title: Li day 7 rat 15

city: Gothenburg

first: Anna

last: Thorfve

address: Arvid Wallgrens backe 20

department: Biomaterials

country: Sweden

institute: University of Gothenburg

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

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

data_processing: The data were analyzed using expression console software version 1.1.2 using default analysis settings and RMA as normalization method.

label: Biotin Allonamide Triphosphate

organism: Rattus norvegicus

source_name: Li-PLGA day 7

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

growth_protocol: The animals were allowed free postoperative movement, with food and water ad libitum

extract_protocol: Qiagen's Qizaol, TissueLyser and Qiagen Rneasy Micro kit

treatment_protocol: Rat tibia fracture model, Li-PLGA or Ctrl-PLGA implants, 7 or 28 days

value: Sprague Dawley

tag: treatment group

value: poly(lactide-co-glycolide acid) (PLGA) implants with incorporated Li+

value: peri-implant bone (tibia)

tag: time point

value: day 7


title: Li day 28 rat 29

status: Public on Jul 21 2014

type: RNA

molecule: total RNA

source_name: Li-PLGA day 28

tag: strain

tag: gender

value: male

tag: tissue

value: day 28


title: Ctrl day 28 rat 27

source_name: Ctrl-PLGA day 28

value: poly(lactide-co-glycolide acid) (PLGA) implants without Li+


title: Li day 28 rat 21


title: Ctrl day 28 rat 28


title: Ctrl day 7 rat 11

source_name: Ctrl-PLGA day


title: Ctrl day 7 rat 15

source_name: Ctrl-PLGA day 7


title: Evolved strain F, time point 5

city: Suita

first: Takaaki

last: Horinouchi

address: 6-2-3, Furuedai

country: Japan

institute: Quantitative biology center, RIKEN

description: Gene expression data from strain F of experimental evolution under ethanol stress in 2496 hours.

hyb_protocol: Hybridization, washing, staining, and scanning were carried out according to the Expression Analysis Technical Manual (provided by Affymetrix). Following fragmentation, 3 ug of cDNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G. Absolute signal intensities of every probe in every sample were generated using GCOS 1.0 software (Affymetrix).

data_processing:
To obtain the absolute expression levels of genes from microarray raw data, we used the Finite Hybridization model (Furusawa et al, 2009; Ono et al, 2008).
Log10 mRNA concentration (pM) data are provided as a supplementary file. Expression levels were normalized using the quantile normalization method (Bolstad et al., 2003).

label: biotin

organism: Escherichia coli

label_protocol: The synthesis of cDNA, fragmentation and end-terminus biotin labeling were carried out in accordance with Affymetrix protocols (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Each strain was inoculated from the frozen stock into 10 mL of M9 medium for preculture. Five-microliter aliquots of preculture medium cells were inoculated into the fresh minimal media, M9 with 5%(v/v) ethanol in 10 mL test tube with screw cap and cultured for 10 generations. When OD600nm reached 0.05 within the exponential growth phase, cell were collected.

extract_protocol: Total RNA was isolated and purified from cells using an RNeasy mini kit with on-column DNA digestion.

treatment_protocol: The cells were collected by centrifugation at 8,000 × g for 5 min at 25°C, and the pelleted cells were stored at –80°C prior to use.

tag: platform_id_id design


title: Evolved strain F, time point 4

description: Gene expression data from strain F of experimental evolution under ethanol stress in 1824 hours.


title: Evolved strain F, time point 2

description: Gene expression data from strain F of experimental evolution under ethanol stress in 744 hours.


title: Evolved strain F, time point 3

description: Gene expression data from strain F of experimental evolution under ethanol stress in 1224 hours.


title: Li day 7 rat 7


title: Ctrl day 28 rat 21


title: Evolved strain F, time point 1

description: Gene expression data from strain F of experimental evolution under ethanol stress in 384 hours.


title: Li day 7 rat 10


title: Ctrl day 28 rat 29


title: Li day 28 rat 27


title: Li day 7 rat 5


title: Ctrl day 28 rat 30


title: Evolved strain E, time point 5

description: Gene expression data from strain E of experimental evolution under ethanol stress in 2496 hours.


title: Ctrl day 7 rat 5


title: Li day 28 rat 23


title: Ctrl day 7 rat 7


title: Li day 7 rat 11


title: Li day 28 rat 28


title: Li day 7 rat 4


title: Ctrl day 7 rat 4


title: Ctrl day 7 rat 10


title: Li day 28 rat 30


title: Evolved strain E, time point 4

description: Gene expression data from strain E of experimental evolution under ethanol stress in 1824 hours.


title: Evolved strain E, time point 3

description: Gene expression data from strain E of experimental evolution under ethanol stress in 1224 hours.


title: Evolved strain E, time point 2

description: Gene expression data from strain E of experimental evolution under ethanol stress in 744 hours.


title: Evolved strain E, time point 1

description: Gene expression data from strain E of experimental evolution under ethanol stress in 384 hours.


title: Evolved strain D, time point 5

description: Gene expression data from strain D of experimental evolution under ethanol stress in 2496 hours.


title: Evolved strain D, time point 4

description: Gene expression data from strain D of experimental evolution under ethanol stress in 1824 hours.


title: Evolved strain D, time point 3

description: Gene expression data from strain D of experimental evolution under ethanol stress in 1224 hours.


title: Evolved strain D, time point 2

description: Gene expression data from strain D of experimental evolution under ethanol stress in 744 hours.


title: Evolved strain C, time point 3

description: Gene expression data from strain C of experimental evolution under ethanol stress in 1224 hours.


title: Ctrl day 28 rat 23


title: Evolved strain D, time point 1

description: Gene expression data from strain D of experimental evolution under ethanol stress in 384 hours.


title: Evolved strain C, time point 4

description: Gene expression data from strain C of experimental evolution under ethanol stress in 1824 hours.


title: Evolved strain C, time point 5

description: Gene expression data from strain C of experimental evolution under ethanol stress in 2496 hours.


title: Evolved strain B, time point 5

description: Gene expression data from strain B of experimental evolution under ethanol stress in 2496 hours.


title: Evolved strain C, time point 2

description: Gene expression data from strain C of experimental evolution under ethanol stress in 744 hours.


title: Evolved strain A, time point 5

description: Gene expression data from strain A of experimental evolution under ethanol stress in 2496 hours.

source_name: Strain A of experimental evolution under ethanol stress in 2496 hours.


title: Evolved strain B, time point 4

description: Gene expression data from strain B of experimental evolution under ethanol stress in 1824 hours.


title: Evolved strain B, time point 2

description: Gene expression data from strain B of experimental evolution under ethanol stress in 744 hours.


title: Evolved strain A, time point 3

description: Gene expression data from strain A of experimental evolution under ethanol stress in 1224 hours.

source_name: Strain A of experimental evolution under ethanol stress in 1224 hours.


title: Evolved strain B, time point 1

description: Gene expression data from strain B of experimental evolution under ethanol stress in 384 hours.


title: Evolved strain C, time point 1

description: Gene expression data from strain C of experimental evolution under ethanol stress in 384 hours.


title: Evolved strain A, time point 1

description: Gene expression data from strain A of experimental evolution under ethanol stress in 384 hours.

source_name: Strain A of experimental evolution under ethanol stress in 384 hours.


title: Evolved strain A, time point 2

description: Gene expression data from strain A of experimental evolution under ethanol stress in 744 hours.

source_name: Strain A of experimental evolution under ethanol stress in 744 hours.


title: Evolved strain B, time point 3

description: Gene expression data from strain B of experimental evolution under ethanol stress in 1224 hours.


title: Evolved strain A, time point 4

description: Gene expression data from strain A of experimental evolution under ethanol stress in 1824 hours.

source_name: Strain A of experimental evolution under ethanol stress in 1824 hours.


title: untreated cells-replicate 4

city: Frederick

first: Dennis

last: Klinman

state: Maryland

address: 1050 Boyles St

department: Cancer and Inflammation Program

country: USA

institute: National Institutes of Health

description: biological replicate 4 of 4, unstimulated MDSC cells 30 min

hyb_protocol: Cy dyed aRNA of control and target samples were combined, denaturated by heating for 2 min at 98o C, and mixed with 18 ul hybridization solution at 42̊C (Ambion, Austin, TX, USA).  Microarrays were overlaid with this solution and hybridized for 18 h at 42̊C using an actively mixing MAUI hybridization system (BioMicro Systems, Salt Lake City, UT) then washed sequentially.

scan_protocol: Arrays were scanned on an Axon genepix 4000B scanner and images were quantified using GenePix software v 5.1

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. GenePix ans BRB arraytools software was used.

organism: Homo sapiens

source_name: FACS sorted MDSC

label_protocol: 200-500 ng of total RNA was amplified through the Amino Allyl MessageAmp II aRNA Kit (Ambion, Life Technologies).  Total RNA is reverse transcribed into cDNA followed by in vitro transcription with T7 RNA polymerase into antisense amplified RNA (aRNA). Aminoallyl modified UTPs are incorporated during in vitro transcription for Cy-dye coupling.  aRNA from mMDSC samples were labeled with Cy5 monoreactive dye (Amersham Biosciences, Piscataway, NJ) .  A reference human sample (Stratagene) was processed in parallel and labeled with Cy3.  For the coupling reaction up to 10ul of aRNA (2000-4000ng) was added to 0.1M sodium bicarbonate buffer (pH 8.7) to a total volume of 20 ul and then added to either Cy3 or Cy5 dissolved in 20ul DMSO for 120 minutes in the dark.  To quench unreacted Cy-dye, 18ul of 4M hydroxylamine was added for 15 minuted in the dark before cleaning up using the Rneasy MinElute kit (Qiagen).

growth_protocol: PBMC were separated from fresh buffy coats from healthy volunteers and separated using density gradient and ficol reagent.  Cells were stained and FACS sorted to isolate mMDSC as defined by the following characteristics: CD33+, Lin-(CD3/19/57-), HLA-DR-, CD11b+ and CD14hi

extract_protocol: total RNA was extracted using Qiagen's Rneasy minikit, following the instuction booklet

treatment_protocol: mMDSC were stimulated in vitro with optimal concentrations (determined by preliminary dose-ranging studies) of PAM3 (1 ug/ml), R848 (3 ug/ml) for 30, 75, and 225 minutes or left untreated.  Some samples were stimulated for 3 days.

value: fresh PBMC collected from donors

tag: cell type

value: myeloid-derived suppressor cells

source_name: total RNA from Stratagene universal reference RNA

tag: control type

value: universal RNA


title: untreated cells-replicate 1

description: biological replicate 1 of 4, unstimulated MDSC cells 30 min


title: r848 treated cells-replicate 3-225min

description: biological replicate 3 of 4, r848 stimulated MDSC cells 225 min stimulation


title: r848 treated cells-replicate 4-75min

description: biological replicate 4 of 4, r848 stimulated MDSC cells 75 min stimulation


title: r848 treated cells-replicate 4-225min

description: biological replicate 4 of 4, r848 stimulated MDSC cells 225 min stimulation


title: r848 treated cells-replicate 3-75min

description: biological replicate 3 of 4, r848 stimulated MDSC cells 75 min stimulation


title: Ustilago maydis- Wild type

city: San Nicolas de los Garza

first: Elva

middle: Teresa

last: Aréchiga-Carvajal

state: Nuevo León

address: Av. Pedro de Alba

country: Mexico

description: This sample is from the Ustilago maydis Wild Type. It is the RNA merge of two separate replicates

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Mycosarcoma maydis

source_name: Ustilago maydis FB2 wild type

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Ustilago maydis WT and ∆Rim101 mutant strain were growth in Minimal Medium at pH 9, buffered with 50mM Tris. 100mM H3PO4, to a cell concentration of  1x107cell/ml

extract_protocol: Total RNA was isolated using a slight modification of the protocol of Jones et al. (1985). DNA was removed with  RNase-Free Dnase.

