis Technical Manual).

value: Evolved L- cells

value: coculture


title: paracancerous tissue of  lung SCC_Patient34

tag: tissue


title: paracancerous tissue of  lung SCC_Patient39


title: paracancerous tissue of  lung SCC_Patient29


title: LE-log-tr

description:
T-19
A technical replicate of LE-log.
DH1 is a recombinant derivative of MM294.
Platform: EcFS_03

source_name: Evolved L- cells at log phase in monoculture, a technical replicate


title: paracancerous tissue of  lung SCC_Patient26


title: LA-log-tr

description:
T-18
A technical replicate of LA-log.
DH1 is a recombinant derivative of MM294.
Platform: EcFS_03

source_name: Ancestral L- cells at log phase in monoculture, a technical replicate

value: Ancestral L- cells


title: paracancerous tissue of  lung SCC_Patient30


title: paracancerous tissue of  lung SCC_Patient23


title: paracancerous tissue of  lung SCC_Patient28


title: paracancerous tissue of  lung SCC_Patient19


title: paracancerous tissue of  lung SCC_Patient20


title: IE-co2

description:
T-16
A biological replicate of IE-co1.
DH1 is a recombinant derivative of MM294.
Platform: EcFS_03

source_name: Evolved I- cells in coculture, a biological replicate

value: Evolved I- cells


title: MCF-10A_Cytoplasm-Nuclei_time 20h

description: The collected MCF-10A cells at 20h were fractionated in cytoplasmic and nuclei fractions. Total RNA were isolated from each fraction. Cytoplasmic RNA and nuclei RNA were labeled with Cy3 and Cy5, respectively.

source_name: MCF-10A cells collected at 20-h after serum shock

tag: time point


title: MCF-10A_Cytoplasm-Nuclei_time 16h

description: The collected MCF-10A cells at 16h were fractionated in cytoplasmic and nuclei fractions. Total RNA were isolated from each fraction. Cytoplasmic RNA and nuclei RNA were labeled with Cy3 and Cy5, respectively.

source_name: MCF-10A cells collected at 16-h after serum shock


title: LE-co1

description:
T-15
L-, Evolved, at 26h in coculture.
DH1 is a recombinant derivative of MM294.
Platform: EcFS_03

source_name: Evolved L- cells in coculture


title: paracancerous tissue of  lung SCC_Patient27


title: paracancerous tissue of  lung SCC_Patient22


title: paracancerous tissue of  lung SCC_Patient25


title: paracancerous tissue of  lung SCC_Patient21


title: paracancerous tissue of  lung SCC_Patient17


title: paracancerous tissue of  lung SCC_Patient18


title: paracancerous tissue of  lung SCC_Patient24


title: paracancerous tissue of  lung SCC_Patient16


title: LA-co2

description:
T-13
A biological replicate of LA-co1.
DH1 is a recombinant derivative of MM294.
Platform: EcFS_03

source_name: Ancestral L- cells in coculture, a biological replicate


title: IA-co2

description:
T-12
A biological replicate of IA-co1.
DH1 is a recombinant derivative of MM294.
Platform: EcFS_03

source_name: Ancestral I- cells in coculture, a biological replicate

value: Ancestral I- cells


title: paracancerous tissue of  lung SCC_Patient15


title: LA-co1

description:
T-11
L-, Ancestral, at 26h in coculture.
DH1 is a recombinant derivative of MM294.
Platform: EcFS_03

source_name: Ancestral L- cells in coculture


title: MCF-10A_Cytoplasm-Nuclei_time 12h

description: The collected MCF-10A cells at 12h were fractionated in cytoplasmic and nuclei fractions. Total RNA were isolated from each fraction. Cytoplasmic RNA and nuclei RNA were labeled with Cy3 and Cy5, respectively.

source_name: MCF-10A cells collected at 12-h after serum shock


title: DH1-log

description:
T-9
Original, prototroph, at log phase in monoculture.
DH1 is a recombinant derivative of MM294.
Platform: EcFS_03

source_name: Original prototroph DH1 cells at log phase in monoculture


title: LE-log

description:
T-8
L-, Evolved, at log phase in monoculture.
DH1 is a recombinant derivative of MM294.
Platform: EcFS_03

source_name: Evolved L- cells at log phase in monoculture


title: IA-co1

description:
T-10
I-, Ancestral, at 26h in coculture.
DH1 is a recombinant derivative of MM294.
Platform: EcFS_03

source_name: Ancestral I- cells in coculture


title: paracancerous tissue of  lung SCC_Patient14

description: Gene expression after surgical resection

source_name: lung SCC patinent


title: paracancerous tissue of  lung SCC_Patient13


title: LA-log

description:
T-6
L-, Ancestral, at log phase in monoculture.
DH1 is a recombinant derivative of MM294.
Platform: EcFS_03

source_name: Ancestral L- cells at log phase in monoculture


title: IE-log

description:
T-7
I-, Evolved, at log phase in monoculture.
DH1 is a recombinant derivative of MM294.
Platform: EcFS_03

