title: Stab5b transgenic F1 8N

city: Augusta

first: Jin-Xiong

last: She

state: GA

department: Center for Biotechnology and Genomic Medicine

institute: Medical College of Georgia

hyb_protocol: Approximately 750ng of labeled cRNA was fragmented, and hybridized to the Illumina MouseRef-8 v2.0 Expression beadchips in accordance to the Illumina technical manual. RNA from each culture was independently analyzed.

scan_protocol: After hybridization, arrays were washed, stained with Cy3-conjugated streptavidin, and scanned. Image data were analyzed with BeadStudio V2.0.

data_processing: The raw data were normalized using Robust Spline Normalization.

source_name: Stab5b transgenic

label_protocol: Total RNA (200 ng) was converted into biotin labeled cRNA using Target Amp cDNA synthesis kit (Epicenter catalog no. TAB1R6924).

extract_protocol: Total RNA was extracted using Qiagen RNeasy minikit

tag: genetic background

value: B6 NOD mixed

value: 4 wk

value: male

value: CD8+ thymocyte

tag: genotype

value: Stab5b transgenic


title: 8888 L

status: Public on Apr 10 2012

type: RNA

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services Department

country: Germany

institute: Miltenyi Biotec GmbH

description:
punch biopsy
SAMPLE 8

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.

molecule: total RNA

organism: Homo sapiens

source_name: Dermal lymphatic 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).

tag: gender

value: female

tag: age

value: 29 years

tag: tissue

value: buttock

tag: cell type

value: Dermal lymphatic endothelial cells


title: TD M disc, replicate 5

city: College Park

first: Gerald

middle: S

last: Wilkinson

state: MD

address: Bldg 144, 4094 Campus Dr

department: Biology

country: USA

institute: University of Maryland

description:
TdM_2.1r
Biological replicate 5 of 10.

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

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

tag: Sex

value: third-instar (wandering) larvae

value: eye disc and brain


title: Stab5b transgenic F1 4N

organism: Mus musculus

value: Female


title: HDBEC_73w.BaB

type: genomic

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

molecule: genomic DNA

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: 73 years

value: breast

value: dermal blood endothelial cells


title: 24h-mmg-G

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 G irradiated with gamma-rays (2.0 Gy) and incubated in modelled microgravity (mmg) 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 G, 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.

tag: donor

value: G

tag: treatment

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


title: 12156 L

description:
punch biopsy
SAMPLE 6


title: 60 B

description:
cosmetic surgery
SAMPLE 11

source_name: Dermal blood endothelial cells, breast

value: 60 years

value: Dermal blood endothelial cells


title: Stab5b transgenic F1 5P

value: B6 NOD mixed

value: 4 wk

value: male

value: CD8+ thymocyte


title: 6062 L

description:
punch biopsy
SAMPLE 5

value: female

value: 66 years

value: buttock


title: 16870 L

description:
punch biopsy
SAMPLE 7

value: 30 years

value: Dermal lymphatic endothelial cells


title: Stab5b transgenic F1 6N

value: Female

value: Stab5b transgenic


title: 24h-mmg-C

source_name: PBL of healthy donor C 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 C, 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: C


title: HDLEC_3222.L

description: punch biopsy

source_name: Dermal lymphatic endothelial cells_buttock

value: 69 years

value: dermal lymphatic endothelial cells


title: HDBEC_60w.Br.B

description: cosmetic surgery

value: breast

value: dermal blood endothelial cells


title: TD F disc, replicate 4

description:
TdF_1.4r
Biological replicate 4 of 10.

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

value: Gombak

value: third-instar (wandering) larvae

value: eye disc and brain


title: 8068 L

description:
punch biopsy
SAMPLE 4

value: 65 years


title: 24h-1g-C

source_name: PBL of healthy donor C 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 C, 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.

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


title: TD M disc, replicate 4

description:
TdM_1.4g
Biological replicate 4 of 10.

value: male


title: Stab5b transgenic F1 7P

value: B6 NOD mixed

value: 4 wk

value: CD8+ thymocyte


title: Stab5b transgenic F1 3P


title: Stab5b transgenic F1 2N


title: NOD 10N

description: NOD

source_name: NOD

value: NOD

value: wild type


title: 20173 L

description:
punch biopsy
SAMPLE 3

value: female

value: 23 years

value: buttock

value: Dermal lymphatic endothelial cells


title: 24h-mmg-A

source_name: PBL of healthy donor A 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 A, 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: A

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


title: 24h-1g-G

source_name: PBL of healthy donor G 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 G, 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.

value: G


title: TD F disc, replicate 2

description:
TdF_1.2r
Biological replicate 2 of 10.

value: Gombak

value: third-instar (wandering) larvae


title: NOD 7N

description: NOD

value: Female


title: 3222 L

description:
punch biopsy
SAMPLE 2

value: 69 years


title: HDLEC_8068.L

description: punch biopsy

value: 65 years

value: dermal lymphatic endothelial cells


title: Stab5b transgenic F1 1P

value: B6 NOD mixed

value: 4 wk

value: Stab5b transgenic


title: TD F disc, replicate 3

description:
TdF_1.3g
Biological replicate 3 of 10.

value: eye disc and brain


title: HDLEC_5112.L

description: punch biopsy

value: female

value: 66 years


title: 5112 L

description:
punch biopsy
SAMPLE 1

value: buttock


title: 24h-1g-A

source_name: PBL of healthy donor A 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 A, 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.

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


title: NOD 13P

description: NOD

value: NOD

value: male

value: CD8+ thymocyte

value: wild type


title: TD M disc, replicate 2

description:
TdM_1.2g
Biological replicate 2 of 10.

value: Gombak

value: third-instar (wandering) larvae


title: Snf2l-Ex6DEL replicate 3

city: Ottawa

first: Alan

last: Mears

state: ON

address: 401 Smyth Rd

department: Research Institute

country: Canada

institute: Children's Hospital of Eastern Ontario

description: Replicate 3 (of 3). Dissected brain cortices at E15.5.

hyb_protocol: Hybridization protocols were followed according to manufacturers guidelines (Genisphere) using the formamide-based buffer.

scan_protocol: Slides were scanned with a ScanArray Express (Perkin Elmer) scanner for the Cy5 and Cy3 channels

data_processing: Background subtracted and LOWESS normalized using the ProScan Array software package (Perkin Elmer) to generate log2 signal ratios

source_name: E15.5 cortices

label_protocol: cDNA synthesis and labeling was performed with the 3DNA Array 900 kit (Genisphere)

extract_protocol: RNA was isolated from brain tissue with the Rneasy mini kit (Qiagen) according to manufacturers protocols

value: brain cortex


title: TD M disc, replicate 1

description:
TdM_1.1r
Biological replicate 1 of 10.


title: NOD 8P

description: NOD


title: NOD 11P

description: NOD

value: Female


title: NOD 12N

description: NOD

value: unknown


title: Snf2l-Ex6DEL replicate 2

description: Replicate 2 (of 3). Dissected brain cortices at E15.5. Technical (dye-flip) replicate of replicate 1.


title: Snf2l-Ex6DEL replicate 1

description: Replicate 1 (of 3). Dissected brain cortices at E15.5.


title: TD F disc, replicate 1

description:
TdF_1.1g
Biological replicate 1 of 10.


