title: Subject 20568, lung, 94 dpc

value: 94 dpc


title: U-204

status: Public on Dec 22 2015

type: RNA

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

hyb_protocol: Affymetrix Human Gene 2.0 ST Array (Cat No. 902112); Affymetrix GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720);  Affymetrix Genechip®  fluidics station 450: protocol FS450_0007 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software  AGCC 3.2.)

data_processing:
Affymetrix Genexpression Console (1.3.1) using Affymetrix default analysis settings for generation of CEL-files.
Data Pre-Processing and Filtering (Partek Software, v.6.6): RMA  (background correction, quantile normalization across all chips in the experiment, log2 transformation, median polish summarization);

label: Biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: NuGen Applause WT-Amp Plus ST System M01199v2-1, (Cat No. 5510); Encore Biotin Module, M01111v6 (Cat No. 4200);

growth_protocol: Monolayer culture PMID 22150225

extract_protocol: Extraction with Trizol

treatment_protocol: Treatment with interleukin-1 and anti-LAMA4-Antibody ( 2A3) as decribed before, PMID 22150225

tag: patient id

tag: tissue

value: Knee joint

tag: cell type

value: chondrocytes

tag: treatment group

value: untreated


title: Subject 20560, lung, 96 dpc

city: Boston

first: Alvin

middle: T.

last: Kho

state: MA

address: 320 Longwood Avenue

department: Informatics Program

country: USA

institute: Boston Children's Hospital

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

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

data_processing: All 316 sample CEL files were inputted into Bioconductor/R to derive Robust Multi-Array Average (RMA) normalized output in base 2 logarithmic scale.

source_name: whole lung human fetus

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

extract_protocol: For each experimental sample, total RNA was extracted using RNeasy Mini Kit (Qiagen, Valencia, CA) and quality was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100. Concentrations may also be determined using a NanoDrop 1000 spectrophotometer. Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371).

tag: subject id

tag: age (days post conception)

value: 96 dpc

tag: gender

value: male

value: lung

tag: cotinine (ng/g placenta)

tag: hybridization batch id


title: Subject 20495, lung, 96 dpc


title: Subject 20492, lung, 74 dpc

value: 74 dpc


title: Subject 20490, lung, 85 dpc

value: 85 dpc


title: L4 Il1-204

description: L4 Il1-204

source_name: chondrocytes_Lama4 + IL1

value: Lama4 + IL1


title: U-193


title: Subject 20559, lung, 78 dpc

value: 78 dpc


title: L4 Il1-193

description: L4 Il1-193


title: Subject 20471, lung, 80 dpc

value: 80 dpc

value: female


title: U Il1-204

description: U Il1-204

source_name: chondrocytes_untreated + IL1

value: untreated + IL1


title: IgM Il1-204

description: IgM Il1-204

source_name: chondrocytes_neg vehicle control + IL1

value: neg vehicle control + IL1


title: Subject 20631, lung, 87 dpc

value: 87 dpc


title: IgM Il1-193

description: IgM Il1-193


title: Subject 20477, lung, 82 dpc

value: 82 dpc


title: Subject 20458, lung, 96 dpc


title: Subject 20445, lung, 72 dpc

value: 72 dpc


title: Subject 20436, lung, 98 dpc

value: 98 dpc


title: U Il1-193

description: U Il1-193

value: Knee joint

value: chondrocytes


title: Subject 20437, lung, 74 dpc


title: Subject 20466, lung, 96 dpc

value: 96 dpc


title: Subject 20468, lung, 91 dpc

value: 91 dpc

value: male


title: Subject 20465, lung, 101 dpc

value: 101 dpc

value: lung


title: Subject 20361, lung, 105 dpc

value: 105 dpc


title: Subject 20319, lung, 96 dpc


title: Subject 20301, lung, 72 dpc


title: Subject 20295, lung, 72 dpc


title: Subject 20299, lung, 56 dpc

value: 56 dpc


title: Subject 20220, lung, 94 dpc

value: 94 dpc


title: Subject 20411, lung, 85 dpc

value: 85 dpc

value: female


title: Subject 20421, lung, 78 dpc

value: 78 dpc


title: Subject 20247, lung, 56 dpc


title: Subject 20248, lung, 82 dpc


title: Subject 20357, lung, 91 dpc


title: Subject 20420, lung, 91 dpc


title: Subject 20250, lung, 103 dpc

value: 103 dpc


title: Subject 20223, lung, 89 dpc

value: 89 dpc


title: Subject 20280, lung, 98 dpc


title: Subject 20245, lung, 101 dpc


title: Subject 20188, lung, 54 dpc

value: 54 dpc


title: Subject 20244, lung, 96 dpc


title: Subject 20187, lung, 72 dpc

value: 72 dpc


title: Subject 20243, lung, 107 dpc

value: 107 dpc


title: Subject 20196, lung, 105 dpc


title: Subject 20197, lung, 110 dpc

value: 110 dpc


title: Subject 20160, lung, 89 dpc


title: Subject 20159, lung, 91 dpc


title: Subject 20183, lung, 89 dpc


title: Subject 20157, lung, 105 dpc


title: Subject 20154, lung, 96 dpc

value: 96 dpc


title: Subject 20153, lung, 74 dpc

value: 74 dpc


title: Subject 20151, lung, 67 dpc

value: 67 dpc

value: male


title: Subject 20136, lung, 67 dpc

value: lung


title: Subject 20150, lung, 80 dpc

value: 80 dpc


title: Subject 20139, lung, 67 dpc


title: Subject 20146, lung, 96 dpc


title: Subject 20107, lung, 103 dpc


title: Subject 20137, lung, 67 dpc


title: Subject 20110, lung, 82 dpc

value: 82 dpc


title: Subject 20114, lung, 94 dpc

value: 94 dpc


title: Subject 20113, lung, 74 dpc


title: Subject 20318, lung, 91 dpc

value: 91 dpc


title: Subject 20135, lung, 72 dpc


title: Subject 20108, lung, 89 dpc

value: female


title: Subject 20050, lung, 117 dpc

value: 117 dpc


title: Subject 20020, lung, 91 dpc


title: Subject 20030, lung, 87 dpc

value: 87 dpc


title: Subject 20149 replicate 1, lung, 80 dpc


title: Subject 20019, lung, 74 dpc


title: Subject 20027, lung, 91 dpc


title: Subject 20049, lung, 117 dpc


title: Subject 20040, lung, 67 dpc


title: Subject 19996, lung, 78 dpc

value: 78 dpc


title: Subject 20044, lung, 87 dpc


title: Subject 20003, lung, 67 dpc


title: Subject 19974, lung, 82 dpc


title: Subject 19969, lung, 94 dpc


title: Subject 20023, lung, 59 dpc

value: 59 dpc


title: Subject 20041, lung, 59 dpc


title: heart of Myh6-MeCP2TG, biological replicate 3

city: Freiburg

first: Ralf

last: Gilsbach

address: Albertstr. 25

country: Germany

institute: Institute of Pharmacology

hyb_protocol: 10 µg of fragmented cRNA were hybridized (16h) to the array. Staining and washing was conducted according to the Affymetrix protocol.

scan_protocol: The processed array was scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data was analyzed using ArrayAssist 5.0 software (Stratagene). Probe levels were calculated using the GCRMA algorithm.

label: biotin

organism: Mus musculus

source_name: heart

label_protocol: Double stranded cDNA was synthesized (GeneChip® Expression 3' Amplification One-Cycle Target Labeling and Control Reagents, 900493) and biotin labeled cRNA was in vitro transcribed (GeneChip® Expression 3' Amplification One-Cycle Target Labeling and Control Reagents, 900493). Cleanup of the cDNA and the fragmented cRNA was carried out with the GeneChip Sample Module (Affymetrix,900371). The integrity of the total RNA and of the subsequent preparation steps was validated using the Agilent 2100 bioanalyzer (Waldbronn, Germany).

growth_protocol: 2-3 week old mice

extract_protocol: Total RNA (5 µg) from hearts was extracted using the RNeasy fibrous tissue kit (Qiagen, Hilden, Germany).

treatment_protocol: No additional treatment was applied.

tag: genotype

value: heart


title: Subject 19322, lung, 82 dpc


title: Subject 19314, lung, 87 dpc


title: Subject 19096, lung, 108 dpc

value: 108 dpc


title: Subject 19912, lung, 54 dpc

value: 54 dpc


title: Subject 19970, lung, 85 dpc

value: 85 dpc


title: Subject 19360, lung, 89 dpc

value: 89 dpc


title: Subject 19099, lung, 105 dpc

value: 105 dpc


title: Subject 19123, lung, 110 dpc

value: 110 dpc


title: Subject 18815, lung, 91 dpc

value: male

value: lung


title: Subject 18853, lung, 78 dpc


title: Subject 18611, lung, 85 dpc


title: Subject 18639, lung, 103 dpc

value: 103 dpc


title: Subject 18730, lung, 96 dpc

value: 96 dpc


title: Subject 18609, lung, 94 dpc

value: 94 dpc


title: Subject 18610, lung, 82 dpc

value: 82 dpc

value: female


title: Subject 18483, lung, 103 dpc


title: Subject 18607, lung, 108 dpc


title: Subject 18404, lung, 105 dpc


title: Subject 18420, lung, 103 dpc


title: Subject 18475, lung, 108 dpc


title: Subject 18481, lung, 91 dpc

value: 91 dpc


title: Subject 18381, lung, 96 dpc


title: Subject 18403, lung, 85 dpc


title: Subject 18390, lung, 94 dpc


title: KO_TAC 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Quantile normalization using GenomeStudio 2011.1
GenomeStudio 2011.1 calculated intensities

label_protocol: Biotinylated cRNA were prepared with Illumina TotalPrep RNA Amplification Kit from Applied Biosystems.