source_name: Evolved I- cells at log phase in monoculture


title: IA-log

description:
T-5
I-, Ancestral, at log phase in monoculture.
DH1 is a recombinant derivative of MM294.
Platform: EcFS_03

source_name: Ancestral I- cells at log phase in monoculture


title: LE-starve

description:
T-4
L-, Evolved, at amino acid starvation in monoculture.
DH1 is a recombinant derivative of MM294.
Platform: EcFS_03

source_name: Evolved L- cells at amino acid starvation in monoculture

value: amino acid starvation


title: LA-starve

description:
T-2
L-, Ancestral, at amino acid starvation in monoculture.
DH1 is a recombinant derivative of MM294.
Platform: EcFS_03

source_name: Ancestral L- cells at amino acid starvation in monoculture


title: 9d ZIKV-infected human brain microvascular endothelial cells

city: Stony Brook

first: Erich

middle: R

last: Mackow

state: NY

address: 100 Nicholls Road

department: Molecular Genetics & Microbiology

institute: Stony Brook University

description: 9d PRV

hyb_protocol: Samples were hybridized to GeneChip Human Clariom S Arrays (Affymetrix) using the  Hydridization, Wash and  Stain kit (Affymetrix). .

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix). Arrays were scanned at the Stony Brook Genomics Core Facility

data_processing:
Raw data was processed with the Expression Console software (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performed with Transcriptome Analysis Console (TAC) Software (Affymetrix)
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

source_name: ZIKV-infected_hBMECs_9d-post infection

label_protocol: Fragmented and labeled single-stranded cDNA was generated from total RNA using the GeneChip WT PLUS Reagent Kit ( Affymetrix)

growth_protocol: human brain microvascular endothelial cells passage 5

extract_protocol: Cell were lysed in Qiagen RLT Buffer and total RNA was purified using Qiagen Rneasy kit.

treatment_protocol: mock-infected or ZIKV infected at an MOI 20

value: human brain microvascular endothelial cells (hBMECs)

tag: passage

value: passage 5

tag: infected with

value: Zka virus (ZIKV) at an MOI 20

value: 9d-post infection


title: IA-starve

description:
T-1
I-, Ancestral, at amino acid starvation in monoculture.
DH1 is a recombinant derivative of MM294.
Platform: EcFS_03

source_name: Ancestral I- cells at amino acid starvation in monoculture


title: 9d mock-infected human brain microvascular endothelial cells

description: 9d Ctrl

source_name: mock-infected_hBMECs_9d-post infection

value: mock


title: 72hr ZIKV-infected human brain microvascular endothelial cells second

description: 72hr PRV RS

value: 72hr-post infection


title: 72hr ZIKV-infected human brain microvascular endothelial cells

description: 72hr PRV


title: 9d mock-infected human brain microvascular endothelial cells second

description: 9d Ctrl RS


title: paracancerous tissue of  lung SCC_Patient7

value: normal lung tissue adjacent to tumor

value: M

tag: age


title: paracancerous tissue of  lung SCC_Patient11

tag: gender


title: paracancerous tissue of  lung SCC_Patient9


title: 9d ZIKV-infected human brain microvascular endothelial cells second

description: 9d PRV RS


title: 48hr ZIKV-infected human brain microvascular endothelial cells

description: 48hr PRV

value: 48hr-post infection


title: paracancerous tissue of  lung SCC_Patient8


title: 48hr mock-infected human brain microvascular endothelial cells second

description: 48hr Ctrl RS


title: IE-starve

description:
T-3
I-, Evolved, at amino acid starvation in monoculture.
DH1 is a recombinant derivative of MM294.
Platform: EcFS_03

source_name: Evolved I- cells at amino acid starvation in monoculture

tag: strain

value: monoculture


title: paracancerous tissue of  lung SCC_Patient10


title: 72hr mock-infected human brain microvascular endothelial cells second

description: 72hr Ctrl RS


title: paracancerous tissue of  lung SCC_Patient12


title: paracancerous tissue of  lung SCC_Patient6


title: paracancerous tissue of  lung SCC_Patient5


title: 72hr mock-infected human brain microvascular endothelial cells

description: 72hr Ctrl


title: 48hr ZIKV-infected human brain microvascular endothelial cells second

description: 48hr PRV RS


title: paracancerous tissue of  lung SCC_Patient4


title: 48hr mock-infected human brain microvascular endothelial cells

description: 48hr Ctrl


title: 24hr ZIKV-infected human brain microvascular endothelial cells second

description: 24hr PRV RS

value: 24hr-post infection


title: 24hr ZIKV-infected human brain microvascular endothelial cells

description: 24hr PRV


title: paracancerous tissue of  lung SCC_Patient2


title: paracancerous tissue of  lung SCC_Patient1


title: 24hr mock-infected brain microvascular endothelial cells second

description: 24hr Ctrl RS


title: IE-co1

description:
T-14
I-, Evolved, at 26h in coculture.
DH1 is a recombinant derivative of MM294.
Platform: EcFS_03

