title: MCF-7 miR-644 (replicate 2)

city: Basel

first: Jitao David

address: Grenzacherstrasse 124

department: Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel

country: Switzerland

institute: F. Hoffmann-La Roche

description:
MCF-7 miR-644  treated with miR-644
BT_644_2_5504654026_F

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: MCF-7 miR-644

label_protocol: Standard protocol of TargetAmp-Nano Labeling Kit

growth_protocol: SK-BR-3 cells were cultured in McCoy's 5a medium (GIBCO BRL). MDA-MB-231 cells were cultured in Leibovitz's L-15 medium (Sigma). MCF-7 cells were cultured in Eagle's Minimial essential medium, All media were supplemented with 50 U/mL penicillin, 50 μg/mL streptomycin sulphate, 1% non-essential amino acids and 10% fetal bovine serum (all media and supplements from Gibco BRL). Additionally, 2.2 g/L sodium bicarbonate was supplemented for MDA-MB-231 cells. In media for MCF-7 cells we added 0.01 mg/mL bovine insulin. The cells were incubated at 37°C with 5% CO2 and split 2–3 times per week in a 1:3 ratio for no more than 20 passages. All cell lines were validated by genotyping.

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

treatment_protocol: Scramble control and miR-644 mimic was transfected using lipofectamin.

tag: microrna mimic


title: hMSC K line in NSS

status: Public on Jul 25 2016

type: RNA

city: Daejeon

first: Bic-Na

last: Song

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea

department: Korean Bioinformation Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

description:
Sample name: 13_K
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Array data processin were performed on Illumina GenomeStudio software.  We normalized gene expression data using Quantile normalization and log2 transformation.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: human bone marrow_non-stimulatory serum

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX).

growth_protocol: MSC cultures were established from BM mononuclear cells and passaged in the Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS) (stimulatory (SS) serum and non-stimulatory (NSS) serums). MSCs that had been maintained in each culture media were sub-cultured for at least two passages before analysis.

extract_protocol: Total RNA was isolated from tissues with TRIzol (Life Technologies, NY) reagent according to the manufacturer's protocol.

tag: gender

value: Female

tag: age

tag: tissue

value: Bone marrow

tag: cell line

value: K


title: LacZ knockdown MCF-7 (clone#112)

city: Kyotanabe

first: Tsuyoshi

last: Waku

address: 1-3 Tatara Miyakodani

country: Japan

institute: Doshisha University

description: Sample data of shLacZ clone

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

scan_protocol: GeneChips were scanned using the AFFYMETRIX GeneChip Scanner GCS3000.

data_processing: The data were analyzed using GeneSpring software with the default settings.

source_name: LacZ knockdown MCF-7, isolated

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

growth_protocol: MCF-7 cells were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (FBS).

extract_protocol: Total RNA was extracted using Fast pure RNA kit (TAKARA) according to the manufacturer's instructions.

treatment_protocol: MCF-7 cells were incubated with the shCHIP- or shLacZ-containing retroviral supernatant in the presence of 8 μg/ml polybrene.  Twenty-four hours after infection, the viral supernatant was replaced with fresh DMEM containing 10% FBS.  The infected cells were selected with 1 mg/ml G418.  Clones were isolated from shLacZ or shCHIP cells.

tag: treatment

value: LacZ knockdown


title: hMSC K line in SS

description:
Sample name: 97_K
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.

source_name: human bone marrow_stimulatory serum


title: hMSC G line in SS

description:
Sample name: 97_G
To export to gene expression data based on probe ID, we use Sample Probe Profile option of Illumina GenomeStudio software.

value: Male

value: G


title: full term delivery sample 5

type: genomic

city: Honolulu

first: Dongmei

last: Li

state: HI

address: 1960 East-West Road

country: USA

institute: University of Hawaii at Manoa

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio Normalized data by background substraction and controls GSR

label: Cy5 and Cy3

molecule: genomic DNA

source_name: placental tissue from decidual membrane rolls of previously formalin fixed sample

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

value: placenta


title: MCF-7 miR-644 (replicate 1)

last: Zhang

description:
MCF-7 miR-644  treated with miR-644
BT_644_1_5504654026_E


title: LacZ knockdown MCF-7 (clone#10)

description: Sample data of shLacZ clone


title: full term delivery sample 4


title: LacZ knockdown MCF-7 (bulk_2)

description: Control data to compare with each shLacZ clone.

source_name: LacZ knockdown MCF-7, non-isolated (bulk)


title: full term delivery sample 2


title: LacZ knockdown MCF-7 (bulk_1)


title: SK-BR-3 miR-644 (replicate 1)

description:
SK-BR-3 miR-644  treated with miR-644
SK_644_1_5504654026_C

source_name: SK-BR-3 miR-644


title: preterm delivery sample 3


title: SK-BR-3 miR-644 (replicate 2)

description:
SK-BR-3 miR-644  treated with miR-644
SK_644_2_5504654026_D


title: full term delivery sample 3


title: MCF-7 control (replicate 1)

description:
MCF-7 control  treated with control
BT_Ctrl_1_5504654026_K

source_name: MCF-7 control

value: control


title: CHIP knockdown MCF-7 (clone#137)

description: Sample data of shCHIP clone

source_name: CHIP knockdown MCF-7, isolated

value: CHIP knockdown


title: CHIP knockdown MCF-7 (clone#134)

description: Sample data of shCHIP clone


title: MCF-7 control (replicate 2)

description:
MCF-7 control  treated with control
BT_Ctrl_2_5504654026_L


title: SK-BR-3 control (replicate 2)

description:
SK-BR-3 control  treated with control
SK_Ctrl_2_5504654026_J

source_name: SK-BR-3 control


title: preterm delivery sample 2


title: CHIP knockdown MCF-7 (clone#130)

description: Sample data of shCHIP clone


title: preterm delivery sample 4


title: CHIP knockdown MCF-7 (clone#141)

description: Sample data of shCHIP clone


title: full term delivery sample 1


title: CHIP knockdown MCF-7 (clone#123)

description: Sample data of shCHIP clone


title: MDA-MB-231 miR-644 (replicate 1)

description:
MDA-MB-231 miR-644  treated with miR-644
MDA_644_1_5504654026_A


title: MDA-MB-231 miR-644 (replicate 2)

description:
MDA-MB-231 miR-644  treated with miR-644
MDA_644_2_5504654026_B


title: SK-BR-3 control (replicate 1)

description:
SK-BR-3 control  treated with control
SK_Ctrl_1_5504654026_I


title: MDA-MB-231 control (replicate 1)

description:
MDA-MB-231 control  treated with control
MDA_Ctrl_1_5504654026_G

source_name: MDA-MB-231 control


title: preterm delivery sample 1

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the Illumina HumanMethylation450 Beadchip using standard Illumina protocol


title: CHIP knockdown MCF-7 (clone#122)

description: Sample data of shCHIP clone


title: CHIP knockdown MCF-7 (clone#115)

description: Sample data of shCHIP clone


title: Candida albicans orf19.5100 KO_6hr_biological rep 2

city: New Delhi

first: Nitesh

middle: Kumar

last: Khandelwal

state: Delhi

address: Near Munirka

department: School of Life Sciences

country: India

institute: Jawaharlal Nehru University

description: Gene expression after 6hr in orf19.5100 KO Candida albicans cells

hyb_protocol: The labeled cRNA samples were hybridized on to a Custom Agilent Candida albicans 8x15k Microarray Gene expression  (AMADID: 026377) designed by Genotypic Technology Private Limited. 600ng of cy3 labeled samples were  fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned using the Agilent Microarray Scanner (AgilentTechnologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX Software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift ( Gene based Analysis was performed)

organism: Candida albicans

source_name: Candida albicans cells

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: C.albicans strains were grown over night in YEPD in biological duplicates. From primary cultures, cells of  0.2 OD600 were inoculated in 15 ml YEPD and allowed to grow for  6 hrs to reach log phase

extract_protocol: RNA was extracted using the Qiagen RNeasy mini kit following the manufacturer's recommendations.

tag: genotype


title: PlusGATA6L_PlusTNF_2

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

institute: University of Virginia

description: HT-29 TetTight-GATA6L neo; 1 µg/ml doxycycline for 24 hr, 100 ng/ml TNF for 2 hr, replicate #2

hyb_protocol: Complementary RNA was hybridized to a HumanHT-12 v4 Expression BeadChip (Illumina) according to the manufacturer's recommendation.

scan_protocol: BeadChip was scanned using an iScan (Illumina) according to the manufacturer's recommendations.

data_processing: The data were processed as variance-stabilized (approximately log2) transformed values with the Bioconductor package lumi (Bioinformatics 24:1547-8 [2008]).

label: Biotin

source_name: HT-29 colon adenocarcinoma cells sensitized with 200 U/ml interferon-gamma for 24 hr

label_protocol: Biotin-labeled complementary RNA was synthesized with the T7-based TotalPrep-96 RNA Amplification kit (Illumina) according to the manufacturer's recommendation.

growth_protocol: HT-29 cells were grown according to ATCC recommendations, plated at 50,000 cells/cm2 for 24 hr, and sensitized with 200 U/ml interferon-gamma with or without 1 µg/ml doxycycline for 24 hr before treatment.

extract_protocol: RNA was isolated with the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer's recommendation, and RNA purity was assessed by absorbance.

treatment_protocol: Cells were stimulated with 0 or 100 ng/ml TNF for 2 hr.

tag: cell type

value: colon adenocarcinoma


title: PlusGATA6L_PlusTNF_4

description: HT-29 TetTight-GATA6L neo; 1 µg/ml doxycycline for 24 hr, 100 ng/ml TNF for 2 hr, replicate #4


title: MDA-MB-231 control (replicate 2)

description:
MDA-MB-231 control  treated with control
MDA_Ctrl_2_5504654026_H


title: Candida albicans WT_6hr_biological rep 1

description: Gene expression after 6hr in SC5314 Candida albicans cells

value: wild type


title: PlusGATA6L_PlusTNF_3

description: HT-29 TetTight-GATA6L neo; 1 µg/ml doxycycline for 24 hr, 100 ng/ml TNF for 2 hr, replicate #3


title: PlusGATA6L_PlusTNF_1

description: HT-29 TetTight-GATA6L neo; 1 µg/ml doxycycline for 24 hr, 100 ng/ml TNF for 2 hr, replicate #1


title: Candida albicans WT_6hr_biological rep 2


title: CHIP knockdown MCF-7 (clone#124)

description: Sample data of shCHIP clone


title: CHIP knockdown MCF-7 (bulk_1)

description: Control data to compare with each shCHIP clone.