tag: genotype/variation

value: Wild type


title: r848 treated cells-replicate 2-225min

description: biological replicate 2 of 4, r848 stimulated MDSC cells 225 min stimulation


title: Parent strain of experimental evolution

description: Gene expression data from parent strain of experimental evolution

source_name: Parent strain of experimental evolution as adaptive evolved E. coli W3110 strain to M9 synthetic medium without ethanol stress


title: r848 treated cells-replicate 2-75min

description: biological replicate 2 of 4, r848 stimulated MDSC cells 75 min stimulation


title: r848 treated cells-replicate 1-75min

description: biological replicate 1 of 4, r848 stimulated MDSC cells 75 min stimulation


title: Ustilago maydis- ∆Rim101 mutant strain

description: This sample is from the Ustilago maydis ∆Rim101 mutant strain. In which the the zinc fingers region of the gene Rim101, is substituted by the Hyg gen resistance. It is the RNA merge of two separate replicates

source_name: Ustilago maydis ∆Rim101 mutant strain

value: ∆Rim101 deletant


title: r848 treated cells-replicate 3-30min

description: biological replicate 3 of 4, r848 stimulated MDSC cells 30 min stimulation


title: r848 treated cells-replicate 2-30min

description: biological replicate 2 of 4, r848 stimulated MDSC cells 30 min stimulation


title: pam3 treated cells-replicate 4-75min

description: biological replicate 4 of 4, pam3 stimulated MDSC cells 75 min stimulation


title: pam3 treated cells-replicate 4-225min

description: biological replicate 4 of 4, pam3 stimulated MDSC cells 225 min stimulation


title: pam3 treated cells-replicate 1-225min

description: biological replicate 1 of 4, pam3 stimulated MDSC cells 225 min stimulation


title: r848 treated cells-replicate 1-30min

description: biological replicate 1 of 4, r848 stimulated MDSC cells 30 min stimulation


title: pam3 treated cells-replicate 2-225min

description: biological replicate 2 of 4, pam3 stimulated MDSC cells 225 min stimulation


title: pam3 treated cells-replicate 4-30min

description: biological replicate 4 of 4, pam3 stimulated MDSC cells 30 min stimulation


title: pam3 treated cells-replicate 3-30min

description: biological replicate 3 of 4, pam3 stimulated MDSC cells 30 min stimulation


title: pam3 treated cells-replicate 1-75min

description: biological replicate 1 of 4, pam3 stimulated MDSC cells 75 min stimulation


title: pam3 treated cells-replicate 3-75min

description: biological replicate 3 of 4, pam3 stimulated MDSC cells 75 min stimulation


title: untreated cells-replicate 2

description: biological replicate 2 of 4, unstimulated MDSC cells 30 min


title: pam3 treated cells-replicate 2-30min

description: biological replicate 2 of 4, pam3 stimulated MDSC cells 30 min stimulation


title: pam3 treated cells-replicate 2-75min

description: biological replicate 2 of 4, pam3 stimulated MDSC cells 75 min stimulation


title: r848 treated cells-replicate 1-225min

description: biological replicate 1 of 4, r848 stimulated MDSC cells 225 min stimulation


title: r848 treated cells-replicate 6-three days

description: biological replicate 6 of 7, r848 stimulated MDSC cells 3 days stimulation


title: r848 treated cells-replicate 4-30min

description: biological replicate 4 of 4, r848 stimulated MDSC cells 30 min stimulation


title: r848 treated cells-replicate 5-three days

description: biological replicate 5 of 7, r848 stimulated MDSC cells 3 days stimulation


title: r848 treated cells-replicate 7-three days

description: biological replicate 7 of 7, r848 stimulated MDSC cells 3 days stimulation


title: pam3 treated cells-replicate 1-30min

description: biological replicate 1 of 4, pam3 stimulated MDSC cells 30 min stimulation


title: pam3 treated cells-replicate 3-225min

description: biological replicate 3 of 4, pam3 stimulated MDSC cells 225 min stimulation


title: r848 treated cells-replicate 4-three days

description: biological replicate 4 of 7, r848 stimulated MDSC cells 3 days stimulation


title: pam3 treated cells-replicate 7-three days

description: biological replicate 7 of 7, pam3 stimulated MDSC cells 3 days stimulation


title: r848 treated cells-replicate 1-three days

description: biological replicate 1 of 7, r848 stimulated MDSC cells 3 days stimulation


title: pam3 treated cells-replicate 6-three days

description: biological replicate 6 of 7, pam3 stimulated MDSC cells 3 days stimulation


title: pam3 treated cells-replicate 4-three days

description: biological replicate 4 of 7, pam3 stimulated MDSC cells 3 days stimulation


title: pam3 treated cells-replicate 5-three days

description: biological replicate 5 of 7, pam3 stimulated MDSC cells 3 days stimulation


title: r848 treated cells-replicate 3-three days

description: biological replicate 3 of 7, r848 stimulated MDSC cells 3 days stimulation


title: r848 treated cells-replicate 2-three days

description: biological replicate 2 of 7, r848 stimulated MDSC cells 3 days stimulation


title: pam3 treated cells-replicate 1-three days

description: biological replicate 1 of 7, pam3 stimulated MDSC cells 3 days stimulation


title: T13_912LT

type: genomic

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

description:
8 x 60
Sample 21

hyb_protocol: 5ug of Cy5-labeled sample was combined with 5ug of Cy3-labeled male reference, and samples were hybridized and washed by following Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol v6.2 on on Agilent SurePrint G3 Human Catalog CGH 8x60K (Design ID 021924) or SurePrint G3 Human Catalog CGH 4x180K (Design ID 022060)

scan_protocol: scanned at a 3um scan resolution and 20 bit tiff file setting on the Agilent DNA Microarray Scanner G2505C

data_processing:
quantified signal intensities and pre-processed data with Agilent Feature Extraction 10.5.1.1
FE files loaded into Nexus Copy Number Software v.7  (Biodiscovery Inc.) for analysis.
CGH data was processed using BioDiscovery’s FASST2 Segmentation Algorithm to estimate copy number state. These state values are then used to make calls based on a log-ratio threshold. The significance threshold for segmentation was set at 5.0E-6 also requiring a minimum of 3 probes per segment and a maximum probe spacing of 1000 between adjacent probes before breaking a segment. The log ratio thresholds for single copy gain and single copy loss were set at 0.2 and -0.23, respectively. The log ratio thresholds for two or more copy gain and homozygous loss were set at 1.14 and -1.1 respectively.   Upon loading of raw data files, signal intensities are normalized via division by mean.  All samples are corrected for GC wave content using a systematic correction algorithm.

molecule: genomic DNA

source_name: Prostate Tumor

label_protocol: 500ng gDNA labeled by following NimbleGen Arrays User’s Guide: CGH Analysis v5.0, which included a 98C heat fragmentation step and labeling with Cy-labeled random nanomers (TriLink Biotechnologies) and Klenow 3'-5'exo-(New England Biolabs).

extract_protocol: Genomic DNA extracted with Promega Wizard Genomic DNA Extraction Kit

tag: sample origin

value: Clinical Patient

tag: tissue type

value: Tumor

tag: patient age at diagnosis (yrs)

tag: gleason score

tag: psa at diagnosis

source_name: male reference DNA (Promega Corp)

tag: sample type

value: reference DNA


title: T17_964RP

description:
8 x 60
Sample 25


title: pam3 treated cells-replicate 2-three days

description: biological replicate 2 of 7, pam3 stimulated MDSC cells 3 days stimulation


title: T11_702LP

description:
8 x 60
Sample 18


title: B11_702LT

description:
8 x 60
Sample 19

value: Adjacent benign


title: B7_585RT

description:
8 x 60
Sample 13


title: T24_927RP

description:
8 x 60
Sample 23


title: T18_974LP

description:
8 x 60
Sample 27


title: pam3 treated cells-replicate 3-three days

description: biological replicate 3 of 7, pam3 stimulated MDSC cells 3 days stimulation


title: T7_585LP

description:
8 x 60
Sample 12


title: B13_912RP

description:
8 x 60
Sample 20


title: T9_650RP

description:
8 x 60
Sample 16


title: T5_536RP

description:
8 x 60
Sample 9


title: T16_963LP

description:
8 x 60
Sample 24


title: T8_616RP

description:
8 x 60
Sample 14


title: T10_689RT

description:
8 x 60
Sample 17


title: T25_971LP

description:
8 x 60
Sample 26


title: T6_569LP

description:
8 x 60
Sample 10


title: T2_332RP

description:
4 x 180
Sample 4


title: T19_518LP

description:
4 x 180
Sample 8


title: T22_917LP

description:
4 x 180
Sample 22


title: B6_569RP

description:
8 x 60
Sample 11


title: SW13 cells with BRG1, UV treated, exp #3

city: Miami

first: Feng

last: Gong

state: FL

address: 1011 NW 15th ST

department: Biochemistry and Molecular Biology

institute: University of Miami

hyb_protocol: Target synthesis and GeneChip hybridization, washing, staining, and scanning were performed at the Molecular Biology Core at Washington State University, according to the  instructions from Affymetrix.

data_processing: Microarray output was examined visually for excessive background noise and physical anomalies. The default MAS statistical values were used for all analyses. All probe sets on each array were scaled to a mean target signal intensity of 125, with the signal correlating to the amount of transcript in the sample. An absolute analysis using MAS was performed to assess the relative abundance of the 47,000 represented transcripts and variants, including 38,500 human genes, based on signal and detection.

source_name: human cancer cells

growth_protocol: SW13 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (CELLGRO, Manassas, VA) supplemented with 10% fetal bovine serum (HyClone, Logan, UT) and penicillin-streptomycin.

extract_protocol: Total RNA was prepared using TRIZOL reagent (Invitrogen, Carlsbad, CA), followed by the RNeasy kit (Qiagen, Valencia, CA), according to the manufacturer’s instructions.

treatment_protocol: SW13+pREP7 (SW13+vector) and SW13+pREP7+BRG1 (SW13+BRG1) cells were irradiated with 10 J/m2 UV or mock treated. After treatment, warm media were added back and cells were incubated for 6 hours before being collected for RNA preparation.

tag: cell line


title: T20_639LP

description:
4 x 180
Sample 15


title: SW13 cells with BRG1, UV treated, exp #2

scan_protocol: Target synthesis and GeneChip hybridization, washing, staining, and scanning were performed at the Molecular Biology Core at Washington State University, according to the  instructions from Affymetrix.


title: LTL311

description:
4 x 180
Sample 28

value: Patient Derived Xenograft


title: T21_1007RT

description:
4 x 180
Sample 1


title: untreated cells-replicate 3

description: biological replicate 3 of 4, unstimulated MDSC cells 30 min


title: SW13 cells with BRG1, mock treated, exp #2

label_protocol: Target synthesis and GeneChip hybridization, washing, staining, and scanning were performed at the Molecular Biology Core at Washington State University, according to the  instructions from Affymetrix.


title: SW13 cells without BRG1, UV treated, exp #3


title: B4_445LP

description:
8 x 60
Sample 6


title: T4_445RT

description:
8 x 60
Sample 7


title: SW13 cells without BRG1, UV treated, exp #2


title: SW13 cells without BRG1, mock treated, exp #3


title: SW13 cells without BRG1, UV treated, exp #1


title: A9

status: Public on Jul 20 2014

city: Hamburg

first: Bastian

last: Spruth

state: Hamburg

address: Unnastr. 48

department: Front End Innovation

country: Germany

institute: Beiersdorf AG

description: Gene expression after 24h incubation on FBLN5cleaved

hyb_protocol: 0.6 ug of Cy3-labelled fragmented cRNA was hybridizated at 65°C for 17 hours in hybridization buffer to Agilent Whole Human Genome Oligo Microarrays 8x60K V2 using Agilent's recommended hybridization chamber and oven.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Mocroarray Scanner System (Sgilent Technologies).