title: GBAM1 CD133- control biological replicate 1

status: Public on Apr 09 2012

city: Bethesda

first: Barbara

middle: Helen

last: Rath

address: 10 Center Drive B3B406

department: National Cancer Institute

institute: National Institute of Health

description: Gene expression data from GBAM1 CD133- cell, (differentiated for 10d from GBAM1 CD133+ cells)

hyb_protocol: Hybridized to GeneChip Human genome U133A 2.0 array chips (Affymetrix) according to manufacturers instruction

scan_protocol: according to manufacturers instruction

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: GBAM1, 10d differentiated

label_protocol: The isolated RNA was amplified using GeneChip 3’ IVT Express Kit (Affymetrix) according to manufacturers instruction

growth_protocol: cells were grown in their respective culture medium

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

treatment_protocol: 48h of co-culture

value: brain

value: GBAM1 CD133-

tag: culture condition

value: control


title: NOD 9P

description: NOD

value: 4 wk


title: GBAM1 CD133- control biological replicate 2


title: GBAM1 CD133- direct co-cultured biological replicate 2

description: Gene expression data from GBAM1 CD133- cell, (differentiated for 10d from GBAM1 CD133+ cells) indirect co-cultured for 48h with astrocytes

value: direct co-cultured


title: GBAM1 CD133+ control biological replicate 2

description: Gene expression data from GBAM1 CD133+ glioma-stem cells

source_name: GBAM1 glioma stem cells

value: GBAM1 CD133+


title: GBAM1 CD133+ direct co-cultured biological replicate 1

description: Gene expression data from GBAM1 CD133+ glioma-stem cell direct co-cultured for 48h with astrocytes


title: GBAM1 CD133+ direct co-cultured biological replicate 2


title: GBAM1 CD133+ indirect co-cultured biological replicate 1

description: Gene expression data from GBAM1 CD133+ glioma-stem cell indirect co-cultured for 48h with astrocytes

value: indirect co-cultured


title: GBAM1 CD133- indirect co-cultured biological replicate 2


title: NSC11 CD133- direct co-cultured biological replicate 1

description: Gene expression data from NSC11 CD133- cell, (differentiated for 10d from NSC11 CD133+ cells) direct co-cultured for 48h with astrocytes

source_name: NSC11, 10d differentiated


title: GBAM1 CD133+ indirect co-cultured biological replicate 2


title: GBAM1 CD133- indirect co-cultured biological replicate 1


title: NSC11 CD133- control biological replicate 2

description: Gene expression data from NSC11 CD133- cells


title: GBAM1 CD133+ control biological replicate 1


title: NSC11 CD133- control biological replicate 1


title: NSC11 CD133- indirect co-cultured biological replicate 1

description: Gene expression data from NSC11 CD133- cell, (differentiated for 10d from NSC11 CD133+ cells) indirect co-cultured for 48h with astrocytes


title: NSC11 CD133+ control biological replicate 2

description: Gene expression data from NSC11 CD133+ glioma-stem cell

source_name: NSC11 glioma stem cells


title: NSC11 CD133- indirect co-cultured biological replicate 2


title: NSC11 CD133+ direct co-cultured biological replicate 2

description: Gene expression data from NSC11 CD133+ glioma-stem cell direct co-cultured for 48h with astrocytes


title: NSC11 CD133- direct co-cultured biological replicate 2


title: NSC11 CD133+ direct co-cultured biological replicate 1


title: NSC11 CD133+ control biological replicate 1


title: TD M disc, replicate 3

description:
TdM_1.3r
Biological replicate 3 of 10.

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

value: eye disc and brain


title: TD M disc, replicate 6

description:
TdM_2.2g
Biological replicate 6 of 10.


title: A23 recipeint replicate1_6

city: Los Angeles

first: Richard

middle: T

last: Wang

state: CA

address: 650 Charles E Young Drive South

institute: UCLA

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Raw values were extracted from BeadStudio 1.5.  Data were median normalized using GeneSpring GX.

organism: Cricetulus griseus

source_name: A23 recipient replicate

label_protocol: Ambion Illumina® TotalPrepTM RNA Amplification Kit was used according to standard Illumina protocol.

growth_protocol: Cells were grown in alpha MEM with 10% FBS, 1x ampicillin and 1x HAT

extract_protocol: Qiagen Mini RNeasy kit using manufacturer's instructions

treatment_protocol: Standard Illumina protocol

tag: cell line

value: hamster fibroblast

value: male/male


title: A23 recipeint replicate1_3


title: RH server number 80_1

description:
technical replicate 1
1547673097_C

organism:
Homo sapiens
Cricetulus griseus

source_name: RH server number 80

value: human lymphoblastoid, hamster fibroblast


title: A23 recipeint replicate1_5


title: TD F disc, replicate 5

description:
TdF_2.1g
Biological replicate 5 of 10.

value: female


title: RH server number 72_1

description:
technical replicate 1
1547673023_D

source_name: RH server number 72


title: RH server number 82_1

description:
technical replicate 1
1547673113_D

source_name: RH server number 82


title: A23 recipeint replicate1_1


title: A23 recipeint replicate1_2


title: NSC11 CD133+ indirect co-cultured biological replicate 2

description: Gene expression data from NSC11 CD133+ glioma-stem cell indirect co-cultured for 48h with astrocytes