source_name: CHIP knockdown MCF-7, non-isolated (bulk)


title: PlusGATA6L_NoTNF_2

description: HT-29 TetTight-GATA6L neo; 1 µg/ml doxycycline for 24 hr, 0 ng/ml TNF for 2 hr, replicate #2


title: PlusGATA6L_NoTNF_1

description: HT-29 TetTight-GATA6L neo; 1 µg/ml doxycycline for 24 hr, 0 ng/ml TNF for 2 hr, replicate #1


title: NoGATA6L_PlusTNF_3

description: HT-29 TetTight-GATA6L neo; 0 µg/ml doxycycline for 24 hr, 100 ng/ml TNF for 2 hr, replicate #3


title: PlusGATA6L_NoTNF_3

description: HT-29 TetTight-GATA6L neo; 1 µg/ml doxycycline for 24 hr, 0 ng/ml TNF for 2 hr, replicate #3


title: CHIP knockdown MCF-7 (bulk_2)


title: NoGATA6L_PlusTNF_4

description: HT-29 TetTight-GATA6L neo; 0 µg/ml doxycycline for 24 hr, 100 ng/ml TNF for 2 hr, replicate #4


title: NoGATA6L_PlusTNF_2

description: HT-29 TetTight-GATA6L neo; 0 µg/ml doxycycline for 24 hr, 100 ng/ml TNF for 2 hr, replicate #2


title: Candida albicans orf19.5100 KO_6hr_biological rep 1


title: CHIP knockdown MCF-7 (clone#109)

description: Sample data of shCHIP clone


title: NoGATA6L_PlusTNF_1

description: HT-29 TetTight-GATA6L neo; 0 µg/ml doxycycline for 24 hr, 100 ng/ml TNF for 2 hr, replicate #1


title: NoGATA6L_NoTNF_4

description: HT-29 TetTight-GATA6L neo; 0 µg/ml doxycycline for 24 hr, 0 ng/ml TNF for 2 hr, replicate #4


title: NoGATA6L_NoTNF_1

description: HT-29 TetTight-GATA6L neo; 0 µg/ml doxycycline for 24 hr, 0 ng/ml TNF for 2 hr, replicate #1


title: Microarray-DE1

status: Public on Jul 24 2016

city: Beijing

first: Jinhua

last: Qin

address: Taiping Road

country: China

institute: Beijing Institute of Transfusion

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Array data were processed and analyzed by using Illumina BeadStudio software.

source_name: definitive endoderm cells differentiated from hESCs

label_protocol: Biotinylated cRNA was generated from total RNA by using the Illumina TotalPrep kit (Ambion) according to the manufacturer’s instruction.

growth_protocol: hGECs and hDECs were cultured in Kubota's medium. hiMESCs which were converted from hGECs/hDECs by small molecules were cultured in advanced DMEM/F12 with 2μM Bay K 8644, 0.5μM Bix01294 , 0.04μM RG108, 2μM SB431542. DEs were induced from hESCs in high Activin media. GSEMFs were cultured in Kubota's medium with 10% FBS.

extract_protocol: Total RNAs were prepared from hGECs,hDECs,hiMESCs, DEs,and GSEMFs using an RNeasy MiniKit (Qiagen) following the manufacturer's recommendations

treatment_protocol: hGECs,hDECs,DEs,and GSEMFs were collected after trypsinized with TrypLE. hiMESCs were collected by manual picking.

value: DE derived from hESCs


title: NoGATA6L_NoTNF_3

description: HT-29 TetTight-GATA6L neo; 0 µg/ml doxycycline for 24 hr, 0 ng/ml TNF for 2 hr, replicate #3


title: Microarray-DE3

description: replicate 3


title: Microarray-DE2

description: replicate 2


title: Microarray-GSEMF2

description: replicate 2

source_name: gastric stromal cells isolated from stomach

value: gastric subepithelial myofibroblasts


title: Microarray-DE4

description: replicate 4


title: Microarray-D-hiEndoPC2

description: replicate 2

source_name: hiMESCs derived from hDECs by reprogramming

value: hiMESCs generated by reprogramming


title: Microarray-G-hiEndoPC

description: replicate 1

source_name: hiMESCs derived from hGECs by reprogramming


title: Microarray-GSEMF3

description: replicate 3


title: Microarray-GSEMF1

description: replicate 1


title: Microarray-hDEC2

description: replicate 2

source_name: duodenum epthelial cells isolated from duodenum

value: primary epithelial cells


title: Microarray-hDEC1

description: replicate 1


title: Microarray-hGEC

description: replicate 1

source_name: gastric epthelial cells isolated from stomach


title: Microarray-D-hiEndoPC1

description: replicate 1


title: ANXA2_8

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

description: Gene expression data from primary GBM cells treated with an ANXA2 neutralizing antibody

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000.

data_processing: The data were normalized using R software [www.r-ptoject.org] with BioConductor package [www.bioconductor.org] using RMA

source_name: Primary Glioblastoma Cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng of Total RNA.

growth_protocol: GBM cells were cultured on fibronectin-coated dishes in DMEM/F12 medium supplemented with BIT9500, 20ng/ml basic Fibroblast Growth Factor and 20ng/ml Epidermal Growth Factor in an atmosphere of 2% oxygen, 5% carbon dioxide and balanced nitrogen in a Ruskinn C300 system for hypoxic cell culture.

extract_protocol: RNA was isolated from cultured cells treated with an isotype control or an ANXA2 neutralizing antibody using Trizol in 4 independent experiments

treatment_protocol: GBM cells were treated with an anti-ANXA2 monoclonal antibody or an Isotype control antibody at a final concentration of 20µg/ml and then cultured for 48 hours before total RNA extraction.

tag: antibody

value: antibody anti-ANXA2

value: primary glioblastoma cells


title: Artery constriction, biological rep3

first: Yiqiang

address: 651 Ilalo St BSB-311D

department: Anatomy, Biochemistry and Physiology

institute: University of Hawaii Manoa

description: Gene expression data in artery constriction SIE flap.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 19 hr at 45C on  GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 7G.

data_processing: The data were analyzed with Affymetrix Expression Console Software using Affymetrix default analysis settings and global scaling as normalization method.

organism: Rattus norvegicus

source_name: Flap from artery constriction

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (3' IVT Expression kit)

extract_protocol: Rneasy (Qiagen) Mini protocol, with Dnase I treatment.

treatment_protocol: SIE flaps were constricted in venous or artery or not (sham control group), for 4 hours before harvested for total RNA extraction.

value: superficial inferior epigastric flap

tag: group

value: artery constriction

value: male

tag: strain

value: Sprague Dawley

tag: constriction time


title: Artery constriction, biological rep4


title: Artery constriction, biological rep2


title: Artery constriction, biological rep1


title: ANXA2_7

description: Gene expression data from primary GBM cells treated with an isotype control antibody

value: isotype control


title: Artery constriction, biological rep5


title: ANXA2_6


title: ANXA2_5


title: ANXA2_4


title: ANXA2_3


title: ANXA2_1


title: ANXA2_2


title: Control, biological rep3

description: Gene expression data in sham operation SIE flap.

source_name: Flap from sham operation

value: sham operation


title: Venous constriction, biological rep3

description: Gene expression data in venous constriction SIE flap.

source_name: Flap from venous constriction

value: venous constriction


title: Control, biological rep1


title: F2 6M 46

city: Sao Paulo

first: Mariz

last: Vainzof

state: Sao Paulo

address: Rua do Matao, 106

department: Genetics and Evolutionary Biology

country: Brazil

institute: University of Sao Paulo

description: Hybrid of Dmdmdx with 129/Sv, generation F2.

hyb_protocol: Samples were hybridized with GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix).

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

data_processing: Data were analyzed with Expression Console (Affymetrix). Normalization was done with RMA method.

organism: Mus musculus

source_name: Hybrid of Duchenne muscular dystrophy model with 129/Sv normal mouse at generation F2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

growth_protocol: The calf muscles were dissected, rapidly frozen in liquid nitrogen and powdered using a pestle and mortar.

extract_protocol: Total RNA was extracted using RNeasy Kit (Qiagen, Hilden, Germany) following the manufacturer's instructions. Quantity and quality of RNA were assessed with NanoDrop 8000 Spectrophotometer (Thermo Scientific, Schwerte, Germany), agarose gel electrophoresis and integrity with Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany). Only samples with 260/280 ratio greater than 1.8, preserved rRNA 28S/18S ratio and RIN (RNA integrity number) >7.0 were used.

treatment_protocol: No treatment.

tag: strain/background

tag: genotype/variation

value: mdx

value: calf muscles

tag: Sex

value: 6 months


title: F3 6M 20C

description: Hybrid of Dmdmdx with 129/Sv, generation F3.

source_name: Hybrid of Duchenne muscular dystrophy model with 129/Sv normal mouse at generation F3


title: Venous constriction, biological rep4


title: Venous constriction, biological rep5


title: F3 6M 10C


title: F3 6M 11C


title: Venous constriction, biological rep2


title: Control, biological rep4


title: PlusGATA6L_NoTNF_4

description: HT-29 TetTight-GATA6L neo; 1 µg/ml doxycycline for 24 hr, 0 ng/ml TNF for 2 hr, replicate #4

value: colon adenocarcinoma


title: F1 6M 8

description: Hybrid of Dmdmdx with 129/Sv, generation F1.

source_name: Hybrid of Duchenne muscular dystrophy model with 129/Sv normal mouse at generation F1


title: F2 6M 45


title: Control, biological rep5


title: F2 6M 44


title: F1 6M 7


title: Venous constriction, biological rep1


title: 129 2

description: 129/Sv normal control

source_name: Normal mouse, 129/Sv

value: WT


title: 129 3

description: 129/Sv normal control


title: Ctl3

description: Adult mouse cardiomyocytes (Ctl)

hyb_protocol: NimbleGen Hybridization protocol

scan_protocol: NimbleGen MS 200 Microarray Scanner, HX1 (2.1M) format.

data_processing:
NimbleScan 2.6.0.0 (to produce .ndf, .pos, and .xys charm inputfiles), charm Bioconductor package
Values in the processed data file on the Series record represent CpG site percentage methylation calculated using the methp function from the 'charm' Bioconductor package (as described by Irizarry et al, PMID 18316654); includes quantile normalization between samples and loess normalization within samples

source_name: enzyme digestion

label_protocol: NimbleGen Dual-Color DNA Labeling Kits; untreated total DNA fraction was labeled with Cy3 and the methyl-depleted DNA fraction was labeled with Cy5.

