title: ZY-mutant

status: Public on Jan 04 2018

city: Wuhan

first: Zhixiong

last: Xie

state: Hubei

address: Bayi Road 299#

department: College of Life Science

institute: Wuhan University

data_processing:
Basecalls performed using Hiseq 4000 sequencing platform
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to bacterial WGS using bowtie v2.2.5.
Gene expression level was calculated by using RSEM v1.2.12.
Genome_build: GenBank: AJJP00000000.1
Supplementary_files_format_and_content: spreadsheet files include expression level of each gene in HYS genome

organism: Pseudomonas donghuensis

source_name: experimental group

growth_protocol: Bacterial were grown in Luria-Bertani (LB) medium with gyratory shaking at 30°C for 12 hours. Then, cultures were spread on nematode growth medium (NGM) agar plates and total RNA was extracted after an incubation of 12 hours at 22°C.

extract_protocol:
Bacterial were removed, flash frozen on dry ice, and total RNA was harvested using  using Trizol reagent.
rRNA was first removed from the total RNAs, and the purified RNAs were digested into 200-nt fragments followed by synthesis of first-strand cDNA and second-strand cDNA. The resulting cDNAs were then subjected to end repair and A-tailing, and then ligated to adapters. By utilizing PCR and gel electrophoresis, the cDNA fragments were enriched and purified to construct the final sequencing cDNA libraries.

tag: strain background

value: HYS

value: crcZ and crcY double deletion mutant

tag: Stage

value: six hours after grown on agar plate


title: HYS-p

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

source_name: control group

tag: genotype/variation

value: wild-type carrying plasmid vector


title: HYS-pc

value: crc overexpression mutant


title: HYS

value: wild-type


title: Overexpression rep3

type: RNA

city: Warsaw

first: Beata

middle: Alicja

last: Kądziołka

address: Pasteur 3 Street

department: Departament of Molecular and Cellular Neurobiology

country: Poland

institute: Nencki Institute of Experimental Biology, Polish Academy of Sciences

description:
Overexpression replicate 3
OV3

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization.

label: biotin

organism: Homo sapiens

source_name: HCT116 cells

label_protocol: Biotinylated cRNA was prepared by Cambridge Genomics Services

growth_protocol: HCT116 cells were maintained in McCoy's 5A with 10% FBS, 100 µg/ml streptomycin and 100 U/ml penicillin

extract_protocol: RNA was extracted using QIAGEN RNeasy Mini Kit

treatment_protocol: Control cells were transfected with p3xFLAG-CMV-10 plasmid, cells overexpressing CacyBP/SIP were transfected with p3xFLAG-CMV-10-CacyBP/SIP plasmid, 24 hrs before RNA isolation

tag: plasmid


title: Overexpression rep2

description:
Overexpression replicate 2
OV2


title: Control rep2

description:
Control replicate 2
WT2


title: Overexpression rep4

description:
Overexpression replicate 4
OV4


title: Control rep3

description:
Control replicate 3
WT3


title: Control rep1

description:
Control replicate 1
WT1


title: Control rep4

description:
Control replicate 4
WT4


title: Overexpression rep1

description:
Overexpression replicate 1
OV1


title: Hose with scramble control KnockIn

city: Boston

first: Shu-Wing

last: Ng

state: MA

address: 221 Longwood Avenue

department: Department of Obstetrics, Gynecology and Reproductive Biology

country: USA

institute: Brigham and Women’s Hospital; Harvard Medical School

description: The whole transcriptome Gene expression data from human Normal ovarian epithelium cell (Hose) with scramble control KnockIn.

hyb_protocol: GeneChips were scanned using the  Affymetrix GeneAtlas hyberzation station according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using the  Affymetrix GeneAtlas Fluidic station according to the manufacturer's instructions.

data_processing: The data were analyzed with Affymetrix Expression Console  using Robust Mutichip Average (RMA) preprocessing followed by “per chip” normalization across all samples. All Affymetrix control genes were removed from the expression data and the remaining Affymetrix probe clusters were imported into the Affymetrix Power Tools software (APT package).

source_name: human ovarian surface epithelial cell line

label_protocol: The quality and quantity of the RNA were tested using Bioanalyzer (Agilent Technologies, Santa Clara, CA). 4.5 μg of RNA from each sample was used for target labeling by a two-round amplification protocol (Expression Analysis Technical Manual, 20012, Affymetrix).

growth_protocol: The knockin and knockdown celllines were screened by puromycin (2 ug/ml)  and got the stable knockin and knockdown celllines. Using the westernblot to valid the knockin and knockdown effect.

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

treatment_protocol: the cell lines  were under the rest conditions and without any extra drug treatment.

tag: cell line

value: Hose

value: scramble control knockin


title: E11-5_EMB_MN_rep1

city: Los Angeles

first: Justin

last: Ichida

state: CA

address: 1425 San Pablo St. Bcc 307

institute: University of Southern California

description:
Sample 5
new6_count_delXY_delLC_4GEO.csv

data_processing:
trimming 8bp of barcode with clipper (https://github.com/mfcovington/adapter-clipper)
trimming reads on basis of quality phred33 (Trimmomatic v0.36)
alignment and genecounts by STAR (v.2.5.3a)
deletion of genes on X or Y chromosome
deletion of genes with an average readcount lower that 3 in the other samples (these samples were added on later as an extended analysis)
Genome_build: mm10
Supplementary_files_format_and_content: csv, genelist with gene counts per Samples 1 to 6

organism: Mus musculus

growth_protocol: Embryoid Body medium was conditioned by incubating 6 mls of media for 48 hours on a confluent 60 mm dish of primary cortical glia that was harvested 2-4 weeks prior to use for conditioning medium. 1 uM retinoic acid and 1 uM Smoothened agonist were added to the mixture and this was incubated with the embryoid bodies. (Samples 1-4) To isolate primary embryonic motor neurons, spinal cords from E11.5 Hb9::GFP embryos were dissected out in PBS and treated with papain/DNase in DMEM/F12 for 15-30 minutes at 37 degree Celsius. They were then triturated 10-20 times using a p1000 pipet before FACS sorting (Sample 5 and 6).

extract_protocol:
RNA was harvested from two biological replicates of each cell type or condition using TRIzol (Invitrogen) according to the manufacturers’ directions. RNA quality was determined using BioAnalyzer (Aligent). RNA integrity numbers above 7.5 were deemed sufficiently high quality to proceed with library preparation.
Amaryllis Nucleics YourSeq Dual (FT & 3'-DGE) RNAseq Library Kit v1.5
3'-DGE (3'-Digital Gene Expression) mode

treatment_protocol: During days 3-7 of directed differentiation, medium conditioned on mixed glia or on a plate without cells (as a negative control) was mixed 1:1 with non-conditioned medium. The medium was replaced with a fresh 1:1 mixture of conditioned and non-conditioned medium every 48 hours until harvest at day 7. (Samples 1-4)

tag: cell type

value: embryonic day 11.5 embryonic motor neurons


title: E11-5_EMB_MN_rep2

description:
Sample 6
new6_count_delXY_delLC_4GEO.csv


title: ESC_MN_nCM_rep1

description:
Sample 3
new6_count_delXY_delLC_4GEO.csv

value: embryonic stem cells derived motor neurons cultured without glial conditioned media


title: ESC_MN_CM_rep2

description:
Sample 2
new6_count_delXY_delLC_4GEO.csv

value: embryonic stem cells derived motor neurons cultured in glial conditioned media


title: ESC_MN_nCM_rep2

description:
Sample 4
new6_count_delXY_delLC_4GEO.csv


title: SK-OV-3 with Scramble Ctrl knockdown

description: The whole transcriptome Gene expression data from human ovarian epithelium Cancer cell (SK-OV-3) with scramble control Knockdown.

source_name: SK-OV-3,  which was derived from ascites of a 64-year-old Caucasian female with adenocarcinoma of the ovary

value: scramble control knockdown


title: B-mutant

value: cbrB deletion mutant


title: MCAS with Pin1 Knockdown

description: The whole transcriptome Gene expression data from human ovarian epithelium Cancer cell (MCAS) with pin1 Knockdown.

source_name: mucinous cystadenocarcinoma of the human ovary

value: MCAS

value: pin1 Knockdown


title: SK-OV-3 with Pin1 KnockDown

description: The whole transcriptome Gene expression data from human ovarian epithelium Cancer cell (SK-OV-3) with pIN1 Knockdown.

source_name: SK-OV-3,  which was derived from ascites of a 64-year-old Caucasian female with adenocarcinoma of the ovary,  with Pin1 knockdown

value: pin1 Knockdown.


title: Hose with Pin1 KnockIn

description: The whole transcriptome Gene expression data from human Normal ovarian epithelium cell (Hose) with Pin1 cDNA KnockIn.

value: Pin1 cDNA KnockIn


title: Caco without interaction - control, replicate 3 [EC472]

status: Public on Jan 05 2018

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

country: Brazil

institute: Faculdade de Medicina da Universidade de Sao Paulo

description:
Gene expression from Caco-2 after 3 hrs without interaction as a control, replicate 3
Caco-CT#27

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 and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent Bundle using one color scan setting for 1x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software version 9.5.3.1 (Agilent) using default parameters (protocol GE1-v5_95 and Grid: 014850_D__F_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities but not included the normalization process.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Caco-2 cell, control

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Microarray-Based Gene Expression Analysis - Quick Amp Labeling (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen). RNA concentration and purity was determined by reading the absorbance at 260 and 280 nm on a spectrophotometer (NanoVue, GE Health Care, USA).

extract_protocol: Total RNA was extracted from cells after lysing with RLT buffer and the RNeasy Mini Kit (Qiagen cat no. 74104, Valencia, CA) according to the manufacturer's instructions. The purity and quantification for all RNA samples were done using the NanoVue spectrophotometer and the RNA quality was assessed on the Agilent BioAnalyzer 2100 (Agilent, Santa Clara, CA). All samples that present RIN > 8.0 were stored at -80°C until used in hybridization experiments.

treatment_protocol: The Caco-2 intestinal cells were maintained in DMEM medium with 10% fetal bovine serum (complete medium) and penicillin-streptomycin in a 5% CO2 incubator at 37°C until cells differentiate in enterocyte-like. Prior to interaction assays Caco-2 cells were washed and incubated with complete medium. After 24 hrs 1/10 volume of bacterial culture were placed on a Caco-2 monolayer and incubated in a 5% CO2 at 37°C for 3 hrs.  After this period Caco-2 cells infected and uninfected (control) were washed 3 times with phosphate buffered saline (PBS) and the cells were recovered with 5 mL of PBS by pipetting. The cells were then centrifuged for 5 min at 5000 xg and the pellet was ressuspended in 600 µL of RNAlater Reagent (Qiagen cat. no. 76154, Valencia, CA) for RNA extraction.

value: intestinal cell line Caco-2

tag: stress

value: control (without interaction)


title: Genes expression in CD49a+ dNK_rep2.

city: Hefei

first: Zhou

last: Yonggang

state: Anhui

address: 443 HuangShan Road

department: School of Life Science and Medical Center

institute: University of Science and Technology of China

description: Genes expression in CD49a+ dNK_rep2.