treatment_protocol: Sham, TAC, rTAC

value: KO

tag: disease

value: TAC


title: Subject 18453, lung, 87 dpc

value: 87 dpc


title: KO_TAC 4

value: heart


title: KO_TAC 2


title: KO_TAC 1


title: WT_for_KO_TAC 4

value: WT


title: WT_for_KO_TAC 3


title: KO_Sham 1

value: Sham


title: KO_Sham 2


title: WT_for_KO_TAC 1


title: KO_Sham 3


title: WT_for_KO_TAC 2


title: WT_for_KO_Sham 2


title: WT_for_KO_Sham 3


title: Liu-UACC3199 Sample6 miR29c

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

description: Breast Cell Line

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-132

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.

data_processing: Data for both channels were Lowess-normalized and then log(2) ratio was taken

source_name: Human Reference B

extract_protocol: Total RNA isolated by stratagene

tag: reference

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

source_name: Liu-UACC3199 Sample6 miR29c

extract_protocol: Qiagen Rneasy Kit

tag: cell line

value: breast cancer


title: Liu-UACC3199 Sample5 Control

description: Breast Cell Line

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-130

source_name: Liu-UACC3199 Sample5 Control


title: Liu-UACC3199 Sample5Repl1 Control

description: Breast Cell Line

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-131

source_name: Liu-UACC3199 Sample5Repl1 Control


title: KO_rTAC 3

value: rTAC


title: Subject 20206, lung, 101 dpc

value: 101 dpc

value: male


title: Liu-UACC3199 Sample4 miR29c

description: Breast Cell Line

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-129

source_name: Liu-UACC3199 Sample4 miR29c


title: Liu-UACC3199 Sample2 miR29c

description: Breast Cell Line

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-127

source_name: Liu-UACC3199 Sample2 miR29c


title: KO_rTAC 5


title: KO_rTAC 6


title: WT_for_KO_Sham 1


title: KO_rTAC 2


title: Category young age, biological replicate 24

city: Rotterdam

first: Dmitry

last: Zubakov

state: ZH

address: Dr. Molewaterplein, 50

department: FMB

country: Netherlands

institute: Erasmus Medical Centre Rotterdam

description: young age donor, whole venous blood sample

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Partek Genomic Suit v. 6.5 software, using RMA algorithm for normalization and Turkey biweight for probe summarization for gene-level analysis
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: whole venous blood

label_protocol: Samples were enzymatically fragmented and biotinylated using a combination of NuGEN kits (NuGEN Technologies, Inc., San Carlos, CA): Ovation Pico WTA System, WT-Ovation EXON Module, Encore Biotin Module recommended for the whole blood RNA samples.

growth_protocol: not applicable

extract_protocol: total RNA was extracted with PAXgene Blood RNA kit (Qiagen) according to the manufacturer's protocol

treatment_protocol: not applicable

tag: age category

value: young

tag: age (years)

value: whole venous blood

value: wild-type


title: Category young age, biological replicate 25


title: Category old age, biological replicate 22

description: old age donor, whole venous blood sample

value: old


title: KO_rTAC 1


title: WT_for_KO_rTAC 4


title: WT_for_KO_rTAC 3


title: Liu-UACC3199 Sample3 Control

description: Breast Cell Line

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-128

source_name: Liu-UACC3199 Sample3 Control


title: Liu-UACC3199 Sample1Repl1 Control

description: Breast Cell Line

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-126

source_name: Liu-UACC3199 Sample1Repl1 Control


title: KO_rTAC 4


title: Category old age, biological replicate 20


title: Category old age, biological replicate 21


title: Liu-UACC3199 Sample1 Control

description: Breast Cell Line

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125

source_name: Liu-UACC3199 Sample1 Control


title: WT_for_KO_rTAC 1


title: Category old age, biological replicate 19


title: WT_for_KO_rTAC 2


title: WT_for_TG_TAC 3


title: Category old age, biological replicate 18


title: genomic DNA from N42 chromosomally normal miscarriage

type: genomic

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

country: Canada

institute: University of British Columbia

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

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

data_processing: GenomeStudio software v2011.1

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted by standard salt method and purified using Qiagen DNeasy Kit according to standard instructions

tag: status/group

value: Chromosomically Normal Miscarriage

tag: fetal sex/sex

value: M

tag: sample tissue

value: placental chorionic villi

tag: fetal gestational age (weeks)/trimester

tag: 450k plate id

tag: 450k sentrix_id

tag: 450k sentrix_position


title: genomic DNA from N39 chromosomally normal miscarriage

value: F


title: Category young age, biological replicate 20

tag: tissue


title: Category young age, biological replicate 23


title: Category young age, biological replicate 21


title: Category old age, biological replicate 17


title: Category young age, biological replicate 22


title: WT_for_TG_TAC 4

value: TAC


title: WT_for_TG_TAC 2

value: heart


title: WT_for_TG_Sham 3

value: WT


title: WT_for_TG_Sham 1

value: Sham


title: genomic DNA from N48 chromosomally normal miscarriage


title: WT_for_TG_Sham 2


title: genomic DNA from N19 chromosomally normal miscarriage


title: WT_for_TG_TAC 1


title: genomic DNA from N28 chromosomally normal miscarriage


title: genomic DNA from pooled complete hydatiform mole

value: CHM

value: complete hydatiform mole


title: Category young age, biological replicate 19


title: Category old age, biological replicate 15


title: genomic DNA from TP9 diandric triploid placental chorionic villi

value: diandric triploid

value: F,XXX


title: WT_for_TG_TAC 5


title: Category old age, biological replicate 11


title: Category old age, biological replicate 12


title: Category young age, biological replicate 18


title: TG_Sham 4


title: Category old age, biological replicate 13


title: TG_TAC 3


title: TG_TAC 2


title: TG_Sham 3


title: TG_Sham 2


title: TG_TAC 1


title: TG_TAC 4


title: Category old age, biological replicate 14


title: genomic DNA from TP60 digynic triploid placental chorionic villi

value: digynic triploid

value: M, XXY


title: genomic DNA from TP76 diandric triploid placental chorionic villi

value: F, XXX

value: 15w by dates 9w size 53d


title: genomic DNA from TP61 digynic triploid placental chorionic villi


title: Category young age, biological replicate 17

value: young

value: whole venous blood

value: wild-type


title: genomic DNA from TP56 digynic triploid placental chorionic villi

value: M,XXY

value: placental chorionic villi

value: 8w 48 days DA


title: genomic DNA from TP7 diandric triploid placental chorionic villi


title: Category old age, biological replicate 16

value: old


title: genomic DNA from TP24 diandric triploid placental chorionic villi


title: genomic DNA from TP6 diandric triploid placental chorionic villi


title: Category young age, biological replicate 16


title: Category old age, biological replicate 10


title: Category old age, biological replicate 9


title: genomic DNA from TP58 digynic triploid placental chorionic villi

value: 8w 37d DA


title: genomic DNA from control pooled placental trophoblast 3

value: control

value: placental trophoblast


title: Category young age, biological replicate 14


title: Category old age, biological replicate 8


title: TG_rTAC 2

value: rTAC

value: heart


title: TG_rTAC 1


title: TG_rTAC 4


title: genomic DNA from control pooled placental trophoblast 2


title: TG_rTAC 5


title: Category young age, biological replicate 15


title: genomic DNA from control pooled placental mesenchyme 3

value: placental mesenchyme


title: Category old age, biological replicate 7


title: genomic DNA from control pooled placental trophoblast 1


title: genomic DNA from TP3 digynic triploid placental chorionic villi

value: digynic triploid


title: WT_for_TG_rTAC 4

value: WT


title: TG_rTAC 3


title: WT_for_TG_rTAC 3


title: genomic DNA from PM83 control chorionic membrane 3

value: M

value: chorionic membrane


title: Category young age, biological replicate 12

value: young


title: genomic DNA from control pooled placental mesenchyme 2


title: genomic DNA from PM110 control chorionic membrane


title: Category old age, biological replicate 6

value: whole venous blood


title: WT_for_TG_rTAC 2


title: genomic DNA from PM139 IUGR chorionic membrane

value: IUGR


title: Category young age, biological replicate 10

value: wild-type


title: Category young age, biological replicate 11


title: WT_for_TG_rTAC 1


title: genomic DNA from control pooled placental mesenchyme 1


title: Category young age, biological replicate 9


title: Empty_Vector_3 mRNA

first: Joshua

middle: David

last: Campbell

address: 72 East Concord St.

institute: Boston University

description: Gene expression data from mouse lung epithelial cells treated with empty vector control

hyb_protocol: The labeled fragmented DNA was hybridized to the Gene Arrays 1.0ST for 16-18 hours in GeneChip Hybridization oven 640 at 45°C with rotation (60 rpm).  The hybridized samples were washed and stained using Affymetrix fluidics station 450.

scan_protocol: Microarrays were scanned using Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing: CEL files were summarized using Affymetrix Expression Console version 1.1. RMA was used to generate gene-level data.

source_name: MLE-15, Empty vector, 48h

label_protocol: RNA (300 ng) was reverse transcribed using Whole Transcript cDNA Synthesis kit (Affymetrix, Santa Clara, CA). The obtained cDNA was used as a template for in vitro transcription using Whole Transcript cDNA Amplification Kit (Affymetrix, Santa Clara, CA). The obtained antisense cRNA was purified using GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA), and used as a template for reverse transcription (Whole Transcript  cDNA Synthesis kit, Affymetrix, Santa Clara, CA) to produce single-stranded DNA in the sense orientation. Quality controls were carried out by running an mRNA Nano assay in the Agilent 2100 Bioanalyzer.

