title: Post-26-AER-F

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Scanned using IlluminaHIscanHQ system

data_processing: Data was processed in Genome Studio, quantile normalized and removal of probes not detacted in atleast 10% of the samples

label: not provided

source_name: Vastus Lateralis

extract_protocol: not provided

tag: male or female

value: F


title: Eµ-myc Lymphoma Test D64

status: Public on Sep 10 2014

type: RNA

city: Durham

first: Daphne

middle: R

last: Friedman

state: NC

address: 101 Science Drive, Room 2121, CIEMAS Bldg

country: USA

institute: Duke University Medical Center

hyb_protocol: The cRNA was fragmented and mixed into a hybridization cocktail before application to the array, which was then hybridized for 16 hours at 45C with rotation at 60 rpm.  This was performed at the Duke University DNA Microarray Core Facility.

scan_protocol: Immediately following hybridization, the arrays underwent an automated washing and staining protocol on the GeneChip FS450 fluidics station and were then scanned on the GeneChip Scanner 3000 7G Plus.  This was performed at the Duke University DNA Microarray Core Facility.

data_processing: The data were analyzed with RMA normalization using the standard settings in the affy package from Bioconductor using R.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Lymphoma

label_protocol: Target preparation from total RNA was performed using T7 primers in the cDNA synthesis step, followed by in vitro transcription to produce biotin-labeled cRNA. This was performed at the Duke University DNA Microarray Core Facility.

extract_protocol: Lymphoma tissue was homogenized with a mortar and pestle and with sonication.  Cell pellets were homogenized with a needle and syringe, Lysing Matrix A tube for tissue (MP Biomedicals), and/or QIAshredder homogenizer column (Qiagen).  RNA was extracted using the Rneasy Mini Kit (Qiagen).

tag: genotype/variation

value: Eµ-myc

tag: tissue type

value: lymphoma tumor


title: Eµ-myc Lymphoma Test D58


title: AER_26_POST

city: Wellington

first: David

last: Rowlands

state: Wellington

address: 63 Wallace St Mt Cook

department: Institute of Food, Nutrition and Human Health

country: New Zealand

institute: Massey University

hyb_protocol: 21.5 µl of high-quality biotin-labeled miRNA sample was hybridized to Affymetrix Gene-Chip® miRNA 2.0 Array for 16 h according to Affymetrix protocol

scan_protocol: The arrays were washed and stained on the Affymetrix Fluidics station 400 and scanned with a Hewlett Packard G2500A gene Array Scanner

data_processing: Affymetrix® miRNA QC Tool v 1.1.1.0 was used for the data summarization, normalization, and microarray quality control

organism: Homo sapiens

source_name: VASTUS LATERALIS

label_protocol: low molecular weight RNA was biotin-labeled with FlashTag™ Biotin HSR RNA Labeling Kit

extract_protocol: A biopsy was collected from the right Vastus Lateralis under local anaesthesia and RNA was isolated from muscle (~10 mg) using mirVana™ Kit , Low molecular weight RNA was biotin-labeled with FlashTag™ Biotin HSR RNA Labeling Kit

value: Vastus Lateralis

tag: sample id

tag: exercise type (aerobic or resistance)

value: AEROBIC

tag: pre exercise/ post exercise

value: POST


title: AER_15_PRE

value: PRE


title: Eµ-myc Lymphoma Test D56


title: AER_19_POST


title: AER_15_POST


title: Pre-26-AER-F

label_protocol: Standard Illumina hybridization protocol


title: Post-25-PRT-F

value: RESISTANCE


title: Eµ-myc Lymphoma Test D57


title: Eµ-myc lymphoma 16

type: genomic

description: harvested lymphoma tumor DNA

hyb_protocol: After removing excess labeling dye, the gDNA was hybridized to Agilent Mouse Genome CGH Microarray 1x244K slides.

scan_protocol: The microarray slides were scanned using an Agilent G2565CA Microarray Scanner.

data_processing:
Copy number changes (log2 ratio of Cy3 to Cy5) are called using Agilent Genomic Workbench 5.0.
Log2 ratio cut-offs were 0.2 for amplification, 0.85 for high amplification (≥ 2 copies), -0.2 for deletion, and -2 for homozygous deletion.

molecule: genomic DNA

source_name: Cluster 1 lymphoma

label_protocol: 1.5 ug of gDNA was fragmented and labeled with ULS-Cy3 for lymphoma gDNA or ULS-Cy5 for reference gDNA (Agilent Genomic DNA ULS Labeling Kit) per the manufacturer’s instructions.

extract_protocol: Genomic DNA (gDNA) was extracted from flash frozen lymphoma pieces and normal tail tissue from background strain mice. Lymphoma tissue was homogenized with a mortar and pestle and then sonicated, and DNA was extracted with the DNeasy Blood and Tissue Kit (Qiagen). Tail tissue was digested, and DNA was extracted with isopropanol and subsequently cleaned up with the DNeasy Blood and Tissue Kit.

value: normal background

value: tail


title: Pre-25-PRT-F


title: Eµ-myc lymphoma 14

description: harvested lymphoma tumor DNA

source_name: normal tail tissue from background strain mice


title: Eµ-myc lymphoma 18

description: harvested lymphoma tumor DNA


title: Eµ-myc lymphoma 17

description: harvested lymphoma tumor DNA


title: AER_14_PRE


title: PRT_4_PRE


title: Eµ-myc lymphoma 15

description: harvested lymphoma tumor DNA


title: AER_14_POST


title: Eµ-myc Lymphoma Test D55


title: Eµ-myc Lymphoma Test D48


title: Eµ-myc Lymphoma Test D53


title: Eµ-myc Lymphoma Test D52


title: Eµ-myc lymphoma 13

description: harvested lymphoma tumor DNA


title: Post-23-PRT-F


title: Post-21-PRT-F


title: PRT_10_PRE


title: PRT_2_PRE


title: Pre-23-PRT-F


title: Eµ-myc lymphoma 12

description: harvested lymphoma tumor DNA


title: PRT_4_POST


title: Post-20-AER-F

description: Post-20 (4 replicates)


title: Eµ-myc Lymphoma Test D47


title: Pre-21-PRT-F


title: Post-19-AER-F

description: This sample not included in final analysis (no normalized data)


title: PRT_10_POST


title: Eµ-myc lymphoma 11

description: harvested lymphoma tumor DNA


title: Pre-19-AER-F


title: Eµ-myc lymphoma 10

description: harvested lymphoma tumor DNA


title: Eµ-myc lymphoma 9

description: harvested lymphoma tumor DNA


title: Eµ-myc Lymphoma Test D46


title: Pre-20-AER-F

description: Pre-20 (4 replicates)


title: Eµ-myc lymphoma 8

description: harvested lymphoma tumor DNA


title: Eµ-myc Lymphoma Test D43


title: PRT_2_POST


title: Eµ-myc Lymphoma Test D34


title: Eµ-myc Lymphoma Test D35


title: PRT_23_POST


title: Eµ-myc lymphoma 7

description: harvested lymphoma tumor DNA


title: Pre-18-PRT-M

value: M


title: PRT_25_PRE


title: Post-18-PRT-M


title: PRT_21_PRE


title: PRT_25_POST


title: PRT_21_POST


title: PRT_23_PRE


title: Post-17-PRT-M

description: Post-17 (2 replicates)


title: Eµ-myc lymphoma 6

description: harvested lymphoma tumor DNA


title: 453960A08 - CRR4_2 vs Col0_2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: A comparative assessment of the Arabidopsis sequencing approach High-throughput sequencing cDNA GAII or HiSeq2000 sequenceur (technology Solexa) and data on CATMA array hybridation (version 6). These different characteristics will be studied through the analysis of control samples but also samples from mutants in genes coding for cytosolic or nuclear PPR proteins

hyb_protocol: Col0_2 Cy5 / CRR4_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: InnoScan900_MAPIX, Cy3:pmt voltage 532nm,650V,laser power 5%, Cy5:635nm,pmt voltage 700V,laser power 5%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: aerial - short days (8 hours), 21°C, 64% hygrometri

extract_protocol: Col0_2:18ug. (miRVana_manuel.pdf)

treatment_protocol: no treatment

value: control

tag: harvest date

tag: tissue

value: aerial portion of plant

growth_protocol: aerial - short days (8 hours light), 21°C, 64% hygrometry, culture room (conviron) on loam media

extract_protocol: CRR4_2:19ug. (miRVana_manuel.pdf)

value: CRR4 mutant


title: Pre-17-PRT-M

description: Pre-17 (2 replicates)


title: Eµ-myc lymphoma 1

description: harvested lymphoma tumor DNA


title: Eµ-myc lymphoma 5

description: harvested lymphoma tumor DNA


title: Eµ-myc lymphoma 3

description: harvested lymphoma tumor DNA


title: Eµ-myc lymphoma 4

description: harvested lymphoma tumor DNA


title: Post-15-AER-F


title: Pre-15-AER-F


title: Eµ-myc lymphoma 2

description: harvested lymphoma tumor DNA


title: 453960A06 - DYW1_2 vs Col0_2

hyb_protocol: Col0_2 Cy5 / DYW1_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: DYW1_2:20ug. (miRVana_manuel.pdf)

value: DYW1 mutant


title: PRT_17_POST


title: Pre-14-AER-M


title: 453960A07 - Col0_2 vs CRR4_2

hyb_protocol: CRR4_2 Cy5 / Col0_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PRT_18_POST


title: PRT_17_PRE


title: Post-11-PRT-F


title: PRT_18_PRE


title: Post-14-AER-M


title: PRT_11_PRE


title: 453960A03 - Col0_1 vs CRR4_1

hyb_protocol: CRR4_1 Cy5 / Col0_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: aerial - short days (8 hours light); 21°C; 64% hygrometry, culture room (conviron) on loam media

extract_protocol: CRR4_1:8ug. (miRVana_manuel.pdf)

extract_protocol: Col0_1:20ug. (miRVana_manuel.pdf)


title: PRT_11_POST


title: 453960A04 - CRR4_1 vs Col0_1

hyb_protocol: Col0_1 Cy5 / CRR4_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 453960A05 - Col0_2 vs DYW1_2

hyb_protocol: DYW1_2 Cy5 / Col0_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 019-Pre

hyb_protocol: DNA was hybridization on Infinium Human Methylation 450 BeadChip (Illumina)

scan_protocol: Scanned using Illumina HiScan SQ

data_processing: Image intensity was extracted using Genome Studio Methylation module 1.8.5, and processed in R using SWAN package

label: Cy3, Cy5

label_protocol: Illumina Standard protocol

extract_protocol: DNA was extracted from 5-10mg muscle using Qiagen DNA kit

tag: exercise type

value: AER

tag: gender

tag: condition

value: Pre

tag: treatment

value: pre-exercise


title: 019-Post

value: F

value: Post

value: post-exercise


title: Post-7-AER-M

value: Vastus Lateralis

value: AEROBIC


title: 453960A02 - DYW1_1 vs Col0_1

hyb_protocol: Col0_1 Cy5 / DYW1_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: DYW1_1:16ug. (miRVana_manuel.pdf)


title: 010-Post

value: PRT


title: 010-Pre


title: Pre-11-PRT-F

value: RESISTANCE

value: PRE


title: Pre-10-PRT-F


title: Post-10-PRT-F

value: POST


title: Pre-8-AER-F


title: Post-8-AER-F


title: Pre-7-AER-M

value: M


title: 453960A01 - Col0_1 vs DYW1_1

hyb_protocol: DYW1_1 Cy5 / Col0_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: control


title: Pre-6-AER-F


title: Pre-2-PRT-M

description:
Pre-2 (4 replicates)
This sample not included in final analysis (no normalized data)


title: 018-Post


title: 002-Pre


title: Post-4-PRT-F


title: Post-6-AER-F


title: 002-Post


title: 018-Pre


title: 015-Pre


title: 014-Pre


title: Mouse lung, CFA treated, pandemic H1N1 (H1N1pdm) infected, on Day 5, biological rep 1

city: Toronto

first: Longsi

last: Ran

state: ON

address: 101 College Street

department: Division of Experimental Therapeutics

country: Canada

institute: Toronto General Research Institute

description: replicate 1

scan_protocol: Standard Illumina scanning protocol

data_processing: Day 3 and Day 5 data were normalized using quantile normalization with Illumina GenomeStudio_2010.3 seperately as the microarray experiments on Day 3 and Day 5 were performed in different batches.