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Human EG 1.0 ST Array in GeneChip® Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: Expression data were generated by Affymetrix Expression Console software and normalized by the RMA(Robust Multi-chip Average ) method.

source_name: Decidua NK cells

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

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit and RNase-Free Dnase Set.

treatment_protocol: NK cells from normal decidua and peripheral blood have been sorted by FACS Aria.

tag: tissue

value: decidua

value: CD56+CD3-CD49a+CD49b- NK cells


title: Genes expression in CD49a+ dNK_rep1.

description: Genes expression in CD49a+ dNK_rep1.


title: Genes expression in CD49b+ pNK_rep1.

description: Genes expression in CD49b+ pNK_rep1.

source_name: Peripheral blood NK cells

value: peripheral blood

value: CD56+CD3-CD49a-CD49b+  NK cells


title: Genes expression in CD49b+ pNK_rep2.

description: Genes expression in CD49b+ pNK_rep2.


title: Brain tumor; SAMPLE 1

type: genomic

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

country: Germany

institute: DKFZ

description: Methylation data from brain tumor sample.

hyb_protocol: Illumina protocol.

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing: Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'

label: biotin/DNP

molecule: genomic DNA

source_name: brain tumor

label_protocol: Illumina protocol.

extract_protocol: Illumina protocol.

treatment_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out by use of a salting-out method or by ultracentrifugation over cesium chloride.

value: brain tumor

tag: histology

value: Anaplastic astrocytoma (WHO grade III)

tag: age

tag: mgmtstatus

value: methylated

tag: os

tag: OS status

tag: pfs


title: MCAS with Scramble Ctrl knockdown

description: The whole transcriptome Gene expression data from human ovarian epithelium Cancer cell (MCAS) with scramble control KnockIn.

value: scramble control knockin


title: A-mutant

value: HYS

value: cbrA deletion mutant

value: six hours after grown on agar plate


title: ESC_MN_CM_rep1

description:
Sample 1
new6_count_delXY_delLC_4GEO.csv

value: embryonic stem cells derived motor neurons cultured in glial conditioned media


title: MUTANT Rep 1

status: Public on Jan 03 2018

city: Iowa City

first: Eric

last: Van Otterloo

state: Iowa

address: 801 Newton Rd

institute: University of Iowa

description:
MUT 1
processed data file: PIPELINE_1_ALL_DATA.xlsx
processed data file: PIPELINE_2_ALL_DATA.xlsx

data_processing:
Pipeline 1: For an initial ‘pipeline’ to identify mRNA-based gene expression changes between control and mutant mandibular prominences, derived fastq sequences were analyzed by applying a custom computational workflow (Baird et al., 2014; Bradford et al., 2015; Henderson et al., 2015; Maycotte et al., 2015) consisting of the open-source gSNAP (Wu and Nacu, 2010), Cufflinks (Trapnell et al., 2010), and R for sequence alignment and ascertainment of differential gene expression. In short, reads generated were mapped to the mouse genome (mm10) by gSNAP, expression (FPKM) derived by Cufflinks, and differential expression analyzed with ANOVA in R.
Pipeline 2: For a secondary ‘pipeline’ to further refine mRNA-based gene expression changes between control and mutant mandibular prominences, fastq sequence reads were first trimmed using the Java software package Trim Galore! (Babraham Bioinformatics, Babraham Institute) and subsequently mapped to the mm10 genome using the HISAT2 software package (Pertea et al., 2016) (both with default settings). Following mapping, RNA expression levels were generated using StringTie (Pertea et al., 2016) and differential expression computed between genotypes using CuffDiff2 (Trapnell et al., 2013), with a significance cut-off value of Q < 0.05 (FDR corrected P-value).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_ALL_DATA.xlsx: Excel files include FPKM values for each sample.

source_name: E10.5 Mandibular prominence

extract_protocol:
RNA was extracted from isolated tissue samples using the microRNA Purification Kit (Norgen Biotek Corp., Thorold, ON), following manufacturer's protocol. Following elution, mRNA was further purified using the Qiagen RNeasy Kit (Qiagen, Valencia, CA), according to manufacturer's protocol.
Quality of extracted mRNA was assessed using DNA Analysis ScreenTape (Agilent Technologies, Santa Clara, CA) to ensure that it was of sufficient quality for library production. Following validation of extracted mRNA, cDNA libraries were generated using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA).
Following library generation and subsequent quality control assessment, cDNA was sequenced using the Illumina HiSeq2500 platform and single-end reads (1x150).

tag: strain/background

value: Black-Swiss

value: Tfap2a;Tfap2b;Wnt1CRE mutant

tag: developmental stage

value: Embryonic day 10.5

value: Mandibular prominence


title: WT Rep 2

description:
CTRL 2
processed data file: PIPELINE_1_ALL_DATA.xlsx
processed data file: PIPELINE_2_ALL_DATA.xlsx

value: Control


title: WT Rep 3

description:
CTRL 3
processed data file: PIPELINE_1_ALL_DATA.xlsx
processed data file: PIPELINE_2_ALL_DATA.xlsx


title: MUTANT Rep 3

description:
MUT 3
processed data file: PIPELINE_1_ALL_DATA.xlsx
processed data file: PIPELINE_2_ALL_DATA.xlsx


title: MUTANT Rep 2

description:
MUT 2
processed data file: PIPELINE_1_ALL_DATA.xlsx
processed data file: PIPELINE_2_ALL_DATA.xlsx


title: RAP_TREAT_90min_RNA-seq

city: Stanford

first: Graeme

last: Gowans

address: Gilbert Building, 371 Serra Mall

department: Biology

institute: Stanford University

data_processing:
Reads were aligned using Bowtie2 and analysed using DESeq2. Replicates were combined for analysis and genes with low reads (< 5 FPKM across all samples) were removed.
Genome_build: sacCer3 (April 2011)
Supplementary_files_format_and_content: FPKM

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: Yeast grown in continuous culture to induce metabolic cycling; samples taken at different times across these metabolic cycles. Samples A and B are replicates.

extract_protocol:
yeast were harvested and flash frozen. RNA was extracted using MasterPure RNA extraction kit (MPY03100).
0.8 µg of RNA was used with the Illumina TruSeq mRNA kit (15031047) using standard protocols.

treatment_protocol: Asynchronous culture was treated in mid-log phase with 30 nM rapamycin for 90 minutes. Pellets were collected, snap-frozen and then processed as per the RNA-seq protocol outlined. Two biological replicates were collected (5 & 6).

tag: genotype

tag: growth phase

value: Asynchronous culture


title: WT Rep 1

description:
CTRL 1
processed data file: PIPELINE_1_ALL_DATA.xlsx
processed data file: PIPELINE_2_ALL_DATA.xlsx


title: Right atrial_AF_1y_rep4

city: Chengdu

first: Peng

last: Liu

state: Sichuan

address: Huimin Road 211#

department: Maize Research Institute

institute: Sichuan Agriculture University

description:
AF-004
LncRNA
Gene expression after AF sustained for 1 year in auricular dextra of patients with rheumatic heart valve disease

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Array with design ID 062918 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 for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: Right atrial, AF, 1y, replicate 4

label_protocol: Total RNA was labeled with the mRNA Complete Labeling and Hyb Kit (Agilent Technologies) and hybridized on the SurePrint G3 Human Gene Expression 8x60K v2 Microarray (Agilent Technologies).

growth_protocol: All patients were diagnosed as mitral stenosis by Doppler ultrasonography, and permanent AF and Sinus rhythm(SR) were diagnosed by dynamic electrocardiogram.

extract_protocol: Total RNA was extracted by the mirVana miRNA Isolation Kit (Apllied Biosystems) according to the manufacturer’s specifications. The concentration of RNAs was determined using NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific), and the integrity of RNAs was determined by Agilent 2100 bioanalyzer and RNA 6000 Nano kit (Agilent Technologies, USA).

treatment_protocol: Specimens of auricular dextra were obtained from patients undergone valve replacement surgery. The harvested specimens were snap-frozen in liquid nitrogen and were stored in an airtight -80℃ freezer.

value: Right atrial tissue

tag: gender

value: male

tag: diagnosis

value: rheumatic heart valve disease

tag: rhythm

value: atrial fibrillation


title: HeLa PA+EIPA 4h-4

city: aarhus

first: Yonglun

last: Luo

address: Wilhelm Meyers Allé 4

country: Denmark

institute: Aarhus University

data_processing:
Sequencing reads that contained adapters and/or had low quality, aligned to rRNA were filtered off before mapping.
We aligned clean reads to the hg19 UCSC RefSeq (RNA sequences, GRCh37) using bowtie2.
Gene level expression was performed by transforming mapped transcript reads to FPKM using RSEM.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: HeLa PA+EIPA 4h

growth_protocol: HeLa cells were cultured in Dulbecco's modified Eagle's medium (DMEM), 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit from QIAGEN.
Integrity and quantity of RNA was evaluated by Agilent 2100, following the manufacturer’s instructions. The mRNA and non-coding RNAs are enriched by removing rRNA using RNaseH. Mixed with the fragmentation buffer, target RNA were fragmented into short fragments and  cDNA was synthesized using the RNA fragments as templates by N6 random primer, followed by  end reparation and ligated with adapters. The quantity and quality of the cDNA libraries were assessed using an Agilent 2100 BioAnalyzer (Agilent Technologies).

treatment_protocol: PA+EIPA means (50mM) propionate plus (25uM) EIPA.

value: HeLa

tag: treated wth

value: 50mM propionate + 25uM EIPA


title: Comparison in human bronchial epithelial cell lines

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shaking (250 rpm). Hybridization buffer and washing protocol were followed by the protocol supplied by TORAY Industries, Inc.

scan_protocol: 3D-Gene Scanner (Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction (Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

label_protocol: cDNA and Amino Allyl aRNA was synthesized by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion #1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc.

growth_protocol: 16HBE14o- cell lines: Grown in fibronectin/bovine serum albumin (BSA)-coated dishes from Invitrogen. MEM were supplemented with 10% fetal bovine serum, 100 U/mL of penicillin, and 100 mg/mL of streptomycin. Cells were cultured in a humidified incubator at 37°C with 5% CO2. NHBE and DHBE-CF cells: following manufacturer's instruction (TaKaRa).

extract_protocol: RNA samples were extracted using RNeasy Mini Kit (QIAGEN, Valencia, CA).

tag: cell line

tag: cell type

value: Normal human bronchial epithelial cell line

source_name: ENaC

value: Epithelial sodium channel (ENaC)-overexpressing human bronchial epithelial cell line


title: Melanocytes Tyrosine

city: Delhi

first: Rajender

last: Motiani

state: Delhi

address: CSIR-IGIB, SUKHDEV VIHAR, MATHURA ROAD DELHI, OPPOSITE SUKHDEV VIHAR BUS DEPOT, ADJACENT TO CRRI DELHI-110020

department: SKIN BIOLOGY

country: India

institute: CSIR-IGIB

hyb_protocol: Agilent’s In situ Hybridzation kit 5188-5242, 1.65µg of cy3 labelled  linearly amplified  cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4140-90040) for 17 hours at 65°C in a rotating Agilent hybridization oven at 10rpm.  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: G4858A-039494 G3 Human Gene Expression 8×60K v2 Microarray (1 slide) AMADID: 39494.Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides.

