title: mock_6h_RLU_M0

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

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 one Agilent 4X44K Rhesus Macaque Gene Expression Array (Agilent-015421).

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505C) 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. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.

organism: Macaca mulatta

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

growth_protocol: Rhesus macaques (Macaca mulatta), aged from 2.5 to 3.5 years and ranging in weight from 2.8 to 4.4 kg, were individually  infected intratracheally with 10^7 EID50 of Anhui/2 in 4 ml of phosphate-buffered saline (PBS). At 6 h, 12 h, 1 d, 3 d, 6 d, and 14 d post-infection (p.i.), lung samples from two animals per time point were isolated for microarray analysis. Mock-infected animals were administered equal volumes of PBS and lung samples were isolated at 6hr.

extract_protocol: All samples processed simultaneously 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: Lung samples from the lower lobes of each animal were harvested and briefly rinse tissue in cold (4ºC) PBS. Following the RNAlater (Ambion) protocol, tissue was cut into small chunks (<0.5cm in any single dimension) and place immediately into a 10-20 volumes (w/v) (e.g. 100mg/ml) RNAlater. After a 4ºC incubation for overnight, samples were stored at -80ºC further processing. Lung 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.

tag: infected

value: none (mock)

tag: animal replicate number

tag: sample collection time post infection

tag: lobe of the lung where sample was taken from

value: right lower lobe


title: M4301-kidney-Resolved, 460974_A02

status: Public on Apr 11 2012

type: RNA

city: Nutley

first: Donavan

last: Cheng

state: NJ

address: 340 Kingsland Ave

department: Translational Research Sciences

country: USA

institute: Hoffmann-LaRoche

description:
460974_A02
mRNA

hyb_protocol: Woodchuck Gene Expression HX3 Microarrays were hybridized with 6.7 μg Cy3-labelled cDNA for 16-20 hours at 42ºC and were washed and dried according to the manufacturer’s instructions.

scan_protocol: Microarrays were scanned using a Roche NimbleGen MS200 Microarray Scanner at 2 μm pixel resolution. Features were extracted using NimbleScan Software.

data_processing: The gene expression data was normalized by the Robust Multichip Average (RMA) algorithm implemented in Partek Genomics Suite 6.5 (Partek, St. Louis MO).

molecule: total RNA

organism: Marmota monax

source_name: Woodchuck kidney, resolved

label_protocol: 10 μg of total RNA was reverse-transcribed using the SuperScript double-stranded cDNA synthesis kit (Invitrogen, Inc., Calsbad, CA). After precipitation, double-stranded cDNA was labelled with Cy3 by using the Roche NimbleGen One-color DNA Labelling Kit (Roche NimbleGen, Inc., Madison, WI).

extract_protocol: Total RNA was isolated using the QIAamp RNA Blood Mini Kit (Qiagen Inc., Valencia, CA).

tag: tissue

value: kidney

tag: whv infection status

value: resolved

tag: sample identifier


title: DLD1 GFP-3

city: Bunkyo-ku

first: Kiichiro

last: Tsuchiya

address: 1-5-45 Yushima

country: Japan

institute: Tokyo Medical and Dental University

hyb_protocol: Hybridization was carried out using the Gene Expression Hybridization Kit. 1.65 μg of cRNA samples were subjected to fragmentation (30 min at 60°C) and then hybridized on a 4×44K Agilent Whole Human Genome Oligo DNA Microarray Ver2.0 in a rotary oven (10 rpm at 65°C for 17 h).

scan_protocol: Slides were scanned with Agilent DNA Microarray Scanner.

data_processing: Gene expression values measured with the microarrays for DLD1_GFP (N=3) and DLD1_5SA-Atoh1 (N=3) were normalized with GeneSpring software by using the 75th percentile value.The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid:　026652_D_F_20110325) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Homo sapiens

source_name: GFP expressing DLD1 cells

label_protocol: RNA samples were labeled using Low Input Quick Amp Labeling Kit (Agilent Technologies). Labeling of 100 ng of total RNA was performed using Cyanine 3-CTP.

growth_protocol: Human sporadic colon cancer-derived DLD-1 cells were cultured in Dubecco’s modified Eagle medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using Trizol reagent. All samples showed RNA Integrity Numbers (RIN) more than 9.5.

treatment_protocol: Either GFP or 5SA-Atoh1 was expressed in DLD1 cells by lenti virus infection system.

tag: cell line

tag: genotype/variation

value: control


title: mock_6h_LLL_M0

value: left lower lobe


title: DLD1 GFP-1

value: sporadic colon cancer-derived DLD-1 cells


title: M4091-kidney-Uninfected, 460971_A01

description:
460971_A01
mRNA

source_name: Woodchuck kidney, uninfected

value: uninfected


title: Anhui-2-05_D6_RLU_M7

value: influenza (A/Anhui/2/2005)


title: Anhui-2-05_D3_LLL_M9


title: Anhui-2-05_D6_LLL_M10


title: Anhui-2-05_D14_LLL_M12


title: M7777-kidney-Chronic, 460973_A03

description:
460973_A03
mRNA

source_name: Woodchuck kidney, chronic

value: chronic


title: M4380-kidney-Resolved, 460961_A02

description:
460961_A02
mRNA


title: Anhui-2-05_D14_LLL_M11


title: M4171-kidney-Chronic, 460969_A03

description:
460969_A03
mRNA


title: Anhui-2-05_6h_RLL_M2


title: Anhui-2-05_D3_LLL_M8


title: M4075-kidney-Uninfected, 460949_A03

description:
460949_A03
mRNA


title: M4091-kidney-Uninfected, 460941_A02

description:
460941_A02
mRNA


title: M4374-kidney-Resolved, 460957_A01

description:
460957_A01
mRNA


title: Anhui-2-05_12h_LLL_M3_3


title: Anhui-2-05_6h_RLL_M1


title: M7780-kidney-Chronic, 460768_A01

description:
460768_A01
mRNA


title: M4301-kidney-Resolved, 460813_A03

description:
460813_A03
mRNA


title: M4046-kidney-Uninfected, 460892_A01

description:
460892_A01
mRNA


title: M4378-kidney-Resolved, 460768_A03

description:
460768_A03
mRNA


title: Anhui-2-05_24h_LLL_M6


title: Anhui-2-05_12h_RLL_M4


title: M4765-liver-Chronic, 461125_A03

description:
461125_A03
mRNA

source_name: Woodchuck liver, chronic

extract_protocol: Total RNA was isolated from woodchuck liver tissues using the QIAamp RNA Blood Mini Kit (Qiagen Inc., Valencia, CA).

value: liver


title: M5616-liver-Chronic, 461116_A01

description:
461116_A01
mRNA


title: M7777-liver-Chronic, 461119_A02

description:
461119_A02
mRNA


title: M4301-liver-Resolved, 461119_A01

description:
461119_A01
mRNA

source_name: Woodchuck liver, resolved


title: M4380-liver-Resolved, 461125_A01

description:
461125_A01
mRNA


title: Anhui-2-05_24h_LLL_M5


title: M4380-kidney-Resolved, 460801_A01

description:
460801_A01
mRNA


title: M4046-kidney-Uninfected, 460927_A02

description:
460927_A02
mRNA


title: M4727-liver-Chronic, 461118_A03

description:
461118_A03
mRNA


title: M4091-liver-Uninfected, 461116_A03

description:
461116_A03
mRNA

source_name: Woodchuck liver, uninfected


title: M4728-liver-Chronic, 461120_A02

description:
461120_A02
mRNA


title: M5415-liver-Resolved, 461116_A02

description:
461116_A02
mRNA


title: M4075-liver-Uninfected, 461114_A02

description:
461114_A02
mRNA


title: M9202-liver-Uninfected, 461112_A01

description:
461112_A01
mRNA


title: M6131-liver-Resolved, 461115_A01

description:
461115_A01
mRNA


title: M3349-liver-Uninfected, 461109_A03

description:
461109_A03
mRNA


title: M3134-liver-Chronic, 461113_A03

description:
461113_A03
mRNA


title: Secretory phase [90-09]

city: CLAYTON

first: HONG

last: NGUYEN

state: VIC

address: 27-31 Wright St

country: Australia

institute: Monash Institute of Medical Research

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Illumina BeadStudio scanner software was used to convert signal. Data analysis and normalisation were performed using Partek Genome Suite 6.5 using robust multichip average algorithm and analysis of variance.
Log2 transformation was performed. Gene list was filterd using p < 0.05 and fold change of > 2. Fold change refers to the level of change above or below the actual value for Post-M samples

label: biotin

source_name: Human endometrium

label_protocol: Biotinylated cRNA of all samples were prepared using Ambion total prep RNA amplification kit for Illumina arrays

extract_protocol: Total RNA was extracted using Ambion RNAqueous Micro kit, followed by DNase treatment using DNase inactivation kit, according to the manufacturer's instructions. RNA quality was assessed using Nanodrop ND1000 Spectrophotometer and Agilent Bioanalyser 2100

value: Full-thickness Pre-menopausal

tag: phase

value: Secretory phase


title: M3353-liver-Uninfected, 461106_A03

description:
461106_A03
mRNA


title: Post-menopausal [54-10]

value: Post-menopausal


title: Secretory phase [88-09]


title: Secretory phase [122-09]


title: M5485-liver-Resolved, 461107_A01

description:
461107_A01
mRNA


title: M5445-liver-Resolved, 461106_A01

description:
461106_A01
mRNA


title: Proliferative phase [109-09]

value: Proliferative phase


title: Proliferative phase [96-09]


title: Secretory phase [115-09]


title: M5415-liver-Resolved, 461103_A03

description:
461103_A03
mRNA


title: Post-menopausal [98-09]


title: M5376-liver-Chronic, 461108_A02

description:
461108_A02
mRNA


title: M4765-liver-Chronic, 461101_A01

description:
461101_A01
mRNA


title: M5376-liver-Chronic, 461105_A01

description:
461105_A01
mRNA


title: Proliferative phase [120-09]


title: Post-menopausal [29-10]


title: M3353-liver-Uninfected, 461105_A02

description:
461105_A02
mRNA


title: DLD1 5SA-Atoh1-2

source_name: 5SA-Atoh1 expressing DLD1 cells

value: Mutated Atoh1 (5SA-Atoh1)


title: M4091-liver-Uninfected, 461106_A02

description:
461106_A02
mRNA


title: M4374-liver-Resolved, 461101_A03

description:
461101_A03
mRNA


title: M4191-kidney-Chronic, 460992_A02

description:
460992_A02
mRNA


title: Proliferative phase [95-09]


title: M5376-liver-Chronic, 461099_A03

description:
461099_A03
mRNA


title: M4727-liver-Chronic, 461100_A02

description:
461100_A02
mRNA


title: WB_Normal19 [validation]

city: Vancouver

first: Bruce

middle: Maxwell

last: McManus

state: BC

address: 1081 Burrard Street

department: UBC James Hogg Research Centre

country: Canada

institute: PROOF Centre of Excellence

description:
control
Raw data file: L769.CEL.  Linked as supplementary file on Series record.

hyb_protocol: Following fragmentation, the cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 array. Equilibrate probe array to room temperature immediately before use.  Then, heat the hybridization cocktail to 99°C for 5 minutes in heatblock.  Next, wet the array by filling it through one of the septa with appropriate volume of 1X MES Hybridization Buffer using a micropipettor and appropriate tips. Last, incubate the probe array for 10 minutes at 45°C in the hybridization oven with rotation.

scan_protocol: The Probe Array is scanned using the Affymetrix System.  The scanner is controlled by the GeneChip software.  The probe array is scanned after the wash protocols are complete

data_processing: Data import, normalization and statistical analysis were performed using the Partek Genomics Suite, version 6.5 (Partek, St Louis, MI).  RMA background correction and quantile normalization were applied followed by log2-transformation.

source_name: healthy volunteer whole blood (WB)

label_protocol: Biotin-labeled cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA.