source_name: Mouse lung

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification kit in accordance with the prescribed protocol provided with the kit

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

treatment_protocol: Complete Freund’s adjuvant (CFA, Sigma) were mixed with PBS in a total volume of 100ul.    Mice were administered intramuscularly (i.m.) in each quadriceps with 50 ul.  Two days after first administration, mice were infected by 10^4 EID50 of A/Mexico/4108/2009.  At day 2 post infection, another administration was performed.

tag: time

value: day 5

tag: infection

value: pandemic H1N1 (H1N1pdm)

value: lung

value: CFA

tag: strain


title: 015-Post

value: AER


title: Mouse lung, CFA treated, pandemic H1N1 (H1N1pdm) infected, on Day 5, biological rep 2

description: replicate 2


title: Post-2-PRT-M

description:
Post-2 (3 replicates)
This sample not included in final analysis (no normalized data)


title: Mouse lung, CFA treated, pandemic H1N1 (H1N1pdm) infected, on Day 5, biological rep 3

description: replicate 3


title: 006-Post


title: 006-Pre

value: Pre

value: pre-exercise


title: 008-Post

value: F

value: Post


title: Mouse lung, PBS  treated, pandemic H1N1 (H1N1pdm) infected, on Day 5, biological rep 3

description: replicate 3

value: PBS


title: Mouse lung, PBS  treated, pandemic H1N1 (H1N1pdm) infected, on Day 5, biological rep 1

description: replicate 1


title: 014-Post

value: Vastus Lateralis

value: post-exercise


title: Mouse lung, CFA treated, pandemic H1N1 (H1N1pdm) infected, on Day 3, biological rep 3

description: replicate 3

value: day 3


title: Mouse lung, CFA treated, pandemic H1N1 (H1N1pdm) infected, on Day 3, biological rep 2

description: replicate 2


title: Mouse lung, PBS  treated, pandemic H1N1 (H1N1pdm) infected, on Day 5, biological rep 2

description: replicate 2


title: 020-Pre


title: Mouse lung, CFA treated, pandemic H1N1 (H1N1pdm) infected, on Day 3, biological rep 1

description: replicate 1


title: Mouse lung, PBS  treated, pandemic H1N1 (H1N1pdm) infected, on Day 3, biological rep 3

description: replicate 3


title: 008-Pre


title: 017-Pre

value: PRT


title: 025-Pre


title: 025-Post


title: 020-Post


title: 017-Post


title: 023-Post


title: Hipex_PPP_6_rep_group_21 6285449007_D

status: Public on Sep 09 2014

city: La Jolla

first: Roy

middle: M

last: Williams

state: CA

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

data_processing: The raw probe expression values were log2 transformed and normalized with quantiles normalization functions as implemented in the GeneSpring package. The R/Bioconductor limma function removeBatchEffects was used to alleviate observed chip dependent fluctuations.

source_name: whole mouse brain

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: replicate group number

value: HIPEX

tag: age months

value: brain

tag: Sex

tag: genotype

tag: line


title: Pre-4-PRT-F

tag: tissue type

tag: male or female

value: RESISTANCE

value: PRE


title: 023-Pre


title: Hipex_PPP_6_rep_group_21 6203239014_F

value: M


title: 011-Post


title: Hipex_PPM_6_rep_group_26 6285449007_E

value: WT


title: 011-Pre


title: Mouse lung, PBS  treated, pandemic H1N1 (H1N1pdm) infected, on Day 3, biological rep 1

description: replicate 1

value: pandemic H1N1 (H1N1pdm)

value: lung


title: 021-Post


title: Hipex_PPP_1.5_rep_group_25 6203239014_E


title: Hipex_MMP_6_rep_group_31 6203239014_D


title: 004-Post


title: 021-Pre

value: Pre


title: Hipex_MMM_6_rep_group_36 6203239014_B


title: 026-Post

value: AER


title: Hipex_MMP_6_rep_group_31 6203239014_C


title: Hipex_MMP_6_rep_group_31 6203239014_A


title: 004-Pre

value: F

value: pre-exercise


title: Hipex_MMP_1.5_rep_group_35 6203221047_D


title: Hipex_MMM_1.5_rep_group_40 6203239010_A


title: Hipex_MMP_3_rep_group_32 6203221047_E


title: Hipex_MMM_6_rep_group_36 6203239010_C


title: 026-Pre


title: Hipex_MMM_1.5_rep_group_40 6203239010_D


title: Hipex_PPM_3_rep_group_27 6203239010_F


title: Hipex_PPP_1.5_rep_group_25 6203221047_A


title: Hipex_PPP_6_rep_group_21 6203239010_B


title: Hipex_MMP_12_rep_group_34 6203221025_C


title: Hipex_MMP_12_rep_group_34 6203221047_F


title: Hipex_PPP_20_rep_group_23 6203221047_C


title: Hipex_PPP_12_rep_group_24 6203221025_F


title: Hipex_PPM_3_rep_group_27 6203239010_E


title: Hipex_PPP_12_rep_group_24 6203221025_E


title: Hipex_MMM_12_rep_group_39 6203212073_F


title: Hipex_MMP_12_rep_group_34 6203221025_D


title: Hipex_MMM_12_rep_group_39 6203221025_A


title: Hipex_PPP_12_rep_group_24 6203221047_B


title: Hipex_PPM_6_rep_group_26 6203212073_C


title: Hipex_MMM_3_rep_group_37 6203212073_E


title: Hipex_PPM_12_rep_group_29 6203212073_D


title: Hipex_PPM_1.5_rep_group_30 6203212073_A


title: Hipex_PPP_3_rep_group_22 6203212023_F


title: Hipex_MMP_3_rep_group_32 6203212023_C


title: Hipex_PPM_3_rep_group_27 6203212073_B


title: Hipex_MMP_3_rep_group_32 6203212023_D


title: Hipex_PPP_6_rep_group_21 5528656054_C


title: Hipex_PPP_3_rep_group_22 6203212023_E


title: Hipex_MMM_12_rep_group_39 6203221025_B


title: Hipex_PPP_12_rep_group_24 5528656054_F


title: Hipex_MMM_3_rep_group_37 6203212023_A


title: Hipex_MMM_12_rep_group_39 5528656054_E


title: Hipex_MMM_1.5_rep_group_40 5528656054_B


title: Hipex_MMP_6_rep_group_31 5528656054_D


title: Hipex_MMM_1.5_rep_group_40 5528656052_F


title: Hipex_MMM_3_rep_group_37 6203212023_B


title: Hipex_PPM_1.5_rep_group_30 5528656052_D


title: Hipex_PPM_6_rep_group_26 6285449007_F


title: Hipex_MMP_1.5_rep_group_35 5528656052_E


title: Hipex_PPM_1.5_rep_group_30 5528656052_C


title: Hipex_MMP_1.5_rep_group_35 5528656054_A


title: Hipex_PPP_20_rep_group_23 5519936030_C


title: Mouse lung, PBS  treated, pandemic H1N1 (H1N1pdm) infected, on Day 3, biological rep 2