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_1105 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
The normalization has been done using GeneSpring GX 12.6 Software. Intra-array normalization deals with variability within a single array. In intra array normalization, gProcessed signal (dye normalized background subtracted signal intensity) is log transformed and then for each of the array the 75th percentile value is calculated separately. In each sample the log transformed intensity values for each probe is subtracted by the calculated 75th percentile value of the respective array and expression values are obtained.

source_name: Melanocytes Tyrosine

label_protocol: T7 promoter based-linear amplification to generate labeled complementary RNA (One-Color Microarray-Based Gene Expression Agilent’s; Quick-Amp labeling Kit (p/n5190-0442)

growth_protocol: Cells were seeded at a density of 125000 cells per T25 in Melanocytes specific M254 media by Invitrogen for 24 hrs at 37° C in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was isolated using Macherey Nagel Nucleospin Triprep Kit according to manufacturer's instructions.

treatment_protocol: Post 24 hrs cells were treated with Phenylthiourea and Tyrosine for 48 hrs at 37°C in a humidified incubator with 5% CO2.

tag: tissue

value: Neonatal Foreskin

tag: treatment

value: 48 hours with 1mM L-Tyrosine treatment


title: Melanocytes Untreated

source_name: Melanocytes Untreated

value: 48 hours without treatment control


title: Melanocytes Phenylthio Urea

source_name: Melanocytes Phenylthio Urea

value: 48 hours with phenylthiourea 200µM treatment


title: Right atrial_SR_rep1

description:
SR-006
LncRNA
Gene expression in auricular dextra of rheumatic heart valve disease patients with sinus rhythm

source_name: Right atrial, SR,  replicate 1

value: female

value: sinus


title: Right atrial_SR_rep3

description:
SR-008
LncRNA
Gene expression in auricular dextra of rheumatic heart valve disease patients with sinus rhythm

source_name: Right atrial, SR,  replicate 3


title: Right atrial_AF_1y_rep2

description:
AF-002
LncRNA
Gene expression after AF sustained for 1 year in auricular dextra of patients with rheumatic heart valve disease

source_name: Right atrial, AF, 1y, replicate 2


title: Comparison in human primary bronchial epithelial cells

source_name: NHBE

value: Normal primary human bronchial epithelial cells

source_name: DHBE-CF

value: Cystic fibrosis (CF) primary human bronchial epithelial cells


title: HeLa Blank-1

source_name: HeLa Blank


title: HeLa PA+EIPA 4h-2


title: HeLa Blank-4


title: HeLa Blank-2


title: Right atrial_SR_rep5

description:
SR-010
LncRNA
Gene expression in auricular dextra of rheumatic heart valve disease patients with sinus rhythm

source_name: Right atrial, SR,  replicate 5


title: HeLa STAT3 KO-3

source_name: HeLa STAT3 KO

tag: genotype/variation

value: STAT3 KO


title: HeLa PA+EIPA 4h-1


title: Right atrial_SR_rep2

description:
SR-007
LncRNA
Gene expression in auricular dextra of rheumatic heart valve disease patients with sinus rhythm

source_name: Right atrial, SR,  replicate 2

value: Right atrial tissue


title: Comparison in mouse lung tissues

source_name: WT

growth_protocol: The mice were housed in a vivarium in accordance with the guidelines of the animal facility center of Kumamoto University and were fed with normal chow ad libitum.

value: normal mouse lung

source_name: ENaC-Tg

value: airway-specific epithelial sodium channel (ENaC)-overexpressing mouse lung


title: Young keratinocytes siCTL biological replicate 1

city: Montreal

first: Simon-Pierre

last: Gravel

state: QC

address: 2940 ch. de la polytechnique

department: Faculty of pharmacy

country: Canada

institute: University of Montreal

hyb_protocol: 3.5µg DNA target was hybridized on GeneChip® Human Gene 2.0ST (Thermo Fisher Scientific) and incubated at 45oC in the Genechip® Hybridization oven 640 (Thermo Fisher Scientific) for 17 hours at 60 rpm. GeneChips were then washed in a GeneChips® Fluidics Station 450 (Thermo Fisher Scientific) using Affymetrix Hybridization Wash and Stain kit according to the manufacturer’s instructions

scan_protocol: The microarrays were scanned on a GeneChip® scanner 3000 (Thermo Fisher Scientific)

data_processing: CHP files were generated from CEL files with the Expression Console (Thermo Fisher Scientific) for gene level studies using default RMA-Sketch workflow.

source_name: Young keratinocytes, 3 days with siRNA control

label_protocol: Sense-strand cDNA was synthesized from 100 ng of total RNA, and fragmentation and labeling were performed to produce ss DNA with the Affymetrix GeneChip® WT Terminal Labeling Kit according to manufacturer’s instructions (Thermo Fisher Scientific)

growth_protocol: NHEK were maintained in keratinocyte growth media (PromoCell). Cells were grown in a humidified 37oC incubator supplied with 5% CO2

extract_protocol: Total RNA was extracted using the Aurum Total RNA Mini Kit (Bio-Rad) following the manufacturer's instructions.

treatment_protocol: Subconfluent cells were transfected with siRNA control (SI03650318, QIAGEN) or siRNA-PGC-1alpha+beta (QIAGEN GeneSolution) at 2.4nM using HiPerfect (QIAGEN). 24h post-transfection, media was changed and cells were allow to grow for an additional 48h.

value: human primary keratinocytes

tag: age of donor (years)

tag: knockdown

value: siRNA control


title: Aged keratinocytes siCTL biological replicate 1

source_name: Aged keratinocytes, 3 days with siRNA control


title: Right atrial_AF_1y_rep3

description:
AF-003
LncRNA
Gene expression after AF sustained for 1 year in auricular dextra of patients with rheumatic heart valve disease

source_name: Right atrial, AF, 1y, replicate 3

value: male

value: rheumatic heart valve disease

value: atrial fibrillation


title: Right atrial_AF_1y_rep5

description:
AF-005
LncRNA
Gene expression after AF sustained for 1 year in auricular dextra of patients with rheumatic heart valve disease

source_name: Right atrial, AF, 1y, replicate 5


title: HeLa STAT3 KO-2

value: HeLa


title: Young keratinocytes siPGC1alpha+beta biological replicate 1

source_name: Young keratinocytes, 3 days with siRNA PGC-1s


title: Right atrial_SR_rep4

description:
SR-009
LncRNA
Gene expression in auricular dextra of rheumatic heart valve disease patients with sinus rhythm

source_name: Right atrial, SR,  replicate 4


title: Aged keratinocytes siCTL biological replicate 2


title: HeLa WT-3

source_name: HeLa WT

value: Wild type


title: Young keratinocytes siPGC1alpha+beta biological replicate 2


title: HeLa WT-2


title: Young keratinocytes siCTL biological replicate 2


title: Right atrial_AF_1y_rep1

description:
AF-001
LncRNA
Gene expression after AF sustained for 1 year in auricular dextra of patients with rheumatic heart valve disease

source_name: Right atrial, AF, 1y, replicate 1


title: HeLa WT-1


title: HeLa STAT3 KO-1


title: spinal_cord_e18.5_31405.1.olig2-ko

status: Public on Jan 02 2018

first: Alvin

middle: T.

last: Kho

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

description: Olig2 -/- spinal cord E18.5.

hyb_protocol: Hybridization is carried out according to the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight. Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.

scan_protocol: Scanning is carried out on an Affymetrix GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System.

data_processing: All sample CEL files were inputted into Bioconductor/R to derive MAS5 normalized output.

label: Biotin

source_name: Olig2 -/- E18.5 spinal cord

label_protocol: In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols. Quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.

growth_protocol: Neurosphere cultures were established from E14.5 ganglionic eminences of Olig1/2+/+ Ink4a/Arf-/-, Olig1/2+/- Ink4a/Arf-/- and Olig1/2-/- Ink4a/Arf-/- backgrounds. Neurospheres were grown in serum-free medium, in the presence of EGF (20ng/mL) and bFGF (20ng/mL). These cells were subsequently infected with epidermal growth factor receptor variant III (EGFRvIII)-encoding retrovirus at first passage (P1) and treated with puromycin (2µg/mL) 48 hours after infection. For the rescue experiment, Ink4a/Arf-/-EGFRvIII neurospheres of various genetic backgrounds were transduced with Olig2 or GFP encoding retroviruses at P3 and selected with blasticidin (2µg/mL).

extract_protocol: For each experimental sample, RNA quality was assessed using an Agilent Bioanalyzer 2100. Total mRNA was isolated using TriZol / RNeasy (Invitrogen) following the standard manufacturer protocol.

treatment_protocol: Cells were harvested at various passages (from P4 to P15) for mRNA extraction.

value: mixed Swiss and C57BL/6J

value: Olig2 -/-

value: spinal cord

tag: age

tag: a260/a280 ratio

tag: microarray hybridization date


title: spinal_cord_e18.5_31405.4.olig2-het

description: Olig2 +/- spinal cord E18.5.

source_name: Olig2 +/- E18.5 spinal cord

tag: strain/background

value: Olig2 +/-


title: olig2_het15gfp

description: Cultures of Ink4a/Arf-/- embryonic neural progenitors E14.5, transduced in vitro with hEGFRvIII.

source_name: Olig1/2+/- Ink4a/Arf-/- EGFRvIII neurospheres overexpressing GFP

value: Olig1/2+/- Ink4a/Arf-/-

value: cultured E14.5 embryonic neural progenitors

tag: in vitro transduction

value: hEGFRvIII

tag: rescue

value: GFP


title: forebrain_e18.5_31405.3.olig2-het

description: Olig2 +/- forebrain E18.5.

source_name: Olig2 +/- E18.5 forebrain

value: forebrain


title: forebrain_e18.5_31405.4.olig2-het

description: Olig2 +/- forebrain E18.5.


title: olig2_ko13o2-rescue

source_name: Olig1/2-/- Ink4a/Arf-/- EGFRvIII neurospheres overexpressing Olig2

value: Olig1/2-/- Ink4a/Arf-/-


title: olig2_het11o2-rescue

source_name: Olig1/2+/- Ink4a/Arf-/- EGFRvIII neurospheres overexpressing Olig2


title: olig2_ko13gfp

source_name: Olig1/2-/- Ink4a/Arf-/- EGFRvIII neurospheres overexpressing GFP


title: forebrain_e18.5_31405.1.olig2-ko

description: Olig2 -/- forebrain E18.5.

