title: SW480 cells (24_SW480) [cell line]

value: SW480 cells


title: LS174T cells (29_LS174T) [cell line]

status: Public on Jun 24 2012

type: RNA

city: Berne

first: Pascale

last: Anderle

state: BE

address: Buehlstrasse 28

department: Institute of Biochemistry and Molecular Medicine

country: Switzerland

institute: University of Berne

hyb_protocol: cRNA was hybridized to Human Genome U133 Plus 2.0 arrays (Affymetrix, Santa Clara, USA).

scan_protocol: Standard Affymetrix protocol

data_processing: Robust multi-array averaging and quantile normalization were used to quantify gene expression (R, Bioconductor, RMA package).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: colon carcinoma derived cell line

label_protocol: 100 ng of total RNA were amplified and labeled using Affymetrix protocols.

growth_protocol: SW480 were cultured in RPMI 1640 containing 10% fetal calf serum (FCS), Caco-2, HT29, LS174T in Dulbecco's modified Eagle essential medium (DMEM) Glutamax containing 10% FCS and T84 in RPMI 1640 containing 10% FCS and 2 mM glutamine. For the culture of Caco-2LD cells antibiotic mixture (100 U/ml penicillin, 100 µg/ml streptomycin) was added to the media. All cell lines were cultured in 37°C and 5% CO2. CacoReadyTM kit cells (Readycell, Barcelona, Spain) were cultured on 24-transwells filters for either 14 days in DMEM Low glucose containing 10% FCS, 1% L-Glutamine and 1% Penicillin/Streptomycin, then 4 days of culture in semi-solid shipping media and again 3 days in culture media (Readycell’s patented technology), or for 3 weeks in the absence of the semi-solid shipping media. Differentiated Caco-2LD cells were grown at low density and then differentiated on 0.4 µm PET filters as described by Natoli et al J Cell Physiol 226, 1531-1543 (2011).

extract_protocol: Total RNA was extracted using the total RNA extraction Nucleospin II kit by Machery-Nagel (Oensingen, Switzerland).

tag: tissue

value: colon

tag: cell line

value: LS174T cells


title: Control 1

city: Stanford

first: May

last: Han

address: 1201 Welch Road

country: USA

institute: Stanford University

description:
Fresh-frozen autopsy brain samples
Gene expression data from healthy control brain samples

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 2.0 array (Affymatrix). GeneChips were washed and stained in the GeneChip Hybridization Oven 640.

scan_protocol: GeneChips were scanned using the Affymatrix Genechip Scanner 3000 7G.

data_processing: The data were analyzed with Affymatrix Gene Expression Console using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

source_name: White matter from age-matched healthy controls

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-5 ug total RNA (3'IVT protocol from Affymatrix ).

growth_protocol: Fresh-frozen autopsy brain samples from MS and control subjects were studied

extract_protocol: Total RNA from MS and control brain samples were extracted utilizing RNAEasy kit from Qiagen.

treatment_protocol: MS brain lesions were characterized histologically according to disease activity as AP (active plaque), CAP (chronic active plaque), CP (chronic plaque). Control brain samples were analyzed to rule out neurological disorders.

tag: histology

value: control

tag: disease state

value: healthy control

value: brain white matter


title: CacoReady cells, grown on filters (69_cacoB) [cell line]

value: CacoReady cells

tag: growth protocol

value: grown on filters


title: SW480 cells (26_SW480) [cell line]


title: LS174T cells (27_LS174T) [cell line]


title: 3-week T84 cells (21_T84) [cell line]

value: colon, metastatic site lung

value: T84 cells


title: 3-week HT29 cells (18_HT29) [cell line]

value: HT29 cells


title: Caco-2 cells (66_caco_JU) [cell line]

value: Caco-2 cells


title: Case seven: invasive breast cancer tissue

status: Public on Jun 23 2012

city: Nottingham

first: Sarkawt

last: Khoshnaw

address: Queens Medical Centre

country: United Kingdom

institute: University of Nottingham

description:
miRNAs expression profiling using Human miRNA Microarrays Release 16.0 (Agilent Technologies)
[3736-3]

hyb_protocol: Cyanine-3-labelled miRNA samples were hybridised to human miRNA microarrays (Release 16.0, 8x60K) (Agilent Technologies, Santa Clara, USA) at 55°C for 20 hrs. Microarray slides were washed with increasing stringency (Gene Expression Wash Buffers, Agilent Technologies, Santa Clara), and subsequently dried with acetonitrile (Sigma-Aldrich, St. Louis, USA).

scan_protocol: Fluorescent signal intensities were detected on an Agilent Microarray Scanner (Agilent Technologies, Santa Clara, USA) using the Scan Control A.8.4.1 Software (Agilent Technologies, Santa Clara, USA).

data_processing: Fluorescent signal intensities were extracted from the images with the Feature Extraction 10.7.3.1 Software (Agilent Technologies, Santa Clara, USA). The raw signal values were 'normalized to the 90th percentile' when importing the FE files into GeneSpring (the analysis software). Only the top 20% of probes on the array typically had any detectable signal so shifting to the 90th percentile meant the median line was around the centre of this expressed set.

source_name: Mastectomy

label_protocol: MiRNAs extracted from laser microdissected tissue components were profiled using Agilent microRNA microarray profiling system (Agilent Technologies, Santa Clara, USA). Total RNA samples were spiked using the MicroRNA Spike-In Kit (Agilent Technologies, Santa Clara, USA) to evaluate efficiencies of labelling and hybridisation. Total RNA was treated with Calf Intestinal Alkaline Phosphatase (CIP), and then 100 ng of total RNA was used per sample to initiate a labelling reaction. Ligation master mix for T4 RNA ligase, which includes Cyanine 3-Cytidine biphosphate (Cyanine 3-pCp) (Complete miRNA Labelling and Hyb Kit, Agilent Technologies, Santa Clara, USA) was used to label the dephosphorylated RNA.

extract_protocol: Twenty μm thick FFPE sections were cut and mounted on PALM Membrane Slides. Under direct microscopic visualization, tissues of interest were micro-dissected using PALM non-contact Laser catapulsion instrument (P.A.L.M. Microlaser Technologies, Carl Zeiss Ltd). Total RNA, including miRNAs, was extracted with the TRIzol reagent (Invitrogen, supplied by Fisher Scientific UK Ltd) according to the manufacturer’s instructions. Total RNA was quantified with Quant-iT RiboGreen RNA Quantitation Kit (Fisher Scientific UK Ltd), which is an accurate method of measuring total RNA with a detection limit of 0.001-1ng/µl. RNA purity and RNA integrity number (RIN) were determined on an Agilent 2100 Bioanalyzer and RNA 6000 NanoLabChip Kits (both Agilent Technologies, Santa Clara, USA).