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

source_name: FBLN5cleaved donor3  replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

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

treatment_protocol: Human neonatal dermal fibroblast were seeded on plates precoated with heat denaturated BSA, FBLN5 or FBLN5cleaved. The cultures were incubated for 24 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: primary cells

value: neonatal dermal fibroblasts

tag: donor tissue

value: caucasion male foreskin


title: SW13 cells with BRG1, mock treated, exp #3


title: A18

source_name: FBLN5cleaved donor3  replicate 2


title: A15


title: A17

description: Gene expression after 24h incubation on FBLN5

source_name: FBLN5 donor3  replicate 2


title: T23_1015LP

description:
8 x 60
Sample 2


title: SW13 cells with BRG1, UV treated, exp #1


title: T1_274LP

description:
8 x 60
Sample 3


title: SW13 cells without BRG1, mock treated, exp #1


title: A14

source_name: FBLN5 donor3  replicate 1


title: A16

description: Gene expression after 24h incubation on denatured BSA

source_name: control donor3  replicate 2


title: A4

source_name: control donor1  replicate 2


title: A8


title: A13

source_name: control donor3  replicate 1


title: A5

source_name: FBLN5 donor1  replicate 2


title: SW13 cells without BRG1, mock treated, exp #2


title: SW13 cells with BRG1, mock treated, exp #1


title: T3_404LT

description:
8 x 60
Sample 5


title: A12

source_name: FBLN5cleaved donor2 replicate 2


title: A6

source_name: FBLN5cleaved donor1  replicate 2


title: A7


title: A11

source_name: FBLN5 donor2  replicate 2


title: A10

source_name: control donor2  replicate 2


title: A1

source_name: control donor1  replicate 1


title: A3

source_name: FBLN5cleaved donor1  replicate 1


title: Baseline (day 0) 5863981135_B

city: Stanford

first: David

last: Furman

address: 279 Campus Dr, B226

department: Microbiology and Immunolgy

institute: Stanford University

description: subject SUB134230 in ImmPort study SDY312

hyb_protocol: Standard illumina protocol

scan_protocol: The hybridized Beadchips were scanned on an Illumina BeadScan confocal scanner

data_processing: Data was analyzed by Illumina's GenomeStudio software, version 2.0. Normalized values are raw values normalized to the overall intensity to the median average intensity for all samples across multiple arrays and chips after background normalization.

source_name: whole blood

label_protocol: For each sample, 750 ng of total RNA were hybridized to Beadchips (HumanHT-12v3 Expression Bead Chip, Illumina, San Diego, CA)

extract_protocol: Total RNA was extracted from PAXgene blood RNA tubes (PreAnalytiX, USA) using the QIAcube automation RNA extraction procedure according to the manufacturer s protocol (Qiagene, Valencia, CA).

tag: Sex

tag: race

value: White

tag: vaccine


title: Baseline (day 0) 5863981136_C

description: subject SUB134153 in ImmPort study SDY312

value: female


title: Baseline (day 0) 5863981136_D

description: subject SUB134154 in ImmPort study SDY312

value: male

value: Asian


title: Baseline (day 0) 5863981136_A

description: subject SUB134210 in ImmPort study SDY312


title: Baseline (day 0) 5863981135_C

description: subject SUB134156 in ImmPort study SDY312


title: Baseline (day 0) 5863981136_E

description: subject SUB134176 in ImmPort study SDY312

value: Other


title: Baseline (day 0) 5863981135_K

description: subject SUB134226 in ImmPort study SDY312


title: Baseline (day 0) 5863981136_G

description: subject SUB134214 in ImmPort study SDY312


title: Baseline (day 0) 5863981136_B

description: subject SUB134195 in ImmPort study SDY312


title: Baseline (day 0) 5863981135_G

description: subject SUB134213 in ImmPort study SDY312


title: Baseline (day 0) 5863981135_E

description: subject SUB134162 in ImmPort study SDY312


title: Baseline (day 0) 5863981135_L

description: subject SUB134220 in ImmPort study SDY312


title: Baseline (day 0) 5863981133_D

description: subject SUB134163 in ImmPort study SDY312


title: A2

source_name: FBLN5 donor1  replicate 1


title: Baseline (day 0) 5863981135_D

description: subject SUB134196 in ImmPort study SDY312


title: Baseline (day 0) 5863981133_K

description: subject SUB134187 in ImmPort study SDY312


title: Baseline (day 0) 5863981136_F

description: subject SUB134197 in ImmPort study SDY312


title: Baseline (day 0) 5863981133_C

description: subject SUB134180 in ImmPort study SDY312


title: Baseline (day 0) 5863981135_H

description: subject SUB134233 in ImmPort study SDY312


title: Baseline (day 0) 5863981133_L

description: subject SUB134223 in ImmPort study SDY312


title: Baseline (day 0) 5863981135_I

description: subject SUB134181 in ImmPort study SDY312


title: Baseline (day 0) 5863981133_H

description: subject SUB134202 in ImmPort study SDY312


title: Baseline (day 0) 5863981133_A

description: subject SUB134172 in ImmPort study SDY312


title: Baseline (day 0) 5863981133_F

description: subject SUB134189 in ImmPort study SDY312


title: Baseline (day 0) 5863981133_B

description: subject SUB134222 in ImmPort study SDY312


title: Baseline (day 0) 5863981135_A

description: subject SUB134207 in ImmPort study SDY312


title: Baseline (day 0) 5863981135_F

description: subject SUB134221 in ImmPort study SDY312


title: Baseline (day 0) 5863981135_J

description: subject SUB134192 in ImmPort study SDY312


title: Baseline (day 0) 5863981133_I

description: subject SUB134205 in ImmPort study SDY312


title: Baseline (day 0) 5863981132_J

description: subject SUB134171 in ImmPort study SDY312


title: Baseline (day 0) 5863981133_G

description: subject SUB134200 in ImmPort study SDY312


title: Baseline (day 0) 5863981132_F

description: subject SUB134203 in ImmPort study SDY312


title: Baseline (day 0) 5863981132_G

description: subject SUB134157 in ImmPort study SDY312


title: Baseline (day 0) 5863981132_A

description: subject SUB134166 in ImmPort study SDY312


title: Baseline (day 0) 5863981132_C

description: subject SUB134215 in ImmPort study SDY312


title: lung transplant patient T24

city: Reno

first: Tong

last: Zhou

state: NV

address: 1664 N Virginia St

institute: University of Nevada School of Medicine

description: Gene expression data from PBMC total RNA from lung transplant patient.

hyb_protocol: Samples were hybridized with Affymetrix GeneChip Human Exon 1.0 ST Arrays per manufacturer’s instructions.

scan_protocol: Array scanning was performed according to the manufacturer's instruction by the University of Chicago Functional Genomics Facility.

data_processing:
The transcript expression data were summarized by RMA using the Affymetrix Power Tools v.1.12.0.
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: Human peripheral blood mononuclear cells

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

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

tag: gender

value: M

tag: ethnicity

value: Caucasian American

tag: treatment

value: lung transplant patient


title: lung transplant patient T23

tag: cell type

value: Human peripheral blood mononuclear cells


title: Baseline (day 0) 5863981132_B

description: subject SUB134177 in ImmPort study SDY312


title: Baseline (day 0) 5863981132_D

description: subject SUB134194 in ImmPort study SDY312


title: Baseline (day 0) 5863981133_E

description: subject SUB134227 in ImmPort study SDY312


title: Baseline (day 0) 5863981132_L

description: subject SUB134208 in ImmPort study SDY312


title: lung transplant patient T20

value: F


title: lung transplant patient T22


title: Baseline (day 0) 5863981130_A

description: subject SUB134184 in ImmPort study SDY312


title: Baseline (day 0) 5863981130_J

description: subject SUB134173 in ImmPort study SDY312


title: Baseline (day 0) 5863981130_K

description: subject SUB134234 in ImmPort study SDY312


title: Baseline (day 0) 5863981132_H

description: subject SUB134186 in ImmPort study SDY312


title: Baseline (day 0) 5863981130_I

description: subject SUB134209 in ImmPort study SDY312


title: lung transplant patient T18


title: Baseline (day 0) 5863981130_E

description: subject SUB134188 in ImmPort study SDY312


title: Baseline (day 0) 5863981130_L

description: subject SUB134178 in ImmPort study SDY312


title: Baseline (day 0) 5863981130_F

description: subject SUB134231 in ImmPort study SDY312


title: Baseline (day 0) 5863981124_D

description: subject SUB134190 in ImmPort study SDY312


title: Baseline (day 0) 5863981130_B

description: subject SUB134169 in ImmPort study SDY312


title: Baseline (day 0) 5863981124_K

description: subject SUB134164 in ImmPort study SDY312


title: Baseline (day 0) 5863981124_A

description: subject SUB134219 in ImmPort study SDY312


title: Baseline (day 0) 5863981124_F

description: subject SUB134160 in ImmPort study SDY312


title: lung transplant patient T15

description: Gene expression data from PBMC total RNA from lung transplant patient.


title: Baseline (day 0) 5863981130_D

description: subject SUB134170 in ImmPort study SDY312


title: lung transplant patient T17


title: Baseline (day 0) 5863981130_H

description: subject SUB134193 in ImmPort study SDY312


title: Baseline (day 0) 5863981130_C

description: subject SUB134175 in ImmPort study SDY312


title: Baseline (day 0) 5863981124_E

description: subject SUB134228 in ImmPort study SDY312


title: lung transplant patient T14


title: Baseline (day 0) 5863981124_J

description: subject SUB134211 in ImmPort study SDY312


title: Baseline (day 0) 5863981124_I

description: subject SUB134204 in ImmPort study SDY312


title: Baseline (day 0) 5863981124_L

description: subject SUB134206 in ImmPort study SDY312


title: lung transplant patient T13


title: lung transplant patient T10

value: African American


title: Baseline (day 0) 5863981124_G

description: subject SUB134199 in ImmPort study SDY312


title: Baseline (day 0) 5863981124_B

description: subject SUB134185 in ImmPort study SDY312


title: lung transplant patient T11


title: lung transplant patient T09


title: Baseline (day 0) 5863981123_L

description: subject SUB134229 in ImmPort study SDY312


title: Baseline (day 0) 5863981123_B

description: subject SUB134225 in ImmPort study SDY312


title: lung transplant patient T12


title: lung transplant patient T07


title: Baseline (day 0) 5863981123_I

description: subject SUB134224 in ImmPort study SDY312


title: lung transplant patient T06


title: Baseline (day 0) 5863981124_H

description: subject SUB134191 in ImmPort study SDY312


title: Baseline (day 0) 5863981123_E

description: subject SUB134179 in ImmPort study SDY312


title: lung transplant patient T04


title: Baseline (day 0) 5863981123_C

description: subject SUB134198 in ImmPort study SDY312


title: Baseline (day 0) 5863981123_F

description: subject SUB134167 in ImmPort study SDY312


title: Baseline (day 0) 5863981123_J

description: subject SUB134217 in ImmPort study SDY312


title: Baseline (day 0) 5863981123_G

description: subject SUB134174 in ImmPort study SDY312


title: Baseline (day 0) 5863981123_K

description: subject SUB134155 in ImmPort study SDY312


title: Baseline (day 0) 5863981123_A

description: subject SUB134232 in ImmPort study SDY312


title: Baseline (day 0) 5863981123_D

description: subject SUB134182 in ImmPort study SDY312


title: lung transplant patient T03

description: Gene expression data from PBMC total RNA from lung transplant patient.