source_name: Olig2 -/- E18.5 forebrain


title: olig2_ko21

source_name: Olig1/2-/- Ink4a/Arf-/- EGFRvIII neurospheres


title: olig2_het15o2-rescue


title: olig2_ko14o2-rescue


title: spinal_cord_e18.5_31405.2.olig2-ko

description: Olig2 -/- spinal cord E18.5.


title: olig2_ko24


title: olig2_ko12gfp


title: olig2_ko12


title: olig2_het11gfp


title: olig2_ko14


title: forebrain_e18.5_31405.2.olig2-ko

description: Olig2 -/- forebrain E18.5.


title: olig2_ko16


title: olig2_ko14gfp


title: olig2_het26

source_name: Olig1/2+/- Ink4a/Arf-/- EGFRvIII neurospheres


title: olig2_het15


title: olig2_ko12o2-rescue


title: olig2_ko13


title: olig2_wt3

source_name: Olig1/2+/+ Ink4a/Arf-/- EGFRvIII neurospheres

value: Olig1/2+/+ Ink4a/Arf-/-


title: olig2_het11


title: spinal_cord_e18.5_31405.3.olig2-het

description: Olig2 +/- spinal cord E18.5.


title: olig2_wt2


title: olig2_wt20


title: Mammary_Tamoxifen_Biological Replicate7 [outcome: NoCancer_Biological Replicate8]

city: Savannah

first: Amy

last: Greene

state: GA

address: 1250 East 66th Street

department: Biomedical Sciences

institute: Mercer University

hyb_protocol: Biomedical Image Processing Laboratory (BIPL) of the University of Minnesota for hybridization with the murine Affymetrix gene chip MG430 plus 2.0.  Fluidics Protocol EukGE-WS2v4_450.

scan_protocol: GeneChips were scanned using a GeneChip 3000 scanner at the University of Minnesota Microarray Facility. Scaner ID 50209060.

data_processing: BioConductor/R with S+ ArrayAnalyzer was used to normalize the raw data (RMA normalization).

source_name: mammary gland from 20.5-21 week old female collected 4 weeks after tamoxifen treatment ended.

label_protocol: Procedures followed the Affymetrix Gene Chip Expression Analysis Manual.  First and second strand cDNA was synthesized from total RNA using a HPLC-purified T7-(dT)24 primer as recommended by Affymetrix and the SuperScript Choice kit (Invitrogen Life Tech).  Double-stranded cDNA was further purified using phase lock gel phenol/chloroform extraction.  cDNA size distribution and yield were determined on a 1% agarose gel and by NanoDrop prior to synthesis of biotin-labeled cRNA.  The synthesis of biotin-labeled cRNA was carried out as recommended by Affymetrix using the Bioarray High Yield RNA Transcript labeling ENZO Kit.  Products of in vitro transcription (before and after purification with the Qiagen RNeasy columns) were analyzed by gel electrophoresis. cRNA was fragmented at 94oC for 35 minutes in Fragmentation Buffer (Affymetrix) and checked by gel electrophoresis.

growth_protocol: NRL-TGFa mice of line 1372-1 TgN(Nrl-tgfa)29EPS in the FVB/N strain were used in this study (RoseHellekant et al., 2007) and transgenic mice were identified by PCR analysis of tail DNA for the TGFalpha transgene (RoseHellekant et al., 2009).  Mice were housed in AAALAC accredited facilities with 14 h on, 10 h off light cycle.  Food (Purina Lab Diet 5001) and water were provided ad libitum.  All procedures were IACUC approved. Transgenic mice evaluated in this study were heterozygous for the transgene.

extract_protocol: Procedures followed the Affymetrix Gene Chip Expression Analysis Manual.  Frozen mammary glands were thawed and homogenized in RLT buffer (RNeasy Qiagen).  Total RNA was prepared according to the Qiagen protocol and quantified using spectrophotometric measurements (NanoDrop).  RNA quality was evaluated using Agilent Lab-on-a Chip bioanalyzer (Paulo Alto, CA).

treatment_protocol: NRL-TGFa mice received subcutaneous implants releasing 5 mg of tamoxifen (hereafter referred to as tamoxifen mice) or containing tamoxifen-free carrier (hereafter known as placebo mice) at 8.5 weeks. Mice were maintained under identical housing conditions, and over a 1-year assignment period every other subject was assigned to tamoxifen or placebo cohort, as they became 8 weeks of age.  A single, nontumorous, number 4, mammary gland was surgically removed, from each isoflurane-anesthetized mouse at 20.5-21 weeks of age, and flash-frozen in liquid nitrogen followed by storage at -70oC.  Mice were held under observation for tumor development for up to 2 years of age.

tag: gender

value: female

tag: strain

value: FVB/N

tag: line

value: 1372-1 TgN(Nrl-tgfalpha)29EPS

value: tamoxifen

value: 20.5-21 week old

value: mammary gland

tag: outcome

value: mammary gland from 20.5-21 week old female collected 4 weeks after tamoxifen treatment ended; no mammary tumors observed.


title: HNE2_TP53 transfection_48 hours

city: Changsha

first: Wei

last: Xiong

state: Hunan

address: 110 Xiangya Road

department: Cancer Research Institute

institute: Central South University

description: Gene expression after 48hr TP53 transfected HNE2 cell

hyb_protocol: 0.6 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 25ul containing 25x Agilent fragmentation buffer and 10x Agient blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 25ul of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent-046065 Mouse miRNA Microarray V19.0 8x60K(Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 100.0 percent of samples in any 1 condition out of 2 conditions have flags in Detected were maintained.

source_name: HNE2_TP53 transfection_48 hours

label_protocol: 0.1ug total RNA were dephosphorylated, denaturated and then labeled with Cyanine-3-CTP（Cy3）using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions,then followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 UV-VIS Spectrophotometer  version 3.2.1.

growth_protocol: Human nasopharyngeal carcinoma (NPC) HNE2 cells were maintained in RPMI-1640 media  supplemented with 10% fetal bovine serum (FBS). Cells were grown at 37°C in a humidified 5% CO2 incubator.

extract_protocol: total RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions

treatment_protocol: HNE2 were transfected with pCMV-p53 plasmid (Clontech Laboratories Inc.) using Lipofectamine 2000 according to the manufacturer’s suggested protocol.

value: nasopharyngeal carcinoma

value: male

tag: cell line

tag: transfection

value: TP53 for 48 hours


title: HNE2_TP53 transfection_12 hours

description: Gene expression after 12hr TP53 transfected HNE2 cell

source_name: HNE2_TP53 transfection_12 hours

tag: tissue

value: TP53 for 12 hours


title: HNE2_TP53 transfection_0 hour

description: Gene expression after 0hr TP53 transfected HNE2 cell

source_name: HNE2_TP53 transfection_0 hour

value: TP53 for 0 hour


title: Mammary_Tamoxifen_Biological Replicate9 [outcome: NoCancer_Biological Replicate10]

tag: treatment


title: Mammary_Tamoxifen_Biological Replicate8 [outcome: NoCancer_Biological Replicate9]


title: Mammary_Tamoxifen_Biological Replicate2 [outcome: Cancer_Biological Replicate5]

value: mammary gland from 20.5-21 week old female collected 4 weeks after tamoxifen treatment ended; animal developed mammary tumor.


title: Mammary_Tamoxifen_Biological Replicate3 [outcome: NoCancer_Biological Replicate3]


title: Mammary_Tamoxifen_Biological Replicate4 [outcome: NoCancer_Biological Replicate4]


title: HNE2_TP53 transfection_24 hours

description: Gene expression after 24hr TP53 transfected HNE2 cell

source_name: HNE2_TP53 transfection_24 hours

value: TP53 for 24 hours


title: Mammary_Placebo_Biological Replicate10 [outcome: Cancer_Biological Replicate10]

source_name: mammary gland from 20.5-21 week old female collected 4 weeks after placebo treatment ended.

value: placebo

value: mammary gland from 20.5-21 week old female collected 4 weeks after placebo treatment ended; animal developed mammary tumor.


title: Mammary_Tamoxifen_Biological Replicate6 [outcome: NoCancer_Biological Replicate7]


title: Mammary_Tamoxifen_Biological Replicate5 [outcome: NoCancer_Biological Replicate5]


title: Mammary_Placebo_Biological Replicate5 [outcome: NoCancer_Biological Replicate2]

value: mammary gland from 20.5-21 week old female collected 4 weeks after placebo treatment ended; no mammary tumors observed.


title: Mammary_Tamoxifen_Biological Replicate1 [outcome: Cancer_Biological Replicate4]

value: female


title: Mammary_Tamoxifen_Biological Replicate10 [outcome: Cancer_Biological Replicate9]

value: FVB/N


title: Mammary_Placebo_Biological Replicate9 [outcome: Cancer_Biological Replicate8]

value: 1372-1 TgN(Nrl-tgfalpha)29EPS


title: Mammary_Placebo_Biological Replicate6 [outcome: NoCancer_Biological Replicate6]


title: Mammary_Placebo_Biological Replicate7 [outcome: Cancer_Biological Replicate6]


title: Mammary_Placebo_Biological Replicate4 [outcome: Cancer_Biological Replicate3]


title: Mammary_Placebo_Biological Replicate8 [outcome: Cancer_Biological Replicate7]


title: Mammary_Placebo_Biological Replicate2 [outcome: Cancer_Biological Replicate2]


title: Mammary_Placebo_Biological Replicate1 [outcome: Cancer_Biological Replicate1]


title: colorectal cancer sample AUS2_430

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

description: SST RMA expression values at the gene-level derived using Expression Console software

hyb_protocol: Samples were hybridized onto Affymetrix Human Transcriptome 2.0 Arrays according to the manufacturer's protocol (Affymetrix).