growth_protocol: We transduced mouse lung epithelial MLE 15 cells with lentivirus expressing shRNAs targeting mouse and human Nkx2-1. We used a mix of three shRNAs cloned in the pLKO.1 lentivirus vector (individual clones TRCN0000020449, TRCN0000020450, and TRCN0000086264) targeting Nkx2-1 mRNA of mouse, rat, and human origin (contained in shRNA sets RHS4533 and RMM4534, Open Biosystems). This combination of shRNAs gave us the greatest down-regulation of Nkx2-1 mRNA. The pLKO.1 lentivirus empty vector (RHS4080, Open Biosystems) was used as non-silencing control. Enhanced GFP shRNA-positive control (RHS4459, Open Biosystems) was used to generate viral particles and calculate infection efficiency and transduction units in MLE-15 cells. To produce the lentiviral particles, we cotransfected the pLKO.1 vectors with packaging plasmids in the Trans-Lentiviral packaging mix (Open Biosystems) in the TLA-HEK293T packaging cell line following the manufacturer's protocols. For the experiments, MLE-15 cells were seeded at 40–50% confluence in P100 tissue culture plates. The mixture, including 80 μl of the viral stock (at 6 × 105 transduction units/ml), 20 μl of fetal bovine serum, 32 μl of 8 μg/ml Polybrene, and 868 μl of serum-free media, was added to 2 ml of serum-free media and incubated at room temperature for 20 min. The viral mixture was added to the cells and incubated at 37 °C for 3–4 h. Then, we removed the transduction viral mix and added Dulbecco's modified Eagle's medium with 10% fetal bovine serum, 100 units/ml penicillin, and 100 μg/ml streptomycin for at least 48 h to allow cells to reach confluence. Cells were trypsinized and cultured in the same media containing 5 μg/ml puromycin dihydrochloride (Sigma) for 48 h to select for transduced cells. Knockdown of Nkx2-1 in MLE-15 cells was quantified at protein levels by Western blot and at mRNA levels by qRT-PCR (Cao et al Journal of Biological Chemistry 2010; Tagne et al PlosOne 2012).

extract_protocol: Total RNA was isolated using QIAGEN’s RNeasy kit (Qiagen, Valencia, CA) and the sample integrity was verified using RNA 6000 Nano Assay RNA chips run in Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: treatment

value: Empty vector control


title: genomic DNA from ch control pooled chorionic membrane 3


title: Empty_Vector_2 mRNA


title: genomic DNA from control pooled amniotic membrane 3

value: amniotic membrane


title: Category young age, biological replicate 8


title: Nkx2-1_shRNA_3 mRNA

description: Gene expression data from mouse lung epithelial cells treated with Nkx2-1 shRNA

source_name: MLE-15, Nkx2-1 shRNA, 48h

value: Nkx2-1 shRNA


title: Empty_Vector_1 mRNA


title: Nkx2-1_shRNA_2 mRNA


title: Category old age, biological replicate 5

value: old


title: Empty_Vector_3 microRNA

description: MicroRNA expression data from mouse lung epithelial cells treated with empty vector control

hyb_protocol: The labeled RNA was hybridized to the microRNA arrays v1 (Affymetrix, Santa Clara, CA) for 16 hours in GeneChip Hybridization oven 640 at 48oC with rotation (60 rpm).  The hybridized samples were washed and stained using Affymetrix fluidics station 450.

data_processing: Affymetrix miRNA QC Tool software version 1.0.33.0 was used for background subtraction, calculation of detection p-value and array normalization.

label_protocol: The RNA was labeled with FlashTag kit (Genisphere Inc., Hatfield, PA) according to the manufacturer’s protocol.

extract_protocol: Total RNA was isolated and enriched for low molecular weight RNA using QIAGEN’s miRNeasy kit (Qiagen, Valencia, CA) and the sample integrity was verified using RNA 6000 Nano Assay RNA chips run in Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).


title: Category young age, biological replicate 13


title: genomic DNA from PM139 IUGR amniotic membrane


title: Category old age, biological replicate 4


title: genomic DNA from PM33_B IUGR placental decidua

value: F

value: placental decidua


title: Category old age, biological replicate 3


title: Nkx2-1_shRNA_2 microRNA

description: MicroRNA expression data from mouse lung epithelial cells treated with Nkx2-1 shRNA


title: Category old age, biological replicate 2


title: Empty_Vector_1 microRNA


title: Nkx2-1_shRNA_3 microRNA


title: Empty_Vector_2 microRNA


title: Nkx2-1_shRNA_1 mRNA


title: Category young age, biological replicate 6


title: Category young age, biological replicate 5


title: genomic DNA from pooled control cord 3

value: control

value: umbilical cord


title: TG_Sham 1

value: Sham

value: heart


title: Category young age, biological replicate 7


title: Nkx2-1_shRNA_1 microRNA


title: genomic DNA from pooled control cord blood

source_name: cord blood

value: cord blood


title: genomic DNA from PM89 control placental decidua


title: Category young age, biological replicate 4


title: genomic DNA from PM110 control amniotic membrane

value: M

value: amnioniotic membrane


title: Category young age, biological replicate 1

value: young


title: Category young age, biological replicate 2

value: whole venous blood


title: genomic DNA from PM234 control maternal blood

value: whole maternal blood


title: genomic DNA from PM252 control maternal blood


title: Category young age, biological replicate 3

value: wild-type


title: genomic DNA from PM214 control maternal blood


title: Category old age, biological replicate 1


title: Eat-2 mutant worms treated with 2% DMSO alone replicate 3

city: Liverpool

first: João Pedro

last: de Magalhães

address: Crown Street,

department: Institute of Integrative Biology

country: United Kingdom

institute: The University of Liverpool

hyb_protocol: Following amplification 15ug of RNA was fragmented and 12.5ug of fragmented labelled RNA was hybridised onto Affymetrix GeneChip C. elegans Genome Arrays as per the manufacturer’s instructions. These were hybridised for 16 hours at 45°C and 60rpm in an Affymetrix hybridisation oven 640. Hybridised arrays were washed using Affymetrix Hybridisation wash and stain kit on a GeneChip Fluidics station 450

scan_protocol: scanned using an Affymetrix GeneChip scanner 3000 7G

data_processing: Affymetrix GeneChip Command Console Software and Affymetric Expression Console were used to generate .CEL files and QC metrics. Analysis of gene expression data was done with the Affymetrix® Transcriptome Analysis Console (TAC) Software. Affymetrix Transcriptome Analysis Console (TAC) Software was used to analyze gene expression data. Normalization was performed using the Robust Multi-chip Average (RMA) method. The data in the matrix table contains the log2 transformed RMA normalized signal from all 15 samples.

organism: Caenorhabditis elegans

source_name: Eat-2 mutant worms syncronised and grown to L4 malt just prior to treatment

label_protocol: labelled using the Affymetric GeneChip 3@ IVT Express labelling kit as per the manufacturer’s instructions using 200ng of total RNA was input into the labelling reaction

growth_protocol: Grown at 20°C on standard nematode growth medium

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

treatment_protocol: Worms were transphered to nematode growth medium containing the drug under study and/or 2% DMSO for 72 hours pre extraction.

value: Whole organism

value: Eat-2 mutant

tag: age

value: 72 hours post L4 malt


title: Eat-2 mutant worms treated with 2% DMSO alone replicate 2


title: genomic DNA from PM193 control maternal blood


title: Wild type worms treated with allantoin in 2% DMSO replicate 3

source_name: Wildtype worms syncronised and grown to L4 malt just prior to treatment

value: N2 Wildtype


title: Wild type worms treated with allantoin in 2% DMSO replicate 2


title: Wild type worms treated with rapamycin in 2% DMSO replicate 3


title: Eat-2 mutant worms treated with rapamycin in 2% DMSO replicate 3


title: Eat-2 mutant worms treated with rapamycin in 2% DMSO replicate 1


title: Wild type worms treated with rapamycin in 2% DMSO replicate 1


title: Wild type worms treated with allantoin in 2% DMSO replicate 1


title: Wild type worms treated with 2% DMSO alone replicate 3


title: Wild type worms treated with 2% DMSO alone replicate 2


title: genomic DNA from PM190 control maternal blood

value: F


title: Wild type worms treated with 2% DMSO alone replicate 1


title: Wild type worms treated with rapamycin in 2% DMSO replicate 2


title: genomic DNA from PM177 control maternal blood


title: CC-11050-vs-Uninfected_12w-4

status: Public on Dec 21 2015

city: Newark

first: Selvakumar

last: Subbian

state: NJ

address: 225 Warren Street

department: Medicine

institute: PHRI, NJMS, Rutgers the State University of NJ

description: Biological replicate

hyb_protocol: standard operating protocol from the Center for Applied Genomics core of the Rutgers Biomedical and Health Sciences, Rutgers university was used for labeling, hybridization and post-hybridization washings for all the experiments

scan_protocol: The rabbit microarray slides were scanned using Agilent scanner

data_processing:
Microarray data from the scanned images were extracted using the software from Agilent technologies, processed with RMA used for downstream analysis with a commercial software.
RMA-corrected and Lowess-error-normalized log2 ratio (Red vs Green Channel) for significant difference in fold change in gene expression was calculated using one-way ANOVA .