title: V6_21_MH

city: London

first: Jordan

middle: Eduard

last: Bisanz

state: Ontario

address: 268 Grosvenor Street, Room F2-116

institute: Lawson Health Research Institute

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA

source_name: Vaginal Epithelium

label_protocol: standard Affymetrix protocol

extract_protocol: Samples collected and stored in 500 µL RNAlater and frozen at -80˚C until extraction. Samples were thawed on ice, vortexed, and centrifuged (5,000 g, 10 min, 4˚C). The supernatant was discarded and the RNA was extracted using TRIzol and Turbo DNase (Life Technologies) according to the manufacturers protocols.

tag: tissue

value: Vaginal Epithelium

tag: visit

tag: first intervention

value: probiotic

tag: second intervention

value: placebo

tag: responder status

value: responder

tag: ph

tag: nugent score


title: Baseline (day 0) 5920711008_F

description:
subject SUB134132 in ImmPort study SDY311
5920711008_F


title: Baseline (day 0) 5920666012_F

description:
subject SUB134152 in ImmPort study SDY311
5920666012_F


title: V5_21_MH


title: healthy control C64

description: Gene expression data from PBMC total RNA from healthy control.

value: healthy control


title: V3_21_MH


title: V6_19_JV

value: nonresponder


title: lung transplant patient T02


title: Baseline (day 0) 5920666012_E

description:
subject SUB134094 in ImmPort study SDY311
5920666012_E


title: Baseline (day 0) 5920666011_J

description:
subject SUB134086 in ImmPort study SDY311
5920666011_J

value: White


title: healthy control C62


title: Baseline (day 0) 5920711019_I

description:
subject SUB134088 in ImmPort study SDY311
5920711019_I

value: female


title: V8_21_MH


title: Baseline (day 0) 5920711019_A

description:
subject SUB134102 in ImmPort study SDY311
5920711019_A


title: Baseline (day 0) 5920666014_K

description:
subject SUB134092 in ImmPort study SDY311
5920666014_K


title: healthy control C63


title: healthy control C61


title: healthy control C60


title: Baseline (day 0) 5920666014_G

description:
subject SUB134126 in ImmPort study SDY311
5920666014_G


title: V6_17_BJ


title: Baseline (day 0) 5920834001_C

description:
subject SUB134141 in ImmPort study SDY311
5920834001_C


title: Baseline (day 0) 5920666012_I

description:
subject SUB134106 in ImmPort study SDY311
5920666012_I

value: male


title: V3_19_JV


title: V8_18_CM


title: Baseline (day 0) 5920711008_B

description:
subject SUB134138 in ImmPort study SDY311
5920711008_B


title: Baseline (day 0) 5920666014_C

description:
subject SUB134093 in ImmPort study SDY311
5920666014_C


title: V5_17_BJ


title: Baseline (day 0) 5920666013_B

description:
subject SUB134115 in ImmPort study SDY311
5920666013_B


title: Baseline (day 0) 5920666011_L

description:
subject SUB134085 in ImmPort study SDY311
5920666011_L


title: healthy control C59


title: Baseline (day 0) 5920711008_I

description:
subject SUB134099 in ImmPort study SDY311
5920711008_I


title: Baseline (day 0) 5920666013_E

description:
subject SUB134091 in ImmPort study SDY311
5920666013_E


title: V4_16_PT


title: Baseline (day 0) 5920834001_G

description:
subject SUB134140 in ImmPort study SDY311
5920834001_G


title: healthy control C58


title: Baseline (day 0) 5920666012_C

description:
subject SUB134110 in ImmPort study SDY311
5920666012_C


title: healthy control C55

description: Gene expression data from PBMC total RNA from healthy control.


title: V3_16_PT


title: Baseline (day 0) 5920666012_G

description:
subject SUB134135 in ImmPort study SDY311
5920666012_G


title: healthy control C54


title: V4_15_GAM


title: Baseline (day 0) 5920711019_H

description:
subject SUB134128 in ImmPort study SDY311
5920711019_H


title: V2_16_PT


title: Baseline (day 0) 5920666013_H

description:
subject SUB134148 in ImmPort study SDY311
5920666013_H


title: healthy control C56


title: V7_14_DIW


title: Baseline (day 0) 5920666014_L

description:
subject SUB134145 in ImmPort study SDY311
5920666014_L

value: Asian


title: Baseline (day 0) 5920666014_F

description:
subject SUB134130 in ImmPort study SDY311
5920666014_F


title: V6_15_GAM


title: Baseline (day 0) 5920711019_D

description:
subject SUB134116 in ImmPort study SDY311
5920711019_D


title: healthy control C53


title: healthy control C52


title: Baseline (day 0) 5920666013_J

description:
subject SUB134117 in ImmPort study SDY311
5920666013_J


title: Baseline (day 0) 5920711019_J

description:
subject SUB134103 in ImmPort study SDY311
5920711019_J

value: Other


title: Baseline (day 0) 5920711019_L

description:
subject SUB134109 in ImmPort study SDY311
5920711019_L


title: V6_14_DIW


title: Baseline (day 0) 5920666014_E

description:
subject SUB134082 in ImmPort study SDY311
5920666014_E


title: Baseline (day 0) 5920666011_K

description:
subject SUB134139 in ImmPort study SDY311
5920666011_K


title: Baseline (day 0) 5920834001_E

description:
subject SUB134129 in ImmPort study SDY311
5920834001_E


title: Baseline (day 0) 5920666012_L

description:
subject SUB134101 in ImmPort study SDY311
5920666012_L


title: healthy control C45

value: M


title: Baseline (day 0) 5920666014_A

description:
subject SUB134095 in ImmPort study SDY311
5920666014_A


title: healthy control C44

value: Caucasian American


title: V4_14_DIW


title: healthy control C57


title: V3_14_DIW


title: Baseline (day 0) 5920666013_A

description:
subject SUB134143 in ImmPort study SDY311
5920666013_A


title: healthy control C41


title: Baseline (day 0) 5920711008_J

description:
subject SUB134124 in ImmPort study SDY311
5920711008_J


title: healthy control C35

description: Gene expression data from PBMC total RNA from healthy control.


title: healthy control C38


title: healthy control C36


title: V7_12_SLG


title: healthy control C37


title: Baseline (day 0) 5920834001_B

description:
subject SUB134130 in ImmPort study SDY311
5920834001_B


title: V5_12_SLG


title: Baseline (day 0) 5920711008_C

description:
subject SUB134150 in ImmPort study SDY311
5920711008_C


title: Baseline (day 0) 5920711019_E

description:
subject SUB134139 in ImmPort study SDY311
5920711019_E


title: Baseline (day 0) 5920666011_H

description:
subject SUB134142 in ImmPort study SDY311
5920666011_H


title: V6_10_POH


title: V3_12_SLG


title: Baseline (day 0) 5920666012_H

description:
subject SUB134129 in ImmPort study SDY311
5920666012_H


title: Baseline (day 0) 5920666013_K

description:
subject SUB134134 in ImmPort study SDY311
5920666013_K


title: Baseline (day 0) 5920666014_I

description:
subject SUB134149 in ImmPort study SDY311
5920666014_I


title: Baseline (day 0) 5920711019_K

description:
subject SUB134140 in ImmPort study SDY311
5920711019_K


title: Baseline (day 0) 5920711019_B

description:
subject SUB134125 in ImmPort study SDY311
5920711019_B


title: Baseline (day 0) 5920711008_E

description:
subject SUB134147 in ImmPort study SDY311
5920711008_E


title: Baseline (day 0) 5920711008_A

description:
subject SUB134113 in ImmPort study SDY311
5920711008_A


title: healthy control C33


title: V2_09_EAE


title: Baseline (day 0) 5920711019_G

description:
subject SUB134151 in ImmPort study SDY311
5920711019_G


title: Baseline (day 0) 5920666012_J

description:
subject SUB134131 in ImmPort study SDY311
5920666012_J


title: Baseline (day 0) 5920711019_F

description:
subject SUB134112 in ImmPort study SDY311
5920711019_F


title: V4_09_EAE


title: healthy control C24


title: healthy control C30


title: V4_07_AR


title: healthy control C23


title: Baseline (day 0) 5920834001_H

description:
subject SUB134131 in ImmPort study SDY311
5920834001_H


title: healthy control C21


title: V2_07_AR


title: Baseline (day 0) 5920711008_K

description:
subject SUB134130 in ImmPort study SDY311
5920711008_K


title: V6_05_JL


title: V7_05_JL


title: Baseline (day 0) 5920666012_D

description:
subject SUB134122 in ImmPort study SDY311
5920666012_D


title: Baseline (day 0) 5920666013_F

description:
subject SUB134114 in ImmPort study SDY311
5920666013_F


title: Baseline (day 0) 5920711008_L

description:
subject SUB134100 in ImmPort study SDY311
5920711008_L


title: Baseline (day 0) 5920666014_H

description:
subject SUB134127 in ImmPort study SDY311
5920666014_H


title: Baseline (day 0) 5920711019_C

description:
subject SUB134137 in ImmPort study SDY311
5920711019_C


title: healthy control C20

description: Gene expression data from PBMC total RNA from healthy control.


title: Baseline (day 0) 5920666014_B

description:
subject SUB134117 in ImmPort study SDY311
5920666014_B


title: healthy control C18


title: healthy control C19


title: Baseline (day 0) 5920666011_I

description:
subject SUB134143 in ImmPort study SDY311
5920666011_I


title: Baseline (day 0) 5920666014_J

description:
subject SUB134119 in ImmPort study SDY311
5920666014_J

value: Fluzone multi-dose vial|49281-386-15


title: Baseline (day 0) 5920666013_C

description:
subject SUB134081 in ImmPort study SDY311
5920666013_C


title: healthy control C17

value: Human peripheral blood mononuclear cells


title: V5_04_KK


title: V6_04_KK


title: V8_05_JL


title: Baseline (day 0) 5920666012_K

description:
subject SUB134087 in ImmPort study SDY311
5920666012_K


title: Baseline (day 0) 5920834001_A

description:
subject SUB134112 in ImmPort study SDY311
5920834001_A


title: Baseline (day 0) 5920666013_G

description:
subject SUB134097 in ImmPort study SDY311
5920666013_G


title: V4_10_POH


title: healthy control C16

value: F


title: healthy control C14


title: healthy control C15

value: African American


title: Baseline (day 0) 5920834001_F

description:
subject SUB134123 in ImmPort study SDY311
5920834001_F


title: Baseline (day 0) 5920666013_L

description:
subject SUB134111 in ImmPort study SDY311
5920666013_L


title: V3_04_KK

value: Vaginal Epithelium


title: Baseline (day 0) 5920666014_D

description:
subject SUB134120 in ImmPort study SDY311
5920666014_D


title: healthy control C12


title: V4_01_MAC


title: Baseline (day 0) 5920666013_I

description:
subject SUB134087 in ImmPort study SDY311
5920666013_I


title: Baseline (day 0) 5920834001_I

description:
subject SUB134089 in ImmPort study SDY311
5920834001_I


title: Baseline (day 0) 5920711008_H

description:
subject SUB134100 in ImmPort study SDY311
5920711008_H


title: Baseline (day 0) 5920666011_G

description:
subject SUB134084 in ImmPort study SDY311
5920666011_G


title: Baseline (day 0) 5920834001_D

description:
subject SUB134098 in ImmPort study SDY311
5920834001_D


title: V3_01_MAC


title: Baseline (day 0) 5920711008_G

description:
subject SUB134105 in ImmPort study SDY311
5920711008_G


title: Baseline (day 0) 5920666012_B

description:
subject SUB134121 in ImmPort study SDY311
5920666012_B


title: Baseline (day 0) 5920834001_J

description:
subject SUB134119 in ImmPort study SDY311
5920834001_J


title: Gemmza variety infected

city: Giza

first: Sameh

middle: El-Sayed

last: Hassanein

state: Giza

address: Gamaa st., Giza, Egypt

department: Bioinformatics and Computer Networks

country: Egypt

institute: Agricultural Genetic Engineering Research Institute

description: Gene expression after one week from infection of one weeks old plantlets

hyb_protocol: Hybridization was performed using the same kit of lableing

scan_protocol: Gene Pix scanner was used to scan the microarray

data_processing: Feature Extraction software provided by Agilent Technologies was used to extract features (protocol: GE1-v5_95_Feb07)

organism: Triticum aestivum

source_name: Gemmza variety infected

label_protocol: 200 ng of total RNA was labled with (One-Color Microarray-Based Gene Expression Analysis(Quick Amp Labeling) with Tecan HS Pro Hybridization) kit. (Agilent Technologies., Cat. No. G4140-90041) using manfucture instruction

growth_protocol: Bread wheat seeds were grown in green house under normal condition

extract_protocol: Total RNA extraction using Trizol following manfuacture's instructions

treatment_protocol: Puccinia triticinae spores were inoculated with 2 weeks old seedling and samples were isolated from infected and non infected planlets

tag: variety

value: GEMMZA 7

value: Leaves

tag: developmental stage

value: Two weeks old plantlets

tag: inoculant


title: V5_01_MAC

value: placebo


title: healthy control C13

description: Gene expression data from PBMC total RNA from healthy control.