treatment_protocol: Mastectomised breast and the axillary lymph nodes kept in formalin

tag: gender

value: female

tag: age

value: 56 years

tag: tissue origin

value: breast

value: invasive breast cancer tissue


title: Case seven: ductal carcinoma in situ

description:
miRNAs expression profiling using Human miRNA Microarrays Release 16.0 (Agilent Technologies)
[3736-2]

value: ductal carcinoma in situ


title: Case five: ductal carcinoma in situ

description:
miRNAs expression profiling using Human miRNA Microarrays Release 16.0 (Agilent Technologies)
[3380-2]

value: 52 years


title: Case seven: normal breast tissue

description:
miRNAs expression profiling using Human miRNA Microarrays Release 16.0 (Agilent Technologies)
[3736-1]

value: normal breast tissue


title: Case six: metastatic breast cancer tissue

description:
miRNAs expression profiling using Human miRNA Microarrays Release 16.0 (Agilent Technologies)
[3424-4]

value: metastatic breast cancer tissue


title: SW480 cells (25_SW480) [cell line]

value: colon

value: SW480 cells


title: Case seven: metastatic breast cancer tissue

description:
miRNAs expression profiling using Human miRNA Microarrays Release 16.0 (Agilent Technologies)
[3736-4]


title: 3-week T84 cells (22_T84) [cell line]


title: Case six: invasive breast cancer tissue

description:
miRNAs expression profiling using Human miRNA Microarrays Release 16.0 (Agilent Technologies)
[3424-3]


title: Case five: invasive breast cancer tissue

description:
miRNAs expression profiling using Human miRNA Microarrays Release 16.0 (Agilent Technologies)
[3380-3]


title: Case five: metastatic breast cancer tissue

description:
miRNAs expression profiling using Human miRNA Microarrays Release 16.0 (Agilent Technologies)
[3380-4]


title: Case six: normal breast tissue

description:
miRNAs expression profiling using Human miRNA Microarrays Release 16.0 (Agilent Technologies)
[3424-1]


title: Case six: ductal carcinoma in situ

description:
miRNAs expression profiling using Human miRNA Microarrays Release 16.0 (Agilent Technologies)
[3424-2]


title: Case five: normal breast tissue

description:
miRNAs expression profiling using Human miRNA Microarrays Release 16.0 (Agilent Technologies)
[3380-1]


title: Case two: metastatic breast cancer tissue

description:
miRNAs expression profiling using Human miRNA Microarrays Release 16.0 (Agilent Technologies)
[2734-4]

value: 36 years


title: Case two: invasive breast cancer tissue

description:
miRNAs expression profiling using Human miRNA Microarrays Release 16.0 (Agilent Technologies)
[2734-3]


title: Case two: ductal carcinoma in situ

description:
miRNAs expression profiling using Human miRNA Microarrays Release 16.0 (Agilent Technologies)
[2734-2]


title: Case two: normal breast tissue

description:
miRNAs expression profiling using Human miRNA Microarrays Release 16.0 (Agilent Technologies)
[2734-1]


title: Case three: metastatic breast cancer tissue

description:
miRNAs expression profiling using Human miRNA Microarrays Release 16.0 (Agilent Technologies)
[2758-4]

value: 38 years


title: Case three: ductal carcinoma in situ

description:
miRNAs expression profiling using Human miRNA Microarrays Release 16.0 (Agilent Technologies)
[2758-2]


title: Case three: invasive breast cancer tissue

description:
miRNAs expression profiling using Human miRNA Microarrays Release 16.0 (Agilent Technologies)
[2758-3]


title: Case three: normal breast tissue

description:
miRNAs expression profiling using Human miRNA Microarrays Release 16.0 (Agilent Technologies)
[2758-1]


title: Case one: metastatic breast cancer tissue

description:
miRNAs expression profiling using Human miRNA Microarrays Release 16.0 (Agilent Technologies)
[2730-4]

value: 62 years


title: Case one: ductal carcinoma in situ

description:
miRNAs expression profiling using Human miRNA Microarrays Release 16.0 (Agilent Technologies)
[2730-2]


title: Case one: invasive breast cancer tissue

description:
miRNAs expression profiling using Human miRNA Microarrays Release 16.0 (Agilent Technologies)
[2730-3]


title: 3-week Caco-2 cells (15_Caco2) [cell line]


title: Caco-2LD cells, grown on filters (64_cacoF) [cell line]

value: Caco-2LD cells

value: grown on filters


title: 3-week Caco-2 cells (16_Caco2) [cell line]


title: 3-week Caco-2 cells (17_Caco2) [cell line]


title: Case one: normal breast tissue

description:
miRNAs expression profiling using Human miRNA Microarrays Release 16.0 (Agilent Technologies)
[2730-1]


title: Tumor_CASE 56

city: Leuven

first: Julio

last: Finalet

address: Herestraat 49

country: Belgium

institute: KULeuven

description: CASE 56

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16hr at 45C on an Affymetrix HG-U133 Plus 2.0 GeneChip. The GeneChip was washed and stained in the Affymetric Fluidics Station 400.

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

data_processing: The data were analyzed with Array Studio version 5.0 (Omicsoft Corporation). Data were normalized using RMA as implemented in the Affy package (version 1.32.1) of Bioconductor. Expression values are represented on a log2-scale. Control probes are discarded.

source_name: Lymph node

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

growth_protocol: Patients diagnosed with PTLD were biopsied and tumor tissues were frozen or paraffin-embedded.

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

treatment_protocol: Frozen tissue sections were immediately dissolved in Trizol.

tag: immune status

value: Immunocompetent lymphoma

value: Lymph node

tag: lymphoma subtype

value: Diffuse large B-cell lymphoma (DLBCL)

tag: ebv status

value: EBV(-)

tag: chip number


title: Tumor_CASE 63

description: CASE 63

value: Burkitt Lymphoma


title: Tumor_CASE 61

description: CASE 61

source_name: Gut-associated lymphoid tissue

value: Gut-associated lymphoid tissue

value: DLBCL (Burkitt-like lymphoma (BLL))


title: Tumor_CASE 54

description: CASE 54


title: Tumor_CASE 42

description: CASE 42


title: Tumor_CASE 55

description: CASE 55


title: Tumor_CASE 58

description: CASE 58


title: Tumor_CASE 64

description: CASE 64


title: Tumor_CASE 43

description: CASE 43


title: Tumor_CASE 53

description: CASE 53


title: Tumor_CASE 41

description: CASE 41


title: Tumor_CASE 57

description: CASE 57


title: Tumor_CASE 59

description: CASE 59


title: Tumor_CASE 62

description: CASE 62


title: Tumor_CASE 47

description: CASE 47


title: Tumor_CASE 65

description: CASE 65

value: EBV(+)


title: Tumor_CASE 50

description: CASE 50


title: Tumor_CASE 45

description: CASE 45


title: Tumor_CASE 52

description: CASE 52


title: Tumor_CASE 60

description: CASE 60


title: Tumor_CASE 49

description: CASE 49


title: Tumor_CASE 48

description: CASE 48


title: Tumor_CASE 40

description: CASE 40

value: Post-transplant lymphoma


title: Tumor_CASE 38

description: CASE 38


title: Tumor_CASE 44

description: CASE 44

source_name: mediastinum

value: mediastinum


title: Tumor_CASE 39

description: CASE 39


title: Tumor_CASE 46

description: CASE 46


title: Tumor_CASE 37

description: CASE 37


title: Tumor_CASE 51

description: CASE 51

source_name: Extracranial fronto-parietal

value: Extracranial fronto-parietal


title: Tumor_CASE 32

description: CASE 32


title: Mesenteric lymphatic_untreated_rep5

city: Temple

first: David

middle: C.