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

data_processing: Gene-level expression signals were obtained from raw data CEL files by the SST RMA procedure implemented in the Affymetrix Expression Console software.

source_name: Colorectal cancer patient

label_protocol: RNA was amplified, fragmented and labelled according to the Affymetrix GeneChip HT WT User Guide.

extract_protocol: Total RNA was isolated from colorectal cancer tissue samples using the Qiagen Allprep DNA/RNA/miRNA Universal kit, according to the manufacturer's protocol (Qiagen).

value: colorectal cancer biopsy


title: Mammary_Placebo_Biological Replicate3 [outcome: NoCancer_Biological Replicate1]

value: 20.5-21 week old


title: colorectal cancer sample AUS2_353


title: colorectal cancer sample AUS2_413


title: colorectal cancer sample AUS2_352


title: colorectal cancer sample AUS2_346


title: colorectal cancer sample AUS2_425


title: ko5B_ATAC-seq

description:
processed data file:
normalized_atac_counts.csv

library_source: genomic

data_processing:
Reads were aligned using Bowtie2. Duplicate reads were removed using Picard tools and replicates were combined for analysis.ATAC-seq signal in promoters was quantified as the number of fragments mapping to the window 400bp upstream to 100bp downstream from the TSS. NucleoATAC and chromVAR were used to assess promoter accessibility and nucleosome positioning resectively.
genome build: sacCer3 (April 2011)
processed data files format and content: Fragments mapped to promoters

source_name: yeast

growth_protocol: Yeast grown in continuous culture to induce metabolic cycling; samples taken at different times across these metabolic cycles. The growth stages are described in Kuang, Z., Cai, L., Zhang, X., Ji, H., Tu, B.P., and Boeke, J.D. (2014). High-temporal-resolution view of transcription and chromatin states across distinct metabolic states in budding yeast. Nat Struct Mol Biol 21, 854   863.  Samples A and B are technical replicates-- RNA was prepared separately from the same culture.

extract_protocol: yeast were harvested and processed immediately as described in the method sections.

tag: genotype

value: CEN.PK ARP5::KAN

tag: growth phase

value: RB start


title: ko6B_ATAC-seq

value: RB late


title: ko6A_ATAC-seq


title: ko3B_ATAC-seq

value: OX mid


title: ko5A_ATAC-seq


title: ko4B_ATAC-seq

value: OX late


title: colorectal cancer sample AUS2_367


title: ko4A_ATAC-seq


title: ko2A_ATAC-seq

value: RC mid


title: colorectal cancer sample AUS2_326


title: colorectal cancer sample AUS2_380


title: colorectal cancer sample AUS2_379


title: ko3A_ATAC-seq


title: ko1B_ATAC-seq

value: RC start


title: colorectal cancer sample AUS2_336


title: colorectal cancer sample AUS2_357


title: colorectal cancer sample AUS2_329


title: colorectal cancer sample AUS2_334


title: colorectal cancer sample AUS2_324


title: colorectal cancer sample AUS2_378


title: ko2B_ATAC-seq


title: colorectal cancer sample AUS2_411


title: colorectal cancer sample AUS2_321


title: ko1A_ATAC-seq


title: wt5B_ATAC-seq


title: wt4B_ATAC-seq


title: wt6A_ATAC-seq


title: wt4A_ATAC-seq


title: wt6B_ATAC-seq


title: wt3A_ATAC-seq


title: wt2B_ATAC-seq


title: wt3B_ATAC-seq


title: wt1B_ATAC-seq


title: wt1A_ATAC-seq


title: ko6B_RNA-seq

description:
processed data file:
fpkmMatrix.csv

data_processing:
Reads were aligned using Bowtie2 and analysed using DESeq2. Replicates were combined for analysis and genes with low reads (< 5 FPKM across all samples) were removed.
genome build: sacCer3 (April 2011)
processed data files format and content: FPKM


title: wt2A_ATAC-seq


title: wt5A_ATAC-seq


title: colorectal cancer sample AUS2_294


title: ko6A_RNA-seq

description:
processed data file:
fpkmMatrix.csv


title: colorectal cancer sample AUS2_285


title: colorectal cancer sample AUS2_282


title: colorectal cancer sample AUS2_293


title: ko4B_RNA-seq

description:
processed data file:
fpkmMatrix.csv


title: ko4A_RNA-seq

description:
processed data file:
fpkmMatrix.csv


title: colorectal cancer sample AUS2_306


title: colorectal cancer sample AUS2_309


title: colorectal cancer sample AUS2_292


title: colorectal cancer sample AUS2_297


title: ko3B_RNA-seq

description:
processed data file:
fpkmMatrix.csv


title: colorectal cancer sample AUS2_280


title: colorectal cancer sample AUS2_295


title: ko3A_RNA-seq

description:
processed data file:
fpkmMatrix.csv


title: colorectal cancer sample AUS2_278


title: colorectal cancer sample AUS2_277


title: colorectal cancer sample AUS2_563


title: colorectal cancer sample AUS2_469


title: colorectal cancer sample AUS2_566


title: colorectal cancer sample AUS2_459


title: colorectal cancer sample AUS2_564


title: ko2A_RNA-seq

description:
processed data file:
fpkmMatrix.csv


title: ko5B_RNA-seq

description:
processed data file:
fpkmMatrix.csv


title: ko5A_RNA-seq

description:
processed data file:
fpkmMatrix.csv


title: ko1B_RNA-seq

description:
processed data file:
fpkmMatrix.csv


title: wt6B_RNA-seq

description:
processed data file:
fpkmMatrix.csv


title: wt5B_RNA-seq

description:
processed data file:
fpkmMatrix.csv


title: ko2B_RNA-seq

description:
processed data file:
fpkmMatrix.csv


title: ko1A_RNA-seq

description:
processed data file:
fpkmMatrix.csv


title: wt6A_RNA-seq

description:
processed data file:
fpkmMatrix.csv


title: wt5A_RNA-seq

description:
processed data file:
fpkmMatrix.csv


title: wt4B_RNA-seq

description:
processed data file:
fpkmMatrix.csv


title: wt4A_RNA-seq

description:
processed data file:
fpkmMatrix.csv


title: wt3B_RNA-seq

description:
processed data file:
fpkmMatrix.csv


title: colorectal cancer sample AUS2_557


title: wt1B_RNA-seq

description:
processed data file:
fpkmMatrix.csv


title: wt2B_RNA-seq

description:
processed data file:
fpkmMatrix.csv


title: wt3A_RNA-seq

description:
processed data file:
fpkmMatrix.csv


title: colorectal cancer sample AUS2_556


title: colorectal cancer sample AUS2_558


title: colorectal cancer sample AUS2_560


title: colorectal cancer sample AUS2_551


title: colorectal cancer sample AUS2_555


title: colorectal cancer sample AUS2_552


title: colorectal cancer sample AUS2_554


title: wt1A_RNA-seq

description:
processed data file:
fpkmMatrix.csv


title: colorectal cancer sample AUS2_549


title: colorectal cancer sample AUS2_543


title: colorectal cancer sample AUS2_542


title: colorectal cancer sample AUS2_544


title: colorectal cancer sample AUS2_541


title: wt2A_RNA-seq

description:
processed data file:
fpkmMatrix.csv


title: colorectal cancer sample AUS2_534


title: colorectal cancer sample AUS2_535


title: colorectal cancer sample AUS2_507


title: colorectal cancer sample AUS2_505


title: colorectal cancer sample AUS2_540


title: colorectal cancer sample AUS2_504


title: colorectal cancer sample AUS2_501


title: colorectal cancer sample AUS2_500


title: colorectal cancer sample AUS2_506


title: colorectal cancer sample AUS2_497


title: colorectal cancer sample AUS2_503


title: colorectal cancer sample AUS2_490


title: colorectal cancer sample AUS2_493


title: colorectal cancer sample AUS2_481


title: colorectal cancer sample AUS2_480


title: colorectal cancer sample AUS2_470


title: colorectal cancer sample AUS2_494


title: colorectal cancer sample AUS2_499


title: colorectal cancer sample AUS2_476


title: colorectal cancer sample AUS2_539


title: colorectal cancer sample AUS2_484


title: colorectal cancer sample AUS2_482


title: colorectal cancer sample AUS2_462


title: colorectal cancer sample AUS2_471


title: colorectal cancer sample AUS2_474


title: colorectal cancer sample AUS2_477


title: colorectal cancer sample AUS2_485


title: colorectal cancer sample AUS2_472


title: colorectal cancer sample AUS2_547


title: colorectal cancer sample AUS2_467


title: colorectal cancer sample AUS2_468


title: colorectal cancer sample AUS2_478


title: colorectal cancer sample AUS2_487


title: colorectal cancer sample AUS2_452


title: colorectal cancer sample AUS2_451


title: colorectal cancer sample AUS2_460


title: colorectal cancer sample AUS2_463


title: colorectal cancer sample AUS2_456


title: colorectal cancer sample AUS2_429


title: colorectal cancer sample AUS2_458


title: colorectal cancer sample AUS2_423


title: colorectal cancer sample AUS2_445


title: colorectal cancer sample AUS2_433


title: colorectal cancer sample AUS2_426


title: colorectal cancer sample AUS2_435


title: colorectal cancer sample AUS2_447


title: colorectal cancer sample AUS2_418


title: colorectal cancer sample AUS2_450


title: colorectal cancer sample AUS2_419


title: colorectal cancer sample AUS2_387


title: colorectal cancer sample AUS2_399


title: colorectal cancer sample AUS2_402


title: Normal -N10_9

first: Julio

middle: C

last: Mantero

address: 72 E Concord St

department: Rheumatology

institute: Boston University School of Medicine

hyb_protocol: The labeled, fragmented DNA was hybridized to the GeneChip HG-U133A 2.0 Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix Fluidics Station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing:
Processed using affy package for R, using MAS5 normalization.
Log2_batch_adjusted.txt: Log2 data in this matrix was adjusted for batch differences using the ComBat algorithm within the sva package for R.
Brainarray custom CDF for HGU133A2 (version 19.0.0, ENTREZG) was utilized for this data set. http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/19.0.0/entrezg.asp

source_name: skin, normal

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

extract_protocol: Skin biopsies placed in RNAlater at bedside were stored at -80 degrees C until processing. RNA was extracted by homogenization in RLT Buffer and purifying over RNeasy columns.

value: skin

tag: dx

value: healthy

tag: batch


title: Normal -N10_7


title: colorectal cancer sample AUS2_382


title: colorectal cancer sample AUS2_398


title: colorectal cancer sample AUS2_361


title: Normal -N10_4


title: Normal -N10_11


title: colorectal cancer sample AUS2_389


title: SSc -SD11_2

source_name: skin, SSc

value: diffuse cutaneous systemic sclerosis


title: colorectal cancer sample AUS2_405


title: colorectal cancer sample AUS2_397


title: colorectal cancer sample AUS2_364


title: colorectal cancer sample AUS2_351


title: colorectal cancer sample AUS2_350


title: colorectal cancer sample AUS2_368


title: SSc -SD10_24


title: SSc -SD10_22


title: SSc -SD10_15


title: Normal -HC_7


title: Normal -HC_8


title: SSc -SD10_9


title: Normal -HC_6


title: Normal -N15_6


title: colorectal cancer sample AUS2_442


title: Normal -N15_8


title: SSc -SD10_5


title: colorectal cancer sample AUS2_337


title: Normal -HC_5


title: colorectal cancer sample AUS2_414


title: Normal -HC_3


title: Normal -N15_4


title: colorectal cancer sample AUS2_431


title: colorectal cancer sample AUS2_432


title: Normal -HC-4


title: colorectal cancer sample AUS2_416


title: colorectal cancer sample AUS2_407


title: SSc -SD10_7


title: colorectal cancer sample AUS2_404


title: colorectal cancer sample AUS2_409


title: colorectal cancer sample AUS2_417


title: colorectal cancer sample AUS2_408


title: colorectal cancer sample AUS2_415


title: colorectal cancer sample AUS2_443


title: RAP_TREAT_45min_RNA-seq

description:
processed data file:
RAP_FPKM.csv

extract_protocol: yeast were harvested and flash frozen. RNA was extracted using MasterPure RNA extraction kit (MPY03100).

treatment_protocol: Asynchronous culture was treated in mid-log phase with 30 nM rapamycin for 45 minutes. Pellets were collected, snap-frozen and then processed as per the RNA-seq protocol outlined. Two biological replicates were collected (3 & 4).