title: RH server number 83_1

description:
technical replicate 1
1553820024_A

source_name: RH server number 83


title: A23 recipeint replicate1_4


title: RH server number 75_1

description:
technical replicate 1
1553820022_H

source_name: RH server number 75


title: A23 recipeint replicate1_7


title: RH server number 74_1

description:
technical replicate 1
1547673113_E

source_name: RH server number 74


title: RH server number 79_1

description:
technical replicate 1
1547673107_B

source_name: RH server number 79


title: NSC11 CD133+ indirect co-cultured biological replicate 1


title: RH server number 81_1

description:
technical replicate 1
1553820022_D

source_name: RH server number 81


title: RH server number 68_1

description:
technical replicate 1
1553820024_B

source_name: RH server number 68


title: RH server number 73_1

description:
technical replicate 1
1547673113_G

source_name: RH server number 73


title: RH server number 77_1

description:
technical replicate 1
1547673115_D

source_name: RH server number 77


title: RH server number 69_1

description:
technical replicate 1
1547673114_B

source_name: RH server number 69


title: RH server number 62_1

description:
technical replicate 1
1547673097_G

source_name: RH server number 62


title: RH server number 63_1

description:
technical replicate 1
1553820037_D

source_name: RH server number 63


title: RH server number 70_1

description:
technical replicate 1
1553820022_F

source_name: RH server number 70


title: RH server number 66_1

description:
technical replicate 1
1547673113_A

source_name: RH server number 66


title: RH server number 64_1

description:
technical replicate 1
1553820037_F

source_name: RH server number 64


title: RH server number 67_1

description:
technical replicate 1
1553820031_B

source_name: RH server number 67


title: RH server number 61_1

description:
technical replicate 1
1547673107_F

source_name: RH server number 61


title: RH server number 65_1

description:
technical replicate 1
1553820022_B

source_name: RH server number 65


title: RH server number 57_1

description:
technical replicate 1
1553820031_H

source_name: RH server number 57


title: RH server number 59_1

description:
technical replicate 1
1553820031_G

source_name: RH server number 59


title: RH server number 60_1

description:
technical replicate 1
1553820031_E

source_name: RH server number 60


title: RH server number 54_1

description:
technical replicate 1
1521406001_B

source_name: RH server number 54


title: RH server number 51_1

description:
technical replicate 1
1547673023_G

source_name: RH server number 51


title: RH server number 50_1

description:
technical replicate 1
1547673097_A

source_name: RH server number 50


title: RH server number 44_1

description:
technical replicate 1
1553820037_B

source_name: RH server number 44


title: RH server number 45_1

description:
technical replicate 1
1553820024_D

source_name: RH server number 45


title: RH server number 55_1

description:
technical replicate 1
1547673097_E

source_name: RH server number 55


title: RH server number 47_1

description:
technical replicate 1
1553820037_C

source_name: RH server number 47


title: RH server number 58_1

description:
technical replicate 1
1553820022_E

source_name: RH server number 58


title: RH server number 56_1

description:
technical replicate 1
1547673097_D

source_name: RH server number 56


title: RH server number 53_1

description:
technical replicate 1
1553820022_G

source_name: RH server number 53


title: RH server number 52_1

description:
technical replicate 1
1547673113_B

source_name: RH server number 52


title: RH server number 46_1

description:
technical replicate 1
1553820037_H

source_name: RH server number 46


title: RH server number 35_1

description:
technical replicate 1
1553820031_F

source_name: RH server number 35


title: RH server number 41_1

description:
technical replicate 1
1547673107_E

source_name: RH server number 41


title: RH server number 49_1

description:
technical replicate 1
1547673114_F

source_name: RH server number 49


title: RH server number 39_1

description:
technical replicate 1
1547673097_B

source_name: RH server number 39


title: RH server number 43_1

description:
technical replicate 1
1553820037_E

source_name: RH server number 43


title: RH server number 42_1

description:
technical replicate 1
1547673107_D

source_name: RH server number 42


title: RH server number 32_1

description:
technical replicate 1
1521406001_C

source_name: RH server number 32


title: RH server number 33_1

description:
technical replicate 1
1553820024_C

source_name: RH server number 33


title: RH server number 36_1

description:
technical replicate 1
1547673023_B

source_name: RH server number 36


title: RH server number 38_1

description:
technical replicate 1
1553820022_A

source_name: RH server number 38


title: RH server number 34_1

description:
technical replicate 1
1547673023_C

source_name: RH server number 34


title: RH server number 30_1

description:
technical replicate 1
1547673114_A

source_name: RH server number 30


title: RH server number 40_1

description:
technical replicate 1
1521406001_A

source_name: RH server number 40


title: RH server number 37_1

description:
technical replicate 1
1547673107_C

source_name: RH server number 37


title: RH server number 29_1

description:
technical replicate 1
1547673107_G

source_name: RH server number 29


title: RH server number 25_1

description:
technical replicate 1
1553820037_A

source_name: RH server number 25


title: RH server number 20_1

description:
technical replicate 1
1521406001_D

source_name: RH server number 20


title: RH server number 23_1

description:
technical replicate 1
1547673114_C

source_name: RH server number 23


title: RH server number 22_1

description:
technical replicate 1
1547673115_A

source_name: RH server number 22


title: RH server number 21_1

description:
technical replicate 1
1547673115_B

source_name: RH server number 21


title: RH server number 26_1

description:
technical replicate 1
1547673115_E

source_name: RH server number 26


title: RH server number 19_1

description:
technical replicate 1
1547673023_F

source_name: RH server number 19


title: RH server number 24_1

description:
technical replicate 1
1553820031_A

source_name: RH server number 24


title: RH server number 27_1

description:
technical replicate 1
1547673097_F

source_name: RH server number 27


title: RH server number 9_1

description:
technical replicate 1
1547673113_C

source_name: RH server number 9


title: RH server number 28_1

description:
technical replicate 1
1521406001_F

source_name: RH server number 28


title: RH server number 15_1

description:
technical replicate 1
1547673115_F

source_name: RH server number 15


title: RH server number 18_1

description:
technical replicate 1
1547673114_G

source_name: RH server number 18


title: RH server number 6_1

description:
technical replicate 1
1553820031_C

source_name: RH server number 6


title: RH server number 16_1

description:
technical replicate 1
1553820024_E

source_name: RH server number 16


title: RH server number 8_1

description:
technical replicate 1
1547673023_E

source_name: RH server number 8


title: RH server number 11_1

description:
technical replicate 1
1553820024_G

source_name: RH server number 11


title: GBAM1 CD133- direct co-cultured biological replicate 1

source_name: GBAM1, 10d differentiated


title: RH server number 4_1

description:
technical replicate 1
1547673115_C

source_name: RH server number 4


title: RH server number 5_1

description:
technical replicate 1
1553820024_H

source_name: RH server number 5


title: RH server number 14_1

description:
technical replicate 1
1553820031_D

source_name: RH server number 14


title: RH server number 12_1

description:
technical replicate 1
1521406001_E

source_name: RH server number 12


title: RH server number 10_1

description:
technical replicate 1
1547673114_D

source_name: RH server number 10


title: RH server number 2_1

description:
technical replicate 1
1547673023_A

source_name: RH server number 2


title: RH server number 13_1

description:
technical replicate 1
1547673107_A

source_name: RH server number 13


title: RH server number 1_1

description:
technical replicate 1
1547673115_G

source_name: RH server number 1


title: RH server number 3_1

description:
technical replicate 1
1547673114_E

source_name: RH server number 3


title: RH server number 7_1

description:
technical replicate 1
1553820024_F

source_name: RH server number 7


title: ES _rep3

city: Shanghai

first: Fu

last: Shijun

address: Halei Road

country: China

institute: China Novartis Institutes for BioMedical Research

description: miRNA expression of undifferentiated ES cells

hyb_protocol: Cy3-labelled cRNA was hybridizated using Agilent’s miRNA Complete Labeling and Hyb Kit (p/n 5190-0456) according to the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner

data_processing: The scanned images were analyzed with Agilent Feature Extraction software version 9.5.3.1. using default parameters

source_name: ES _rep3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug RNA using Agilent’s miRNA Complete Labeling and Hyb Kit (p/n 5190-0456)according to the manufacturer's instructions.

growth_protocol: mESCs were maintained on mitomycin C-treated MEF feeder layers in DMEM medium supplemented with 15% FBS, 1mM L-glutamine, 1mM nonessential amino acids, 0.1mM beta-mercaptoethanol, 1% Penicillin:streptomycin (all from Invitrogen, Carisbad, USA), and 1000unit/ml LIF(Millipore, Billerica, USA) under a standard gas atmosphere of humidified air/5% CO2.

extract_protocol: All samples were lysed in Trizol and RNA was extracted using the procedure recommended by the manufacture (Invitrogen, Carisbad, USA). RNA quality was confirmed by Agilent bioanalyzer 2100

treatment_protocol: Mouse ESCs were maintained on MEF feeder cells until they reached about 80% confluence. Prior to differentiation, mouse ESCs were passaged onto gelatin-coated plates for 1 hour to remove feeders, and afterwards, ESCs were seeded at 80000 cells per well on collagen-coated 6 well plate. After overnight culture, cells were treated with 100ng/ml Activin A (R&D system, Minneapolis,USA), or 50ng/ml Wnt3a (R&D system, Minneapolis,USA), or 100ng/ml Activin A plus 50ng/ml Wnt3a (R&D system, Minneapolis,USA) in RPMI 1640(Invitrogen, Carisbad, USA) supplemented with 1XB27 and 1X sodium butyrate (Invitrogen, Carisbad, USA) for 3 to 5 days for endoderm differentiation.

value: embryonic stem cells


title: ES _rep2

source_name: ES _rep2


title: ES _rep1

source_name: ES _rep1


title: ES treated without growth factors_5d_rep3

description: miRNA expression after 5d in growth factor treated differentiated ES cells

value: differentiated embryonic stem cells


title: Hamster Liver_4

source_name: Hamster Liver

value: liver


title: ES treated without growth factors_5d_rep2


title: ES treated without growth factors_5d_rep1


title: Hamster Liver_1


title: Hamster Liver_2


title: ES treated without growth factors_3d_rep2

description: miRNA expression after 3d in growth factor treated differentiated ES cells


title: ES treated without growth factors_3d_rep1


title: Hamster Liver_3


title: ES treated without growth factors_1d_rep3

description: miRNA expression after 1d in growth factor treated differentiated ES cells


