title: Vietnam nasopharyngeal swabs discharge RSVco 14

city: Ho Chi Minh City

first: Lien Anh Ha

last: Do

address: 764 Vo Van Kiet, Ward 1, District 5

country: Viet Nam

institute: Oxford University Clinical Research Unit, Vietnam

scan_protocol: Standard Illumina scanning protocol with iScan confocal scanner

data_processing: We applied a probe quality filtering with a cut-off for the detection p-value less than 0.01. After filtering, the data were normalised using a robust spline normalization (RSN) algorithm with R and the the Bioconductor lumi package

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA amplification kit.

extract_protocol: RNA was extracted with PAXgene blood RNA isolation kit (PreAnalyti X). Quality control was performed with Agilent Bioanalyser.

tag: subject status

value: Respiratory Syncitial Virus co-infections (RSVco)

tag: phase

value: discharge

value: f

tag: sample type

value: Nasopharyngeal swabs


title: Vietnam nasopharyngeal swabs acute RSVco 14

status: Public on Apr 14 2017

type: RNA

hyb_protocol: Standard Illumina hybridization protocol

label: biotin

molecule: total RNA

organism: Homo sapiens

value: acute

tag: age

tag: Sex


title: Vietnam nasopharyngeal swabs discharge hRV 29

value: Rhinovirus infection (hRV)

value: m


title: C01 (Control 1)

city: Columbus

first: Haiyan

last: Fu

state: Ohio

address: 700 Children's Dive

department: Center for Gene Therapy

country: USA

institute: Research Institute at Nationwide Childrens Hospital

description: gene expression in human blood

hyb_protocol: The labeled test and control RNA samples were fragmented and hybridized to the array overnight. Microarray slides were then washed and scanned with the Agilent G2505C Microarray Scanner, at 2 µM resolution.

scan_protocol: Microarray slides were washed and scanned with the Agilent G2505C Microarray Scanner, at 2 µM resolution.

data_processing: Images were analyzed with Feature Extraction 10.10 (Agilent Technologies). Median foreground intensities were then obtained for each spot and imported into the mathematical software package “R”, which was used for all data input, diagnostic plots, normalization and quality checking steps of the analysis process using scripts developed in-house for this analysis. The data was normalized by the loess method using the LIMMA (Linear models for microarray data) package in “R” as described

source_name: Peripheral blood, replica 1

label_protocol: The RNA samples were labeled with Cy3, purified using Qiagen columns and checked for labeling efficiency using the NanoDrop spectrophotometer (NanoDrop products).

extract_protocol: Paxgene Blood RNA kit (Qiagen)

treatment_protocol: peripheral blood

tag: tissue

value: whole blood

tag: gender

value: Female

tag: disease

value: healthy


title: Vietnam nasopharyngeal swabs discharge RSVsi 37

value: Single Respiratory Syncitial Virus infection (RSVsi)


title: CKO-adCM-rep4

city: Chicago

first: Yong

last: Peng

state: IL

address: 929 E 57th Street

department: Department of Chemistry

institute: University of Chicago

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: The data were analyzed using Bioconductor version 3.1 with oligo package version 1.32.0, pd.mogene.1.0.st.v1 package version 3.14.1 and mogene10sttranscriptcluster.db package version 8.3.1

organism: Mus musculus

source_name: heart

label_protocol: Affymetrix protocol

extract_protocol: Total RNAs were extracted using Trizol according to the manufacturer's instructions.

tag: strain

tag: cell type

value: cardiomyocytes

tag: genotype/variation

value: cardiac conditional EED knock-out


title: Vietnam nasopharyngeal swabs acute RSVco 15


title: Vietnam nasopharyngeal swabs discharge RSVco 13


title: Vietnam nasopharyngeal swabs acute hRV 30

source_name: Vietnam nasopharyngeal swabs acute hRV


title: CKO-adCM-rep5


title: Vietnam nasopharyngeal swabs discharge RSVco 15


title: Vietnam nasopharyngeal swabs acute hRV 29


title: Vietnam nasopharyngeal swabs discharge hRV 30


title: Vietnam nasopharyngeal swabs discharge RSVsi 38


title: CKO-adCM-rep2


title: WT-adCM-rep1

value: Wildtype


title: Vietnam nasopharyngeal swabs acute RSVsi 38


title: C04 (Control 4)