description: replicate 2

value: PBS


title: Hipex_PPP_1.5_rep_group_25 5528656052_A


title: Hipex_PPM_3_rep_group_27 5519936020_B


title: Hipex_MMP_20_rep_group_33 5519936030_A


title: Hipex_PPP_3_rep_group_22 5519936030_F


title: Hipex_MMP_3_rep_group_32 5519936012_F


title: Hipex_MMM_3_rep_group_37 5519936012_C


title: Hipex_MMM_3_rep_group_37 5519936012_B


title: Hipex_MMP_3_rep_group_32 5519936030_D


title: Hipex_MMP_3_rep_group_32 5519936012_E


title: Hipex_PPP_3_rep_group_22 5519936030_E


title: Hipex_PPP_1.5_rep_group_25 5528656052_B


title: Hipex_PPP_3_rep_group_22 5519936020_F


title: Hipex_PPP_20_rep_group_23 5519936030_B


title: Hipex_PPM_3_rep_group_27 5519936020_A


title: Hipex_PPM_3_rep_group_27 5519936020_C


title: Hipex_PPP_3_rep_group_22 5519936020_D


title: Hipex_MMM_3_rep_group_37 5519936012_A


title: Hipex_PPP_20_rep_group_23 5519936009_E


title: Hipex_PPP_20_rep_group_23 5519936009_D


title: Hipex_MMP_20_rep_group_33 5519936008_E


title: Hipex_PPM_20_rep_group_28 5519936009_B


title: Hipex_PPM_20_rep_group_28 5519936009_A


title: 007-Post

value: Post

value: Vastus Lateralis


title: Hipex_MMM_20_rep_group_38 5519936008_C


title: Hipex_PPP_20_rep_group_23 5519936009_F


title: Hipex_PPM_20_rep_group_28 5519936009_C


title: Hipex_MMM_12_rep_group_39 5519936007_A


title: 007-Pre


title: Hipex_MMP_12_rep_group_34 5519936007_C


title: Hipex_MMM_20_rep_group_38 5519936008_B


title: Hipex_MMM_12_rep_group_39 5448533024_B


title: Hipex_MMP_12_rep_group_34 5448533024_D


title: Hipex_PPP_12_rep_group_24 5519936007_F


title: Hipex_MMP_12_rep_group_34 5519936007_B


title: Hipex_MMP_12_rep_group_34 5448533024_E


title: Hipex_PPM_12_rep_group_29 5519936007_E


title: Hipex_PPP_3_rep_group_22 5519936020_E


title: Hipex_MMM_20_rep_group_38 5519936008_A


title: Hipex_MMP_12_rep_group_34 5448533024_F


title: Hipex_MMM_12_rep_group_39 5448533024_A


title: Hipex_MMP_20_rep_group_33 5519936008_D


title: Hipex_PPM_12_rep_group_29 5519936007_D


title: Hipex_MMM_12_rep_group_39 5448533024_C


title: Hipex_PPP_12_rep_group_24 5448533022_E


title: Hipex_PPM_12_rep_group_29 5448533022_C


title: Hipex_PPM_12_rep_group_29 5448533022_B


title: Hipex_PPP_1.5_rep_group_25 5320054005_F


title: Hipex_PPP_12_rep_group_24 5448533022_D


title: Hipex_MMP_20_rep_group_33 5519936008_F


title: Hipex_PPP_1.5_rep_group_25 5320054005_E


title: Hipex_PPM_12_rep_group_29 5448533022_A


title: Hipex_PPM_1.5_rep_group_30 5320054005_C


title: Hipex_MMP_1.5_rep_group_35 5320054004_F


title: Hipex_PPM_1.5_rep_group_30 5320054005_B


title: Hipex_PPM_1.5_rep_group_30 5320054005_A


title: Hipex_MMM_1.5_rep_group_40 5320054004_C


title: Hipex_PPM_1.5_rep_group_30 5320054005_D


title: Hipex_PPM_6_rep_group_26 4457278044_E


title: Hipex_PPP_6_rep_group_21 4457278044_B


title: Hipex_MMM_6_rep_group_36 4457278003_F


title: Hipex_MMP_1.5_rep_group_35 5320054004_D


title: Hipex_PPP_6_rep_group_21 4457278044_A


title: Hipex_MMP_6_rep_group_31 4457278003_D


title: Hipex_MMP_6_rep_group_31 4457278003_B


title: Hipex_MMM_6_rep_group_36 4457278003_E


title: LAV_PPM_4_rep_group_7 6285449007_C

value: LAV


title: Hipex_MMP_1.5_rep_group_35 5320054004_E


title: LAV_MMP_12_rep_group_14 5613738018_F


title: Hipex_MMP_3_rep_group_32 5519936012_D


title: Hipex_PPP_6_rep_group_21 4457278044_C


title: LAV_PPM_12_rep_group_9 5613738018_C


title: Hipex_MMM_1.5_rep_group_40 5320054004_A


title: LAV_PPP_12_rep_group_4 5613738018_D


title: LAV_MMP_4_rep_group_12 6285449007_A


title: LAV_PPP_1.5_rep_group_5 5613738018_E


title: LAV_PPM_20_rep_group_8 5613738018_B


title: Hipex_MMM_1.5_rep_group_40 5320054004_B


title: LAV_PPP_4_rep_group_2 5502448048_E


title: LAV_PPM_4_rep_group_7 5502448048_C


title: Hipex_MMP_6_rep_group_31 4457278003_C


title: Hipex_PPM_6_rep_group_26 4457278044_D


title: LAV_MMP_12_rep_group_14 5613738018_A


title: LAV_PPM_4_rep_group_7 5502448048_B


title: LAV_PPP_4_rep_group_2 5502448048_F


title: LAV_PPP_4_rep_group_2 5502448047_E


title: LAV_PPP_4_rep_group_2 5502448048_D


title: LAV_MMP_4_rep_group_12 5502448047_D


title: LAV_PPP_4_rep_group_2 6285449007_B


title: LAV_PPP_4_rep_group_2 5502448047_F


title: LAV_PPP_12_rep_group_4 5502448048_A


title: LAV_MMM_4_rep_group_17 5502448047_B


title: LAV_MMM_4_rep_group_17 5502448047_A


title: LAV_MMP_1.5_rep_group_15 5502448046_F


title: LAV_MMP_1.5_rep_group_15 5502448046_E


title: LAV_PPM_1.5_rep_group_10 5502448046_D


title: LAV_PPM_20_rep_group_8 5502448042_E


title: LAV_PPM_20_rep_group_8 5502448042_F


title: LAV_PPM_1.5_rep_group_10 5502448042_D


title: LAV_PPP_1.5_rep_group_5 5502448042_C


title: LAV_MMP_4_rep_group_12 5502448047_C


title: LAV_MMM_6_rep_group_16 5502448042_A


title: LAV_MMM_6_rep_group_16 5502448006_F


title: LAV_PPP_6_rep_group_1 5502448006_C


title: LAV_PPM_1.5_rep_group_10 5502448046_C


title: LAV_PPP_1.5_rep_group_5 5502448046_A


title: LAV_PPP_1.5_rep_group_5 5502448046_B


title: LAV_MMM_6_rep_group_16 5502448006_E


title: LAV_PPM_4_rep_group_7 5417796090_E


title: LAV_PPM_6_rep_group_6 5502448006_B


title: LAV_MMM_4_rep_group_17 5417796090_A


title: Hipex_PPP_12_rep_group_24 5448533022_F


title: LAV_PPM_4_rep_group_7 5417796090_F


title: LAV_PPM_4_rep_group_7 5417796090_D


title: LAV_PPM_20_rep_group_8 5417796089_E


title: LAV_PPP_6_rep_group_1 5502448006_D


title: LAV_MMM_4_rep_group_17 5417796090_C


title: LAV_PPM_20_rep_group_8 5417796089_D


title: LAV_PPP_20_rep_group_3 5417796089_C


title: LAV_MMP_6_rep_group_11 5502448042_B


title: LAV_PPM_6_rep_group_6 5502448006_A


title: LAV_PPP_20_rep_group_3 5355492012_D


title: LAV_MMP_20_rep_group_13 5355492011_A


title: LAV_MMM_20_rep_group_18 5417796089_A


title: LAV_MMM_4_rep_group_17 5417796090_B


title: LAV_PPP_20_rep_group_3 5355492012_E


title: LAV_MMM_20_rep_group_18 5355492011_F


title: LAV_MMM_20_rep_group_18 5355492011_E


title: LAV_PPP_20_rep_group_3 5417796089_B


title: LAV_MMM_20_rep_group_18 5355492012_C


title: LAV_PPM_20_rep_group_8 5417796089_F


title: LAV_MMM_20_rep_group_18 5355492011_D


title: LAV_MMP_20_rep_group_13 5355492011_B


title: LAV_MMP_20_rep_group_13 5355492012_A


title: LAV_PPP_20_rep_group_3 5355492012_F


title: LAV_MMP_20_rep_group_13 5355492011_C


title: LAV_PPP_12_rep_group_4 5355492010_F


title: LAV_MMP_20_rep_group_13 5355492012_B


title: LAV_PPM_12_rep_group_9 5355492010_D


title: LAV_MMM_12_rep_group_19 5355492010_B


title: LAV_PPP_12_rep_group_4 5355492003_F


title: LAV_MMM_12_rep_group_19 5355492010_A


title: LAV_PPM_12_rep_group_9 5355492003_B


title: LAV_MMM_1.5_rep_group_20 5216898009_C


title: LAV_PPP_12_rep_group_4 5355492003_E


title: LAV_PPP_1.5_rep_group_5 5216898005_B


title: LAV_MMM_12_rep_group_19 5355492001_A


title: LAV_MMP_12_rep_group_14 5355492010_C


title: LAV_PPP_12_rep_group_4 5355492003_D


title: LAV_MMM_12_rep_group_19 5355492001_B


title: LAV_MMM_1.5_rep_group_20 5216898009_B


title: LAV_PPP_1.5_rep_group_5 5216898005_A


title: LAV_MMM_1.5_rep_group_20 5216898009_A


title: LAV_PPM_12_rep_group_9 5355492010_E


title: LAV_MMP_12_rep_group_14 5355492001_F


title: LAV_MMP_12_rep_group_14 5355492001_D


title: LAV_PPM_1.5_rep_group_10 5216898005_F


title: LAV_MMP_1.5_rep_group_15 5216898009_E


title: LAV_MMP_1.5_rep_group_15 5216898009_D


title: LAV_PPP_1.5_rep_group_5 5216898005_C


title: LAV_PPM_1.5_rep_group_10 5216898005_E


title: LAV_MMP_6_rep_group_11 5212037036_F


title: LAV_MMM_12_rep_group_19 5355492001_C


title: LAV_PPM_12_rep_group_9 5355492003_A


title: LAV_MMP_1.5_rep_group_15 5216898009_F


title: LAV_MMP_12_rep_group_14 5355492001_E


title: LAV_MMP_6_rep_group_11 5212037036_E


title: LAV_PPM_1.5_rep_group_10 5216898005_D


title: LAV_PPP_6_rep_group_1 5212037035_F


title: LAV_MMM_6_rep_group_16 5212037036_C


title: LAV_MMM_6_rep_group_16 5212037036_A


title: LAV_MMM_6_rep_group_16 5212037036_B


title: LAV_PPM_6_rep_group_6 5212037035_A


title: LAV_PPP_6_rep_group_1 5212037035_E


title: Tmprss2-/-TRAMP_APE1

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description: microdissected antierior prostate tumor from  Tmprss2-/-;TRAMP mouse pool 1

hyb_protocol: Experimental and reference probes were combined and competitively hybridized to MPEDB microarrays under a coverslip for 16 h at 63°C.

scan_protocol: Fluorescent array images were collected for Cy3 and Cy5 emissions using a GenePix 4000B fluorescent scanner (Axon Instruments, Foster City, CA). Image intensity data were extracted and analyzed using GenePix Pro v4.1.1.44 software.

data_processing: We normalized the raw data within arrays using the printtiploess function (span=0.2, bc.method=subtract, offset=10) from the Limma package in R.  We assigned a value of NA to poor quality spots (these are represented in the GSM tables as NULL).

source_name: MGS

label_protocol: cDNA probe pairs were prepared by amino-allyl reverse transcription using 2 μg of amplified RNA and labeling with Cy3-dCTP or Cy5-dCTP fluorescent dyes (Amersham Bioscience, Piscataway, NJ.)

extract_protocol: Reference RNA was purified using Trizol (Life Technologies, Rockville, MD) following the manufacturer’s protocol. The RNA was then further purified by RNeasy maxi kit (Qiagen Inc, Valencia, CA) and treated with DNAse using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by one round of mRNA amplification with amino-allyl incorporation using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

value: male

value: Swiss-Webster

tag: age

value: Adult

value: reference pool of normal adult tissues (10% prostate and 30% each testis, liver, and kidney)

extract_protocol: Approximately 10,000 cells were laser-capture microdissected using the Veritas LCM system (Arcturus Mountain View, CA). Total RNA from LCM experimental samples were isolated using the Arcturus PicoPure RNA Isolation kit (Molecular Devices, Sunnyvale, CA) and DNAse-treated using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by two rounds of mRNA amplification using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

value: anterior prostate tumor pool


title: LAV_PPP_6_rep_group_1 5212037035_D

value: brain


title: LAV_MMP_6_rep_group_11 5212037036_D


title: Tmprss2+/+TRAMP_APE3

description: microdissected antierior prostate tumor from Tmprss2+/+;TRAMP mouse pool 3


title: Tmprss2-/-TRAMP_APE3

description: microdissected antierior prostate tumor from  Tmprss2-/-;TRAMP mouse pool 3


title: Tmprss2+/+TRAMP_APE2

description: microdissected antierior prostate tumor from Tmprss2+/+;TRAMP mouse pool 2


title: Benign_APE1

description: microdissected benign antierior prostate epithelium from strain-matched control mouse pool 1

value: benign anterior prostate pool


title: Tmprss2-/-TRAMP_APE2

description: microdissected antierior prostate tumor from  Tmprss2-/-;TRAMP mouse pool 2


title: Benign_APE2

description: microdissected benign antierior prostate epithelium from strain-matched control mouse pool 2


title: Benign_APE3

description: microdissected benign antierior prostate epithelium from strain-matched control mouse pool 3


title: WT_8hDEX_rep3

city: Zwijnaarde

first: Liesbeth

last: Vercruyssen

address: Technologiepark 927

department: Plant Systems Biology

country: Belgium

institute: VIB / Ghent University

description: Transcript profile of wild-type leaves that are in the transition from cell proliferation to expansion

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Background correction, normalization, and summarization were done with robust multichip average (RMA) as implemented in BioConductor (Irizarry et al, 2003a; 2003b; Gentleman et al, 2004). Ath1121501attairgcdf_14.0.0 was used as chip definition file (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp). The BioConductor package Limma was used to identify differentially expressed genes (Smyth, 2004). P-values were corrected for multiple testing according to Benjamini and Hochberg (1995).

source_name: Wild type, 8h DEX leaves 1&2, rep3

label_protocol: Standard Affymetrix protocol

growth_protocol: Plants were grown in vitro on 1/2MS, overlaid with nylon meshes, in long day conditions (16h light/8h dark).

extract_protocol: RNA was extracted according to a combined protocol of TRI Reagent RT (Molecular Research Center) and the RNeasy kit (QIAGEN) with on-column DNase digestion.