last: Zawieja

state: TX

address: 702 SW HK Dodgen Loop

department: Dept. of Systems Biology and Translational Medicine

institute: Texas A&M Health Science Center

hyb_protocol: Spotted arrays were incubated 45 min @48ºC with 35 rpm orbital agitation in prehybridization buffer (5X SSC , 0.1% SDS, 0.2% BSA) and then gently agitated 2 x 5 min in nuclease-free water followed by 2 x 5 min in isopropanol before being spun dry and maintained at 48ºC until hybridization. Equal mass, dye-coupled amplified RNA samples were mixed, column purified, and fragmented by hydrolysis (Fragmentation Reagents, Ambion, Austin, TX) prior to hybridization. The sample was then diluted to approximately 0.25X with Slidehyb Glass Hybridization buffer (Ambion) and applied directly to the array surface. The sample was then covered with a Hybrislip (Grace Biolabs, Bend, OR) and incubated for 18hrs @48ºC. Following hybridization, the arrays were gently agitated in 48ºC 1X SSC, 0.1% SDS for 6 min followed by room temperature 1X SSC, 0.1% SDS for 6 min followed room temperature 0.1X SSC for 2 x 6 min. The slides were then scanned immediately.

scan_protocol: The array is scanned at 635 nm and 532 nm wavelengths with a 10 µm resolution using GenePix 4000A scanner (Molecular Devices, Sunnyvale, CA). Image analysis and data extraction was performed using GenePix Pro 6.0 software (Molecular Devices).

data_processing: Unprocessed fluorescence intensity data was exported to Microsoft Excel 11.2 software for quality control evaluation. Data points were flagged as absent if the Cy3 (reference) channel failed any of the following requirements: 1) at least 40% of feature pixels exhibiting fluorescent intensity greater than local mean background+2SD, 2) median feature intensity greater than median local background intensity by at least 10 units, 3) ratio of median feature intensity to median local background intensity greater than 2.5. The flagged raw feature and GenePix-specified local background intensity values for both dye channels were then imported into GeneSpring GX 7.3 software (Agilent Technologies) and normalized by 1) subtracting the local background intensity from the feature intensity for each channel, 2) setting all Cy5 measurements less than 0.5 to 0.5, 3) applying a per-gene and per-array, intensity-dependent (LOWESS) normalization utilizing 20% of data for smoothing and a Cy3 channel cutoff of 0.5, and 4) dividing each normalized Cy5:Cy3 ratio by the median normalized Cy5:Cy3 ratio for that gene across all arrays. Values obtained from replicate oligos on the same array were averaged. Because every sample is compared to the same arbitrary reference sample, the normalized Cy5:Cy3 ratios for each gene were directly comparable across all arrays. Those measurements flagged as absent in the reference channel were excluded from further analysis

organism: Rattus norvegicus

source_name: mesenteric lymphatic

label_protocol: Total cellular RNA was subjected to two rounds of linear amplification using the Amino Allyl MessageAmp aRNA Kit (Ambion, Austin, TX). Briefly, mRNA is reverse transcribed to form cDNA containing a T7 promoter. After conversion of the cDNA to double-stranded DNA, T7 RNA Polymerase is used to generate numerous antisense copies of each mRNA. During the second round of in vitro transcription, 5-(3-aminoallyl)-UTP is incorporated into the amplified RNA, which is then chemically coupled to NHS esters of Cy dye (GE Healthcare, Piscataway, NJ).

growth_protocol: The animals were housed in facilities that were accredited by the Association for the Assessment and Accreditation of Laboratory Animal Care (AAALAC International) and adhere to the regulations, policies and principles detailed in the Public Health Service Policy for the Humane Care and Use of Laboratory Animals (PHS Policy, 1996) and the United States Department of Agriculture's Animal Welfare Regulations (Animal Welfare Act, AWA, 9CFR, 1985, 1992). The animals were exposed to a 12 hr light/dark cycle and given open access to food and water. The animal procedures performed for this study were reviewed and approved by the institutional animal care and use committee of Texas A&M University, College Station, TX.

extract_protocol: The tissue of interest was rapidly isolated by microdisection and transferred to RNAlater (Ambion, Austin, TX) to stop endogenous RNase activity. The tissue was then cleaned of all extraneous tissue prior to RNA extraction. Total vessel RNA was isolated using a rotor-stator homogenizer and TRIzol Reagent (Invitrogen, Carlsbad, CA) according to the manufacturers protocol. The RNA was subsequently DNase-treated with DNA-free (Ambion) and analyzed for integrity and quantity using the Agilent 2100 Bioanalyzer and RNA6000 Pico LabChip Kit (Agilent Technologies, Santa Clara, CA).

value: male

tag: strain

value: Sprague-Dawley

value: mesenteric lymphatic

tag: organism weight

source_name: Rat Universal Reference RNA

tag: sample type

value: reference


title: Mesenteric lymphatic_untreated_rep6


title: Tumor_CASE 35

description: CASE 35

source_name: Waldeyer

value: Waldeyer


title: Tumor_CASE 33

description: CASE 33


title: Mesenteric lymphatic_untreated_rep1


title: Mesenteric vein_untreated_rep6

source_name: mesenteric vein

value: mesenteric vein


title: Tumor_CASE 30

description: CASE 30


title: Mesenteric lymphatic_untreated_rep3


title: Mesenteric vein_untreated_rep2


title: Mesenteric vein_untreated_rep1


title: Mesenteric lymphatic_untreated_rep2


title: Tumor_CASE 34

description: CASE 34


title: Tumor_CASE 27

description: CASE 27

source_name: BALT

value: BALT


title: Tumor_CASE 29

description: CASE 29

source_name: Urinary tract

value: Urinary tract


title: Tumor_CASE 31

description: CASE 31

value: Lymph node

value: Diffuse large B-cell lymphoma (DLBCL)


title: Mesenteric vein_untreated_rep4


title: Tumor_CASE 26

description: CASE 26


title: Mesenteric vein_untreated_rep5


title: Tumor_CASE 28

description: CASE 28


title: Mesenteric vein_untreated_rep3


title: Tumor_CASE 25

description: CASE 25


title: Tumor_CASE 23

description: CASE 23


title: Mesenteric artery_untreated_rep6

source_name: mesenteric artery

value: mesenteric artery


title: Mesenteric artery_untreated_rep5


title: Tumor_CASE 24

description: CASE 24


title: Tumor_CASE 22

description: CASE 22


title: Mesenteric lymphatic_untreated_rep4


title: Mesenteric artery_untreated_rep4


title: Mesenteric artery_untreated_rep1


title: Tumor_CASE 19

description: CASE 19


title: Tumor_CASE 21

description: CASE 21


title: Tumor_CASE 20

description: CASE 20


title: Tumor_CASE 17

description: CASE 17


title: Tumor_CASE 11

description: CASE 11


title: Tumor_CASE 14

description: CASE 14

value: Gut-associated lymphoid tissue


title: Thoracic duct_untreated_rep2

source_name: thoracic duct

value: thoracic duct


title: Tumor_CASE 18

description: CASE 18

value: EBV(+)