description: gene expression in human blood

source_name: Peripheral blood, replica 4


title: Vietnam nasopharyngeal swabs acute RSVsi 37


title: Vietnam nasopharyngeal swabs discharge RSVsi 36


title: Vietnam nasopharyngeal swabs discharge RSVsi 34


title: Vietnam nasopharyngeal swabs acute RSVsi 36


title: Vietnam nasopharyngeal swabs acute RSVco 13


title: Vietnam nasopharyngeal swabs discharge hRV 28


title: Vietnam nasopharyngeal swabs discharge RSVsi 33


title: Vietnam nasopharyngeal swabs acute RSVsi 35


title: Vietnam nasopharyngeal swabs discharge RSVsi 35


title: Vietnam nasopharyngeal swabs discharge RSVsi 31


title: Vietnam nasopharyngeal swabs acute hRV 28


title: Vietnam nasopharyngeal swabs acute RSVsi 34


title: Vietnam nasopharyngeal swabs acute RSVsi 30


title: Vietnam nasopharyngeal swabs acute RSVsi 33


title: Vietnam nasopharyngeal swabs discharge hRV 26


title: Vietnam nasopharyngeal swabs acute RSVsi 29


title: Vietnam nasopharyngeal swabs discharge RSVsi 28


title: Vietnam nasopharyngeal swabs discharge RSVsi 32


title: Vietnam nasopharyngeal swabs discharge hRV 27


title: Vietnam nasopharyngeal swabs acute RSVsi 31


title: Vietnam nasopharyngeal swabs discharge RSVco 12


title: Vietnam nasopharyngeal swabs discharge RSVsi 30


title: Vietnam nasopharyngeal swabs discharge RSVco 11


title: Vietnam nasopharyngeal swabs discharge RSVsi 27


title: Vietnam nasopharyngeal swabs acute hRV 27


title: Vietnam nasopharyngeal swabs discharge RSVsi 29


title: Vietnam nasopharyngeal swabs acute RSVco 11


title: Vietnam nasopharyngeal swabs acute RSVco 12


title: Vietnam nasopharyngeal swabs acute RSVsi 32


title: Vietnam nasopharyngeal swabs acute hRV 26


title: Vietnam nasopharyngeal swabs acute RSVsi 28


title: Vietnam nasopharyngeal swabs discharge RSVsi 26


title: Vietnam nasopharyngeal swabs acute RSVsi 27


title: Vietnam nasopharyngeal swabs acute RSVsi 26


title: Vietnam nasopharyngeal swabs discharge RSVsi 23


title: Vietnam nasopharyngeal swabs discharge RSVsi 25


title: Vietnam nasopharyngeal swabs acute RSVsi 25


title: Vietnam nasopharyngeal swabs discharge RSVsi 24


title: Vietnam nasopharyngeal swabs discharge RSVsi 21


title: Vietnam nasopharyngeal swabs acute RSVsi 23


title: Vietnam nasopharyngeal swabs discharge RSVsi 22


title: Vietnam nasopharyngeal swabs acute RSVsi 24


title: Vietnam nasopharyngeal swabs acute RSVsi 21


title: Vietnam nasopharyngeal swabs acute RSVsi 22


title: Vietnam nasopharyngeal swabs discharge hRV 25


title: Vietnam nasopharyngeal swabs discharge hRV 23


title: Vietnam nasopharyngeal swabs acute hRV 25


title: Vietnam nasopharyngeal swabs acute hRV 23


title: Vietnam nasopharyngeal swabs acute RSVsi 20


title: Vietnam nasopharyngeal swabs discharge RSVsi 20


title: Vietnam nasopharyngeal swabs discharge hRV 24


title: Vietnam nasopharyngeal swabs discharge hRV 22


title: Vietnam nasopharyngeal swabs acute hRV 24


title: Vietnam nasopharyngeal swabs acute hRV 20


title: Vietnam nasopharyngeal swabs acute hRV 22


title: Vietnam nasopharyngeal swabs discharge hRV 19


title: Vietnam nasopharyngeal swabs discharge hRV 21


title: Vietnam nasopharyngeal swabs discharge hRV 20


title: Vietnam nasopharyngeal swabs acute RSVsi 19


title: Vietnam nasopharyngeal swabs discharge RSVsi 18


title: Vietnam nasopharyngeal swabs acute hRV 21


title: Vietnam nasopharyngeal swabs acute hRV 19


title: Vietnam nasopharyngeal swabs acute RSVsi 18


title: Vietnam nasopharyngeal swabs discharge RSVsi 19


title: Vietnam nasopharyngeal swabs discharge hRV 18


title: Vietnam nasopharyngeal swabs discharge RSVsi 16


title: Vietnam nasopharyngeal swabs acute hRV 18


title: Vietnam nasopharyngeal swabs discharge RSVsi 17


title: Vietnam nasopharyngeal swabs discharge hRV 15


title: Vietnam nasopharyngeal swabs acute RSVsi 17


title: Vietnam nasopharyngeal swabs acute hRV 16


title: Vietnam nasopharyngeal swabs discharge hRV 16


title: Vietnam nasopharyngeal swabs discharge hRV 13


title: Vietnam nasopharyngeal swabs discharge RSVsi 15


title: Vietnam nasopharyngeal swabs acute RSVco 10


title: Vietnam nasopharyngeal swabs discharge hRV 14


title: Vietnam nasopharyngeal swabs acute hRV 17


title: Vietnam nasopharyngeal swabs discharge hRV 17


title: Vietnam nasopharyngeal swabs acute RSVsi 16


title: Vietnam nasopharyngeal swabs discharge RSVco 10


title: Vietnam nasopharyngeal swabs discharge RSVsi 14


title: Vietnam nasopharyngeal swabs acute hRV 13


title: Vietnam nasopharyngeal swabs acute RSVsi 15


title: Vietnam nasopharyngeal swabs discharge RSVsi 13


title: Vietnam nasopharyngeal swabs acute RSVsi 13


title: Vietnam nasopharyngeal swabs discharge RSVco 9


title: Vietnam nasopharyngeal swabs acute hRV 11


title: Vietnam nasopharyngeal swabs discharge hRV 11


title: Vietnam nasopharyngeal swabs acute hRV 14


title: Vietnam nasopharyngeal swabs acute hRV 12


title: Vietnam nasopharyngeal swabs acute RSVco 9


title: Vietnam nasopharyngeal swabs acute hRV 15


title: Vietnam nasopharyngeal swabs discharge hRV 12


title: Vietnam nasopharyngeal swabs acute RSVsi 14


title: Vietnam nasopharyngeal swabs discharge RSVco 8


title: Vietnam nasopharyngeal swabs discharge hRV 10


title: Vietnam nasopharyngeal swabs acute RSVco 6


title: Vietnam nasopharyngeal swabs acute RSVsi 12


title: Vietnam nasopharyngeal swabs discharge RSVsi 11


title: Vietnam nasopharyngeal swabs acute RSVsi 11


title: Vietnam nasopharyngeal swabs discharge RSVco 6


title: Vietnam nasopharyngeal swabs discharge hRV 8


title: Vietnam nasopharyngeal swabs acute hRV 10


title: Vietnam nasopharyngeal swabs discharge hRV 9


title: Vietnam nasopharyngeal swabs discharge RSVco 7


title: Vietnam nasopharyngeal swabs acute hRV 8


title: Vietnam nasopharyngeal swabs acute RSVco 8


title: Vietnam nasopharyngeal swabs acute hRV 9


title: Vietnam nasopharyngeal swabs discharge RSVsi 12


title: Vietnam nasopharyngeal swabs discharge RSVco 5


title: Vietnam nasopharyngeal swabs acute RSVco 5


title: Vietnam nasopharyngeal swabs acute RSVsi 10


title: Vietnam nasopharyngeal swabs acute RSVco 7


title: Vietnam nasopharyngeal swabs acute RSVsi 9


title: Vietnam nasopharyngeal swabs discharge RSVsi 10


title: Vietnam nasopharyngeal swabs acute RSVco 4


title: Vietnam nasopharyngeal swabs acute RSVsi 6


title: Vietnam nasopharyngeal swabs discharge RSVsi 9


title: Vietnam nasopharyngeal swabs discharge RSVsi 8


title: Vietnam nasopharyngeal swabs discharge RSVsi 7


title: Vietnam nasopharyngeal swabs acute RSVsi 7


title: Vietnam nasopharyngeal swabs discharge RSVsi 5


title: Vietnam nasopharyngeal swabs acute RSVsi 8


title: Vietnam nasopharyngeal swabs discharge hRV 6


title: Vietnam nasopharyngeal swabs discharge hRV 7


title: Vietnam nasopharyngeal swabs discharge hRV 2


title: Vietnam nasopharyngeal swabs acute RSVsi 5


title: Vietnam nasopharyngeal swabs acute RSVco 3


title: Vietnam nasopharyngeal swabs discharge hRV 5


title: Vietnam nasopharyngeal swabs discharge hRV 3


title: Vietnam nasopharyngeal swabs acute hRV 4


title: Vietnam nasopharyngeal swabs discharge RSVsi 4


title: Vietnam nasopharyngeal swabs discharge hRV 4


title: Vietnam nasopharyngeal swabs acute hRV 3


title: Vietnam nasopharyngeal swabs acute hRV 5


title: Vietnam nasopharyngeal swabs acute hRV 7


title: Vietnam nasopharyngeal swabs acute hRV 6


title: Vietnam nasopharyngeal swabs discharge RSVco 3


title: Vietnam nasopharyngeal swabs discharge RSVco 4


title: Vietnam nasopharyngeal swabs acute hRV 2


title: Vietnam nasopharyngeal swabs acute hRV 1


title: Vietnam nasopharyngeal swabs discharge hRV 1


title: Vietnam nasopharyngeal swabs discharge RSVsi 6


title: Vietnam nasopharyngeal swabs discharge RSVsi 3


title: Vietnam nasopharyngeal swabs acute RSVsi 3


title: Vietnam nasopharyngeal swabs acute RSVco 1


title: Vietnam nasopharyngeal swabs discharge RSVco 1


title: Vietnam whole blood acute RSVco 15

source_name: Vietnam whole blood acute RSVco

value: Whole blood


title: Vietnam nasopharyngeal swabs discharge RSVsi 1


title: Vietnam whole blood discharge RSVco 15

source_name: Vietnam whole blood discharge RSVco


title: Vietnam nasopharyngeal swabs acute RSVsi 1


title: Vietnam whole blood acute hRV 29

source_name: Vietnam whole blood acute hRV


title: Vietnam whole blood acute RSVsi 37

source_name: Vietnam whole blood acute RSVsi


title: Vietnam whole blood acute hRV 30


title: Vietnam nasopharyngeal swabs acute RSVsi 4


title: Vietnam whole blood acute RSVco 13


title: Vietnam whole blood discharge RSVsi 37

source_name: Vietnam whole blood discharge RSVsi


title: Vietnam whole blood discharge RSVsi 36


title: Vietnam nasopharyngeal swabs discharge RSVco 2


title: Vietnam whole blood discharge RSVsi 38


title: Vietnam whole blood acute RSVsi 36


title: Vietnam nasopharyngeal swabs discharge RSVsi 2


title: Vietnam whole blood acute RSVco 14


title: Vietnam nasopharyngeal swabs acute RSVco 2


title: Vietnam whole blood discharge RSVco 14


title: Vietnam whole blood discharge hRV 29

source_name: Vietnam whole blood discharge hRV


title: Vietnam nasopharyngeal swabs acute RSVsi 2


title: Vietnam whole blood discharge hRV 30


title: Vietnam whole blood acute RSVsi 35


title: Vietnam whole blood discharge RSVco 13


title: Vietnam whole blood acute hRV 28


title: Vietnam whole blood discharge RSVsi 35


title: Vietnam whole blood discharge hRV 28


title: Vietnam whole blood discharge RSVsi 33


title: Vietnam whole blood acute RSVsi 33


title: Vietnam whole blood acute RSVsi 34


title: Vietnam whole blood acute RSVsi 32


title: Vietnam whole blood discharge RSVsi 34


title: Vietnam whole blood acute RSVsi 31


title: Vietnam whole blood discharge RSVsi 32


title: Vietnam whole blood discharge RSVco 11


title: Vietnam whole blood acute RSVsi 29


title: Vietnam whole blood acute hRV 27


title: Vietnam whole blood discharge RSVsi 29


title: Vietnam whole blood acute RSVsi 30


title: Vietnam whole blood discharge RSVsi 30


title: Vietnam whole blood discharge hRV 27


title: Vietnam whole blood acute RSVsi 28


title: Vietnam whole blood acute RSVco 12


title: Vietnam whole blood discharge RSVsi 27


title: Vietnam whole blood discharge RSVsi 31


title: Vietnam whole blood acute RSVco 11


title: Vietnam whole blood acute RSVsi 26


title: Vietnam whole blood discharge RSVco 12


title: Vietnam whole blood acute RSVsi 25


title: Vietnam whole blood discharge RSVsi 25


title: Vietnam whole blood discharge RSVsi 26


title: Vietnam whole blood discharge RSVsi 28


title: Vietnam whole blood discharge hRV 26


title: Vietnam whole blood discharge RSVsi 23


title: Vietnam whole blood acute RSVsi 27


title: Vietnam whole blood acute hRV 26


title: Vietnam whole blood acute RSVsi 23


title: Vietnam whole blood acute RSVsi 24


title: Vietnam whole blood acute RSVsi 20


title: Vietnam whole blood acute RSVsi 21


title: Vietnam whole blood acute hRV 25


title: Vietnam whole blood discharge hRV 24


title: Vietnam whole blood discharge RSVsi 24


title: Vietnam whole blood discharge hRV 25


title: Vietnam whole blood discharge RSVsi 20


title: Vietnam whole blood acute RSVsi 19


title: Vietnam whole blood acute hRV 24


title: Vietnam whole blood acute RSVsi 22


title: Vietnam whole blood discharge RSVsi 22


title: Vietnam whole blood acute hRV 22


title: Vietnam whole blood acute hRV 23


title: Vietnam whole blood discharge hRV 19


title: Vietnam whole blood acute hRV 19


title: Vietnam whole blood acute hRV 20


title: Vietnam whole blood discharge hRV 18


title: Vietnam whole blood discharge hRV 17


title: Vietnam whole blood discharge hRV 22


title: Vietnam whole blood discharge hRV 23


title: Vietnam whole blood discharge hRV 21


title: Vietnam whole blood acute hRV 21


title: Vietnam whole blood discharge hRV 20


title: Vietnam whole blood acute hRV 17


title: Vietnam whole blood discharge hRV 16


title: Vietnam whole blood discharge RSVsi 16


title: Vietnam whole blood acute RSVsi 15


title: Vietnam whole blood discharge RSVsi 19


title: Vietnam whole blood acute hRV 18


title: Vietnam whole blood acute RSVsi 17


title: Vietnam whole blood discharge RSVsi 18


title: Vietnam whole blood discharge RSVsi 17


title: Vietnam whole blood acute RSVsi 16


title: Vietnam whole blood discharge RSVco 10


title: Vietnam whole blood acute hRV 16


title: Vietnam whole blood acute RSVsi 14


title: Vietnam whole blood discharge RSVsi 15


title: Vietnam whole blood discharge RSVsi 14


title: Vietnam whole blood discharge hRV 15


title: Vietnam whole blood acute RSVco 10


title: Vietnam whole blood acute RSVsi 13


title: Vietnam whole blood acute hRV 15


title: Vietnam whole blood discharge RSVco 9


title: Vietnam whole blood acute RSVco 9


title: Vietnam whole blood acute hRV 14


title: Vietnam whole blood discharge hRV 10


title: Vietnam whole blood discharge RSVsi 13


title: Vietnam whole blood discharge hRV 12


title: Vietnam whole blood acute hRV 13


title: Vietnam whole blood discharge hRV 14


title: Brain_WT_non-treated Brain, half sphere_replica 2

description: Gene expression

value: Male

value: 8 months


title: Vietnam whole blood acute hRV 11


title: Vietnam whole blood acute hRV 10


title: Vietnam whole blood acute hRV 12


title: Vietnam whole blood acute RSVsi 12

value: Respiratory Syncitial Virus co-infections (RSVco)


title: Vietnam whole blood discharge hRV 11

value: discharge


title: Brain_WT_non-treated Brain, half sphere_replica 1

description: Gene expression


title: Brain_WT_non-treated Brain, half sphere_replica 4

description: Gene expression


title: Brain_MPS IIIA_IV-AAV Brain, half sphere_replica 3

description: Gene expression, 7m post IV AAVrh74-hSGSH gene delivery

source_name: Brain_MPS IIIA_IV-AAV


title: Vietnam whole blood acute RSVco 7


title: Brain_MPS IIIA_IV-AAV Brain, half sphere_replica 4


title: Vietnam whole blood discharge RSVco 6


title: Vietnam whole blood acute RSVco 8


title: Vietnam whole blood discharge hRV 9

value: f


title: Brain_WT_non-treated Brain, half sphere_replica 3

description: Gene expression


title: Vietnam whole blood acute hRV 9


title: Peripheral blood_WT_non-treated Peripheral blood_replica 4

description: Gene expression

source_name: Peripheral blood_WT_non-treated


title: Brain_MPS IIIA_non-treated Brain, half sphere_replica 4

description: Gene expression

source_name: Brain_MPS IIIA_non-treated


title: Brain_MPS IIIA_non-treated Brain, half sphere_replica 1

description: Gene expression


title: Vietnam whole blood discharge RSVco 8


title: Vietnam whole blood discharge RSVsi 11


title: Peripheral blood_WT_non-treated Peripheral blood_replica 2

description: Gene expression


title: Brain_MPS IIIA_IV-AAV Brain, half sphere_replica 2


title: Vietnam whole blood discharge RSVsi 21


title: Vietnam whole blood acute hRV 8


title: Brain_MPS IIIA_IV-AAV Brain, half sphere_replica 1


title: Vietnam whole blood discharge RSVsi 12


title: Vietnam whole blood acute RSVco 6


title: Brain_MPS IIIA_non-treated Brain, half sphere_replica 3

description: Gene expression


title: Peripheral blood_MPS IIIA_IV-AAV Peripheral blood_replica 3

source_name: Peripheral blood_MPS IIIA_IV-AAV


title: Vietnam whole blood discharge hRV 8


title: Vietnam whole blood acute RSVsi 11


title: Vietnam whole blood acute RSVsi 18


title: Vietnam whole blood discharge hRV 13


title: Peripheral blood_MPS IIIA_IV-AAV Peripheral blood_replica 2


title: Brain_MPS IIIA_non-treated Brain, half sphere_replica 2

description: Gene expression


title: Peripheral blood_MPS IIIA_non-treated Peripheral blood_replica 3

description: Gene expression

source_name: Peripheral blood_MPS IIIA_non-treated


title: Peripheral blood_MPS IIIA_IV-AAV Peripheral blood_replica 4


title: Vietnam whole blood discharge RSVco 7


title: Vietnam whole blood acute RSVsi 10


title: Peripheral blood_WT_non-treated Peripheral blood_replica 3

description: Gene expression


title: Peripheral blood_MPS IIIA_IV-AAV Peripheral blood_replica 1


title: Vietnam whole blood acute RSVsi 8


title: Peripheral blood_MPS IIIA_non-treated Peripheral blood_replica 1

description: Gene expression


title: Vietnam whole blood discharge RSVsi 8


title: Vietnam whole blood discharge RSVsi 9


title: Vietnam whole blood discharge RSVco 5


title: Vietnam whole blood discharge RSVsi 10


title: LPS high dose 2

city: Lexington

first: Phillip

middle: J

last: Bridges

state: KY

address: 206 WP Garrigus Building

department: Animal and Food Sciences

institute: University of Kentucky

description: On the day of estrus, mice were treated with 0 (control), 2 µg (low dose) or 10 µg (high dose) of LPS from E. Coli serotype 055:B5 in 100 mL PBS (Sigma-Aldrich, Saint Louis MO) via intraperitoneal (IP) injection

hyb_protocol: 100 ng of total RNA from each sample was hybridized with reporter and capture probes which hybridize directly to target molecules. The reporter probe carries the fluorescent barcode and the Capture probe contains a biotin moiety that immobilizes the hybridized complex for data collection.