treatment_protocol: At 8 DAS, the plants were transferred to 1/2MS medium + 5µM Dexamethasone, by gently lifting the nylon meshes with forceps. After 8h, the plants were harvested and leaves 1&2 were micro-dissected in RNAlater solution (AM7021; AMBION),  incubated at 4ºC for at least one night, and frozen in liquid nitrogen.

tag: ecotype

value: 8 days after stratification

value: Leaves 1 and 2

value: WT


title: AN3GR_8hDEX_rep2

description: Transcript profile after activation of AN3 function during the transition from cell proliferation to expansion

source_name: AN3-GR, 8h DEX leaves 1&2, rep2

tag: tissue


title: WT_8hDEX_rep2

source_name: Wild type, 8h DEX leaves 1&2, rep2


title: LAV_PPM_6_rep_group_6 5212037035_C


title: Tmprss2+/+TRAMP_APE1

description: microdissected antierior prostate tumor from Tmprss2+/+;TRAMP mouse pool 1


title: miR-Neg 72hrs Rep1

city: Riyadh

first: Nehad

last: Alajez

address: 1st floor College of Medicne

department: Anatomy

country: Saudi Arabia

institute: King Saud University College of Medicine

description: Gene expression in MSCs transfectd with miR-negative control (72hrs)

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul following the manufacturer’s instructions. On completion of the fragmentation reaction, 55 ul of 2× Hi-RPM Hybridization Buffer (Agilent) was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome GE 4x44K v2 Microarray chip for 17 hours at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0 (Agilent) using default parameters. Dat were analyzed using Agilent GeneSpring X software

source_name: miR-Neg 72hrs

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Cells were grown in DMEM 4.5g/l glucose supplemented with 10% fetal bovine serum, 1% NEAA, 1% L-glutamine, 100 mg/l penicillin, and 100 mg/l streptomycin

extract_protocol: Total RNA were isolated from transfected hMSC-TERT cells using Total RNA Purification Kit (Norgen-Biotek Corp., Canada) according to the manufacturer’s instructions. The concentrations of total RNA were measured using NanoDrop 2000 (Thermo-Scientific).

treatment_protocol: hMSC cells were transfected with the indicated microRNA precursors (pre-miR-Neg, pre-miR-320c, Ambion) using reverse transfection protocol and lipofectamine™2000 (Invitrogen). Briefly, 0.05x106 cells were reverse-transfected with 30 nM of the indicated pre-miRs complexed with 1.5 ul of lipofectamine 2000 in a 24-well tissue culture plate. Transfection cocktail was subsequently replaced after 4 hours with normal DMEM without antibiotics.

tag: cell line

value: hMSC-TERT


title: miR-320c 72hrs Rep3

description: Gene expression in MSCs transfectd with miR-320c (72hrs)

source_name: miR-320c 72hrs

value: transfectd with miR-320c (72hrs)


title: miR-Neg 72hrs Rep2

value: transfectd with miR-negative control (72hrs)


title: AN3GR_8hDEX_rep3

source_name: AN3-GR, 8h DEX leaves 1&2, rep3


title: WT_8hDEX_rep1

source_name: Wild type, 8h DEX leaves 1&2, rep1


title: AN3GR_8hDEX_rep1

source_name: AN3-GR, 8h DEX leaves 1&2, rep1


title: miR-Neg 72hrs Rep3


title: miR-320c 72hrs Rep2


title: miR-320c 72hrs Rep1


title: pregnant_breast_tumor_54

city: Brussels

first: Sylvain

last: Brohée

address: Boulevard de Waterloo 127

institute: Institut Jules Bordet

description: Gene expression data from breast tumor in pregnant patient

hyb_protocol: Following fragmentation, 132 ng of cRNA were hybridized overnight at 45C on HG U219 96-array plate.

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

data_processing: The data were analyzed with R-Bioconductor statistical suite. Data were normalized using the RMA function (affy package) and a batch effect correction was applied via the ComBat function of the sva package.

molecule: polyA RNA

source_name: breast tumor, pregnant patient

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: mRNA extraction was performed using ZYMO research pinpoint slide RNA isolation system II. Pinpoint solution was added ro the tissue on a glass slide. After air-dry, a thin blue film that embeds the tissue underneath is formed. This was then lifted from the slide and transferred to a tube. Following the treatment of the tissue with Proteinase K and RNA digestions and extraction buffers, the extracted RNA was washed and concentered using the Zymo-Spin TM IC Column

tag: rfs

tag: rfsevent

tag: grade

tag: er

value: Basal

tag: pgr

tag: pn


title: pregnant_breast_tumor_51


title: Control D0 Rep2

description: Gene expression on control MSCs (day 7)

source_name: Control D0 Rep2

extract_protocol: Total RNA were isolated from hMSC-TERT cells using Total RNA Purification Kit (Norgen-Biotek Corp., Canada) according to the manufacturer’s instructions. The concentrations of total RNA were measured using NanoDrop 2000 (Thermo-Scientific).

treatment_protocol: hMSC-TERT cells were cultured in basal medium in 24-well tissue culture plates. When cells reached 80-90% confluence, medium was replaced with Adipogenic induction medium (AIM) (DMEM medium supplemented with 10 % FBS, 10 % Horse Serum (Sigma, St. Louis, MO, USA), 1 % Penicillin-Streptomycin, 100 nM dexamethasone, 0.45 mM isobutyl methyl xanthine [(IBMX) (Sigma)], 3 μg/mL insulin (Sigma), and 1 μM Rosiglitazone (BRL49653). The adipogenic induction medium was replaced every 3 days. Control cells were cultured in parallel in normal DMEM medium. Cells were assessed for adipogenic differentiation on day 7.

tag: treatment

value: control MSCs (day 7)


title: Control D0 Rep3

description: Gene expression on control MSCs (day 7)

source_name: Control D0 Rep3


title: pregnant_breast_tumor_53


title: Adipo D7 Rep2

description: Gene expression on MSCs differentiated into adipocytes (day 7)

source_name: Adipo D7 Rep2

value: differentiated into adipocytes (day 7)


title: pregnant_breast_tumor_52


title: Control D0 Rep1

description: Gene expression on control MSCs (day 7)

source_name: Control D0 Rep1


title: pregnant_breast_tumor_49

value: LumA


title: pregnant_breast_tumor_47

value: LumB


title: pregnant_breast_tumor_48


title: Adipo D7 Rep1

source_name: Adipo D7 Rep1


title: Adipo D7 Rep3

source_name: Adipo D7 Rep3


title: pregnant_breast_tumor_50


title: pregnant_breast_tumor_45


title: Uveal_melanoma_derivative_cell_line_T142_passage60_rep1

city: Québec

first: Karine

last: Zaniolo

state: Québec

address: 1050 Chemin Sainte-Foy

department: CUO-Recherche

institute: Centre de recherche du CHU de Québec

description: Gene expression after 60 cell passages

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole SurePrint G3 Human GE 8x60K (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScanner (G4900DA) using one color scan setting for 1x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10,7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Uveal melanoma derivative cell line T142, passage 60,replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color LLowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification  (QIAGEN, Toronto, ON).  Dye incorporation and cRNA yield were checked with the Nanophotometer pearl(Montréal Biotech).

extract_protocol: Total RNA was isolated directly from two UM primary tumors (patients 142 and 143) and the corresponding cell lines (T142 and T143) cultured to near 100% confluency at passages P4, P20 and P60 using the RNeasy Mini Kit (QIAGEN, Toronto, ON).

tag: cell type

value: Uveal melanoma derivative cell line

tag: gender

value: male


title: Uveal_melanoma_derivative_cell_line_T143_passage60_rep1

description: Gene expression after 60 cell passages

source_name: Uveal melanoma derivative cell line T143, passage 60,replicate 1


title: LAV_PPM_12_rep_group_9 5355492003_C

hyb_protocol: Standard Illumina hybridization protocol

source_name: whole mouse brain

tag: replicate group number

tag: strain

value: LAV

tag: age months

tag: Sex

value: F

tag: genotype


title: pregnant_breast_tumor_44

tag: age


title: Uveal_melanoma_derivative_cell_line_T142_passage20_rep1

description: Gene expression after 20 cell passages

source_name: Uveal melanoma derivative cell line T142, passage 20,replicate 1


title: pregnant_breast_tumor_46


title: pregnant_breast_tumor_41


title: Uveal_melanoma_derivative_cell_line_T143_passage20_rep1

description: Gene expression after 20 cell passages

source_name: Uveal melanoma derivative cell line T143, passage 20,replicate 1


title: Uveal_melanoma_derivative_cell_line_T142_passage4_rep1

description: Gene expression after 4 cell passages

source_name: Uveal melanoma derivative cell line T142, passage 4,replicate 1


title: pregnant_breast_tumor_43


title: pregnant_breast_tumor_42


title: Primary_uveal_melanoma_tumor_143_rep1

description: Gene expression after tumor prelevement

source_name: Primary uveal melanoma tumor 143, replicate 1

tag: tissue

value: Primary uveal melanoma tumor


title: pregnant_breast_tumor_39


title: Primary_uveal_melanoma_tumor_142_rep1

description: Gene expression after tumor prelevement

source_name: Primary uveal melanoma tumor 142, replicate 1


title: Uveal_melanoma_derivative_cell_line_T143_passage4_rep1

description: Gene expression after 4 cell passages

source_name: Uveal melanoma derivative cell line T143, passage 4,replicate 1


title: pregnant_breast_tumor_35


title: pregnant_breast_tumor_37


title: pregnant_breast_tumor_38


title: pregnant_breast_tumor_33


title: pregnant_breast_tumor_26

value: Normal


title: pregnant_breast_tumor_30


title: pregnant_breast_tumor_27


title: pregnant_breast_tumor_31


title: pregnant_breast_tumor_25


title: pregnant_breast_tumor_29


title: pregnant_breast_tumor_28


title: pregnant_breast_tumor_17


title: pregnant_breast_tumor_40


title: pregnant_breast_tumor_19


title: pregnant_breast_tumor_23


title: pregnant_breast_tumor_34


title: pregnant_breast_tumor_21


title: pregnant_breast_tumor_32


title: pregnant_breast_tumor_18


title: pregnant_breast_tumor_12


title: pregnant_breast_tumor_24


title: pregnant_breast_tumor_16


title: pregnant_breast_tumor_14


title: pregnant_breast_tumor_15


title: pregnant_breast_tumor_13


title: pregnant_breast_tumor_22


title: pregnant_breast_tumor_20


title: Untreated [9479628085_H]

city: Brisbane

first: Glen

last: Boyle

state: Queensland

address: 300 Herston Road Herston

department: Department of Cell and Molecular Biology, Cancer Program

country: Australia

institute: QIMR Berghofer Medical Research Insitute

hyb_protocol: Labelled cRNA was hybridized to HumanHT-12 v4 BeadChip Arrays (Illumina Inc, San Diego, CA, USA), and then washed and scanned according to standard Illumina protocols.

data_processing: Data were extracted in GenomeStudio (Illumina) using default analysis settings and no normalization method.  Resulting data were imported into GeneSpring GX v12.5 (Agilent Technologies, Santa Clara, CA, USA).  Expression values were normalized using quantile normalization with default settings.

source_name: Monocytes from untreated patient

label_protocol: Biotinylated cRNA was prepared with the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX, USA).

extract_protocol: RNA was extracted using Qiagen RNeasy mini kit as per manufacturer’s instructions, then DNase treated and purified.  RNA concentration was determined using the NanoDrop 2000 (Thermo Scientific, Wilmington, DE, USA).