value: Asynchronous culture


title: RAP_CTRL_RNA-seq

description:
processed data file:
RAP_FPKM.csv

treatment_protocol: Asynchronous culture was treated in mid-log phase with 30 nM rapamycin for 45 minutes. Pellets were collected, snap-frozen and then processed as per the RNA-seq protocol outlined. Two biological replicates were collected (1 & 2)


title: colorectal cancer sample AUS2_403


title: SSc -SD9_3


title: Normal -HC_1


title: SSc -SD7_4A


title: SSc -SD8_4A


title: SSc -SD8_2A


title: colorectal cancer sample AUS2_391


title: colorectal cancer sample AUS2_395


title: colorectal cancer sample AUS2_316


title: colorectal cancer sample AUS2_369


title: colorectal cancer sample AUS2_383


title: colorectal cancer sample AUS2_371


title: SSc -SD6_5A


title: colorectal cancer sample AUS2_365


title: colorectal cancer sample AUS2_363


title: Normal -HC_2


title: MCM1DLN_SR-BI KD

city: Wien

first: Katharina

middle: M.

last: Pichler

state: Wien

address: Odoakergasse

department: Department of Orthopedics and Trauma Surgery

country: Austria

institute: Medical University of Vienna

description: metastatic

hyb_protocol: Affymetrix GeneChip® Human PrimeView arrays were washed, stained and scanned according to the protocol described in GeneChip® 3` IVT Plus Reagent Kit User Manual (Fluidics Protocol FS450_0002)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.1

source_name: MCM1DLN SR-BI siRNA + DMSO

label_protocol: 100ng of total RNA were amplified and labeled using the Affymetrix 3` IVT Plus Reagent Kit (Catalog Number 902416), Affymetrix, Santa Clara, CA)

growth_protocol: Cells were grown in melanoma isolation media containing 10% FCS. (https://www.wistar.org/lab/meenhard-herlyn-dvm-dsc/page/melanoma-isolation-media)

extract_protocol: Total RNA was extracted according to the manufacturer's instructions (PEQ Gold Total RNA) 44 hours post transfection. RNA from 2 biologic replicates were pooled to yield a single sample for further analysis.

treatment_protocol: Cells were treated either with control siRNA + DMSO, control siRNA + BLT-1 [1µM] or SR-BI siRNA + DMSO in melanoma isolation media containing 10% FCS for 24 hours. Media was changed to growing media after 24 hours of transfection. 45 hours after medium change cells were harvested.


title: 1205Lu_BLT-1

description: metastatic

source_name: 1205Lu Control siRNA + BLT-1


title: MCM1DLN_Control

description: metastatic

source_name: MCM1DLN Control siRNA + DMSO


title: 1205Lu_Control

description: metastatic

source_name: 1205Lu Control siRNA + DMSO


title: 1205Lu_SR-BI KD

description: metastatic

source_name: 1205Lu SR-BI siRNA + DMSO


title: SSc -SD7_1A


title: MCM1DLN_BLT-1

description: metastatic

source_name: MCM1DLN Control siRNA + BLT-1


title: SSc -SD5_11A


title: colorectal cancer sample AUS2_359


title: SSc -SD6_4A


title: SSc -SD5_16A


title: colorectal cancer sample AUS2_356


title: SSc -SD5_10A


title: colorectal cancer sample AUS2_358


title: colorectal cancer sample AUS2_355


title: 451Lu_BLT-1

description: metastatic

source_name: 451Lu Control siRNA + BLT-1


title: 451Lu_SR-BI KD

description: metastatic

source_name: 451Lu SR-BI siRNA + DMSO


title: 451Lu_Control

description: metastatic

source_name: 451Lu Control siRNA + DMSO


title: Kras; Brg1flox acinar cell explants

status: Public on Jan 01 2018

city: kyoto

first: Motoyuki

last: Tsuda

state: Please Select

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

department: Department of Gastroenterology and Hepatology

institute: Graduate School of Medicine, Kyoto university

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray Ver2.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

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

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Data were normalized   on GeneSpring GX 14.5 (Agilent). Features flagged in Feature Extraction as not positive and significant or not above background were excluded.

source_name: isolated acinar cell, Ad-Cre, 24h culture

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 20ug Total RNA using the Pico WTA System(Ovation) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

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

value: isolated acinar cell


title: exosomes derived from hypoxic-MSCs supplemented with GW4869

city: Hangzhou

first: Jin

middle: Yun

last: Zhu

state: zhejiang

address: Jiefang road 88

institute: Second Affiliated Hospital, College of Medicine, Zhejiang University.

description: miRNAs expression in exosomes secreted from MSCs after 24-hr hypoxia exposure and supplement with GW4869

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

scan_protocol: After washing, the arrays were scanned with the Agilent Scanner G2505C (Agilent Technologies)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: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Next, Genespring software (version 13.1, Agilent Technologies) was employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 100.0 percent of samples in any 1 condition out of 2 conditions have flags in Detected were chosen for further data analysis. Differentially expressed miRNAs were then identified through fold change. The threshold set for up- and down-regulated genes was a fold change>= 1.5. Target genes of differentially expressed miRNAs were the intersection predicted with 3 databases（Targetscan，microRNAorg，PITA）

source_name: bone-marrow derived MSCs

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

growth_protocol: Mouse MSCs were isolated from bone marrow of 4–6 week old male wild type C57BL/6 mice. Mice were sacrificed by isoflurane inhalation and cervical dislocation. In brief, total bone marrow cells were ﬂushed with culture medium from the femur and tibia and seeded in culture dishes containing Dulbecco’s modiﬁed Eagle’s medium-low glucose (DMED-LG) supplemented with 10% fetal bovine serum (FBS) and penicillin (100 U/mL)/streptomycin (100 mg/mL). Cells were incubated at 37°C in a humidiﬁed atmosphere containing 5% CO2. The ﬁrst medium change was performed to remove the non-adherent cells at 48 hours. Fresh complete medium was added and replaced every 3 days. Each primary culture was sub-cultured 1:3 when MSCs grew to approximately 80% confluence. MSCs at Passages 3-6 were used.

extract_protocol: RNA was isolated by TRIzol reagent (Invitrogen, Life Technology) according to the manufacturer’s protocol. PrimeScript™ 1st Strand cDNA Synthesis Kit (TaKaRa, Dalian, China) was applied to reverse total RNA (1 μg) transcription to synthesize cDNA.Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: For isolation of exosomes derived from MSCs under culture condition of normoxia, or hypoxia, or hypoxia with GW4869 (N-Exo, H-Exo, H+G-Exo), the conditioned supernatant derived from 10-dish MSCs after 24-hr hypoxia or normoxia exposure were collected and centrifuged. Cells and debris were removed by differential centrifugation at 300x g for 10 min, 2000x g for 10 min respectively; and macrovesicles were removed at 13000x g for 30 min. The conditioned media were then filtered (0.2 µm), and concentrated using Ultracel-100K (Millipore) by centrifugation at 4000x g for 15 min. Exosomes were isolated by ultracentrifugation at 100, 000x g for 70 minutes to obtain the crude exosome pellet. The pellet was subsequently washed with phosphate buffered saline (PBS pH7.4) followed by repeat ultracentrifugation for 70 minutes at the same speed.

value: male

tag: cell type

value: MSCs

value: hypoxia + GW4869

tag: time

tag: sample type

value: exosome


title: exosomes derived from normoxic-MSCs

description: miRNAs expression in exosomes secreted from MSCs after 24-hr normoxia exposure

value: normoxia


title: Kras acinar cell explants


title: exosomes derived from hypoxic-MSCs

description: miRNAs expression in exosomes secreted from MSCs after 24-hr hypoxia exposure

value: hypoxia


title: lymph node 10y

city: Basel

first: David

middle: Christian

last: Müller

address: Schönbeinstrasse 40

department: Institute for Pathology

country: Switzerland

institute: University Hospital Basel

hyb_protocol: Labeled DNAs were hybridized in an ozone free environment in a rotisserie oven at 20 rpm for 40 hours then washed according to array supplier's (Agilent)protocol

scan_protocol: All arrays were  scanned using an Agilent 2565C Scanner and default settings for CGH.

data_processing:
Data was extracted from the TIFF files using Agilent FE 10.5.  The data quality was assessed using the QC Report output in F.E. 10.5.  All arrays that passed the experimental Q.C. were then visualized and analyzed using DNA Analytics 4.0.85 and the ADM2 step gram algorithm.
For normalization, we applied GC-correction and diploid peak-centralization using the Agilent Workbench 7.0.4.0.

source_name: Frozen tissue biopsy

label_protocol: A 1 microgram aliquot of each sample and reference DNA was digested with DNAse 1 then labeled with a fluorescent nucleotide (Cy5 for tumor and Cy3 for normal reference) using the BioPrime labeling kit (Invitrogen)according to manufacturer's protocol.

growth_protocol: Tumor samples from the patient from different locations and different timepoints with urothelial carcinoma were either snap-frozen and maintaned at -80 degrees C or FFPE archived until processed for flow sorting

extract_protocol: 25-100 mg of tumor was thawed then minced in the presence of NST and DAPI.  Each sample was then mechanically sheared then filtered through a 30 micron mesh filter prior to sorting. All sorting was done with an Influx Flow Cytometer equiped with a UV laser. DNA was extracted from each sorted fraction using Qiagen DNA micro kits. All phi29 amplifications were done with a 100ng aliquot of either sample or reference genomic DNA using the GenomiPhi kit (G.E Health Care).

tag: disease state

value: Urothelial cancer

value: tumor (Frozen tissue biopsy)

tag: location

value: lymph

tag: timepoint

source_name: Reference pooled 46XX

tag: reference

value: Normal female genome


title: SSc -SD11_1

city: Boston


title: Caski-NC

city: chongqing

first: haiyu

last: li

address: Yixueyuan Road1#, Yuzhong District, Chongqing

institute: chongqing medical university

description: Wild type CaSki cells

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Human Transcriptome Array 2.0 in GeneChip® Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method.

source_name: NCK1-AS1 negative control cells

growth_protocol: CaSki cells were maintained in Dulbecco’s modiﬁed Eagle’s medium (Gibco) supplemented with 10% FBS.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit and RNase-Free Dnase Set.

treatment_protocol: CaSki cells were transfected with Lentivirous3-shNCK1-AS1 or control, and 3ug/ml puromycin-resistant transfectants were selected.