title: Thoracic duct_untreated_rep5


title: Tumor_CASE 12

description: CASE 12

value: Post-transplant lymphoma


title: Tumor_CASE 16

description: CASE 16


title: Thoracic duct_untreated_rep6


title: Axillary vein_untreated_rep6

source_name: axillary vein

value: axillary vein


title: Thoracic duct_untreated_rep1


title: Tumor_CASE 13

description: CASE 13


title: Mesenteric artery_untreated_rep2


title: Thoracic duct_untreated_rep3


title: Mesenteric artery_untreated_rep3


title: Tumor_CASE 15

description: CASE 15


title: Thoracic duct_untreated_rep4


title: Axillary vein_untreated_rep5


title: Axillary vein_untreated_rep4


title: Axillary vein_untreated_rep3


title: Tumor_CASE 10

description: CASE 10

value: EBV(-)


title: Axillary vein_untreated_rep2

value: male


title: Tumor_CASE 9

description: CASE 9


title: BDEsp Tumor-Derived Epithelial cells in Co-Culture with BDEsp Tumor-Derived Fibroblastic cells

city: Jacksonville

first: Catherine

last: Dumur

state: FL

address: 5008 Mustang Rd

department: Anatomic Pathology

institute: Sonic Healthcare USA

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

scan_protocol: GeneChips were scanned using the Affymetrix GC3000 scanner.

data_processing: After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries was performed using the log-scale Robust Multiarray Analysis (RMA) method.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: Tissues were snap-frozen immediately after extirpation from the animal.

treatment_protocol: BDEsp tumor-derived cells lines were grown in a rat tail type I collagen gel matrix, alone or in co-culture. For the co-cultures, cholangiocarcinoma (Epithelial) cells were plated at a density of  1 x 105 cells/mL and with a-SMA positive CAF (Fibroblasts) at various plating densities, ranging 0–8 x 105 cells/gel.

tag: genetic background

value: Fischer 344

tag: cell type


title: BDEsp Tumor-Derived Fibroblastic cells in Co-Culture with BDEsp Tumor-Derived Epithelial cells


title: Tumor_CASE 36

description: CASE 36

tag: tissue

value: DLBCL (Burkitt-like lymphoma (BLL))


title: Axillary vein_untreated_rep1

value: Sprague-Dawley

value: reference


title: Endometrium receptive rep3

city: Valencia

first: Jose

middle: Antonio

last: Martinez-Conejero

address: C/ Guadassuar 1, bajo

country: Spain

institute: iGenomix

hyb_protocol: The sample were then loaded onto the microarray and incubated for 20 h at 55 °C rotating at 20 rpm.

scan_protocol: The microarrays were washed in 3 steps of 5 min and scanned on Axon 4100A scanner (Molecular Devices, Sunnyvale, CA, USA). The GenePix Pro 6.0 software (Molecular Devices, Sunnyvale, CA, USA) was used to analyse the images obtained after scanning the microarrays as described in our previous study (Altmäe, et al. 2010).

data_processing:
Differential miRNA expression
Data analyses were performed by using the R-statistical software system (Free Software Foundation, Boston, MA, USA). miRNA expression profiles were determined by comparing the pre-receptive and receptive groups (2 by 2 comparisons) with the rank product non-parametric test implemented in the Bioconductor RankProd package. Two criteria were used to define the miRNAs that had altered miRNA abundance among the different sample sets: an absolute fold change (Fc) > 2.0 and a proportion of false positives (PFP) < 0.05. The latter is used to control errors in multiple tests, where it effectively controls the accumulation of false-positives relative to the total number of positive results (Fernando, et al. 2004).
In silico analysis of miRNA target genes
For computational prediction of miRNA target genes, we used different algorithms: miRanda (August 2010 release, www.microrna.org), PicTar (pictar.mdc-berlin.de/) (Krek, et al. 2005), and TargetScan 5.1 (April 2009 release, www.targetscan.org) (Lewis, et al. 2005). Based on the three different algorithms, we created the list of common target genes for each miRNA in order to narrow down the gene list of thousands of targets. These common targets were further annotated by using functional annotation tools at IPA software and The Database for Annotation, Visualization and Integrated Discovery (DAVID) (Dennis, et al. 2003). DAVID is a gene set-based algorithm that detects functionally related genes in lists of genes ordered according to the differential expression. DAVID can search blocks of functionally related genes according to different criteria such as the Gene Ontology (GO) terms: biological process, cellular component and molecular function. P-values were adjusted with the false discovery rate (FDR) correction (Benjamini, et al. 2001) based on the number of GO categories that were tested; a FDR of < 5.0 was considered statistically significant.
Additionally, we compared the obtained list of predicted target genes with our previous mRNA microarray data of the same group of women, LH+7 vs. LH+2 (Riesewijk, et al. 2003), with parameters of fold change ≥ 2, p < 0.05. The common genes of these two distinct lists of differentially regulated genes were further annotated by using functional annotation tools IPA and DAVID.

source_name: Receptive endometrium

label_protocol: In general, Agilent protocol generates fluorescent miRNA from an initial amount of 100 ng of total RNA. This method involves the binding of molecules of cyanine 3-pCp at the 3'-ends of RNA molecules with efficiency above 90%. The first step of the protocol was dephosphorylation reaction, by taking 100 ng of total RNA, adding bovine intestinal alkaline phosphatase, and incubating at 37 °C for 30 min in a circulating water bath. Next, DMSO was added to 100% at 100 °C to denature the RNAs. The ligation reaction of the marked RNAs was performed by adding the RNA ligase of phage T4 and Cy3-pCp, incubated 2 h at 16 °C and dried completely in vacuum centrifuge for 3 h at 45 °C. After that, the samples were resuspended in 18 ul of water, added a blocking agent and the hybridization buffer, incubated 5 min at 100 °C, and transferred to ice for another 5 min.

extract_protocol: For miRNA array and real-time PCR analysis, total RNA was extracted from the endometrial biopsy samples by the ‘TRIzol method’ and extracted RNA quality was assessed using Agilent Bioanalyzer as described before (Altmäe, et al. 2010).

value: female

value: endometrium

tag: day

value: seven days after the LH peak


title: Tumor_CASE 8

description: CASE 8

value: Lymph node


title: Endometrium receptive rep1


title: Axillary artery_untreated_rep6

source_name: axillary artery

value: axillary artery


title: Endometrium pre-receptive rep4

source_name: Pre-receptive endometrium

value: five days after the LH peak


title: Tumor_CASE 6

description: CASE 6

value: Gut-associated lymphoid tissue

value: Diffuse large B-cell lymphoma (DLBCL)


title: Axillary artery_untreated_rep2


title: Tumor arising from BDEsp cells rep2

description: Intrahepatic cholangiocarcinoma from Fischer 344 male rat, young adult

source_name: Tumor arising from BDEsp cells

value: BDEsp ICC Tumor

value: Intrahepatic cholangiocarcinoma


title: Tumor arising from BDEsp cells rep3


title: Axillary artery_untreated_rep5


title: Endometrium receptive rep2


title: Tumor_CASE 3

description: CASE 3

source_name: Testis

value: Post-transplant lymphoma

value: Testis


title: Axillary artery_untreated_rep3

value: male


title: Tumor arising from BDEsp cells rep1

value: Fischer 344


title: Tumor arising from BDEsp cells rep4


title: Tumor_CASE 4

description: CASE 4

source_name: Lymph node

value: EBV(-)