extract_protocol: Isolation begins with a centrifugation step to pellet nucleic acids in the PAXgene Blood RNA Tube. The pellet is washed, resuspended, and incubated in optimized buffers containing Proteinase K to digest proteins. A second centrifugation step is carried out to remove residual cell debris, and the supernatant is transferred to a fresh microcentrifuge tube. Ethanol is added to adjust binding conditions, and the lysate is applied to a PAXgene RNA spin column. During a brief centrifugation, RNA is selectively bound to the silica-gel membrane of the spin column as contaminants pass through. Remaining contaminants are removed in three wash steps, and pure RNA is then eluted in Buffer BR5. Generally, DNase digestion is not required for RNA purified with the PAXgene Blood RNA Kit, since PAXgene silica-gel–membrane technology efficiently removes most of the DNA without DNase treatment. However, further DNA removal is recommended for RNA applications that are sensitive to DNA contamination. In these cases, residual DNA can be removed either by using the RNase-Free DNase Set for on-column DNase digestion, or by treating the eluted RNA with DNase.

tag: disease state

value: healthy control

value: whole blood (WB)

tag: Sex

value: M

tag: race

value: Caucasian


title: WB_Normal20 [validation]

description:
control
Raw data file: L770.CEL.  Linked as supplementary file on Series record.


title: M4191-liver-Chronic, 461099_A01

description:
461099_A01
mRNA


title: WB_Normal16 [validation]

description:
control
Raw data file: L473.CEL.  Linked as supplementary file on Series record.

value: F

value: Asian Oriental


title: M6109-liver-Resolved, 461099_A02

description:
461099_A02
mRNA

value: resolved


title: M4046-liver-Uninfected, 461098_A02

description:
461098_A02
mRNA


title: M5429-liver-Resolved, 461097_A02

description:
461097_A02
mRNA


title: M4728-liver-Chronic, 461097_A03

description:
461097_A03
mRNA


title: M5429-liver-Resolved, 461098_A03

description:
461098_A03
mRNA


title: WB_Normal15 [validation]

description:
control
Raw data file: L765.CEL.  Linked as supplementary file on Series record.


title: WB_Normal17 [validation]

description:
control
Raw data file: L766.CEL.  Linked as supplementary file on Series record.


title: WB_Normal14 [validation]

description:
control
Raw data file: L764.CEL.  Linked as supplementary file on Series record.

value: Other/multiracial


title: WB_Normal12 [validation]

description:
control
Raw data file: L472.CEL.  Linked as supplementary file on Series record.


title: M4378-liver-Resolved, 461061_A01

description:
461061_A01
mRNA


title: WB_Normal18 [validation]

description:
control
Raw data file: L767.CEL.  Linked as supplementary file on Series record.


title: WB_Normal13 [validation]

description:
control
Raw data file: L763.CEL.  Linked as supplementary file on Series record.


title: M7780-liver-Chronic, 461097_A01

description:
461097_A01
mRNA


title: M5485-liver-Resolved, 461060_A01

description:
461060_A01
mRNA


title: M4378-kidney-Resolved, 460829_A02

description:
460829_A02
mRNA

value: kidney


title: M4765-liver-Chronic, 461061_A02

description:
461061_A02
mRNA


title: WB_Normal9 [validation]

description:
control
Raw data file: L470.CEL.  Linked as supplementary file on Series record.


title: M3349-liver-Uninfected, 461060_A03

description:
461060_A03
mRNA

value: uninfected


title: M4374-kidney-Resolved, 460802_A03

description:
460802_A03
mRNA


title: WB_Normal8 [validation]

description:
control
Raw data file: L469.CEL.  Linked as supplementary file on Series record.


title: WB_Normal11 [validation]

description:
control
Raw data file: L471.CEL.  Linked as supplementary file on Series record.


title: WB_Normal10 [validation]

description:
control
Raw data file: L762.CEL.  Linked as supplementary file on Series record.


title: M3134-liver-Chronic, 461059_A03

description:
461059_A03
mRNA

value: chronic


title: WB_Normal7 [validation]

description:
control
Raw data file: L468.CEL.  Linked as supplementary file on Series record.


title: M4324-liver-Chronic, 461059_A02

description:
461059_A02
mRNA

value: liver


title: WB_Normal6 [validation]

description:
control
Raw data file: L761.CEL.  Linked as supplementary file on Series record.


title: M4388-liver-Chronic, 461059_A01

description:
461059_A01
mRNA


title: WB_Normal4 [validation]

description:
control
Raw data file: L771.CEL.  Linked as supplementary file on Series record.


title: WB_Normal1 [validation]

description:
control
Raw data file: L464.CEL.  Linked as supplementary file on Series record.


title: M4374-liver-Resolved, 461058_A02

description:
461058_A02
mRNA


title: WB_Normal2 [validation]

description:
control
Raw data file: L465.CEL.  Linked as supplementary file on Series record.


title: WB_Normal20 [discovery]

description:
control
Raw data file: L770.CEL.  Linked as supplementary file on Series record.


title: WB_Normal3 [validation]

description:
control
Raw data file: L760.CEL.  Linked as supplementary file on Series record.


title: WB_Normal5 [validation]

description:
control
Raw data file: L772.CEL.  Linked as supplementary file on Series record.


title: M4790-liver-Chronic, 461043_A03

description:
461043_A03
mRNA


title: M4378-liver-Resolved, 461058_A03

description:
461058_A03
mRNA


title: WB_Normal19 [discovery]

description:
control
Raw data file: L769.CEL.  Linked as supplementary file on Series record.


title: M3350-liver-Uninfected, 461043_A01

description:
461043_A01
mRNA


title: M4728-liver-Chronic, 461043_A02

description:
461043_A02
mRNA


title: M6023-liver-Uninfected, 461036_A01

description:
461036_A01
mRNA


title: M4171-liver-Chronic, 461036_A02

description:
461036_A02
mRNA


title: M4765-liver-Chronic, 461036_A03

description:
461036_A03
mRNA


title: WB_Normal15 [discovery]

description:
control
Raw data file: L765.CEL.  Linked as supplementary file on Series record.


title: WB_Normal13 [discovery]


title: WB_Normal14 [discovery]

description:
control
Raw data file: L764.CEL.  Linked as supplementary file on Series record.


title: M5376-liver-Chronic, 460989_A02

description:
460989_A02
mRNA


title: WB_Normal17 [discovery]

description:
control
Raw data file: L766.CEL.  Linked as supplementary file on Series record.


title: WB_Normal16 [discovery]

description:
control
Raw data file: L473.CEL.  Linked as supplementary file on Series record.


title: WB_Normal18 [discovery]

description:
control
Raw data file: L767.CEL.  Linked as supplementary file on Series record.


title: M4046-liver-Uninfected, 461034_A01

description:
461034_A01
mRNA


title: WB_Normal12 [discovery]

description:
control
Raw data file: L472.CEL.  Linked as supplementary file on Series record.


title: M3134-liver-Chronic, 460989_A01

description:
460989_A01
mRNA


title: WB_Normal11 [discovery]

description:
control
Raw data file: L471.CEL.  Linked as supplementary file on Series record.


title: M6023-liver-Uninfected, 461034_A03

description:
461034_A03
mRNA


title: M4790-liver-Chronic, 460990_A02

description:
460990_A02
mRNA


title: WB_Normal10 [discovery]

description:
control
Raw data file: L762.CEL.  Linked as supplementary file on Series record.


title: M3134-liver-Chronic, 460987_A01

description:
460987_A01
mRNA


title: WB_Normal8 [discovery]

description:
control
Raw data file: L469.CEL.  Linked as supplementary file on Series record.


title: WB_Normal9 [discovery]

description:
control
Raw data file: L470.CEL.  Linked as supplementary file on Series record.


title: mESCs 28 hours after differentiation start

city: Berlin

first: Nils

last: Blüthgen

address: Chariteplatz 1

department: Institute of Pathology

country: Germany

institute: Charite Universitätsmedizin Berlin

hyb_protocol: Affymetrix GeneChip Mouse Exon 1.0 ST microarrays were hybridized with 4.7 µg of labelled DNA

scan_protocol: Washes, staining and scan of microarrays were conducted using an Affymetrix GCS3000 platform

data_processing:
Microarrays were normalized using RMA (Robust Multi-array Analysis) as available in the bioconductor affy package (http://www.bioconductor.org), and annotated using the xmapcore database for Ensembl mouse version 62 (http://annmap.picr.man.ac.uk/download/). For each gene the expression is calculated by averaging over probesets that detect the maximum number of transcripts per gene
probe group file: MoEx-1_0-st-v1.r2.pgf

organism: Mus musculus

label_protocol: Affymetrix mouse Exon 1.0 ST arrays were hybridised according to Affymetrix's recommendations using the Ambion WT protocol (Life technologies) and Affymetrix labelling and hybridization kits. 100ng of total RNA (RIN=10) were processed and amplified in parallel with an external Universal Mouse Reference RNA (Agielent, #740100) to control robustness of the data. The mean yield of labelled DNA was   7.2 µg (min: 6.4µg; max: 7.7µg).

growth_protocol: Pgk12.1 ES cells were adapted, during passages 21-26, to 2i culture conditions, consisting of N2B27 medium (50% DMEM/F12 (Invitrogen), 50% Neurobasal medium (Invitrogen), NDiff supplement (Millipore), B27 supplement (Invitrogen), 2mM Glutamine, 100 µM β-Mercaptoethanol), supplemented with 3 µM Gsk3 inhibitor CT-99021, 1 µM Mek1 inhibitor PD-0325901 and 100U/ml LIF (Millipore).

extract_protocol: 200 µl of Chloroform was added and after 15 min centrifugation (12000xg, 4°C) the aqueous phase was mixed with 700 µl 70% ethanol and applied to a Silica column (Qiagen RNAeasy Mini kit). RNA was then purified according to the instruction of the manufacturer, including on-column DNAse digestion.

treatment_protocol: For EpiSC differentiation9 8*10^5 cells per well were seeded in a Fibronectin coated (10 µg/ml, Millipore) 6-well plate in differentiation medium (N2B27 medium, 20ng/ml Activin A, 12 ng/ml Fgf-basic, R&D), subsequently the medium was changed daily. At 6, 12, 18, 24, 28, 32, 36, 40, 44, 48, 52, 56, 60, 66, 72 and 84 hours of differentiation, cells were lysed by direct addition of 1 ml Trizol to the wells

tag: hours


title: M4171-liver-Chronic, 460988_A01

description:
460988_A01
mRNA


title: M4765-liver-Chronic, 460979_A03

description:
460979_A03
mRNA


title: M5445-liver-Resolved, 460987_A03

description:
460987_A03
mRNA


title: M6109-liver-Resolved, 460977_A03

description:
460977_A03
mRNA


title: M4324-liver-Chronic, 460982_A03

description:
460982_A03
mRNA


title: M5485-liver-Resolved, 460978_A03

description:
460978_A03
mRNA


title: M3350-liver-Uninfected, 460978_A02

description:
460978_A02
mRNA


title: M4728-liver-Chronic, 460979_A02

description:
460979_A02
mRNA


title: WB_Normal7 [discovery]

description:
control
Raw data file: L468.CEL.  Linked as supplementary file on Series record.


title: WB_Normal4 [discovery]

description:
control
Raw data file: L771.CEL.  Linked as supplementary file on Series record.


title: M9202-liver-Uninfected, 460975_A01

description:
460975_A01
mRNA


title: M4380-liver-Resolved, 460977_A01

description:
460977_A01
mRNA


title: M5616-liver-Chronic, 460971_A03

description:
460971_A03
mRNA


title: WB_Normal1 [discovery]

description:
control
Raw data file: L464.CEL.  Linked as supplementary file on Series record.


title: M6009-liver-Uninfected, 460970_A03

description:
460970_A03
mRNA


title: WB_Normal2 [discovery]

description:
control
Raw data file: L465.CEL.  Linked as supplementary file on Series record.


title: WB_Normal5 [discovery]


title: WB_Normal6 [discovery]

description:
control
Raw data file: L761.CEL.  Linked as supplementary file on Series record.


title: WB_Uremia74 [validation]

description: validation

source_name: pre-transplant uremic whole blood (WB)

value: uremia

value: CAPD


title: WB_Uremia75 [validation]

description: validation

value: Conventional Haemo


title: WB_Normal3 [discovery]

description:
control
Raw data file: L760.CEL.  Linked as supplementary file on Series record.