organism: Oryctolagus cuniculus

source_name: Lung, uninfected

label_protocol: cDNA was synthesised from total RNA using First strand synthesis kit (Invitrogen) and was labelled with either Cy3 or Cy5 using the kit from the manufacturer (Agilent Technologies)

extract_protocol: Total RNA from the rabbit lungs were isolated using TRIzol reagent (Invitrogen, CA, USA) according to the instructions of the manufacturers and purified through a Qiagen RNA kit.

treatment_protocol:
[Infection protocol] New Zealand White rabbits were infected with Mtb HN878 at about 3.2log10 (on day 0).  One group of rabbits each were treated with CC-11050 for 8 weeks (i.e, 12 weeks post infection).  Infected but not treated and uninfected rabbits were included as controls.
Lung samples were snap frozen at -80oC before isolation of total RNA (using TRIzol method)

tag: infection

value: No infection

value: no treatment

tag: time

value: 12 wks

value: lung

source_name: Lung, infected

value: Mtb HN878

value: 12 wks post infection


title: Eat-2 mutant worms treated with 2% DMSO alone replicate 1

tag: genotype


title: CC-11050-vs-Uninfected_12w-3

description: Biological replicate


title: genomic DNA from PM151 control maternal blood

value: control


title: genomic DNA from PM135 control maternal blood


title: slide 346836

city: Jena

first: Akos

middle: T

last: Kovacs

address: Neugasse 23

department: Institute of Microbiology

institute: Friedrich Schiller University of Jena

description: comparison of wild type and floA mutant at stationer phase

hyb_protocol: The protocol was performed as described in Lulko, et. al. J. Mol. Microbiol. Biotechnol. 12:82-95 PMID: 17183215

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner

data_processing: Dual-channel array images were analyzed with ArrayPro 4.5 software (Media Cybernetics Inc.). Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP as previously described (den Hengst et al J. Biol. Chem. 280:34332-34342; PMID: 16040604). Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets.Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of mutant strain over the wild-type strain were calculated. Further analysis was performed with a Cyber-T Student t test for paired data.

organism: Bacillus subtilis

source_name: Net{A}

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using NucleoSpin Extract II columns

growth_protocol: B subtilis NCIB 3610 wild type and its floT, floA, and floT-floA derivative strains were grown in MSgg medium and cells were harvested at late exponential phase (OD600 ~1.0-1.2).  For each strains, 3 biological replicates were used, resulting 3 slides per comparison.  RNA purification was performed on the samples as previosuly described Kovacs and Kuipers 2011 J Bacteriol 193(4): 998-1002.

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Kovacs and Kuipers 2011 JBacteriol 193(4): 998-1002 PMID: 21097620). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

treatment_protocol: no treatment

tag: strain

source_name: Net{B}

value: floA


title: CC-11050-vs-Uninfected_12w-2

description: Biological replicate


title: slide 346843

description: comparison of wild type and floT floA double mutant at stationer phase

value: floT-floA


title: slide 346837


title: slide 346840


title: Untreated-vs-UnInfected_12w-4

description: Biological replicate

value: untreated


title: Untreated-vs-UnInfected_12w-2

description: Biological replicate


title: slide 347183


title: Eat-2 mutant worms treated with rapamycin in 2% DMSO replicate 2


title: Untreated-vs-UnInfected_12w-3

description: Biological replicate


title: CC-11050-vs-Uninfected_12w-1

description: Biological replicate


title: Untreated-vs-UnInfected_12w-1

description: Biological replicate


title: Seedlings untreated, biological rep1

city: Madrid

first: Maria

last: FernandezMarcos

state: Madrid

address: Darwin 3

department: Genomic

country: Spain

institute: CNB-CSIC

description: Gene expression data from seedlings of Arabidopsis thaliana

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Analysis was performed using the affylmaGUI R package (Wettenhall et al., 2006). Robust Multi-array Analysis (RMA) algorithm was used for background correction, normalization and expression levels summarization (Irizarry et al., 2003). Next, differential expression analysis was performed with the Bayes t-statistics from the linear models for Microarray data (limma), included in the affylmGUI package. P-values were corrected for multiple-testing using the Benjamini-Hochberg’s method (False Discovery Rate) (Benjamini and Hochberg, 1995; Reiner et al., 2003).

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana ecotype Columbia-0

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The Arabidopsis plants used throughout this work were routinely grown in a growth chamber under 50-60% humidity, a temperature of 22°C, and with a 16-h light/8-h dark photoperiod at 80 to 100 µE m-2 s-1 in pots containing a 1:3 vermiculite:soil mixture.

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

treatment_protocol: After 3 days seedlings were placed under different treatments in open plastic dishes (receiver dish). Three receiver dishes were introduced in a 15 cm Petri dish together with one open, 5 cm Petri dish (donor dish) that contained 15 ml of the solution to be tested, 100 uM sodium nitroprusside (SNP). Three receiver dishes were introduced in another 15 cm Petri dish and 2 ml of 1 mM 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (cPTIO) solution were added into the receiver dishes. The 15 cm Petri dishes were sealed. After 5 days of treatment, tissues were collected and frozen (-80 ºC).

tag: agent

value: seedlings

tag: ecotype

value: seedlings of 8 days


title: Seedlings treated with SNP, biological rep2

value: sodium nitroprusside


title: ASC unstim Repl2

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

description: ASC 23.3 p11 U

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were quantile normalised using Illumina BeadStudio software (V2010.1, Gene Expression module v.1.6.0).

source_name: unstimulated adipose stem cells

label_protocol: Biotinylated cRNA was prepared with the Illumina TotalPrep RNA Amplification Kit

growth_protocol: Adipose stem cells were cultured in DMEM/F12 Glutamax containing 10% FCS and 1 % PenStrep.

extract_protocol: RNA was extracted using the RNeasy Mini Kit (Qiagen) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: For stim treatment, cells were treated with KO DMEM with 20 ng/ml EGF, 20 ng/ml bFGF and B27 for 2-3 weeks, for unstim, cells were treated with DMEM/F12 in parallel. Cells were trypsinized once per week

value: Adipose tissue

tag: cell type

value: mesenchymal stem cells (MSCs)

tag: stimulated with

value: none (unstimulated control)


title: Seedlings untreated, biological rep2


title: slide 347177

description: comparison of wild type and floT mutant at stationer phase

tag: stain

value: floT


title: Seedlings treated with cPTIO, biological rep2


title: Seedlings treated with SNP, biological rep1


title: Seedlings treated with SNP, biological rep3


title: Seedlings untreated, biological rep3


title: slide 346850


title: Seedlings treated with cPTIO, biological rep3


title: slide 347026


title: Seedlings treated with cPTIO, biological rep1


title: slide 347180


title: ASC unstim Repl3

description: FSC2 p3 U


title: ASC unstim Repl1

description: ASC 18.2 p13 U


title: genomic DNA from PM83 control amniotic membrane

tag: status/group

tag: fetal sex/sex

value: M

tag: sample tissue

value: amniotic membrane

tag: age (years)


title: 6D-Mock.2

city: Jouy en Josas

first: Aude

last: Remot

address: Domaine de Vilvert

department: VIM

country: France

institute: INRA

hyb_protocol: We followed Agilent monocolor hybridization protocol, as adviced by the manufacturer.

scan_protocol: Raw data were extracted from scanned microarray images (.tif) using Feature Extraction Software v9.5 (Agilent)

data_processing: Data were normalized using intra-array median substraction and log2 transformation

source_name: Lung, 2 days post-infection from a 6 days old BALB/C pup

label_protocol: Total RNAs (200 ng) were amplified by linear PCR and the amplification products were labeled with Cy3 (5190-2305, LowInput QuickAmp Labeling Kit One-Color, Agilent)

growth_protocol: SPF Mice were bred and housed under FELASA condition

extract_protocol: Total RNA was extracted from lung homogenate using RNA minikit columns (Qiagen), with a 15 min DNase treatment (Rnase free DNase set, Qiagen), according to the manufacturer’s instructions.

treatment_protocol: Animals were sacrificed by cervical dislocation, lung were collected and frozen in liquid nitrogen, stored at -80°C until RNA extraction

value: BALB/C

value: Mock


title: 6W-Mock.1

source_name: Lung, 2 days post-infection from a 6 weeks old BALB/C mouse


title: 6D-Mock.3


title: 6W-Mock.4


title: 6D-RSV.3

value: RSV


title: 6W-RSV.3


title: 6W-RSV.2


title: 6W-Mock.2


title: 6D-Mock.4


title: 6D-RSV.2


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 60hrs, Biological replicate3

city: Seattle

first: Richard

last: Gelinas

address: 401 Terry Avenue North

institute: Institute for Systems Biology

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 60hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_60hrs_rep3

hyb_protocol: Labeled target was hybridized overnight to Affymetrix U219-96 plates followed by washing, staining on the Affymetrix GeneTitan instrument following the manufacturer’s protocol.

scan_protocol: Scanning was also performed on the Affymetrix GeneTitan instrument following the manufacturer’s protocol.

data_processing: Cel files were preprocessed with RMA method from R/Bioconductor for background correction, quantile normalization and summarization

source_name: BEAS-2B, 60hrs after Both Influenza & Rhino virus infection

label_protocol: Purified RNA was stored at -80°C until use in the Genechip experiments. For the Genechip experiments, 250 ng of total RNA was converted to Genechip targets using the Affymetrix HT 3’ IVT Express (Santa Clara, CA) protocol optimized for use on the Beckman Coulter Biomek FXp automation workstation (Indianapolis, IN).

growth_protocol: Human bronchial epithelial cells (BEAS-2B; ATCC® CRL-9609™) were seeded into 12-well plates at a density of 2.8 x 105 cells/well and placed overnight in the 37oC incubator with 5% CO2 and 90% humidity.