growth_protocol: NA/Freshly isolated

extract_protocol: Genomic DNA isolated using Qiagen Dneasy Kit

value: adult mouse cardiomyocytes

source_name: INPUT

tag: sample type

value: reference


title: 129 1

description: 129/Sv normal control


title: MDX2 6m

description: Dmdmdx

source_name: Duchenne muscular dystrophy model


title: F1 6M 6


title: MDX3 6m

description: Dmdmdx


title: MDX1 6m

description: Dmdmdx


title: C57BL49 6m

description: C57BL/6 normal control

source_name: Normal mouse, C57BL/6


title: Ctl1

description: Adult mouse cardiomyocytes (Ctl)


title: CPC1

description: mouse myocyte-derived cardiac progenitor cells (CPC)

growth_protocol: Mitogen-rich medium for dedifferentiation/proliferation

value: cardiomyocyte-derived progenitor cells


title: MDX36 6m

description: Dmdmdx


title: CPC2


title: C57BL7 6m

description: C57BL/6 normal control


title: Ctl2

description: Adult mouse cardiomyocytes (Ctl)


title: CPC3


title: C57BL6 6m

description: C57BL/6 normal control


title: Normal tissue_pooled

city: Guangzhou

first: Weihua

last: Jia

state: Guangdong

institute: SYSUCC

description: pooled 10 normal esophageal tissues

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

scan_protocol: The hybridized arrays were washed, fixed and scanned with the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies).

source_name: normal esophageal tissue

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was extracted from ten tumor tissues and ten adjacent normal tissues with TRIzol® Reagent (Invitrogen life technologies). Each RNA sample was quantified using the NanoDrop ND-1000 and RNA integrity was assessed using denaturing agarose gel electrophoresis. The pooled tumor RNA sample was generated by mixing an equal amount of each tumor RNA. The pooled normal RNA sample was generated from the normal RNA using the same method.

value: pooled 10 normal esophageal tissues


title: Ctl3

description: Adult mouse cardiomyocytes (Ctl)

scan_protocol: NimbleGen MS 200 Microarray Scanner, HX3 (3x720k) format.

data_processing:
NimbleScan 2.6.0.0 (to produce .ndf, .pos, and .xys charm inputfiles), charm Bioconductor package
CpG site percentage methylation calculated using the methp function from the 'charm' Bioconductor package (as described by Irizarry et al, PMID 18316654); includes quantile normalization between samples and loess normalization within samples

growth_protocol: Freshly isolated


title: Ctl2

description: Adult mouse cardiomyocytes (Ctl)


title: MDX35 6m

description: Dmdmdx


title: Ctl1

description: Adult mouse cardiomyocytes (Ctl)


title: C57BL8 6m

description: C57BL/6 normal control


title: ESCC tissue _pooled

description: pooled 10 esophageal squamous cell carcinoma tissues


title: C57BL5 6m

description: C57BL/6 normal control


title: CPC3


title: CPC2


title: CPC1


title: Brain CD11b+ cells [08_WT-4]

status: Public on Jul 23 2016

city: NORTH CHICAGO

first: Rahul

last: Vijay

state: IL

address: 3333 GreenBay Road, BSB 2.450

department: Microbiology and Immunology

institute: Rosalind Franklin University

hyb_protocol: RNA for the microarray was processed using a NuGEN WT-Ovation Pico RNA Amplification System together with a NuGEN WT-Ovation Exon Module. Samples were hybridized and loaded onto Affymetrix Mouse gene 2.0. Arrays

scan_protocol: scanned with a HiScan bead array system, and data were collected using GeneChip Operating Software

data_processing: Data from Affymetrix Mouse gene 2.0 Expression BeadChip were normalized and median polished using Robust Multichip Average background correction with log2-adjusted values. After obtaining the log2 expression values for genes, significance testing was performed comparing the two groups (CD11b+ cells from brains of WT and DP1 KO mice). Significance of expression differences was assessed using a false discovery rate (FDR) cutoff of 0.05 and a twofold change. Analysis and visualization of data and pathway analysis were performed using PartekGS software and Ingenuity Pathway Analysis software.

source_name: Mouse Brain_3dpi

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

value: Brain

tag: agent


title: Brain CD11b+ cells [07_WT-3]


title: Brain CD11b+ cells [06_WT-2]


title: Brain CD11b+ cells [04_DP1_KO-4]

value: DP1 KO


title: Brain CD11b+ cells [02_DP1_KO-2]


title: Brain CD11b+ cells [05_WT-1]


title: Wild Type base crypt cells 2

city: New York

first: Loukia

last: Lili

state: NY

address: 770 Lexington Ave, 14-07 14th floor

department: Icahn School of Medicine at Mount Sinai

institute: The Institute for Next Generation Healthcare

description: replicate 2

data_processing: The data were normalised using quantile normalisation and log2 transformation with Illumina Genome Studio

source_name: epithelial cells from the base of the colonic crypt of wild-type mouse

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

extract_protocol: RNA extraction was performed with the Arcturus PicoPure RNA extraction kit (Applied Biosystems/Life Technologies) according to manufucturer's protocols, treated with DNase (Qiagen, Valencia, CA), and amplified twice using a Nugen WT-Ovation kit (San Carlos, CA). RNA integrity was confirmed by Agilent 2100 Bioanayzer (Santa Clara, CA).

value: 10-12 weeks

tag: cell population

value: crypt-base


title: Wild Type surface cells 2

description: replicate 2

source_name: epithelial cells from the surface of the colonic crypt of wild-type mouse

value: surface


title: Col upon normoxia 0h, biological rep2

first: Lujun

last: Yu

state: Guandong

address: xingangxilu 135

institute: Sun Yat-sen University

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, and the date were analyzed with Gene Spring Software

organism: Arabidopsis thaliana

source_name: leaves_normoxia 0h

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: plants grown under LD cycles (16 h light, 23C/8 h dark, 22C)

treatment_protocol: 4-week-old plants were submerged at depths of 5-10 cm under the water surface for 48 h under normal growth conditions (light and submergence; LS)

tag: ecotype

value: Columbia

value: 4-week old

value: normoxia 0h (untreated control)

value: leaves


title: Col upon hypoxia under light submergence for 48 h, biological rep1

source_name: leaves_hypoxia under light submergence for 48 h

tag: age


title: Col upon normoxia 0h, biological rep3

tag: tissue


title: Wild Type base crypt cells 4

description: replicate 4


title: Brain CD11b+ cells [03_DP1_KO-3]


title: Col upon hypoxia under light submergence for 48 h, biological rep3


title: Col upon normoxia 0h, biological rep1


title: Brain CD11b+ cells [01_DP1_KO-1]


title: NoGATA6L_NoTNF_2

description: HT-29 TetTight-GATA6L neo; 0 µg/ml doxycycline for 24 hr, 0 ng/ml TNF for 2 hr, replicate #2

source_name: HT-29 colon adenocarcinoma cells sensitized with 200 U/ml interferon-gamma for 24 hr

tag: cell line


title: S-miR-135a-3p

city: Fukuoka

first: Satoshi

last: Fukagawa

state: Fukuoka

address: 7-45-1 Nanakuma, Jonan-ku

department: Fuculty of Medicine

institute: Fukuoka University

description: target

hyb_protocol: Following fragmentation, 4.7 ug of cDNA were hybridized on the GeneChip Human Gene 2.0 ST Array using  the GeneChip Hybridization Oven 645. GeneChips were washed and stained in the  GeneChip Fluidics Station 450.

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

data_processing: The data were analyzed with Expression Console v1.4(Affymetrix) and Transcriptome Analysis Console v3.0 (Affymetrix). RMA was used as summarization algorithm.

label_protocol: cDNA synthesis, amplification and labeling were performed with WT PLUS Reagent Kit (Affymetrix).

extract_protocol: Total RNA extraction was performed by using RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer's instructions.

tag: miRNA

value: ovarian cancer


title: Wild Type surface cells 3

description: replicate 3


title: PTE_model_rep1

city: Nantong

first: Songshi

last: Ni

state: Jiangsu

address: No.20 Xisi Road Chongchuan District

department: Department of Respiratory Medicine

institute: Affiliated Hospital of Nantong University

description: Gene expression of pulmonary artery in a rabbit model of pulmonary thromboembolism

hyb_protocol: The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: The hybridized arrays were scanned by the Agilent Scanner G2505C.  A total of 8 RNA samples (4 control samples and 4 experimental samples) were analyzed by the expression microarray.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 4 out of 8 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance were identified through Volcano Plot filtering.Finally, Hierarchical Clustering was performed to show the distinguishable gene expression profiling between samples.

organism: Oryctolagus cuniculus

source_name: Pulmonary artery, acute pulmonary thromboembolism, replicate 1

label_protocol: The sample preparation and microarray hybridization were performed according to the manufacturer’s standard protocols. Briefly, total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies). The labeled cRNAs were hybridized onto the Whole Rabbit Genome Oligo Microarray covering 14,765 genes (4x44K, Agilent Technologies).

growth_protocol: Twenty healthy China big-ear rabbits, specific-pathogen-free (SPF) grade and weighing between 2.5 and 3 kg, were purchased from the Center of experimental animals of the Nantong University.

extract_protocol: RNA was isolated from frozen pulmonary artery using the Trizol method.  Total RNA from each sample was quantified using the NanoDrop ND-1000 and the RNA integrity was assessed using standard denaturing agarose gel electrophoresis.

treatment_protocol: In the experimental group, the blood clot in 10 mL of saline was injected into the femoral vein. An additional 5 mL of saline were used to flush the catheter. In the control group, 15 mL of saline were injected into the femoral vein.

value: pulmonary artery


title: Col upon hypoxia under light submergence for 48 h, biological rep2

tag: treatment


title: Wild Type base crypt cells 3

description: replicate 3


title: PTE_model_rep2

source_name: Pulmonary artery, acute pulmonary thromboembolism, replicate 2


title: PTE_model_rep3

source_name: Pulmonary artery, acute pulmonary thromboembolism, replicate 3


title: S-miR-blank

description: control

value: miR-blank


title: PTE_control_rep4

description: Gene expression of pulmonary artery in a normal rabbitthromboembolism

source_name: Pulmonary artery, untreated, replicate 4


title: Wild Type surface cells 1

description: replicate 1


title: PTE_control_rep3

source_name: Pulmonary artery, untreated, replicate 3


title: Wild Type base crypt cells 1

description: replicate 1


title: O-miR-135a-3p

description: target


title: PTE_model_rep4

source_name: Pulmonary artery, acute pulmonary thromboembolism, replicate 4


title: Wild Type surface cells 4

description: replicate 4


title: Sѐzary syndrome tumour 15

status: Public on Jul 22 2016

city: London

first: Venu

middle: Madhav

last: Pullabhatla

address: Great Maze Pond

department: Guy's Hospital

country: United Kingdom

institute: Biomedical Research Centre

hyb_protocol: Standard illumina hybridization protocol

scan_protocol: Arrays were imaged using Illumina's iScan System using standard recommended Illumina scanner setting

data_processing:
The iDat files were processed using custom illumina Genome Studio software using default parameters (Gen Call Threshold = 0.15) using the manifest file provided by manufacturer. The cluster positions were imported using the EGT file provided by illumina. The data was imported using the import data option provided by the software.
Genotype: AA,AB,BB,or NC (No Call), Score, Thera, R, B Allele, Log R Ratio

label: C-Bio and A-DNP

source_name: Sѐzary syndrome

label_protocol: Standard illumina labelling protocol

growth_protocol: No growth protocol was applied, samples were extracted directly from patient blood samples.