source_name: Evolved I- cells in coculture


title: paracancerous tissue of  lung SCC_Patient3


title: 12hr ZIKV-infected human brain microvascular endothelial cells second

description: 12hr PRV RS

value: 12hr-post infection


title: 12hr ZIKV-infected human brain microvascular endothelial cells

description: 12hr PRV


title: 24hr mock-infected brain microvascular endothelial cells

description: 24hr Ctrl


title: 12hr mock-infected human brain microvascular endothelial cells

description: 12hr Ctrl


title: HeLa cell line, replicate 01

status: Public on Jul 14 2017

city: Cambridge

first: Martin

middle: Lee

last: Miller

state: Cambridgeshire

address: Robinson Way

department: Cancer Research UK Cambridge Institute

institute: University of Cambridge

description:
HeLa 1
Affymetrix internal control

hyb_protocol: Hybridization was performed using the following protocol: "GeneChip WT Pico Reagent Kit Manual Target Preparation for GeneChip Whole-Transcript Expression Arrays".

scan_protocol: The Affymetrix GCS3000 scanner was used along with Affymetrix GeneChip Command Console software for imaging processing.

data_processing:
Affymetrix Expression Console software version 1.4.1.46 was used for primary analysis, and SST-RMA was used as the processing algorithm. To define whether a gene was expressed or not we used the Affymetrix Transcriptome Analysis Console version 3.1.0.5 and implemented an alternative-splicing analysis, which gives an Expressed column with True or False values. For genes for which this approach gives an ambiguous result (e.g. since some genes have more than one probe aligning to it, if one probe gives True and the other False), then we used the median expression level (accross probes) of the SRY gene for each sample as threshold for that tumor sample. For indivudal gene expression level analysis, we first filtered the probes that hybridize with protein coding genes. Then we assigned the median gene expression value for each gene. Then we normalize the gene expression values using the normalize.loess function of the R package affy, and we selected the distributions that were not statistically significant between them. The gene expression levels obtained were then compared between samples. Here we provide the CHP files with the SST-RMA normalization alone, but we can provide the SST-RMA+loess normalize gene expression values upon request. The HeLa cell lines were used only by Affymetrix as their internal controls and were not incorporated in any analysis in the study.
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = Clariom_D_Human
program-name = Expression Console
program-version = 1.4.1.46

source_name: Cell line

label_protocol: Labeling was performed using the following protocol: "GeneChip WT Pico Reagent Kit Manual Target Preparation for GeneChip Whole-Trascript Expression Arrays".

extract_protocol: RNA was extracted from FFPE samples using the RecoverAll Total Nucleic Acid Isolation from Thermo Fisher Scientific (Catalog Number: AM1975).

value: female

value: Cell line

tag: condition

value: Cervical adenocarcinoma

tag: tumor type

tag: sample type

value: Control


title: HLSEC_GATA4_biological rep3

status: Public on Jul 13 2017

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description:
Gene expression data from GATA4-transduced HLSEC
Gata_III

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 7, from SAS. Gene expression profiling was performed using arrays of human Hugene-2_0-type from Affymetrix. A Custom CDF Version 21 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

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

growth_protocol: Human GATA4 from cDNA IMAGE:8144111(BC105108) and human LMO3 from cDNA IMAGE:5720992(BC026311) were cloned into pBabePuro vector using EcoRI restriction sites. Phoenix producer cells (Gary Nolan, Stanford, CA, USA) were transfected with pBabePuro vector using lipofectamine.

extract_protocol: RNA from HLSEC was extracted using E.Z.N.A. TM Total-RNA-Kit I (OMEGA Biotec, Norcross, GA, USA).

treatment_protocol: Filtered conditioned supernatants were applied to the cells three times during day 1 and 2. Selection with 1-2µg/ml Puromycin (Invivogen, San Diego, CA, USA) was carried out on day 5 for 24h. RNA was isolated on day 7.

value: LSEC

tag: treatment

value: Gata


title: 12hr mock-infected human brain microvascular endothelial cells second

description: 12hr Ctrl RS

value: human brain microvascular endothelial cells (hBMECs)

value: passage 5


title: Spleen metastasis, Growing

description:
Spleen-9-5
Gene expression data from spleen metastasis

source_name: Growing spleen metastasis resected 6 years after primary tumor and after 12 different chemotherapy drugs

value: Spleen

value: Malignant

value: High grade serous ovarian cancer

tag: tumor stage

value: Metastasis

value: FFPE


title: sgr1 vs wild type replicate 1

city: Nagoya

first: Miyo

middle: Terao

last: Morita

address: Furocho, Chikusa

department: Graduate School of Bioagricultural Sciences

institute: Nagoya University

description:
Biological replicate 1 of 1
sgr1_vs_WT_rep1

hyb_protocol: Hybridized at 60°C for 17 hr. After hybridizetion, slides were washed sequential.

scan_protocol: Scanned on Agilent Technologies Microarray Scanner (resolution: 10µm)

data_processing: Extracted  features which fulfill the next confditions; ControlType=0, gIsSaturated=0, rIsSaturated=0, gIsPosAndSingnif=1, rIsPosAnd Singnif=1, gIsWellAvoveBG=1, rIsWellAvoveBG=1 and P value <0.01.