title: Human Liver_4

source_name: Human Liver


title: Human Liver_3


title: Human Liver_2


title: Human Liver_1


title: Human Heart_2

source_name: Human Heart

value: heart


title: ES treated with Activin A_5d_rep3

source_name: ES treated with Activin A_5d_rep3


title: ES treated without growth factors_1d_rep1


title: Human Heart_1


title: ES treated with Activin A_5d_rep2

source_name: ES treated with Activin A_5d_rep2


title: Hamster Heart_1

source_name: Hamster Heart


title: ES treated without growth factors_1d_rep2


title: ES treated with Activin A_3d_rep3

source_name: ES treated with Activin A_3d_rep3


title: ES treated with Activin A_3d_rep1

source_name: ES treated with Activin A_3d_rep1


title: ES treated with Activin A_3d_rep2

source_name: ES treated with Activin A_3d_rep2


title: Human Kidney_2

source_name: Human Kidney

value: kidney


title: Hamster Kidney_1

source_name: Hamster Kidney


title: Hamster Kidney_2


title: ES treated with Activin A_5d_rep1

source_name: ES treated with Activin A_5d_rep1


title: Human Kidney_1


title: Hamster Heart_2


title: ES treated with Activin A_1d_rep3

source_name: ES treated with Activin A_1d_rep3


title: a23 recipient replicate2_8

source_name: a23 recipient replicate

value: male


title: a23 recipient replicate2_7


title: ES treated with Activin A_1d_rep2

source_name: ES treated with Activin A_1d_rep2


title: a23 recipient replicate2_6


title: ES treated with Activin A_1d_rep1

source_name: ES treated with Activin A_1d_rep1


title: ES treated with Activin A and wnt3a_3d_rep3


title: ES treated with Activin A and wnt3a_5d_rep2


title: ES treated with Activin A and wnt3a_5d_rep1


title: a23 recipient replicate2_5


title: a23 recipient replicate2_3


title: a23 recipient replicate2_4


title: ES treated without growth factors_3d_rep3


title: a23 recipient replicate2_1


title: a23 recipient replicate2_2


title: RH server number 31_1

description:
technical replicate 1
1553820022_C

source_name: RH server number 31


title: ES treated with Activin A and wnt3a_5d_rep3


title: ES treated with Activin A and wnt3a_1d_rep3


title: ES treated with Activin A and wnt3a_1d_rep2


title: ES treated with Activin A and wnt3a_1d_rep1


title: ES treated with wnt3a_5d_rep1

source_name: ES treated with wnt3a_5d_rep1


title: ES treated with wnt3a_5d_rep3

source_name: ES treated with wnt3a_5d_rep3


title: ES treated with wnt3a_5d_rep2

source_name: ES treated with wnt3a_5d_rep2


title: ES treated with wnt3a_3d_rep3

source_name: ES treated with wnt3a_3d_rep3


title: RH server number 81_2

description:
technical replicate 2
1553838024_B

source_name: RH server number 81


title: RH server number 83_2

description:
technical replicate 2
1553820049_C

source_name: RH server number 83


title: ES treated with wnt3a_3d_rep2

source_name: ES treated with wnt3a_3d_rep2


title: ES treated with wnt3a_1d_rep3

source_name: ES treated with wnt3a_1d_rep3


title: ES treated with wnt3a_3d_rep1

source_name: ES treated with wnt3a_3d_rep1


title: RH server number 80_2

description:
technical replicate 2
1553838032_D

source_name: RH server number 80


title: RH server number 77_2

description:
technical replicate 2
1553838031_H

source_name: RH server number 77


title: RH server number 73_2

description:
technical replicate 2
1553820053_F

source_name: RH server number 73


title: RH server number 75_2

description:
technical replicate 2
1553820049_F

source_name: RH server number 75


title: RH server number 82_2

description:
technical replicate 2
1553838031_F

source_name: RH server number 82


title: RH server number 74_2

description:
technical replicate 2
1553820057_F

source_name: RH server number 74


title: ES treated with wnt3a_1d_rep2

source_name: ES treated with wnt3a_1d_rep2


title: RH server number 72_2

description:
technical replicate 2
1553838031_C

source_name: RH server number 72


title: RH server number 68_2

description:
technical replicate 2
1553820043_C

source_name: RH server number 68


title: RH server number 79_2

description:
technical replicate 2
1553838025_E

source_name: RH server number 79


title: RH server number 65_2

description:
technical replicate 2
1553820043_B

source_name: RH server number 65


title: RH server number 67_2

description:
technical replicate 2
1553820043_D

source_name: RH server number 67


title: RH server number 70_2

description:
technical replicate 2
1553838023_F

source_name: RH server number 70


title: ES treated with wnt3a_1d_rep1

source_name: ES treated with wnt3a_1d_rep1


title: RH server number 69_2

description:
technical replicate 2
1553838025_G

source_name: RH server number 69


title: RH server number 66_2

description:
technical replicate 2
1553838026_F

source_name: RH server number 66


title: RH server number 63_2

description:
technical replicate 2
1553838024_E

source_name: RH server number 63


title: RH server number 60_2

description:
technical replicate 2
1553838024_H

source_name: RH server number 60


title: RH server number 61_2

description:
technical replicate 2
1553820055_E

source_name: RH server number 61


title: RH server number 64_2

description:
technical replicate 2
1553838024_A

source_name: RH server number 64


title: RH server number 57_2

description:
technical replicate 2
1553820049_H

source_name: RH server number 57


title: RH server number 56_2

description:
technical replicate 2
1553838031_D

source_name: RH server number 56


title: RH server number 17_1

description:
technical replicate 1
1547673113_F

source_name: RH server number 17


title: RH server number 52_2

description:
technical replicate 2
1553838025_F

source_name: RH server number 52


title: RH server number 54_2

description:
technical replicate 2
1553838025_B

source_name: RH server number 54


title: RH server number 58_2

description:
technical replicate 2
1553838024_F

source_name: RH server number 58


title: RH server number 62_2

description:
technical replicate 2
1553820053_D

source_name: RH server number 62


title: RH server number 49_2

description:
technical replicate 2
1553820055_G

source_name: RH server number 49


title: RH server number 55_2

description:
technical replicate 2
1553820057_D

source_name: RH server number 55


title: RH server number 50_2

description:
technical replicate 2
1553838026_D

source_name: RH server number 50


title: RH server number 59_2

description:
technical replicate 2
1553820043_H

source_name: RH server number 59


title: RH server number 53_2

description:
technical replicate 2
1553820043_F

source_name: RH server number 53


title: RH server number 45_2

description:
technical replicate 2
1553838024_C

source_name: RH server number 45


title: RH server number 51_2

description:
technical replicate 2
1553820053_C

source_name: RH server number 51


title: RH server number 43_2

description:
technical replicate 2
1553820053_B

source_name: RH server number 43


title: RH server number 46_2

description:
technical replicate 2
1553820043_A

source_name: RH server number 46


title: RH server number 47_2

description:
technical replicate 2
1553838023_E

source_name: RH server number 47


title: RH server number 44_2

description:
technical replicate 2
1553820043_E

source_name: RH server number 44


title: RH server number 42_2

description:
technical replicate 2
1553838031_E

source_name: RH server number 42


title: RH server number 41_2

description:
technical replicate 2
1553820057_E

source_name: RH server number 41


title: RH server number 79

description: US23502366_251469327875_S01_CGH-v4_95_Feb07.txt

hyb_protocol: The samples were hybridized for 40 hours using the Agilent Oligo aCGH Hybridization Kit according to the manufacturer's instructions.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software version 9.5.1.1

data_processing: Data from each array was mean centered. The data across all arrays was aggregated and bimodal. The data was scaled so that the second mode was centered at log10(3/2) for autosomes and log10(2/1) for sex chromosomes.

source_name: RH server number 79

label_protocol: The samples were labeled using the Agilent Geomic DNA Labeling Kit PLUS (Agilent p/n 5188-5309) according to manufacturer's instructions. Genomic DNA was fragmented using restriction exzymes. Random hexamers were used to prime an Exo-Klenow fragment DNA polymerase reaction incorporating cy5/cy3 labeled dUTP.

extract_protocol: DNA was extracted using the Qiagen DNeasy Tissue kit according to the manufacturer's instructions

value: G3 radiation hybrid

source_name: A23 cell line


title: RH server number 80

description: US23502366_251469327876_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 80


title: RH server number 40_2

description:
technical replicate 2
1553838026_B

source_name: RH server number 40


title: RH server number 39_2

description:
technical replicate 2
1553838025_D

source_name: RH server number 39


title: RH server number 38_2

description:
technical replicate 2
1553820049_B

source_name: RH server number 38


title: RH server number 37_2

description:
technical replicate 2
1553838032_E

source_name: RH server number 37


title: 24h-mmg-M

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

hyb_protocol: Labeled RNA was hybridized to Agilent miRNA arrays for 22 hours at 55°C using the Agilent's Hybridization Oven that is suited for bubble-mixing and microarray hybridization processes. Washing was performed using the Gene Expression Wash Buffer kit (Agilent Technologies) following the manufacturer's instructions.

scan_protocol: Slides were scanned on an Agilent microarray scanner (model G2565CA) at 100% and 5% 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 60% of detected spots across all arrays were removed from the analysis. Background corrected intensities of replicated spots on each array were averaged. Data were and inter-array normalized with cyclic Lowess (Bolstad BM et al., Bioinformatics (2003), 19(2):185-93) and then log2-transformed.

source_name: PBL of healthy donor M irradiated with gamma-rays (0.2 Gy) and incubated in modelled microgravity (mmg) for 24h.

label_protocol: We performed miRNA expression profiling from 200 ng of total RNA and following the miRNA Microarray System protocol v. 1.5 (Agilent Technologies). Total RNA was dephosphorylated and ligated with pCp-Cy3. Unincorporated dyes were removed with MicroBioSpin6 columns (BioRad) . Labeled RNA was hybridized to Agilent miRNA arrays for 22 hours at 55°C using the Agilent's Hybridization Oven that is suited for bubble-mixing and microarray hybridization processes.

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 and the Small RNA Nano LabChip respectively using the Agilent Bioanalyzer 2100 (Agilent Technologies). Only total RNA samples with R.I.N. (RNA Integrity Number) values of 6, or higher, and the percentage of miRNA < 20% 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 M, 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 (0.2 Gy) and then incubated in modelled microgravity (mmg) for 24h.


title: 24h-1g-M

source_name: PBL of healthy donor M irradiated with gamma-rays (0.2 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 M, 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 (0.2 Gy) and then kept parallel ground conditions (1g) for 24h.


title: RH server number 74

description: US23502366_251469327266_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 74


title: RH server number 75

description: US23502366_251469327267_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 75


title: RH server number 81

description: US23502366_251469327877_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 81


title: RH server number 83

description: US23502366_251469327302_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 83


title: RH server number 36_2

description:
technical replicate 2
1553838025_C

source_name: RH server number 36


title: RH server number 82

description: US23502366_251469327878_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 82


title: RH server number 32_2

description:
technical replicate 2
1553838032_B

source_name: RH server number 32


title: 4h-mmg-M

source_name: PBL of healthy donor M irradiated with gamma-rays (0.2 Gy) and incubated in modelled microgravity (mmg) for 4h.