extract_protocol: Total RNA (including small RNAs) was isolated from BEAS-2B cells with QIAgen (Helden, Germany) miRNeasy Mini columns using the manufacturer’s protocol.  In brief, monolayer BEAS-2B cells were rinsed once with ice-cold phosphate buffered saline (pH 7.4) followed by extraction in QIAzol lysis reagent and brief vortexing.  Lysates were frozen at -80°C until RNA isolation.  For RNA isolation, lysates were thawed on ice and then extracted once in chloroform.  Ethanol was added to the aqueous phase of the extract and this mixture was added to RNeasy spin columns.  Columns were washed to remove contaminants and purified total RNA was eluted with nuclease-free water.  RNA quantity was determined using a NanoDrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA).

treatment_protocol: On the day of infection, the rhinovirus strain RV16 (RV) and the influenza virus (IV) (H1N1, strain A/WS/33, ATCC IV-1520) stocks were removed from a -80oC freezer, and diluted in serum-free medium. After removing the cell culture medium from the BEAS-2B cells, 300 μl of the diluted virus (either RV, IV or RV+IV) was added to each well. A similar volume of medium alone was added to the control wells. A multiplicity of infection of 2 was used for each virus. All plates were incubated at 33oC with 5% CO2 and 90% humidity. All infected and uninfected (control) samples were collected at the scheduled time points (2, 4, 8, 12, 24, 36, 48, 60 and 78 hours post-infection) and processed according to a randomized schedule to minimize the possibility of experimentally induced batch effects.

tag: virus infection

value: Influenza & Rhino virus infected

tag: virus serotype

tag: time point


title: 6D-RSV.4


title: 6W-Mock.3


title: 6W-RSV.1


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 72hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 72hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_72hrs_rep5

source_name: BEAS-2B, 72hrs after Both Influenza & Rhino virus infection


title: 6W-RSV.4


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 60hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 60hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_60hrs_rep5


title: 6D-Mock.1


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 48hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 48hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_48hrs_rep5

source_name: BEAS-2B, 48hrs after Both Influenza & Rhino virus infection


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 72hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 72hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_72hrs_rep3


title: 6D-RSV.1


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 72hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 72hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_72hrs_rep4


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 48hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 48hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_48hrs_rep3


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 60hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 60hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_60hrs_rep2


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 60hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 60hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_60hrs_rep4


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 72hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 72hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_72hrs_rep1


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 48hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 48hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_48hrs_rep4


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 60hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 60hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_60hrs_rep1


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 72hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 72hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_72hrs_rep2


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 48hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 48hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_48hrs_rep2


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 36hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 36hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_36hrs_rep2

source_name: BEAS-2B, 36hrs after Both Influenza & Rhino virus infection


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 36hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 36hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_36hrs_rep4


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 24hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 24hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_24hrs_rep5

source_name: BEAS-2B, 24hrs after Both Influenza & Rhino virus infection


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 8hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 8hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_8hrs_rep2

source_name: BEAS-2B, 8hrs after Both Influenza & Rhino virus infection


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 12hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 12hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_12hrs_rep1

source_name: BEAS-2B, 12hrs after Both Influenza & Rhino virus infection


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 8hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 8hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_8hrs_rep4


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 8hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 8hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_8hrs_rep3


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 4hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 4hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_4hrs_rep5

source_name: BEAS-2B, 4hrs after Both Influenza & Rhino virus infection


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 48hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 48hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_48hrs_rep1


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 12hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 12hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_12hrs_rep2


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 36hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 36hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_36hrs_rep5


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 24hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 24hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_24hrs_rep2


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 36hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 36hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_36hrs_rep3


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 24hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 24hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_24hrs_rep4


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 8hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 8hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_8hrs_rep1


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 2hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 2hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_2hrs_rep3

source_name: BEAS-2B, 2hrs after Both Influenza & Rhino virus infection


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 8hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 8hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_8hrs_rep5


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 24hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 24hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_24hrs_rep1


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 4hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 4hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_4hrs_rep4


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 12hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 12hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_12hrs_rep4


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 4hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 4hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_4hrs_rep1


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 2hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 2hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_2hrs_rep4


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 4hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 4hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_4hrs_rep2


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 2hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 2hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_2hrs_rep5


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 4hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 4hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_4hrs_rep3


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 12hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 12hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_12hrs_rep3


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 12hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 12hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_12hrs_rep5


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 2hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 2hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_2hrs_rep2


title: BEAS-2B, RhinoVirus 72hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 72hrs after Rhino virus infection
RhinoVirus_72hrs_rep5

source_name: BEAS-2B, 72hrs after Rhino virus infection

value: Rhino virus infected


title: BEAS-2B, RhinoVirus 72hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 72hrs after Rhino virus infection
RhinoVirus_72hrs_rep3


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 2hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 2hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_2hrs_rep1


title: BEAS-2B, RhinoVirus 72hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 72hrs after Rhino virus infection
RhinoVirus_72hrs_rep4


title: BEAS-2B, RhinoVirus 48hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 48hrs after Rhino virus infection
RhinoVirus_48hrs_rep2

source_name: BEAS-2B, 48hrs after Rhino virus infection


title: BEAS-2B, RhinoVirus 48hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 48hrs after Rhino virus infection
RhinoVirus_48hrs_rep4


title: BEAS-2B, RhinoVirus 60hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 60hrs after Rhino virus infection
RhinoVirus_60hrs_rep3

source_name: BEAS-2B, 60hrs after Rhino virus infection


title: BEAS-2B, RhinoVirus 60hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 60hrs after Rhino virus infection
RhinoVirus_60hrs_rep5


title: BEAS-2B, RhinoVirus 72hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 72hrs after Rhino virus infection
RhinoVirus_72hrs_rep2


title: BEAS-2B, RhinoVirus 72hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 72hrs after Rhino virus infection
RhinoVirus_72hrs_rep1


title: BEAS-2B, RhinoVirus 60hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 60hrs after Rhino virus infection
RhinoVirus_60hrs_rep4


title: BEAS-2B, RhinoVirus 36hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 36hrs after Rhino virus infection
RhinoVirus_36hrs_rep5

source_name: BEAS-2B, 36hrs after Rhino virus infection


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 36hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 36hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_36hrs_rep1


title: BEAS-2B, RhinoVirus 12hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 12hrs after Rhino virus infection
RhinoVirus_12hrs_rep2

source_name: BEAS-2B, 12hrs after Rhino virus infection


title: BEAS-2B, RhinoVirus 48hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 48hrs after Rhino virus infection
RhinoVirus_48hrs_rep5


title: BEAS-2B, RhinoVirus 60hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 60hrs after Rhino virus infection
RhinoVirus_60hrs_rep2


title: BEAS-2B, RhinoVirus 12hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 12hrs after Rhino virus infection
RhinoVirus_12hrs_rep3


title: BEAS-2B, RhinoVirus 12hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 12hrs after Rhino virus infection
RhinoVirus_12hrs_rep5


title: BEAS-2B, RhinoVirus 36hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 36hrs after Rhino virus infection
RhinoVirus_36hrs_rep3


title: BEAS-2B, RhinoVirus 60hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 60hrs after Rhino virus infection
RhinoVirus_60hrs_rep1


title: BEAS-2B, RhinoVirus 48hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 48hrs after Rhino virus infection
RhinoVirus_48hrs_rep3


title: BEAS-2B, RhinoVirus 24hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 24hrs after Rhino virus infection
RhinoVirus_24hrs_rep4

source_name: BEAS-2B, 24hrs after Rhino virus infection


title: BEAS-2B, RhinoVirus 36hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 36hrs after Rhino virus infection
RhinoVirus_36hrs_rep2


title: BEAS-2B, RhinoVirus 24hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 24hrs after Rhino virus infection
RhinoVirus_24hrs_rep1


title: BEAS-2B, RhinoVirus 24hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 24hrs after Rhino virus infection
RhinoVirus_24hrs_rep2


title: BEAS-2B, RhinoVirus 48hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 48hrs after Rhino virus infection
RhinoVirus_48hrs_rep1


title: BEAS-2B, RhinoVirus 8hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 8hrs after Rhino virus infection
RhinoVirus_8hrs_rep5

source_name: BEAS-2B, 8hrs after Rhino virus infection


title: BEAS-2B, RhinoVirus 24hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 24hrs after Rhino virus infection
RhinoVirus_24hrs_rep3


title: BEAS-2B, RhinoVirus 12hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 12hrs after Rhino virus infection
RhinoVirus_12hrs_rep4


title: BEAS-2B, RhinoVirus 36hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 36hrs after Rhino virus infection
RhinoVirus_36hrs_rep4


title: BEAS-2B, RhinoVirus 36hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 36hrs after Rhino virus infection
RhinoVirus_36hrs_rep1


title: BEAS-2B, RhinoVirus 24hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 24hrs after Rhino virus infection
RhinoVirus_24hrs_rep5


title: BEAS-2B, RhinoVirus 4hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 4hrs after Rhino virus infection
RhinoVirus_4hrs_rep5

source_name: BEAS-2B, 4hrs after Rhino virus infection


title: BEAS-2B, RhinoVirus 8hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 8hrs after Rhino virus infection
RhinoVirus_8hrs_rep4


title: BEAS-2B, InfluenzaVirus 60hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 60hrs after Influenza virus infection
InfluenzaVirus_60hrs_rep3

source_name: BEAS-2B, 60hrs after Influenza virus infection

value: Influenza virus infected


title: BEAS-2B, RhinoVirus 12hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 12hrs after Rhino virus infection
RhinoVirus_12hrs_rep1