value: healthy control


title: Misr variety infected

source_name: Misr variety infected

value: MISR 1


title: Control epithelial cells

city: Urbana

first: Shanmugasundaram

last: Nallasamy

state: IL

address: 2001 S Lincoln Ave

department: Comparative Biosciences

institute: University of illinois at Urbana-Champaign

description: uterus, D4 of pregnancy, implantation, stromal-epithelial communication, Wnts

hyb_protocol: 10 micrograms of labeled aRNA were hybridized to a Mouse Genome 430 2.0 Affymetrix 3' Expression Analysis Array.  Wash and stain were performed on Affymetrix Fluidics Station 450 with protocol EukGE_WS2v5 using Affymetrix GeneChip Command Console Fluidics Control software and solutions prepared by Keck Center,Comparative and Functional Genomics Unit, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign.

scan_protocol: Arrays were scanned on Affymetrix GeneChip Scanner model 3000 7G Plus using GeneChip Command Console Scan Control software to generate DAT and CEL files.

data_processing: To generate quality control metrics the Keck Center generated CHP files using the MAS5 algorithm with Affymetrix Expression Console version 1_1.

organism: Mus musculus

source_name: uteirne epithelial cells from Floxed control mice on day4 of pregnancy

label_protocol: The Keck Center Comparative and Functional Genomics Unit, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign prepared amplified, biotin-labeled, fragmented antisense RNA from 100 nanograms of sample total RNA using the Affymetrix 3' Express Kit (Affymetrix, Inc., Santa Clara, CA) according to manufacturer’s instructions.

growth_protocol: Mice were maintained in the designated animal care facility at University of Illinois at Urbana-Champaign according to the institutional guidelines for the care and use of laboratory animals. Msx1Msx2 floxed mice obtained from Dr. Robert E Maxson (University of Southern California) were crossed with PRcre mice (provided by Dr. Francceso DeMayo, (Baylor College of Medicine) to conditionally ablate Msx1Msx2 in the uterus.

extract_protocol: Total RNA was extracted from uterine stromal cells (n=4 for each genotype) using the Qiagen RNAeasy total RNA isolation kit according to the manufacturer's instructions.

treatment_protocol: Msx1Msx2-null mice (n=5) and the corresponding controls (n=5) were mated to fertile male mice. The presence of vaginal plug after mating was designated as Day1 of pregnancy. On day4 of pregnancy, uterine horns were excised. The uterine horns were cut into 3-4 mm pieces and were incubated in a solution of 1% trypsin (Difco, Dertroit, MI) in HBSS for 90 min at 40 C and then for 30 min at room temperature. After that the tissues were rinsed with 10% FBS. Under a dissecting microscope each enzyme treated piece of uterus was squeezed by iris forceps to separate the epithelium. After washing with HBSS, cells were lysed with Trizol to extract RNA.

tag: strain

tag: genotype/variation

value: Msx1Msx2 Floxed Control

value: uteirne epithelial cells

value: D4 of pregnancy


title: Baseline (day 0) 5920711008_D

description:
subject SUB134118 in ImmPort study SDY311
5920711008_D

tag: Sex

value: female

tag: race

value: White

tag: vaccine


title: DKO stromal cells

description: uterus, D4 of pregnancy, implantation, stromal-epithelial communication, FGFs, Wnts

source_name: uteirne stromal cells from KO mice on day4 of pregnancy

treatment_protocol: Msx1Msx2-null mice (n=5) and the corresponding controls (n=5) were mated to fertile male mice. The presence of vaginal plug after mating was designated as Day1 of pregnancy. On day4 of pregnancy, uterine horns were excised and cut into  3-5 mm pieces, then placed in HBSS containing 6g/L dispase (Gibico BRL), 25g/L pancreatin (Sigma), and 100 U/L penicillin, 0.1 g/L streptomycin, 1.25 mg/L fungizone (Gibico BRL) for 1h on ice followed by 1h at room temperature and then 10 min at 37⁰C. The tubes were gently mixed and the supernatant was discarded to remove the emdometrial epithelial clumps. The partially digested tissues were then washed twice in HBSS and placed in HBSS containing 0.5g/L collagenase (Sigma). After incubation for 45 min at 37⁰C, the tubes were mixed for 10-12 seconds by vortexing until the supernatant became turbid with dispersed endometrial stromal cells. The content of the tube was then passed through a 70 m gauze filter (Millipore). After washing with HBSS, pellet was lysed with Trizol to extract RNA.

value: uteirne stromal cells


title: Gemmza variety non infected

description: Gene expression after 2 weeks old non infected plantlets

source_name: Gemmza variety non infected

value: Puccinia triticinae


title: DKO epithelial cells

source_name: uteirne epithelial cells from KO mice on day4 of pregnancy


title: healthy control C11

value: Human peripheral blood mononuclear cells

tag: gender

value: M

tag: ethnicity

tag: treatment


title: PI3K 4 hours_biological rep 3

status: Public on Jul 19 2014

city: MADRID

first: Teresa

last: Fernandez-Acero

address: PLAZA DE RAMÓN Y CAJAL S/N

department: Departamento de Microbiología II

country: Spain

institute: Facultad de Farmacia UCM

description: All the procedure for microarrays experiments was carried out following the instructions of affymetrix for each of the steps

hyb_protocol: Following affymetrix hybridation instructions

scan_protocol: Following affymetrix scanning instructions

data_processing: CEL files from scanner were analyzed using GCRMA algorithm from Bioconductor software

organism: Saccharomyces cerevisiae

source_name: yeast

label_protocol: Following affymetrix labelling instructions

growth_protocol: Transformants of Saccharomyces cerevisiae strain BY4741 were grown overnight in SC-Raffinose and dilluted to 0.3 OD with fresh medium prior to treatment.

extract_protocol: Total RNA was isolated from exponentially growing cells by the “mechanical disruption protocol” using the RNeasy kit (Qiagen, Hilden, Germany), following the instructions of the manufacturer. RNA concentrations were determined by measuring absorbance at 260 nm. RNA purity and integrity were assessed using RNA Nano Labchips in an Agilent 2100B Bioanalyzer (Agilent Technologies, Palo Alto, CA) following the manufacturer’s instructions.

treatment_protocol: Galactose was added to the cultures to a final concentration of 2% and cultures were incubated for 4 hours at 30°C to induce GAL-PI3K (p110α-CAAX) /KD (p110α-CAAX K802R)-driven expression.


title: PI3K-KD 4 hours_biological rep 2


title: PI3K-KD 4 hours_biological rep 3


title: Control stromal cells

source_name: uteirne stromal cells from Floxed control mice on day4 of pregnancy

tag: cell type


title: PI3K 4 hours_biological rep 2


title: PI3K 4 hours_biological rep 1


title: PI3K-KD 4 hours_biological rep 1


title: Misr variety non infected

source_name: Misr variety non infected

tag: tissue


title: Baseline (day 0) 5920666012_A

description:
subject SUB134104 in ImmPort study SDY311
5920666012_A


title: CCd27 Post

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

hyb_protocol: A mixture of fragmented biotinylated cDNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix GeneChip Human Gene 2.0 ST Arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: Data were processed with RMA as implemented in the XPS package of Bioconductor. Reported values are on log2-scale.

source_name: coculture CD27+CD1a- TCRαβ-transduced, expanded

label_protocol: RNA concentration was determined with the Qubit RNA Assay using the Qubit 2.0 Fluorometer (Life Technologies), RNA purity was determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Using the Ambion WT Expression Kit, per sample, an amount of 100 ng of total RNA spiked with bacterial poly-A RNA positive controls (Affymetrix) was converted to double stranded cDNA in a reverse transcription reaction. Next the sample was converted and amplified to antisense cRNA in an in vitro transcription reaction which was subsequently converted to single stranded sense cDNA. Finally, samples were fragmented and labeled with biotin in a terminal labeling reaction according to the Affymetrix WT Terminal Labeling Kit.

growth_protocol: Cultured cells were cultured in alphaMEM supplemented with SCF, flt3 and interleukin-7.

extract_protocol: miRNeasy kit (Qiagen), following manufacturer's instructions.

treatment_protocol: No treatment applied.

value: child

tag: culture type

value: in vitro culture from thymus stem cells

value: CD27+CD1a- TCRαβ-transduced, expanded


title: CTX-14d myogenic cells

city: suita

first: so-ichiro

last: fukada

address: 1-6 yamadaoka

institute: osaka University

description: SM/C-2.6 is described in Exp. Cell Res. 2004 296(2); 245-255. Mouse 430A array was used.

hyb_protocol: Following fragmentation, 10 mg of labeled cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array (MOE430A). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Affymetrix MAS 5.0 with p-value cuttoffs of 0.04 and 0.06 for present, marginal, and absent.

source_name: Myogenic cells at CTX-14d

label_protocol: GeneChip® Eukayotic Small Sample Target Labeling Assay Version II.

growth_protocol: These samples were directly isolated from mouse skeletal muscle. Therefore, the cells were not cultured in vitro.

extract_protocol: Used Qiagen Rneasy Mini Kit according to instructions therein.

treatment_protocol: Hind limb muscle were injured by cardiotoxin (CTX).

tag: age

value: 8-12 weeks

value: cardiotoxin (CTX)

value: myogenic cells

tag: time post-ctx


title: CTX-3d myogenic cells

source_name: Myogenic cells at CTX-3d


title: CCd20 SP8

source_name: coculture CD27+CD1a- TCRαβ-transduced

value: CD27+CD1a- TCRαβ-transduced


title: PBMC CD8 POST

value: adult

value: peripheral blood


title: Thymus DPCD3+

source_name: thymus CD8β+CD4+CD3+CD27-CD1a+CD69-

value: thymus


title: RtCaud_0.15_4w_rep5

city: Raleigh

first: Alina

last: Efremenko

state: North Carolina

address: 6 Davis Dr

institute: The Hamner Institutes for Health Sciences

description: HT Rat Right Caudal Lung Cells

hyb_protocol: Fifteen μg of labeled cRNA was fragmented and hybridized to HT RG-230 PM Array Plate (16, 24, or 96 plate) for 16 h at 45°C. The hybridization, washing and scanning was carried out within the Gene Titan instrumentation.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan array scanner to generate CEL files with corresponding intensity values.

data_processing: Initial gene expression analysis was performed with Partek® (Partek Genome Suite 6.5; Partek Incorporated, St. Louis, MO). Arrays were robust multi-array average (RMA) normalized (Irizarry et al., 2003) and a standard 2 way analysis of variance (2-way ANOVA) was performed with factors including inhalation exposure concentrations (0.04, 0.08, 0.15, and 0.6 mg/m3) and length of exposure (1 or 4 weeks). Orthogonal linear contrasts were used to assess significance of differential gene expression at each concentration. Each individual rat was used as a replicate.