value: cervical cancer cell


title: Perilesion_Inactive MS lesion_6

city: Amsterdam

first: Inge

last: Huitinga

address: meibergdreef 47

department: Neuroimmunology

country: Netherlands

institute: NIN

hyb_protocol: Samples were hybridized to an Agilent Human Gene Expression 4x44K v2 Microarray (Part Number G4845A) for 17 h at 65°C in a rotating hybridization chamber. Arrays were washed in 6 x saline sodium phosphate–EDTA (SSPE)/0.005% N-lauroylsarcosine (Sigma-Aldrich, St. Louis, MO, USA) for 5 min, then in 0.06 x SSPE/0.005% N-lauroylsarcosine for 1 min, and finally in acetonitrile (Sigma-Aldrich) for 30 sec, followed by drying in a nitrogen flow

scan_protocol: Arrays were scanned using an Agilent DNA Microarray Scanner at 5 mm resolution and 100% photomultiplier tube setting

data_processing: Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA

source_name: frozen post-mortem brain tissue

label_protocol: The Low Input Quick Amp Labeling Kit (Agilent Technologies) was used for sample amplification and fluorescent labeling according to manufacturer’s instructions. 100 ng experimental RNA input and 50 ng reference pool RNA input was used for linear amplification and fluorescent labeling. Experimental samples were labeled with Cy5-CTP, and the reference pool was labeled with Cy3-CTP (Perkin Elmer, Waltham, MA, USA)

extract_protocol: Total RNA extracted using Trisure following manufacturer's instructions

treatment_protocol: The rim and peri-lesional (PL)-NAWM were dissected by laser dissection microscopy. Control tissue was dissected inside the cryostat using a pre-chilled scalpel

value: brain

value: multiple sclerosis (MS)

tag: lesion type

tag: gender

value: M

tag: age

source_name: pooled tissue from control and MS brains, including MS lesions and NAWM and tonsil


title: RIM_Inactive MS lesion_7

value: F


title: Perilesion_Inactive MS lesion_4


title: bladder 10y

value: bladder


title: Perilesion_Inactive MS lesion_1


title: Perilesion_Inactive MS lesion_7


title: Perilesion_Inactive MS lesion_8


title: Perilesion_Chronic active MS lesion_7

value: Perilesion_Chronic active


title: Caski-shAS1

description: NCK1-AS1  knockdown CaSki cells

source_name: NCK1-AS1 knockdown CaSki cells


title: RIM_Inactive MS lesion_8


title: Perilesion_Inactive MS lesion_5


title: RIM_Inactive MS lesion_4


title: Perilesion_Inactive MS lesion_3


title: Perilesion_Inactive MS lesion_2


title: bladder 9y

source_name: FFPE tissue biopsy

value: tumor (FFPE tissue biopsy)


title: RIM_Inactive MS lesion_6


title: RIM_Inactive MS lesion_1


title: RIM_Inactive MS lesion_3


title: bladder 8y


title: RIM_Inactive MS lesion_5


title: RIM_Inactive MS lesion_2


title: kidney 10y

value: kidney


title: Perilesion_Chronic active MS lesion_6


title: Perilesion_Chronic active MS lesion_5


title: Perilesion_Chronic active MS lesion_4


title: Perilesion_Chronic active MS lesion_3


title: RIM_Chronic active MS lesion_6

value: RIM_Chronic active


title: Perilesion_Chronic active MS lesion_1


title: Control 10_white matter tissue

source_name: frozen post-mortem brain tissue_control

value: control


title: RIM_Chronic active MS lesion_3


title: RIM_Chronic active MS lesion_5


title: RIM_Chronic active MS lesion_7


title: Perilesion_Chronic active MS lesion_2


title: Day 30_rep5

city: New York

first: Shanaz

middle: Adi

last: Ghandhi

state: NY

address: 630, W 168th street

department: Center for Radiological Research

institute: Columbia University Medical Center

description: Gene expression in blood, day 30 after irradiation

hyb_protocol: Agilent recommended protocols were used for hybridizations

scan_protocol: Slides were  scanned with the Agilent DNA Microarray Scanner (G2505B), and the images were analyzed (Agilent Feature Extraction Software ver. 10.7) with default parameters for background correction and flagging non-uniform features.

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

organism: Macaca mulatta

source_name: NHP, day 30, rep5

label_protocol: We processed 5 samples from each of the following groups: pre-irradiation, day 2, day 5 and day 30 RNA for microarray hybridization. Previous studies have shown the usefulness of human microarray platforms for the detection of non-human primate gene expression [6, 7].  We used Agilent Whole Human Genome 4X44K v2 microarrays for measurement of levels of Rhesus transcripts, following the Agilent recommended protocol.

growth_protocol: We obtained whole blood samples pre-irradiation and post-irradiation (days 2, 5 and 30) from 8 NHP exposed to 10 Gy X-rays to the thoracic region

extract_protocol: We isolated RNA from the blood using the PAXgene Blood RNA method (PreAnalytix GmBH, catalog#762165), and then depleted Globin transcripts using the Ambion GLOBINclear-Human kit (Life Technologies, Grand Island, NY, catalog#AM1980). We evaluated the samples for RNA integrity using the Agilent 2100 bioanalyzer and samples with RINs >8.0 were used for further analysis.

treatment_protocol: The intent of irradiation was to deliver 10 Gy to the anterior-posterior midplane of the thorax, covering the superior aspect of the lungs and including inferior lung to 4cm below the xyphoid.

value: whole blood


title: Day 30_rep3

source_name: NHP, day 30, rep3


title: Day 30_rep4

source_name: NHP, day 30, rep4


title: Day 30_rep1

source_name: NHP, day 30, rep1


title: RIM_Chronic active MS lesion_4


title: Day 5_rep3

description: Gene expression in blood, day 5 after irradiation

source_name: NHP, day 5, rep3


title: Control 5_white matter tissue


title: RIM_Chronic active MS lesion_2


title: Control 7_white matter tissue


title: Control 4_white matter tissue


title: Day 5_rep2

source_name: NHP, day 5, rep2


title: Day 5_rep1

source_name: NHP, day 5, rep1


title: Day 30_rep2

source_name: NHP, day 30, rep2


title: RIM_Chronic active MS lesion_1


title: Control 2_white matter tissue


title: Day 5_rep4

source_name: NHP, day 5, rep4


title: Control 9_white matter tissue


title: Day 5_rep5

source_name: NHP, day 5, rep5


title: Control 6_white matter tissue


title: Control 3_white matter tissue


title: Control 1_white matter tissue


title: Control 8_white matter tissue


title: Day 2_rep3

description: Gene expression in blood, day 2 after irradiation

source_name: NHP, day 2, rep3


title: Day 2_rep4

source_name: NHP, day 2, rep4


title: Pre-irradiation_rep4

description: Gene expression in blood, pre-irradiation control

source_name: NHP, pre-irradiation control, rep4


title: Day 2_rep5

source_name: NHP, day 2, rep5


title: Pre-irradiation_rep2

source_name: NHP, pre-irradiation control, rep2


title: Pre-irradiation_rep1

source_name: NHP, pre-irradiation control, rep1


title: Day 2_rep2

source_name: NHP, day 2, rep2


title: Pre-irradiation_rep5

source_name: NHP, pre-irradiation control, rep5


title: Day 2_rep1

source_name: NHP, day 2, rep1


title: rainbow trout, anterior intestine, fasted

type: SAGE

anchor: NlaIII

city: Talence

first: Patrick

middle: J.

last: BABIN

address: Avenue des facultés

department: UFR Biologie

country: France

institute: Université Bordeaux

description: 30 micrograms of total RNAs of the pool of 8 animals were used to generate the long-SAGE library using the I-SAGE Long kit (Invitrogen, Cergy Pointoise, France).

data_processing: SAGE-tag extraction, counting and quality control were undertaken by Skuld-Tech (Montpellier, France, http://www.skuldtech.com)

organism: Oncorhynchus mykiss

source_name: anterior intestine, fasted

growth_protocol: Rainbow trouts were reared at constant water temperature (17 to 18°C) under natural photoperiod conditions (French National Institute for Agricultural Research (INRA) experimental fish farm, Donzacq, Landes, France).

extract_protocol: The anterior intestine was isolated from 8 animals. Total RNA were extracted from the intestines using the WIZTM RNA isolation reagent (Ambion, France).

treatment_protocol: Rainbow trouts were deprived of food during 3 days.

value: diploid

tag: developmental stage

value: juvenile

value: anterior intestine

value: fasted


title: Pre-irradiation_rep3

source_name: NHP, pre-irradiation control, rep3

tag: tissue


title: Patient 05 - 7477_pre

city: Durham

last: Chen

state: NC

address: 101 Science Drive

department: Center for Genomic and Computational Biology

institute: Duke University

description:
Microarray analysis of human samples. The same FFPE samples were also used for RNA extraction in a subset of the human tumors (n=9 patients, 18 paired samples) using the RNeasy FFPE kit from Qiagen (catalog # 73504). The SensationPlus 3' IVT A&L FFPE kit was used for the labeling and amplification of the RNA (Affymetrix, Inc. catalog # 902028). The Almac Xcel™ Array was used for profiling of the FFPE samples (Affymetrix, Inc. catalog # 902016). The Xcel™arrays provide a 3’ gene expression array designed and optimized for use with FFPE tissues with probe sets for over 97,000 transcripts. The RNA Gene expression estimates were obtained using the Robust Multi-array Average (RMA) algorithm. Next, gene filtering was performed to select the top 10% of the probe sets with the highest coefficient of variation across all 18 samples. Paired samples t-tests were performed using the Bioconductor limma package (13) to identify differentially expressed probe sets caused by radiation. Probe sets with q-values less than 5% were selected as differentially expressed.
Formalin fixed and paraffin-embedded (FFPE) samples were obtained at the time of diagnosis. Patients then received a single large dose of radiation to the intact tumor and proceeded to surgical resection within 10 days of treatment. A second post-radiation sample was obtained at the time of surgical excision.
7477

hyb_protocol: Hybridization of samples to Affymetrix GeneChip arrays was performed according to Affymetrix manual instructions .

scan_protocol: Scanning of Affymetrix GeneChip arrays was performed according to the Affmetrix manual instructions.

data_processing: The Almac Xcel™ Array was used for profiling of the FFPE samples (Affymetrix, Inc. catalog # 902016). The Xcel™arrays provide a 3’ gene expression array designed and optimized for use with FFPE tissues with probe sets for over 97,000 transcripts.   The RNA Gene expression estimates were obtained using the Robust Multi-array Average (RMA) algorithm. Next, gene filtering was performed to select the top 10% of the probe sets with the highest coefficient of variation across all 18 samples. Paired samples t-tests were performed using the Bioconductor limma package  to identify differentially expressed probe sets caused by radiation. Probe sets with q-values less than 5% were selected as differentially expressed.

source_name: Patients with biologically favorable early stage breast cancer participating in an IRB approved phase I dose-escalation preoperative radiotherapy protocol at Duke University Medical Center.

label_protocol: Affymetrix  SensationPlus 3' IVT A&L FFPE  for the human FFPE samples (for the Xcel™ Array ).

extract_protocol: Microarray analysis of human samples: The same FFPE samples were also used for RNA extraction in a subset of the human tumors (n=9 patients, 18 paired samples) using the RNeasy FFPE kit from Qiagen (catalog # 73504). The SensationPlus 3' IVT A&L FFPE kit was used for the labeling and amplification of the RNA (Affymetrix, Inc. catalog # 902028).

value: breast

value: breast cancer


title: rainbow trout, anterior intestine, fed

source_name: anterior intestine, fed

treatment_protocol: Rainbow trouts were deprived of food during 3 days, and subsequently fed during 8 hours.