organism: Arabidopsis thaliana

source_name: elongation zone

label_protocol: 500 ng of total RNA was used for cDNA synthesis and cRNA labeling reaction with Agilent Low RNA Input Fluorescent Linear Amplification Kit. In this reaction, each cRNA was labeled both cyanine-3 and cyanine-5 in separate reactions.

growth_protocol: Seeds were sterilized and plated on Murashige and Skoog (MS) plates followed by treatment at 4°C for 3days. Seedlings were germinated under constant light at 23°C for 10 days. Plant were transplanted and grown on soil under constant white light at 23°C.

extract_protocol: Total RNA extracted using Rneasy Plant Mini kit (Qiagen) following manufacturer's instructions

treatment_protocol: Stem samples 1.5 cm long were excised 0.3−1.8 cm from apices of primary inflorescence stems grown to 5-8 cm, from which lateral organs were removed. At least ten individuals were used for RNA sample preparations.

tag: genotype

value: WT(Col)

value: Inflorescence stems


title: HUVEC_GATA4_Noggin_biological rep1

description:
Gene expression data from GATA4-transduced HUVEC + Noggin
Gata_Noggin_I

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 7, from SAS. Gene expression profiling was performed using arrays of human Hugene-1_0-type from Affymetrix. A Custom CDF Version 21 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

growth_protocol: Human GATA4 from cDNA IMAGE:8144111(BC105108) were cloned into pBabePuro vector using EcoRI restriction sites. Phoenix producer cells (Gary Nolan, Stanford, CA, USA) were transfected with pBabePuro vector using lipofectamine.

extract_protocol: RNA from HUVEC was extracted using E.Z.N.A. TM Total-RNA-Kit I (OMEGA Biotec, Norcross, GA, USA).

treatment_protocol: Filtered conditioned supernatants were applied to the cells three times during day 1 and 2. Selection with 1-2µg/ml Puromycin (Invivogen, San Diego, CA, USA) was carried out on day 5 for 24h. RNA was isolated on day 7. For stimulation Recombinant human BMP2 (50 ng/ml) (R&D Systems, Minneapolis, MN, USA) or human Noggin (50 ng/ml) (R&D Systems) was added to the medium.

value: HUVEC

tag: genotype/variation

tag: stimulation

value: Noggin


title: Primary high grade serous ovarian cancer, Growing

description:
Primary-IIIG
Gene expression data from primary high grade serous ovarian cancer

source_name: Primary high-grade serous ovarian cancer resected before any therapy or treatment

value: female

value: Bladder

value: Primary tumor stage IV


title: HUVEC_GATA4_Noggin_biological rep2

description:
Gene expression data from GATA4-transduced HUVEC + Noggin
Gata_Noggin_II

tag: cell type


title: HUVEC_GATA4_Noggin_biological rep3

description:
Gene expression data from GATA4-transduced HUVEC + Noggin
Gata_Noggin_III


title: eal1-1 vs wild type replicate 2 (dye swapped)

description:
Biological replicate 1 of 2
eal1-1_vs_WT_rep2


title: eal1-2 vs wild type replicate 2 (dye swapped)

description:
Biological replicate 1 of 2
eal1-2_vs_WT_rep2


title: sgr1 vs wild type replicate 2 (dye swapped)

description:
Biological replicate 1 of 1
sgr1_vs_WT_rep2


title: HUVEC_GATA4_biological rep2

description:
Gene expression data from GATA4-transduced HUVEC
Gata_II

value: control


title: HeLa cell line, replicate 02

description:
HeLa 2
Affymetrix internal control

value: Cell line

value: Cervical adenocarcinoma

value: Control


title: eal1-1 vs wild type replicate 1

description:
Biological replicate 1 of 2
eal1-1_vs_WT_rep1


title: Vaginal cuff metastasis, Growing

description:
VagCuff-4-1
Gene expression data from vaginal cuff metastasis

source_name: Growing vaginal cuff metastasis resected 6 years after primary tumor and after 12 different chemotherapy drugs

value: Vaginal Cuff


title: eal1-2 vs wild type replicate 1

description:
Biological replicate 1 of 2
eal1-2_vs_WT_rep1


title: Liver metastasis, Stable

description:
LiverSeg5-7-1
Gene expression data from liver metastasis

source_name: Stable liver metastasis resected 6 years after primary tumor and after 12 different chemotherapy drugs

value: Liver


title: HUVEC_GATA4_biological rep3

description:
Gene expression data from GATA4-transduced HUVEC
Gata_III


title: HLSEC_GATA4_biological rep2

description:
Gene expression data from GATA4-transduced HLSEC
Gata_II

value: LSEC

value: Gata


title: Right upper quadrant metastasis, Shrinking

description:
RUQ-1-4
Gene expression data from right upper quadrant metastasis

source_name: Shrinking right upper quadrant metastasis resected 6 years after primary tumor and after 12 different chemotherapy drugs

value: Right Upper Quadrant

value: Malignant

value: High grade serous ovarian cancer

value: Metastasis


title: HLSEC_GATA4_LMO3_biological rep3

description:
Gene expression data from GATA4/LMO3-transduced HLSEC
Gata_Lmo3_III

value: GATA4 and LMO3


title: HLSEC_GATA4_biological rep1

description:
Gene expression data from GATA4-transduced HLSEC
Gata_I


title: HUVEC_GATA4_BMP2_biological rep2

description:
Gene expression data from GATA4-transduced HUVEC + BMP2
Gata4_BMP2_II