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 M, 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 (0.2 Gy) and then incubated in modelled microgravity (mmg) for 4h.


title: RH server number 77

description: US23502366_251469327873_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 77


title: RH server number 35_2

description:
technical replicate 2
1553838023_H

source_name: RH server number 35


title: RH server number 33_2

description:
technical replicate 2
1553838023_C

source_name: RH server number 33


title: RH server number 34_2

description:
technical replicate 2
1553838032_C

source_name: RH server number 34


title: ES treated with Activin A and wnt3a_3d_rep1


title: 4h-1g-M

source_name: PBL of healthy donor M irradiated with gamma-rays (0.2 Gy) in parallel ground conditions (1g) for 4h.

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 M, 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 (0.2 Gy) and then kept parallel ground conditions (1g) for 4h.


title: ES treated with Activin A and wnt3a_3d_rep2


title: RH server number 30_2

description:
technical replicate 2
1553838026_G

source_name: RH server number 30


title: RH server number 31_2

description:
technical replicate 2
1553838023_B

source_name: RH server number 31


title: RH server number 29_2

description:
technical replicate 2
1553820053_E

source_name: RH server number 29


title: RH server number 72

description: US23502366_251469326988_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 72

source_name: A23 cell line


title: RH server number 27_2

description:
technical replicate 2
1553820055_D

source_name: RH server number 27


title: RH server number 71

description: US23502366_251469326987_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 71


title: RH server number 73

description: US23502366_251469327265_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 73


title: RH server number 25_2

description:
technical replicate 2
1553820049_E

source_name: RH server number 25


title: RH server number 70

description: US23502366_251469326986_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 70


title: RH server number 26_2

description:
technical replicate 2
1553820057_H

source_name: RH server number 26


title: RH server number 69

description: US23502366_251469326985_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 69


title: RH server number 28_2

description:
technical replicate 2
1553820055_B

source_name: RH server number 28


title: 24h-mmg-L

source_name: PBL of healthy donor L irradiated with gamma-rays (0.2 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 L, 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 (0.2 Gy) and then incubated in modelled microgravity (mmg) for 24h.


title: RH server number 23_2

description:
technical replicate 2
1553838032_G

source_name: RH server number 23


title: 24h-1g-L

source_name: PBL of healthy donor L irradiated with gamma-rays (0.2 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 L, 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 (0.2 Gy) and then kept parallel ground conditions (1g) for 24h.


title: RH server number 24_2

description:
technical replicate 2
1553820049_D

source_name: RH server number 24


title: RH server number 22_2

description:
technical replicate 2
1553838026_H

source_name: RH server number 22


title: 4h-mmg-L

source_name: PBL of healthy donor L irradiated with gamma-rays (0.2 Gy) and incubated in modelled microgravity (mmg) for 4h.

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 L, 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 (0.2 Gy) and then incubated in modelled microgravity (mmg) for 4h.


title: RH server number 21_2

description:
technical replicate 2
1553838025_H

source_name: RH server number 21


title: RH server number 20_2

description:
technical replicate 2
1553838031_B

source_name: RH server number 20


title: RH server number 18_2

description:
technical replicate 2
1553820053_G

source_name: RH server number 18


title: RH server number 68

description: US23502366_251469326984_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 68

source_name: A23 cell line


title: RH server number 19_2

description:
technical replicate 2
1553820055_C

source_name: RH server number 19


title: RH server number 67

description: US23502366_251469327975_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 67


title: 4h-1g-L

source_name: PBL of healthy donor L irradiated with gamma-rays (0.2 Gy) in parallel ground conditions (1g) for 4h.

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 L, 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 (0.2 Gy) and then kept parallel ground conditions (1g) for 4h.


title: RH server number 17_2

description:
technical replicate 2
1553820055_F

source_name: RH server number 17


title: RH server number 65

description: US23502366_251469327973_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 65


title: RH server number 13_2

description:
technical replicate 2
1553838026_E

source_name: RH server number 13


title: RH server number 15_2

description:
technical replicate 2
1553820055_H

source_name: RH server number 15


title: RH server number 16_2

description:
technical replicate 2
1553838024_G

source_name: RH server number 16


title: RH server number 8_2

description:
technical replicate 2
1553820057_C

source_name: RH server number 8


title: RH server number 14_2

description:
technical replicate 2
1553838024_D

source_name: RH server number 14


title: 24h-mmg-I

source_name: PBL of healthy donor I irradiated with gamma-rays (0.2 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 I, 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 (0.2 Gy) and then incubated in modelled microgravity (mmg) for 24h.


title: RH server number 64

description: US23502366_251469327972_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 64


title: 4h-mmg-I

source_name: PBL of healthy donor I irradiated with gamma-rays (0.2 Gy) and incubated in modelled microgravity (mmg) for 4h.

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 I, 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 (0.2 Gy) and then incubated in modelled microgravity (mmg) for 4h.


title: RH server number 63

description: US23502366_251469327971_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 63


title: 24h-1g-I

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

source_name: PBL of healthy donor I irradiated with gamma-rays (0.2 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 I, 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 (0.2 Gy) and then kept parallel ground conditions (1g) for 24h.


title: RH server number 62

description: US23502366_251469327933_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 66


title: RH server number 11_2

description:
technical replicate 2
1553820043_G

source_name: RH server number 11


title: RH server number 66

description: US23502366_251469327974_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 62

source_name: A23 cell line


title: RH server number 6_2

description:
technical replicate 2
1553838023_D

source_name: RH server number 6


title: RH server number 7_2

description:
technical replicate 2
1553838023_G

source_name: RH server number 7


title: RH server number 5_2

description:
technical replicate 2
1553820049_G

source_name: RH server number 5


title: RH server number 9_2

description:
technical replicate 2
1553838032_F

source_name: RH server number 9


title: RH server number 10_2

description:
technical replicate 2
1553838031_G

source_name: RH server number 10


title: RH server number 4_2

description:
technical replicate 2
1553838032_H

source_name: RH server number 4


title: 4h-1g-I

source_name: PBL of healthy donor I irradiated with gamma-rays (0.2 Gy) in parallel ground conditions (1g) for 4h.

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 I, 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 (0.2 Gy) and then kept parallel ground conditions (1g) for 4h.


title: RH server number 61

description: US23502366_251469327932_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 61


title: RH server number 12_2

description:
technical replicate 2
1553820057_B

source_name: RH server number 12


title: RH server number 58

description: US23502366_251469327929_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 58


title: RH server number 3_2

description:
technical replicate 2
1553820057_G

source_name: RH server number 3


title: RH server number 1_2

description:
technical replicate 2
1553820053_H

source_name: RH server number 1


title: RH server number 60

description: US23502366_251469327931_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 60


title: RH server number 2_2

description:
technical replicate 2
1553838026_C

source_name: RH server number 2


title: RH server number 59

description: US23502366_251469327930_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 59


title: RH server number 57

description: US23502366_251469327928_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 57


title: 24h-1g-F

source_name: PBL of healthy donor F irradiated with gamma-rays (0.2 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 F, 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 (0.2 Gy) and then kept parallel ground conditions (1g) for 24h.


title: 4h-mmg-F

source_name: PBL of healthy donor F irradiated with gamma-rays (0.2 Gy) and incubated in modelled microgravity (mmg) for 4h.

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 F, 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 (0.2 Gy) and then incubated in modelled microgravity (mmg) for 4h.


title: 4h-1g-F

source_name: PBL of healthy donor F irradiated with gamma-rays (0.2 Gy) in parallel ground conditions (1g) for 4h.