title: M7777-liver-Chronic, 460970_A01

description:
460970_A01
mRNA


title: M5616-liver-Chronic, 460968_A03

description:
460968_A03
mRNA


title: WB_Uremia72 [validation]

description: validation


title: M4790-liver-Chronic, 460968_A01

description:
460968_A01
mRNA


title: M7777-liver-Chronic, 460967_A01

description:
460967_A01
mRNA


title: M4171-liver-Chronic, 460961_A03

description:
460961_A03
mRNA


title: M6023-liver-Uninfected, 460967_A03

description:
460967_A03
mRNA


title: WB_Uremia67 [discovery]

description: discovery

value: CCPD (Automated PD)


title: WB_Uremia70 [discovery]

description: discovery

value: Pre Dialysis


title: WB_Uremia69 [discovery]

description: discovery


title: WB_Uremia73 [validation]

description: validation

value: Home Haemo


title: M6130-liver-Resolved, 460967_A02

description:
460967_A02
mRNA


title: M6131-liver-Resolved, 460971_A02

description:
460971_A02
mRNA


title: WB_Uremia71 [validation]

description: validation

value: whole blood (WB)


title: M6130-liver-Resolved, 460957_A03

description:
460957_A03
mRNA


title: WB_Uremia68 [discovery]

description: discovery

value: M


title: M4790-liver-Chronic, 460956_A02

description:
460956_A02
mRNA


title: M6109-liver-Resolved, 460951_A01

description:
460951_A01
mRNA


title: WB_Uremia66 [discovery]

description: discovery

value: Caucasian


title: WB_Uremia63 [discovery]

description: discovery


title: WB_Uremia65 [discovery]

description: discovery

value: F


title: WB_Uremia62 [discovery]

description: discovery


title: M6130-liver-Resolved, 460949_A01

description:
460949_A01
mRNA


title: M5376-liver-Chronic, 460950_A01

description:
460950_A01
mRNA


title: WB_Uremia64 [discovery]

description: discovery


title: M4046-liver-Uninfected, 460956_A01

description:
460956_A01
mRNA


title: M4301-liver-Resolved, 460944_A03

description:
460944_A03
mRNA


title: M5429-liver-Resolved, 460950_A03

description:
460950_A03
mRNA


title: M7780-liver-Chronic, 460948_A03

description:
460948_A03
mRNA


title: MCF-7, Insx24h-2

city: Nashville

first: Todd

middle: W

last: Miller

state: TN

address: 2220 Pierce Ave, 777 PRB

department: Medicine

institute: Vanderbilt Univ

description: Gene expression data from cells treated with serum-free medium x 24 hrs, then with 10 ug/mL insulin x 24 hrs

hyb_protocol: 15 ug biotinylated cRNA was fragmented and hybridizied to an Affymetrix Genechip Human Genome Plus 2.0-PM array

scan_protocol: Hybridized cRNA was detected using streptavidin coupled to phycoerythrin. Genechips were scanned using Genechip Scanner 3000 7G Plus 2 and Genechip Operating System (Affymetrix)

data_processing: Default values were used to grid images (.DAT) and generate .CEL and .CHP files.

source_name: MCF-7 cells

label_protocol: GeneChip One-Cycle Target Labeling and Control reagents kit (Affymetrix)

growth_protocol: MCF-7 cells are maintained in IMEM + 10% FBS.

extract_protocol: Trizol extraction followed by Qiagen RNeasy column clean-up with on-column DNase digestion

treatment_protocol: Cells were seeded in 100 mm dishes in triplicate. The following day, cells were washed with PBS, and treated with serum-free IMEM. Twenty-four hrs later, cells were treated +/- 10 ug/mL insulin. RNA was harvested after 4 or 24 hrs of insulin stimulation.

tag: treatment


title: MCF-7, Insx24h-3

value: serum-free medium x 24 hrs, then with 10 ug/mL insulin x 24 hrs


title: MCF-7, Insx4h-3

description: Gene expression data from cells treated with serum-free medium x 44 hrs, then with 10 ug/mL insulin x 4 hrs


title: M4191-liver-Chronic, 460949_A02

description:
460949_A02
mRNA


title: WB_Uremia59 [discovery]

description: discovery

value: Black


title: WB_Uremia58 [discovery]

description: discovery


title: WB_Uremia57 [discovery]

description: discovery

value: North American Indian


title: WB_Uremia60 [discovery]

description: discovery


title: MCF-7, Insx4h-1

value: serum-free medium x 44 hrs, then with 10 ug/mL insulin x 4 hrs


title: MCF-7, Insx24h-1


title: M4727-liver-Chronic, 460941_A03

description:
460941_A03
mRNA


title: WB_Uremia56 [discovery]

description: discovery


title: M5616-liver-Chronic, 460944_A02

description:
460944_A02
mRNA


title: M4727-liver-Chronic, 460948_A01

description:
460948_A01
mRNA


title: MCF-7, Insx4h-2


title: M9202-liver-Uninfected, 460941_A01

description:
460941_A01
mRNA

value: uninfected


title: M6009-liver-Uninfected, 460935_A01

description:
460935_A01
mRNA


title: WB_Uremia54 [discovery]

description: discovery


title: WB_Uremia53 [discovery]

description: discovery


title: WB_Uremia55 [discovery]

description: discovery


title: M5616-liver-Chronic, 460935_A03

description:
460935_A03
mRNA

value: chronic


title: M9189-liver-Uninfected, 460935_A02

description:
460935_A02
mRNA

value: liver


title: M4301-liver-Resolved, 460928_A01

description:
460928_A01
mRNA

value: resolved


title: M4191-liver-Chronic, 460928_A02

description:
460928_A02
mRNA


title: M4388-liver-Chronic, 460929_A01

description:
460929_A01
mRNA


title: MCF-7, control-3

description: Gene expression data from cells treated with serum-free medium x 48 hrs

value: serum-free medium x 48 hrs


title: WB_Uremia52 [discovery]

description: discovery

value: uremia

value: Conventional Haemo


title: M4727-liver-Chronic, 460894_A03

description:
460894_A03
mRNA


title: M4378-liver-Resolved, 460894_A02

description:
460894_A02
mRNA


title: M5415-liver-Resolved, 460928_A03

description:
460928_A03
mRNA


title: MCF-7, control-2


title: MCF-7, control-1


title: M9189-liver-Uninfected, 460929_A02

description:
460929_A02
mRNA


title: M6131-liver-Resolved, 460927_A01

description:
460927_A01
mRNA


title: M3350-liver-Uninfected, 460892_A03

description:
460892_A03
mRNA


title: WB_Uremia51 [discovery]

description: discovery

value: CAPD


title: M4374-liver-Resolved, 460891_A03

description:
460891_A03
mRNA


title: M5445-liver-Resolved, 460891_A02

description:
460891_A02
mRNA


title: M4380-liver-Resolved, 460872_A03

description:
460872_A03
mRNA


title: WB_Uremia48 [discovery]

description: discovery

value: PD Combined with Haemo


title: WB_Uremia50 [discovery]

description: discovery

value: whole blood (WB)

value: Asian Filipino


title: M4790-liver-Chronic, 460872_A01

description:
460872_A01
mRNA


title: M9189-liver-Uninfected, 460872_A02

description:
460872_A02
mRNA


title: M4075-liver-Uninfected, 460891_A01

description:
460891_A01
mRNA


title: WB_Uremia49 [discovery]

description: discovery

value: Caucasian


title: M4727-liver-Chronic, 460868_A02

description:
460868_A02
mRNA


title: WB_Uremia46 [discovery]

description: discovery

value: F


title: M4790-liver-Chronic, 460829_A03

description:
460829_A03
mRNA


title: WB_Uremia45 [discovery]

description: discovery

value: CCPD (Automated PD)


title: M5616-liver-Chronic, 460828_A02

description:
460828_A02
mRNA


title: M4091-liver-Uninfected, 460830_A02

description:
460830_A02
mRNA


title: M6009-liver-Uninfected, 460802_A02

description:
460802_A02
mRNA


title: M4765-liver-Chronic, 460828_A01

description:
460828_A01
mRNA


title: M4728-liver-Chronic, 460868_A01

description:
460868_A01
mRNA


title: WB_Uremia44 [discovery]

description: discovery

value: M

value: Pre Dialysis


title: M7780-liver-Chronic, 460808_A03

description:
460808_A03
mRNA


title: M4388-liver-Chronic, 460868_A03

description:
460868_A03
mRNA


title: WB_Uremia43 [discovery]

description: discovery

value: Asian Indian


title: M3349-liver-Uninfected, 460808_A02

description:
460808_A02
mRNA

value: uninfected


title: M4728-liver-Chronic, 460830_A03

description:
460830_A03
mRNA

value: chronic


title: WB_Uremia47 [validation]

description: validation


title: M4324-liver-Chronic, 460802_A01

description:
460802_A01
mRNA

value: liver


title: M5376-liver-Chronic, 460781_A02

description:
460781_A02
mRNA


title: WB_Uremia41 [discovery]

description: discovery

value: North American Indian


title: M4075-liver-Uninfected, 460781_A03

description:
460781_A03
mRNA


title: M3134-liver-Chronic, 460801_A03

description:
460801_A03
mRNA


title: M3353-liver-Uninfected, 460771_A02

description:
460771_A02
mRNA


title: M3134-liver-Chronic, 460771_A03

description:
460771_A03
mRNA


title: WB_Uremia61 [discovery]

description: discovery

value: Asian Oriental

value: Slow Nocturnal Haemo


title: WB_Uremia37 [discovery]

description: discovery

value: uremia


title: WB_Uremia38 [discovery]

description: discovery


title: WB_Uremia35 [discovery]

description: discovery


title: WB_Uremia40 [discovery]

description: discovery

value: Conventional Haemo


title: WB_Uremia34 [discovery]

description: discovery


title: EAC_44T

city: Ann Arbor

first: David

middle: G

last: Beer

state: Michigan

address: 1500 E Medical Center Dr. CCGC 6431

department: Surgery

institute: University of Michigan Medical School

description: Gene expression data from esophageal adenocarcinoma.

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Data was analyzed using the affy Bioconductor package implemented in the R-statistical environment. RMA was used to normalize the data and fit log2 transformed expression values.

source_name: Esophagectomy specimen with no preoperative chemoradiation therapy.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNAs from primary tissues were isolated using Trizol reagent from Invitrogen and the RNeasy mini kit from QIAGEN following the manufacturers' instructions.  Total RNA was isolated using the RNeasy mini kit from Qiagen, following the manufacturer’s instructions.

value: Esophageal adenocarcinoma

tag: age

tag: gender

tag: ethnicity

tag: Stage

value: IIA

value: esophagectomy specimen


title: BE_43B

description: Gene expression data from Barrett’s esophageal tissues.

value: Barrett’s esophageal tissues

value: Caucasian


title: BE_42B


title: BE_36B

value: F

value: Unknown


title: WB_Uremia36 [discovery]

description: discovery

value: whole blood (WB)

value: M

value: CAPD


title: WB_Uremia39 [discovery]

description: discovery


title: BE_38B


title: EAC_33T

value: III


title: BE_39B


title: BE_45B


title: BE_34B


title: WB_Uremia33 [discovery]

description: discovery


title: WB_Uremia42 [discovery]

description: discovery


title: BE_40B


title: EAC_37T


title: BE_46B


title: BE_31B


title: EAC_30T

value: I


title: BE_32B


title: EAC_41T


title: BE_35B


title: WB_Uremia31 [discovery]

description: discovery


title: WB_Uremia32 [discovery]

description: discovery


title: BE_28B


title: EAC_27T


title: WB_Uremia30 [discovery]

description: discovery

value: North American Indian


title: EAC_29T


title: WB_Uremia29 [discovery]

description: discovery


title: BE_26B


title: BE_23B


title: BE_24B


title: EAC_20T

value: IV


title: BE_21B


title: EAC_17T


title: BE_15B


title: BE_16B


title: BE_14B


title: WB_Uremia25 [discovery]

description: discovery

value: Pre Dialysis


title: WB_Uremia27 [discovery]

description: discovery

value: uremia


title: WB_Uremia24 [validation]

description: validation


title: EAC_19T


title: BE_12B


title: BE_25B


title: BE_22B


title: EAC_13T


title: WB_Uremia26 [discovery]

description: discovery


title: EAC_11T


title: WB_Uremia23 [validation]

description: validation

value: Asian Oriental

value: Conventional Haemo


title: WB_Uremia28 [discovery]

description: discovery

value: Asian Indian


title: BE_10B

value: esophagectomy specimen


title: BE_18B

value: Barrett’s esophageal tissues


title: BE_07B

value: Caucasian


title: BE_08B


title: BE_05B

value: F


title: WB_Uremia21 [validation]

description: validation

value: Slow Nocturnal Haemo


title: BE_09B


title: WB_Uremia22 [validation]

description: validation

value: whole blood (WB)


title: EAC_04T

value: Esophageal adenocarcinoma

value: M


title: EAC_67T

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human HG-U133A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data was analyzed using the affy and limma Bioconductor package implemented in the R-statistical environment. RMA was used to normalize the data and fit log2 transformed expression values.