title: Endometrium pre-receptive rep2

value: two days after the LH peak


title: Tumor_CASE 5

description: CASE 5


title: Axillary artery_untreated_rep4

value: Sprague-Dawley

value: reference


title: Tumor_CASE 1

description: CASE 1

source_name: Gut-associated lymphoid tissue


title: RIS5_control

status: Public on Jun 22 2012

city: São Paulo

first: Renato

middle: David

last: Puga

state: São Paulo

address: Dr Ovidio Pires de Campos,785

department: Instituto de Psiquiatria

country: Brazil

institute: Universidade de São Paulo

description: Blood samples from 10 male patients, aging between 18-65 years, diagnosed with schizophrenia and treated with Risperidone were used for total RNA extraction. Study protocol was approved by the Ethics Committee of the Hospital, and performed in accordance with the Declaration of Helsinki. A two-round linear amplification procedure based on T7-driven amplification was carried out. Amplified RNA was then used in a transcriptase reverse reaction into cDNA in the presence of Alexa 555 or Alexa 647. Dye swap was performed for each sample analyzed and used as replicate samples.

hyb_protocol: Hibridization - Solution: 5 X SSC; 0,1% SDS; 4 ug poly A DNA; 4 ug Cot1 DNA; 5X Denhardts ; 10 ug Esperma de salmao,  Formamida 25%. / Temperature:14 a 24 hs / Time:42 C / Touch Down: Washing - Round 1 - Solution: SSC 2X / Temperature:42 / Time:10 / Washing Number: 1 Washing - Round 2 - Solution: SSC 0.1X, SDS 0.1% / Temperature:42 / Time:10 / Washing Number: 2 Washing - Round 3 - Solution: SSC 0.1X / Temperature:42 / Time:10 / Washing Number: 2

scan_protocol: Hardware: Perkinelmer / Software: ScanArray

data_processing: Lowesss

label: Alexa Fluor succinimidyl ester 555

label_protocol: Protocol Cy3/Cy5

extract_protocol: kit Pico Pure RNA Isolation Kit

value: male, disease state:schizophrenia, agent:risperidone

label: Alexa Fluor succinimidyl ester 647

source_name: Reference

extract_protocol: Trizol

value: pool of 15 human cell lines


title: Tumor_CASE 2

description: CASE 2


title: RIS6_control


title: RIS6_swap

description: A pool of RNAs obtained from 15 distinct human cell lines (Daudi from Burkitt's lymphoma, DLD-1 from colorectal adenocarcinoma, DU 145 from prostate carcinoma, FaDu from pharinx squamous cell carcinoma, GM-637 from fibroblast, H-146 from small cell lung carcinoma, HT-1080 from fibrosarcoma, HB4a from normal mammary luminal epithelium, HEK from human embryonic kidney, Jurkat from acute T cell leukemia, Saos-2 from osteosarcoma, SK-BR-3 from breast adenocarcinoma, SK-MEL-28 from melanoma, T24 from bladder transitional cell carcinoma and T98G from glioblastoma multiforme) were used as reference. Total RNA was amplified following the same protocol and used as reference for microarray hybridizations.


title: RIS7_control


title: RIS7_swap


title: RIS9_swap


title: RIS8_control


title: Tumor_CASE 7

description: CASE 7

value: Lymph node


title: RIS9_control


title: RIS8_swap


title: RIS5_swap


title: RIS4_swap


title: Endometrium pre-receptive rep1

value: female

value: endometrium

value: one day after the LH peak


title: RIS4_control


title: RIS10_swap


title: HAL9_control

description: Blood samples from 9 male patients, aging between 18-65 years, diagnosed with schizophrenia and treated with Haloperidol were used for total RNA extraction. Study protocol was approved by the Ethics Committee of the Hospital, and performed in accordance with the Declaration of Helsinki. A two-round linear amplification procedure based on T7-driven amplification was carried out. Amplified RNA was then used in a transcriptase reverse reaction into cDNA in the presence of Alexa 555 or Alexa 647. Dye swap was performed for each sample analyzed and used as replicate samples.

value: male, disease state:schizophrenia, agent:haloperidol


title: RIS2_swap


title: Axillary artery_untreated_rep1

value: axillary artery


title: HAL9_swap


title: RIS1_swap


title: RIS3_swap


title: RIS1_control


title: HAL8_swap


title: RIS3_control


title: RIS10_control


title: RIS2_control


title: HAL8_control

description: Blood samples from9 male patients, aging between 18-65 years, diagnosed with schizophrenia and treated with Haloperidol were used for total RNA extraction. Study protocol was approved by the Ethics Committee of the Hospital, and performed in accordance with the Declaration of Helsinki. A two-round linear amplification procedure based on T7-driven amplification was carried out. Amplified RNA was then used in a transcriptase reverse reaction into cDNA in the presence of Alexa 555 or Alexa 647. Dye swap was performed for each sample analyzed and used as replicate samples.


title: HAL7_swap


title: HAL3_swap


title: CLO11_swap


title: HAL7_control


title: HAL1_control


title: CLO11_control


title: HAL3_control


title: HAL2_control


title: HAL10_control


title: CON9_swap

value: male, disease state:control


title: HAL1_swap


title: HAL10_swap


title: CON7_swap


title: HAL6_swap


title: HAL2_swap


title: CON4_control

description: Total RNA was extracted from blood samples from 10 male patients and used as control samples. Study protocol was approved by the Ethics Committee of the Hospital, and performed in accordance with the Declaration of Helsinki. A two-round linear amplification procedure based on T7-driven amplification was carried out. Amplified RNA was then used in a transcriptase reverse reaction into cDNA in the presence of Alexa 555 or Alexa 647. Dye swap was performed for each sample analyzed and used as replicate samples.


title: CON9_control


title: CON6_swap


title: HAL6_control


title: CON5_swap


title: CON6_control


title: CON8_swap


title: CON8_control


title: CON4_swap


title: CON5_control


title: CON3_swap


title: CON3_control


title: CON7_control


title: CON2_control


title: CON2_swap


title: CON10_control


title: CON10_swap


title: CLO6_swap

value: male, disease state:schizophrenia, agent:clozapine


title: CLO9_control

description: Blood samples from 9 male patients, aging between 18-65 years, diagnosed with schizophrenia and treated with Clozapine were used for total RNA extraction. Study protocol was approved by the Ethics Committee of the Hospital, and performed in accordance with the Declaration of Helsinki. A two-round linear amplification procedure based on T7-driven amplification was carried out. Amplified RNA was then used in a transcriptase reverse reaction into cDNA in the presence of Alexa 555 or Alexa 647. Dye swap was performed for each sample analyzed and used as replicate samples.