scan_protocol: After hybridization, sample processing allows for probe/target complexes to be immobilized on the nCounter cartridge and unbound probes removed.  After sample processing, digital data acquisition allows for barcodes on reporter probes to be tabulated for each target molecule.

data_processing: The raw reported code count data generated from the nCounter Digital Analyzer was then exported to nSolver software (NanoString Technologies) for normalization, background assessment, and molecule count summarization

label: Fluorescent barcode and biotin moiety

source_name: Oviduct

label_protocol: Not supplied

growth_protocol: Animal procedures involved in this study were approved by the University of Kentucky Animal Care and Use Committee.  Prior to treatment, the progression of normal estrous cycles was confirmed in 6-8 week old CD1 mice by analysis of vaginal cytology.  Briefly, vaginal smears were collected daily, at the same time each day, using PBS and a bent, blunted borosilicate glass pipette.  Vaginal Cytology’s were evaluated under a Motic AE21 inverted microscope (Motic Instruments, Richmond, British Columbia, Canada) and classified according to well-established morphological criteria and digital images recorded for later reference.

extract_protocol: To determine the effect of treatment on the expression of inflammatory mRNA, total RNA was extracted from oviducts (n=4 mice/treatment) using Trizol reagent (Invitrogen Corporation, Carlsbad, CA) and purified with RNeasy columns (Qiagen, Valencia, CA, USA) according to manufacturer’s instructions.  RNA quality was analyzed by determining the RNA integrity number (RIN) using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) at the University of Kentucky Microarray Core Facility.  RNA integrity numbers were greater than 9.7 and 28S/18S rRNA absorbance ratios greater than 2.0 for all samples.  All samples passed the quality control measurements outlined by Nanostring Technologies (Seattle, WA).

treatment_protocol: On the day of estrus, mice were treated with 0 (control), 2 µg (low dose) or 10 µg (high dose) of LPS from E. Coli serotype 055:B5 in 100 μL PBS (Sigma-Aldrich, Saint Louis MO) via intraperitoneal (IP) injection.  The rationale for treatment on the day of estrus was that treatment at estradiol-induced sexual receptivity will induce an inflammatory response at the time of normal exposure of the oviduct to freshly ovulated cumulus-oocyte complexes, associated follicular debris, spermatozoa, seminal fluids and putatively, any foreign pathogens introduced at mating.  To investigate the acute response to LPS-induced inflammation, mice were killed 24 h later and their oviducts collected and snap-frozen on dry ice for later extraction of total RNA.

value: Oviduct

value: 6-8 week old


title: Vietnam whole blood acute RSVco 5

value: acute


title: Peripheral blood_WT_non-treated Peripheral blood_replica 1

description: Gene expression


title: LPS high dose 4


title: LPS high dose 3


title: LPS high dose 1


title: Vietnam whole blood discharge RSVco 4


title: LPS low dose 4


title: Peripheral blood_MPS IIIA_non-treated Peripheral blood_replica 4

description: Gene expression


title: Peripheral blood_MPS IIIA_non-treated Peripheral blood_replica 2

description: Gene expression


title: LPS low dose 2


title: Vietnam whole blood acute RSVsi 7

value: m


title: LPS low dose 3


title: Vietnam whole blood acute RSVsi 9


title: Vietnam whole blood discharge RSVsi 7


title: Vietnam whole blood acute RSVsi 5


title: Vietnam whole blood acute RSVsi 6


title: Vietnam whole blood acute RSVco 4


title: Vietnam whole blood discharge RSVsi 6


title: Vietnam whole blood discharge RSVsi 5


title: LPS low dose 1


title: LPS control 4


title: LPS control 3


title: LPS control 1


title: LPS high dose 4

extract_protocol: To determine the effect of treatment on the expression of miRNAs, total RNA was extracted from oviducts (n=4 mice/treatment) using the miRNeasy Mini Kit (Qiagen, Valencia, CA) according to manufacturer’s instructions.  RNA quality was analyzed by determining the RNA integrity number (RIN) using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) at the University of Kentucky Microarray Core Facility.  RNA integrity numbers were greater than 9.8 and 28S/18S rRNA absorbance ratios greater than 1.7 for all samples.  All samples passed the quality control measurements outlined by Nanostring Technologies (Seattle, WA).

tag: sample id


title: LPS high dose 3


title: Vietnam whole blood acute hRV 7

value: Rhinovirus infection (hRV)


title: Vietnam whole blood discharge RSVco 3


title: Vietnam whole blood acute RSVco 3


title: Vietnam whole blood acute RSVsi 4


title: Vietnam whole blood discharge hRV 7


title: Vietnam whole blood acute hRV 6


title: Vietnam whole blood discharge hRV 6


title: LPS control 2

value: Female


title: LPS low dose 3


title: LPS high dose 2


title: LPS high dose 1


title: LPS low dose 4


title: LPS low dose 1


title: LPS low dose 2


title: LPS control 2


title: LPS control 3


title: LPS control 1


title: SE16

city: Moscow

first: Maria

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

country: Russia

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

description: SAMPLE 20

hyb_protocol: Hybridization was performed according to CustomArray ElectraSense™ Hybridization and Detection protocol. Hybridization mix contained 2.5 ug of labeleled DNA library, 6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt solution, 100 ng/ul sonicated calf thymus gDNA, 0,05% SDS. Hybridization mix was incubated with chip overnight at 50ºC.

scan_protocol: Hybridization efficiency was detected electrochemically using CustomArray ElectraSense™ Detection Kit and ElectraSense™ 4X2K/12K Reader.

data_processing: The data were normalised using quantile normalisation in R.

source_name: SKOV3 cell line

label_protocol: Complete Whole Transcriptome Amplification WTA2 Kit  (Sigma) was used for reverse transcription and library amplification. Manufacturer's protocol was modified by adding to amplification reaction dNTP mix containing biotinylated dUTP, resulting to final proportion dTTP/biotin-dUTP as 5/1.

growth_protocol: Cells were grown in complete medium supplemented with the appropriate concentrations of the drugs (or without drugs in control line) up to 16 weeks.

extract_protocol: Attached cells were treated with trypsin and collected by centrifugation. Cell pellets (approximately 10^6 cells per sample) were resuspended with  500 ul of  TRI Reagent (MRC). RNA extraction was performed using Direct-zol™ RNA MiniPrep (Zymo Research) kit. RNA was quantified with Nanodrop (Thermo Fisher Scientific).

treatment_protocol: SKOV3 cells resistant to five target anticancer drugs were generated by growing naive cells serially treated with an increasing doses of Sunitinib up to 6 µM, Pazopanib up to 25 µM, Sorafenib up to 10 µM, Everolimus up to 20 µM and Temsirolimus up to 15 µM (Selleckchem, USA).

tag: treatment

value: Everolimus

tag: weeks


title: ST4

description: SAMPLE 21

value: Temsirolimus


title: SE12

description: SAMPLE 19


title: SE4

description: SAMPLE 18


title: Vietnam whole blood discharge hRV 5

value: Single Respiratory Syncitial Virus infection (RSVsi)


title: Vietnam whole blood discharge RSVsi 3


title: ST16

description: SAMPLE 23


title: Vietnam whole blood acute hRV 3


title: Vietnam whole blood discharge hRV 3


title: Vietnam whole blood acute hRV 4


title: Vietnam whole blood acute RSVco 2


title: Vietnam whole blood discharge hRV 4


title: Vietnam whole blood acute RSVsi 3


title: SP12

description: SAMPLE 16

value: Pazopanib


title: ST8

description: SAMPLE 22


title: Vietnam whole blood discharge hRV 2


title: Vietnam whole blood acute hRV 2


title: Vietnam whole blood discharge hRV 1


title: SP16

description: SAMPLE 17


title: Vietnam whole blood discharge RSVsi 4


title: Vietnam whole blood acute hRV 1


title: Vietnam whole blood discharge RSVco 2


title: Vietnam whole blood discharge RSVsi 2


title: SP8

description: SAMPLE 15


title: Vietnam whole blood acute RSVsi 2


title: Vietnam whole blood acute RSVsi 1


title: Vietnam whole blood acute RSVco 1


title: SSu16

description: SAMPLE 13

value: Sunitinib


title: SP4

description: SAMPLE 14


title: Vietnam whole blood discharge RSVco 1

value: Whole blood


title: SSu12

description: SAMPLE 12


title: SSu4

description: SAMPLE 10


title: SSo16

description: SAMPLE 9

value: Sorafenib


title: SSu8

description: SAMPLE 11


title: Vietnam whole blood acute RSVsi 38


title: SSo8

description: SAMPLE 7


title: Vietnam whole blood discharge RSVsi 1


title: SC14

description: SAMPLE 4

value: No treatment


title: SSo12

description: SAMPLE 8


title: SC16

description: SAMPLE 5


title: SC10

description: SAMPLE 2


title: Vietnam whole blood acute hRV 5


title: SSo4

description: SAMPLE 6


title: NE14

description: SAMPLE 19

source_name: NGP-127 cell line

growth_protocol: Cells were grown in complete medium supplemented with the appropriate concentrations of the drugs (or without drugs in control line) up to 18 weeks.

treatment_protocol: NGP-127 cells resistant to five target anticancer drugs were generated by growing naive cells serially treated with an increasing doses of Sunitinib up to 6 µM, Pazopanib up to 25 µM, Sorafenib up to 10 µM, Everolimus up to 20 µM and Temsirolimus up to 15 µM (Selleckchem, USA).


title: NE18

description: SAMPLE 20


title: SC8

description: SAMPLE 1


title: NT4

description: SAMPLE 21


title: NT8

description: SAMPLE 22


title: NT18

description: SAMPLE 24


title: NT14

description: SAMPLE 23


title: NE8

description: SAMPLE 18


title: NP14

description: SAMPLE 15


title: NP18

description: SAMPLE 16


title: SC12

description: SAMPLE 3


title: NE4

description: SAMPLE 17


title: NP4

description: SAMPLE 13


title: K562_mv_5

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

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

country: Italy

institute: università di padova

description: Gene expression data from K562 microvesicles derived from parental K562 cell line

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

scan_protocol: GeneChips were scanned using the Scan GCS3000.