extract_protocol: CD4+ enrichment was performed using Rosettesep and lymphoprep and genomic DNA extraction by proteinase K and phenol chloroform

treatment_protocol: No treatment was performed on extracted DNA

tag: cell type

value: PBMC


title: Sѐzary syndrome tumour 16


title: Sѐzary syndrome tumour 14


title: Sѐzary syndrome tumour 13


title: Sѐzary syndrome tumour 12


title: Sѐzary syndrome tumour 11


title: Sѐzary syndrome tumour 10


title: Sѐzary syndrome tumour 9


title: Sѐzary syndrome tumour 8


title: Sѐzary syndrome tumour 5


title: Sѐzary syndrome tumour 7


title: Sѐzary syndrome tumour 6


title: Sѐzary syndrome tumour 4


title: Sѐzary syndrome tumour 2


title: E-miR-blank

description: control


title: O-miR-blank

description: control


title: PTE_control_rep1

source_name: Pulmonary artery, untreated, replicate 1


title: E-miR-135a-3p

description: target


title: Sѐzary syndrome tumour 1


title: PTE_control_rep2

source_name: Pulmonary artery, untreated, replicate 2


title: MCF10A.B2 shRNA Pak1 cells #2

city: Tlalnepantla

first: Luis

middle: E.

last: Arias-Romero

address: Avenida de los Barrios #1

country: Mexico

institute: UBIMED

description: Gene expression of Pak1 deficient cells #2

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) 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: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95) and Grid: 026652_D_F_20110325).  Mean Signals (without background subtraction) were quantile normalized. The following probes were removed: (i) Control probes; (ii) Probes which were absent across all arrays (gIsPosAndSignif, gIsWellAboveBG, and gIsFound not all TRUE); (iii) Probes flagged as Saturated, feature non-uniform or population outliers in any array; (iv) Probes lacking an Entrez identifier.

source_name: human breast epithelial cell line

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: Cells were grown in DMEM/F12 plus 5% horse serum

extract_protocol: RNA was extracted with Rneasymini kit (QIAGEN) following the manufacturer's recommendations.

treatment_protocol: serum starved by 3 hr and stimulated with AP1510 crosslinker (to promote Her2 activation) 15 min

tag: diagnosis

value: breast cancer

value: shRNA targeting Pak1


title: Her2 positive : Pak1 +/+ cells #2

description: Gene expression of Pak1 +/+ cells #2

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95) and Grid: 026655_D_F_20100123).  Mean Signals (without background subtraction) were quantile normalized. The following probes were removed: (i) Control probes; (ii) Probes which were absent across all arrays (gIsPosAndSignif, gIsWellAboveBG, and gIsFound not all TRUE); (iii) Probes flagged as Saturated, feature non-uniform or population outliers in any array; (iv) Probes lacking an Entrez identifier.

source_name: Tumor derived breast cancer cells from MMTV-Neu Pak1 wt mice

growth_protocol: Cells were grown in Low Calcium media plus 5% horse serum

treatment_protocol: serum starved by 3 hr and stimulated with EGF 15 min


title: MCF10A.B2 control cells #2

description: Gene expression of Pak1 wild type cells #2

value: Ctrl


title: Her2 positive : Pak1 -/- cells #2

description: Gene expression of Pak1 -/- cells #2

source_name: Tumor derived breast cancer cells from MMTV-Neu Pak1 KO mice


title: MCF10A.B2 control cells #1

description: Gene expression of Pak1 wild type cells #1


title: MCF10A.B2 shRNA Pak1 cells #1

description: Gene expression of Pak1 deficient cells #1


title: Her2 positive : Pak1 -/- cells #1

description: Gene expression of Pak1 -/- cells #1


title: Her2 positive : Pak1 +/+ cells #1

description: Gene expression of Pak1 +/+ cells #1


title: CG4EPOR 5A_EPO+LIF_1h_rep1

city: Brighton

first: Pietro

last: Ghezzi

address: BSMS Teaching Building

institute: Brighton & Sussex Medical School

description: Gene expression in EPO+LIF-treated differentiating cells at 1h

hyb_protocol: Amplified labeled RNA was hybridised onto Single Colour SurePrint G3 Rat GE 8x60K Microarrays (AMADID:028279; Agilent)

scan_protocol: Slides were scanned immediately after washing on the Agilent C microarray Scanner (G2505B) for G3 microarray format scan setting for 8 X 60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Red and Green PMT).

data_processing: The scanned images were analysed with Feature Extraction software v10.7.3.1 to generate the array data from the images

source_name: CG4EPOR cells, 1h, EPO+LIF, replicate 1

label_protocol: RNA was amplified and labeled with Cyanine-3 (Cy3)

growth_protocol: CG4-EPOR cells were cultured in growth medium (DMEM+N1+FGF 5ng/ml+PDGF 1ng/ml+biotin 10ng/ml+B104-conditioned medium 30%), then differentiated in differentiation medium (DMEM/F12+progesterone 3ng/ml+putrescine 5µg/ml+sodium selenite 4µg/ml+insulin 12.5µg/ml+transferrin 50µg/ml+biotin 10ng/ml+thyroxine 0.4µg/ml+glucose 0.3%). The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Cells were lysed with QIAzol (QIAGEN) and total RNA was extracted by using the miRNeasy system and protocol (QIAGEN)

treatment_protocol: Cells were treated with EPO 10ng/ml, LIF 0.2ng/ml, LIF 10ng/ml or the combination of EPO and LIF both at 10 ng/ml for 1h and 20h.

value: rat glial precursor cell line


title: CG4EPOR 10A_EPO+LIF_20h_rep1

description: Gene expression in EPO+LIF-treated differentiating cells at 20h

source_name: CG4EPOR cells, 20h, EPO+LIF, replicate 1


title: CG4EPOR 10B_EPO+LIF_20h_rep2

source_name: CG4EPOR cells, 20h, EPO+LIF, replicate 2


title: CG4EPOR 5B_EPO+LIF_1h_rep2

source_name: CG4EPOR cells, 1h, EPO+LIF, replicate 2


title: CG4EPOR 9A_LIF_20h_rep1

description: Gene expression in  LIF-treated differentiating cells at 20h

source_name: CG4EPOR cells, 20h, LIF, replicate 1


title: CG4EPOR 6A_ctr_20h_rep1

description: Gene expression in differentiating cells at 20h

source_name: CG4EPOR cells, 20h, control, replicate 1


title: CG4EPOR 7A_EPO_20h_rep1

description: Gene expression in  EPO-treated differentiating cells at 20h

source_name: CG4EPOR cells, 20h, EPO, replicate 1


title: CG4EPOR 1A_ctr_1h_rep1

description: Gene expression in differentiating cells at 1h

source_name: CG4EPOR cells, 1h, control, replicate 1


title: CG4EPOR 5C_EPO+LIF_1h_rep3

source_name: CG4EPOR cells, 1h, EPO+LIF, replicate 3


title: CG4EPOR 2A_EPO_1h_rep1

description: Gene expression in  EPO-treated differentiating cells at 1h

source_name: CG4EPOR cells, 1h, EPO, replicate 1


title: CG4EPOR 10C_EPO+LIF_20h_rep3

source_name: CG4EPOR cells, 20h, EPO+LIF, replicate 3


title: CG4EPOR 7B_EPO_20h_rep2

source_name: CG4EPOR cells, 20h, EPO, replicate 2


title: Sѐzary syndrome tumour 3

source_name: Sѐzary syndrome


title: CG4EPOR 6B_ctr_20h_rep2

source_name: CG4EPOR cells, 20h, control, replicate 2


title: CG4EPOR 9B_LIF_20h_rep2

source_name: CG4EPOR cells, 20h, LIF, replicate 2


title: CG4EPOR 7C_EPO_20h_rep3

description: Gene expression in EPO-treated differentiating cells at 20h

source_name: CG4EPOR cells, 20h, EPO, replicate 3


title: CG4EPOR 2C_EPO_1h_rep3

source_name: CG4EPOR cells, 1h, EPO, replicate 3


title: CG4EPOR 1B_ctr_1h_rep2

source_name: CG4EPOR cells, 1h, control, replicate 2


title: CG4EPOR 4A_LIF_1h_rep1

description: Gene expression in  LIF-treated differentiating cells at 1h

source_name: CG4EPOR cells, 1h, LIF, replicate 1


title: CG4EPOR 6C_ctr_20h_rep3

source_name: CG4EPOR cells, 20h, control, replicate 3


title: CG4EPOR 1C_ctr_1h_rep3

source_name: CG4EPOR cells, 1h, control, replicate 3


title: CG4EPOR 9C_LIF_20h_rep3

source_name: CG4EPOR cells, 20h, LIF, replicate 3


title: CG4EPOR 4B_LIF_1h_rep2

source_name: CG4EPOR cells, 1h, LIF, replicate 2


title: CG4EPOR 11A_undif_rep1

description: Gene expression in undifferentiated cells

source_name: CG4EPOR cells, undifferentiated, replicate 1


title: CG4EPOR 3B_LIFlow_1h_rep2

description: Gene expression in LIFlow-treated differentiating cells at 1h

source_name: CG4EPOR cells, 1h, LIFlow, replicate 2


title: CG4EPOR 8B_LIFlow_20h_rep2

description: Gene expression in LIFlow-treated differentiating cells at 20h

source_name: CG4EPOR cells, 20h, LIFlow, replicate 2


title: CG4EPOR 5D_EPO+LIF_1h_rep4

source_name: CG4EPOR cells, 1h, EPO+LIF, replicate 4


title: CG4EPOR 2B_EPO_1h_rep2

source_name: CG4EPOR cells, 1h, EPO, replicate 2


title: CG4EPOR 4C_LIF_1h_rep3

source_name: CG4EPOR cells, 1h, LIF, replicate 3


title: CG4EPOR 3C_LIFlow_1h_rep3

source_name: CG4EPOR cells, 1h, LIFlow, replicate 3


title: Amyloidosis sample 111

city: Pamplona

first: Bruno

last: Paiva

address: Av. Pio XII, 55

country: Spain

institute: Clinica Universidad de Navarra

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

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

data_processing:
ChAS console from Affymetrix was used to assess genome wide copy number frequencies
primary data description: Weighted Log2 Ratios from ChAS console

source_name: Bone marrow

label_protocol: Labelling and hybridizations were performed according to protocols from Affymetrix

extract_protocol: not provided

value: Amyloidosis

value: Clonal plasma cells


title: Amyloidosis sample 127


title: Amyloidosis sample 164


title: Amyloidosis sample 17


title: CG4EPOR 4D_LIF_1h_rep4

source_name: CG4EPOR cells, 1h, LIF, replicate 4


title: p:DonS overexpression strain-mucin media rep1

city: Greenville

first: Charles

middle: Jeffrey

last: Smith

state: NC

address: 600 Moye Blvd.