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 F, 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 (0.2 Gy) and then kept parallel ground conditions (1g) for 4h.


title: 24h-mmg-F

source_name: PBL of healthy donor F irradiated with gamma-rays (0.2 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 F, 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 (0.2 Gy) and then incubated in modelled microgravity (mmg) for 24h.


title: RH server number 55

description: US23502366_251469327059_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 55

source_name: A23 cell line


title: RH server number 56

description: US23502366_251469327927_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 56


title: choroid plexus - Add1 null - rep5

city: Bar Harbor

first: Raymond

middle: F

last: Robledo

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

hyb_protocol: 5.5 ug of biotin-labeled cDNA was fragmented and hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 DT Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 as per manufacturer's instructions.

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 laser confocal slide scanner.

data_processing: Average signal intensities for each probe set within arrays were calculated by and exported from Affymetrix’s Expression Console (Version 1.1) software using the RMA method which incorporates convolution background correction, sketch-quantile normalization, and summarization based on a multi-array model fit robustly using the median polish algorithm.  For this experiment, four pairwise comparisons were used to statistically resolve gene expression differences between genotype groups using the R/maanova analysis package.  Specifically, differentially expressed genes were detected by using Fs, a modified F-statistic incorporating shrinkage estimates of variance components from within the R/maanova package.  Statistical significance levels of the pairwise comparisons were calculated by permutation analysis (1000 permutations) and adjusted for multiple testing using the false discovery rate (FDR), q-value, method.  Differentially expressed genes were declared at an FDR q-value threshold of 0.05.

source_name: choroid plexus, Add1 null

label_protocol: 250 ng of total RNA was biotin labeled using the Ambion WT Expression Kit as per manufacturer's instructions.

extract_protocol: Choroid plexi were dissected out and placed into Trizol.  Invitrogen  Pure Link RNA Micro Kits were used to extract RNA as per manufacturer's instructions.

value: null (knockout)

value: choroid plexus

tag: strain

value: 3 weeks


title: RH server number 53

description: US23502366_251469327303_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 53


title: choroid plexus - Add1 null - rep4


title: choroid plexus - Add1 null - rep2


title: choroid plexus - Add1 null - rep3


title: choroid plexus - Add1 heterozygote - rep5

source_name: choroid plexus, Add1 heterozygote

value: heterozygous


title: 24h-1g-E

source_name: PBL of healthy donor E irradiated with gamma-rays (0.2 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 E, 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 (0.2 Gy) and then kept parallel ground conditions (1g) for 24h.


title: choroid plexus - Add1 wild -type - rep4

source_name: choroid plexus, Add1 wild-type

value: wild-type


title: choroid plexus - Add1 wild -type - rep5


title: choroid plexus - Add1 heterozygote - rep4


title: 24h-mmg-E

source_name: PBL of healthy donor E irradiated with gamma-rays (0.2 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 E, 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 (0.2 Gy) and then incubated in modelled microgravity (mmg) for 24h.


title: RH server number 54

description: US23502366_251469327058_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 54


title: choroid plexus - Add1 heterozygote - rep3


title: choroid plexus - Add1 null - rep1


title: RH server number 51

description: US23502366_251469327091_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 51


title: 4h-mmg-E

source_name: PBL of healthy donor E irradiated with gamma-rays (0.2 Gy) and incubated in modelled microgravity (mmg) for 4h.

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 E, 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 (0.2 Gy) and then incubated in modelled microgravity (mmg) for 4h.


title: choroid plexus - Add1 heterozygote -rep2


title: choroid plexus - Add1 wild -type - rep2


title: choroid plexus - Add1 wild -type - rep1


title: RH server number 52

description: US23502366_251469332919_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 52


title: 4h-1g-E

source_name: PBL of healthy donor E irradiated with gamma-rays (0.2 Gy) in parallel ground conditions (1g) for 4h.

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 E, 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 (0.2 Gy) and then kept parallel ground conditions (1g) for 4h.


title: Wbp7-/-, LPS 2hrs, replicate 3

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

hyb_protocol: GeneChip Hybridization, Wash and Stain Kit (Affymetrix cat #900720) is used to prepare the Hybridization Cocktail. The kit contains mix for target dilution, DMSO at a final concentration of 7% and pre-mixed biotin-labelled control oligo B2 and bioB, bioC, bioD and Cre controls (Affymetrix cat #900299) at a final concentration of 50 pM, 1.5 pM, 5 pM, 25 pM and 100 pM, respectively. These control oligos serve as positive controls for hybridization. Biotin-labeled sense targets were diluted in hybridization buffer at a concentration of 25 ng/ul and denatured at 99 °C for 5 minutes. Hybridization cocktails were incubated at 45 °C for 5 minutes and centrifuged at maximum speed for 1 minute prior to loading into the GeneChip array cartridge.  Hybridizations were performed for 16 h at 45 °C in a rotisserie oven at 60 RPM. Upon hybridization, GeneChip cartridges were washed and stained with GeneChip Hybridization, Wash and Stain Kit in the Affymetrix Fluidics Station 450 following the FS450_0007 standard protocol. The cartridge is then loaded into the GeneChip Scanner 3000 7G.

scan_protocol: GeneChip arrays are scanned using default parameters. Affymetrix GeneChip Command Console software (AGCC) was used to acquire GeneChip images and generate .DAT and .CEL files.

data_processing: CELs files were imported into Partek Genomics Suite software 6.5 (build 6.11.0321) and RMA normalized. Analysis was limited to probesets matching a known transcript.

molecule: polyA RNA

source_name: Wbp7-/-, LPS 2hrs

label_protocol: Biotin-labeled cDNA targets were synthesized starting from 150 ng of totRNA. Double stranded cDNA synthesis and related cRNA amplification was performed with Ambion® WT Expression Kit (Ambion, Austin, TX). cRNA was reverse transcribed to cDNA fragmented and terminal labeled with Affymetrix GeneChip® WT Teminal Labeling Kit (Affymetrix, Santa Clara, CA). All steps of the protocol were performed according to manufacturer’s specifications. Efficacy of fragmentation procedure was checked on Agilent Bioanalyzer 2100.

growth_protocol: Bone marrow cells isolated from mixed C57BL/6 (94%) and 129/Ola (6%) mice were plated in 10 cm plates in 5ml of BM-medium (high glucose DMEM supplemented with 20% low endotoxin fetal bovine serum, 30% L929-conditioned medium, 1% glutamine, 1%, Pen/Strep, 0.5% Sodium Pyruvate, 0.1% β-mercaptoethanol). Cultures were fed with 2.5 ml of fresh medium every two days.

extract_protocol: RNeasy from Qiagen with DNAse I treatment

treatment_protocol: Macrophages were stimulated with lipopolysaccharide (LPS, 10 ug/ml)

tag: strain background

tag: genotype/variation

value: Primary BMDM cells (7th day of differentiation)

value: LPS (10 ug/ml) for 2hrs


title: Wbp7-/-, LPS 4hrs, replicate 3

source_name: Wbp7-/-, LPS 4hrs

value: LPS (10 ug/ml) for 4hrs


title: choroid plexus - Add1 heterozygote - rep1


title: RH server number 50

description: US23502366_251469327090_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 50

value: male/male


title: Wbp7-/-, LPS 4hrs, replicate 2


title: choroid plexus - Add1 wild -type - rep3


title: RH server number 47

description: US23502366_251469327263_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 47


title: RH server number 49

description: US23502366_251469327045_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 49

source_name: A23 cell line


title: RH server number 46

description: US23502366_251469327262_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 46


title: RH server number 45

description: US23502366_251469332918_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 45


title: 24h-mmg-D

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

source_name: PBL of healthy donor D irradiated with gamma-rays (0.2 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 D, 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 (0.2 Gy) and then incubated in modelled microgravity (mmg) for 24h.


title: 24h-1g-D

source_name: PBL of healthy donor D irradiated with gamma-rays (0.2 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 D, 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 (0.2 Gy) and then kept parallel ground conditions (1g) for 24h.


title: 4h-mmg-D

source_name: PBL of healthy donor D irradiated with gamma-rays (0.2 Gy) and incubated in modelled microgravity (mmg) for 4h.

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 D, 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 (0.2 Gy) and then incubated in modelled microgravity (mmg) for 4h.


title: Wbp7-/-, untreated, replicate 3

source_name: Wbp7-/-, untreated

value: No treatment


title: 4h-1g-D

source_name: PBL of healthy donor D irradiated with gamma-rays (0.2 Gy) in parallel ground conditions (1g) for 4h.