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

source_name: K562 cell line

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

extract_protocol: RNA was isolated from K562 cultured cells and microvesicles released by parental cell line using Trizol in 5 independent experiments.

tag: type of cells

value: Microvesicles

tag: cell line


title: NP8

description: SAMPLE 14


title: NSu14

description: SAMPLE 11


title: NSu8

description: SAMPLE 10


title: NSu4

description: SAMPLE 9


title: NSo18

description: SAMPLE 8


title: NSo8

description: SAMPLE 6


title: NSo14

description: SAMPLE 7


title: bCL_6

city: Midlothian

first: Xavier

last: Donadeu

address: Easter Bush

country: United Kingdom

institute: Roslin Institute, University of Edinburgh

description:
microRNA expression in early CL
SAMPLE D6
ch1:Hy3 array = 1_Exiqon_*_S01.txt
ch2:Hy5 array = 0_Exiqon_*_S01.txt

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA™ microRNA Array 6th gen (Exiqon, Denmark), which contains capture probes targeting all microRNAs for human, mouse or rat registered in the miRBASE 16.0.

scan_protocol: The hybridization was performed according to the miRCURY LNA™ microRNA Array Instruction manual using a Tecan HS4800™ hybridization station (Tecan, Austria). After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in  order to prevent potential bleaching of the fluorescent dyes. The miRCURY LNA™ microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene® 9 (miRCURY LNA™ microRNA Array Analysis Software, Exiqon, Denmark).

data_processing:
The quantified signals were background corrected (Normexp with offset value 10, see Ritchie et al. 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.
The processed data matrix contains Normalized signal intensity, log2transformed normalized median ratios (Cy3/Cy5)

organism: Bos taurus

source_name: Early corpus luteum

label_protocol: Six-hundred ng of total RNA from both sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark) following the procedure described by the manufacturer.

extract_protocol: Total RNA from whole follicles devoid of follicular fluid and CL was extracted using miRNeasy mini kit (Qiagen) according to manufacturer’s instructions (Qiagen, UK) and analysed using the Nano Drop and Agilent Bioanalyzer 2100 (Agilent Technologies).

tag: developmental stage

value: Early Corpus Luteum

value: whole follicles

source_name: Pool of follicular and luteal tissues

tag: developmental stages

value: Small follicles+Large healthy follicles+Large atretic follicles+Early Corpus Luteum


title: NSu18

description: SAMPLE 12


title: bCL_4

description:
microRNA expression in early CL
SAMPLE D4
ch1:Hy3 array = 1_Exiqon_*_S01.txt
ch2:Hy5 array = 0_Exiqon_*_S01.txt


title: K562_Cell Line_4

description: Gene expression data from K562 cell line

value: Cell Line


title: bCL_3

description:
microRNA expression in early CL
SAMPLE D3
ch1:Hy3 array = 1_Exiqon_*_S01.txt
ch2:Hy5 array = 0_Exiqon_*_S01.txt


title: bCL_5

description:
microRNA expression in early CL
SAMPLE D5
ch1:Hy3 array = 1_Exiqon_*_S01.txt
ch2:Hy5 array = 0_Exiqon_*_S01.txt


title: NC14

description: SAMPLE 4


title: NC18

description: SAMPLE 5


title: NC10

description: SAMPLE 3


title: K562_Cell Line_3


title: K562_Cell Line_5


title: K562_mv_4


title: K562_mv_1


title: bCL_2

description:
microRNA expression in early CL
SAMPLE D2
ch1:Hy3 array = 1_Exiqon_*_S01.txt
ch2:Hy5 array = 0_Exiqon_*_S01.txt


title: K562_Cell Line_1


title: Trachea MUT3

city: Los Angeles

first: Brendan

middle: H

last: Grubbs

state: CA

address: 4661 W. Sunset Blvd.

department: Obstetrics and Gynecology

institute: University of Southern California

scan_protocol: Standard Illumina scanning protocol

data_processing:
limma (version 3.26.9), R ( version 3.2.3), Bioconductor (version 2.3)
limma function ‘neqc’- “Performs background correction followed by quantile normalization, using negative control probes for background correction and both negative and positive controls for normalization.”
Description of background correction and normalization using the limma ‘neqc’ function, http://nar.oxfordjournals.org/content/38/22/e204
Reduced dataset for ‘LimmaData’ and differential expression testing was generated by filtering out rows which had less than two samples with detection p.values greater than 0.05

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

extract_protocol: Total RNA was extracted with Trizol. Upon arrival UCLA core technicians treated samples with Dnase and re-purified the RNA with Qiagen Colum.

treatment_protocol: The mutant trachea were missing mesenchymal expression of Sox9 gene, which results in the lack of cartilage rings.

tag: strain background

value: trachea


title: NC8

description: SAMPLE 2


title: Trachea MUT1


title: Trachea MUT2


title: K562_mv_2


title: bCL_1

description:
microRNA expression in early CL
SAMPLE D1
ch1:Hy3 array = 1_Exiqon_*_S01.txt
ch2:Hy5 array = 0_Exiqon_*_S01.txt


title: NC4

description: SAMPLE 1


title: Trachea WT2


title: K562_Cell Line_2


title: Trachea WT1


title: K562_mv_3


title: Trachea WT3


title: W0029L-1_Control

status: Public on Apr 13 2017

type: genomic

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450k Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio software V2011.1 with GenomeStudio Methylation Analysis Module Version 1.9.1000 (background-subtraction, colour-correction). The file unmethylated_and_methylated_signal.txt contains the raw unmethylated (A) and methylated (B) signal intensities.

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated using the Isohelix DNA isolation kit and bisulfite converted with the Zymo EZ DNA Methylation Kit, as per manufacturer’s instructions.

value: Buccal epithelial cells

tag: date run

value: Male

tag: disease status

value: Control

tag: disease subgroup

tag: self-reported ethnicity

value: caucasian

tag: sentrix id

tag: sentrix position

tag: sentrix row


title: W0025_Control

tag: cell type

tag: Sex

value: Female

tag: age


title: W0028_Control


title: W0032_Control


title: W0018_FASD

value: FASD

value: pFAS

value: first nations


title: W0035_Control


title: W0017_FASD

value: metis


title: W0024_Control


title: W0021_FASD

value: ARND

value: indian


title: W0019_FASD


title: W0023_Control


title: W0034_Control


title: W0026_Control


title: W0027_Control


title: W0015_FASD


title: W0010_FASD


title: W0013_FASD


title: W0036_Control


title: W0011_FASD

value: Metis


title: W0020_FASD


title: W0014_FASD


title: W0012_FASD


title: W0029L-2_Control


title: W0007_FASD

value: first nations/caucasian


title: W0031_Control


title: W0030_Control


title: W0005_FASD


title: W0022_Control


title: W0016_FASD


title: W0033_Control


title: W0004_FASD


title: W0001_FASD


title: V0044_Control


title: W0003_FASD


title: W0002_FASD


title: IM104_Etoposide_H1N1_D6_4_RNA

city: Richland

first: Natalie

last: Heller

address: 902 Battelle Blvd.

institute: PNNL

hyb_protocol: Hybridization was performed according to Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 x Blocking Agent and 2.2 μl of 25x Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 x GE Hybridization buffer was added to dilute the labeled cRNA. 100μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

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

data_processing: Scanned images were analyzed using Agilent Feature Extraction Software (v11.0.1.1). The limma package for R (available on Bioconductor) was used to perform background correction, quantile normalization (normalizeBetweenArrays), and summarization (avereps) to derive a single normalized intensity value per probe. Outlier samples were detected using PCA and by visual inspection of heatmaps, and all data was re-processed after removing outlier samples. All data processing for each of the biological replicates was performed independently of the other.

source_name: Lung tissue, Etoposide, H1N1-inoculated, 6 days, bioreplicate 4

label_protocol: Total RNA was labeled according to Agilent’s Quick Amp Labeling protocol as part of the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). Total RNA from each sample was linearly amplified and labeled with Cy3-UTP.

extract_protocol: Total RNA was isolated from TRIzol homogenate of mouse lung.

treatment_protocol: Mice were anesthetized with isoflurane and inoculated with PBS or PBS containing virus in a volume of 50 μl.

tag: strain

value: 22 weeks

tag: tissue

value: lung

tag: time (days)