tag: subject group

value: untreated patient

tag: graft source

value: Sibling

tag: conditioning received

value: High Intensity Conditioning (Cyclophosphamide/Total Body Irradiation)

value: Monocyte


title: pregnant_breast_tumor_9

source_name: breast tumor, pregnant patient

tag: rfs

tag: rfsevent

tag: grade


title: Untreated [9479628085_F]

scan_protocol: Labelled cRNA was hybridized to HumanHT-12 v4 BeadChip Arrays (Illumina Inc, San Diego, CA, USA), and then washed and scanned according to standard Illumina protocols.

value: Volunteer Unrelated Donor

value: Reduced Intensity Conditioning (Fludarabine/Melphalan)


title: pregnant_breast_tumor_11

tag: er

tag: pgr

tag: pn


title: pregnant_breast_tumor_8


title: Untreated [9479628085_B]


title: pregnant_breast_tumor_4


title: Untreated [9479628085_J]


title: pregnant_breast_tumor_10

value: Basal


title: pregnant_breast_tumor_6


title: Untreated [9479628085_I]


title: pregnant_breast_tumor_5


title: Untreated [9479628085_D]


title: Untreated [9479628078_L]


title: Untreated [9479628085_C]


title: Untreated [9479628085_K]


title: Untreated [9479628085_G]


title: pregnant_breast_tumor_2


title: non_pregnant_breast_tumor_113

description: Gene expression data from breast tumor in non pregnant patient

source_name: breast tumor, non pregnant patient


title: Untreated [9479628085_E]


title: Untreated [9479628078_K]


title: pregnant_breast_tumor_7


title: non_pregnant_breast_tumor_112


title: pregnant_breast_tumor_1


title: Untreated [9479628078_I]


title: Untreated [9479628078_J]


title: non_pregnant_breast_tumor_111


title: pregnant_breast_tumor_3


title: Untreated [9479628085_A]


title: non_pregnant_breast_tumor_110


title: Untreated [9479628078_G]


title: Untreated [9479628078_H]


title: non_pregnant_breast_tumor_108


title: pregnant_breast_tumor_36


title: non_pregnant_breast_tumor_107


title: Untreated [9479628078_F]


title: non_pregnant_breast_tumor_101


title: Untreated [9479628078_D]


title: Untreated [9479628078_E]


title: non_pregnant_breast_tumor_102


title: non_pregnant_breast_tumor_104


title: Untreated [9479628078_C]


title: non_pregnant_breast_tumor_105


title: non_pregnant_breast_tumor_100


title: non_pregnant_breast_tumor_106


title: IL-6R mAb [9479628078_A]

source_name: Monocytes from patient treated with IL-6R mAb

value: patient treated with IL-6R mAb


title: IL-6R mAb [9479628078_B]


title: IL-6R mAb [9479614025_K]


title: non_pregnant_breast_tumor_109


title: non_pregnant_breast_tumor_103


title: non_pregnant_breast_tumor_97


title: non_pregnant_breast_tumor_99


title: IL-6R mAb [9479614025_F]


title: IL-6R mAb [9479614025_I]


title: IL-6R mAb [9479614025_G]


title: IL-6R mAb [9479614025_L]


title: IL-6R mAb [9479614025_J]


title: IL-6R mAb [9479614025_H]


title: non_pregnant_breast_tumor_98


title: IL-6R mAb [9479614025_E]


title: non_pregnant_breast_tumor_94


title: non_pregnant_breast_tumor_92


title: IL-6R mAb [9479614025_C]


title: non_pregnant_breast_tumor_93


title: non_pregnant_breast_tumor_89


title: non_pregnant_breast_tumor_87


title: IL-6R mAb [9479614025_D]


title: IL-6R mAb [9479187135_K]


title: IL-6R mAb [9479187135_H]


title: IL-6R mAb [9479614025_B]


title: IL-6R mAb [9479187135_I]


title: non_pregnant_breast_tumor_91


title: IL-6R mAb [9479187135_G]


title: IL-6R mAb [9479614025_A]


title: non_pregnant_breast_tumor_88


title: non_pregnant_breast_tumor_86


title: IL-6R mAb [9479187135_L]


title: non_pregnant_breast_tumor_96


title: non_pregnant_breast_tumor_84


title: non_pregnant_breast_tumor_90


title: IL-6R mAb [9479187135_J]


title: IL-6R mAb [9479187135_E]


title: IL-6R mAb [9479187135_F]


title: IL-6R mAb [9479187135_C]


title: non_pregnant_breast_tumor_83


title: non_pregnant_breast_tumor_95


title: non_pregnant_breast_tumor_82


title: non_pregnant_breast_tumor_85


title: IL-6R mAb [9479187135_D]


title: INTS11sh_rep3

city: Miami

first: Alessandro

last: Gardini

state: FL

address: 1501 NW 10 Avenue

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

hyb_protocol: Biotin labeled aRNA at 750ng was hybridized  to  Illumina HumanHT-12V4 expression Beadchip with Illumina  HumanHT-12 v4 Expression BeadChip Kit(cat# BD-103-0204 )         Subsequent steps include washing, blocking, and streptavadin-Cy3 staining of the beadchip.

scan_protocol: Fluorescence emission by Cy3 is quantitatively detected with Illumina BeadArray Reader( scan software : Illumina BeadSacn) and GenomeStudio  software provides results in standard file format

data_processing: Intensity raw data were log2 transformed and normalized by quantile normalization using BeadArray (version 2.8.1) package on R

source_name: Hela

label_protocol: samples were biotin-labeled using the TargetAmp™-Nano Labeling Kit for Illumina Expression BeadChip (Epicentre)

growth_protocol: Hela cells were transfected with sh vectors and selected in puromycin, medium was DMEM + 10% FBS

extract_protocol: cells were harvested and lysed in RLT buffer (Qiagen), total RNA was extracted with Rneasy mini kit

treatment_protocol: cells were starved in 1% serum for 48h, then treated with 100 ng/microl of recombinant EGF

tag: knockdown

value: INTS11 depleted cells

tag: cell line

value: HeLa

tag: treatment

value: untreated


title: non_pregnant_breast_tumor_80


title: non_pregnant_breast_tumor_81


title: IL-6R mAb [9479187135_B]


title: non_pregnant_breast_tumor_74


title: non_pregnant_breast_tumor_79

value: LumA


title: IL-6R mAb [9479187135_A]


title: non_pregnant_breast_tumor_69

value: LumB


title: INTS11sh_EGF_rep3

value: EGF


title: non_pregnant_breast_tumor_75


title: INTS11sh_rep2


title: INTS1sh_EGF_rep3

value: INTS1 depleted cells


title: INTS11sh_EGF_rep2


title: CTRLsh_EGF_rep3

value: control cells


title: non_pregnant_breast_tumor_70


title: non_pregnant_breast_tumor_73


title: non_pregnant_breast_tumor_78


title: CTRLsh_rep3


title: non_pregnant_breast_tumor_77


title: non_pregnant_breast_tumor_67


title: CTRLsh_EGF_rep2


title: CTRLsh_rep2


title: INTS1sh_rep3


title: INTS1sh_rep2


title: non_pregnant_breast_tumor_72


title: non_pregnant_breast_tumor_76


title: non_pregnant_breast_tumor_71


title: non_pregnant_breast_tumor_68


title: INTS1sh_EGF_rep2


title: INTS11sh_EGF_rep1


title: INTS11sh_rep1


title: non_pregnant_breast_tumor_63


title: INTS1sh_rep1


title: non_pregnant_breast_tumor_64


title: non_pregnant_breast_tumor_65


title: INTS1sh_EGF_rep1


title: non_pregnant_breast_tumor_62


title: non_pregnant_breast_tumor_66


title: non_pregnant_breast_tumor_61


title: non_pregnant_breast_tumor_58


title: Zeb2_3

city: Madrid

first: Gema

last: Moreno-Bueno

state: Madrid

address: Arturo Duperier

department: Biochemistry

country: Spain

institute: IIB

description: Biological replicate

hyb_protocol: The arrays hybridization was performed using In Situ Hybridization Kit Plus (Agilent technologies) according to Peinado et al, Cancer Research 2008.

scan_protocol: After hybridization and washing, the slides were scanned in an Axon GenePix Scanner (Axon Instruments), according to manufacturer´s protocol.

data_processing: The slides were analyzed using Feature Extraction Software 10.0 (Agilent technologies), following manufacturer’s protocol. A hierarchical clustering method was applied to group the genes and samples on the basis of the similarities in expression and the unsupervised analyses were visualized using the SOTA and TreeView software assuming euclidean distances between genes (http://bioinfo.cnio.es/cgi-bin/tools/clustering/sotarray). Genes with potentially significant changes in expression were identified using the POMELO program (http://www.genoma.wi.mit.edu/MPR/software). We tested the null hypothesis of equal means among groups using T-test, computing p-values using a permutation test. To select differentially expressed genes, we adjusted for multiple testing using the False Discovery Rate (FDR) method (Chung et al, 2004)

organism: Canis lupus familiaris

source_name: MDCK-control

label_protocol: 1mg from tRNA was labelled and array hybridized using the Low RNA Linear Amplification Kit (Agilent) following manufacturer’s protocol.

growth_protocol: MDCK-II (Madin Darby canine kidney type II) were obtained from the American Type Cell Culture (ATCC) (LGC Standards-SLU; Barcelona, Spain) and  were cultured in Dulbecco’s modified Eagle medium  supplemented with 10% fetal calf serum and antibiotics (100 mg mL21 ampicillin and 30 mg mL21 gentamicin, Sigma– Aldrich) in a humidified chamber with 5% CO2, at 37 C. For clone generation, cells were grown in the presence of G418 (400 lg mL21) or puromycin (1 lg mL21) for 2 weeks and individual clones isolated with cloning rings.

extract_protocol: 1mg of total RNA from each independent tumours were labelled with Cy5-dUTP and as control a pooled RNA obtained from equal concentration of each RNA tumor sample labelled with Cy3-dUTP was used. The amplification and labelling of mRNA were performed using   Low RNA Linear Amplification Kit (Agilent technologies),  following manufacturer’s protocol

value: MDCK-II

tag: reference

value: over-expression pLKO empty vector

source_name: MDCK cells over-expressing Zeb2 transcription factor

tag: transcription factor


title: non_pregnant_breast_tumor_56


title: CTRLsh_EGF_rep1


title: non_pregnant_breast_tumor_57


title: non_pregnant_breast_tumor_55

value: Normal


title: CTRLsh_rep1


title: Zeb1_3

description: Biological replicate

source_name: MDCK cells over-expressing Zeb1 transcription factor


title: non_pregnant_breast_tumor_59


title: Zeb2_2

description: Biological replicate

value: over-expressing Zeb2 transcription factor


title: Zeb1_2

description: Biological replicate

value: over-expressing Zeb1 transcription factor


title: Zeb2_1

description: Biological replicate


title: non_pregnant_breast_tumor_53


title: non_pregnant_breast_tumor_60


title: Twist2_3

description: Biological replicate

source_name: MDCK cells over-expressing Twist2 transcription factor


title: Twist2_1

description: Biological replicate

value: over-expressing Twist2 transcription factor


title: Zeb1_1

description: Biological replicate


title: non_pregnant_breast_tumor_52


title: non_pregnant_breast_tumor_50


title: Twist1_1

description: Biological replicate

source_name: MDCK cells over-expressing Twist1  transcription factor


title: Twist2_2

description: Biological replicate


title: non_pregnant_breast_tumor_51


title: Snail1_2

description: Biological replicate

source_name: MDCK cells over-expressing Snail1 transcription factor


title: non_pregnant_breast_tumor_54


title: Twist1_2

description: Biological replicate

value: over-expressing Twist1  transcription factor


title: Snail1_1

description: Biological replicate

value: over-expressing Snail1 transcription factor


title: non_pregnant_breast_tumor_47


title: Snail2_2

description: Biological replicate

source_name: MDCK cells over-expressing Snail2 transcription factor


title: Twist1_3

description: Biological replicate


title: Snail2_3

description: Biological replicate

value: over-expressing Snail2 transcription factor


title: non_pregnant_breast_tumor_48

value: Basal


title: Snail1_3

description: Biological replicate


title: non_pregnant_breast_tumor_46


title: non_pregnant_breast_tumor_45


title: 10666_Time-3

city: Baltimore

first: Ashwin

last: Balagopal

state: MD

address: 855 North Wolf Street, Rangos Building Room 520

department: Medicine

institute: Johns Hopkins Univ. School of Medicine

description: Test

data_processing:
Crt values from the Expression Suite® (Life Technologies)  below 35 were quantile normalized using R (v.3.0.2)/Bioconductor (v.2.12).
Quantile normalized Crts are presented in the normalized matrix and 2^deltaCrt  values (using the pre-infection level as a reference) are shown in the fold-change matrix.
Please note that the normalized data set does not include controls and only includes genes that were detected in at least one sample of the non-normalized data set.