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 D, 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 (0.2 Gy) and then kept parallel ground conditions (1g) for 4h.


title: Wbp7-/-, LPS 2hrs, replicate 1


title: Wbp7-/-, LPS 2hrs, replicate 2


title: Wbp7-/-, untreated, replicate 2


title: Wbp7-/-, untreated, replicate 1


title: Wbp7-/-, LPS 4hrs, replicate 1


title: Wbp7+/-, LPS 4hrs, replicate 3

source_name: Wbp7+/-, LPS 4hrs


title: Wbp7+/-, LPS 2hrs, replicate 3

source_name: Wbp7+/-, LPS 2hrs


title: Wbp7+/-, untreated, replicate 2

source_name: Wbp7+/-, untreated


title: RH server number 44

description: US23502366_251469327074_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 44


title: Wbp7+/-, LPS 2hrs, replicate 1


title: Wbp7+/-, LPS 4hrs, replicate 2


title: Wbp7+/-, untreated, replicate 3


title: RH server number 43

description: US23502366_251469327073_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 43


title: Wbp7+/-, LPS 4hrs, replicate 1


title: Wbp7+/-, LPS 2hrs, replicate 2


title: RH server number 41

description: US23502366_251469327013_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 41


title: Wbp7+/-, untreated, replicate 1


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.


title: RH server number 42

description: US23502366_251469332917_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 42


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: RH server number 39

description: US23502366_251469327925_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 39

source_name: A23 cell line


title: RH server number 38

description: US23502366_251469327173_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 38


title: RH server number 37

description: US23502366_251469327060_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 37


title: IDR-1018-treated, mouse 17 (infected), Spleen

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

hyb_protocol: A total of 1.5ug of labelled cRNA was then prepared for hybridisation to the Sentrix Mouse-6 Expression Beadchip (v1.1) by preparing a probe cocktail (cRNA @ 0.05ug/ul) that includes GEX-HYB Hybridisation Buffer (supplied with the beadchip). A total hybridisation volume of 30ul is prepared for each sample and 30ul loaded into a single array on the Sentrix Mouse-6 Expression Beadchip (v1.1).  A total of 6 different labelled samples can be loaded into 6 individual arrays per beadchip.  The chip is hybridised at 58C for 16 hours in an oven with a rocking platform.  After hybridisation, the chip is washed using the appropriate protocols as outlined in the Illumina manual.

scan_protocol: Upon completion of the washing, the chips are then coupled with Cy3 and scanned in the illumina BeadArray Reader.  The scanner operating software, BeadStudio, converts the signal on the array into a TXT file for analysis.

data_processing: Un-normalized summary probe profiles were output from BeadStudio and analysed using the limma package of Bioconductor open-source software project (http://www.bioconductor.org). Brain and spleen samples were processed separately, where raw intensities were neqc background corrected with offset 50, quantile normalized then log2-transformed.

source_name: IDR-1018-treated, infected, Spleen

label_protocol: A total of 500ng was labelled using the Ambion Total Prep RNA amplification kit (Cat. No. – IL1791).  The quantity of labelled product was ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol.

growth_protocol: Female 8-week-old C57BL/6 mice, were maintained under conventional conditions. The two infected groups were injected i.p. with 1x10^5 P. berghei ANKA-infected red blood cells. IDR-1018 or saline was injected i.v. into the tail vein at 8 mg/kg in 200 µL saline at 48-hour intervals starting 24 h prior to infection. Brains and spleens were taken from three uninfected mice, three saline-treated infected mice and nine IDR-1018-treated infected mice at day 3 of infection.

extract_protocol: Up to one third of the brain or spleen was macerated in 1 ml Trizol with a tissue homogenizer and extracted with chloroform and isopropanol. Samples were washed twice in 75% ethanol and resuspended in RNAse-free water. A maximum of 100 µg RNA was purified by spin columns using the RNeasy Mini kit (Qiagen), following the manufacturer’s instructions and including DNAse digestion. Quality and quantity of RNA was assessed using a Bioanalyser 2100 (Agilent Technologies, Forest Hill, Victoria, Australia).

treatment_protocol: Tissue was stored in RNAlater (Ambion, Applied Biosystems, CA, USA) for 1 day at 4˚C and then at -20˚C until processing.

tag: background strain

tag: mouse

value: Spleen

tag: p. berghei anka-infected

value: infected

tag: brain section

tag: beadchip barcode

tag: beadchip section

value: D


title: IDR-1018-treated, mouse 14 (infected), Brain

source_name: IDR-1018-treated, infected, Brain

tag: tissue

value: Brain

value: back

value: F


title: RH server number 40

description: US23502366_251469327926_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 40

value: G3 radiation hybrid

tag: gender

value: male


title: 4h-mmg-H

source_name: PBL of healthy donor H irradiated with gamma-rays (2.0 Gy) and incubated in modelled microgravity (mmg) for 4h.

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 4h.

tag: cell type


title: 4h-1g-H

source_name: PBL of healthy donor H irradiated with gamma-rays (2.0 Gy) in parallel ground conditions (1g) for 4h.

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 4h.


title: RH server number 36

description: US23502366_251469327044_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 36


title: IDR-1018-treated, mouse 19 (infected), Spleen

value: B


title: non-treated, mouse 37 (uninfected), Spleen

source_name: non-treated, uninfected, Spleen

value: uninfected

value: A


title: IDR-1018-treated, mouse 15 (infected), Brain

value: front

value: C


title: saline-treated, mouse 22 (infected), Brain

source_name: saline-treated, infected, Brain

value: saline

value: E


title: RH server number 35

description: US23502366_251469327043_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 35

value: male/male


title: RH server number 34

description: US23502366_251469327019_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 34


title: saline-treated, mouse 22 (infected), Spleen

source_name: saline-treated, infected, Spleen


title: non-treated, mouse 38 (uninfected), Spleen


title: 24h-mmg-G

source_name: PBL of healthy donor G 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 G, 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 incubated in modelled microgravity (mmg) for 24h.


title: IDR-1018-treated, mouse 16 (infected), Spleen


title: 24h-1g-G

source_name: PBL of healthy donor G 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 G, 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: IDR-1018-treated, mouse 19 (infected), Brain


title: RH server number 33

description: US23502366_251469327018_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 33


title: RH server number 32

description: US23502366_251469327017_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 32

source_name: A23 cell line


title: IDR-1018-treated, mouse 18 (infected), Brain


title: IDR-1018-treated, mouse 15 (infected), Spleen


title: non-treated, mouse 40 (uninfected), Brain

source_name: non-treated, uninfected, Brain


title: IDR-1018-treated, mouse 21 (infected), Brain


title: IDR-1018-treated, mouse 20 (infected), Brain


title: 4g-mmg-G

source_name: PBL of healthy donor G irradiated with gamma-rays (2.0 Gy) and incubated in modelled microgravity (mmg) for 4h.

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 G, 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 incubated in modelled microgravity (mmg) for 4h.


title: RH server number 31

description: US23502366_251469327016_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 31


title: non-treated, mouse 38 (uninfected), Brain


title: IDR-1018-treated, mouse 18 (infected), Spleen

source_name: IDR-1018-treated, infected, Spleen


title: RH server number 30

description: US23502366_251469327015_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 30


title: 4h-1g-G

source_name: PBL of healthy donor G irradiated with gamma-rays (2.0 Gy) in parallel ground conditions (1g) for 4h.

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 G, 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 4h.


title: RH server number 29

description: US23502366_251469327009_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 29


title: RH server number 27

description: US23502366_251469327007_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 27


title: RH server number 28

description: US23502366_251469327008_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 28


title: 24h-mmg-C

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

source_name: PBL of healthy donor C 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 C, 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 incubated in modelled microgravity (mmg) for 24h.


title: saline-treated, mouse 24 (infected), Spleen


title: IDR-1018-treated, mouse 13 (infected), Spleen


title: 24h-1g-C

source_name: PBL of healthy donor C 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 C, 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: non-treated, mouse 40 (uninfected), Spleen

source_name: non-treated, uninfected, Spleen


title: IDR-1018-treated, mouse 16 (infected), Brain

source_name: IDR-1018-treated, infected, Brain


title: 4h-mmg-C

source_name: PBL of healthy donor C irradiated with gamma-rays (2.0 Gy) and incubated in modelled microgravity (mmg) for 4h.