tag: treatment

value: Etoposide

tag: virus


title: V0040_FASD

value: FAS


title: IM104_Etoposide_H1N1_D6_5_RNA

source_name: Lung tissue, Etoposide, H1N1-inoculated, 6 days, bioreplicate 5


title: V0043_Control

value: Buccal epithelial cells


title: V0038_Control


title: IM104_Etoposide_H1N1_D6_3_RNA

source_name: Lung tissue, Etoposide, H1N1-inoculated, 6 days, bioreplicate 3


title: IM104_Etoposide_H1N1_D6_1_RNA

source_name: Lung tissue, Etoposide, H1N1-inoculated, 6 days, bioreplicate 1


title: V0041_FASD

value: PAE


title: IM104_Etoposide_H1N1_D6_2_RNA

source_name: Lung tissue, Etoposide, H1N1-inoculated, 6 days, bioreplicate 2


title: V0032_

value: Male


title: V0021_FASD

value: caucasian


title: V0028_FASD

value: Female


title: V0022_FASD

value: FASD

value: Caucasian/Jamaican


title: V0037_Control

value: Control


title: V0030_Control

value: caucasian/Sikh


title: V0033_Control

value: Pakistani


title: V0029_FASD


title: V0017_FASD

value: first nations


title: V0031_Control

value: Sikh/Caucasian


title: V0023_FASD

value: caucasian/Jewish


title: V0018_FASD

value: ARND


title: V0027_FASD


title: V0019_FASD

value: pFAS


title: V0034_FASD


title: IM104_Etoposide_Mock_D6_3_RNA

source_name: Lung tissue, Etoposide, Mock-inoculated, 6 days, bioreplicate 3

value: 22 weeks

value: lung

value: Etoposide

value: Mock


title: IM104_Etoposide_Mock_D6_4_RNA

source_name: Lung tissue, Etoposide, Mock-inoculated, 6 days, bioreplicate 4


title: V0035_FASD

value: Buccal epithelial cells

value: Male


title: IM104_Etoposide_Mock_D6_2_RNA

source_name: Lung tissue, Etoposide, Mock-inoculated, 6 days, bioreplicate 2


title: V0026_Control

value: Female

value: unknown


title: V0013_FASD

value: FASD

value: first nations/Hondorian


title: IM104_Etoposide_Mock_D6_5_RNA

source_name: Lung tissue, Etoposide, Mock-inoculated, 6 days, bioreplicate 5


title: V0016_Control

value: Control

value: asian


title: V0036_Control

value: caucasian


title: IM104_Vehicle_H1N1_D6_5_RNA

source_name: Lung tissue, Vehicle, H1N1-inoculated, 6 days, bioreplicate 5

value: Vehicle


title: IM104_Etoposide_Mock_D6_1_RNA

source_name: Lung tissue, Etoposide, Mock-inoculated, 6 days, bioreplicate 1


title: V0010_FASD

value: first nations/German


title: IM104_Vehicle_H1N1_D6_4_RNA

source_name: Lung tissue, Vehicle, H1N1-inoculated, 6 days, bioreplicate 4


title: V0015_FASD

value: ARND

value: first nations


title: V0012_FASD

value: PAE


title: V0011_FASD


title: V0014_FASD


title: IM104_Vehicle_H1N1_D6_2_RNA

source_name: Lung tissue, Vehicle, H1N1-inoculated, 6 days, bioreplicate 2

value: 22 weeks

value: lung


title: V0005_Control


title: V0039_Control

value: caucasian/Latino


title: V0007_Control

value: Buccal epithelial cells


title: IM104_Vehicle_Mock_D6_5_RNA

source_name: Lung tissue, Vehicle, Mock-inoculated, 6 days, bioreplicate 5

value: Mock


title: V0008_Control

value: Female

value: French


title: IM104_Vehicle_H1N1_D6_3_RNA

source_name: Lung tissue, Vehicle, H1N1-inoculated, 6 days, bioreplicate 3


title: V0003R-1_Control


title: V0006_Control

value: Male


title: IM104_Vehicle_Mock_D6_3_RNA

source_name: Lung tissue, Vehicle, Mock-inoculated, 6 days, bioreplicate 3


title: IM104_Vehicle_Mock_D6_2_RNA

source_name: Lung tissue, Vehicle, Mock-inoculated, 6 days, bioreplicate 2


title: IM104_Vehicle_Mock_D6_1_RNA

source_name: Lung tissue, Vehicle, Mock-inoculated, 6 days, bioreplicate 1


title: V0004_Control


title: IM104_Vehicle_H1N1_D6_1_RNA

source_name: Lung tissue, Vehicle, H1N1-inoculated, 6 days, bioreplicate 1


title: L0018_FASD

value: FASD

value: FAS


title: V0002_Control

value: Control


title: V0001_Control

value: caucasian


title: V0003R-2_Control


title: L0017_FASD


title: L0014_FASD


title: IM104_Etoposide_H1N1_D3_5_RNA

source_name: Lung tissue, Etoposide, H1N1-inoculated, 3 days, bioreplicate 5

value: Etoposide


title: L0015_FASD


title: L0016_FASD


title: L0010_FASD

value: caucasian/metis


title: L0009_FASD

value: ARND


title: L0011_FASD

value: first nations


title: IM104_Etoposide_H1N1_D3_4_RNA

source_name: Lung tissue, Etoposide, H1N1-inoculated, 3 days, bioreplicate 4


title: IM104_Vehicle_Mock_D6_4_RNA

source_name: Lung tissue, Vehicle, Mock-inoculated, 6 days, bioreplicate 4

value: Vehicle


title: IM104_Etoposide_H1N1_D3_3_RNA

source_name: Lung tissue, Etoposide, H1N1-inoculated, 3 days, bioreplicate 3

value: 22 weeks


title: IM104_Etoposide_H1N1_D3_2_RNA

source_name: Lung tissue, Etoposide, H1N1-inoculated, 3 days, bioreplicate 2

value: lung


title: L0012_FASD

value: PAE


title: L0020_FASD

value: Buccal epithelial cells


title: IM104_Etoposide_Mock_D3_5_RNA

source_name: Lung tissue, Etoposide, Mock-inoculated, 3 days, bioreplicate 5

value: Mock


title: IM104_Etoposide_H1N1_D3_1_RNA

source_name: Lung tissue, Etoposide, H1N1-inoculated, 3 days, bioreplicate 1


title: L0005_FASD


title: L0002_Control

value: Female


title: L0003_FASD


title: L0019_FASD


title: K0046_FASD


title: L0013_FASD


title: IM104_Etoposide_Mock_D3_4_RNA

source_name: Lung tissue, Etoposide, Mock-inoculated, 3 days, bioreplicate 4


title: K0045_Control


title: IM104_Etoposide_Mock_D3_3_RNA

source_name: Lung tissue, Etoposide, Mock-inoculated, 3 days, bioreplicate 3


title: IM104_Etoposide_Mock_D3_2_RNA

source_name: Lung tissue, Etoposide, Mock-inoculated, 3 days, bioreplicate 2


title: L0004_FASD


title: L0001_Control


title: K0044_FASD


title: IM104_Vehicle_H1N1_D3_4_RNA

source_name: Lung tissue, Vehicle, H1N1-inoculated, 3 days, bioreplicate 4


title: IM104_Vehicle_H1N1_D3_5_RNA

source_name: Lung tissue, Vehicle, H1N1-inoculated, 3 days, bioreplicate 5


title: K0043_FASD

value: pFAS


title: K0039_Control

value: Male


title: K0042_FASD

value: FASD

value: unknown/possible greek or hispanic


title: IM104_Etoposide_Mock_D3_1_RNA

source_name: Lung tissue, Etoposide, Mock-inoculated, 3 days, bioreplicate 1


title: K0034_FASD


title: K0041_Control

value: Control


title: K0036_FASD

value: caucasian


title: IM104_Vehicle_H1N1_D3_3_RNA

source_name: Lung tissue, Vehicle, H1N1-inoculated, 3 days, bioreplicate 3


title: K0035_FASD


title: K0040_Control


title: K0031_Control


title: K0037_Control


title: IM104_Vehicle_H1N1_D3_1_RNA

source_name: Lung tissue, Vehicle, H1N1-inoculated, 3 days, bioreplicate 1


title: K0033_FASD


title: K0028_Control


title: K0025_Control


title: IM104_Vehicle_Mock_D3_5_RNA

source_name: Lung tissue, Vehicle, Mock-inoculated, 3 days, bioreplicate 5


title: IM104_Vehicle_H1N1_D3_2_RNA

source_name: Lung tissue, Vehicle, H1N1-inoculated, 3 days, bioreplicate 2


title: K0026_Control


title: IM104_Vehicle_Mock_D3_3_RNA

source_name: Lung tissue, Vehicle, Mock-inoculated, 3 days, bioreplicate 3


title: K0024_FASD

value: FAS

value: first nations/caucasian


title: K0029_Control


title: IM104_Vehicle_Mock_D3_4_RNA

source_name: Lung tissue, Vehicle, Mock-inoculated, 3 days, bioreplicate 4


title: K0032_Control


title: K0022_Control


title: K0018_FASD

value: ARND


title: IM104_Vehicle_Mock_D3_1_RNA

source_name: Lung tissue, Vehicle, Mock-inoculated, 3 days, bioreplicate 1


title: K0020_FASD


title: IM104_Vehicle_Mock_D3_2_RNA

source_name: Lung tissue, Vehicle, Mock-inoculated, 3 days, bioreplicate 2


title: K0030_Control


title: IM104_No treatment_No infection_D0_4_RNA

source_name: Lung tissue, No Treatment, No Infection-inoculated, 0 days, bioreplicate 4

value: No Treatment

value: No Infection


title: IM104_No treatment_No infection_D0_5_RNA

source_name: Lung tissue, No Treatment, No Infection-inoculated, 0 days, bioreplicate 5

value: 22 weeks


title: K0016_Control


title: K0019_Control


title: K0021_FASD


title: K0012_Control


title: K0007_Control


title: K0008_Control


title: K0014_FASD

value: first nations


title: K0027_Control


title: K0015_FASD


title: IM104_No treatment_No infection_D0_2_RNA

source_name: Lung tissue, No Treatment, No Infection-inoculated, 0 days, bioreplicate 2

value: lung


title: IM104_No treatment_No infection_D0_3_RNA

source_name: Lung tissue, No Treatment, No Infection-inoculated, 0 days, bioreplicate 3


title: K0011_Control

value: Buccal epithelial cells


title: K0006_FASD


title: IM104_Etoposide_No infection_D0_5_RNA

source_name: Lung tissue, Etoposide, No Infection-inoculated, 0 days, bioreplicate 5

value: Etoposide


title: K0005_Control


title: K0001_Control


title: IM104_Etoposide_No infection_D0_4_RNA

source_name: Lung tissue, Etoposide, No Infection-inoculated, 0 days, bioreplicate 4


title: IM104_Etoposide_No infection_D0_3_RNA

source_name: Lung tissue, Etoposide, No Infection-inoculated, 0 days, bioreplicate 3


title: K0004_Control


title: E0109_Control

value: Female


title: E0107_Control


title: IM104_Etoposide_No infection_D0_2_RNA

source_name: Lung tissue, Etoposide, No Infection-inoculated, 0 days, bioreplicate 2


title: K0013_Control


title: IM104_No treatment_No infection_D0_1_RNA

source_name: Lung tissue, No Treatment, No Infection-inoculated, 0 days, bioreplicate 1


title: K0003_Control


title: E0108_Control


title: E0106_Control


title: K0017_FASD

value: PAE


title: IM104_Etoposide_No infection_D0_1_RNA

source_name: Lung tissue, Etoposide, No Infection-inoculated, 0 days, bioreplicate 1


title: E0104_Control


title: IM104_Vehicle_No infection_D0_2_RNA

source_name: Lung tissue, Vehicle, No Infection-inoculated, 0 days, bioreplicate 2

value: Vehicle


title: IM104_Vehicle_No infection_D0_5_RNA

source_name: Lung tissue, Vehicle, No Infection-inoculated, 0 days, bioreplicate 5


title: IM104_Vehicle_No infection_D0_4_RNA

source_name: Lung tissue, Vehicle, No Infection-inoculated, 0 days, bioreplicate 4


title: E0105_Control


title: E0101_Control

value: Male


title: E0102_Control


title: IM104_Vehicle_No infection_D0_3_RNA

source_name: Lung tissue, Vehicle, No Infection-inoculated, 0 days, bioreplicate 3


title: E0097_FASD

value: FASD


title: E0100_Control

value: Control


title: E0089_Control

value: caucasian


title: E0081_Control


title: E0096_Control


title: E0080_Control


title: E0103_Control


title: E0098_Control


title: E0095_Control


title: E0079_Control


title: E0078_Control


title: IM104_Vehicle_No infection_D0_1_RNA

source_name: Lung tissue, Vehicle, No Infection-inoculated, 0 days, bioreplicate 1


title: E0075_Control


title: E0077_Control


title: E0072_Control


title: E0074_Control


title: E0069_Control


title: E0070_Control

value: Metis


title: E0073_FASD

value: first nations/caucasian


title: E0071_Control


title: E0051_FASD


title: E0059_FASD

value: ARND


title: E0046_FASD


title: E0068_Control


title: E0052_Control


title: E0034_Control


title: E0066_Control


title: E0030_FASD

value: caucasian/african american


title: E0038_Control


title: E0036_Control


title: E0067_Control


title: E0019_Control


title: E0025_Control


title: E0058_FASD

value: pFAS


title: E0026_FASD


title: E0054_Control


title: E0024_FASD


title: E0020_FASD

value: metis/Vietnamese


title: E0035_FASD

value: first nations


title: E0033_Control


title: E0040_FASD


title: E0014_FASD

value: pFASD


title: NoAsthma-CBMC-Rep15

city: Tucson

first: Donata

last: Vercelli

state: Arizona

address: 1657 E. Helen Street

institute: University of Arizona

description:
DNA from cord blood mononuclear cells from a non-asthmatic child (by age 9), biological replicate 15 of 18
66960902

hyb_protocol: Labeling and hybridization  were performed at Roche-NimbleGen. Briefly, WGA-input and WGA-enriched samples were labeled with Cy3 and Cy5 respectively, and co-hybridized to 2.1M Human Promoter Deluxe microarrays (Roche-NimbleGen). Hybridization intensities were extracted separately for the Cy3 and Cy5 channels and used for subsequent processing and analysis.

scan_protocol: Scanning and quality control were performed at Roche-NimbleGen.

data_processing:
For each sample, the hybridization intensities of the input and enriched channels were quantile-normalized separately to remove technical noise. Probes mapping to sex chromosomes were excluded from the analysis. Log2 ratios of enriched/input probe intensities were then calculated from the normalized data.
Regions that were differentially methylated between asthmatics and non-asthmatics (DMRs) were detected using a Probe Sliding Window-ANOVA [Roche-NimbleGen (van Breda, Claessen et al. 2015)] that identifies maximal inter-group differences in signal intensities relative to a user-defined threshold. Probability scores (P-values) are then assigned to each probe on the array using a repeated measure ANOVA model. In this study, DMRs were defined by region length ≥300 bp, magnitude (between-group mean log2 ratio difference) ≥0.2, significance threshold (adjusted using the Benjamini Hochberg False Discovery Rate method to account for multiple testing) = 0.01, using a sliding window size = 750 bp. A positive magnitude difference indicated hypermethylation in asthmatics relative to non-asthmatics. DMRs containing ≤5 CpG sites within a 750 bp window centered on the DMR [a configuration likely to result in sub-optimal capture of methylated DNA (Yegnasubramanian, Lin et al. 2006)] were excluded from further analyses.
Normalized log2 ratios of enriched/input probe intensities

source_name: Input DNA from CBMCs from Non-asthmatic child, replicate 15 of 18

label_protocol: The MethylCollector Ultra Kit (Active Motif) was then used for methyl binding protein-dependent capture (MBDCap) (Rauch and Pfeifer 2010) of methylated DNA (enriched fraction). The protocol is a modification of the Methylated CpG Island Recovery Assay (MIRA)(Rauch and Pfeifer 2010) and has the advantage of requiring limited amounts of DNA. For each sample, enriched and input DNA underwent one round of whole genome amplification (WGA) using the GenomePlex Whole Genome Amplification Kit (Sigma). The entire output of the MethylCollector capture (for enriched DNA) or 20 ng of input DNA were used as starting material. WGA reactions were run on 1% agarose gels (1x TBE) to assess fragment size distribution and purified with the QiaQuick PCR Purification Kit (Qiagen).    The efficiency of methylated DNA enrichment was evaluated by quantitative (q) PCR analysis of three control regions that are typically methylated (XIST and NBR2) and unmethylated (APC) across tissues. Primers are provided with the MethylCollector Kit. WGA-input and WGA-enriched DNA (5 ng/ul, 5 ul) were amplified using PerfeCTa SYBR Green FastMix ROX (Quanta BioSciences) and optimal cycling conditions. Samples were run in triplicate and their Ct values averaged. Fold-enrichment was calculated as 2^(Ct WGA input – Ct WGA enriched). All samples met the required quality control criteria (≥3-fold enrichment in XIST and NBR2, methylation depletion in APC).

extract_protocol: High molecular weight genomic DNA was isolated from CBMCs using the DNeasy Blood and Tissue Kit (Qiagen) and fragmented with a Bioruptor sonicator (Diagenode) to produce fragments of 200-700 bp.  For each sample, a DNA aliquot was set aside to serve as the non-enriched, input DNA fraction.