value: HUVEC


title: HUVEC_GATA4_BMP2_biological rep3

description:
Gene expression data from GATA4-transduced HUVEC + BMP2
Gata4_BMP2_III


title: HUVEC_GATA4_biological rep1

description:
Gene expression data from GATA4-transduced HUVEC
Gata_I


title: HUVEC_EV_biological rep2

description:
Gene expression data from EV-transduced HUVEC
EV_II

value: EV


title: yeast_TFM_treated_120min_rep1 (YPD)

status: Public on Jul 12 2017

city: Northfield

first: Darlene

middle: M

last: Olsen

state: VT

address: 158 Harmon Drive

department: Mathematics

institute: Norwich University

description:
Gene expression data from TFM exposure (2 h)
TFM_120_r1

hyb_protocol: Fragmented cRNA was hybridized to Yeast 2.0 GeneChips (Affymetrix) and subsequently stained with streptavidin-phycoerytherin and biotinylated anti-phycoerytherin antibody.

scan_protocol: GeneChips were scanned in a high resolution GS3000 scanner.

data_processing: The robust multi-array analysis (RMA) normalization method was used to preprocess the probe level data using the AffyPLM R/Bioconductor package.

organism: Saccharomyces cerevisiae

source_name: Saturated S. cerevisiae cultures, fermentable media

label_protocol: cRNA was prepared using an Enzo bioarray kit and fragmented using the hammerhead cleavage reaction (Tighe et al., J Vis Exp, 2011).

growth_protocol: The wild type S. cerevisiae strain BY4741 were grown in yeast peptone dextrose (YPD), a fermentable medium (1% yeast extract, 2% peptone, and 2% dextrose), at 30°C to saturation.

extract_protocol: Total RNA was isolated from S. cerevisiae using RNeasy Mini Kits (Qiagen) per manufacturer’s instructions.

treatment_protocol: Treated for 1, 2, or 4 hours with 0.05mM TFM.

tag: agent

value: TFM

tag: time

value: 2 h


title: yeast_TFM_treated_120min_rep2 (YPD)

description:
Gene expression data from TFM exposure (2 h)
TFM_120_r2


title: HLSEC_GATA4_LMO3_biological rep2

description:
Gene expression data from GATA4/LMO3-transduced HLSEC
Gata_Lmo3_II


title: yeast_TFM_treated_240min_rep1 (YPD)

description:
Gene expression data from TFM exposure (4 h)
TFM_240_r1

value: 4 h


title: HLSEC_GATA4_LMO3_biological rep1

description:
Gene expression data from GATA4/LMO3-transduced HLSEC
Gata_Lmo3_I


title: HUVEC_EV_biological rep3

description:
Gene expression data from EV-transduced HUVEC
EV_III

value: control


title: yeast_untreated_0min_rep1 (YPD)

description:
Gene expression data from 2% isopropanol exposure
Control_r1


title: HUVEC_GATA4_BMP2_biological rep1

description:
Gene expression data from GATA4-transduced HUVEC + BMP2
Gata4_BMP2_I


title: yeast_TFM_treated_60min_rep2 (YPD)

description:
Gene expression data from TFM exposure (1 h)
TFM_60_r2

value: 1 h


title: HLSEC_EV_biological rep3

description:
Gene expression data from EV-transduced HLSEC
EV_III


title: HUVEC_EV_biological rep1

description:
Gene expression data from EV-transduced HUVEC
EV_I


title: yeast_untreated_0min_rep2 (YPD)

description:
Gene expression data from 2% isopropanol exposure
Control_r2


title: yeast_TFM_treated_60min_rep1 (YPD)

description:
Gene expression data from TFM exposure (1 h)
TFM_60_r1


title: yeast_TFM_treated_240min_rep2 (YPD)

description:
Gene expression data from TFM exposure (4 h)
TFM_240_r2


title: REH transduced with empty vector, replicate 2

city: Los Angeles

first: Norma

middle: Iris

last: Rodriguez-Malave

state: California

address: 8723 Alden Drive

institute: Cedars-Sinai Medical Center

description:
Gene expression data after succesful knockout of CASC15, control line with no CASC15 knockout
REH-VECTOR_2

hyb_protocol: Standard Affymetrix Protocol

scan_protocol: Standard Affymetrix Protocol

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: flouresens

source_name: REH transduced with empty vector

label_protocol: Fluoresens, standard Affymetrix protocol

growth_protocol: Cells were grown in RPMI 1640 media supplemented with 10% FBS and passaged as necessary to maintain a cell density between 1 X 10^5 and 1 X 10^6 viable cells/mL

extract_protocol: RNA was extracted using Tryzol as per manufacturer's instructions, and then RNA was DNAse treated and purified using RNeasy Minielute Cleanup Kit