value: III


title: BE_03B


title: WB_Uremia20 [discovery]

description: discovery

value: CAPD


title: BE_01B


title: EAC_64T

value: Unknown

value: IIB


title: EAC_65T


title: EAC_63T


title: EAC_06T


title: EAC_66T

value: IV


title: EAC_61T


title: WB_Uremia18 [discovery]

description: discovery

value: uremia


title: WB_Uremia17 [discovery]

description: discovery

value: Asian Filipino


title: EAC_62T


title: WB_Uremia16 [discovery]

description: discovery

value: CCPD (Automated PD)


title: EAC_60T

value: IIA


title: WB_Uremia19 [discovery]

description: discovery

value: Conventional Haemo


title: WB_Uremia13 [discovery]

description: discovery

value: Pre Dialysis


title: WB_Uremia14 [discovery]

description: discovery

value: Caucasian


title: EAC_02T

value: esophagectomy specimen


title: EAC_68T

value: F


title: EAC_59T


title: EAC_54T


title: EAC_58T


title: EAC_57T

value: I


title: EAC_53T

value: Esophageal adenocarcinoma


title: EAC_56T

value: M


title: EAC_49T

value: III


title: WB_Uremia10 [validation]

description: validation

value: whole blood (WB)


title: EAC_51T


title: EAC_52T


title: WB_Uremia12 [discovery]

description: discovery

value: Asian Indian


title: WB_Uremia8 [discovery]

description: discovery

value: North American Indian

value: CAPD


title: WB_Uremia11 [validation]

description: validation

value: uremia


title: EAC_50T

value: Unknown


title: WB_Uremia9 [discovery]

description: discovery


title: EAC_55T


title: WB_Uremia6 [discovery]

description: discovery


title: EAC_48T

value: IIB


title: WB_Uremia7 [discovery]

description: discovery


title: Testis CREMKO 0h batch 2 [TeKOh00.12]

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

description: Gene expression data from testis Crem-/- sample taken at 0h

hyb_protocol: 100 ng of total RNA was used for hybridization of Affymetrix Gene Chip Mouse 1.0 ST Arrays according to manufacturer’s instructions (Genechip® Whole Transcript (wt) Sense Ttarget Labeling Assay Manual – P/N 701880 Rev 4). Labled samples were injected into Affymetrix arrays and hybridized at 45°C and 60 rpm for 16 h in an Affymetrix Hybridization Oven. Arrays were stained and washed in the Affymetrix GeneChip Fluidic Station 450.

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

data_processing:
GeneChip data was processed and analyzed using R/Bioconductor packages. Data were summarized (w.r.t. core meta-probeset annotations and AFFX control probes, probes grouped to the level of transcripts) and quantile-normalized (background computed from antigenomic probes) using RMA algorithm from XPS package.
probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.r4.mps

source_name: Whole testis RNA from Crem-/- mouse #143 at 0h

label_protocol: Total RNA was used to synthesize double-stranded cDNA with random hexamer primers tagged with a T7 promoter sequence. The double-stranded cDNA was subsequently used as a template and amplified by T7 RNA polymerase producing cRNA. In the second cycle of cDNA synthesis, random hexamers were used to prime reverse transcription of the cRNA and dUTP was incorporated to produce single-stranded DNA. This single-stranded DNA sample were then treated with a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) that specifically recognized the unnatural dUTP residues and broke the DNA strand. DNA was labeled by terminal eoxynucleotidyl transferase (TdT) with the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.

growth_protocol: WT and Crem-/- animals of the mixed strain (129Pas x C57Bl/J ) [Nantel F, Monaco L, Foulkes NS, Masquilier D, LeMeur M, Henriksén K, Dierich A, Parvinen M, Sassone-Corsi P: Spermiogenesis deficiency and germ-cell apoptosis in CREM-mutant mice. Nature 1996, 380:159-162] were maintained in a temperature and humidity controlled room under a 12:12 h light:dark cycle (light on at 7:00 am, light off at 7:00 pm) with free access to food (Harland Tekland 2916) and water.

extract_protocol: 8 weeks old mice were sacrificed with cervical dislocation at 7 am (0h circadian time). Tissue samples from testis were excised, snap frozen in liquid nitrogen and stored at -80°C for subsequent analysis. Samples were first pulverized and then homogenized in 1000 μl of TRI Reagent (Sigma) and total RNA was isolated according to the manufacturer’s instructions. RNA quantity and quality were assessed with NanoDrop and Agilent 2100 Bioanalyzer instruments, all samples isolated fulfilled the minimum requirements (OD260/280 and OD230/280 > 1.8) for microarray hybridization.

treatment_protocol: Mice were not treated.

value: Testis

tag: strain

value: 129Pas x C57Bl/J

value: CREMKO

tag: animal

tag: time

tag: batch


title: Testis WT 0h batch 4 [TeWTh00.25]

description: Gene expression data from testis WT sample taken at 0h

source_name: Whole testis RNA from WT mouse #145 at 0h

tag: tissue

value: WT


title: Testis CREMKO 0h batch 4 [TeKOh00.29]

source_name: Whole testis RNA from Crem-/- mouse #77 at 0h


title: WB_Uremia5 [discovery]

description: discovery

value: CCPD (Automated PD)


title: EAC_47T

value: Caucasian

value: esophagectomy specimen


title: WB_Uremia3 [discovery]

description: discovery


title: Testis WT 0h batch 3 [TeWTh00.20]

source_name: Whole testis RNA from WT mouse #78 at 0h


title: Testis WT 0h batch 2 [TeWTh00.11]

source_name: Whole testis RNA from WT mouse #146 at 0h


title: Testis CREMKO 0h batch 4 [TeKOh00.28]

source_name: Whole testis RNA from Crem-/- mouse #76 at 0h


title: Testis WT 0h batch 2 [TeWTh00.13]

source_name: Whole testis RNA from WT mouse #147 at 0h


title: WB_Uremia1 [discovery]

description: discovery

value: F

value: Conventional Haemo


title: WB_Uremia2 [discovery]

description: discovery

value: M

value: Pre Dialysis


title: rabbit_day4

city: Lynchburg

middle: S

last: Price

state: VA

address: 1971 University Blvd.

department: Biology & Chemistry

institute: Liberty University

description: raw data files: slide3-day4.gpr available as Series Suppelementary files

hyb_protocol: Hybridization was performed at the Duke University Microarray Facility following the Hybridization protocol (http://www.genome.duke.edu/cores/microarray/).

scan_protocol: Slides were scanned at the Duke University Microarray Facility using an Axon Genepix 4000B scanner (http://www.genome.duke.edu/cores/microarray/).

data_processing: Data was analyzed using JMP genomics (SAS institute, Cary NC) and initial background subtraction was performed. Data were normalized using the Loess Normalization process in JMP.

organism: Cryptococcus neoformans

source_name: H99-inoculated rabbit cerebrospinal fluid

label_protocol: Labeling was performed at the Duke University Microarray Facility following the 1 Round Amp Labeling protocol for spotted arrays (http://www.genome.duke.edu/cores/microarray/).

growth_protocol: New Zealand White rabbits were inoculated with WT strain H99 and harvested by intracisternal spinal tap on days 1, 3, 4, and 7 as previously described (Lee, et al., 2010, Infection and Immunity).  For the human sample, RNA was extracted from yeast obtained from the CSF of a de-identified patient with cryptococcal meningitis as previously described (Price, et al., 2011, mBio).

extract_protocol: RNA for all samples were obtained from lyophilized cells using the TriZol extraction protocol (Invitrogen, Carlsbad, CA) followed by purification using the Qiagen RNeasy kit (Qiagen, Valencia, CA).

tag: treatment/sample type

value: harvested from H99-inoculated rabbit at day4


title: rabbit_day7_reanalysis

description: raw data files: slide4-day7.gpr available as Series Suppelementary files

value: harvested from H99-inoculated rabbit at day7


title: human_HC1

description: raw data files: HC1US-h_h99.gpr available as Series Suppelementary files

source_name: cerebrospinal fluid from a cryptococcal meningitis patient

value: obtained from a de-identified patient with cryptococcal meningitis


title: Serum_24hr_H99

description: raw data files: 1045_9106r_CU_025_CNWash2_H99-sera-24_H99-CSF-24.gpr, 1045_9108r_CU_027_CNWash2_IAI0-sera-24_H99-sera-24.gpr available as Series Supplementary files

data_processing: Data was analyzed using JMP genomics (SAS institute, Cary NC) and initial background subtraction was performed. Data were normalized using the ANOVA Normalization process in JMP.

growth_protocol: WT strain H99, mutant strains 1A10 (ena1∆, CNAG_00531), and 14A4 (pik1∆, CNAG_07744) were incubated in two 50mL YPD broth cultures each for 24 hours at 30°C with shaking, washed once and resuspended in 50mL sterile distilled water.  The cultures were then split in half and pelleted by centrifugation, with half of the cultures resuspended in filter-sterilized human CSF or serum from anonymous human donors.  These cultures were then incubated at 37°C with shaking, and harvested at either 1 or 24 hours post-resuspension in each biological fluid for RNA extraction.

tag: background strain

tag: genotype/variation

value: wild type

tag: incubated in

value: filter-sterilized human ex vivo serum

tag: incubation time


title: rabbit_day3

description: raw data files: slide2-day3.gpr  available as Series Suppelementary files

value: harvested from H99-inoculated rabbit at day3


title: Testis CREMKO 0h batch 4 [TeKOh00.5]

source_name: Whole testis RNA from Crem-/- mouse #144 at 0h

value: Testis


title: Serum_24hr_1A10

description: raw data files: 1045_9108r_CU_027_CNWash2_IAI0-sera-24_H99-sera-24.gpr, 1045_9109r_CU_028_CNWash2_IAI0-CSF-24_IAI0-sera-24.gpr available as Series Supplementary files

value: mutant 1A10 (ena1∆, CNAG_00531)


title: Testis WT 0h batch 2 [TeWTh00.9]

source_name: Whole testis RNA from WT mouse #80 at 0h

value: 129Pas x C57Bl/J


title: Testis CREMKO 0h batch 1 [TeKOh00.6]

source_name: Whole testis RNA from Crem-/- mouse #151 at 0h

value: CREMKO


title: Serum_24hr_14A4

description: raw data files: 1045_9103r_CU_022_CNWash2_I4A4-sera-24_I4A4-CSF-24.gpr, 1045_9104r_CU_023_CNWash2_H99-Ref_I4A4-sera-24.gpr available as Series Supplementary files

value: mutant 14A4 (pik1∆, CNAG_07744)


title: rabbit_day1_reanalysis

description: raw data files: slide1-day1.gpr available as Series Suppelementary files

value: harvested from H99-inoculated rabbit at day1


title: pooled_REF-1

description: raw data files: slide1-day1.gpr, slide2-day3.gpr, slide3-day4.gpr, slide4-day7.gpr, HC1US-h_h99.gpr available as Series Suppelementary files

source_name: Pooled reference RNA

value: pooled RNA from C. neoformans grown under 9 different culture conditions


title: 185cl3 tiEBV-neg (cl. 10-14) biological rep 1

city: Shreveport

first: Rona

middle: S.