label: FAM

extract_protocol: 100 uL of plasma was extracted using the miRvana PARIS miRNA isolation kit (Life Technologies) according to the manufacturer's protocol for total RNA isolation. 5pmol of synthetic ath-miR-159a was added to each sample's lysis buffer prior to extraction.

tag: subject id

tag: acute hcv outcome

value: Persist

tag: time point

value: plasma


title: 10666_Time-4

description: Test


title: non_pregnant_breast_tumor_44

tag: age

value: LumA


title: 10666_Initial-Viremia

description: Test

source_name: Initial-Viremia

value: Initial-Viremia


title: 70470_Time-4

description: Test

value: Clear


title: 70470_Time-3

description: Test


title: 10666_Pre-Infection

description: Control

source_name: Pre-Infection

value: Pre-Infection


title: 70470_Initial-Viremia

description: Test


title: non_pregnant_breast_tumor_43


title: Snail2_1

description: Biological replicate


title: non_pregnant_breast_tumor_41


title: E47_3

description: Biological replicate

source_name: MDCK cells over-expressing E47 transcription factor


title: non_pregnant_breast_tumor_42


title: E47_2

description: Biological replicate

value: over-expressing E47 transcription factor


title: 70470_Pre-Infection

description: Control


title: non_pregnant_breast_tumor_40


title: 70154_Initial-Viremia

description: Test


title: E47_1

description: Biological replicate

value: MDCK-II


title: 70154_Pre-Infection

description: Control


title: non_pregnant_breast_tumor_39


title: non_pregnant_breast_tumor_38


title: non_pregnant_breast_tumor_35


title: 50075_Time-4

description: Test


title: 70154_Time-4

description: Test


title: non_pregnant_breast_tumor_37


title: 50075_Time-3

description: Test


title: non_pregnant_breast_tumor_33

value: LumB


title: non_pregnant_breast_tumor_36


title: 50075_Initial-Viremia

description: Test


title: 50075_Pre-Infection

description: Control


title: non_pregnant_breast_tumor_31


title: 70154_Time-3

description: Test


title: non_pregnant_breast_tumor_30


title: 70301_Time-3

description: Test


title: 70301_Time-4

description: Test


title: non_pregnant_breast_tumor_28


title: non_pregnant_breast_tumor_29


title: non_pregnant_breast_tumor_34


title: 50000_Pre-Infection

description: Control


title: 50000_Time-4

description: Test


title: 50000_Initial-Viremia

description: Test


title: 50000_Time-3

description: Test


title: non_pregnant_breast_tumor_32


title: 70518_Time-4

description: Test


title: non_pregnant_breast_tumor_26


title: non_pregnant_breast_tumor_23


title: non_pregnant_breast_tumor_24


title: 70301_Initial-Viremia

description: Test


title: 70301_Pre-Infection

description: Control


title: 70518_Time-3

description: Test


title: non_pregnant_breast_tumor_22


title: 70518_Initial-Viremia

description: Test


title: non_pregnant_breast_tumor_25


title: 70518_Pre-Infection

description: Control


title: 50163_Time-4

description: Test


title: non_pregnant_breast_tumor_20


title: non_pregnant_breast_tumor_19


title: non_pregnant_breast_tumor_17


title: non_pregnant_breast_tumor_18


title: non_pregnant_breast_tumor_21


title: 50163_Time-3

description: Test


title: non_pregnant_breast_tumor_15


title: non_pregnant_breast_tumor_14


title: non_pregnant_breast_tumor_16


title: 50179_Pre-Infection

description: Control


title: 50163_Initial-Viremia

description: Test


title: 50163_Pre-Infection

description: Control


title: 50179_Time-4

description: Test


title: 50105_Time-4

description: Test


title: 50179_Initial-Viremia

description: Test


title: non_pregnant_breast_tumor_11


title: non_pregnant_breast_tumor_9


title: non_pregnant_breast_tumor_7


title: 50105_Initial-Viremia

description: Test


title: 50179_Time-3

description: Test


title: non_pregnant_breast_tumor_6


title: non_pregnant_breast_tumor_12


title: non_pregnant_breast_tumor_8


title: 50105_Time-3

description: Test


title: non_pregnant_breast_tumor_4


title: 70226_Time-4

description: Test


title: non_pregnant_breast_tumor_10


title: non_pregnant_breast_tumor_3


title: 50105_Pre-Infection

description: Control


title: non_pregnant_breast_tumor_13


title: non_pregnant_breast_tumor_5


title: non_pregnant_breast_tumor_49


title: non_pregnant_breast_tumor_2


title: non_pregnant_breast_tumor_1


title: 70226_Pre-Infection

description: Control


title: 11187_Time-4

description: Test


title: 70226_Time-3

description: Test


title: 70226_Initial-Viremia

description: Test


title: 4-act R69 [miRNA]

city: montpellier

first: martin

last: villalba

address: CHU Montpellier Hôpital Saint-Eloi 80, av. Augustin Fliche.

department: INSERM U1040

institute: Institut for Research in Biotherapy of Montpellier

description:
SAMPLE 16
11SE249_(miRNA-2_0).CEL

hyb_protocol: Following recommendations of Genisphere, we prepared a mixture of hybridization, which included Eukaryotic Hybridization Controls 20x and control oligonucleotide B2 (Affymetrix). Development of chips took place in an Affymetrix Fluidics Station, using the Hybridization, Wash and Stain kit from Affymetrix.

scan_protocol: GeneChips were scanned using the Scanner 3000 7G (Affymetrix)

data_processing:
Affymetrix GeneChip Command Console Software v3.0 (AGCC 3.0, Affymetrix ®) and the miRNA QC Tool Software (Affymetrix ®) were used for processing of chips and results.
We used the software dChip (www.dchip.org) to determine the existence of cross-hybridization and image contamination. We applied the program Expression Console ofAffymetrix (Gene arrays) and Partek Genomics Suite (miRNA arrays) to obtain the RLE (Relative Log Expression), in which the expression of each probe is normalized with an array of reference built with the average of all arrays for each probe set. The intensity values for each probe were processed and normalized by Robust Multichip Average (RMA). We eliminated sequences with intensities close to the background and, after normalization, those ones that did not change during the experiment in order to reduce the number of genes and the false positives. For the Gene Array we finally obtained a work list of 8711 sequences and for the miRNA we obtained 4581 (selection of all human miRNA present in the microarray).
Th softwares consider as present all p-values under 0.06.

source_name: NK cells_act R69

label_protocol: We used 400ng of each sample to join a tail of Poly (A) with a PolyA Polymerase and then labeled with biotin following the protocol of FlashTag Biotin HSR RNA Labeling Kit for Affymetrix GeneChip miRNA arrays (Genisphere®). Just as indicated by the protocol, as a first step, RNA was added to a mixture of the starting Spike RNA controls included in the kit to allow quality control after hybridization to verify that the processing had occurred as expected.

growth_protocol: 5 days RPMI 5%CO2, 37 C, 1 million/ml

extract_protocol: microRNA were isolated from enriched ex vivo or activated NK cells (more than 90% purity) by using the mirVana miRNA (Invitrogen) Isolation Kit

treatment_protocol: PBLs from 4 different donors were activated by 100 U/ml IL-2; K562+IL-2 or R69 cells. After 5 days we obtained RNA and miRNA from naïve NK cells or from NK cells activated with the above mentioned stimuli. The 16 RNA samples were used to generate cDNA libraries that were hybridized on Human Gene 1.1ST arrays (Affymetrix) and analyzed with the Affymetrix Gene Chip Command Console Software v3.0 (AGCC 3.0, Affymetrix®) and the Expression Console Software v1.1 (Affymetrix®).

tag: donor id

value: donor 4

tag: activated by

value: peripheral blood lymphocytes (PBLs)

tag: cell type

value: EBV-target cell (R69)

tag: cell subtype

value: purified NK cells

tag: molecule subtype

value: miRNA


title: 11187_Time-3

description: Test


title: 2-act R69 [miRNA]

description:
SAMPLE 14
11SE247_(miRNA-2_0).CEL

value: donor 2


title: 2-act K562+IL-2 [miRNA]

description:
SAMPLE 10
11SE243_(miRNA-2_0).CEL

source_name: NK cells_act K562+IL-2

value: MHC-I-deficient target cell (K562)+IL-2


title: 4-act K562+IL-2 [miRNA]

description:
SAMPLE 12
11SE245_(miRNA-2_0).CEL


title: 11187_Initial-Viremia

description: Test


title: 1-act K562+IL-2 [miRNA]

description:
SAMPLE 9
11SE242_(miRNA-2_0).CEL

value: donor 1


title: 1-act R69 [miRNA]

description:
SAMPLE 13
11SE246_(miRNA-2_0).CEL


title: 2-act IL-2 [miRNA]

description:
SAMPLE 6
11SE239_(miRNA-2_0).CEL

source_name: NK cells_act IL-2


title: 3-act K562+IL-2 [miRNA]

description:
SAMPLE 11
11SE244_(miRNA-2_0).CEL

value: donor 3


title: 2-naïve [miRNA]

description:
SAMPLE 2
11SE231_(miRNA-2_0).CEL

source_name: NK cells_naive

value: none(naïve control)


title: 11187_Pre-Infection

description: Control

value: plasma


title: 3-act R69 [miRNA]

description:
SAMPLE 15
11SE248_(miRNA-2_0).CEL


title: 4-act IL-2 [miRNA]

description:
SAMPLE 8
11SE241_(miRNA-2_0).CEL


title: 3-act IL-2 [miRNA]

description:
SAMPLE 7
11SE240_(miRNA-2_0).CEL


title: 50040_Time-4

description: Test

value: Persist


title: 50040_Time-3

description: Test


title: 4-naive [miRNA]

description:
SAMPLE 4
11SE233_(miRNA-2_0).CEL


title: 1-act IL-2 [miRNA]

description:
SAMPLE 5
11SE238_(miRNA-2_0).CEL


title: 3-naive [miRNA]

description:
SAMPLE 3
11SE232_(miRNA-2_0).CEL


title: non_pregnant_breast_tumor_27

source_name: breast tumor, non pregnant patient

tag: rfs

tag: rfsevent

tag: grade

tag: er

value: Basal


title: 50040_Initial-Viremia

description: Test

value: Initial-Viremia


title: Sperm-Blastocyst Replicate 4

city: Quebec

first: Eric

last: Fournier

state: Quebec

address: 2325 Rue de l'Universite

department: Departement des sciences animales

institute: Universite Laval

hyb_protocol: Hybridizations were performed according to the microarray manufacturer's instructions (Agilent Technologies, Santa Clara, USA). Briefly, 1 µg of labeled sample (in 40 µL) was mixed with 158 µL of hybridization master mix containing 25 µL of bovine Cot-1 DNA (1.0 mg/mL, Bovine Hybloc competitor DNA, Applied Genetics Laboratories, Melbourne, FL, USA), 2.6 µL of Agilent 100x Blocking Agent and 130 µL of Agilent 2x HI-RPM Hybridization Buffer (Agilent Technologies, Santa Clara, USA). Samples were held at 95 °C for 3 min and at 37 °C for 30 min followed by addition of 65 µL of Agilent-CGHBlock (final volume 260 µL). The samples were loaded onto the microarray and hybridization was carried out in a hybridization oven (Shel Lab, Cornelius, OR, USA) for 40 h at 65 °C and 20 rpm. Washing was carried out according to the microarray manufacturer's instructions

scan_protocol: Slides were scanned with the PowerScanner (Tecan, Männedorf, Switzerland)

data_processing: Intensity values were obtained from slide images using the Array-Pro Analyzer 6.3 software (MediaCybernetics, Bethesda, MD, USA). Raw intensities were subjected to within-array normalization(loess) followed by between-array normalization (quantile) using the limma library from Bioconductor.