department: Microbiology & Immunology

institute: East Carolina University

hyb_protocol: Hybridization was performed by at the FSU NimbleGen Microarray Facility, using standard protocols as described previously (Sund et al., 2008, Mol. Microbiol. 67:129-142)

scan_protocol: Scanning was performed by at the FSU NimbleGen Microarray Facility, using standard protocols as described previously (Sund et al., 2008, Mol. Microbiol. 67:129-142)

data_processing: Raw data (pair files) were subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185) using NimbleGen Systems DEVA 1.1 software as described on their web site.  The RMA processed data was averaged and log2 transformed (see *.calls files).

organism: Bacteroides fragilis 638R

source_name: grown in vitro to mid-log phase in defined media with mucin glycans

label_protocol: Labeling was performed by at the FSU NimbleGen Microarray Facility, using standard protocols as described previously (Sund et al., 2008, Mol. Microbiol. 67:129-142).

growth_protocol: Overnight cultures of Bacteroides fragilis 638R wild type strain or mutant strains were diluted into defined media containing 2% mucin glycans, and grown to mid-logarithmic phase at A550 of 0.5 ( Rocha et al. 1996, J. Bacteriol. 178:6895)

extract_protocol: Total RNA was isolated by the hot phenol method and treated as described by Sund et al, 2008, Mol. Microbiol.67:129-142.

tag: genotype

value: with p:DonS

tag: growth conditions

value: In vitro cultures grown in defined media with mucin glycans as sole carbon source


title: Amyloidosis sample 23


title: Amyloidosis sample 25


title: Amyloidosis sample 29


title: Amyloidosis sample 26


title: CG4EPOR 2D_EPO_1h_rep4

source_name: CG4EPOR cells, 1h, EPO, replicate 4


title: Amyloidosis sample 2


title: CG4EPOR 1D_ctr_1h_rep4

source_name: CG4EPOR cells, 1h, control, replicate 4


title: donS null mutant-mucin media rep1

value: donS null mutant


title: CG4EPOR 3D_LIFlow_1h_rep4

source_name: CG4EPOR cells, 1h, LIFlow, replicate 4


title: CG4EPOR 8C_LIFlow_20h_rep3

source_name: CG4EPOR cells, 20h, LIFlow, replicate 3


title: Control sample 12

value: Healthy

value: T lymphocytes


title: CG4EPOR 11B_undif_rep2

source_name: CG4EPOR cells, undifferentiated, replicate 2


title: Amyloidosis sample 197


title: Control sample 137


title: CG4EPOR 10D_EPO+LIF_20h_rep4

source_name: CG4EPOR cells, 20h, EPO+LIF, replicate 4


title: CG4EPOR 11C_undif_rep3

source_name: CG4EPOR cells, undifferentiated, replicate 3


title: CG4EPOR 6D_ctr_20h_rep4

source_name: CG4EPOR cells, 20h, control, replicate 4


title: CG4EPOR 7D_EPO_20h_rep4

source_name: CG4EPOR cells, 20h, EPO, replicate 4


title: Control sample 139


title: CG4EPOR 8D_LIFlow_20h_rep4

source_name: CG4EPOR cells, 20h, LIFlow, replicate 4


title: VeryLowDose 48h rep4

city: MASON

first: Jay

middle: Patrick

last: Tiesman

state: OH

address: PO BOX 8006

department: Global Biotechnology

institute: Procter & Gamble

description: Cells known to possess both estrogen and progesterone receptors

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on GeneChip Human U133plus2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1500.

source_name: Ishikawa Cell Line

label_protocol: Purified RNA was converted to cDNA target using SuperScript Choice system (Invitrogen Corp, Carlsbad, CA) and cDNA was converted to biotinylated cRNA probes using the ENZO BioArray transcript labeling kit (ENZO Life Sciences, Farmingdale, NY).

growth_protocol: Ishikawa cells were maintained and grown (to confluency or at a desired cell density between 500,000 - 1 million cells/mL) in DMEM/F-12 Medium (supplemented with 10% Fetal Bovine Serum + 1X penicillin/streptomycin) in xenoestrogen-free Corning plasticware.

extract_protocol: Total RNA was extracted using TRI-Reagent and protocol provided by supplier (Molecular Research Center, Cincinnati, OH).  Extracted RNA was further purified using Qiagen RNEasy columns and protocol provided by supplier (QIAgen, Valencia, CA).  Quadruplicate samples were advanced to target preparation and GeneChip processing.

treatment_protocol: Cells were gently washed in warm PBS and transferred to phenol red-free DMEM/F-12 Medium (supplemented with 10% Charcoal-Stripped Fetal Bovine Serum + 1X penicillin/streptomycin) in Corning Cell Culture Cluster wells overnight and then challenged with 10pM (very low, vL), 1nM (low, L), 100nM (high, H), and 1uM (very high, vH) levels of Genistein.  Prior to collection, cells were washed in warm PBS, resuspended & briefly incubated in TRI-Reagent, & finally collected (in quintuplicate replicates) at time each specific time point: 8 hours, 24 hours, and 48 hours.

value: 10 pM Genistein

tag: time period

value: 48 Hour Treatment

tag: source

value: cells derived from 39yo parous Japanese female diagnosed with endometrial adenocarcinoma stage 2


title: VeryLowDose 48h rep3


title: VeryLowDose 24h rep3

value: 24 Hour Treatment


title: VeryLowDose 48h rep1


title: Amyloidosis sample 8


title: Control sample 199


title: Control sample 3


title: Control sample 4


title: VeryLowDose 24h rep4


title: VeryLowDose 48h rep2


title: VeryLowDose 8h rep4

value: 8 Hour Treatment


title: VeryLowDose 24h rep1


title: Control sample 140


title: VeryLowDose 24h rep2


title: VeryHighDose 24h rep1

value: 10 uM Genistein


title: VeryLowDose 8h rep2


title: VeryHighDose 8h rep4


title: VeryLowDose 8h rep1


title: LowDose 24h rep3

value: 1 nM Genistein


title: VeryHighDose 48h rep2


title: LowDose 48h rep4


title: VeryHighDose 24h rep4


title: VeryHighDose 48h rep3


title: LowDose 8h rep1


title: VeryHighDose 8h rep3


title: VeryHighDose 24h rep3


title: LowDose 8h rep3


title: VeryLowDose 8h rep3


title: LowDose 24h rep1


title: VeryHighDose 48h rep4


title: VeryHighDose 8h rep1


title: LowDose 48h rep1


title: LowDose 8h rep2


title: LowDose 48h rep2


title: VeryHighDose 8h rep2


title: VeryHighDose 24h rep2


title: LowDose 8h rep4


title: LowDose 24h rep2


title: HighDose 48h rep4

value: 100 nM Genistein


title: LowDose 48h rep3


title: VeryHighDose 48h rep1


title: HighDose 48h rep3


title: HighDose 48h rep2


title: HighDose 24h rep3


title: HighDose 48h rep1


title: HighDose 8h rep4


title: Control 24h rep4

value: Vehicle Control


title: Control 48h rep2


title: HighDose 24h rep1


title: HighDose 24h rep2


title: Control 48h rep4


title: Control 24h rep2


title: Control 48h rep1


title: HighDose 24h rep4


title: LowDose 24h rep4


title: HighDose 8h rep2


title: HighDose 8h rep1


title: Control 24h rep3


title: Control 48h rep3


title: PBMC_3

city: Rennes

first: Colette

last: DESERT

address: 65 Rue de St Brieuc

country: France

institute: Agrocampus INRA UMR1348 PEGASE

description: Gene expression

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 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 custom 8 x 60K chicken gene expression microarray (GPL19630) 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 the Agilent DNA Mmicroarray scanner  using one color scan setting for 8x60k array slides (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.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Normalization was performed by centering on the median

organism: Gallus gallus

source_name: PBMC, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150ng RNA using the Low Input Quick Amp Labeling 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: Broilers were reared under standard conditions. They were fed a conventional diet ad libitum.

extract_protocol: Total RNA was extracted using TRIzol®. The quantity and quality of extracted RNA was evaluated using the NanoDrop ND-1000 spectrophotometer and the Agilent 2100 BioAnalyzer.

treatment_protocol: Peripheral blood mononucleated cells (PBMC) were  isolated, just after sampling by density gradient centrifugation (Ficoll Histopaque)

value: PBMC

tag: gender

value: male

value: 9 weeks old


title: Control 8h rep3


title: HighDose 8h rep3


title: PBMC_4

description: Gene expression

source_name: PBMC, replicate 4


title: PBMC_1

description: Gene expression

source_name: PBMC, replicate 1


title: Control 24h rep1


title: Control 8h rep4


title: Control 8h rep1


title: C98

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

institute: Juntendo University

description:
Gene expression profile of surgically resected material
C98

hyb_protocol: Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.

source_name: patient 098, cancer, LCM

label_protocol: cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).

treatment_protocol: Gene expression profiles for 152 cancer tissues from colorectal cancer patients were used.

tag: metastasis

value: distant metastasis

value: colorectal cancer


title: Control 8h rep2


title: PBMC_2

description: Gene expression

source_name: PBMC, replicate 2


title: Whole Blood_4

description: Gene expression

source_name: Peripheral Whole Blood, replicate 4

value: Whole blood


title: Whole Blood_2

description: Gene expression

source_name: Peripheral Whole Blood, replicate 2


title: Whole Blood_1

description: Gene expression

source_name: Peripheral Whole Blood, replicate 1


title: C99

description:
Gene expression profile of surgically resected material
C99

source_name: patient 099, cancer, LCM


title: C97

description:
Gene expression profile of surgically resected material
C97

source_name: patient 097, cancer, LCM


title: 2dsstimp1ko8_TIMP1KO_acute_DSS

city: Leuven

first: Ingrid

last: Arijs

address: Herestraat 49

department: Clinical and Experimental Medicine

country: Belgium

institute: KULeuven

description: Colonic gene expression data of TIMP1 knock out (KO) acute colitis mouse

hyb_protocol: After fragmentation of DNA, labeled DNA was hybridized for 16h at 45°C on Affymetrix mouse Gene 1.0 ST arrays.

scan_protocol: The arrays were washed and stained in a fluidics station using the GeneChip hybridization, Wash end Stain kit (Affymetrix) and scanned using the Affymetrix 3000 GeneScanner.

data_processing: Probe level analysis was performed on the Affymetrix raw data (.cel files) with the robust multichip average (RMA) method implemented in the Bioconductor package 'aroma.affymetrix' to obtain a log2 expression value for each gene probe set

label_protocol: Biotin-labeled single-stranded DNA was synthesized using the Affymetrix GeneChip WT terminal Labeling kit (Affymetrix), according to manufacturer's instructions.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Benelux B.V.), according to the manufacturer’s instructions.