value: cord blood mononuclear cells (CBMCs)

tag: sample type

value: Input DNA

tag: asthma diagnosis (2-9 years)

value: Non-asthmatic

source_name: Methylation-Enriched DNA from CBMCs from Non-asthmatic child, replicate 15 of 18

tag: enrichment

value: Methyl binding-protein dependent capture (MethylCollector Ultra Kit, Active Motif, Rauch et al (2010), PMID:20304072)

value: Methylation-Enriched DNA


title: NoAsthma-CBMC-Rep16

description:
DNA from cord blood mononuclear cells from a non-asthmatic child (by age 9), biological replicate 16 of 18
66961802

source_name: Input DNA from CBMCs from Non-asthmatic child, replicate 16 of 18

value: Male

source_name: Methylation-Enriched DNA from CBMCs from Non-asthmatic child, replicate 16 of 18


title: NoAsthma-CBMC-Rep17

description:
DNA from cord blood mononuclear cells from a non-asthmatic child (by age 9), biological replicate 17 of 18
66982602

source_name: Input DNA from CBMCs from Non-asthmatic child, replicate 17 of 18

value: Female

source_name: Methylation-Enriched DNA from CBMCs from Non-asthmatic child, replicate 17 of 18


title: NoAsthma-CBMC-Rep18

description:
DNA from cord blood mononuclear cells from a non-asthmatic child (by age 9), biological replicate 18 of 18
67423702

source_name: Input DNA from CBMCs from Non-asthmatic child, replicate 18 of 18

source_name: Methylation-Enriched DNA from CBMCs from Non-asthmatic child, replicate 18 of 18


title: E0017_Control

value: Buccal epithelial cells

tag: date run

tag: disease status

value: Control


title: E0037_Control

tag: disease subgroup

tag: self-reported ethnicity

value: caucasian


title: E0008_FASD

value: FASD

tag: sentrix id

tag: sentrix position


title: E0013_FASD

tag: cell type

value: PAE

tag: sentrix row


title: E0015_FASD

tag: Sex

value: ARND

tag: age


title: E0009_FASD


title: E0018_FASD

value: aboriginal/ african american


title: Asthma-CBMC-Rep17

description:
DNA from cord blood mononuclear cells from an asthmatic child (by age 9), biological replicate 17 of 18
66909502

source_name: Input DNA from CBMCs from Asthmatic child, replicate 17 of 18

tag: tissue

value: Asthmatic

source_name: Methylation-Enriched DNA from CBMCs from Asthmatic child, replicate 17 of 18


title: NoAsthma-CBMC-Rep14

description:
DNA from cord blood mononuclear cells from a non-asthmatic child (by age 9), biological replicate 14 of 18
66909802

source_name: Input DNA from CBMCs from Non-asthmatic child, replicate 14 of 18

source_name: Methylation-Enriched DNA from CBMCs from Non-asthmatic child, replicate 14 of 18


title: Asthma-CBMC-Rep18

description:
DNA from cord blood mononuclear cells from an asthmatic child (by age 9), biological replicate 18 of 18
66910102

source_name: Input DNA from CBMCs from Asthmatic child, replicate 18 of 18

source_name: Methylation-Enriched DNA from CBMCs from Asthmatic child, replicate 18 of 18


title: E0011_FASD

value: first nations


title: E0007_FASD


title: E0010_FASD


title: E0016_FASD


title: E0006_FASD


title: NoAsthma-CBMC-Rep13

description:
DNA from cord blood mononuclear cells from a non-asthmatic child (by age 9), biological replicate 13 of 18
66909202

source_name: Input DNA from CBMCs from Non-asthmatic child, replicate 13 of 18

source_name: Methylation-Enriched DNA from CBMCs from Non-asthmatic child, replicate 13 of 18


title: Asthma-CBMC-Rep15

description:
DNA from cord blood mononuclear cells from an asthmatic child (by age 9), biological replicate 15 of 18
63804902

source_name: Input DNA from CBMCs from Asthmatic child, replicate 15 of 18

source_name: Methylation-Enriched DNA from CBMCs from Asthmatic child, replicate 15 of 18


title: Asthma-CBMC-Rep16

description:
DNA from cord blood mononuclear cells from an asthmatic child (by age 9), biological replicate 16 of 18
63805502

source_name: Input DNA from CBMCs from Asthmatic child, replicate 16 of 18

source_name: Methylation-Enriched DNA from CBMCs from Asthmatic child, replicate 16 of 18


title: C0019_FASD


title: NoAsthma-CBMC-Rep11

description:
DNA from cord blood mononuclear cells from a non-asthmatic child (by age 9), biological replicate 11 of 18
66904802

source_name: Input DNA from CBMCs from Non-asthmatic child, replicate 11 of 18

source_name: Methylation-Enriched DNA from CBMCs from Non-asthmatic child, replicate 11 of 18


title: Asthma-CBMC-Rep14

description:
DNA from cord blood mononuclear cells from an asthmatic child (by age 9), biological replicate 14 of 18
63804602

source_name: Input DNA from CBMCs from Asthmatic child, replicate 14 of 18

source_name: Methylation-Enriched DNA from CBMCs from Asthmatic child, replicate 14 of 18


title: Asthma-CBMC-Rep13

description:
DNA from cord blood mononuclear cells from an asthmatic child (by age 9), biological replicate 13 of 18
63783602

source_name: Input DNA from CBMCs from Asthmatic child, replicate 13 of 18

source_name: Methylation-Enriched DNA from CBMCs from Asthmatic child, replicate 13 of 18


title: C0015_FASD

value: pFAS


title: E0001_FASD

value: Metis/Italian


title: Asthma-CBMC-Rep11

description:
DNA from cord blood mononuclear cells from an asthmatic child (by age 9), biological replicate 11 of 18
63782902

source_name: Input DNA from CBMCs from Asthmatic child, replicate 11 of 18

value: cord blood mononuclear cells (CBMCs)

value: Input DNA

source_name: Methylation-Enriched DNA from CBMCs from Asthmatic child, replicate 11 of 18


title: C0018_FASD


title: NoAsthma-CBMC-Rep12

description:
DNA from cord blood mononuclear cells from a non-asthmatic child (by age 9), biological replicate 12 of 18
66908902

source_name: Input DNA from CBMCs from Non-asthmatic child, replicate 12 of 18

value: Non-asthmatic

source_name: Methylation-Enriched DNA from CBMCs from Non-asthmatic child, replicate 12 of 18

value: Methyl binding-protein dependent capture (MethylCollector Ultra Kit, Active Motif, Rauch et al (2010), PMID:20304072)


title: E0003_FASD


title: C0017_FASD

value: FAS

value: Metis


title: C0022_FASD

value: Buccal epithelial cells

value: Female

value: Inuit


title: Asthma-CBMC-Rep8

description:
DNA from cord blood mononuclear cells from an asthmatic child (by age 9), biological replicate 8 of 18
61650402

source_name: Input DNA from CBMCs from Asthmatic child, replicate 8 of 18

value: Male

source_name: Methylation-Enriched DNA from CBMCs from Asthmatic child, replicate 8 of 18

value: Methylation-Enriched DNA


title: C0028_FASD

value: FASD

value: ARND

value: caucasian


title: Asthma-CBMC-Rep7

description:
DNA from cord blood mononuclear cells from an asthmatic child (by age 9), biological replicate 7 of 18
61649802

source_name: Input DNA from CBMCs from Asthmatic child, replicate 7 of 18

value: Asthmatic

source_name: Methylation-Enriched DNA from CBMCs from Asthmatic child, replicate 7 of 18


title: Asthma-CBMC-Rep6

description:
DNA from cord blood mononuclear cells from an asthmatic child (by age 9), biological replicate 6 of 18
60912902

source_name: Input DNA from CBMCs from Asthmatic child, replicate 6 of 18

source_name: Methylation-Enriched DNA from CBMCs from Asthmatic child, replicate 6 of 18


title: Asthma-CBMC-Rep10

description:
DNA from cord blood mononuclear cells from an asthmatic child (by age 9), biological replicate 10 of 18
63782602

source_name: Input DNA from CBMCs from Asthmatic child, replicate 10 of 18

source_name: Methylation-Enriched DNA from CBMCs from Asthmatic child, replicate 10 of 18


title: Asthma-CBMC-Rep9

description:
DNA from cord blood mononuclear cells from an asthmatic child (by age 9), biological replicate 9 of 18
61650702

source_name: Input DNA from CBMCs from Asthmatic child, replicate 9 of 18

source_name: Methylation-Enriched DNA from CBMCs from Asthmatic child, replicate 9 of 18


title: Asthma-CBMC-Rep12

description:
DNA from cord blood mononuclear cells from an asthmatic child (by age 9), biological replicate 12 of 18
63783202

source_name: Input DNA from CBMCs from Asthmatic child, replicate 12 of 18

source_name: Methylation-Enriched DNA from CBMCs from Asthmatic child, replicate 12 of 18


title: C0013_FASD

value: pFAS


title: E0002_FASD

value: Metis/Italian


title: C0016_FASD

value: PAE


title: E0004_FASD

value: first nations


title: Asthma-CBMC-Rep5

description:
DNA from cord blood mononuclear cells from an asthmatic child (by age 9), biological replicate 5 of 18
60870902

source_name: Input DNA from CBMCs from Asthmatic child, replicate 5 of 18

value: cord blood mononuclear cells (CBMCs)

value: Input DNA

source_name: Methylation-Enriched DNA from CBMCs from Asthmatic child, replicate 5 of 18


title: Asthma-CBMC-Rep4

description:
DNA from cord blood mononuclear cells from an asthmatic child (by age 9), biological replicate 4 of 18
60870602

source_name: Input DNA from CBMCs from Asthmatic child, replicate 4 of 18

source_name: Methylation-Enriched DNA from CBMCs from Asthmatic child, replicate 4 of 18

value: Methyl binding-protein dependent capture (MethylCollector Ultra Kit, Active Motif, Rauch et al (2010), PMID:20304072)


title: Asthma-CBMC-Rep3

description:
DNA from cord blood mononuclear cells from an asthmatic child (by age 9), biological replicate 3 of 18
60868802

source_name: Input DNA from CBMCs from Asthmatic child, replicate 3 of 18

source_name: Methylation-Enriched DNA from CBMCs from Asthmatic child, replicate 3 of 18


title: Asthma-CBMC-Rep2

description:
DNA from cord blood mononuclear cells from an asthmatic child (by age 9), biological replicate 2 of 18
60868502

source_name: Input DNA from CBMCs from Asthmatic child, replicate 2 of 18

source_name: Methylation-Enriched DNA from CBMCs from Asthmatic child, replicate 2 of 18


title: C0014_Control

value: Control


title: C0023_FASD

value: Buccal epithelial cells


title: NoAsthma-CBMC-Rep10

description:
DNA from cord blood mononuclear cells from a non-asthmatic child (by age 9), biological replicate 10 of 18
58934702

source_name: Input DNA from CBMCs from Non-asthmatic child, replicate 10 of 18

value: Non-asthmatic

source_name: Methylation-Enriched DNA from CBMCs from Non-asthmatic child, replicate 10 of 18


title: C0005_Control

value: Female


title: Asthma-CBMC-Rep1

description:
DNA from cord blood mononuclear cells from an asthmatic child (by age 9), biological replicate 1 of 18
60866302

source_name: Input DNA from CBMCs from Asthmatic child, replicate 1 of 18

source_name: Methylation-Enriched DNA from CBMCs from Asthmatic child, replicate 1 of 18


title: NoAsthma-CBMC-Rep8

description:
DNA from cord blood mononuclear cells from a non-asthmatic child (by age 9), biological replicate 8 of 18
58934102

source_name: Input DNA from CBMCs from Non-asthmatic child, replicate 8 of 18

value: Male

source_name: Methylation-Enriched DNA from CBMCs from Non-asthmatic child, replicate 8 of 18


title: NoAsthma-CBMC-Rep7

description:
DNA from cord blood mononuclear cells from a non-asthmatic child (by age 9), biological replicate 7 of 18
58933802

source_name: Input DNA from CBMCs from Non-asthmatic child, replicate 7 of 18

source_name: Methylation-Enriched DNA from CBMCs from Non-asthmatic child, replicate 7 of 18