last: Scott

state: LA

address: 1501 Kings Highway

department: Microbiology and Immunology

institute: Louisiana State University Health Sciences Center-Shreveport

description: Gene expression data from transiently-infected, EBV-negative clone

hyb_protocol: Following fragmentation, 13.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GCOS version 1.4 using Affymetrix default analysis settings and global scaling with target intensity value of 2500 as normalization method.

source_name: CCL185/A549 carcinoma cell line, transiently-infected EBV-negative clone

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: Cells were seeded at a density of 5x10^5 cells in a T-75 flask containing DMEM containing 4.5g/L glucose and L-glutamine, supplemented with 10% fetal bovine serum.  Cells were allowed to grow for 3 days before RNA harvest.

extract_protocol: RNA extraction was performed with RNA Stat-60 according to manucturer's protocol (Tel-test)

tag: cell line

tag: cell type

value: lung carcinoma


title: rabbit_day7

description:
Lsmean Treatment day7
raw data files: slide4-day7.gpr available as Series Supplementary files

growth_protocol: WT strain H99 was incubated in two 50mL YPD broth cultures each for 24 hours at 30°C with shaking, washed once and resuspended in 50mL sterile distilled water.  The cultures were then resuspended in ex vivo CSF for 24 hours, and harvested for RNA extraction.  For the rabbit samples, New Zealand White rabbits were inoculated with WT strain H99 and harvested by intracisternal spinal tap on days 1 and 7 as previously described (Lee, et al., 2010, Infection and Immunity).


title: 185cl3 tiEBV-neg (cl. 10-10) biological rep 1


title: 185cl3 tiEBV-neg (cl. 10-10) biological rep 2


title: Serum_1hr_1A10

description: raw data files: 1045_9101r_CU_020_CNWash2_IAI0-CSF-1_IAI0-sera-1.gpr, 1045_9110r_CU_029_CNWash2_IAI0-sera-1_IAI0-CSF-24.gpr available as Series Supplementary files


title: pooled_REF

description:
Lsmean Treatment REF
raw data files: slide1-day1.gpr, slide4-day7.gpr, CSF1-24h_Ref-H99.gpr, CSF2-24h_Ref-H99.gpr, CSF3-24h_Ref-H99.gpr available as Series Supplementary files


title: Serum_1hr_H99

description: raw data files: 1045_9100r_CU_019_CNWash2_H99-sera-1_H99-CSF-1.gpr, 1045_9107r_CU_026_CNWash2_H99-CSF-24_H99-sera-1.gpr available as Series Supplementary files


title: rabbit_day1

description:
Lsmean Treatment day1
raw data files: slide1-day1.gpr available as Series Supplementary files


title: ex_vivo_CSF

description:
Lsmean Treatment CSF
raw data files: CSF1-24h_Ref-H99.gpr, CSF2-24h_Ref-H99.gpr, CSF3-24h_Ref-H99.gpr available as Series Supplementary files

source_name: ex vivo human cerebrospinal fluid

value: incubated in pooled ex vivo human CSF


title: 185cl3 tiEBV-neg (cl. 10-14) biological rep 2


title: CSF_24hr_1A10

description: raw data files: 1045_9109r_CU_028_CNWash2_IAI0-CSF-24_IAI0-sera-24.gpr, 1045_9110r_CU_029_CNWash2_IAI0-sera-1_IAI0-CSF-24.gpr available as Series Supplementary files

value: filter-sterilized human ex vivo cerebrospinal fluid (CSF)


title: Serum_1hr_14A4

description: raw data files: 1045_9111r_CU_030_CNWash2_I4A4-sera-1_I4A4-CSF-1.gpr, 1045_9112r_CU_031_CNWash2_I4A4-CSF-24_I4A4-sera-1.gpr available as Series Supplementary files


title: CSF_24hr_H99

description: raw data files: 1045_9106r_CU_025_CNWash2_H99-sera-24_H99-CSF-24.gpr, 1045_9107r_CU_026_CNWash2_H99-CSF-24_H99-sera-1.gpr available as Series Supplementary files


title: 185cl3 tiEBV-neg (cl. 10-9) biological rep 2


title: 185cl3 pcDNA3 biological rep2

description: Gene expression data from uninfected, transfected vector control

source_name: CCL185/A549 carcinoma cell line, uninfected  clone, tranfected with pCDN3 plasmid to control for selection


title: CSF_24hr_14A4

description: raw data files: 1045_9103r_CU_022_CNWash2_I4A4-sera-24_I4A4-CSF-24.gpr, 1045_9112r_CU_031_CNWash2_I4A4-CSF-24_I4A4-sera-1.gpr available as Series Supplementary files


title: 185cl3 pcDNA3 biological rep1


title: 185cl3 UN biological rep2

description: Gene expression data from uninfected parental clone

source_name: CCL185/A549 carcinoma cell line, uninfected parental clone


title: 185cl3 tiEBV-neg (cl. 10-9) biological rep 1


title: 185cl3 UN biological rep1


title: DV infected ECs at 48 hours

city: Stony Brook

first: Nadine

last: Dalrymple

state: NY

address: 126 Life Sciences Building

department: Molecular Genetics and Microbiology

institute: Stony Brook University

description: gene expression from infected HUVECs

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized overnight at 45C on GeneChip Human U133 PLUS 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChip Human U133 PLUS 2.0 Arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Affymetrix GCOS software v1.4.0.036 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 250.

source_name: HUVECs, dengue infected, 48 hr

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (GeneChip 3' IVT Express Kit, Affymetrix).

growth_protocol: HUVECs were maintained at 37C and 5% CO2 prior to infection. Monolayers were then mock or dengue infected for 1.5 h at 25C and then incubated at 37C and 5% CO2 until RNA extration at 12, 24, or 48 hours.

extract_protocol: Total RNA was extracted using a RNeasy kit according to the manufacturer's protocol.

treatment_protocol: Primary HUVECs were mock infected or infected with dengue virus and incubated for 12, 24, or 48 hours. At each timepoint, HUVEC monolayers were washed twice with PBSprior to addition of RNeasy lysis reagent (Qiagen).

tag: infection

value: dengue

value: 48 hours

value: primary human umbilical vein endothelial cells

tag: passage

value: passage 6


title: CSF_1hr_H99

description: raw data files: 1045_9100r_CU_019_CNWash2_H99-sera-1_H99-CSF-1.gpr, 1045_9105r_CU_024_CNWash2_H99-CSF-1_H99-Ref.gpr available as Series Supplementary files

value: wild type


title: CSF_1hr_1A10

description: raw data files: 1045_9101r_CU_020_CNWash2_IAI0-CSF-1_IAI0-sera-1.gpr, 1045_9102r_CU_021_CNWash2_I4A4-CSF-1_IAI0-CSF-1.gpr available as Series Supplementary files


title: CSF_1hr_14A4

description: raw data files: 1045_9102r_CU_021_CNWash2_I4A4-CSF-1_IAI0-CSF-1.gpr, 1045_9111r_CU_030_CNWash2_I4A4-sera-1_I4A4-CSF-1.gpr available as Series Supplementary files


title: Mock infected ECs at 48 hours

description: gene expression from uninfected HUVECs

source_name: HUVECs, mock infected, 48 hr

value: mock


title: Mock infected ECs at 24 hours

description: gene expression from uninfected HUVECs

source_name: HUVECs, mock infected, 24 hr

value: 24 hours


title: DV infected ECs at 24 hours

description: gene expression from infected HUVECs

source_name: HUVECs, dengue infected, 24 hr


title: WB_Uremia4 [discovery]

description: discovery

source_name: pre-transplant uremic whole blood (WB)

tag: disease state

value: uremia

value: whole blood (WB)

tag: Sex

value: F

tag: race

value: Caucasian

value: Conventional Haemo


title: ubp5delta_30C

description:
raw data file: 2995_10431_V2_057_CNWash2_ubp5-30-1_H99-30-1_scan2.gpr
raw data file: 2995_10432_V2_058_CNWash2_ubp5-37-1_ubp5-30-1.gpr
raw data file: 2995_10437_V2_063_CNWash2_ubp5-30-2_ubp5-37-2.gpr
raw data file: 2995_10438_V2_065_CNWash2_H99-30-2_ubp5-30-2.gpr

data_processing: Data was analyzed using JMP genomics (SAS institute, Cary NC) and initial background subtraction was performed. Data were normalized using the Array Normalization process in JMP.

organism: Cryptococcus neoformans H99

source_name: yeast culture

growth_protocol: ubp5delta mutant and wild-type strains were inoculated in 50 mL YPD medium and grown to mid-log phase(OD600～1.5) at 30°C.  The cultures were then split into two parts and pelleted by centrifugation.   One part of the cultures resuspended in 25 mL fresh YPD medium and incubated for 1h at 37°C. RNA was isolated from each culture and compared in a dye-swap experiment.  Two biological replicates of the experiment were performed.

extract_protocol: RNA for all samples was obtained from lyophilized cells using the TriZol extraction protocol (Invitrogen, Carlsbad, CA) followed by purification using the Qiagen RNeasy kit (Qiagen, Valencia, CA).

value: ubp5 deletion mutant

tag: temperature


title: hour 72 post infection, 4

status: Public on Apr 10 2012

first: Victoria

last: Svinti

address: 2350 Health Sciences Mall

institute: University of British Columbia

description: Sample name: h72.4

hyb_protocol: Samples were hybridized on Illumina HumanHT-12 v3 BeadChips following the Illumina Whole-Genome Gene Expression Direct Hybridization Assay Guide (11286331).

scan_protocol: BeadChips were imaged and quantified with the Illumina iScan scanner.

data_processing: Illumina GenomeStudio v2010.2 was used for data processing, which included averaging signal intensities for each unique Beadtype. GeneSpring 7.3.1 (Agilent Technologies) was used to median-normalize data to the 25th percentile. Analysis of the normalized data was carried out using R. The microarray profiling was performed at the Vancouver Prostate Centre Laboratory for Advanced Genome Analysis.

source_name: Total RNA from infected A549 cells

label_protocol: An input of 200 ng of total RNA was used to generate biotin-labeled cRNA following the Illumina TotalPrep RNA Amplification Kit (Ambion, Inc.)

growth_protocol: All experiments with live influenza virus were performed at the National Center for Foreign Animal Diseases under biosafety level 3 (BSL3+) conditions. A/Mexico/InDRE4487/2009 (H1N1) stocks were propagated on MDCK (Madin Darby canine kidney) cells.

extract_protocol: Total RNA was isolated using the miRvana isolation kit (Ambion) following the instructions of the supplier.

treatment_protocol: A549 cells were infected with the H1N1 virus at a multiplicity of infection (MOI) of 0.1. Infection with S-OIV 2009 H1N1 was performed in the presence of 1 μg/ml TPCK-trypsin. Cell supernatant and RNA were collected at 0, 4, 8, 24, 48, and 72 hours post-infection (hpi). The 0-hour time-point corresponds to samples collected immediately after the 1-hour virus incubation with additional time-points numbered with regard to the end of viral incubation. Mock-infected A549 cells were propagated for each experiment with samples collected at the 72-hour time-point.

value: A549 cells

value: H1N1 infection

tag: time [post-infection]

value: hour 72


title: Mock infected ECs at 12 hours

description: gene expression from uninfected HUVECs

source_name: HUVECs, mock infected, 12 hr

tag: time

value: 12 hours


title: Human CD34+ Hematopoetic Stem cells expressing TEL-PDGFRb oncogene treated with Glivec for 4 hours – replicate 3

city: Brussels

first: Jean-Baptiste

last: Demoulin

address: av Hippocrate 75, B1.74.05

department: de Duve Institute

country: Belgium

institute: Université catholique de Louvain

description: CD34+ HSCs isolated from fresh cord blood and infected with lentivrus coding for TEL-PDGFRb

hyb_protocol: cRNA was hybridized to human genome U133 A 2.0 PLUS arrays (Affymetrix, Santa Clara, USA)

scan_protocol: Affymetrix standard

data_processing: The MAS5 algorithm was run using GCOS® Affymetrix software as follows: the scaling factor using all probe sets was set to 100, the normalize factor was set to 1 and the baseline comparison was done for each replicate with the Glivec treated condition.