treatment_protocol: Cell lines were stably transduced with lentivirus to express vectors with siRNAs or sgRNAS against CASC15 or expressing empty vectors as controls

tag: cell line

value: REH ALL cell line

tag: karyotype

tag: source

value: Established from the peripheral blood of a patient with acute lymphoblastic leukemia

value: control line with no CASC15 knockout


title: REH transduced with sgRNAs vectors, replicate 3

description:
Gene expression data after succesful knockout of CASC15
REH-C19_3

source_name: REH transduced with sgRNAs vectors

value: knockout of CASC15


title: HLSEC_EV_biological rep2

description:
Gene expression data from EV-transduced HLSEC
EV_II

value: LSEC


title: REH transduced with sgRNAs vectors, replicate 2

description:
Gene expression data after succesful knockout of CASC15
REH-C19_2


title: REH transduced with sgRNAs vectors, replicate 1

description:
Gene expression data after succesful knockout of CASC15
REH-C19_1


title: HLSEC_EV_biological rep1

description:
Gene expression data from EV-transduced HLSEC
EV_I


title: RS4,11 transduced with siRNA3 vector

description:
Gene expression data after succesful knockdown of CASC15
RS4;11-siRNA3

source_name: RS4,11 transduced with siRNA3 vector

value: RS4;11 ALL cell line

value: Established from the bone marrow of a patient with acute lymphoblastic leukemia

value: knockdown of CASC15


title: RS4,11 transduced with siRNA2 vector

description:
Gene expression data after succesful knockdown of CASC15
RS4;11-siRNA2

source_name: RS4,11 transduced with siRNA2 vector


title: REH transduced with empty vector, replicate 3

description:
Gene expression data after succesful knockout of CASC15, control line with no CASC15 knockout
REH-VECTOR_3


title: RS4,11 transduced with siRNA1 vector

description:
Gene expression data after succesful knockdown of CASC15
RS4;11-siRNA1

source_name: RS4,11 transduced with siRNA1 vector


title: RS4,11 transduced with empty vector

description:
Gene expression data after succesful knockdown of CASC15, control line with no CASC15 knockdown
RS4;11-VECTOR

source_name: RS4,11 transduced with empty vector

value: control line with no CASC15 knockdown


title: REH transduced with empty vector, replicate 1

description:
Gene expression data after succesful knockout of CASC15, control line with no CASC15 knockout
REH-VECTOR_1


title: term_amniotic_fluid_MMC 6

city: Boston

first: Tomo

last: Tarui

state: MA

address: 800 Washington St.

department: Pediatric Neurology

institute: Tufts Medical Center

description: gene expression data from control

hyb_protocol: Arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).

data_processing: Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method.  Identification of individual differentially-expressed genes was performed via two-sided, paired t-tests using the multtest package in BioConductor, with the Benjamini-Hochberg adjustment for multiple testing.

source_name: cell free mRNA from term amniotic fluid

label_protocol: Samples were labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN, San Carlos, CA).

extract_protocol: RNA was extracted from 10 mL AF with 30 mL TRIzol LS Reagent (Invitrogen, Carlsbad, CA) and 8 mL chloroform. After RNA extraction, RNA was purified and DNA was removed using the RNeasy® Maxi Kit, including the DNase step according to the manufacturer’s protocol (QIAGEN, Valencia, CA).  RNA was precipitated using 3M NaOAc and 100% ethanol, and 80% ethanol was added after 4 hours incubation at -20 °C. cDNA, synthesized from extracted RNA, was amplified and purified using the WT-Ovation™ Pico RNA Amplification System (NuGEN, San Carlos, CA) and the DNA Clean & Concentrator™-25 (Zymo Research, Orange, CA).

tag: gestational age

value: Second Trimester Control


title: term_amniotic_fluid_MMC 9

description: gene expression data from control


title: ChIP-seq from fibroblast of arm (ENCLB419HWH)

city: Stanford

description:
https://www.encodeproject.org/experiments/ENCSR673OPX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR673OPX
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR922FLS
encode release date: 2017-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB419HWH
size range: 200-600
nucleic acid starting quantity: 837.5
nucleic acid starting quantity units: ng

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens fibroblast of arm primary cell male adult (53 years)

tag: antibody

value: fibroblast of arm

value: primary cell

tag: description

value: These are primary fibroblasts taken from the PGP1 donor from the Personal Genome Project (PGP).

tag: biosample encode accession

tag: age

value: 53 year

tag: dev stage

value: adult

tag: Sex

value: male

tag: lab

value: Thomas Gingeras, CSHL

tag: link

value: ENCBS372AAA at ENCODE; https://www.encodeproject.org/ENCBS372AAA/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_F183; http://web.expasy.org/cellosaurus/CVCL_F183