title: CON1_swap


title: CLO4_control


title: CLO8_swap


title: CON1_control


title: CLO5_swap


title: CLO5_control


title: CLO6_control


title: CLO9_swap


title: CLO3_swap


title: CLO8_control


title: CLO7_control


title: CLO7_swap


title: CLO2_swap


title: CL01_swap


title: CLO3_control


title: chick insulin neutralized, biological rep5

city: Knoxville

first: Bo

last: Ji

state: TN

address: 2640 Morgan Circle Drive

department: Animal Science

institute: University of Tennessee

description: Gene expression data from adipose tissue of 16-17 day chick injected injected at 0, 2 and 4 hours with porcine anti-insulin serum

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Statistical analysis of the microarray data was performed using R 2.9.0 and routines contained in Bioconductor (bioconductor.org). GC robust multi-array average (GCRMA) was used to normalize and scale the raw data from CEL files.

organism: Gallus gallus

source_name: chick was fed but injected at 0, 2 and 4 hours with porcine anti-insulin serum

label_protocol: Affymetrix protocol

extract_protocol: Total RNA was isolated from chicken adipose samples using the RNeasy Lipid kit and incorporating an on-column DNase treated with the RNase-free DNase Set according to the manufacturer's protocol.

treatment_protocol: At 16-17 days of age, chicks of similar body weights were either allowed to continue feeding (ad libitum fed controls), fasted for five hours, or fed but injected at 0, 2 and 4 hours with porcine anti-insulin serum (insulin neutralized). Both the fed and fasted groups received injections of normal porcine serum as a vehicle control.

value: adipose tissue


title: chick insulin neutralized, biological rep4


title: chick insulin neutralized, biological rep3


title: chick insulin neutralized, biological rep2


title: CLO2_control

description:
Clozapine
Blood samples from 9 male patients, aging between 18-65 years, diagnosed with schizophrenia and treated with Clozapine were used for total RNA extraction. Study protocol was approved by the Ethics Committee of the Hospital, and performed in accordance with the Declaration of Helsinki. A two-round linear amplification procedure based on T7-driven amplification was carried out. Amplified RNA was then used in a transcriptase reverse reaction into cDNA in the presence of Alexa 555 or Alexa 647. Dye swap was performed for each sample analyzed and used as replicate samples.


title: CLO4_swap


title: chick fed ad libitum, biological rep5

description: Gene expression data from adipose tissue of 16-17 day chick fed ad libitum

source_name: chick fed ad libitum


title: CLO1_control


title: chick fed ad libitum, biological rep4


title: chick fasted for 5 hours, biological rep4

description: Gene expression data from adipose tissue of 16-17 day chick fasted for 5 hours

source_name: chick fasted for 5 hours


title: chick fasted for 5 hours, biological rep5


title: chick fed ad libitum, biological rep2


title: chick fasted for 5 hours, biological rep2


title: GTL16 R1 clone, gene expression array U133Plus2, replicate

city: San Diego

first: Keith

middle: A

last: Ching

state: CA

address: 10777 Science Center Dr.

department: Computational Sciences

institute: Pfizer, Inc.

hyb_protocol: Protocol per manufacturer's protocol (Affymetrix, Santa Clara, CA).

data_processing: Data were normalized using Bioconductor and the R package gcrma.

source_name: GTL16 R1 clone

extract_protocol: RNA were isolated using an RNeasy kit (Qiagen, Germantown, MD).

tag: cell line

value: GTL16 R1 clone

tag: origin

value: gastric

tag: resistant


title: GTL16, gene expression array U133Plus2, replicate

scan_protocol: Protocol per manufacturer's protocol (Affymetrix, Santa Clara, CA).


title: GTL16, gene expression array U133Plus2

label_protocol: Protocol per manufacturer's protocol (Affymetrix, Santa Clara, CA).


title: GTL16 R1 clone, gene expression array U133Plus2


title: GTL16 R3 clone, gene expression array U133Plus2, replicate

source_name: GTL16 R3 clone

value: GTL16 R3 clone


title: chick fasted for 5 hours, biological rep3


title: newborn tap rep2

city: Louisville

first: J.

middle: Christopher

last: States

state: KY

address: 505 S. Hancock St., Rm 304

department: Department of Pharmacology & Toxicology

institute: University of Louisville

hyb_protocol: Slides were hybridized according to manufacturers protocol (Two-Color Microarray-Based Genr Expression Analysis Protocol,  Product # G4140-90050, Version 5.0.1, August 2006)

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5um.

data_processing:
Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal,rDyeNormSignal in the raw files and log-transform them using: log10(max(x,1)). These values will be referenced below as Xgi and Xri where i is array number.
(2) Take average of Xri's for the oligo among 15 arrays in the series:  AverXr = average(Xri).
(3) For each array estimate Yi = Xgi-Xri+AverXr
(4) Round Yi to 4 decimal digits. This is used as the normalized VALUE.
More detailed information with error correction can be found at http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

organism: Mus musculus

source_name: newborn tap

label_protocol: Total RNA was labeled using Agilents Low RNA Input Fluorescent Linear Amplification kit, according to manufacturers instructions.

extract_protocol: Total RNA was purified from samples of frozen livers using the miRVana kit from Ambion (now Life Technologies).

treatment_protocol: Pregnant dams were provided drinking water containing 49 ppm arsenic (85 mg/L sodium arsenite) from gestational day 8 (GD) 8 to day of parturition. The dams were then provided arsenic-free tap water as were the pups. The pups from these litters are designated As/Tap. On day of birth, 3 pups, each from a separate litter, were sacrificed and the livers dissected and snap frozen. These are designated newborn As/Tap or PND1 As/Tap. Other pups were allowed to wean and then maintained on arsenic free tap water until sacrifice at age 10 weeks (10w As/Tap or PND70 As/Tap).Alternatively, pregnant dams were provided only arsenic-free tap water. On the day of birth, 3 pups were taken from separate litters and the livers dissected and snap frozen. These are designated newborn tap/tap or PND1 Tap/Tap. Other pups were maintained on arsenic-free tap water until weaning at PND21. Three mice from separate litters were continued on arsenic-free tap water until age 10 weeks when they were sacrificed and livers were dissected and snap frozen. These mice are designated 10w tap/tap or PND70 tap/tap. An additional 3 mice, each from separate litters, were provided  drinking water containing 49 ppm arsenic (85 mg/L sodium arsenite) from PND21 to age 10 weeks when were sacrificed and livers were dissected and snap frozen. These mice are designated 10w tap/as or PND70 tap/as.

value: newborn

tag: individual identifier

source_name: Universal Mouse Reference Cell Line Pool

label_protocol: Total RNA was labeled using Agilents Fluorescent Linear Amplification kit, according to manufacturers instructions (Product Number G2554A or P/N G2556-66002, Version 3.0, June 2002).