source_name: lung broncho-alveolar cells

label_protocol: Total RNA was isolated from the distal airway tissue using Trizol reagent (Invitrogen, Carlsbad, CA) according to manufactures instructions.  The isolated RNA was further purified using the QIAcube automated system and RNeasy columns (Qiagen, Valencia, CA).  The RNA was quantified and integrity of the RNA was verified spectrophotometrically with the Nanodrop (ThermoFisher Scientific, Waltham, MA) and the Agilent 2100 Bioanalyzer (Palo Alto, CA) respectively.  Double-stranded cDNA was synthesized from 50-150 ng (dependent on RNA yield) of total RNA, then transcribed to biotin-labeled cRNA using the 3’ Express IVT kit (Affymetrix, Santa Clara, CA).

growth_protocol: Male Fischer-344 (CDF) rats (approximately 7-8 weeks of age on receipt) were obtained from Charles River Laboratories, Kingston, NY.

extract_protocol: Five of 13 rats in each group were used for broncho-alveolar lavage fluid (BALF) evaluation and lung histopathology.  The remaining eight rats per group were used for lung gene expression analysis and lung nickel burden analysis. For gene expression analysis, five (of eight) samples containing the best RNA quality were used for gene expression microarray measurements.

treatment_protocol: Group size was 13 animals per each time point-exposure level combination. Atmospheres of Ni3S2 aerosol were generated at target concentrations of 0 (control), 0.04, 0.08, 0.15, and 0.60 mg/m3 (approximately 0.03, 0.06, 0.11, and 0.44 mg Ni/m3) in air.  Animals were exposed to the target concentrations for 6 hr/day, 5 d/wk for either 1 or 4 weeks (5 or 20 exposure days).

value: Fischer 344

value: Ni3S2 at 0.15 mg/m3

tag: time point

value: 4 week


title: RtCaud_0.15_4w_rep1

description: HT Rat Right Caudal Lung Cells


title: RtCaud_0.15_4w_rep3

description: HT Rat Right Caudal Lung Cells


title: RtCaud_0.15_4w_rep4

description: HT Rat Right Caudal Lung Cells


title: RtCaud_0.15_1w_rep5

description: HT Rat Right Caudal Lung Cells

value: 1 week


title: RtCaud_0.15_4w_rep2

description: HT Rat Right Caudal Lung Cells


title: CCd14 DPCD3+

value: CD8β+CD4+CD27-CD1a+ TCRαβ-transduced


title: RtCaud_0.15_1w_rep4

description: HT Rat Right Caudal Lung Cells


title: Thymus SP8

source_name: thymus CD8β+CD4-CD1a-TCRαβ+


title: RtCaud_0.15_1w_rep2

description: HT Rat Right Caudal Lung Cells


title: RtCaud_0.15_1w_rep3

description: HT Rat Right Caudal Lung Cells


title: RtCaud_0.15_1w_rep1

description: HT Rat Right Caudal Lung Cells


title: RtCaud_0.08_4w_rep5

description: HT Rat Right Caudal Lung Cells

value: Ni3S2 at 0.08 mg/m3


title: RtCaud_0.08_4w_rep4

description: HT Rat Right Caudal Lung Cells


title: RtCaud_0.08_4w_rep3

description: HT Rat Right Caudal Lung Cells


title: RtCaud_0.08_4w_rep1

description: HT Rat Right Caudal Lung Cells


title: Mouse Dermal Endothelial Cells

city: Chapel Hill

first: James

last: Dunleavey

state: NC

address: 111 Mason Farm Road

institute: University of North Carolina- Chapel Hill

hyb_protocol: cRNA was hybridized according to Affymetrix protocols to a Mouse Gene ST1.0 Array

scan_protocol: Array was imaged using a Affymetrix GeneChip Scanner 3000-7Gplus with Autoloader

data_processing: The data was normalized globally using Partek Genomics Suite using default settings and used global scaling to normalize data

source_name: Mouse Dermal Endothelial Cells

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

growth_protocol: B16F10 and derived cell lines were maintained in DMEM with 10% FBS and 1% Antibiotic/Antimycotic. MDEC were maintained in DMEM with Endothelial Growth Supplement Bullet Kit (Lonza).

extract_protocol: Total RNA was harvested according to manufacturuer's instructions with the Qiagen Rneasy isolation kit.

treatment_protocol: Cells were harvested with Accutase, washed in PBS, and total RNA was extracted using a Qiagen Rneasy isolation kit (Qiagen).

tag: pecam status


title: RtCaud_0.08_1w_rep5

description: HT Rat Right Caudal Lung Cells


title: RtCaud_0.08_1w_rep4

description: HT Rat Right Caudal Lung Cells


title: RtCaud_0.08_1w_rep3

description: HT Rat Right Caudal Lung Cells


title: RtCaud_0.08_1w_rep1

description: HT Rat Right Caudal Lung Cells


title: RtCaud_0.6_4w_rep4

description: HT Rat Right Caudal Lung Cells

value: Ni3S2 at 0.60 mg/m3


title: RtCaud_0.08_4w_rep2

description: HT Rat Right Caudal Lung Cells


title: B16F10 Clone A4 PECAM1+

source_name: B16F10 PECAM+ clone

tag: cell line


title: RtCaud_0.6_4w_rep5

description: HT Rat Right Caudal Lung Cells


title: RtCaud_0.08_1w_rep2

description: HT Rat Right Caudal Lung Cells


title: B16F10 Clone A5 PECAM1+


title: RtCaud_0.6_4w_rep3

description: HT Rat Right Caudal Lung Cells


title: RtCaud_0.6_4w_rep1

description: HT Rat Right Caudal Lung Cells


title: RtCaud_0.6_1w_rep3

description: HT Rat Right Caudal Lung Cells


title: B16F10 Clone A3 PECAM1+


title: RtCaud_0.6_1w_rep2

description: HT Rat Right Caudal Lung Cells


title: B16F10 Clone A1 PECAM1-

source_name: B16F10 PECAM- clone


title: RtCaud_0.6_4w_rep2

description: HT Rat Right Caudal Lung Cells


title: B16F10 Parental

source_name: B16F10 Cell Line


title: B16F10 Clone A2 PECAM1+


title: RtCaud_0.6_1w_rep4

description: HT Rat Right Caudal Lung Cells


title: RtCaud_0.6_1w_rep5

description: HT Rat Right Caudal Lung Cells


title: RtCaud_0.04_4w_rep3

description: HT Rat Right Caudal Lung Cells

value: Ni3S2 at 0.04 mg/m3


title: RtCaud_0.04_4w_rep5

description: HT Rat Right Caudal Lung Cells


title: RtCaud_0.04_4w_rep2

description: HT Rat Right Caudal Lung Cells


title: RtCaud_0.6_1w_rep1

description: HT Rat Right Caudal Lung Cells


title: PPoP_array_SL16

city: Amsterdam

first: Tjalf

last: de Boer

address: Science Park 406

country: Netherlands

institute: MicroLife Solutions

hyb_protocol: 300 ng of Cy3-labeled or Cy5-labeled cRNA (specific activity >8.0 pmol dye/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Custom Gene Expression Microarrays with 8 - 15 k format (GPL7150) for 17 hours at 65°C in a rotating Agilent hybridization oven (10 rpm)  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), washed in acetonitril for 10 seconds, then dried immediately by air.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting for 2x11k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Red&Green and PMT is set to 100%, XDR Hi 100%, XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (protocol GE2_11kx2_1205 and Grid: 014597_D_F_20060427) to obtain mean Red or Green intensities and median Red or Green background intesities. In limma, edwards method for background correction was used (offset = 30), and global loess normalizion was done.

organism: Folsomia candida

source_name: whole animal

label_protocol: Cyanine-3 (Cy3) or Cyanine-5 (Cy5) labeled cRNA was prepared from 500 ng total RNA using the Quick Amp Labeling Kit, two-color (Agilent Technologies) according to the manufacturer's guidelines with a slight modification where the transcription (labeling) reactions were done in half the volume, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cultures were first age synchronized before exposure to soil: 20 adult animals were incubated per container; containing a plaster of Paris base mixed with charcoal, to lay eggs for 2 days. The incubation conditions were 20°C, 75% RH and 12:12 hour dark:light cycle

extract_protocol: Total RNA was extracted from all animals (~30) per jar, using SV Total RNA isolation System (Promega).

treatment_protocol: Approximately 30 animals, 23 days old, were exposed for two days in glass jars containing ~30 g of soil at 50% of the soil WHC. Exposure was done at same conditions as incubation. After exposure the animals were extracted from soil with tap water via floatation, put in 1.5 mL tubes and frozen in liquid N2.

value: cadmium spiked soil exposure

value: whole animal

value: LUFA2.2 spiked soil exposure


title: NG-Ptch-rep4

city: Bar Harbor

first: Vivek

last: Philip

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description: gene expression from NG subtype of Ptch medulloblastoma

hyb_protocol: Following fragmentation and labeling, ~25ng/µl (according to manual) cDNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. (GeneChip Whole Transcript (WT) Sense Target Labeling Assay, Affymetrix© 2005-2009) & (GeneChip Expression Wash, Stain and Scan User Manual, Affymetrix © 2008)

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

data_processing: The data were analyzed with Partek Genomics suite 6.6  using Affymetrix default analysis settings. The processes included  background correction on the PM values, quantile normalization across all  the chips in the experiment, Log2 transformation and median polish  summarization.

source_name: NG-Ptch

label_protocol: Biotinylated cDNA were prepared according to the Ambion WT Expression Kit & Affymetrix GeneChip WT Terminal Labeling Kit protocols from 250ng total RNA (Ambion® WT Expression Kit for use with: Affymetrix® GeneChip® Whole Transcript (WT) Expression Arrays, Life Technologies © ) & (GeneChip Whole Transcript (WT) Sense Target Labeling Assay, Affymetrix© 2005-2009) & (GeneChip WT Terminal Labeling and Hybridization User Manual © 2009-2011)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturers instructions.

value: ND

value: medulloblastoma

tag: subtype

value: NG subtype of Ptch medulloblastoma


title: RtCaud_0.04_4w_rep4

description: HT Rat Right Caudal Lung Cells

tag: strain


title: NG-Ptch-rep5


title: GFD-Smo;GFAP-cre-rep4

description: gene expression from GFD subtype of Smo;GFAP-cre medulloblastoma

source_name: GFD-Smo;GFAP-cre


title: RtCaud_0.04_4w_rep1

description: HT Rat Right Caudal Lung Cells


title: RtCaud_0.04_1w_rep5

description: HT Rat Right Caudal Lung Cells


title: PPoP_array_SL15

value: LUFA2.2 soil exposure


title: VAT_5958031032_R05C01

city: Quebec

first: Frederic

last: Guenard

address: 2440, Hochelage blvd

institute: Laval University

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing:
The GenomeStudio software version 2011.1 (Illumina Inc.) and the Methylation Module were used.
Normalization method described in: Fortin, J.-P. et al. Functional normalization of 450k methylation array data improves replication in large cancer studies. bioRxiv (2014).

source_name: Visceral adipose tissue

label_protocol: Illumina protocol

growth_protocol: Visceral adipose tissue was obtained during biliopancreatic diversion surgery, rapidly frozen in liquid N2 and stored at -80 oC.