title: BEAS-2B, RhinoVirus 8hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 8hrs after Rhino virus infection
RhinoVirus_8hrs_rep3


title: BEAS-2B, RhinoVirus 8hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 8hrs after Rhino virus infection
RhinoVirus_8hrs_rep2


title: BEAS-2B, RhinoVirus 8hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 8hrs after Rhino virus infection
RhinoVirus_8hrs_rep1


title: BEAS-2B, RhinoVirus 4hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 4hrs after Rhino virus infection
RhinoVirus_4hrs_rep3


title: BEAS-2B, RhinoVirus 2hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 2hrs after Rhino virus infection
RhinoVirus_2hrs_rep2

source_name: BEAS-2B, 2hrs after Rhino virus infection


title: BEAS-2B, InfluenzaVirus 72hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 72hrs after Influenza virus infection
InfluenzaVirus_72hrs_rep3

source_name: BEAS-2B, 72hrs after Influenza virus infection


title: BEAS-2B, InfluenzaVirus 72hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 72hrs after Influenza virus infection
InfluenzaVirus_72hrs_rep2


title: BEAS-2B, RhinoVirus 4hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 4hrs after Rhino virus infection
RhinoVirus_4hrs_rep4


title: BEAS-2B, RhinoVirus 2hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 2hrs after Rhino virus infection
RhinoVirus_2hrs_rep4


title: BEAS-2B, RhinoVirus 4hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 4hrs after Rhino virus infection
RhinoVirus_4hrs_rep2


title: BEAS-2B, RhinoVirus 4hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 4hrs after Rhino virus infection
RhinoVirus_4hrs_rep1


title: BEAS-2B, InfluenzaVirus 60hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 60hrs after Influenza virus infection
InfluenzaVirus_60hrs_rep4


title: BEAS-2B, InfluenzaVirus 72hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 72hrs after Influenza virus infection
InfluenzaVirus_72hrs_rep1


title: BEAS-2B, InfluenzaVirus 72hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 72hrs after Influenza virus infection
InfluenzaVirus_72hrs_rep4


title: BEAS-2B, InfluenzaVirus 60hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 60hrs after Influenza virus infection
InfluenzaVirus_60hrs_rep2


title: BEAS-2B, InfluenzaVirus 48hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 48hrs after Influenza virus infection
InfluenzaVirus_48hrs_rep2

source_name: BEAS-2B, 48hrs after Influenza virus infection


title: BEAS-2B, RhinoVirus 2hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 2hrs after Rhino virus infection
RhinoVirus_2hrs_rep1


title: BEAS-2B, InfluenzaVirus 60hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 60hrs after Influenza virus infection
InfluenzaVirus_60hrs_rep5


title: BEAS-2B, InfluenzaVirus 72hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 72hrs after Influenza virus infection
InfluenzaVirus_72hrs_rep5


title: BEAS-2B, InfluenzaVirus 60hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 60hrs after Influenza virus infection
InfluenzaVirus_60hrs_rep1


title: BEAS-2B, RhinoVirus 2hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 2hrs after Rhino virus infection
RhinoVirus_2hrs_rep5


title: BEAS-2B, RhinoVirus 2hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 2hrs after Rhino virus infection
RhinoVirus_2hrs_rep3


title: BEAS-2B, Both InfluenzaVirus and RhinoVirus 24hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 24hrs after both Influenza and Rhino virus infection
Both_Rhino_InfluenzaVirus_24hrs_rep3

source_name: BEAS-2B, 24hrs after Both Influenza & Rhino virus infection


title: BEAS-2B, InfluenzaVirus 48hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 48hrs after Influenza virus infection
InfluenzaVirus_48hrs_rep5


title: BEAS-2B, InfluenzaVirus 48hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 48hrs after Influenza virus infection
InfluenzaVirus_48hrs_rep3


title: BEAS-2B, InfluenzaVirus 48hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 48hrs after Influenza virus infection
InfluenzaVirus_48hrs_rep4


title: BEAS-2B, InfluenzaVirus 48hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 48hrs after Influenza virus infection
InfluenzaVirus_48hrs_rep1


title: BEAS-2B, InfluenzaVirus 36hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 36hrs after Influenza virus infection
InfluenzaVirus_36hrs_rep3

source_name: BEAS-2B, 36hrs after Influenza virus infection


title: BEAS-2B, InfluenzaVirus 36hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 36hrs after Influenza virus infection
InfluenzaVirus_36hrs_rep4


title: BEAS-2B, InfluenzaVirus 36hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 36hrs after Influenza virus infection
InfluenzaVirus_36hrs_rep2


title: BEAS-2B, InfluenzaVirus 36hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 36hrs after Influenza virus infection
InfluenzaVirus_36hrs_rep5


title: BEAS-2B, InfluenzaVirus 24hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 24hrs after Influenza virus infection
InfluenzaVirus_24hrs_rep3

source_name: BEAS-2B, 24hrs after Influenza virus infection


title: BEAS-2B, InfluenzaVirus 24hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 24hrs after Influenza virus infection
InfluenzaVirus_24hrs_rep5


title: BEAS-2B, InfluenzaVirus 24hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 24hrs after Influenza virus infection
InfluenzaVirus_24hrs_rep1


title: liver_patient_14_CCC_rep1 (miRNA)

city: Tokyo

first: Y-H.

last: Taguchi

state: Non-US/Canada

address: 1-13-27 Kasuga,Bukyo-ku

department: Physics

country: Japan

institute: Chuo University

description:
CCC
miRNA_27

hyb_protocol: For miRNA microarray, 100 ng of RNA was labeled and hybridized using the Human microRNA Microarray Kit (Rel 14.0) (Agilent Technologies, CA, USA) according to manufacturer’s protocol for use with Agilent microRNA microarrays Version 1.0.For mRNA micaroarray, 100 ng of RNA was labeled and hybridized using the SurePrint G3 Human GE microarray kit (G4851B) (Agilent Technologies, CA, USA) according to manufacturer’s protocol for use with Agilent microarrays.

scan_protocol: For miRNA microarray, hybridization signals were detected with Agilent DNA microarray scanner G2539B and the scanned images were analyzed using Agilent feature extraction software (v10.10.1.1). For mRNA microarray, hybridization signals were detected with Agilent DNA microarray scanner G2539A and the scanned images were analyzed using Agilent feature extraction software (v10.10.1.1).

data_processing: For miRNA and mRNA microarray, gProcessedSignal was extracted and normalized so as to have zero mean and variance of 1.

source_name: liver microRNA CCC tumor part

extract_protocol: RNA was prepared using the mirVana miRNA isolation kit (Life Technologies, CA, USA) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Surgically resected hepatocellular carcinoma (HCC) samples and surrounded non-tumor samples, and cholangiocarcinoma (CCC) samples and surrounded non-tumor samples

tag: patient

value: patient 14

tag: disease state

value: CCC

tag: tissue

value: liver_CCC tumor part

tag: gender

value: male

tag: age

tag: date of birth

tag: hospotal id


title: BEAS-2B, InfluenzaVirus 36hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 36hrs after Influenza virus infection
InfluenzaVirus_36hrs_rep1

tag: strain


title: BEAS-2B, InfluenzaVirus 24hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 24hrs after Influenza virus infection
InfluenzaVirus_24hrs_rep4


title: liver_patient_14_non_tumor_rep1 (miRNA)

description:
non-tumor
miRNA_28

source_name: liver microRNA non-tumor part

label_protocol: For miRNA microarray, 100 ng of RNA was labeled and hybridized using the Human microRNA Microarray Kit (Rel 14.0) (Agilent Technologies, CA, USA) according to manufacturer’s protocol for use with Agilent microRNA microarrays Version 1.0.For mRNA micaroarray, 100 ng of RNA was labeled and hybridized using the SurePrint G3 Human GE microarray kit (G4851B) (Agilent Technologies, CA, USA) according to manufacturer’s protocol for use with Agilent microarrays.

value: liver_non-tumor part


title: BEAS-2B, InfluenzaVirus 12hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 12hrs after Influenza virus infection
InfluenzaVirus_12hrs_rep4

source_name: BEAS-2B, 12hrs after Influenza virus infection


title: liver_patient_15_non_tumor_rep1 (miRNA)

description:
non-tumor
miRNA_30

value: patient 15

value: female


title: liver_patient_15_CCC_rep1 (miRNA)

description:
CCC
miRNA_29


title: BEAS-2B, InfluenzaVirus 8hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 8hrs after Influenza virus infection
InfluenzaVirus_8hrs_rep3

source_name: BEAS-2B, 8hrs after Influenza virus infection


title: liver_patient_16_non_tumor_rep1 (miRNA)

description:
non-tumor
miRNA_32

value: patient 16


title: liver_patient_13_non_tumor_rep1 (miRNA)

description:
non-tumor
miRNA_26

value: patient 13


title: liver_patient_12_non_tumor_rep1 (miRNA)

description:
non-tumor
miRNA_24

value: patient 12

tag: histol information

value: Moderately

tag: afp

tag: pivka-ii

tag: cea

tag: tumor size


title: BEAS-2B, InfluenzaVirus 12hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 12hrs after Influenza virus infection
InfluenzaVirus_12hrs_rep2


title: BEAS-2B, InfluenzaVirus 8hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 8hrs after Influenza virus infection
InfluenzaVirus_8hrs_rep5


title: liver_patient_13_CCC_rep1 (miRNA)

description:
CCC
miRNA_25


title: BEAS-2B, InfluenzaVirus 12hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 12hrs after Influenza virus infection
InfluenzaVirus_12hrs_rep3