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23248&PgId=166


title: ChIP-seq from fibroblast of arm (ENCLB027KPP)

description:
https://www.encodeproject.org/experiments/ENCSR673OPX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR673OPX
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR922FLS
encode release date: 2017-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB027KPP
size range: 200-600
nucleic acid starting quantity: 615
nucleic acid starting quantity units: ng

value: ENCBS367AAA at ENCODE; https://www.encodeproject.org/ENCBS367AAA/


title: term_amniotic_fluid_MMC 4

description: gene expression data from control


title: term_amniotic_fluid_MMC 7

description: gene expression data from control


title: term_amniotic_fluid_MMC 3

description: gene expression data from control


title: second_trimester_amniotic_fluid_MMC 7

description: gene expression data from second trimester fetus with MMC

source_name: cell free mRNA from second trimester amniotic fluid

value: Second Trimester MMC


title: term_amniotic_fluid_MMC 5

description: gene expression data from control


title: ChIP-seq from neuroepithelial stem cell (ENCLB597CQD)

description:
https://www.encodeproject.org/experiments/ENCSR662PLB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR662PLB
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR803UDX
encode release date: 2016-05-20
lab: Bradley Bernstein, Broad
library encode accession: ENCLB597CQD
size range: 300-1000

source_name: Homo sapiens neuroepithelial stem in vitro differentiated cells female embryo (5 days) derived from H9 stably expressing C-terminal eGFP-HES5 fusion protein

value: neuroepithelial stem cell

value: in vitro differentiated cells

value: Neuroepithelial cells were collected at day 12 of differentiation (see protocol)

value: embryonic

value: female

value: 5 day

tag: health state

value: healthy

tag: passage number

value: Bradley Bernstein, Broad

value: ENCBS363SWF at ENCODE; https://www.encodeproject.org/ENCBS363SWF/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: term_amniotic_fluid_MMC 8

description: gene expression data from control

value: Second Trimester Control


title: term_amniotic_fluid_MMC 2

description: gene expression data from control


title: shctl2

city: Augusta

first: Yiming

last: Xu

state: Georgia

address: 1459 Laney Walker Blvd

department: Vascular Biology Center

institute: Augusta University

hyb_protocol: Following labeling, cDNAs were hybridized for 16 hr at 45C on Human Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: CEL files were imported into Partek Genomics Suite v6.6, and gene-level log2 intensities were obtained through RMA background correction, adjustment for GC content, quantile normalization, and median polish probeset summarization.  Differential expressions were calculated using ANOVA of Partek package.

label_protocol: Biotinylated cDNAs were prepared according to the standard Affymetrix protocol from 250 ng of total RNA (The GeneChip WT PLUS Reagent kit, Affymetrix).

growth_protocol: HUVECs (ATCC, Manassas, VA, USA), at passage 4, were cultured in endothelial growth medium 2 (EGM-2; Lonza, Basel, Switzerland).

extract_protocol: The total RNA from HUVECs was extracted with an RNeasy Mini Kit (Qiagen, Venlo, Netherlands) according to the manufacturer's instructions.

treatment_protocol: When reaching 70% confluency, HUVECs were infected with human ADK shRNA or control adenovirus.

tag: cell type

value: HUVEC

tag: shRNA

value: control


title: second_trimester_amniotic_fluid_MMC 3


title: second_trimester_amniotic_fluid_MMC 5


title: shADK1

value: ADK shRNA


title: shctl3


title: second_trimester_amniotic_fluid_MMC 6


title: second_trimester_amniotic_fluid_MMC 2


title: shADK2


title: shADK3


title: second_trimester_amniotic_fluid_MMC 4


title: shctl1


title: second_trimester_amniotic_fluid_MMC 9


title: second_trimester_amniotic_fluid_MMC 10


title: second_trimester_amniotic_fluid_MMC 1


title: second_trimester_amniotic_fluid_MMC 8


title: il7r-/- larvae at 4dpf rep3

city: tianjin

first: shijiao

last: cai

address: Qixiangtai road

institute: Tianjin Medical University

description: Gene expression data from il7r-/- larvae at 4dpf

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on on Zebrafish Gene 1.0 ST Array. GeneChips were washed and stained in GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip2 Scanner 30007G (Affymetrix).

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

organism: Danio rerio

source_name: il7r-/- zebrafish larvae

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

growth_protocol: Zebrafish larvae were raised at 28.5°C under a 10/14h dark/light cycle . Embryos were collected after natural spawning and staged developmentally by hours post fertilization (hpf) or days post fertilization (dpf).

treatment_protocol: We generated il7r-/- homozygous mutant by clustered regularly interspaced short palindromic repeats (CRISPR) / Cas9 technology. Tu and il7r-/- larvae at 4dpf were collected and rinsed with E3 medium . They were put in 1.5 mL RNase tube after discarding excess water and stored in liquid nitrogen.

tag: tissue

value: larvae

value: 4 days post hybridization (dpf)

tag: genotype


title: Tu larvae at 4dpf rep3

description: Gene expression data from  TU larvae at 4dpf

source_name: Tu zebrafish larvae

value: Tu


title: FL1GR_8dD_INP2

city: Davis

first: John

last: Harada

address: One Shields Avenue

department: Plant Biology

institute: University of California

hyb_protocol: Samples were prepared and hybridized to GeneChip Arabidopsis Tiling 1.0R Array, according to Affymetrix specifications.