extract_protocol: Genomic DNA was extracted from the VAT using the DNeasy Blood & Tissue kit, as recommended by the manufacturer

value: Male


title: PPoP_array_SL13


title: PPoP_array_SL14


title: GFD-Smo;GFAP-cre-rep2

value: F

value: GFD subtype of Smo;GFAP-cre medulloblastoma


title: RtCaud_0.04_1w_rep4

description: HT Rat Right Caudal Lung Cells

value: Fischer 344


title: NG-Smo;Atoh1-CreER-rep4

description: gene expression from NG subtype of Smo;Atoh1-CreER medulloblastoma


title: PPoP_array_SL12

value: Noyelle spiked soil exposure


title: GFD-Smo;GFAP-cre-rep1


title: NG-Smo;Atoh1-CreER-rep3

value: NG subtype of Smo;Atoh1-CreER medulloblastoma


title: RtCaud_0.04_1w_rep3

description: HT Rat Right Caudal Lung Cells

value: 1 week


title: GFD-Smo;GFAP-cre-rep3

value: M


title: RtCaud_0.04_1w_rep1

description: HT Rat Right Caudal Lung Cells


title: PPoP_array_SL11


title: VAT_5958091029_R05C01


title: VAT_5958091030_R05C01


title: PPoP_array_SL10

value: Noyelle soil exposure


title: NG-Smo;Atoh1-CreER-rep2


title: RtCaud_0.0_4w_rep5

description: HT Rat Right Caudal Lung Cells

value: Ni3S2 at 0.0 mg/m3

value: 4 week


title: VAT_5958091030_R04C01


title: PPoP_array_SL08

value: Stolberg soil exposure

value: whole animal


title: RtCaud_0.0_4w_rep4

description: HT Rat Right Caudal Lung Cells


title: NG-Smo;Atoh1-CreER-rep1


title: PPoP_array_SL09

value: LUFA2.2 spiked soil exposure


title: PPoP_array_SL07

value: Stolberg spiked soil exposure


title: RtCaud_0.0_4w_rep3

description: HT Rat Right Caudal Lung Cells


title: RtCaud_0.0_4w_rep2

description: HT Rat Right Caudal Lung Cells


title: VAT_5958031032_R04C01


title: PPoP_array_SL06


title: GFI-Ptch-rep3

description: gene expression from GFI subtype of Ptch medullolbastoma

source_name: GFI-Ptch

value: medulloblastoma

value: GFI subtype of Ptch medullolbastoma


title: GFI-Ptch-rep2


title: VAT_5958091029_R04C01

value: Male


title: VAT_5958091028_R05C01


title: GFI-Ptch-rep4

description: gene expression from GFI subtype, progressed from X4200, host=NSG female


title: VAT_5958031032_R02C01


title: GFI-Ptch-rep1

value: F


title: RtCaud_0.0_1w_rep5

description: HT Rat Right Caudal Lung Cells


title: VAT_5958091028_R04C01


title: PPoP_array_SL03

value: LUFA2.2 soil exposure

value: Marchienne spiked soil exposure


title: RtCaud_0.0_1w_rep3

description: HT Rat Right Caudal Lung Cells

value: Fischer 344


title: NG-Ptch-rep2

value: ND

value: NG subtype of Ptch medulloblastoma


title: PPoP_array_SL02

value: Marchienne soil exposure


title: GFD-Ptch-rep1

description: gene expression from GFD subtype of Ptch medullolbastoma

source_name: GFD-Ptch

value: M

value: GFD subtype of Ptch medullolbastoma


title: VAT_5958031032_R03C01


title: RtCaud_0.0_4w_rep1

description: HT Rat Right Caudal Lung Cells

value: Ni3S2 at 0.0 mg/m3

value: 4 week


title: PPoP_array_SL04

value: whole animal


title: VAT_5958091030_R02C01


title: VAT_5958091029_R06C02


title: RtCaud_0.0_1w_rep2

description: HT Rat Right Caudal Lung Cells

value: 1 week


title: PPoP_array_SL01

value: LUFA2.2 spiked soil exposure


title: VAT_5958091028_R03C01


title: GFD-Ptch-rep2

value: medulloblastoma


title: VAT_5958091030_R06C02


title: VAT_5958091028_R06C02


title: VAT_5958091029_R03C01


title: PPoP_array_SL05

value: Stolberg spiked soil exposure


title: X520_V4_T8_475585A01

status: Public on Jul 18 2014

city: Madison

first: Robert

middle: C

last: Landick

state: WI

address: 1550 Linden Dr

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

hyb_protocol: hybridization protocol was conducted according to the manufacturer’s instructions (Roche NimbleGen)

scan_protocol: Hybridized arrays were scanned with a NimbleGen MS 200 microarray scanner, and the probe signal intensities were determined using NimbleScan v 2.6 (Roche NimbleGen).

data_processing: Probe signal intensities were preprocessed using robust multichip averaging (RMA) in the program ArrayStar (DNASTAR), and the resulting gene expression signals were quantile-normalized across all samples using the normalize.quantiles function in the Bioconductor package for R.

source_name: Escherichia coli GLBRCE1

label_protocol: cDNA labeling protocol was conducted according to the manufacturer’s instructions (Roche NimbleGen)

growth_protocol: Fermentations were carried out in 3L bioreactors (Applikon Biotechnology) containing 2.45L of ACSH, SynH, SynH+LT, or SynH + Acid/Amide LTs, and cultures were diluted into ACSH or SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2

extract_protocol: RNA was obtained from cells pellets by lysozyme treatment and phenol-chloroform extraction, analyzed by agarose gel electrophoresis to confirm integrity, quantified using a Nanodrop spectrophotometer (Thermo Scientific), and stored at -80°C

treatment_protocol: Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol/vol) unbuffered phenol in ethanol (EP) and pelleted by centrifugation (10,000 g, 4°C, 3 min). To remove residual traces of hydrolysate, cell pellets were twice resuspended in ice-cold GMM plus 0.125 volume of EP, repelleted, then flash frozen in dry ice-ethanol, and stored at -80°C.

tag: medium

tag: growth phase

value: Stat


title: RtCaud_0.0_1w_rep1

description: HT Rat Right Caudal Lung Cells


title: VAT_5958091030_R03C01

tag: Sex

value: Male


title: X515_V4_T8_475655A04

value: ACSH


title: X520_V4_T7_475644A03

value: Trans


title: VAT_5958031032_R01C01


title: VAT_5958091028_R02C01


title: X520_V3_T7_475644A02s


title: X515_V4_T6_424221A03


title: RtCaud_0.04_1w_rep2

description: HT Rat Right Caudal Lung Cells

value: Fischer 344

value: Ni3S2 at 0.04 mg/m3


title: X515_V3_T6_424221A04


title: X520_V3_T4_475654A04


title: X515_V4_T4_475585A03

value: Exp


title: X515_V4_T4_475644A01


title: VAT_5958031032_R05C02


title: X515_V3_T4_475585A02s


title: X520_V2_T8_424219A02

value: SynH


title: X520_V3_T8_424219A03


title: VAT_5958091029_R01C01


title: X515_V3_T8_475641A04


title: X515_V2_T8_424219A01s


title: X520_V4_T6_424287A01


title: X515_V4_T7_424287A04


title: VAT_5958091030_R01C01


title: VAT_5958091029_R02C01


title: X520_V4_T4_475654A03


title: VAT_5958091028_R01C01


title: X520_V2_T6_424287A02


title: X515_V2_T4_475655A03


title: X515_V2_T6_475644A04


title: X515_V2_T7_475649A01


title: X520_V2_T7_475654A01


title: NG-Ptch-rep1

value: F

value: NG subtype of Ptch medulloblastoma


title: X515_V2_T4_424219A04


title: X520_V2_T4_475641A03


title: RtCaud_0.0_1w_rep4

description: HT Rat Right Caudal Lung Cells

value: Ni3S2 at 0.0 mg/m3


title: tumor DNA_pair 16_late lesion

city: Birmingham

first: Farida

last: Latif

address: College of Medical and Dental Sciences

country: United Kingdom

institute: University of Birmingham

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybrdised to Illumina Infinium HumanMethyaltion450 bead chip using standard Illumina protocol

scan_protocol: Arrays were imaged using Bead Array Reader using recommended Illumina protocol

data_processing: Illumina Genome Studio software; non_normalized data matrix contains unmethylated and methylated signal intensities.

source_name: tumor DNA_pair 16_late lesion

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted using QIAmp DNA mini kit 50 (Qiagen) according to manufacturer's instructions

tag: tumour stage

value: secondary glioblastoma grade IV


title: tumor DNA_pair 15_early lesion

source_name: tumor DNA_pair 15_early lesion

value: astrocytoma grade II


title: X520_V3_T6_475641A02


title: X515_V3_T7_475649A02


title: tumor DNA_pair 20_late lesion

source_name: tumor DNA_pair 20_late lesion


title: tumor DNA_pair 15_late lesion

source_name: tumor DNA_pair 15_late lesion

value: astrocytoma grade III


title: tumor DNA_pair 18_early lesion

source_name: tumor DNA_pair 18_early lesion


title: tumor DNA_pair 19_late lesion

source_name: tumor DNA_pair 19_late lesion


title: tumor DNA_pair 14_early lesion

source_name: tumor DNA_pair 14_early lesion


title: tumor DNA_pair 11_early lesion

source_name: tumor DNA_pair 11_early lesion


title: tumor DNA_pair 14_late lesion

source_name: tumor DNA_pair 14_late lesion


title: tumor DNA_pair 10_late lesion

source_name: tumor DNA_pair 10_late lesion


title: tumor DNA_pair 18_late lesion

source_name: tumor DNA_pair 18_late lesion


title: tumor DNA_pair 16_early lesion

source_name: tumor DNA_pair 16_early lesion


title: tumor DNA_pair 7_late lesion

source_name: tumor DNA_pair 7_late lesion


title: tumor DNA_pair 8_early lesion

source_name: tumor DNA_pair 8_early lesion


title: tumor DNA_pair 17_late lesion

source_name: tumor DNA_pair 17_late lesion


title: tumor DNA_pair 12_late lesion

source_name: tumor DNA_pair 12_late lesion


title: tumor DNA_pair 17_early lesion

source_name: tumor DNA_pair 17_early lesion


title: tumor DNA_pair 12_early lesion

source_name: tumor DNA_pair 12_early lesion


title: tumor DNA_pair 10_early lesion

source_name: tumor DNA_pair 10_early lesion


title: tumor DNA_pair 8_late lesion

source_name: tumor DNA_pair 8_late lesion


title: tumor DNA_pair 9_late lesion

source_name: tumor DNA_pair 9_late lesion


title: tumor DNA_pair 9_early lesion

source_name: tumor DNA_pair 9_early lesion


title: tumor DNA_pair 19_early lesion

source_name: tumor DNA_pair 19_early lesion


title: tumor DNA_pair 20_early lesion

source_name: tumor DNA_pair 20_early lesion


title: X515_V1_T8_475585A04

source_name: Escherichia coli GLBRCE1


title: X520_V1_T7_475655A01


title: tumor DNA_pair 7_early lesion

source_name: tumor DNA_pair 7_early lesion

value: astrocyotma grade II


title: X520_V2_T3_424221A02


title: X515_V1_T7_475654A02


title: X520_V1_T8_475641A01


title: tumor DNA_pair 13_late lesion

source_name: tumor DNA_pair 13_late lesion


title: tumor DNA_pair 6_late lesion

source_name: tumor DNA_pair 6_late lesion


title: LIMS484_S5_T8

growth_protocol: Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH or SynH media, and cultures were diluted into ACSH or SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2

value: SynH w/o osmoprotectants + LTs

value: stat 2


title: LIMS484_S6_T6

value: SynH + LTs

value: transition


title: X515_V1_T6_475649A04s


title: X520_V1_T6_475649A03

value: ACSH


title: X515_V1_T4_475655A02


title: X515_V1_T4_424287A03


title: tumor DNA_pair 6_early lesion

source_name: tumor DNA_pair 6_early lesion


title: LIMS484_S6_T4

value: log phase


title: tumor DNA_pair 13_early lesion

source_name: tumor DNA_pair 13_early lesion


title: LIMS484_S2_T8


title: tumor DNA_pair 5_early lesion

source_name: tumor DNA_pair 5_early lesion


title: LIMS484_S6_T8


title: tumor DNA_pair 5_late lesion

source_name: tumor DNA_pair 5_late lesion


title: tumor DNA_pair 4_late lesion

source_name: tumor DNA_pair 4_late lesion


title: LIMS484_S5_T2


title: LIMS484_S2_T6


title: tumor DNA_pair 3_early lesion

source_name: tumor DNA_pair 3_early lesion


title: LIMS484_S2_T2


title: IF002_CF_WT_NB#5

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

description: We designed an oligonucleotide microarray using Agilent eArray Web portal (https://earray.chem.agilent.com/earray) to profile both Ensembl annotated transcripts and intergenic transcripts derived from ferret RNA-seq data. The longest isoform of each locus was selected for probe design with the ‘Design with 3’ Bias’ checked, and probe length was set to 60nt.  For the version of microarray (design ID: 048471) 36,950 probes were selected to target Ensembl annotated genes and intergenic transcripts uncovered from mRNA-seq data, which was intended to work with conventional experimental protocols using polyA priming for cDNA synthesis.