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts

value: Universale Mouse Reference


title: chick fed ad libitum, biological rep3


title: Endometrium pre-receptive rep3

tag: gender

value: four days after the LH peak


title: chick insulin neutralized, biological rep1


title: chick fed ad libitum, biological rep1


title: newborn tap rep3

tag: age


title: chick fasted for 5 hours, biological rep1


title: newborn as rep3

source_name: newborn as


title: MSC_IL

first: Francisco

middle: García

last: García

address: Eduardo Primo Yúfera, 3

department: Bionformatics & Biostatistics Unit

institute: CIPF

description: Mesenchymal stem cell in response IL-1β

hyb_protocol: Based on the protocol for One-Color Microarray-Based Gene Expression Analysis Version 5.5 (Agilent p/n 5188-5977), 3μg of labeled cRNA was hybridized with Whole Human Genome Oligo Microarray Kit (Agilent p/n G4112F) containing 41,000+ unique human genes and transcripts.

scan_protocol: Arrays were scanned in an Agilent Microarray Scanner (Agilent G2565BA) according to the manufacturer’s protocol and data extracted using Agilent Feature Extraction Software 9.5.1 (http://www.chem.agilent.com/en-us/products/instruments/dnamicroarrays/featureextractionsoftware/pages/default.aspx).

data_processing: Signal was standardized across arrays using quantile normalization. Differential gene expression was carried out using the fold change. Gene set analysis was carried out for the Gene Ontology terms using FatiScan

source_name: Mesenchymal stem cell,  IL-1β

label_protocol: 800 ng of total RNA were used to produce Cyanine 3-CTP-labeled cRNA using the Low RNA Input Linear Amplification Kit, PLUS, One-Color (Agilent p/n 5188-5339) according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted from BM-MSC using the High Pure RNA Isolation kit (Roche) and was quantified by spectrometry (NanoDrop ND-1000, NanoDrop Technologies).

treatment_protocol: Human bone marrow MSC were treated or not with IL-1β (25 ng/mL) for twenty four hours at 37 ºC in a humidified incubator with 5% CO2

tag: treatment

value: IL-1β for 24 hours at 37C

value: Mesenchymal stem cell


title: Spontaneous_lung_tumor_6

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Spontaneous Lung tumor in untreated animals

hyb_protocol: 15 μg of amplified biotin-cRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files.

source_name: Spontaneous lung tumor

label_protocol: One μg of total RNA was amplified as directed in the Affymetrix One-Cycle cDNA Synthesis protocol.

growth_protocol: NA; tumors and tissue collected from B6C3F1 mice on 2-year National Toxicology Program bioassay.

extract_protocol: RNA extraction was performed using the Invitrogen PureLink Mini kit (Invitrogen cat# 12183-018A). Frozen tissue samples were lysed and homogenized in TRIzol reagent using a rotor-stator homogenizer. RNA isolation was performed according to the mini kit protocol. On column DNase treatment was performed using the Invitrogen PureLink DNase kit (Invitrogen cat# 12185-010) to purify the RNA samples.   RNA concentration and 260/280 ratio were measured on a bioanalyzer (Agilent Technologies). RNA quality was checked on Embi Tec Precast RNA gels (Embec cat# GE-6010). Samples were aliquoted and stored at -80C.

treatment_protocol: NA; no treatment was performed.

tag: disease state

value: Spontaneous lung tumor


title: GTL16 R3 clone, gene expression array U133Plus2


title: newborn tap rep1


title: MSC

description: Mesenchymal stem cell

source_name: Mesenchymal stem cell


title: Spontaneous_lung_tumor_5


title: L5 DRG-inflamed-biological rep 4

city: Cincinnati

first: Judith

middle: Ann

last: Strong

state: OH

address: 231 Albert Sabin Way

department: Anesthesiology

institute: University of Cincinnati

hyb_protocol: The standard Probe Array Cartridge (GeneChip Rat Gene 1.0 Exon Array– Affymetrix) was used for hybridization of the cDNA.  Hybridization was for 18 hours at 45 degrees C.

scan_protocol: Scanning was done with an Affymetrix GeneChip Scanner 3000 7G using Genechip Operating Software.

data_processing:
Gene-level expression analysis was conducted using GeneSpring (Agilent Technologies) version 11.5 for gene-level analysis of core transcripts. The standard workflow was used to determine genes whose expression was significantly different between sham animals and animals with local inflammation of the DRG.  Probes were retained in which at least 1 sample had an expression level above a 20% cutoff, using a 0.05 p value cut-off value with the Benjamini-Hochberg correction for multiple testing, The summarization algorithm used was RMA16; the normalization method was quantile baseline transformation to median of all samples.
Probe Group File: RaEx-1_0-st-v1.r2.pgf
meta-probeset file: RaEx-1_0-st-v1.r2.dt1.rn4.core.mps
Normalized intensity values for each sample from GeneSpring version 11.5 gene level analysis of core transcripts using 20% expression level cutoff.   The summarization algorithm used was RMA16; the normalization method was quantile baseline transformation to median of all samples.

source_name: inflamed L5 DRG_post-operative day 3

label_protocol: Labeling and microarray analysis of the samples  were conducted by the Gene Expression Microarray Core facility of Cincinnati Children’s Hospital Medical Center, Cincinnati, OH.  Labeling was done with the Ambion WT expression kit (Applied Biosystems) combined with the GeneChip® WT Terminal Labeling Kit (Affymetrix) to create biotin – labeled sense-strand cDNA targets for hybridization to the array

growth_protocol: single L5 DRG dissected from adult male rats 3 days after surgery for local inflammation of the DRG or sham control surgery

extract_protocol: DRGs were placed onto dry ice then homogenized, after which RNA isolation was done using commercially available column based kits (Norgen Biotek Corp, Thorold, Ontario, Canada,  Cat #24100, or Stratagene,La Jolla, CA, Cat. # 400800), including a DNA digestion step.   Some samples were further concentrated by centrifugation under vacuum.  Before being used for a microarray, a small aliquot from each sample was subjected to a quality control test using an Agilent Bioanalyzer to confirm that the 28S and 18S ribosomal RNA peaks were sharp, distinct, and in the proper ratio, and that the concentration and quantity were suitable for use in the microarray.

treatment_protocol: DRG inflammation by injecting the immune activator zymosan (10 microliters, concentration 2 mg/ml, in Incomplete Freund's Adjuvant) beneath the intervertebral foramen, onto the L5 DRG on one side (PMID 16887276  and 22265726 for more details).  Behavioral sensitivity was confirmed with von Frey testing.  Sham animals received the same incision and intervertebral foramen exposure but no zymosan injection.

value: Sprague Dawley

value: adult

value: male

value: lumbar dorsal root ganglion


title: L5 DRG-inflamed-biological rep 3


title: L5 DRG-inflamed-biological rep 6


title: L5 DRG-inflamed-biological rep 5


title: L5 DRG-inflamed-biological rep 1


title: newborn as rep2


title: Spontaneous_lung_tumor_3


title: L5 DRG-inflamed-biological rep 2


title: Spontaneous_lung_tumor_4


title: L5 DRG-sham-biological rep 5

source_name: shame operated L5 DRG_post-operative day 3


title: L5 DRG-sham-biological rep 6


title: L5 DRG-sham-biological rep 4


title: 10 week tap/as rep1

source_name: 10 week tap/as

value: 10 week


title: newborn as rep1


title: 10 week tap/as rep3


title: Spontaneous_lung_tumor_1


title: Spontaneous_lung_tumor_2


title: Lung_normal_5

description: Control lung

source_name: Normal lung

value: Normal


title: 10 week as/tap rep1

source_name: 10 week as/tap


title: 10 week as/tap rep3


title: 10 week as/tap rep2


title: L5 DRG-sham-biological rep 1


title: L5 DRG-sham-biological rep 3


title: SKOV/ip-FuEP2/Ex2 (in vivo)

city: Tokushima

first: Tetsuyuki

last: Takahashi

state: Tokushima

country: Japan

institute: Tokushima University

description: Gene expression data from human ovarian cancer cell

hyb_protocol: We used GeneChip Hybridization 640 according to the manufacturer's protocol.