organism: Bos taurus

source_name: Expanded blastocyst

label_protocol: Comparable DNA inputs (10 ng) were used for both embryo and sperm samples. For quality control purposes, all samples were spiked with a mixture of six synthetic DNA constructs all bearing an MseI restriction site at each end. One pair of constructs was designed for each methyl-sensitive restriction enzyme (HpaII, HinP1I and Aci1I) to be used in the fragment selection process. For each pair, one control DNA fragment was methylated in vitro using CpG methyltransferase M.SssI (New England Biolabs, Ipswich, MA, USA). The difference between the extents of cleavage obtained with each pair was used to calculate cleavage efficiency. Residual MseI sites within the fragments were measured after processing to determine the extent of genomic fragmentation.  Sample (in 30 µL of phosphate buffered saline) plus 0.5 µL of bovine serum albumin (New England Biolabs, Ipswich, MA, USA), 5 µL of 10X Buffer 4 (New England Biolabs, Ipswich, MA, USA) and 28 µL of DNAse/RNAse free water were divided into two equal fractions and fragmented using 10 U of MseI restriction enzyme (New England Biolabs, Ipswich, MA, USA) and incubated for 16 h at 37 °C following enzyme inactivation (heating to 65 °C for 20 min). The two fractions were combined and DNA was concentrated by ethanol precipitation following addition of 1 µL of linear acrylamide solution (5 mg/mL, Ambion, Austin, TX, USA) as carrier and 5 µL of sodium acetate buffer (3 M, pH 5.5, Ambion Inc., Austin, TX, USA). The pellet was washed twice with 70 % ethanol and air-dried before dissolution in 5 µL of DNAse/RNAse free water.   Adaptors were ligated as described previously (Klein et al. , 1999) to the fragment cohesive ends left by MseI. Briefly, 0.5 µL of 100 µM stock solution of each primer (MseLig 21: 5’-AGT GGG ATT CCG CAT GCT AGT-3’, MseLig 12: 5’-TAA CTA GCA TGC-3’, IDT DNA, Coralville, IA, USA), 0.5 µL of One-Phor-All plus Buffer (Pharmacia Biotech, Piscataway, NJ) and 1.5 µL of nuclease-free water were added to the sample.  Annealing was begun at 65 °C and the temperature was ramped at 1 °C/min down to 15 °C. T4 DNA ligase (5 units, Boehringer Mannheim) and 10 nmol of ATP were added and the reaction mixture was held at 15 °C for 16 h.  The ligated sample was triple-cleaved with FastDigest™ methyl-sensitive restriction endonucleases (MSRE) HpaII (C/CGG), HinP1I (GC/GC), Aci1I (C/CGC) from Fermentas Thermo Fisher Scientific, Waltham, MA, USA. A first cleavage in 50 µL including 10 µL of sample, 0.5 µL of HpaII, 0.5 µL of HinP1I, 5 µL of 10X FastDigest buffer and 34 µL of nuclease-free water was performed at 37 °C for 12 h. A second cleavage was performed by adding 0.5 µL of Aci1I, 5 µL of 10X FastDigest buffer and 44.5 µL of nuclease-free water and incubating at 37 °C for 4 h, followed by thermal inactivation at 85 °C for 10 min.   Amplicon specificity was determined from the shape of the melting curve and the difference in threshold cycle (Δ Ct) between methylated and unprotected templates was used to calculate cleavage efficiency. The DNA samples were then precipitated in ethanol, washed and dissolved in 10 µL of nuclease-free water.  Selective amplification of methylated fragments was performed using two rounds of ligation-mediated PCR (LM-PCR) as described previously (Klein et al., 1999), with some modifications. The first LM-PCR amplification was carried out in 50 µL using 10 µL of sample to which 0.5 µL of primer solution (MseLig12 and MseLig21, 100 µM) was added, 0.5 µL of One-Phor-All plus Buffer (Pharmacia Biotech, Piscataway, NJ), 3 µL of 10X Ex Taq™ buffer without Mg2+ (TaKaRa, Madison, WI, USA), 1 µL (5 U) of Ex Taq™ enzyme (TaKaRa, Madison, WI, USA), 3 µL of MgCl2 (25 mM), 8 µL of dNTP (2.5 mM ), and 23.5 µL of nuclease-free water. The mixture was then subjected to thermal cycling as follows:  94 °C (40 sec), 57 °C (30 sec) and 72 °C (1 min 15 sec) for 15 cycles; 94 °C (40 sec), 57 °C (30 sec) and 72 °C (1 min, 45 sec) for 34 cycles; and 94 °C (40 sec), 57 °C (30 sec) and 72 °C (5 min) for the final cycle. The PCR products were resolved on 1 % agarose gel to assess the quality. Samples DNA content was quantified using the NanoDrop ND-1000 spectrophotometer before proceeding to the next enrichment round.  To obtain sufficient DNA for downstream processing, three PCR reactions were carried out using 0.75 µL aliquots from the first LM PCR, to which 0.75 µL of MseLig21 primer (100 µM ) was added, plus 5 µL of 10X Buffer 1 (Roche/Boehringer Mannheim, Expand Long Template), 4 µL of dNTPs (2.5 mM ), 0.8 µL of Expand Long Template Enzyme Mix (Roche/ Boehringer Mannheim) and 38.7 µL of nuclease-free water. The following four-step programs were used: 94 °C (60 sec), 65 °C (30 sec), and 72 °C (2 min) for 1 cycle; 94 °C (40 sec), 65 °C (30 sec) and 72 °C (90 sec) for14 cycles; 94 °C (40 sec), 65 °C (30 sec) and 72 °C (2 min) for 9 cycles and 72 °C (5 min) as the final cycle. The quality and concentration of DNA were evaluated as described above.    The amplified product from the second LM-PCR was first purified using a QIAquick PCR Purification Kit (Qiagen, Chatsworth, CA, USA) according to the manufacturer's instructions with minor modifications. Final elution volume was 41.5 µL, of which 1.5 µL was used for quantification by absorbance measurement. The rest was divided in two separate 20 µL aliquots. Adaptors were removed by digestion for 16 h at 37 °C with 5 U of MseI (New England Biolabs, Ipswich, MA, USA). The mixture also contained 0.5 µL of bovine serum albumin (New England Biolabs, Ipswich, MA, USA), 5 µL of 10X Buffer 4 (New England Biolabs, Ipswich, MA, USA), and 24 µL of nuclease-free water. The reaction was terminating by heating for 20 min at 65 °C. The sample was then purified using a QIAquick PCR Purification Kit (Qiagen, Chatsworth, CA, USA), eluted in 23.5 µL of nuclease-free water and quantified by absorbance.  For each sample, 2.5 µg of DNA was labeled using the Universal Linkage System (ULS) labeling kit (Kreatech Biotechnology, Amsterdam, Netherlands) according to the manufacturer's instructions with minor modifications: 1 µL of Cy-ULS dye was added per 1 µg of genomic DNA adjusted with 10X labeling buffer. The labelling mixture was then held for 30 min at 85 °C in a thermocycler, followed by 3 min on ice. Non-reacted ULS-Cy3/5 was removed by purification using a QIAquick PCR Purification Kit and samples were eluted in 23.5 µL nuclease-free water.  A 1.5 µL aliquot was used to determine DNA concentration and dye incorporation using the ND-1000 NanoDrop.

growth_protocol: Blastocysts: dairy cattle ovaries from a commercial slaughterhouse were transported to the laboratory in saline (0.9% NaCl) containing 1% antimycotic agent. Cumulus oocyte complex (COC) collection was conducted within 2 h of reception. COCs were aspirated from 2–6 mm follicles. Healthy COCs with at least five layers of cumulus were selected for maturation. Cumulus-oocyte complexes with fragmented cytoplasm, pyknotic cumulus, pale nuclei and abnormal morphology were rejected. The COCs were washed in HEPES-buffered Tyrode’s medium (TLH) supplemented with 10% bovine serum, 200 μM pyruvate and 50 μg/mL of gentamycin. Groups of ten healthy COCs were placed in 50-μL droplets of medium under 9 mL of filtered mineral oil. Maturation medium was composed of TCM199 (Gibco 11150–059; Invitrogen, Burlington, ON, CAN), 10% foetal bovine serum (Sterile Fetal Bovine Serum for Cell Culture, Medicorp, Montréal, QC, CAN), 200 μm pyruvate, 50 μg/mL of gentamycin and 0.1 μg/mL of follicle stimulating hormone (FSH) (Gonal-f, Serono Canada Inc., Mississauga, QC, CAN). Droplets containing COCs were incubated for 24 h at 38.5°C with 5% CO2, 20% O2 and high humidity. Matured COCs were washed twice in TLH. Groups of five matured COCs were added to 50-μL droplets of medium under filtered mineral oil. Each droplet consisted of modified Tyrode’s lactate medium, supplemented with 0.6% bovine serum albumin (Sigma fraction V), 40 mM pyruvate and 50 μg/mL gentamycin. A solution 1 mM hypotaurine, 2 mM penicillamine and 250 mM epinephrine was then added (2 μL) to the COC-containing droplets. The cryo-preserved pool of spermatozoa came from five Holstein bulls (Centre d’insémination artificielle du Québec). Semen was thawed in water at 37°C, laid on a discontinuous Percoll gradient (2 mL of 45% Percoll over 2 mL of 90% Percoll) and centrifuged at 700 × g for 30 min at room temperature. The pellets were re-suspended in in vitro fertilization medium to obtain a ratio of 50,000 spermatozoa/droplet. Fertilization took place in an incubator for 15–18 h at 38.5°C with 5% CO2, 20% O2 and high humidity. Zygotes and unfertilized COCs were mechanically denuded by repeated pipeting and washed twice in TLH to ensure complete removal of cumulus cells. For standard culture conditions, groups of ten embryos were placed in 10-μL droplets of modified synthetic oviduct fluid (SOF) under filtered mineral oil [68]. Sequential SOF media were used as described previously [69]. The embryos were first placed in SOF#1 (6 mM lactate, 0.2 mM glucose). The embryo culture dishes were incubated 38.5°C with 6.5% CO2, 5% O2 and high humidity. Embryos were transferred to droplets of SOF#2 (1 mM lactate, 0.5 mM glucose) 72 h after fertilization and to droplets of SOF#3 (1 mM lactate, 2.5 mM glucose) 120 h after fertilization. On day 7 post-fertilization, blastocysts were collected, washed three times in nuclease-free phosphate-buffered saline (PBS) and frozen at −80°C until DNA extraction.