source_name: Hematopoetic Stem Cells

label_protocol: Biotin-labeled cRNA was synthesized using GeneChip IVT labelling kit (Affymetrix, Santa Clara, USA)

growth_protocol: Cord blood units unsuitable for preservation were used following a procedure approved by the ethics committee of the medical faculty (reference B40320108411) within 24 h of collection. Leukocytes were isolated from fresh cord blood by centrifugation over a Ficoll-Paque density-gradient (GE Healthcare) and CD34+ cells were purified using the EasySep kit (StemCell Technologies, Vancouver, Canada). Cell purity was routinely checked by flow cytometry with an anti-CD34 antibody (Becton Dickinson) and was above 80%. Cells were cultured in Iscove-modified Dulbecco’s medium (IMDM), supplemented with 20% FBS, 10 U/ml penicillin, 1.0 µg/mL streptomycin, and 0.24 mM L-asparagine, 0.55 mM L-arginine, 1.5 mM L-glutamine in presence of 25 ng/ml rhSCF and 25 ng/ml of rhFLT3 ligand. One day after isolation, 5.105 CD34+ cells were resuspended in 0.5 ml of growth medium and incubated for 24 h with concentrated lentiviral particles (0.3 ml) in the presence of polybrene (8 μg/ml). Then, cells were washed and resuspended in fresh growth medium (0.5 ml) and new viral supernatant (0.3 ml) and polybrene (8 μg/ml). Cells were centrifugated at 400 x g for 2 h. Cell were then washed and cultured as described above. After CD34+ cells transduction the percentage of GFP-positive cells was routinely 80% for TEL-PDGFRb as evaluated by flow cytometry.

extract_protocol: Total RNA were extracted from transduced CD34+ cells using Trizol reagent (Invitrogen) and the RNeasy kit (QIAGEN). The quality of RNA was checked using Bioanalyzer.

treatment_protocol: CD34+ cells were transduced with TEL-PDGFRb and cultured for 7 days in the absence of cytokines. Cells were either treated or not for 4 h with low dose imatinib, a potent PDGFR inhibitor, to switch off TELPDGFRb signaling.

tag: treatment

value: Glivec


title: ubp5delta_37C

description:
raw data file: 2995_10432_V2_058_CNWash2_ubp5-37-1_ubp5-30-1.gpr
raw data file: 2995_10433_V2_059_CNWash2_H99-37-1_ubp5-37-1.gpr
raw data file: 2995_10436_V2_062_CNWash2_ubp5-37-2_H99-37-2.gpr
raw data file: 2995_10437_V2_063_CNWash2_ubp5-30-2_ubp5-37-2.gpr


title: hour 72 post infection, 3

description: Sample name: h72.3


title: H99_30C

description:
raw data file: 2995_10431_V2_057_CNWash2_ubp5-30-1_H99-30-1_scan2.gpr
raw data file: 2995_10434_V2_060_CNWash2_H99-30-1_H99-37-1.gpr
raw data file: 2995_10435_V2_061_CNWash2_H99-37-2_H99-30-2.gpr
raw data file: 2995_10438_V2_065_CNWash2_H99-30-2_ubp5-30-2.gpr


title: H99_37C

description:
raw data file: 2995_10433_V2_059_CNWash2_H99-37-1_ubp5-37-1.gpr
raw data file: 2995_10434_V2_060_CNWash2_H99-30-1_H99-37-1.gpr
raw data file: 2995_10435_V2_061_CNWash2_H99-37-2_H99-30-2.gpr
raw data file: 2995_10436_V2_062_CNWash2_ubp5-37-2_H99-37-2.gpr


title: WB_Uremia15 [discovery]

description: discovery

tag: tissue

value: Asian Indian

value: CCPD (Automated PD)


title: Human CD34+ Hematopoetic Stem cells expressing TEL-PDGFRb oncogene – replicate 3

value: control

value: CD34+ HSCs isolated from fresh cord blood


title: Human CD34+ Hematopoetic Stem cells expressing TEL-PDGFRb oncogene treated with Glivec for 4 hours – replicate 1


title: hour 48 post infection, 1

description: Sample name: h48.1

value: hour 48


title: hour 72 post infection, 5

description: Sample name: h72.5


title: hour 48 post infection, 5

description: Sample name: h48.5


title: hour 72 post infection, 1

description: Sample name: h72.1


title: hour 48 post infection, 6

description: Sample name: h48.6


title: hour 72 post infection, 6

description: Sample name: h72.6


title: hour 72 post infection, 2

description: Sample name: h72.2


title: Human CD34+ Hematopoetic Stem cells expressing TEL-PDGFRb oncogene treated with Glivec for 4 hours – replicate 2


title: Human CD34+ Hematopoetic Stem cells expressing TEL-PDGFRb oncogene – replicate 2


title: hour 48 post infection, 4

description: Sample name: h48.4


title: hour 24 post infection, 5

description: Sample name: h24.5

value: hour 24


title: hour 48 post infection, 2

description: Sample name: h48.2


title: Human CD34+ Hematopoetic Stem cells expressing TEL-PDGFRb oncogene – replicate 1


title: DV infected ECs at 12 hours

description: gene expression from infected HUVECs

source_name: HUVECS, dengue infected, 12hr

value: dengue

value: primary human umbilical vein endothelial cells

value: passage 6


title: hour 24 post infection, 6

description: Sample name: h24.6


title: hour 48 post infection, 3

description: Sample name: h48.3


title: hour 24 post infection, 1

description: Sample name: h24.1


title: hour 8 post infection, 6

description: Sample name: h8.6

value: hour 8


title: hour 24 post infection, 3

description: Sample name: h24.3


title: hour 0 post infection, 5

description: Sample name: h0.5

value: hour 0


title: hour 8 post infection, 1

description: Sample name: h8.1


title: hour 8 post infection, 2

description: Sample name: h8.2


title: hour 0 post infection, 3

description: Sample name: h0.3


title: hour 0 post infection, 6

description: Sample name: h0.6


title: hour 8 post infection, 5

description: Sample name: h8.5


title: hour 4 post infection, 1

description: Sample name: h4.1

value: hour 4


title: hour 4 post infection, 4

description: Sample name: h4.4

value: A549 cells


title: hour 8 post infection, 4

description: Sample name: h8.4

value: H1N1 infection


title: hour 0 post infection, 4

description: Sample name: h0.4


title: hour 4 post infection, 6

description: Sample name: h4.6


title: hour 24 post infection, 4

description: Sample name: h24.4


title: hour 4 post infection, 5

description: Sample name: h4.5


title: hour 72 post infection_6

description:
Raw data file: run6.txt
See raw data file 'Array ID' column: 8

hyb_protocol: As per the manufacturers instructions, hybridizations were performed overnight in the Febit GRTA(16 hours) at 42°C.

scan_protocol: Slides were scanned using a Geniom Real Time Analyzer (febit biomed gmbh). Wizard software on standard Microsoft Windows Workstation PC.

data_processing: For each array, the signal intensities for all miRNAs were extracted from the raw data file. As each miRNA was spotted in seven replicates, we obtained seven intensity values for each miRNA. The raw data files were used to obtain the median signal intensity of all features for each array. The values were background-corrected using the median for each array of blank controls. One intensity value was retained for each miRNA by calculating the median for all the corresponding replicates. Variance stabilizing normalization (VSN) was applied to normalize the data across different arrays. Analyses were carried out using R.

label_protocol: After a preincubation with 1× Klenow buffer, the enzymatic elongation was done with 0.25 U/μl Klenow Fragment (3′–5′ exo-) in a 1× buffer with biotinylated nucleotide (biotin-11-dATP, biotin-11-dCTP, biotin-11-dGTP or biotin-11-dUTP) at 37°C. The elongation was stopped using 6× SSPE buffer. Labeling of nucleotides utilized biotin with streptavidin–phwcoerythrin (SAPE) and a signal amplification step using biotinylated antistreptavidin antibodies and a second incubation with SAPE.

growth_protocol: All experiments with live influenza virus were performed at the National Center for Foreign Animal Diseases under biosafety level 3 (BSL3+) conditions. A/Chicken/Germany/R28/2003 (H7N7) virus stocks were propagated on QT-35 cells.

extract_protocol: Total RNA was isolated using the miRvana miRNA isolation kit (Ambion) following the instructions of the supplier.