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G according to manufacturer's instruction.

data_processing:
Probe signal intensity data was processed and standardized using Model-based Analysis of Tiling-array software (MAT; BandWidth=200, MaxGap=150, MinProbe=8, Tvalue=0) to generate the .bar files containing the matscore for each probe on the array.  The bar files were then used as input for CisGenome v1.2 to call significant regions (sample_peaks.bed) using the HMM algorithm and using a posterior probability (PP) > 0.99999 as threshold.
BAR files contain standardized probe intensity generated with Model-based Analysis of Tiling-array software (MAT; BandWidth=200, MaxGap=150, MinProbe=8, Tvalue=0).  BED files contain the peaks called using CisGenome (v1.2) HMM algorithm, posterior probability > 0.99999.  Chromosomal locations refer back to the TAIR8 genome assembly.

source_name: 8d sdlg, 8d DEX

label_protocol: ChIP and Input control DNAs were prepared according to O'Geen, Nicolet, Bahnik, Green and Farnham, BioTechniques 41:577-580 (November 2006). 7.5 ug of DNA were fragmented to an average size of 100bp using RQ1 DNAseI (Promega), biotin-labelled using Affymetrix GeneChip WT Double Stranded DNA Terminal Labelling kit and following the manufacturer's instructions.

growth_protocol: Plants were grown in a Percival cabinet under 16h day/8h night with fluorescent lamps at 20°C.

extract_protocol: Chromatin isolation and immunoprecipitation were performed as described in Gendrel AV, Lippman Z, Martienssen R, Colot V. Nat Methods. 2005;2:213–218, except that the isolated nuclei were resuspended in lysis buffer described in by Johnson et al. (2002) and sonicated to achieve chromatin fragments ranging from 100 to 500 bp.  Nuclear extracts were either set aside for whole genome extracts (input control) or incubated overnight with 10ug of the anti-FLAG (Sigma F1804) antibody.  Crosslinks were reversed and protein digested as in Dahl and Collas, Nat Protoc. 2008;3(6):1032-45, extracted with phenol:chloroform and precipitated using standard procedures.

treatment_protocol: 35S:FLAG-LEC1-GR seedlings were either (1) grown for 8 days on GM media (1X MS salts, 1% sucrose, 1X B5 vitamins, 0.8% Bactoagar, pH 5.7) and incubated for 4h in liquid GM media (same as solid, without Bactoagar) containing 30uM dexamethasone (DEX) or (2) germinated and grown on solid GM media containing 30 uM DEX for 8 days.  Tissues were crosslinked under vaccuum for 10 minutes in Buffer A (0.4M sucrose, 10 mM Tris pH 8.0, 1mM EDTA pH 8.0) containing 1% formaldehyde, at room temperature, then quenched in 100 mM Glycine for 5 minutes.  Crosslinked tissues were rinsed twice with deionized water, ground in liquid nitrogen and stored at -80C until use.

value: Ws-0, 35S:FLAG-LEC1-GR

tag: treatment

value: DEX

tag: time


title: FL1GR_8dD_FLAG2

source_name: 8d sdlg, 8d DEX, anti-FLAG

value: anti-FLAG


title: FL1GR_8dD_INP1


title: Tu larvae at 4dpf rep1


title: JAZi VIGS floral stage 3_rep3

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

institute: Max-Planck-Institute for Chemical Ecology

description:
JAZi VIGS flower, stage 3, replicate 3
Gene expression in developing flower
JAZi VIGS-3-3

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 platform GPL21138 for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and at 37°C with GE Wash buffer 2 (Agilent) as outlined in the One-Color Microarray-Based Gene Expression Analysis manual (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Data was acquired with the Agilent Scan Control software (version A.7.0.1 for the B scanner) and extracted using the Agilent Feature Extraction software (version 9.5). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. 75 percentile normalization was performed for each array of raw data (keeping the controls in the list). Log transformation was done. Controls were removed from the list. All replicated probes were averaged.

organism: Nicotiana attenuata

source_name: JAZi VIGS flower, stage 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp labeling kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Hilden, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: N. attenuata wild type were grown inclimate chamber with a constant temperature of 20ºC set to a 16 h day/8 h night light regime.

extract_protocol: Total RNA was extracted from leaves using the Plant RNeasy kit (Qiagen, Hilden, Germany) and its quality checked by spectrophotometry (NanoDrop, Wilmington, DE). Genomic DNA was removed by DNAse treatment following commercial instructions (Turbo DNase; Ambion, Europe), RNA was cleaned up with RNeasy MinElute columns (Qiagen) and the RNA quality was checked with the RNA 6000 Nano kit (Agilent, Santa Clara, CA) using an Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: Flowers from stage 1 and 3 in JAZi VIGS and control plants were collected at around 10 am.

tag: genotype/variation

value: JAZi VIGS

tag: Stage

value: floral stage 3

value: leaves


title: JAZi VIGS floral stage 1_rep2

description:
JAZi VIGS flower, stage 1, replicate 2
Gene expression in developing flower
JAZi VIGS-1-2

source_name: JAZi VIGS flower, stage 1

value: floral stage 1


title: Control floral stage 1_rep3

description:
Control flower, stage 1, replicate 3
Gene expression in developing flower
Control-1-3

source_name: Control flower, stage 1

value: Control