tag: treatment

value: fed


title: Patient 07 - 7597_post

description:
Microarray analysis of human samples. The same FFPE samples were also used for RNA extraction in a subset of the human tumors (n=9 patients, 18 paired samples) using the RNeasy FFPE kit from Qiagen (catalog # 73504). The SensationPlus 3' IVT A&L FFPE kit was used for the labeling and amplification of the RNA (Affymetrix, Inc. catalog # 902028). The Almac Xcel™ Array was used for profiling of the FFPE samples (Affymetrix, Inc. catalog # 902016). The Xcel™arrays provide a 3’ gene expression array designed and optimized for use with FFPE tissues with probe sets for over 97,000 transcripts. The RNA Gene expression estimates were obtained using the Robust Multi-array Average (RMA) algorithm. Next, gene filtering was performed to select the top 10% of the probe sets with the highest coefficient of variation across all 18 samples. Paired samples t-tests were performed using the Bioconductor limma package (13) to identify differentially expressed probe sets caused by radiation. Probe sets with q-values less than 5% were selected as differentially expressed.
Formalin fixed and paraffin-embedded (FFPE) samples were obtained at the time of diagnosis. Patients then received a single large dose of radiation to the intact tumor and proceeded to surgical resection within 10 days of treatment. A second post-radiation sample was obtained at the time of surgical excision.
7597


title: Patient 03 - 1090_pre

description:
Microarray analysis of human samples. The same FFPE samples were also used for RNA extraction in a subset of the human tumors (n=9 patients, 18 paired samples) using the RNeasy FFPE kit from Qiagen (catalog # 73504). The SensationPlus 3' IVT A&L FFPE kit was used for the labeling and amplification of the RNA (Affymetrix, Inc. catalog # 902028). The Almac Xcel™ Array was used for profiling of the FFPE samples (Affymetrix, Inc. catalog # 902016). The Xcel™arrays provide a 3’ gene expression array designed and optimized for use with FFPE tissues with probe sets for over 97,000 transcripts. The RNA Gene expression estimates were obtained using the Robust Multi-array Average (RMA) algorithm. Next, gene filtering was performed to select the top 10% of the probe sets with the highest coefficient of variation across all 18 samples. Paired samples t-tests were performed using the Bioconductor limma package (13) to identify differentially expressed probe sets caused by radiation. Probe sets with q-values less than 5% were selected as differentially expressed.
Formalin fixed and paraffin-embedded (FFPE) samples were obtained at the time of diagnosis. Patients then received a single large dose of radiation to the intact tumor and proceeded to surgical resection within 10 days of treatment. A second post-radiation sample was obtained at the time of surgical excision.
1090


title: Patient 09 - 24618_pre

description:
Microarray analysis of human samples. The same FFPE samples were also used for RNA extraction in a subset of the human tumors (n=9 patients, 18 paired samples) using the RNeasy FFPE kit from Qiagen (catalog # 73504). The SensationPlus 3' IVT A&L FFPE kit was used for the labeling and amplification of the RNA (Affymetrix, Inc. catalog # 902028). The Almac Xcel™ Array was used for profiling of the FFPE samples (Affymetrix, Inc. catalog # 902016). The Xcel™arrays provide a 3’ gene expression array designed and optimized for use with FFPE tissues with probe sets for over 97,000 transcripts. The RNA Gene expression estimates were obtained using the Robust Multi-array Average (RMA) algorithm. Next, gene filtering was performed to select the top 10% of the probe sets with the highest coefficient of variation across all 18 samples. Paired samples t-tests were performed using the Bioconductor limma package (13) to identify differentially expressed probe sets caused by radiation. Probe sets with q-values less than 5% were selected as differentially expressed.
Formalin fixed and paraffin-embedded (FFPE) samples were obtained at the time of diagnosis. Patients then received a single large dose of radiation to the intact tumor and proceeded to surgical resection within 10 days of treatment. A second post-radiation sample was obtained at the time of surgical excision.
24618


title: HEC1A-sh KD

city: LA

first: Madhuri

last: Wadehra

address: 675 Charles Young Dr. South/ 4726 MRL

department: Pathology and Lab Medicine

institute: UCLA

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials

scan_protocol: Standard Affymetrix protocol. GeneChip Scanner 3000 7G Scanner type: M10 Hardware version: 1.0 Software version: 4.0.0.16

data_processing: Data were analyzed with Partek genomics Suite 6.6

source_name: knockdown of EMP2

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: McCoys + 10% FBS

extract_protocol: Qiagen total RNA purification

treatment_protocol: untreated

tag: cell line

tag: genotype/variation

value: EMP2 knockdown


title: Patient 02 - 1243_pre

description:
Microarray analysis of human samples. The same FFPE samples were also used for RNA extraction in a subset of the human tumors (n=9 patients, 18 paired samples) using the RNeasy FFPE kit from Qiagen (catalog # 73504). The SensationPlus 3' IVT A&L FFPE kit was used for the labeling and amplification of the RNA (Affymetrix, Inc. catalog # 902028). The Almac Xcel™ Array was used for profiling of the FFPE samples (Affymetrix, Inc. catalog # 902016). The Xcel™arrays provide a 3’ gene expression array designed and optimized for use with FFPE tissues with probe sets for over 97,000 transcripts. The RNA Gene expression estimates were obtained using the Robust Multi-array Average (RMA) algorithm. Next, gene filtering was performed to select the top 10% of the probe sets with the highest coefficient of variation across all 18 samples. Paired samples t-tests were performed using the Bioconductor limma package (13) to identify differentially expressed probe sets caused by radiation. Probe sets with q-values less than 5% were selected as differentially expressed.
Formalin fixed and paraffin-embedded (FFPE) samples were obtained at the time of diagnosis. Patients then received a single large dose of radiation to the intact tumor and proceeded to surgical resection within 10 days of treatment. A second post-radiation sample was obtained at the time of surgical excision.
1243


title: Patient 10 - 6832_pre

description:
Microarray analysis of human samples. The same FFPE samples were also used for RNA extraction in a subset of the human tumors (n=9 patients, 18 paired samples) using the RNeasy FFPE kit from Qiagen (catalog # 73504). The SensationPlus 3' IVT A&L FFPE kit was used for the labeling and amplification of the RNA (Affymetrix, Inc. catalog # 902028). The Almac Xcel™ Array was used for profiling of the FFPE samples (Affymetrix, Inc. catalog # 902016). The Xcel™arrays provide a 3’ gene expression array designed and optimized for use with FFPE tissues with probe sets for over 97,000 transcripts. The RNA Gene expression estimates were obtained using the Robust Multi-array Average (RMA) algorithm. Next, gene filtering was performed to select the top 10% of the probe sets with the highest coefficient of variation across all 18 samples. Paired samples t-tests were performed using the Bioconductor limma package (13) to identify differentially expressed probe sets caused by radiation. Probe sets with q-values less than 5% were selected as differentially expressed.
Formalin fixed and paraffin-embedded (FFPE) samples were obtained at the time of diagnosis. Patients then received a single large dose of radiation to the intact tumor and proceeded to surgical resection within 10 days of treatment. A second post-radiation sample was obtained at the time of surgical excision.
6832


title: Patient 07 - 1995_pre

description:
Microarray analysis of human samples. The same FFPE samples were also used for RNA extraction in a subset of the human tumors (n=9 patients, 18 paired samples) using the RNeasy FFPE kit from Qiagen (catalog # 73504). The SensationPlus 3' IVT A&L FFPE kit was used for the labeling and amplification of the RNA (Affymetrix, Inc. catalog # 902028). The Almac Xcel™ Array was used for profiling of the FFPE samples (Affymetrix, Inc. catalog # 902016). The Xcel™arrays provide a 3’ gene expression array designed and optimized for use with FFPE tissues with probe sets for over 97,000 transcripts. The RNA Gene expression estimates were obtained using the Robust Multi-array Average (RMA) algorithm. Next, gene filtering was performed to select the top 10% of the probe sets with the highest coefficient of variation across all 18 samples. Paired samples t-tests were performed using the Bioconductor limma package (13) to identify differentially expressed probe sets caused by radiation. Probe sets with q-values less than 5% were selected as differentially expressed.
Formalin fixed and paraffin-embedded (FFPE) samples were obtained at the time of diagnosis. Patients then received a single large dose of radiation to the intact tumor and proceeded to surgical resection within 10 days of treatment. A second post-radiation sample was obtained at the time of surgical excision.
1995


title: Patient 05 - 3332_post

description:
Microarray analysis of human samples. The same FFPE samples were also used for RNA extraction in a subset of the human tumors (n=9 patients, 18 paired samples) using the RNeasy FFPE kit from Qiagen (catalog # 73504). The SensationPlus 3' IVT A&L FFPE kit was used for the labeling and amplification of the RNA (Affymetrix, Inc. catalog # 902028). The Almac Xcel™ Array was used for profiling of the FFPE samples (Affymetrix, Inc. catalog # 902016). The Xcel™arrays provide a 3’ gene expression array designed and optimized for use with FFPE tissues with probe sets for over 97,000 transcripts. The RNA Gene expression estimates were obtained using the Robust Multi-array Average (RMA) algorithm. Next, gene filtering was performed to select the top 10% of the probe sets with the highest coefficient of variation across all 18 samples. Paired samples t-tests were performed using the Bioconductor limma package (13) to identify differentially expressed probe sets caused by radiation. Probe sets with q-values less than 5% were selected as differentially expressed.
Formalin fixed and paraffin-embedded (FFPE) samples were obtained at the time of diagnosis. Patients then received a single large dose of radiation to the intact tumor and proceeded to surgical resection within 10 days of treatment. A second post-radiation sample was obtained at the time of surgical excision.
3332


title: Patient 06 - 1348_post

description:
Microarray analysis of human samples. The same FFPE samples were also used for RNA extraction in a subset of the human tumors (n=9 patients, 18 paired samples) using the RNeasy FFPE kit from Qiagen (catalog # 73504). The SensationPlus 3' IVT A&L FFPE kit was used for the labeling and amplification of the RNA (Affymetrix, Inc. catalog # 902028). The Almac Xcel™ Array was used for profiling of the FFPE samples (Affymetrix, Inc. catalog # 902016). The Xcel™arrays provide a 3’ gene expression array designed and optimized for use with FFPE tissues with probe sets for over 97,000 transcripts. The RNA Gene expression estimates were obtained using the Robust Multi-array Average (RMA) algorithm. Next, gene filtering was performed to select the top 10% of the probe sets with the highest coefficient of variation across all 18 samples. Paired samples t-tests were performed using the Bioconductor limma package (13) to identify differentially expressed probe sets caused by radiation. Probe sets with q-values less than 5% were selected as differentially expressed.
Formalin fixed and paraffin-embedded (FFPE) samples were obtained at the time of diagnosis. Patients then received a single large dose of radiation to the intact tumor and proceeded to surgical resection within 10 days of treatment. A second post-radiation sample was obtained at the time of surgical excision.
1348