value: H7N7 infection

value: hour 72


title: hour 24 post infection, 2

description: Sample name: h24.2


title: hour 48 post infection_6

description:
Raw data file: run6.txt
See raw data file 'Array ID' column: 7


title: hour 0 post infection, 2

description: Sample name: h0.2


title: hour 24 post infection_6

description:
Raw data file: run6.txt
See raw data file 'Array ID' column: 6


title: mock-infected, 3

description: Sample name: ut.3

value: mock-infected


title: hour 0 post infection, 1

description: Sample name: h0.1


title: hour 4 post infection, 3

description: Sample name: h4.3


title: mock-infected, 6

description: Sample name: ut.6


title: hour 8 post infection, 3

description: Sample name: h8.3


title: mock-infected, 4

description: Sample name: ut.4


title: mock-infected, 5

description: Sample name: ut.5


title: mock-infected, 2

description: Sample name: ut.2


title: hour 8 post infection_6

description:
Raw data file: run6.txt
See raw data file 'Array ID' column: 5


title: hour 4 post infection_6

description:
Raw data file: run6.txt
See raw data file 'Array ID' column: 4


title: hour 0 post infection_6

description:
Raw data file: run6.txt
See raw data file 'Array ID' column: 3


title: mock-infected_6.2

description:
Raw data file: run6.txt
See raw data file 'Array ID' column: 2


title: mock-infected_6.1

description:
Raw data file: run6.txt
See raw data file 'Array ID' column: 1


title: hour 24 post infection_5

description:
Raw data file: run5.txt
See raw data file 'Array ID' column: 6


title: hour 4 post infection_5

description:
Raw data file: run5.txt
See raw data file 'Array ID' column: 4


title: hour 72 post infection_5

description:
Raw data file: run5.txt
See raw data file 'Array ID' column: 8


title: hour 0 post infection_5

description:
Raw data file: run5.txt
See raw data file 'Array ID' column: 3


title: mock-infected_5.2

description:
Raw data file: run5.txt
See raw data file 'Array ID' column: 2


title: hour 48 post infection_4

description:
Raw data file: run4.txt
See raw data file 'Array ID' column: 7


title: hour 72 post infection_4

description:
Raw data file: run4.txt
See raw data file 'Array ID' column: 8


title: mock-infected_5.1

description:
Raw data file: run5.txt
See raw data file 'Array ID' column: 1


title: hour 24 post infection_4

description:
Raw data file: run4.txt
See raw data file 'Array ID' column: 6


title: hour 48 post infection_3

description:
Raw data file: run3.txt
See raw data file 'Array ID' column: 7


title: hour 72 post infection_3

description:
Raw data file: run3.txt
See raw data file 'Array ID' column: 8


title: mock-infected_4.1

description:
Raw data file: run4.txt
See raw data file 'Array ID' column: 1


title: mock-infected_4.2

description:
Raw data file: run4.txt
See raw data file 'Array ID' column: 2


title: hour 0 post infection_4

description:
Raw data file: run4.txt
See raw data file 'Array ID' column: 3


title: hour 8 post infection_3

description:
Raw data file: run3.txt
See raw data file 'Array ID' column: 5


title: hour 24 post infection_3

description:
Raw data file: run3.txt
See raw data file 'Array ID' column: 6


title: hour 48 post infection_5

description:
Raw data file: run5.txt
See raw data file 'Array ID' column: 7


title: hour 0 post infection_3

description:
Raw data file: run3.txt
See raw data file 'Array ID' column: 3


title: hour 72 post infection_2

description:
Raw data file: run2.txt
See raw data file 'Array ID' column: 8


title: mock-infected_3.2

description:
Raw data file: run3.txt
See raw data file 'Array ID' column: 2


title: mock-infected_3.1

description:
Raw data file: run3.txt
See raw data file 'Array ID' column: 1


title: hour 4 post infection_3

description:
Raw data file: run3.txt
See raw data file 'Array ID' column: 4


title: hour 8 post infection_5

description:
Raw data file: run5.txt
See raw data file 'Array ID' column: 5


title: hour 4 post infection_4

description:
Raw data file: run4.txt
See raw data file 'Array ID' column: 4


title: hour 48 post infection_2

description:
Raw data file: run2.txt
See raw data file 'Array ID' column: 7


title: hour 8 post infection_4

description:
Raw data file: run4.txt
See raw data file 'Array ID' column: 5


title: hour 24 post infection_2

description:
Raw data file: run2.txt
See raw data file 'Array ID' column: 6


title: hour 0 post infection_2

description:
Raw data file: run2.txt
See raw data file 'Array ID' column: 3


title: hour 8 post infection_2

description:
Raw data file: run2.txt
See raw data file 'Array ID' column: 5


title: hour 48 post infection_1

description:
Raw data file: run1.txt
See raw data file 'Array ID' column: 7


title: hour 24 post infection_1

description:
Raw data file: run1.txt
See raw data file 'Array ID' column: 6


title: hour 8 post infection_1

description:
Raw data file: run1.txt
See raw data file 'Array ID' column: 5


title: hour 4 post infection_1

description:
Raw data file: run1.txt
See raw data file 'Array ID' column: 4


title: hour 72 post infection_1

description:
Raw data file: run1.txt
See raw data file 'Array ID' column: 8


title: mock-infected_2.1

description:
Raw data file: run2.txt
See raw data file 'Array ID' column: 1


title: mock-infected_2.2

description:
Raw data file: run2.txt
See raw data file 'Array ID' column: 2


title: mock-infected_1.2

description:
Raw data file: run1.txt
See raw data file 'Array ID' column: 2


title: hour 0 post infection_1

description:
Raw data file: run1.txt
See raw data file 'Array ID' column: 3


title: hour 4 post infection_2

description:
Raw data file: run2.txt
See raw data file 'Array ID' column: 4


title: hour 8 post infection, 6

description:
Raw data file: run6.txt
See raw data file 'Array ID' column: 5

data_processing: For each array, the signal intensities for all miRNAs were extracted from the raw data file. As each miRNA was spotted in seven replicates, we obtained seven intensity values for each miRNA. The raw data files were used to obtain the median signal intensity of all features for each array. The values were background-corrected using the median for each array of blank controls. One intensity value was retained for each miRNA by calculating the median for all the corresponding replicates. Variance stabilizing normalization (VSN) was applied to normalize the data across different arrays. The H1N1 RNA in the uninfected samples in chip 1 and the hour 4 samples in chip 2 were found to be degraded during the mRNA profiling; therefore, they were excluded from the statistical analysis.  Analyses were carried out using R.


title: hour 4 post infection, 6

description:
Raw data file: run6.txt
See raw data file 'Array ID' column: 4


title: hour 48 post infection, 6

description:
Raw data file: run6.txt
See raw data file 'Array ID' column: 7


title: hour 4 post infection, 5

description:
Raw data file: run5.txt
See raw data file 'Array ID' column: 4


title: mock-infected, 6.2

description:
Raw data file: run6.txt
See raw data file 'Array ID' column: 2


title: hour 8 post infection, 5

description:
Raw data file: run5.txt
See raw data file 'Array ID' column: 5


title: hour 0 post infection, 6

description:
Raw data file: run6.txt
See raw data file 'Array ID' column: 3


title: hour 48 post infection, 5

description:
Raw data file: run5.txt
See raw data file 'Array ID' column: 7


title: mock-infected, 6.1

description:
Raw data file: run6.txt
See raw data file 'Array ID' column: 1


title: hour 24 post infection, 5

description:
Raw data file: run5.txt
See raw data file 'Array ID' column: 6


title: hour 72 post infection, 5

description:
Raw data file: run5.txt
See raw data file 'Array ID' column: 8


title: mock-infected, 5.2

description:
Raw data file: run5.txt
See raw data file 'Array ID' column: 2


title: hour 0 post infection, 5

description:
Raw data file: run5.txt
See raw data file 'Array ID' column: 3


title: hour 72 post infection, 6

description:
Raw data file: run6.txt
See raw data file 'Array ID' column: 8


title: hour 72 post infection, 4

description:
Raw data file: run4.txt
See raw data file 'Array ID' column: 8


title: hour 24 post infection, 6

description:
Raw data file: run6.txt
See raw data file 'Array ID' column: 6


title: mock-infected, 5.1

description:
Raw data file: run5.txt
See raw data file 'Array ID' column: 1


title: mock-infected_1.1

description:
Raw data file: run1.txt
See raw data file 'Array ID' column: 1


title: hour 48 post infection, 4

description:
Raw data file: run4.txt
See raw data file 'Array ID' column: 7


title: hour 24 post infection, 4

description:
Raw data file: run4.txt
See raw data file 'Array ID' column: 6


title: hour 4 post infection, 4

description:
Raw data file: run4.txt
See raw data file 'Array ID' column: 4


title: hour 72 post infection, 3

description:
Raw data file: run3.txt
See raw data file 'Array ID' column: 8


title: mock-infected, 4.1

description:
Raw data file: run4.txt
See raw data file 'Array ID' column: 1


title: hour 0 post infection, 4

description:
Raw data file: run4.txt
See raw data file 'Array ID' column: 3


title: hour 48 post infection, 3

description:
Raw data file: run3.txt
See raw data file 'Array ID' column: 7


title: hour 24 post infection, 3

description:
Raw data file: run3.txt
See raw data file 'Array ID' column: 6


title: hour 8 post infection, 3

description:
Raw data file: run3.txt
See raw data file 'Array ID' column: 5


title: hour 4 post infection, 3

description:
Raw data file: run3.txt
See raw data file 'Array ID' column: 4


title: hour 0 post infection, 3

description:
Raw data file: run3.txt
See raw data file 'Array ID' column: 3


title: mock-infected, 3.2

description:
Raw data file: run3.txt
See raw data file 'Array ID' column: 2


title: mock-infected, 3.1

description:
Raw data file: run3.txt
See raw data file 'Array ID' column: 1


title: hour 24 post infection, 2

description:
Raw data file: run2.txt
See raw data file 'Array ID' column: 6


title: mock-infected, 2.2

description:
Raw data file: run2.txt
See raw data file 'Array ID' column: 2


title: hour 8 post infection, 2

description:
Raw data file: run2.txt
See raw data file 'Array ID' column: 5


title: mock-infected, 2.1

description:
Raw data file: run2.txt
See raw data file 'Array ID' column: 1


title: hour 72 post infection, 1

description:
Raw data file: run1.txt
See raw data file 'Array ID' column: 8


title: hour 0 post infection, 2

description:
Raw data file: run2.txt
See raw data file 'Array ID' column: 3


title: hour 72 post infection, 2

description:
Raw data file: run2.txt
See raw data file 'Array ID' column: 8


title: hour 48 post infection, 2

description:
Raw data file: run2.txt
See raw data file 'Array ID' column: 7


title: mock-infected, 4.2

description:
Raw data file: run4.txt
See raw data file 'Array ID' column: 2


title: hour 48 post infection, 1

description:
Raw data file: run1.txt
See raw data file 'Array ID' column: 7


title: hour 8 post infection, 4

description:
Raw data file: run4.txt
See raw data file 'Array ID' column: 5


title: hour 8 post infection, 1

description:
Raw data file: run1.txt
See raw data file 'Array ID' column: 5


title: hour 24 post infection, 1

description:
Raw data file: run1.txt
See raw data file 'Array ID' column: 6


title: hour 0 post infection, 1

description:
Raw data file: run1.txt
See raw data file 'Array ID' column: 3


title: hour 4 post infection, 1

description:
Raw data file: run1.txt
See raw data file 'Array ID' column: 4


title: TD F head, replicate 10

city: College Park

first: Gerald

last: Wilkinson

state: MD

address: Bldg 144, 4094 Campus Dr

department: Biology

institute: University of Maryland

description:
TdFH_12g
Biological replicate 10 of 11.

hyb_protocol: Using Agilent's recommended protocol, hybridizations were mixed with equal amounts of labeled nucleic acid. The ratio of the amount of labeled dye to nucleic acid (pmol/ug) was adjusted so that the same amount of red and green signal was acquired in each channel.

scan_protocol: Scanned using an Agilent G2505C microarray scanner in an ozone scrubbed room. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used. This software flags spots if pixel variation is too high or if the spot intensity is an outlier. Flagged features were subsequently removed from further analysis.  The processed signal intensities were calculated using a spatial detrend value for background subtraction and a combination of linear and lowess dye normalization.

organism: Teleopsis dalmanni

source_name: 6 heads, female, adult

label_protocol: We used T7 to amplify messenger RNA prior to labeling. This procedure uses reverse transcription to make single-stranded cDNA and then DNA polymerization to make double-stranded (ds) cDNA, which is then amplified using a linear amplification procedure. Each pair of samples was alternately labeled with Cy3 and Cy5 dyes with regard to sex.

growth_protocol: Each sample consisted of 25 eye discs sampled from male or female wandering larvae, or heads from 6 male or female adult flies, that were taken from population cages maintained at the University of Maryland, College Park, derived from flies originally collected from SE Asia.

extract_protocol: Total RNA was extracted from larval tissue using the SV Total RNA Isolation System (Promega). Adult heads were ground with a pestle under liquid nitrogen, and total RNA was extracted using the mirVANA Total RNA extraction kit (Ambion).

tag: population

value: Gombak

value: female

tag: age

value: adult

value: head


title: TD F head, replicate 11

description:
TdFH_13r
Biological replicate 11 of 11.


title: TD M head, replicate 10

description:
TdMH_12r
Biological replicate 10 of 11.

source_name: 6 heads, male, adult

value: male


title: TD M head, replicate 11

description:
TdMH_13g
Biological replicate 11 of 11.


title: TD F head, replicate 7

description:
TdFH_9r
Biological replicate 7 of 11.


title: TD F head, replicate 8

description:
TdFH_10g
Biological replicate 8 of 11.


title: TD M head, replicate 8

description:
TdMH_10r
Biological replicate 8 of 11.


title: TD M head, replicate 9

description:
TdMH_11g
Biological replicate 9 of 11.


title: TD M head, replicate 6

description:
TdMH_8r
Biological replicate 6 of 11.


title: TD M head, replicate 7

description:
TdMH_9g
Biological replicate 7 of 11.


title: TD F head, replicate 6

description:
TdFH_8g
Biological replicate 6 of 11.


title: TD F head, replicate 5

description:
TdFH_7r
Biological replicate 5 of 11.


title: TD M head, replicate 5

description:
TdMH_7g
Biological replicate 5 of 11.


title: TD F head, replicate 4

description:
TdFH_6r
Biological replicate 4 of 11.


title: TD M head, replicate 4

description:
TdMH_6g
Biological replicate 4 of 11.


title: TD F head, replicate 9

description:
TdFH_11r
Biological replicate 9 of 11.


title: TD F head, replicate 3

description:
TdFH_4g
Biological replicate 3 of 11.


title: Family branch A_healthy individual A-VII1

type: genomic

city: Bergen

first: Torunn

last: Fiskerstrand

address: Jonas Lies vei

department: Center for medical genetics and molecular medicine

country: Norway

institute: Haukeland University Hospital

description: Family branch A_healthy individual

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing:
CHP files and CEL files (generated by Affymetrix GTYPE using the BRLMM algorithm) were processed by the programs Progeny lab and  linkage analysis using the program Allegro 2.0 was used to identify the candidate region for the family mutation.
The data in the CHP-files are from 11 affected and 14 healthy individuals in the first branch of a large Norwegian family with a chronic diarrhea. See publication (figure 2A) for relation between individuals, where the same unique identifiers are used as the sample names given here. Linkage analysis was performed on the CHP-data using the program Allegro 2.0.

label: Biotin

molecule: genomic DNA

source_name: Lymphocytes

label_protocol: Standard Affymetrix procedures

extract_protocol: Genomic DNA was extracted from lymphocytes obtained from peripheral blood using the M48 DNA purification system (Qiagen, Germany).

value: lymphocytes

tag: disease stage

value: healthy


title: TD M head, replicate 3

description:
TdMH_4r
Biological replicate 3 of 11.