title: BEAS-2B, InfluenzaVirus 8hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 8hrs after Influenza virus infection
InfluenzaVirus_8hrs_rep2


title: BEAS-2B, InfluenzaVirus 8hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 8hrs after Influenza virus infection
InfluenzaVirus_8hrs_rep1


title: liver_patient_12_CCC_rep1 (miRNA)

description:
CCC
miRNA_23


title: BEAS-2B, InfluenzaVirus 12hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 12hrs after Influenza virus infection
InfluenzaVirus_12hrs_rep5


title: BEAS-2B, InfluenzaVirus 8hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 8hrs after Influenza virus infection
InfluenzaVirus_8hrs_rep4


title: BEAS-2B, InfluenzaVirus 12hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 12hrs after Influenza virus infection
InfluenzaVirus_12hrs_rep1


title: liver_patient_16_CCC_rep1 (miRNA)

description:
CCC
miRNA_31


title: liver_patient_10_HCC_rep1 (miRNA)

description:
HCC
miRNA_19

source_name: liver microRNA HCC tumor part

value: patient 10

value: HCC

value: liver_HCC tumor part


title: liver_patient_9_HCC_rep1 (miRNA)

description:
HCC
miRNA_17

value: patient 9


title: liver_patient_8_HCC_rep1 (miRNA)

description:
HCC
miRNA_15

value: patient 8


title: BEAS-2B, InfluenzaVirus 2hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 2hrs after Influenza virus infection
InfluenzaVirus_2hrs_rep1

source_name: BEAS-2B, 2hrs after Influenza virus infection

value: Influenza virus infected


title: liver_patient_6_HCC_rep1 (miRNA)

description:
HCC
miRNA_10

value: patient 6

value: Poorly


title: BEAS-2B, InfluenzaVirus 24hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 24hrs after Influenza virus infection
InfluenzaVirus_24hrs_rep2


title: liver_patient_11_CCC_rep1 (miRNA)

description:
CCC
miRNA_21

value: patient 11

value: CCC

value: liver_CCC tumor part

value: moderate tubular


title: BEAS-2B, InfluenzaVirus 2hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 2hrs after Influenza virus infection
InfluenzaVirus_2hrs_rep2


title: BEAS-2B, InfluenzaVirus 4hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 4hrs after Influenza virus infection
InfluenzaVirus_4hrs_rep5

source_name: BEAS-2B, 4hrs after Influenza virus infection


title: BEAS-2B, control 72hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 72hrs
Control_72hrs_rep5

source_name: BEAS-2B, control 72hrs

value: uninfected


title: BEAS-2B, InfluenzaVirus 4hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 4hrs after Influenza virus infection
InfluenzaVirus_4hrs_rep2


title: liver_patient_6_non_tumor_rep1 (miRNA)

description:
non-tumor
miRNA_12

value: liver_non-tumor part

value: male


title: liver_patient_10_non_tumor_rep1 (miRNA)

description:
non-tumor
miRNA_20


title: BEAS-2B, control 72hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 72hrs
Control_72hrs_rep4


title: liver_patient_11_non_tumor_rep1 (miRNA)

description:
non-tumor
miRNA_22

value: female


title: BEAS-2B, InfluenzaVirus 2hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 2hrs after Influenza virus infection
InfluenzaVirus_2hrs_rep4


title: BEAS-2B, InfluenzaVirus 4hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 4hrs after Influenza virus infection
InfluenzaVirus_4hrs_rep4


title: liver_patient_7_non_tumor_rep1 (miRNA)

description:
non-tumor
miRNA_14

value: patient 7

value: Moderately


title: liver_patient_8_non_tumor_rep1 (miRNA)

description:
non-tumor
miRNA_16

value: HCC


title: BEAS-2B, InfluenzaVirus 4hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 4hrs after Influenza virus infection
InfluenzaVirus_4hrs_rep1


title: BEAS-2B, control 72hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 72hrs
Control_72hrs_rep3


title: liver_patient_7_HCC_rep1 (miRNA)

description:
HCC
miRNA_13

value: liver_HCC tumor part


title: BEAS-2B, InfluenzaVirus 2hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 2hrs after Influenza virus infection
InfluenzaVirus_2hrs_rep5


title: liver_patient_5_non_tumor_rep1 (miRNA)

description:
non-tumor
miRNA_11

value: patient 5


title: BEAS-2B, InfluenzaVirus 2hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 2hrs after Influenza virus infection
InfluenzaVirus_2hrs_rep3


title: liver_patient_9_non_tumor_rep1 (miRNA)

description:
non-tumor
miRNA_18

value: patient 9


title: BEAS-2B, InfluenzaVirus 4hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) 4hrs after Influenza virus infection
InfluenzaVirus_4hrs_rep3

value: Influenza virus infected


title: liver_patient_4_CCC_rep1 (miRNA)

description:
CCC
miRNA_7

value: patient 4


title: liver_patient_3_CCC_rep1 (miRNA)

description:
CCC
miRNA_5

value: patient 3


title: BEAS-2B, control 60hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 60hrs
Control_60hrs_rep1

source_name: BEAS-2B, control 60hrs


title: BEAS-2B, control 60hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 60hrs
Control_60hrs_rep4


title: BEAS-2B, control 48hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 48hrs
Control_48hrs_rep4

source_name: BEAS-2B, control 48hrs


title: BEAS-2B, control 60hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 60hrs
Control_60hrs_rep2


title: liver_patient_2_non_tumor_rep1 (miRNA)

description:
non-tumor
miRNA_4

value: patient 2


title: BEAS-2B, control 36hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 36hrs
Control_36hrs_rep2

source_name: BEAS-2B, control 36hrs


title: liver_patient_1_CCC_rep1 (miRNA)

description:
CCC
miRNA_1

value: patient 1

value: CCC


title: BEAS-2B, control 48hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 48hrs
Control_48hrs_rep3


title: liver_patient_1_non_tumor_rep1 (miRNA)

description:
non-tumor
miRNA_2

value: moderate tubular


title: BEAS-2B, control 36hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 36hrs
Control_36hrs_rep3

value: uninfected


title: liver_patient_3_non_tumor_rep1 (miRNA)

description:
non-tumor
miRNA_6

value: liver_non-tumor part


title: liver_patient_4_non_tumor_rep1 (miRNA)

description:
non-tumor
miRNA_8

value: male


title: BEAS-2B, control 72hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 72hrs
Control_72hrs_rep1


title: BEAS-2B, control 48hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 48hrs
Control_48hrs_rep5


title: BEAS-2B, control 60hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 60hrs
Control_60hrs_rep5


title: BEAS-2B, control 48hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 48hrs
Control_48hrs_rep2


title: BEAS-2B, control 60hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 60hrs
Control_60hrs_rep3


title: BEAS-2B, control 36hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 36hrs
Control_36hrs_rep4


title: BEAS-2B, control 48hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 48hrs
Control_48hrs_rep1


title: BEAS-2B, control 36hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 36hrs
Control_36hrs_rep5


title: liver_patient_5_CCC_rep1 (miRNA)

description:
CCC
miRNA_9

value: liver_CCC tumor part


title: liver_patient_2_CCC_rep1 (miRNA)

description:
CCC
miRNA_3


title: BEAS-2B, control 72hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 72hrs
Control_72hrs_rep2


title: CD, biological rep1 (AS level)

city: Chongqing

first: Jin

last: Shang

address: No. 183, Xinqiao Main Street

country: China

institute: Third Military Medical University

description: Alternative splicing data from human CESCs

hyb_protocol: After fragmentation, 5 ug cDNA were hybridized for 16hr at 45C in 60rpm of spanning on Human Transcriptome Array 2.0. The microarray was washed and stained using Affymetrix GeneChip Command Console (AGCC) software.

scan_protocol: The microarray was scanned using AGCC software.

data_processing: We used Expression Console software to pre-treat .CEL files through Robust Multichip Analysis (RMA) algorithm (3), including background correction, probeset signal integration, quantile normalization. After pretreatment, the obtained chp files were analyzed by Transcriptome Analysis Console software to identify differentially expressed genes (DEGs) and alternatively spliced genes (ASGs).

source_name: Chondrogenic differentiation of CESCs

label_protocol: Fragmented single-stranded DNA was labeled using DNA labeling reagent according to standard Affymetrix protocol.

tag: cell type

value: Chondrogenic differentiation of CESCs


title: BEAS-2B, control 12hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 12hrs
Control_12hrs_rep5

source_name: BEAS-2B, control 12hrs

tag: virus infection


title: BEAS-2B, control 24hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 24hrs
Control_24hrs_rep3

source_name: BEAS-2B, control 24hrs

tag: virus serotype


title: UD, biological rep1 (AS level)

source_name: Undifferentiated CESCs

value: Undifferentiated CESCs


title: Hepatocyte B6T

hyb_protocol: Hybridization done by Nimblegen as per normal service protocol. MeDIP and input DNA samples were hybridized onto Roche-Nimblegen human HG18 RefSeq 720K Promoter arrays covering 5 kb of all human promoters (C4226-00-01; www.nimblegen.com).