value: Methylation-Enriched DNA


title: NoAsthma-CBMC-Rep6

description:
DNA from cord blood mononuclear cells from a non-asthmatic child (by age 9), biological replicate 6 of 18
57530202

source_name: Input DNA from CBMCs from Non-asthmatic child, replicate 6 of 18

source_name: Methylation-Enriched DNA from CBMCs from Non-asthmatic child, replicate 6 of 18


title: C0012_FASD

value: FASD


title: E0031_Control

value: Pakistani


title: NoAsthma-CBMC-Rep4

description:
DNA from cord blood mononuclear cells from a non-asthmatic child (by age 9), biological replicate 4 of 18
55343302

source_name: Input DNA from CBMCs from Non-asthmatic child, replicate 4 of 18

source_name: Methylation-Enriched DNA from CBMCs from Non-asthmatic child, replicate 4 of 18


title: NoAsthma-CBMC-Rep2

description:
DNA from cord blood mononuclear cells from a non-asthmatic child (by age 9), biological replicate 2 of 18
53472802

source_name: Input DNA from CBMCs from Non-asthmatic child, replicate 2 of 18

source_name: Methylation-Enriched DNA from CBMCs from Non-asthmatic child, replicate 2 of 18


title: NoAsthma-CBMC-Rep3

description:
DNA from cord blood mononuclear cells from a non-asthmatic child (by age 9), biological replicate 3 of 18
55343002

source_name: Input DNA from CBMCs from Non-asthmatic child, replicate 3 of 18

source_name: Methylation-Enriched DNA from CBMCs from Non-asthmatic child, replicate 3 of 18


title: NoAsthma-CBMC-Rep1

description:
DNA from cord blood mononuclear cells from a non-asthmatic child (by age 9), biological replicate 1 of 18
53468602

source_name: Input DNA from CBMCs from Non-asthmatic child, replicate 1 of 18

source_name: Methylation-Enriched DNA from CBMCs from Non-asthmatic child, replicate 1 of 18


title: C0011_FASD

value: ARND

value: caucasian


title: C0007_FASD


title: human osteosarcoma cell line ZOSM

status: Public on Apr 12 2017

city: Guangzhou

first: Weihai

last: Liu

state: Guangdong

address: 58 Zhongshan Road 2

department: Department of Musculoskeletal Oncology

country: China

institute: The First Affiliated Hospital, Sun Yat-sen University

description: The concentrations of the RNA samples were determined by OD260 using a NanoDrop ND-1007 instrument. The integrity of RNA were assessed by electrophoresis on a denaturing agarose gel.

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The circRNAs that at least 1 out of 8 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses.

source_name: osteosarcoma

label_protocol: Total RNA from each sample was treated with Rnase R to enrich circular RNA. The enriched circular RNA was then amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

extract_protocol: Total RNA was extracted using TRIZOL reagent (Invitrogen, NY, USA) in accordance with the manufacturer’s protocol. And then total RNA from each sample was quantified using the NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA). RNA integrity and gDNA contamination of each sample was assessed by denaturing agarose gel electrophoresis.

tag: cell line

value: ZOSM

tag: molecule type

value: circular RNA


title: C0004_FASD

value: Inuit


title: C0010_FASD


title: NoAsthma-CBMC-Rep5

description:
DNA from cord blood mononuclear cells from a non-asthmatic child (by age 9), biological replicate 5 of 18
56828302

source_name: Input DNA from CBMCs from Non-asthmatic child, replicate 5 of 18

source_name: Methylation-Enriched DNA from CBMCs from Non-asthmatic child, replicate 5 of 18


title: human osteosarcoma cell line HOS

description: The concentrations of the RNA samples were determined by OD260 using a NanoDrop ND-1003 instrument. The integrity of RNA were assessed by electrophoresis on a denaturing agarose gel.

value: HOS


title: human osteosarcoma cell line 143B

description: The concentrations of the RNA samples were determined by OD260 using a NanoDrop ND-1005 instrument. The integrity of RNA were assessed by electrophoresis on a denaturing agarose gel.


title: human osteosarcoma cell line U2OS/MTX300

description: The concentrations of the RNA samples were determined by OD260 using a NanoDrop ND-1002 instrument. The integrity of RNA were assessed by electrophoresis on a denaturing agarose gel.


title: human osteosarcoma cell line U2OS

description: The concentrations of the RNA samples were determined by OD260 using a NanoDrop ND-1001 instrument. The integrity of RNA were assessed by electrophoresis on a denaturing agarose gel.


title: human osteosarcoma cell line MG63

description: The concentrations of the RNA samples were determined by OD260 using a NanoDrop ND-1004 instrument. The integrity of RNA were assessed by electrophoresis on a denaturing agarose gel.


title: human osteosarcoma cell line ZOS

description: The concentrations of the RNA samples were determined by OD260 using a NanoDrop ND-1006 instrument. The integrity of RNA were assessed by electrophoresis on a denaturing agarose gel.

value: ZOS


title: human osteoblast hFOB1.19

description: The concentrations of the RNA samples were determined by OD260 using a NanoDrop ND-1000 instrument. The integrity of RNA were assessed by electrophoresis on a denaturing agarose gel.

source_name: osteoblast


title: C0003_FASD

value: first nations/caucasian


title: naive_14d_animal49

city: Indianapolis

first: Keith

middle: M

last: Goldstein

state: IN

address: Lilly Corporate Center

department: Investigative Toxicology

institute: Eli Lilly & Co.

hyb_protocol: Affymetrix hyb protocol: EukGE-WS2v5_450

scan_protocol: .CEL files were generated using Affymetrix GeneChip Command Console

data_processing: MAS5 signal intensities were generated using Bioconductor's Affy package. Data was scaled to a target of 1500.

organism: Rattus norvegicus

source_name: naïve animals, no BDL or sham surgery, 14 days after surgery of BDL/sham animals

label_protocol: RNA was then labeled and hybridized to RG230-2 microarrays (Affymetrix) according to the manufacturer’s instructions

extract_protocol: Samples were homogenized in Qiagen RLT buffer, and RNA isolated using Qiagen RNeasy columns per manufacturer's protocol.

treatment_protocol: We conducted a rat bile duct ligation (BDL) study, a common model for cholestatic liver injury and BDH, and monitored injury and expression changes from 3 hours through 14 days

value: Liver

tag: surgery

value: no surgery

tag: time following surgery

tag: gender

value: male

tag: strain

value: Sprague-Dawley CD/IGS

tag: animal number

tag: excluded animal

value: No


title: sham_14d_animal47

source_name: liver from animals with sham surgery, 14days after surgery

value: sham


title: BDL_14d_animal45

source_name: liver from animals with ligated bile duct, 14days after surgery

value: bile duct ligation


title: naive_14d_animal50


title: BDL_10d_animal39

source_name: liver from animals with ligated bile duct, 10days after surgery


title: BDL_14d_animal44


title: BDL_10d_animal37


title: sham_14d_animal46


title: sham_10d_animal42

source_name: liver from animals with sham surgery, 10days after surgery


title: naive_14d_animal51


title: BDL_14d_animal43


title: sham_10d_animal41


title: BDL_10d_animal38


title: C0002_FASD

value: Buccal epithelial cells

tag: date run

value: Female

tag: disease status

value: FASD

tag: disease subgroup

value: pFAS


title: sham_10d_animal40


title: sham_5d_animal34

source_name: liver from animals with sham surgery, 5days after surgery


title: sham_14d_animal48


title: NoAsthma-CBMC-Rep9

description:
DNA from cord blood mononuclear cells from a non-asthmatic child (by age 9), biological replicate 9 of 18
58934402

source_name: Input DNA from CBMCs from Non-asthmatic child, replicate 9 of 18

value: cord blood mononuclear cells (CBMCs)

tag: sample type

value: Input DNA

tag: asthma diagnosis (2-9 years)

value: Non-asthmatic

source_name: Methylation-Enriched DNA from CBMCs from Non-asthmatic child, replicate 9 of 18

tag: enrichment

value: Methyl binding-protein dependent capture (MethylCollector Ultra Kit, Active Motif, Rauch et al (2010), PMID:20304072)

value: Methylation-Enriched DNA


title: BDL_5d_animal33

source_name: liver from animals with ligated bile duct, 5days after surgery


title: sham_5d_animal36


title: BDL_5d_animal32


title: BDL_3d_animal27

source_name: liver from animals with ligated bile duct, 3days after surgery


title: BDL_5d_animal31

value: Yes


title: sham_3d_animal29

source_name: liver from animals with sham surgery, 3days after surgery

value: Liver


title: sham_3d_animal30


title: BDL_3d_animal26


title: sham_3d_animal28


title: sham_5d_animal35


title: sham_24hr_animal23

source_name: liver from animals with sham surgery, 24hours after surgery


title: sham_24hr_animal24


title: sham_12hr_animal18

source_name: liver from animals with sham surgery, 12hours after surgery


title: BDL_24hr_animal21

source_name: liver from animals with ligated bile duct, 24hours after surgery


title: sham_12hr_animal16


title: sham_6hr_animal12

source_name: liver from animals with sham surgery, 6hours after surgery


title: sham_6hr_animal10


title: sham_3hr_animal4

source_name: liver from animals with sham surgery, 3hours after surgery


title: sham_12hr_animal17


title: sham_3hr_animal6


title: BDL_6hr_animal8

source_name: liver from animals with ligated bile duct, 6hours after surgery


title: BDL_3d_animal25


title: BDL_24hr_animal19


title: BDL_12hr_animal15

source_name: liver from animals with ligated bile duct, 12hours after surgery


title: sham_24hr_animal22


title: sham_3hr_animal5


title: BDL_24hr_animal20


title: BDL_12hr_animal14


title: sham_6hr_animal11


title: BDL_6hr_animal9


title: BDL_12hr_animal13


title: BDL_3hr_animal1

source_name: liver from animals with ligated bile duct, 3hours after surgery


title: siREST replicate 2 NHEK [siREST-proliferation]

city: Irvine

first: Bogi

last: Andersen

address: 839 Health Sciences Dr.

department: Medicine

institute: University of California, Irvine

hyb_protocol: 2ug of the labeled, fragmented single stranded cDNA is hybridized at 45C with rotation for 17 hours (Affymetrix GenechIP Hybridization Oven 640) to probe sets present on an Affymetrix GeneChIP 1.0ST array. The GeneChIP arrays were washed and then stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 450 (Fluidics protocol FS450_007)

scan_protocol: Arrays were scanned using GeneChIP Scanner 3000 7G and Command Console Software v. 3.2.3 to produce .CEL intensity files.

data_processing:
The probe cell intensity files (*.CEL) were analyzed in Affymetrix Expression Console software v1.1.1 using the PLIER algorithm to generate probe level summarization files (*.CHIP). The settings used were algorithm-PLIER v2.0; quantification scale-Linear;quantification type-signal and detection p-value; background-PM-GCBG; normalization method-sketch-quantile.
Raw values lower than 200 were not considered expressed

source_name: NHEK

label_protocol: The Ambion WT expression kit (Life Technologies) was used to prepare RNA samples for whole transcriptome microarray analysis

growth_protocol: Normal Human Epidermal Keratinocytes (NHEK) were purchased from LifeLine Technologies and grown according to the manufacturer’s instructions in DermaLife medium (LifeLine Tech) supplemented with DermaLife growth factors (LifeLine Tech).

extract_protocol: Cells were collected and lysed in Trizol, followed purification with Zymo RNA extraction kit.  RNA concentration and quality were quantified on a NanoDrop.

treatment_protocol: 100,000 cells were plated in each well of a 12 well plate, and were transfected with 30nM control (Dharmacon D-001810-10-05), REST (Qiagen hs_REST_5: S104153765, hs_REST_1: s100701407). Cells were collected 72 hours after transfection.

tag: cell type

value: proliferating

value: NHEK


title: BDL_3hr_animal2

value: male

value: Sprague-Dawley CD/IGS


title: BDL_6hr_animal7

value: No


title: BDL_3hr_animal3

value: bile duct ligation


title: scramble control replicate 2 NHEK [siREST-migration]

treatment_protocol: 100,000 cells were plated in each well of a 12 well plate, and were transfected with 30nM control (Dharmacon D-001810-10-05), REST (Qiagen hs_REST_5: S104153765, hs_REST_1: s100701407). To induce migration, cells were grown to a confluent monolayer and scratched with a p200 pipette tip. Scratches were made approximately every 1 cm horizontally and vertically, resulting in a grid of scratches. Migration was induced 60 hours after transfection, and cells were collected 12 hours later (72 hours after transfection).