title: Family branch A_healthy individual A-VI3

description: Family branch A_healthy individual

tag: gender

value: M


title: Family branch A_healthy individual A-VI4

description: Family branch A_healthy individual


title: Family branch A_affected individual A-VI2

description: Family branch A_affected individual

value: F

value: affected


title: Family branch A_affected individual A-VI6

description: Family branch A_affected individual


title: Family branch A_healthy individual A-VI5

description: Family branch A_healthy individual


title: Family branch A_affected individual A-V8

description: Family branch A_affected individual


title: Family branch A_affected individual A-VI7

description: Family branch A_affected individual


title: Family branch A_healthy individual A-VI1

description: Family branch A_healthy individual


title: TD F head, replicate 2

description:
TdFH_3r
Biological replicate 2 of 11.


title: HDBEC_65.w.Br.B

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services Department

institute: Miltenyi Biotec GmbH

description: cosmetic surgery

hyb_protocol: bisulphite conversion and subsequent cleanup was carried out using EZ DNA Methylation™ Kit  (D5001), Zymo Research; converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using the standard Illumina protocol

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

data_processing: BeadStudio software 2011.1 and R statistical software vers. 2.12.1  Non_normalized data matrix contains unmethylated (signal A) and methylated (signal B) signal intensities.

label: Cy5 and Cy3

source_name: Dermal blood endothelial cells_breast

label_protocol: Standard Illumina Protocol

growth_protocol: Endothelial cells were grown in EGM-2 MV contained Endothelial Cell Basal Medium-2 (EBM-2) supplemented with 25 ml FBS, 0.2 ml hydrocortisone, 2 ml hFGF, 0.5 ml VEGF, 0.5 ml R3-IGF-1, 0.5

extract_protocol: Genomic DNA was extracted and purified from skin biopsy samples using QIAamp DNA Investigator Kit according to standard instructions

value: 65 years

value: breast

value: dermal blood endothelial cells


title: Family branch A_healthy individual A-V7

description: Family branch A_healthy individual


title: Family branch A_healthy individual A-VI8

description: Family branch A_healthy individual


title: TD M head, replicate 2

description:
TdMH_3g
Biological replicate 2 of 11.


title: HDLEC_3307.L

description: punch biopsy

source_name: Dermal lymphatic endothelial cells_buttock

value: 70 years

value: buttock

value: dermal lymphatic endothelial cells


title: Family branch A_healthy individual A-V9

description: Family branch A_healthy individual


title: HDLEC_8888.L

description: punch biopsy

value: 29 years


title: Family branch A_affected individual A-V6

description: Family branch A_affected individual


title: Family branch A_healthy individual A-V11

description: Family branch A_healthy individual


title: HDLEC_17955.L

description: punch biopsy

value: 22 years


title: Family branch A_healthy individual A-V4

description: Family branch A_healthy individual


title: HDLEC_6062.L

description: punch biopsy

value: female

value: 66 years


title: TD M head, replicate 1

description:
TdMH_2r
Biological replicate 1 of 11.

value: Gombak

value: adult

value: head


title: TD F head, replicate 1

description:
TdFH_2g
Biological replicate 1 of 11.


title: Family branch A_affected individual A-V1

description: Family branch A_affected individual

value: lymphocytes


title: TD F disc, replicate 10

description:
TdF_4.4r
Biological replicate 10 of 10.

source_name: 25 pairs of eye-antennal discs, female, third-instar larvae

value: third-instar (wandering) larvae

value: eye disc and brain


title: Family branch A_affected individual A-V3

description: Family branch A_affected individual

value: M

value: affected


title: 24h-1g-P

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description: Agilent Feature Extraction software version 10.5.1.1 was used for image analysis.

hyb_protocol: Samples were hybridized to Whole Human Genome Microarray 4 x 44K (G4112F, Agilent Technologies). 1.65 ug of Cy3 labelled aRNA were hybridized for 17 hours at 65ºC in a hybridization oven (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies). Arrays were washed with Agilent Gene Expression wash buffers and Stabilization and Drying Solution as suggest by the supplier.

scan_protocol: Slides were scanned on an Agilent microarray scanner (model G2565CA) at 100% and 10% sensitivity settings.

data_processing: Only spots with signal minus background flagged as positive and significant (flag=1) were used in the following analysis as “detected” spot while probes with flag equal to 0 were noted as “null”. Probes with less than 90% of detected spots across all arrays were removed from the analysis. Background corrected intensities of replicated spots on each array were averaged. Data were inter-array normalized with Quantile normalization (Bolstad BM et al., Bioinformatics (2003), 19(2):185-93) and then log2-transformed. Principal component analysis, cluster analysis and profile similarity searching were performed with tMev that is part of the TM4 Microarray Software Suite (Saeed AI, Bhagabati NK, Braisted JC, Liang W, Sharov V, Howe EA, et al. Methods in Enzymology. 2006;411:134-93). Identification of differentially expressed genes was performed with one and two class Significance Analysis of Microarray (SAM) program (Tusher VG, Tibshirani R, Chu G. Proc Natl Acad Sci USA 2001;98:5116-121) with default settings. SAM uses a permutation-based multiple testing algorithm and identifies significant genes with variable false-discovery rates (FDR). This can be manually adjusted to include a reasonable number of candidate genes with acceptable and well defined error probabilities.

source_name: PBL of healthy donor P irradiated with gamma-rays (2.0 Gy) in parallel ground conditions (1g) for 24h.

label_protocol: Eight hundred nanograms of total RNA were labelled with “Agilent One-Color Microarray-Based Gene Expression protocol” (Agilent) according to the manufacturer’s instructions. The synthesized cDNA was transcribed into cRNA and labelled with cyanine 3-labelled nucleotide. Labelled cRNA was purified with RNeasy Mini columns (Qiagen). The quality of each cRNA sample was verified by total yield and specificity calculated with NanoDrop ND-1000 spectrophotometer measurement (NanoDrop Technologies).

extract_protocol: Total RNA was isolated from 107 cells by using Trizol® Reagent (Invitrogen) according to the manufacturer’s protocol. Total RNA was quantified using the ND-1000 spectrophotometer (Nanodrop), while RNA integrity and content of microRNAs (%) in each samples were assessed by capillary electrophoresis using the RNA 6000 Nano LabChip using the Agilent Bioanalyzer 2100 (Agilent Technologies). Only total RNA samples with R.I.N. (RNA Integrity Number) values of 6, or higher, were used for microarray analysis.

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named P, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes, were irradiated with gamma-rays (2.0 Gy) and then kept parallel ground conditions (1g) for 24h.

tag: donor

value: P

value: irradiated with gamma-rays (20 Gy) and then kept parallel ground conditions (1g) for 24h


title: 24h-mmg-P

source_name: PBL of healthy donor P irradiated with gamma-rays (2.0 Gy) and incubated in modelled microgravity (mmg) for 24h.

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named P, provided by the Blood Centre of Padova's Hospital. After a overnight incuation, PBL, consisting of peripheral mononuclear cells depleted of monocytes, were irradiated with gamma-rays (2.0 Gy) and then incubated in modelled microgravity (mmg) for 24h.

value: irradiated with gamma-rays (20 Gy) and then incubated in modelled microgravity (mmg) for 24h


title: TD M disc, replicate 10

description:
TdM_4.4g
Biological replicate 10 of 10.

source_name: 25 pairs of eye-antennal discs, male, third-instar larvae

value: male


title: TD M disc, replicate 9

description:
TdM_4.3r
Biological replicate 9 of 10.


title: 8068 B

description:
punch biopsy
SAMPLE 15

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to Agilent Whole Human Genome Oligo Microarrays (44K) using Agilent's recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.5.1.1 ) was used to read out and process the microarray image files.

source_name: Dermal blood endothelial cells, buttock

label_protocol: 100 ng of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer's protocol.

growth_protocol: Endothelial cells were grown in EGM-2 MV contained Endothelial Cell Basal Medium-2 (EBM-2) supplemented with 25 ml FBS, 0.2 ml hydrocortisone, 2 ml hFGF, 0.5 ml VEGF, 0.5 ml R3-IGF-1, 0.5 ml ascorbic acid, 0.5 ml hEGF, and 0.5 ml GA-1000 (all Lonza).

extract_protocol: Endothelial cells were trypsinized and total cellular RNA was isolated after centrifugation using the RNeasy Mini Kit (Qiagen).

value: 65 years

value: buttock

value: Dermal blood endothelial cells


title: Family branch A_affected individual A-V10

description: Family branch A_affected individual


title: 5112 B

description:
punch biopsy
SAMPLE 14

value: female


title: HDBEC_36.w.B

description: cosmetic surgery

value: 36 years

value: breast

value: dermal blood endothelial cells


title: TD F disc, replicate 9

description:
TdF_4.3g
Biological replicate 9 of 10.

value: Gombak


title: Family branch A_healthy individual A-V13

description: Family branch A_healthy individual

value: lymphocytes

value: healthy


title: Family branch A_healthy individual A-IV7

description: Family branch A_healthy individual


title: Family branch A_affected individual A-IV4

description: Family branch A_affected individual

value: F


title: 24h-mmg-H

source_name: PBL of healthy donor H irradiated with gamma-rays (2.0 Gy) and incubated in modelled microgravity (mmg) for 24h.

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named H, provided by the Blood Centre of Padova's Hospital. After a overnight incuation, PBL, consisting of peripheral mononuclear cells depleted of monocytes, were irradiated with gamma-rays (2.0 Gy) and then incubated in modelled microgravity (mmg) for 24h.

value: H


title: 73 B

description:
cosmetic surgery
SAMPLE 12

source_name: Dermal blood endothelial cells, breast

value: 73 years


title: 24h-1g-H

source_name: PBL of healthy donor H irradiated with gamma-rays (2.0 Gy) in parallel ground conditions (1g) for 24h

treatment_protocol: Human Peripheral blood lymphocytes (PBL) were isolated by separation on Biocoll density gradient from freshly collected buffy coats from one healthy donor, named H, provided by the Blood Centre of Padova's Hospital. After a overnight incubation, PBL, consisting of peripheral mononuclear cells depleted of monocytes, were irradiated with gamma-rays (2.0 Gy) and then kept parallel ground conditions (1g) for 24h.


title: 65 B

description:
cosmetic surgery
SAMPLE 13


title: TD F disc, replicate 8

description:
TdF_3.2r
Biological replicate 8 of 10.

value: third-instar (wandering) larvae

value: eye disc and brain


title: Family branch A_healthy individual A-IV8

description: Family branch A_healthy individual


title: HDLEC_12156.L

description: punch biopsy

value: 29 years

value: dermal lymphatic endothelial cells


title: HDBEC_5112.b.B

description: punch biopsy

source_name: Dermal blood endothelial cells_buttock

value: 66 years


title: Family branch A_healthy individual A-V12

description: Family branch A_healthy individual


title: TD M disc, replicate 8

description:
TdM_3.2g
Biological replicate 8 of 10.

value: male


title: HDLEC_20173.L

description: punch biopsy

value: 23 years

value: buttock


title: 17955 L

description:
punch biopsy
SAMPLE 10

source_name: Dermal lymphatic endothelial cells, buttock

value: female

value: 22 years

value: Dermal lymphatic endothelial cells


title: TD M disc, replicate 7

description:
TdM_3.1r
Biological replicate 7 of 10.

value: Gombak


title: Family branch A_affected individual A-V5

description: Family branch A_affected individual

value: lymphocytes

value: affected


title: HDBEC_8068.BEC.P3

description: punch biopsy

value: 65 years

value: dermal blood endothelial cells


title: HDLEC_16870.L

description: punch biopsy

value: 30 years


title: Family branch A_affected individual A-IV1

description: Family branch A_affected individual

value: F


title: 3953+ B

description:
punch biopsy
SAMPLE 16

value: 28 years

value: Dermal blood endothelial cells


title: TD F disc, replicate 6

description:
TdF_2.2r
Biological replicate 6 of 10.

value: third-instar (wandering) larvae

value: eye disc and brain


title: TD F disc, replicate 7

description:
TdF_3.1g
Biological replicate 7 of 10.


title: 3307 L

description:
punch biopsy
SAMPLE 9

value: 70 years