treatment_protocol: Total RNA was isolated from snap frozen colon

tag: strain

tag: genotype/variation

value: B6.129S4-Timp1tm1Pds/J knock-out

tag: group


title: 2dsstimp1ko6_TIMP1KO_acute_DSS


title: C89

description:
Gene expression profile of surgically resected material
C89

source_name: patient 089, cancer, LCM


title: 7_WT_acute_control

description: Colonic gene expression data of wild type (WT) acute control mouse

value: wild-type


title: C95

description:
Gene expression profile of surgically resected material
C95

source_name: patient 095, cancer, LCM


title: C94

description:
Gene expression profile of surgically resected material
C94

source_name: patient 094, cancer, LCM


title: 8_WT_acute_control


title: C96

description:
Gene expression profile of surgically resected material
C96

source_name: patient 096, cancer, LCM


title: 2dsstimp1ko21_TIMP1KO_acute_control

description: Colonic gene expression data of TIMP1 knock out (KO) acute control mouse


title: 2dsstimp1ko24_TIMP1KO_acute_DSS


title: C86

description:
Gene expression profile of surgically resected material
C86

source_name: patient 086, cancer, LCM


title: C88

description:
Gene expression profile of surgically resected material
C88

source_name: patient 088, cancer, LCM


title: 26_WT_acute_DSS

description: Colonic gene expression data of wild type (WT) acute colitis mouse


title: 2dsstimp1ko2_TIMP1KO_acute_control


title: 24_WT_acute_DSS


title: C84

description:
Gene expression profile of surgically resected material
C84

source_name: patient 084, cancer, LCM


title: C82

description:
Gene expression profile of surgically resected material
C82

source_name: patient 082, cancer, LCM


title: 23_WT_acute_DSS


title: C78

description:
Gene expression profile of surgically resected material
C78

source_name: patient 078, cancer, LCM


title: C83

description:
Gene expression profile of surgically resected material
C83

source_name: patient 083, cancer, LCM


title: 27_WT_acute_DSS


title: C77

description:
Gene expression profile of surgically resected material
C77

source_name: patient 077, cancer, LCM


title: 2dsstimp1ko3_TIMP1KO_acute_control


title: 28_WT_acute_DSS


title: C90

description:
Gene expression profile of surgically resected material
C90

source_name: patient 090, cancer, LCM


title: 21_TIMP1KO_acute_DSS


title: 18_TIMP1KO_acute_DSS


title: C73

description:
Gene expression profile of surgically resected material
C73

source_name: patient 073, cancer, LCM


title: C72

description:
Gene expression profile of surgically resected material
C72

source_name: patient 072, cancer, LCM


title: 16_TIMP1KO_acute_DSS

description: Colonic gene expression data of TIMP1 knock out (KO) acute colitis mouse


title: 14e5_WT_chronic_control

description: Colonic gene expression data of wild type (WT) chronic control mouse


title: C68

description:
Gene expression profile of surgically resected material
C68

source_name: patient 068, cancer, LCM


title: C70

description:
Gene expression profile of surgically resected material
C70

source_name: patient 070, cancer, LCM


title: 14d5_TIMP1KO_chronic_control

description: Colonic gene expression data of TIMP1 knock out (KO) chronic control mouse


title: C64

description:
Gene expression profile of surgically resected material
C64

source_name: patient 064, cancer, LCM


title: 14e2_WT_chronic_control


title: C65

description:
Gene expression profile of surgically resected material
C65

source_name: patient 065, cancer, LCM


title: 14c5_TIMP1KO_chronic_DSS

description: Colonic gene expression data of TIMP1 knock out (KO) chronic colitis mouse


title: 14d4_2_TIMP1KO_chronic_control


title: 11g3_WT_chronic_control


title: 14a5_TIMP1KO_chronic_DSS


title: C63

description:
Gene expression profile of surgically resected material
C63

source_name: patient 063, cancer, LCM


title: C53

description:
Gene expression profile of surgically resected material
C53

source_name: patient 053, cancer, LCM


title: C61

description:
Gene expression profile of surgically resected material
C61

source_name: patient 061, cancer, LCM


title: C48

description:
Gene expression profile of surgically resected material
C48

source_name: patient 048, cancer, LCM


title: 14b4_TIMP1KO_chronic_control


title: 14a4_TIMP1KO_chronic_DSS


title: 14d3_TIMP1KO_chronic_control


title: 14b2_TIMP1KO_chronic_control


title: C59

description:
Gene expression profile of surgically resected material
C59

source_name: patient 059, cancer, LCM


title: 14a2_TIMP1KO_chronic_DSS


title: C46

description:
Gene expression profile of surgically resected material
C46

source_name: patient 046, cancer, LCM


title: C52

description:
Gene expression profile of surgically resected material
C52

source_name: patient 052, cancer, LCM


title: C45

description:
Gene expression profile of surgically resected material
C45

source_name: patient 045, cancer, LCM


title: C57

description:
Gene expression profile of surgically resected material
C57

source_name: patient 057, cancer, LCM


title: 14c4_TIMP1KO_chronic_DSS


title: C55

description:
Gene expression profile of surgically resected material
C55

source_name: patient 055, cancer, LCM


title: C42

description:
Gene expression profile of surgically resected material
C42

source_name: patient 042, cancer, LCM


title: 11e5_WT_chronic_DSS

description: Colonic gene expression data of wild type (WT) chronic colitis mouse


title: C44

description:
Gene expression profile of surgically resected material
C44

source_name: patient 044, cancer, LCM


title: 11e3_WT_chronic_DSS


title: C37

description:
Gene expression profile of surgically resected material
C37

source_name: patient 037, cancer, LCM


title: 11f4_WT_chronic_control

description: Colonic gene expression data of wild type (WT) chronic control mouse


title: 11g1_WT_chronic_control


title: C41

description:
Gene expression profile of surgically resected material
C41

source_name: patient 041, cancer, LCM


title: C36

description:
Gene expression profile of surgically resected material
C36

source_name: patient 036, cancer, LCM


title: 11b2_WT_chronic_DSS


title: 11b4_WT_chronic_DSS


title: 11a2_WT_chronic_DSS


title: C32

description:
Gene expression profile of surgically resected material
C32

source_name: patient 032, cancer, LCM


title: C31

description:
Gene expression profile of surgically resected material
C31

source_name: patient 031, cancer, LCM


title: C33

description:
Gene expression profile of surgically resected material
C33

source_name: patient 033, cancer, LCM


title: C34

description:
Gene expression profile of surgically resected material
C34

source_name: patient 034, cancer, LCM


title: Whole Blood_3

description: Gene expression

source_name: Peripheral Whole Blood, replicate 3


title: C30

description:
Gene expression profile of surgically resected material
C30

source_name: patient 030, cancer, LCM


title: C28

description:
Gene expression profile of surgically resected material
C28

source_name: patient 028, cancer, LCM


title: Murine pro-B cell lymphomas from 18-moth-old Emu-NKX2-3 transgenes rep4

first: Victor

last: Segura

state: Navarra

address: Avda. Pío XII, 55

department: Unit of Proteomics, Genomics and Bioinformatics

institute: FIMA

hyb_protocol: Labeled sense cDNA was hybridized to the Affymetrix MoGene-1_0-st chip according to the the manufacturer protocols and using GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000.

data_processing: The data were normalized with Bioconductor software using RMA algorithm.

source_name: CD19 isolated B cells from abdominal pro-B cell lymphomas

label_protocol: The sense cDNA was prepared from 300 ng of total RNA using the Ambion® WT Expression Kit. The sense strand cDNA was then fragmented and biotinylated with the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671).

growth_protocol: Cell sorting of different subpopulations in C57BL/6 wild type adn Emu-transgenic mice were performed using a FACSAria (BD Biosceinces) with corresponding MoAb antibodies or using the AutoMACs separation system with th corresponding microbeads .

extract_protocol: The RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: The cells were harvested with TRIzol Reagent (Invitrogen) and frozen at -80º upon extraction

value: pEmuSR-NKX2-3 mice

tag: genetic background


title: Murine pro-B cell lymphomas from 18-moth-old Emu-NKX2-3 transgenes rep3

tag: age

value: CD19 isolated B cells from abdominal pro-B cell lymphomas


title: Murine pro-B cell lymphomas from 18-moth-old Emu-NKX2-3 transgenes rep5


title: Murine pro-B cell lymphomas from 18-moth-old Emu-NKX2-3 transgenes rep1


title: Murine pro-B cell lymphomas from 18-moth-old Emu-NKX2-3 transgenes rep2


title: 10_WT_acute_control

description: Colonic gene expression data of wild type (WT) acute control mouse


title: C26

description:
Gene expression profile of surgically resected material
C26

source_name: patient 026, cancer, LCM

tag: tissue


title: Murine bone marow pro-B lymphocytes (from wild type mice) rep1

source_name: B220+cKit+ isolated pro-B cells from bone marrow

value: wild type


title: C27

description:
Gene expression profile of surgically resected material
C27

source_name: patient 027, cancer, LCM


title: C243

description:
Gene expression profile of surgically resected material
C243

source_name: patient 243, cancer, LCM


title: C25

description:
Gene expression profile of surgically resected material
C25

source_name: patient 025, cancer, LCM


title: C244

description:
Gene expression profile of surgically resected material
C244

source_name: patient 244, cancer, LCM


title: Murine bone marow pro-B lymphocytes (from wild type mice) rep2

value: B220+cKit+ isolated pro-B cells from bone marrow


title: Murine bone marow pro-B lymphocytes (from wild type mice) rep3


title: Murine splenic  B-cell from 18-month-old Emu-NKX2-3 transgenes rep2

source_name: CD19 isolated B cells from splenic lymphomas


title: Murine bone marow pro-B lymphocytes (from wild type mice) rep4


title: Murine splenic  B-cell from 12-month-old Emu-NKX2-3 transgenes rep4

value: CD19 isolated B cells from splenic lymphomas


title: C23

description:
Gene expression profile of surgically resected material
C23

source_name: patient 023, cancer, LCM


title: Amyloidosis sample 7

hyb_protocol: Labeled RNA was hybridized to Human Gene 1.0 ST Array

scan_protocol: Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing:
Expression value for each probe set was calculated using Affymetrix Expression Console that uses RMA (Robust Multi-Array Average) algorithm.
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps

source_name: Bone marrow

label_protocol: Labelling and hybridizations were performed according to protocols from Affymetrix. Briefly, 100-300 ng of total RNA were amplified and labeled using the WT Sense Target labelling and control reagents kit (Affymetrix Inc., Santa Clara, CA, USA)