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to both Agilent 8X60K (Design ID 048471) and Agilent 4X180K (Design ID 048472) arrays.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags.  The whole ferret expression data was re-processed together using Bioconductor package ‘limma’. The ‘normexp’ method was for background correction, and the ‘quantile’ method was used for normalizing intensities across all arrays. The log2 fold changes were calculated for each infection condition relative to matched wild type samples, and used for further analysis.

organism: Mustela putorius furo

source_name: Study#, cystic fibrosis, wild type, new born #

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

extract_protocol: All Trizol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: Specific lobes of the lung as well as trachea tissue from each animal were harvested and briefly rinsed in cold (4ºC) PBS. Following the RNALater (Ambion) protocol, tissue was cut into small chunks (<0.5cm in any single dimension) and placed immediately into a 10-20 volumes (w/v) (e.g. 100mg/ml) RNALater. After a 4ºC incubation for overnight, samples were stored at -80ºC until processing. Tissue was removed from RNALater, washed in a small volume of Trizol, homogenized in 10-20 volumes (w/v) Trizol and stored at -80°C until RNA isolation.

value: lung-Trachea

tag: genotype

value: Wild Type

value: Newborn


title: IF002_CF_KO_3875

source_name: Study#, cystic fibrosis, knock out, animal#

value: lung

value: 15 Day


title: LIMS484_S1_T8

value: SynH w/o osmoprotectants


title: IF002_CF_KO_NB#4

source_name: Study#, cystic fibrosis, knock out, new born #


title: LIMS484_S1_T6


title: LIMS484_S1_T3


title: tumor DNA_pair 2_late lesion

source_name: tumor DNA_pair 2_late lesion


title: IF002_CF_KO_NB#3


title: IF002_CF_WT_NB#3


title: tumor DNA_pair 11_late lesion

source_name: tumor DNA_pair 11_late lesion


title: tumor DNA_pair 1_early lesion

source_name: tumor DNA_pair 1_early lesion


title: tumor DNA_pair 1_late lesion

source_name: tumor DNA_pair 1_late lesion


title: LIMS477_S5_T8

source_name: Escherichia coli GLBRCE1

value: SynH

value: stat 1


title: LIMS477_S5_T6


title: tumor DNA_pair 2_early lesion

source_name: tumor DNA_pair 2_early lesion


title: IF002_CF_WT_NB#2


title: LIMS477_S5_T4


title: IF002_CF_KO_3938


title: tumor DNA_pair 3_late lesion

source_name: tumor DNA_pair 3_late lesion

value: secondary glioblastoma grade IV


title: IF002_CF_KO_NB#6


title: LIMS484_S5_T6


title: LIMS477_S3_T6


title: LIMS477_S3_T3


title: tumor DNA_pair 4_early lesion

source_name: tumor DNA_pair 4_early lesion

value: astrocytoma grade III


title: LIMS477_S2_T8


title: IF002_CF_KO_3519


title: short_day_rep4

city: Leicester

first: Eran

last: Tauber

address: University Road

department: Genetics

institute: University of Leicester

hyb_protocol: 10 ug of fragmented biotin-labelled cRNA was used in the hybridisation cocktail for the Drosophila array (total volume of hybridisation cocktail = 200 ul). 130 ul of the hybridisation cocktail was used with Affymetrix GeneChip Drosophila Genome 2.0 Array. The hybridisations were carried by the NERC microarray facility at the University of Liverpool.

scan_protocol: The scaning was carried by the NERC microarray facility at the University of Liverpool following the Affymetrix recommendations.

data_processing: The data were analysed using the R/Bioconductor affylmGUI package (version 1.8.0). GCRMA normalisation was applied.

organism: Drosophila melanogaster

growth_protocol: Within 8 hr after eclosion, flies were transferred to vials and maintained in light boxes illuminated by a 4W fluorescent bulb at 12.5°C under light-dark cycle (LD) of either long (16:8) or short (10:14) day. After 12 days, flies were dissected and head RNA was extracted.

value: female


title: long_day_rep4


title: LIMS477_S2_T6


title: IF002_CF_WT_NB#6


title: long_day_rep3


title: long_day_rep2


title: long_day_rep1


title: LIMS477_S2_T4


title: Non-Diapause rep2

hyb_protocol: 10 ug of fragmented biotin-labelled cRNA was used in the hybridisation cocktail for the Drosophila array (total volume of hybridisation cocktail = 200 ul). 130 ul of the hybridisation cocktail was used with Affymetrix GeneChip Drosophila Genome 2.0 Array. The hybridisations  were carried by the microarray facility at the University of Glasgow.

scan_protocol: The scaning was carried by the microarray facility at the University of Glasgo following the Affymetrix recommendations.

data_processing: The data were analysed using the  R/Bioconductor affylmGUI package (version 1.8.0). GCRMA normalisation was applied.

growth_protocol: Within 8 hr after eclosion, flies were transferred to vials and maintained in light boxes illuminated by a 4W fluorescent bulb at 12.5°C under light-dark cycle (LD) 14:10. After 12 days, flies were dissected and ovaries status (diapause vs. non-diapause) was determined.

value: Canton S

value: heads

tag: developmental state

value: non-diapause


title: IF002_CF_KO_NB#2


title: Diapause rep4

value: diapause


title: IF002_CF_WT_4653

source_name: Study#, cystic fibrosis, wild type, animal#


title: LIMS477_S1_T6

value: transition


title: short_day_rep1


title: Non-Diapause rep3


title: LIMS477_S3_T11

value: SynH w/o osmoprotectants + LTs

value: stat 2


title: X520_V1_T4_424221A01

value: ACSH

value: Exp


title: IF002_CF_HET_3940

source_name: Study#, cystic fibrosis, Heterzygote, animal#

value: lung


title: short_day_rep2


title: Diapause rep3


title: Non-Diapause rep1


title: Diapause rep1


title: LIMS477_S1_T3

value: log phase


title: LIMS477_S1_T10

value: SynH w/o osmoprotectants


title: Long (cy3) - Short (cy5) rep 2 dye swap

description: Biological replicate 4 of 4.

hyb_protocol: labelled miRNAs were co-hybridized with the NCode TM multi-species miRNA microarray V2 (Invitrogen) as a two-colour experiment.

scan_protocol: Images were quantified using GenePix 4.1 software.

data_processing: LOWESS normalized, background subtracted data (minimum) obtained from log2 of processed Red signal/processed Green signal. Between-arrays (scale) normalisation was applied.

source_name: female heads, long day

label_protocol: 250 ng of enriched miRNA from each sample were labelled either with Alexa Flour® 3 or 5 using the NCode TM rapid miRNA labelling system (Invitrogen).

growth_protocol: Drosophlia strain Canton-S flies were maintened on standard sugar media at 12.5°C for 12 days.

extract_protocol: The microRNA fraction was isolated using the pureLinkTM miRNA isolation kit (Invitrogen).

treatment_protocol: Flies were maintened under either short  day (10 hr) or long (16 hr).

tag: gender

value: head

tag: treatment

value: long day

value: Canton-S

source_name: female heads, short day

value: short day


title: Diapause rep2

tag: tissue


title: GLBRCE1_pBBR_ACSH_Exp

source_name: Escherichia coli GLBRCE1_pBBR

growth_protocol: E.coli ethanologen strain GLBRCE1 or GLBRCE1 lacking the plasmid-borne PET cassette (GLBRCE1_pBBR) was grown in AFEX corn stover hydrolysate (ACSH). Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH and cultures were diluted into ACSH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2.  One biological replicate was grown in each medium.  RNA samples were obtained at 3 time points, corresponding to mid-exponential (Exp), transitional (Trans), and stationary (Stat) growth phases.


title: Long (cy3) - Short (cy5) rep 1 dye swap

description: Biological replicate 2 of 4.

value: female


title: Short (cy3) - Long (cy5) rep 1

description: Biological replicate 1 of 4.


title: Non-Diapause rep4

value: Canton S


title: Short (cy3) - Long (cy5) rep 2

description: Biological replicate 3 of 4.


title: GLBRCE1_pBBR_ACSH_Stat

value: Stat


title: IF001_292_trachea_1918_d1_1_B

description: We designed two versions of oligonucleotide microarray using Agilent eArray Web portal (https://earray.chem.agilent.com/earray) to profile both Ensembl annotated transcripts and intergenic transcripts derived from ferret RNA-seq data. In both cases, the longest isoform of each locus was selected for probe design with the ‘Design with 3’ Bias’ checked, and probe length was set to 60nt.  For first version of microarray (design ID: 048471) 36,950 probes were selected to target Ensembl annotated genes and intergenic transcripts uncovered from mRNA-seq data, which was intended to work with conventional experimental protocols using polyA priming for cDNA synthesis. For the second version (design ID: 048472) 64,238 probes were selected to target Ensembl annotated genes, intergenic transcripts uncovered from both mRNA-seq and Total RNA-seq data, which was intended to work with experimental protocols using random priming for cDNA synthesis to capture both polyA and non-polyA transcripts.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags.  The whole ferret expression data was re-processed together using Bioconductor package ‘limma’. The ‘normexp’ method was for background correction, and the ‘quantile’ method was used for normalizing intensities across all arrays. The log2 fold changes were calculated for each infection condition relative to matched mock samples, and used for further analysis.

source_name: Study#, animal#, trachea, infection, day 1, biological replicate, technical replicate

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

value: trachea

value: Female

value: 4-8 month-old

tag: infection


title: short_day_rep3


title: IF001_290_lung_PBS_d1_2_A

source_name: Study#, animal#, lung, infection, day 1, biological replicate, technical replicate

tag: age

value: PBS


title: IF001_292_lung_1918_d1_1_B


title: IF001_292_trachea_1918_d1_1_A


title: IF002_CF_HET_3788

value: 15 Day


title: IF001_292_lung_1918_d1_1_A


title: IF002_CF_WT_3520

value: Wild Type


title: IF001_290_trachea_PBS_d1_2_B


title: IF002_CF_HET_3873


title: IF001_290_lung_PBS_d1_2_B


title: GLBRCE1_ACSH_Stat2_rep320_1

source_name: GLBRCE1, ACSH, Stat2

value: ACSH

tag: biological replicate

tag: technical replicate


title: GLBRCE1_ACSH_Stat2_rep327_1


title: GLBRCE1_ACSH_Trans

value: Trans


title: GLBRCE1_ACSH_Stat2_rep318_1


title: GLBRCE1_pBBR_ACSH_Trans


title: GLBRCE1_ACSH_Exp

value: Exp


title: GLBRCE1_ACSH_Stat


title: GLBRCE1_ACSH_Stat1_rep327_1

source_name: GLBRCE1, ACSH, Stat1


title: GLBRCE1_ACSH_Stat1_rep320_1


title: GLBRCE1_ACSH_Stat1_rep318_1


title: GLBRCE1_ACSH_Trans_rep327_1

source_name: GLBRCE1, ACSH, Trans