value: migrating


title: scramble control replicate 1 NHEK [siREST-migration]


title: siREST replicate 1 NHEK [siREST-proliferation]


title: scramble control replicate 1 NHEK [siREST-proliferation]


title: siREST replicate 1 NHEK [siREST-migration]

description: siREST 1


title: scramble control replicate 1, 0 hours migration, NHEK [siGRHL3-migration]

treatment_protocol: 100,000 cells were plated in each well of a 12 well plate, and were transfected with 30nM control (Dharmacon D-001810-10-05), or GRHL3 (Dharmacon L-014017-02). To induce migration, cells were grown to a confluent monolayer and scratched with a p200 pipette tip. Scratches were made approximately every 1 cm horizontally and vertically, resulting in a grid of scratches. Migration was induced 60 hours after transfection, and cells were collected 12 hours later (72 hours after transfection).


title: siGRHL3 replicate 1, 12 hours migration, NHEK [siGRHL3-migration]


title: Ebola-Day 180-replicate 1

city: Seattle

first: kathie

last: walters

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

description: Gene expression profilign of peripheral blood from Ebola infected patient

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Ebola-Day 180

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.3 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from approximately 2.5 mls of peripheral blood in Paxgene tubes according to manufacturer's protocol under BSL4 conditions.  RNA quality was assessed using Agilent Bioanalyzer.

treatment_protocol: Peripheral blood was collected from either a patient infected with Ebola virus or healthy volunteers and stored in Paxgene tubes (Qiagen) according to manufacturer's instructions.

value: Peripheral blood

tag: virus strain

value: Ebola


title: scramble control replicate 2, 0 hours migration, NHEK [siGRHL3-migration]


title: Ebola-Day 59-replicate 2

source_name: Ebola-Day 59

tag: tissue


title: Ebola-Day 103-replicate 2

source_name: Ebola-Day 103


title: siGRHL3 replicate 2, 12 hours migration, NHEK [siGRHL3-migration]

tag: cell line


title: scramble control replicate 2 NHEK [siREST-proliferation]


title: Ebola-Day 59-replicate 1


title: Ebola-Day 33-replicate 2

source_name: Ebola-Day 33


title: scramble control replicate 2, 12 hours migration, NHEK [siGRHL3-migration]


title: scramble control replicate 1, 12 hours migration, NHEK [siGRHL3-migration]


title: Ebola-Day 270-replicate 1

source_name: Ebola-Day 270


title: Ebola-Day 270-replicate 2


title: Ebola-Day 33-replicate 1


title: Ebola-Day 28-replicate 1

source_name: Ebola-Day 28


title: Ebola-Day 28-replicate 2


title: Ebola-Day 24-replicate 1

source_name: Ebola-Day 24


title: Ebola-Day 31-replicate 2

source_name: Ebola-Day 31


title: Ebola-Day 24-replicate 2


title: Ebola-Day 31-replicate 1


title: Ebola-Day 22-replicate 1

source_name: Ebola-Day 22


title: Ebola-Day 21-replicate 1

source_name: Ebola-Day 21


title: Ebola-Day 103-replicate 1


title: Ebola-Day 20-replicate 1

source_name: Ebola-Day 20


title: Ebola-Day 21-replicate 2


title: Ebola-Day 20-replicate 2


title: Ebola-Day 15-replicate 2

source_name: Ebola-Day 15


title: Ebola-Day 18-replicate 1

source_name: Ebola-Day 18


title: Ebola-Day 17-replicate 2

source_name: Ebola-Day 17


title: Ebola-Day 16-replicate 2

source_name: Ebola-Day 16


title: Ebola-Day 19-replicate 1

source_name: Ebola-Day 19


title: Ebola-Day 17-replicate 1


title: Ebola-Day 16-replicate 1


title: Ebola-Day 18-replicate 2


title: Ebola-Day 19-replicate 2


title: Ebola-Day 14-replicate 1

source_name: Ebola-Day 14


title: Ebola-Day 14-replicate 2


title: Ebola-Day 11-replicate 1

source_name: Ebola-Day 11


title: Ebola-Day 12-replicate 2

source_name: Ebola-Day 12


title: Ebola-Day 10-replicate 3

source_name: Ebola-Day 10


title: Ebola-Day 13-replicate 1

source_name: Ebola-Day 13


title: Ebola-Day 12-replicate 1


title: Ebola-Day 13-replicate 2


title: Ebola-Day 15-replicate 1


title: Ebola-Day 10-replicate 1


title: Ebola-Day 11-replicate 2


title: Ebola-Day 9-replicate 1

source_name: Ebola-Day 9


title: Ebola-Day 10-replicate 2


title: Ebola-Day 9-replicate 2


title: Ebola-Day 7-replicate 2

source_name: Ebola-Day 7


title: Ebola-Day 8-replicate 2

source_name: Ebola-Day 8


title: Ebola-Day 8-replicate 1


title: PD47B-healthy blood-replicate 1

description: Gene expression profiling of peripheral blood from healthy volunteers

source_name: PD47-B-healthy blood


title: siREST replicate 2 NHEK [siREST-migration]

description: siREST 2

source_name: NHEK


title: PD65-healthy blood-replicate 1

source_name: PD65-healthy blood


title: PD44-healthy blood-replicate 1

source_name: PD44-healthy blood


title: PD45B-healthy blood-replicate 1

source_name: PD45-B-healthy blood


title: PD57-healthy blood-replicate 1

source_name: PD57-healthy blood


title: PD41-healthy blood-replicate 1

source_name: PD41-healthy blood


title: PD42-healthy blood-replicate 1

source_name: PD42-healthy blood


title: PD46-healthy blood-replicate 1

source_name: PD46-healthy blood


title: PD47-healthy blood-replicate 1

source_name: PD47-healthy blood


title: PD43-healthy blood-replicate 1

source_name: PD43-healthy blood


title: PD48-healthy blood-replicate 1

source_name: PD48-healthy blood


title: PD38-healthy blood-replicate 1

source_name: PD38-healthy blood


title: PD37-healthy blood-replicate 1

source_name: PD37-healthy blood


title: PD45-healthy blood-replicate 1

source_name: PD45-healthy blood


title: PD34-healthy blood-replicate 1

source_name: PD34-healthy blood


title: PD55-healthy blood-replicate 1

source_name: PD55-healthy blood


title: PD60-healthy blood-replicate 1

source_name: PD60-healthy blood


title: PD64-healthy blood-replicate 1

source_name: PD64-healthy blood


title: PD49-healthy blood-replicate 1

source_name: PD49-healthy blood


title: PD24-healthy blood-replicate 1

source_name: PD24-healthy blood


title: PD27-healthy blood-replicate 1

source_name: PD27-healthy blood


title: PD21-healthy blood-replicate 1

source_name: PD21-healthy blood


title: PD36-healthy blood-replicate 1

source_name: PD36-healthy blood


title: PD28-healthy blood-replicate 1

source_name: PD28-healthy blood


title: PD16-healthy blood-replicate 1

source_name: PD16-healthy blood


title: PD17-healthy blood-replicate 1

source_name: PD17-healthy blood


title: PD15-healthy blood-replicate 1

source_name: PD15-healthy blood


title: PD6-healthy blood-replicate 1

source_name: PD6-healthy blood


title: PD40-healthy blood-replicate 1

source_name: PD40-healthy blood


title: PD20-healthy blood-replicate 1

source_name: PD20-healthy blood


title: Ebola-Day 22-replicate 2

source_name: Ebola-Day 22


title: t=48h post activation, rep2

city: Edinburgh

first: Jose

middle: Ignacio

last: de las Heras

address: Max Born Crescent

department: Wellcome Trust Centre

institute: University of Edinburgh

scan_protocol: Standard Protocols (Clinical Research Facility Edinburgh), Scanner: HiScan H166

data_processing: Data were log2 transformed and quantile normalised using the BioConductor package Limma.

source_name: Jurkat T-cell cell line_t=48h post activation

label_protocol: Ambion Illumina TotalPrep kit

growth_protocol: Jurkat clone E6-1 T-cells and Raji B-cells were cultured inn RPMI 1640 with 10% FBS, 100u/ml penicillin and 100ug/ml streptomycin. Jurkat and raji cells were diluted 1:6 and 1:10 respectively in fresh media every 2-3 days. Cellular debris was removed by centrifugation.

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

treatment_protocol: Raji B-cells were incubated for 30min at a concentration of 1E06 cells/ml in medium containing 0.5ug/ml SEE (Toxin Technologies, EP404). SEE loaded Raji cells were pelleted, washed in PBS and resuspended in medium, then mixed at a 1:10 ratio with Jurkat cells to a total density of 1E06 cells/ml. Naive CD4+ cells were isolated by FACS. Activation was performed by incubation with 20ng/ml PMA. Activation was determined and selected for by FACS staining for CD69-APC. Activated cell samples were used if they were CD69+ for at least 78% of the population.

value: Jurkat T-cell cell line

tag: activated with

value: 20ng/ml PMA

tag: time point

value: t=48h post activation


title: t=48h post activation, rep1

hyb_protocol: Standard Protocols (Clinical Research Facility Edinburgh)


title: t=8h post activation, rep2

source_name: Jurkat T-cell cell line_t=8h post activation

value: t=8h post activation


title: t=8h post activation, rep3


title: untreated control, t0, rep2

source_name: Jurkat T-cell cell line_untreated control_t0

value: none (untreated control)

value: untreated control, t0


title: t=48h post activation, rep3


title: untreated control, t0, rep1


title: t=24h post activation, rep3

source_name: Jurkat T-cell cell line_t=24h post activation

value: t=24h post activation


title: t=24h post activation, rep1


title: t=24h post activation, rep2


title: t=8h post activation, rep1


title: Ebola-Day 25-replicate 1

source_name: Ebola-Day 25


title: untreated control, t0, rep3


title: TCF7L2

description: 253452510007_201107280954_S01 [1_2]

hyb_protocol: The labeled cRNA is fragmented and placed on the human 8x15K microarray and hybridized at 65oC for ~17 hours.

scan_protocol: The arrays are washed and scanned at 5 μM resolution on an Agilent G2565CA High Resolution Scanner.

data_processing: Data was processed through Agilent’s Feature Extraction software version 10.7.31.

source_name: neonatal human epidermal keratintocyes

label_protocol: One-color labeling reactions were prepared using the Agilent One-Color Protocol (Version 5.7) with 300 ng total RNA input. RNA with the appropriate concentration of RNA spike-in controls is converted into double stranded cDNA using an olido (dT) primer linked to the T7 promoter sequence and MMLV-RT. The double stranded cDNA is then in vitro transcribed by T7 RNA polymerase, which simultaneously amplifies and incorporates cyanine 3-labeled CTP into the resulting cRNA. Labeled cRNA is then purified using Qiagen RNeasy columns and the labeling efficiency determined by the NanoDrop spectrophotometer.

growth_protocol: Normal Human Epidermal Keratinocytes (NHEK) were purchased from LifeLine Technologies and grown according to the manufacturer’s instructions in DermaLife medium (LifeLine Tech) supplemented with DermaLife growth factors (LifeLine Tech). Cells were induced to differentiate by addition of high calcium medium (1.8mM Ca2+).

treatment_protocol: Lipofectamine RNAi Max (Life Technologies) in OptiMEM medium was used for siRNA transfections. Pooled siRNA for each factor (Dharmacon) were used for knockdown in NHEK. 24 hours after knockdown, cells were induced to differentiate by the addition of high calcium media, and collected 24 hours later.

tag: transcription factor


title: TP63

description: 253452510007_201107280954_S01 [1_1]


title: STAT6

description: 253452510007_201107280954_S01 [1_4]


title: NEG4

description: 253452510007_201107280954_S01 [2_4]


title: NEG1

description: 253452510007_201107280954_S01 [2_1]