value: Amyloidosis

value: Clonal plasma cells


title: C242

description:
Gene expression profile of surgically resected material
C242

source_name: patient 242, cancer, LCM


title: Murine splenic  B-cell from 18-month-old Emu-NKX2-3 transgenes rep3


title: Murine splenic  B-cell from 12-month-old Emu-NKX2-3 transgenes rep1


title: Murine splenic  B-cell from 12-month-old Emu-NKX2-3 transgenes rep2


title: Murine splenic  B-cell from 12-month-old Emu-NKX2-3 transgenes rep3


title: C235

description:
Gene expression profile of surgically resected material
C235

source_name: patient 235, cancer, LCM


title: Murine splenic B lymphocytes (from wild type mice) rep1

source_name: CD19 isolated B cells from spleen

value: CD19 isolated B cells from spleen


title: Amyloidosis sample 29


title: Murine splenic B lymphocytes (from wild type mice) rep2


title: C234

description:
Gene expression profile of surgically resected material
C234

source_name: patient 234, cancer, LCM


title: C240

description:
Gene expression profile of surgically resected material
C240

source_name: patient 240, cancer, LCM


title: C231

description:
Gene expression profile of surgically resected material
C231

source_name: patient 231, cancer, LCM


title: Amyloidosis sample 8


title: Murine splenic B lymphocytes (from wild type mice) rep4


title: Murine splenic B lymphocytes (from wild type mice) rep3


title: C241

description:
Gene expression profile of surgically resected material
C241

source_name: patient 241, cancer, LCM


title: C233

description:
Gene expression profile of surgically resected material
C233

source_name: patient 233, cancer, LCM


title: Amyloidosis sample 2


title: Amyloidosis sample 197


title: Murine splenic  B-cell from 18-month-old Emu-NKX2-3 transgenes rep1


title: C22

description:
Gene expression profile of surgically resected material
C22

source_name: patient 022, cancer, LCM


title: C230

description:
Gene expression profile of surgically resected material
C230

source_name: patient 230, cancer, LCM


title: Amyloidosis sample 27


title: Amyloidosis sample 16


title: C229

description:
Gene expression profile of surgically resected material
C229

source_name: patient 229, cancer, LCM


title: Amyloidosis sample 127


title: Amyloidosis sample 111


title: C226

description:
Gene expression profile of surgically resected material
C226

source_name: patient 226, cancer, LCM


title: C217

description:
Gene expression profile of surgically resected material
C217

source_name: patient 217, cancer, LCM


title: CHF+Keto, CK1

city: Toronto

first: Claudia

middle: Chimisso

last: dos Santos

state: ON

address: 30, Bond Street, room 4-011

department: University of Toronto

country: Canada

institute: Saint Michaels Hospital

description: Gene expression of CHF+Keto rats.

hyb_protocol: RNA samples were processed for hybridization on Affymetrix Rat Genome 230 2.0 array (Affymetrix, Inc.) GeneChip following standard procedures.

scan_protocol: Arrays were scanned.

data_processing: Data were analyzed using the Bioconductor collection for R (version 2.5.0) and pre-processed and log-transformed by GC-RMA. Genes were defined as differentially expressed if expression levels between control and banded rats varied with a log2-ratio of less than -2 (down-regulation) or greater than 2 (up-regulation), and p<0.05 (two-tailed Student's t-test).

source_name: Whole lung, CHF, ketotifen

label_protocol: Biotin, as per manufacturer's default protocol.

growth_protocol: Age matched. Male Sprague-Dawley rats were obtained from Charles River Laboratories (Sulzfeld, Germany).

extract_protocol: Lungs from banded and control rats were excised and total RNA was extracted (Stratagene Absolutely RNA Miniprep Kit; Stratagene, La Jolla, USA). Three µg total RNA from three control and three banded rats each were processed according to the One-Cycle Target Labeling protocol (GeneChip Expression Analysis, Affymetrix, Santa Clara, USA). Before and after amplifications, the total RNA/complementary RNA concentrations were checked with NanoDrop ND-1000 (Thermo Scientific, Wilmington, USA) and quality was controlled (Experion electrophoresis station, BioRad; Hercules, USA). Samples were hybridized to GeneChip® Rat Genome 230 2.0 arrays (Affymetrix; Santa Clara, USA) containing 31,000 probe sets covering 28,000 rat genes.

treatment_protocol: For Pulmonary Hypertension owing to left heart disease, congestive heart failure was induced in juvenile rats with a body weight (bw) of 91±9 g by supracoronary aortic banding nine weeks prior to investigations. Sham-operated rats of similar body weight served as controls. Rats randomized to receive the mast cell stabilizer ketotifen fumarate (Sigma Aldrich) or placebo given at a dose of 1 mg/kg bw/day with the drinking water from day 1 after aortic banding or MCT injection, respectively.

tag: strain/background

value: Sprague-Dawley

value: Male

value: Whole lung

tag: surgery

value: congestive heart failure (CHF) induction

tag: disease state

value: left heart disease (LHD) with pulmonary hypertension (PH)

value: Ketotifen


title: Sham+Keto, SK3

description: Gene expression of Sham+Keto rats.

source_name: Whole lung, sham, ketotifen

value: Sham

tag: treatment


title: CHF+Keto, CK2

description: Gene expression of CHF+Keto rats.


title: C224

description:
Gene expression profile of surgically resected material
C224

source_name: patient 224, cancer, LCM

value: colorectal cancer


title: C211

description:
Gene expression profile of surgically resected material
C211

source_name: patient 211, cancer, LCM

value: distant metastasis


title: Sham+Keto, SK1

description: Gene expression of Sham+Keto rats.


title: C225

description:
Gene expression profile of surgically resected material
C225

source_name: patient 225, cancer, LCM


title: C223

description:
Gene expression profile of surgically resected material
C223

source_name: patient 223, cancer, LCM


title: CHF+Keto, CK3

description: Gene expression of CHF+Keto rats.


title: C227

description:
Gene expression profile of surgically resected material
C227

source_name: patient 227, cancer, LCM


title: C215

description:
Gene expression profile of surgically resected material
C215

source_name: patient 215, cancer, LCM


title: C221

description:
Gene expression profile of surgically resected material
C221

source_name: patient 221, cancer, LCM


title: C216

description:
Gene expression profile of surgically resected material
C216

source_name: patient 216, cancer, LCM


title: C213

description:
Gene expression profile of surgically resected material
C213

source_name: patient 213, cancer, LCM


title: Sham+Keto, SK2

description: Gene expression of Sham+Keto rats.


title: C222

description:
Gene expression profile of surgically resected material
C222

source_name: patient 222, cancer, LCM


title: CHF, C3

description: Gene expression of CHF rats.

source_name: Whole lung, CHF, placebo

value: Placebo


title: C209

description:
Gene expression profile of surgically resected material
C209

source_name: patient 209, cancer, LCM


title: CHF, C2

description: Gene expression of CHF rats.


title: C210

description:
Gene expression profile of surgically resected material
C210

source_name: patient 210, cancer, LCM


title: C220

description:
Gene expression profile of surgically resected material
C220

source_name: patient 220, cancer, LCM


title: C207

description:
Gene expression profile of surgically resected material
C207

source_name: patient 207, cancer, LCM


title: C214

description:
Gene expression profile of surgically resected material
C214

source_name: patient 214, cancer, LCM


title: C219

description:
Gene expression profile of surgically resected material
C219

source_name: patient 219, cancer, LCM


title: CHF, C1

description: Gene expression of CHF rats.


title: Sham, S2

description: Gene expression of Sham rats.

source_name: Whole lung, sham, placebo


title: Sham, S1

description: Gene expression of Sham rats.


title: C202

description:
Gene expression profile of surgically resected material
C202

source_name: patient 202, cancer, LCM


title: C200

description:
Gene expression profile of surgically resected material
C200

source_name: patient 200, cancer, LCM


title: C204

description:
Gene expression profile of surgically resected material
C204

source_name: patient 204, cancer, LCM


title: C196

description:
Gene expression profile of surgically resected material
C196

source_name: patient 196, cancer, LCM


title: C201

description:
Gene expression profile of surgically resected material
C201

source_name: patient 201, cancer, LCM


title: C194

description:
Gene expression profile of surgically resected material
C194

source_name: patient 194, cancer, LCM


title: C184

description:
Gene expression profile of surgically resected material
C184

source_name: patient 184, cancer, LCM


title: C193

description:
Gene expression profile of surgically resected material
C193

source_name: patient 193, cancer, LCM


title: C183

description:
Gene expression profile of surgically resected material
C183

source_name: patient 183, cancer, LCM


title: C203

description:
Gene expression profile of surgically resected material
C203

source_name: patient 203, cancer, LCM


title: C197

description:
Gene expression profile of surgically resected material
C197

source_name: patient 197, cancer, LCM


title: C188

description:
Gene expression profile of surgically resected material
C188

source_name: patient 188, cancer, LCM


title: Sham, S3

description: Gene expression of Sham rats.


title: C182

description:
Gene expression profile of surgically resected material
C182

source_name: patient 182, cancer, LCM


title: C191

description:
Gene expression profile of surgically resected material
C191

source_name: patient 191, cancer, LCM


title: C17

description:
Gene expression profile of surgically resected material
C17

source_name: patient 017, cancer, LCM


title: C181

description:
Gene expression profile of surgically resected material
C181

source_name: patient 181, cancer, LCM


title: C190

description:
Gene expression profile of surgically resected material
C190

source_name: patient 190, cancer, LCM


title: C195

description:
Gene expression profile of surgically resected material
C195

source_name: patient 195, cancer, LCM


title: C180

description:
Gene expression profile of surgically resected material
C180

source_name: patient 180, cancer, LCM


title: C187

description:
Gene expression profile of surgically resected material
C187

source_name: patient 187, cancer, LCM


title: C185

description:
Gene expression profile of surgically resected material
C185

source_name: patient 185, cancer, LCM


title: Gene profile of Reference

city: Chennai

first: Thulasi

middle: bai

last: K

state: Tamilnadu

address: 39 Vellalar Street,

department: Bioinformatics

institute: Loyola College

description:
N_Ref
140602AE-01
up and down regulated genes

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

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

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)

molecule: polyA RNA

source_name: Reference

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

extract_protocol: Total RNA was extracted using NucleoSpin® RNA Blood Midi kit

tag: diagnosis

value: healthy control

value: 18 years

value: Peripheral blood


title: Gene profile of MR Female

description:
N_F
140507AE-01
up and down regulated genes

source_name: MR  Female

value: mentally retarded

value: 17 years

tag: Sex

value: female


title: C179

description:
Gene expression profile of surgically resected material
C179

source_name: patient 179, cancer, LCM


title: Gene profile of MR Male

description:
N_M
140507AE-01
up and down regulated genes

source_name: MR  Male

value: male


title: C178

description:
Gene expression profile of surgically resected material
C178

source_name: patient 178, cancer, LCM


title: C176

description:
Gene expression profile of surgically resected material
C176

source_name: patient 176, cancer, LCM


title: C186

description:
Gene expression profile of surgically resected material
C186

source_name: patient 186, cancer, LCM


title: LOX1+.CC.2

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

institute: The Wistar Institute

description: LOX1+ cells, from colon cancer patient LOX.CC.2

hyb_protocol: Hybridized on Illumina Human-HT12 v4 Expression BeadChip Kit using Illumina whole-Genome Gene Exprssion with Intellihyb Seal system which detect signal with streptavidin-Cy3

scan_protocol: Illumina Setting with PMTFactor=2

data_processing: Illumina GenomeStudio software was used to export expression levels and detection p-values for each probe of each sample. Signal intensity data was quantile normalized and  genes that showed insignificant detection p-value (p>0.05) in all samples were removed from further analysis.