scan_protocol: Scanning done by Nimblegen as per normal service protocol

data_processing: log2 (MeDIP/Input) with biweight mean of values subtracted

source_name: Isolated non-cultured hepatocytes_IP

label_protocol: Labeling done by Nimblegen as per normal service protocol

growth_protocol: Uncultured isolated cells

extract_protocol: MeDIP was performed in duplicate from 4 µg DNA as described (Sørensen and Collas, 2009). In brief, genomic DNA was treated with 30 µg/ml RNase A for 2 h at 37oC, and fragmented to ~200-800 base pairs by sonication. Sonicated DNA was ethanol-precipitated using glycogen as a carrier and dissolved in 60 µl MilliQ H2O. Two microgram sonicated DNA were diluted in 450 µl TE buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA), denatured for 10 min in boiling water and immediately chilled on ice for 10 min. Fifty-one microliters of 10x IP buffer (1x: 140 mM NaCl, 10 mM Na-Phosphate, pH 7.0, 0.05% Triton X-100) and 10 µl 5-methylcytosine antibodies (Diagenode) were added and incubated for 2 h at 4oC on a rotator. Pre-washed Dynabeads® M-280 sheep anti-mouse IgG (Invitrogen) in 40 µl IP buffer were added and incubated for 2 h at 4oC on a rotator. Samples were collected by magnetic separation, washed and immune complexes digested with Proteinase K for 3 h at 50oC. DNA was extracted with phenol-chloroform isoamylalcohol, ethanol-precipitated and dissolved in 15 µl H2O overnight. Input DNA was fragmented and treated as above except that no immunoprecipitation step was performed. Precipitated and input DNA was amplified using the WGA-2 Whole Genome Amplification kit (Sigma-Aldrich) and cleaned up using the Qiagen MinElute PCR Purification kit.

treatment_protocol: Genomic DNA was fragmented by sonication to 200-500 bp in a Bioruptor (Diagenode), and methylated fragments immunoprecipitated using the anti-5-methylC antibody.

tag: cell state / treatment

value: Freshly isolated cells, frozen and processed for meDIP

tag: medip antibody

value: Diagenode MAb-5MCYT

value: hepatocyte

value: liver

source_name: Isolated non-cultured hepatocytes_input

treatment_protocol: Genomic DNA was fragmented by sonication to 200-500 bp in a Bioruptor (Diagenode).

value: hepatocytes


title: liver_patient_15_non_tumor_rep1 (mRNA)

description:
non-tumor
mRNA_30

source_name: liver mRNA non-tumor part

tag: patient

value: patient 15

tag: disease state

value: female


title: BEAS-2B, control 24hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 24hrs
Control_24hrs_rep5

tag: time point


title: BEAS-2B, control 12hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 12hrs
Control_12hrs_rep1


title: BEAS-2B, control 8hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 8hrs
Control_8hrs_rep5

source_name: BEAS-2B, control 8hrs


title: BEAS-2B, control 24hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 24hrs
Control_24hrs_rep2


title: BEAS-2B, control 8hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 8hrs
Control_8hrs_rep4


title: liver_patient_16_non_tumor_rep1 (mRNA)

description:
non-tumor
mRNA_32

value: patient 16

tag: tissue

tag: gender

tag: age


title: BEAS-2B, control 12hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 12hrs
Control_12hrs_rep2

tag: strain


title: BEAS-2B, control 24hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 24hrs
Control_24hrs_rep1


title: BEAS-2B, control 8hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 8hrs
Control_8hrs_rep3


title: BEAS-2B, control 12hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 12hrs
Control_12hrs_rep3


title: BEAS-2B, control 24hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 24hrs
Control_24hrs_rep4


title: liver_patient_13_non_tumor_rep1 (mRNA)

description:
non-tumor
mRNA_26

value: patient 13

tag: date of birth

tag: hospotal id


title: BEAS-2B, control 36hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 36hrs
Control_36hrs_rep1


title: BEAS-2B, control 12hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 12hrs
Control_12hrs_rep4


title: Hepatocyte B5O


title: BEAS-2B, control 2hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 2hrs
Control_2hrs_rep5

source_name: BEAS-2B, control 2hrs


title: liver_patient_12_non_tumor_rep1 (mRNA)

description:
non-tumor
mRNA_24

value: patient 12

value: CCC

tag: histol information

value: Moderately

tag: afp

tag: pivka-ii


title: BEAS-2B, control baseline, Biological replicate6

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control baseline
Control_Baseline_rep6

source_name: BEAS-2B, control baseline

value: uninfected

value: baseline


title: BEAS-2B, control 4hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 4hrs
Control_4hrs_rep2

source_name: BEAS-2B, control 4hrs


title: BEAS-2B, control 4hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 4hrs
Control_4hrs_rep3


title: liver_patient_7_non_tumor_rep1 (mRNA)

description:
non-tumor
mRNA_14

value: patient 7

value: HCC

value: liver_non-tumor part

value: male

tag: cea

tag: tumor size


title: liver_patient_8_non_tumor_rep1 (mRNA)

description:
non-tumor
mRNA_16

value: patient 8


title: BEAS-2B, control 4hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 4hrs
Control_4hrs_rep4

tag: virus infection

tag: virus serotype


title: BEAS-2B, control 2hrs, Biological replicate3

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 2hrs
Control_2hrs_rep3


title: BEAS-2B, control 4hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 4hrs
Control_4hrs_rep1


title: BEAS-2B, control 2hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 2hrs
Control_2hrs_rep1


title: liver_patient_10_non_tumor_rep1 (mRNA)

description:
non-tumor
mRNA_20

value: patient 10


title: BEAS-2B, control 4hrs, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 4hrs
Control_4hrs_rep5


title: BEAS-2B, control 2hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 2hrs
Control_2hrs_rep2


title: BEAS-2B, control 8hrs, Biological replicate2

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 8hrs
Control_8hrs_rep2


title: BEAS-2B, control 8hrs, Biological replicate1

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 8hrs
Control_8hrs_rep1


title: liver_patient_14_non_tumor_rep1 (mRNA)

description:
non-tumor
mRNA_28

value: patient 14


title: liver_patient_9_non_tumor_rep1 (mRNA)

description:
non-tumor
mRNA_18

value: patient 9


title: Liver sinusoidal endothelial cell Patient L11

source_name: Isolated non-cultured liver sinusoidal endothelial cells_IP

tag: cell state / treatment

value: Freshly isolated cells, frozen and processed for meDIP

tag: medip antibody

value: Diagenode MAb-5MCYT

tag: cell type

value: liver sinusoidal endothelial cells

value: liver

source_name: Isolated non-cultured liver sinusoidal endothelial cells_input


title: Activated hepatic stellate cell Patient L11

source_name: Cultured hepatic stellate cells_IP

growth_protocol: Culture in DMEM/10& fetal calf serum  for 4-5 passages

value: Proliferating, untreated

value: hepatic stellate cell

source_name: Cultured hepatic stellate cells_input

value: hepatic stellate cells


title: Liver sinusoidal endothelial cell Patient L4


title: BEAS-2B, control 2hrs, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control 2hrs
Control_2hrs_rep4

value: uninfected

tag: time point


title: BEAS-2B, control baseline, Biological replicate5

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control baseline
Control_Baseline_rep5

value: baseline


title: OD, biological rep1 (AS level)

description: Alternative splicing data from human CESCs

source_name: Osteogenic differentiation

value: Osteogenic differentiation


title: liver_patient_6_non_tumor_rep1 (mRNA)

description:
non-tumor
mRNA_12

tag: patient

value: patient 6

tag: disease state

value: HCC

tag: tissue

value: Poorly


title: Quiescent hepatic stellate cell Patient L11

source_name: Isolated non-cultured hepatic stellate cells_IP

source_name: Isolated non-cultured hepatic stellate cells_input


title: Activated hepatic stellate cell Patient L8


title: Bacteria_heat_rep3

city: Evora

first: Marta

last: Laranjo

address: Apartado 94

department: ICAAM

country: Portugal

institute: Universidade de Evora

hyb_protocol: One-Color Microarray-Based Gene Expression Analysis (Agilent) - Manufacturer's protocol

data_processing: The signal intensity for each spot was extracted using QuantArray Analysis Software (GSI Lumonics). Analysis of raw data was performed using BRB-ArrayTools v3.4.0, where each gene’s measured intensity was median normalized to correct for differences in the labelling efficiency between samples. The normalized dataset was then subjected to statistical analysis and clustering using MeV software to identified the diferencially expressed genes. The same dataset was also used to calculate the M-value and Fold-change variation.

organism: Mesorhizobium japonicum MAFF 303099

source_name: bacterial cells, heat shock

label_protocol:
aRNA amplification protocol: MessageAmp™ II-Bacteria Kit (Ambion) - Manufacturer's protocol
Quick Amp Labeling Kit (Agilent) - Manufacturer's protocol

growth_protocol: 10 ml of cells with an OD(540 nm)=0.3, which corresponds to approximately 6x10exp8 cells per ml were used.

extract_protocol:
RNeasy Mini Kit (Qiagen) manufacturer's protocol
mRNA enrichment protocol: MICROBExpress™ Bacterial mRNA Enrichment Kit (Ambion) - Manufacturer's protocol

treatment_protocol: Cells grown overnight at 28 ºC and maintained at 28 ºC for the 30 min were used as control. For heat shock experiments, cells were grown overnight at 28 ºC and transferred to 48 ºC for 30 min.

tag: treatment

value: heat shock


title: Activated hepatic stellate cell Patient L4


title: Activated hepatic stellate cell Patient L10


title: Bacteria_heat_rep2

scan_protocol: One-Color Microarray-Based Gene Expression Analysis (Agilent) - Manufacturer's protocol


title: Bacteria_control_rep3

source_name: bacterial cells, control conditions

value: control conditions


title: Bacteria_heat_rep1


title: BEAS-2B, control baseline, Biological replicate4

description:
Gene expression data from Human bronchial epithelial cell (BEAS-2B) control baseline
Control_Baseline_rep4

tag: strain


title: Bacteria_control_rep2


title: Bacteria_control_rep1