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 C, 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 incubated in modelled microgravity (mmg) for 4h.


title: saline-treated, mouse 23 (infected), Brain

source_name: saline-treated, infected, Brain


title: non-treated, mouse 37 (uninfected), Brain


title: IDR-1018-treated, mouse 14 (infected), Spleen


title: RH server number 26

description: US23502366_251469327006_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 26


title: RH server number 25

description: US23502366_251469327005_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 25

source_name: A23 cell line


title: IDR-1018-treated, mouse 17 (infected), Brain


title: saline-treated, mouse 23 (infected), Spleen

source_name: saline-treated, infected, Spleen


title: miR-NC_HEY 2

city: Atlanta

first: Shubin

last: Shahab

address: 310 Ferst Drive

institute: Georgia Institute of Technology

description: Biological replicate 2 of 2.

hyb_protocol: Hybridization with GeneChip miRNA Array chips (Affymetrix, Santa Clara, CA) was carried out according to the manufacturer's instructions.

scan_protocol: Scanning was performed according to Affymetrix-recommended procedures using the GeneChip scanner 3000.

data_processing: Raw data in the form of CEL files were produced by the Affymetrix GeneChip Operating System (GCOS) software and analyzed using miRNA QC Tool software (Affymetrix). Normalization was performed using the default workflow of the miRNA QC Tool software. Briefly, probesets were tested for detection above background using a Wilcoxon Rank-Sum test (p <0.06) and then normalized using quantile normalization. Probesets with ‘FALSE’ call in all groups were removed from statistical analysis. A constant (16) is added for variance stabilization and then values are summarized using the median polish method. The log base 2 transformed expression values were then normalized across samples by Z-score calculations using Spotfire DecisionSite for Microarray Analysis (DSMA). Probeset intensities were filtered with DSMA using a modulation threshold of 0.5 to include only those probesets with at least a fold change ≥ 1.4. Differentially expressed probesets were identified using the SAM algorithm at a threshold 5% false discovery rate correction.

source_name: Cultured HEY epithelial ovarian carcinoma cell line, control miRNA transfected

label_protocol: MiRNAs were labeled with the Genisphere FlashTag HSR Biotin RNA labeling kit (Genisphere, Hatfield, PA).

growth_protocol: The cells (duplicates or triplicates per transfection, 1.5 × 10^5 per well) were seeded on six-well plates in growth medium RPMI 1640 (Mediatech, Manassas, VA) supplemented with 10 % v/v heat-inactivated fetal calf serum (Invitrogen, Carlsbad, CA), 2 mM L-glutamine (Mediatech), 10 mM HEPES buffer (Mediatech), penicillin (100 U/ml), and streptomycin (100 μg/mL) and were allowed to adhere overnight at 37°C in a 5 % CO2 atmosphere.

extract_protocol: Total RNA was isolated from the transfected HEY cells using the mirVana miRNA isolation kit according to the manufacturer's instructions (Applied Biosystems, Foster City, CA).

treatment_protocol: Approximately 16h after seeding, the wells were washed with PBS and the growth medium was replaced with Opti-MEM (Invitrogen), followed by transfection of hsa-miR-7 miRIDIAN mimic or miRIDIAN miRNA mimic negative control #1 (miR-NC, a C.elegans miRNA, cel-miR-67, with confirmed minimal sequence identity in humans) using the Lipofectamine 2000 transfection agent (Invitrogen) according to the manufacturer's instructions at a final concentration of 25nM. Following 4 hours of  incubation in the reduced serum Opti-MEM medium, the cells were switched back to complete growth medium (RPMI 1640) and allowed to grow for another 48 hours before RNA extraction.

value: HEY

value: epithelial ovarian carcinoma

value: negative control miRNA


title: IDR-1018-treated, mouse 21 (infected), Spleen

source_name: IDR-1018-treated, infected, Spleen

value: Spleen

value: infected


title: miR-NC_HEY 1

description: Biological replicate 1 of 2.


title: saline-treated, mouse 24 (infected), Brain

value: Brain

value: back


title: IDR-1018-treated, mouse 20 (infected), Spleen

value: F


title: 4h-1g-C

source_name: PBL of healthy donor C irradiated with gamma-rays (2.0 Gy) in parallel ground conditions (1g) for 4h.

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 C, 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 4h.


title: RH server number 24

description: US23502366_251469327132_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 24

value: G3 radiation hybrid

value: male


title: RH server number 23

description: US23502366_251469327172_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 23


title: RH server number 22

description: US23502366_251469327171_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 22


title: miR-7_HEY 2

description: Biological replicate 2 of 2.

source_name: Cultured HEY epithelial ovarian carcinoma cell line, miR7 transfected

value: hsa-miR-7 mimic


title: RH server number 21

description: US23502366_251469327146_S01_CGH-v4_95_Feb07.txt

source_name: RH server number 21


title: 4h-mmg-B

source_name: PBL of healthy donor B irradiated with gamma-rays (2.0 Gy) and incubated in modelled microgravity (mmg) for 4h.

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 B, 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 incubated in modelled microgravity (mmg) for 4h.


title: 4h-1g-B

source_name: PBL of healthy donor B irradiated with gamma-rays (2.0 Gy) in parallel ground conditions (1g) for 4h.

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 B, 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 4h.


title: 24h-1g-B

source_name: PBL of healthy donor B 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 B, 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: miRNA HEY 1

description: Biological replicate 1 of 2.

data_processing: Raw data in the form of CEL files were produced by the Affymetrix GeneChip Operating System (GCOS) software and analyzed using miRNA QC Tool software (Affymetrix). Normalization was performed using the default workflow of the miRNA QC Tool software. Briefly, probesets were tested for detection above background using a Wilcoxon Rank-Sum test (p <0.06) and then normalized using quantile normalization. Probesets with ‘FALSE’ call in all groups were removed from statistical analysis. A constant (16) is added for variance stabilization and then values are summarized using the median polish method. The log base 2 transformed expression values were then used for calculations.

source_name: Cultured HEY epithelial ovarian carcinoma cell line, pre-transfected

growth_protocol: The cells (1.5 × 10^5 per well) were seeded on six-well plates in growth medium RPMI 1640 (Mediatech, Manassas, VA) supplemented with 10 % v/v heat-inactivated fetal calf serum (Invitrogen, Carlsbad, CA), 2 mM L-glutamine (Mediatech), 10 mM HEPES buffer (Mediatech), penicillin (100 U/ml), and streptomycin (100 μg/mL) and were allowed to adhere overnight at 37°C in a 5 % CO2 atmosphere.

extract_protocol: Total RNA was isolated from the pre-transfected HEY cells using the mirVana miRNA isolation kit according to the manufacturer's instructions (Applied Biosystems, Foster City, CA).

treatment_protocol: Approximately 16h after seeding, the wells were washed with PBS and the growth medium was replaced with Opti-MEM (Invitrogen) to simulate identical conditions of transfection. Following 4 hours of  incubation in the reduced serum Opti-MEM medium, the cells were switched back to complete growth medium (RPMI 1640) and allowed to grow for another 48 hours before RNA extraction.

value: pre-transfected


title: miRNA HEY 2

description: Biological replicate 2 of 2.


city: Rennes

first: Delphine

last: Rossille

address: 2 avenue du Pr. Léon Bernard

country: France

institute: INSERM U1236-MOBIDIC

description: Gene expression of Subject 55, Day4 stimulated NBCs, CSFEhi fraction, IL-2 positive

hyb_protocol: Extracted RNAs were hybridized onto Illumina Human HT-12 v4 Whole-Genome Gene Expression BeadChips according to standard Illumina protocols (Illumina Inc., San Diego, CA)

scan_protocol: Standard Illumina scanning protocol (iScan system)

data_processing: Raw data is the output from Illumina GenomeStudio version 1.7.0. Processed data is log2 transformed and batch effect corrected (Partek GS, St Louis, MO). The processed data were not normalized for the analysis.

source_name: in vitro cultivated naive B cells (NBCs)

label_protocol: Total RNA was amplified and labeled with biotinylated nucleotides using the Illumina TotalPrep RNA Amplification Kit from Ambion (PN AMIL1791)

growth_protocol: We developed a two-step B cell culture model. CD19+CD27- NBCs were first cultured with F(ab’)2 anti-Ig(A+G+M), CD40L, CpG and IL-2. At D4, activated B cells were washed and then reseeded with IL-2, IL-4 & IL-10 in the absence of CD40L

extract_protocol: Total RNA was extracted with Qiagen RNeasy kit (Qiagen Inc.)

tag: pathology

value: Healthy donor

tag: subject

value: purified naive B cells from blood

tag: growth protocol

value: stimulated

tag: il-2 treatment

value: 50 U/ml IL-2 (added at Day0+16h)

tag: time point

tag: cell fraction

value: CSFEhi