source_name: LOX1+ cells from Colon cancer patient

label_protocol: Biotin Labeling of RNA at 400ng with Ambion Illumina® TotalPrep RNA Amplification Kit

growth_protocol: Samples of peripheral blood were collected from patients at Helen F. Graham Cancer Center and University of Pennsylvania.

extract_protocol: total RNA from purified cells was isolated with TRIzol reagent according to the manufacturer’s recommendations

treatment_protocol: PMN-MDSC and PMN were isolated by centrifugation over on double density gradient Histopaque (Sigma) (1.077 to collect PBMC and 1.119 to collect PMN) followed by labeling with CD15-PE mAb (BD Biosciences) and then separated using anti-PE beads and MACS column (Miltenyi). For LOX1+/- isolation, whole blood was enriched for PMNs using MACSxpress® Neutrophil Isolation Kit (Miltenyi) following the protocol provided by the manufacturer.  Cells were then labeled with anti-Lox1-PE mAb (Biolegend) and then separated using anti-PE beads and MACS column (Miltenyi).

tag: selection

tag: cancer

value: colon cancer

tag: subject id


title: LOX1+.CC.1

description: LOX1+ cells, from colon cancer patient LOX.CC.1


title: STAT1 KO IFN lambda

city: Eiheiji

first: Shota

last: Yamauchi

state: Fukui

address: 23-3 Matsuokashimoaizuki

department: Faculty of Medical Sciences

institute: University of Fukui

description: Gene expression data from Huh-7.5 cells

hyb_protocol: Labeled cDNA were hybridized for 16 h at 45C on GeneChip HuGene 2.0 ST Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned using GCS3000-7G Scanner.

data_processing: Data were analyzed with Affymetrix GCS3000 system.

source_name: STAT1 knockout Huh-7.5 cells treated with interferon lambda

label_protocol: Labeled, Sense-strand cDNA were generated from 200 ng of total RNA using a CHIP WT plus kit (Affymetrix) according to the manufacture's instruction.

growth_protocol: Huh-7.5 cells  were cultured in DMEM containig 10% FBS and NEAA.

extract_protocol: Total RNA was extracted using an RNeasy mini kit (Qiagen) according to the manufacture's instruction.

treatment_protocol: Control and STAT1 knockout Huh-7.5 hepatoma cells were left untreated or treated with 1000 U/ml of human interferon alpha 2a or interferon lambda 1 (PBL) for 24 h.

tag: cell line

value: treated with interferon lambda

value: STAT1 knockout


title: C171

description:
Gene expression profile of surgically resected material
C171

source_name: patient 171, cancer, LCM

tag: metastasis


title: C172

description:
Gene expression profile of surgically resected material
C172

source_name: patient 172, cancer, LCM


title: C164

description:
Gene expression profile of surgically resected material
C164

source_name: patient 164, cancer, LCM


title: C169

description:
Gene expression profile of surgically resected material
C169

source_name: patient 169, cancer, LCM


title: LOX1+.NSCLC.1

description: LOX1+ cells, from non-small cell lung cancer patient LOX.NSCLC.1

source_name: LOX1+ cells from Lung cancer patient

value: non-small cell lung cancer


title: LOX1-.CC.1

description: LOX1- cells, from colon cancer patient LOX.CC.1

source_name: LOX1- cells from Colon cancer patient


title: PMN-MDSC.HNC.7

description: PMN-MDSC cells, from head and neck cancer patient PMN.HNC.7

source_name: PMN-MDSC cells from Head and Neck cancer patient

value: PMN-MDSC

value: head and neck cancer


title: LOX1-.NSCLC.1

description: LOX1- cells, from non-small cell lung cancer patient LOX.NSCLC.1

source_name: LOX1- cells from Lung cancer patient


title: STAT1 KO IFN alpha

description: Gene expression data from Huh-7.5 cells

source_name: STAT1 knockout Huh-7.5 cells treated with interferon alpha

value: treated with interferon alpha


title: C166

description:
Gene expression profile of surgically resected material
C166

source_name: patient 166, cancer, LCM

value: colorectal cancer


title: C161

description:
Gene expression profile of surgically resected material
C161

source_name: patient 161, cancer, LCM


title: LOX1+.NSCLC.2

description: LOX1+ cells, from non-small cell lung cancer patient LOX.NSCLC.2


title: C173

description:
Gene expression profile of surgically resected material
C173

source_name: patient 173, cancer, LCM


title: C162

description:
Gene expression profile of surgically resected material
C162

source_name: patient 162, cancer, LCM


title: C175

description:
Gene expression profile of surgically resected material
C175

source_name: patient 175, cancer, LCM


title: LOX1-.CC.2

description: LOX1- cells, from colon cancer patient LOX.CC.2


title: LOX1-.NSCLC.2

description: LOX1- cells, from non-small cell lung cancer patient LOX.NSCLC.2


title: PMN-MDSC.NSCLC.2

description: PMN-MDSC cells, from non-small cell lung cancer patient PMN.NSCLC.2

source_name: PMN-MDSC cells from Lung cancer patient


title: C15

description:
Gene expression profile of surgically resected material
C15

source_name: patient 015, cancer, LCM


title: PMN-MDSC.NSCLC.3

description: PMN-MDSC cells, from non-small cell lung cancer patient PMN.NSCLC.3


title: STAT1 KO

description: Gene expression data from Huh-7.5 cells

source_name: STAT1 knockout Huh-7.5 cells, untreated

value: untreated


title: PMN-MDSC.HNC.6

description: PMN-MDSC cells, from head and neck cancer patient PMN.HNC.6


title: C174

description:
Gene expression profile of surgically resected material
C174

source_name: patient 174, cancer, LCM


title: C168

description:
Gene expression profile of surgically resected material
C168

source_name: patient 168, cancer, LCM


title: PMN-MDSC.HNC.4

description: PMN-MDSC cells, from head and neck cancer patient PMN.HNC.4


title: NT IFN lambda

description: Gene expression data from Huh-7.5 cells

source_name: Control Huh-7.5 cells treated with interferon lambda

value: control


title: NT IFN alpha

description: Gene expression data from Huh-7.5 cells

source_name: Control Huh-7.5 cells treated with interferon alpha


title: C57BL/6_diabetes_4 weeks_rep4

city: Stanford

first: Vivek

last: Bhalla

state: CA

address: 777 Welch Road, Suite DE

institute: Stanford University School of Medicine

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: C57BL/6 glomeruli_diabetes_4 weeks

label_protocol: Not provided

growth_protocol: Mouse were acclimated in standard animal housing facility, with free access to normal food and water.

extract_protocol: RNA were isolated from mouse glomeruli by Tri-reagent (Sigma), 1ug total RNA were applied to the microarray.

treatment_protocol: After 1 week acclimation, we injected streptozotocin (or vehicle- sodium citrate, pH 4.5) i.p. in 6 hour fasted mice daily for 5 consecutive days (40mg/kg body weight for DBA/2 mice, and 50mg/kg body weight for C57BL/6 mice). Mice were supplemented with 10% sucrose water for 1 week to prevent hypoglycemia. Four weeks after injection, we sacrificed mice to prepare glomerular total RNA.

tag: strain

tag: diabetic nephropathy susceptability

value: resistant


title: PMN.NSCLC.2

description: PMN cells, from non-small cell lung cancer patient PMN.NSCLC.2

source_name: PMN cells from Lung cancer patient

value: PMN


title: C155

description:
Gene expression profile of surgically resected material
C155

source_name: patient 155, cancer, LCM

value: distant metastasis


title: C157

description:
Gene expression profile of surgically resected material
C157

source_name: patient 157, cancer, LCM


title: C158

description:
Gene expression profile of surgically resected material
C158

source_name: patient 158, cancer, LCM


title: PMN.NSCLC.3

description: PMN cells, from non-small cell lung cancer patient PMN.NSCLC.3


title: C156

description:
Gene expression profile of surgically resected material
C156

source_name: patient 156, cancer, LCM


title: C154

description:
Gene expression profile of surgically resected material
C154

source_name: patient 154, cancer, LCM


title: PMN-MDSC.HNC.5

description: PMN-MDSC cells, from head and neck cancer patient PMN.HNC.5

source_name: PMN-MDSC cells from Head and Neck cancer patient


title: PMN.HNC.4

description: PMN cells, from head and neck cancer patient PMN.HNC.4

source_name: PMN cells from Head and Neck cancer patient


title: PMN.HNC.6

description: PMN cells, from head and neck cancer patient PMN.HNC.6


title: C150

description:
Gene expression profile of surgically resected material
C150

source_name: patient 150, cancer, LCM


title: PMN.HNC.5

description: PMN cells, from head and neck cancer patient PMN.HNC.5


title: Brain CD11b+ cells [08_03-10-16_S2]

city: NORTH CHICAGO

first: Rahul

last: Vijay

address: 3333 GreenBay Road, BSB 2.450

institute: Rosalind Franklin University

hyb_protocol: RNA for the microarray was processed using a NuGEN WT-Ovation Pico RNA Amplification System together with a NuGEN WT-Ovation Exon Module. Samples were hybridized and loaded onto Affymetrix Mouse gene 2.0. Arrays

scan_protocol: scanned with a HiScan bead array system, and data were collected using GeneChip Operating Software

data_processing: Data from Affymetrix Mouse gene 2.0 Expression BeadChip were normalized and median polished using Robust Multichip Average background correction with log2-adjusted values. After obtaining the log2 expression values for genes, significance testing was performed comparing the two groups (CD11b+ cells from brains of WT and DP1 KO mice). Significance of expression differences was assessed using a false discovery rate (FDR) cutoff of 0.05 and a twofold change. Analysis and visualization of data and pathway analysis were performed using PartekGS software and Ingenuity Pathway Analysis software.

source_name: Naïve mouse brain

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

value: Brain

tag: genotype

value: WT


title: PMN.HNC.7

description: PMN cells, from head and neck cancer patient PMN.HNC.7


title: Brain CD11b+ cells [05_03-10-16_S2]


title: C148

description:
Gene expression profile of surgically resected material
C148

source_name: patient 148, cancer, LCM


title: C57BL/6_diabetes_4 weeks_rep3


title: C57BL/6_diabetes_4 weeks_rep2


title: C57BL/6_diabetes_4 weeks_rep1


title: PMN.hd.4

description: PMN cells, from heathy donor PMN.hd.4

source_name: PMN cells from healthy donors

value: heathy donor


title: NT

description: Gene expression data from Huh-7.5 cells

source_name: Control Huh-7.5 cells, untreated

tag: genotype/variation


title: Brain CD11b+ cells [04_03-10-16_S2]

value: DP1 KO