extract_protocol: Extraction of genomic DNA was carried out  using an AllPrep DNA/RNA Mini Kit (Qiagen) and samples were eluted in 30 μL. Straws containing frozen semen from Holstein bulls were obtained from L'Alliance Boviteq Inc (Saint-Hyacinthe, QC, Canada).   Sperm genomic DNA was extracted using lysis buffer, followed by ethanol precipitation. The quality and quantity of extracted DNA were analyzed by optical absorbance using a Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies Inc.) and by electrophoresis on 0.5% agarose gel at 45 volts for 2 h.

tag: pool

tag: tissue

value: Expanded blastocyst

source_name: Sperm

value: Sperm


title: mESC differentiation exposed to VPA for 24h, biological rep1

city: Laurel

first: Xiugong

last: Gao

address: 8301 Muirkirk Rd

department: HFP/OLOAS/OCT/DT

institute: US FDA

description: Gene expression data after exposure to VPA

hyb_protocol: Hybridization, wash, and staining were carried out using the Affymetrix GeneChip Hybridization, Wash, and Stain Kit on an Affymetrix Fluidics Station 450 following the manufacturer’s protocols.

scan_protocol: The chips were scanned on Affymetrix GeneChip Scanner 3000 7G and the image (.DAT) files were preprocessed using the Affymetrix GeneChip Command Console (AGCC) software v.4.0 to generate cell intensity (.CEL) files.

data_processing: The values of individual probes belonging to one probe set in .CEL files were summarized using the robust multi-array average (RMA) algorithm embedded in the Expression Console software v.1.3 (Affymetrix), which comprises of convolution background correction, quantile normalization, and median polish summarization.

source_name: mESC exposed to VPA

label_protocol: The total RNA samples (50 ng each) were labeled using the GeneChip WT PLUS Reagent Kit (Affymetrix) following the manufacturer’s protocol.

growth_protocol: Pluripotent C57BL/6 mouse ESCs were seeded on 0.1% gelatin-coated flasks, and maintained at 37 °C in a 5% CO2 humidified incubator at standard densities (i.e., between 5×104/cm2 and 5×105/cm2) in ESGRO Complete Plus Clonal Grade Medium (EMD Millipore). The medium contains leukemia inhibitory factor (LIF), bone morphogenic protein 4 (BMP-4), and a glycogen synthase kinase-3b inhibitor (GSK3b-I) to help maintain pluripotency and self-renewal of the ESCs. Cells were passaged every 2-3 days (when reaching 60% confluence) with ESGRO Complete Accutase (EMD Millipore) at about 1:6 ratio.

extract_protocol: EBs were lysed in RLT buffer (Qiagen) supplemented with β-mercaptoethanol, homogenized by QIAshredder (Qiagen), and kept in a -80 °C freezer until further processing. Total RNA was isolated on the EZ1 Advanced XL (Qiagen) automated RNA purification instrument using the EZ1 RNA Cell Mini Kit (Qiagen) following the manufacturer’s protocol, including an on-column DNase digestion.

treatment_protocol: ESC differentiation cultures were exposed from the EB stage on day 3 for 24 h to 0.25 mM thalidomide (THD), 2.0 mM monobutyl phthalate (MBP), 1.0 mM valproic acid (VPA), or vehicle (0.25% DMSO).

tag: strain

value: embryonic stem cell


title: mESC differentiation exposed to VPA for 24h, biological rep2


title: 50040_Pre-Infection

description: Control

value: Pre-Infection


title: 1-naïve [miRNA]

description:
SAMPLE 1
11SE230_(miRNA-2_0).CEL

value: peripheral blood lymphocytes (PBLs)


title: 11108_Time-4

description: Test

value: Clear


title: mESC differentiation exposed to VPA for 24h, biological rep3


title: mESC differentiation exposed to THD for 24h, biological rep3

description: Gene expression data after exposure to THD

source_name: mESC exposed to THD


title: 11108_Time-3

description: Test


title: Biopsy from SVZ of Naive rat, rep 3

city: Stockholm

first: Ruxandra

last: Covacu

country: Sweden

institute: Karolinska Institutet

description: Healthy rats

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

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data processing involved background signal correction using the GC composition-based background correction algorithm (PM-GCBG), array normalization with global median and signal summarization using the probe logarithmic intensity error estimation (plier), all steps performed in the GeneChip Expression console from Affymetrix.
To calculate the statistical significance between naïve and EAE groups two-sided unpaired student’s t-test was used. The false discovery rate (FDR) was calculated using the q-value plugin for R and an FDR level of 5% was set.  The functional analysis and canonical pathway analysis of the entire data set was generated with Ingenuity Pathway Analysis
probe group file: RaGene-1_0-st-v1.r4.pgf
meta-probeset file: RaGene-1_0-st-v1.r4.mps

organism: Rattus norvegicus

source_name: SVZ Naive

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: NPC cultures propagated from different segments of the central nervous system: subventricular zone (SVZ) and the cervical, thoracic and caudal parts of the spinal cord. The segments were isolated from either healthy (naive) rats or rats with EAE.

extract_protocol: Total RNA extraction and on-column DNase treatment was performed using the RNeasy mini kit from Qiagen.

value: Biopsy

tag: biopsy taken from

value: SVZ

tag: differentiation stage

value: Not applicable

tag: disease state

value: Healthy


title: Sperm-Blastocyst Replicate 3


title: 11108_Initial-Viremia

description: Test

tag: subject id

tag: acute hcv outcome

tag: time point


title: mESC differentiation exposed to MBP for 24h, biological rep2

description: Gene expression data after exposure to MBP

source_name: mESC exposed to MBP


title: mESC differentiation exposed to THD for 24h, biological rep1


title: Biopsy from SVZ of Naive rat, rep 1

description: Healthy rats


title: 11108_Pre-Infection

description: Control


title: 50067_Time-4

description: Test


title: mESC differentiation exposed to MBP for 24h, biological rep3


title: 4-act R69

description: SAMPLE 16

hyb_protocol: For the preparation of mixtures of hybridization, washing, and detection of the arrays, GeneTitan Hybridization, Wash and Stain kit for WT Array Plates were used. Hybridization, developing, washing and scanning of 1.1STHuman Gene arrays was performed on an automated GeneTitan System, as recommended by Affymetrix.

scan_protocol: GeneChips were scanned using the Gene Titan System.

data_processing:
Software used for the processing of the chips and the results were the Affymetrix GeneChip Command Console Software v3.0 (AGCC 3.0, Affymetrix®) and the Expression Console Software v1.1 (Affymetrix®).
We used the software dChip (www.dchip.org) to determine the existence of cross-hybridization and image contamination. We applied the program Expression Console ofAffymetrix (Gene arrays) and Partek Genomics Suite (miRNA arrays) to obtain the RLE (Relative Log Expression), in which the expression of each probe is normalized with an array of reference built with the average of all arrays for each probe set. The intensity values for each probe were processed and normalized by Robust Multichip Average (RMA). We eliminated sequences with intensities close to the background and, after normalization, those ones that did not change during the experiment in order to reduce the number of genes and the false positives. For the Gene Array we finally obtained a work list of 8711 sequences and for the miRNA we obtained 4581 (selection of all human miRNA present in the microarray).
The softwares consider as present all p-values under 0.06.

label_protocol: cDNA was synthesized from total RNA and, after fragmentation, hybridized with the chips, following the protocol proposed by Affymetrix. Specifically, 16 total RNA samples were used to generate cDNA with the Ambion® WT Expression kit. The main steps of the protocol were: synthesis of cDNA with random oligonucleotides including the T7 promoter, transcription in vitro; new synthesis of cDNA from the resulting cRNA from above, including dUTP. The obtained cDNA was fragmented using UDG (uracil DNA glycosylase) and APE1 (apurinic/apyrimidinic endonuclease1) and labeled with terminal transferase using the terminal WT Labeling kit.

tag: donor id

value: donor 4

value: peripheral blood lymphocytes

tag: activated by

value: EBV-target cell (R69)

value: purified NK cells


title: Biopsy from SVZ of Naive rat, rep 2

description: Healthy rats


title: mESC differentiation exposed to THD for 24h, biological rep2

tag: cell type


title: 3-act R69

description: SAMPLE 15

value: donor 3

tag: cell subtype


title: Biopsy from SVZ of EAE rat, rep 3

description: Rats with EAE

source_name: SVZ EAE

value: EAE


title: 1-act R69

description: SAMPLE 13

value: donor 1


title: 50067_Time-3

description: Test

value: Persist

value: plasma


title: mESC differentiation at 168h, biological rep3

description: Gene expression data during spontaneous differentiation

source_name: mESC 168h after EB formation

value: embryonic stem cell


title: Biopsy from SVZ of EAE rat, rep 2

description: Rats with EAE


title: Sperm-Blastocyst Replicate 1

value: Sperm

value: Expanded blastocyst


title: Biopsy from SVZ of EAE rat, rep 1

description: Rats with EAE


title: Sperm-Blastocyst Replicate 2


title: mESC differentiation exposed to MBP for 24h, biological rep1


title: 2-act R69

description: SAMPLE 14

value: donor 2


title: mESC differentiation at 168h, biological rep1


title: 50067_Pre-Infection

description: Control

value: Pre-Infection


title: mESC differentiation at 168h, biological rep2


title: Differentiated NPC culture from Caudal Spinal cord (Sp.c) of Naive rat, rep 3

description:
NPC culture harvested after second passage and 5 days of differentiation
Healthy rats

source_name: Sp.c Caudal Naive

value: Dark Agouti

value: NPC culture

tag: npc culture propagated from

value: Caudal Spinal cord

value: Differentiated


title: 4-act K562+IL-2

description: SAMPLE 12

value: donor 4

value: peripheral blood lymphocytes

value: MHC-I-deficient target cell (K562)+IL-2


title: 3-act K562+IL-2

description: SAMPLE 11

value: donor 3

value: purified NK cells


title: 10301_Time-4

description: Test

value: Clear


title: Differentiated NPC culture from Caudal Spinal cord (Sp.c) of Naive rat, rep 2

value: Healthy


title: Differentiated NPC culture from Caudal Spinal cord (Sp.c) of EAE rat, rep 3

description:
NPC culture harvested after second passage and 5 days of differentiation
Rats with EAE

source_name: Sp.c Caudal EAE

value: EAE


title: 10301_Initial-Viremia

description: Test

source_name: Initial-Viremia

value: Initial-Viremia

value: plasma


title: 10301_Time-3

description: Test


title: mESC differentiation at 120h, biological rep2

source_name: mESC 120h after EB formation

value: embryonic stem cell


title: mESC differentiation at 120h, biological rep3


title: Differentiated NPC culture from Caudal Spinal cord (Sp.c) of Naive rat, rep 1


title: Differentiated NPC culture from Caudal Spinal cord (Sp.c) of EAE rat, rep 2


title: 1-act K562+IL-2

description: SAMPLE 9

value: donor 1


title: mESC differentiation at 120h, biological rep1


title: 4-act IL-2

description: SAMPLE 8


title: 50067_Initial-Viremia

description: Test

value: Persist


title: 10301_Pre-Infection

description: Control

source_name: Pre-Infection

value: Pre-Infection