scan_protocol: We used GeneChip Scanner 3000 7G according to the manufacturer's protocol.

data_processing: Expression Console software (HuGene-1_0-st-v1).rma-gene-default.

source_name: SKOV/ip-FuEP2/Ex2 tumor

label_protocol: We used GeneChip WT Terminal Labelling kit according to the manufacturer's protocol.

growth_protocol: We intraperitoneally injected SKOV/ip-Fumock or SKOV/ip-FuEP2/Ex2 and observed for 4 weeks

extract_protocol: RNeasy Mini kit was used according to the manufacturer's protocol.

value: SKOV/ip-FuEP2/Ex2 tumor


title: 10 week tap/as rep2


title: Lung_normal_6

description: Control lung


title: Lung_normal_4

description: Control lung


title: 10 week tap/tap rep2

source_name: 10 week tap/tap


title: SKOV/ip-Fumock (in vivo)

source_name: SKOV/ip-Fumock-derived tumor

value: SKOV/ip-Fumock-derived tumor


title: SKOV/ip-FuEP2/Ex2 (in vitro)

source_name: SKOV/ip-FuEP2/Ex2 cells

value: SKOV/ip-FuEP2/Ex2 cells


title: L5 DRG-sham-biological rep 2


title: Lung_normal_1

description: Control lung


title: Lung_normal_3

description: Control lung


title: 10 week tap/tap rep3


title: Lung_normal_2

description: Control lung


title: BDEspT [AS65]

status: Public on Jun 21 2012

description: intrahepatic cholangiocarcinoma from Fischer 344 male rat, young adult

source_name: Tumor arising from BDEsp cells

tag: cell line origin

value: BDEsp (spontaneously-transformed low grade malignant)

value: Fischer 344


title: BDEspT [AS63]


title: BDEsp [AS54]

description: transformed cholangiocite cell line from Fischer 344 male rat, young adult

source_name: BDEsp cells cultured on plastic


title: 10 week tap/tap rep1


title: BDEspT [AS61]


title: SKOV/ip-Fumock (in vitro)

source_name: SKOV/ip-Fumock cells

value: SKOV/ip-Fumock cells


title: BDEsp [AS53]


title: BDEsp [AS55]


title: BDEsp [AS50]


title: BDEneu [AS41]

source_name: BDEneu cells cultured on plastic

value: BDEneu (high grade malignant)


title: BDEspT [AS59]


title: BDEsp [AS43]


title: BDEneu [AS49]


title: BDEneu [AS42]


title: BDEspT [AS30]


title: BDEneuM [AS11]

description: peritoneal metastatsis from Fischer 344 male rat, young adult

source_name: Metastatic mass from from BDEneu tumor


title: BDEneu [AS34]


title: BDEneuT [AS5]

source_name: Tumor arising from BDEneu cells


title: BDEneu [AS35]


title: BDEsp [AS36]


title: BDEneu [AS48]


title: BDEneuM [AS12]


title: BDEspT [AS28]


title: rny mutant biological replicate 3

first: Gabriella

last: Marincola

address: Elfriede Auhlornstr. 6

country: Germany

institute: IMIT - Interfaculty Institute for Microbiology and Infection Medicine

description: Gene expression data from S. aureus NewmanHG rny mutant at late exponential growth phase

hyb_protocol: Standard affymetrix hybridization protocol for GeneChip S. aureus Genome Array

scan_protocol: Standard scanning protocol for affymetrix GeneChip Scanner 3000 7G system

data_processing: GC-RMA normalization and t-test statistics was performed with GenespringGX 11.5.1 software.

label: biotin-streptavidin

organism: Staphylococcus aureus

source_name: S. aureus rny mutant_late exponential growth phase

label_protocol: Standard affymetrix labelling protocol for prokaryotic organism

growth_protocol: S. aureus strains were grown in complex medium. Bacteria from an overnight culture were diluted to an initial optical density at 600 nm (OD600) of 0.05 in fresh medium and grown with shaking (220 rpm) at 37°C till late exponential growth phase (OD600 = 1.5).

extract_protocol: Bacteria were lysed in Trizol reagent (Invitrogen) with 0.5 ml of zirconia-silica beads (0.1-mm diameter) in a high-speed homogenizer. RNA was then isolated as described in the instructions provided by the manufacturer of Trizol.

treatment_protocol: 5 ml of cultures were harvested by centrifugation

tag: background strain

value: NewmanHG

tag: genotype/variation

value: rny (cvfA) mutant

tag: growth phase

value: late exponential phase


title: Wild type biological replicate 3

description: Gene expression data from S. aureus NewmanHG wild type at late exponential growth phase

source_name: S. aureus wt_late exponential growth phase

value: wild type


title: Wild type biological replicate 2


title: rny mutant biological replicate 1


title: rny mutant biological replicate 2


title: BDEneuT [AS1]

tag: strain


title: Wild type biological replicate 1


title: BDEneuT [AS3]


title: BDEneuT [AS4]


title: BDEneuM [AS10]


title: GTL16 R3 clone, copy number variation SNP6.0

type: genomic

data_processing: Affymetrix SNP6.0 data were processed using the aroma.affymetrix R package according to the methods of H. Bengtsson et al., (Bengtsson, Irizarry et al. 2008 [PMID 18204055]).

molecule: genomic DNA

source_name: GTL16 R3 clone

extract_protocol: DNA were isolated using a DNeasy kit (Qiagen, Germantown, MD).

value: GTL16 R3 clone

value: gastric


title: GTL16 R1 clone, copy number variation SNP6.0

source_name: GTL16 R1 clone

value: GTL16 R1 clone


title: Lin minus cKit plus CX3CR1 minus sample 3

city: Chicago

first: Syamal

middle: Kumar

last: Datta

state: IL

address: MCGAW 240 E Huron

institute: Northwestern Univ.

description: LinminuscKitplusCX3CR1minus sample

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: Lumi Bioconductor package

source_name: lineageminusCD117plusCX3CR1minus cell

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

tag: source tissue

value: spleen

value: Lin minus cKit plus CX3CR1 minus

tag: genetic background

value: NZB x SWR


title: Lin minus cKit plus CX3CR1 minus sample 1

description: LinminuscKitplusCX3CR1minus sample

tag: cell type


title: GTL16, copy number variation SNP6.0


title: Lin minus cKit plus CX3CR1 minus sample 2

description: LinminuscKitplusCX3CR1minus sample


title: Lin minus cKit minus CX3CR1 plus sample 2

description: LinminuscKitminusCX3CR1plus sample

source_name: lineageminusCD117minusCX3CR1plus cell

value: Lin minus cKit minus CX3CR1 plus


title: Day: 3; Drug: Methamphetamine; Phase: Drug treatment; Replicate: 1

city: Krakow

first: Marcin

last: Piechota

address: Smetna 12

department: Molecular Neuropharmacology

country: Poland

institute: Institute of Pharmacology PAS

description: microarray name: 5216513057_A

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in R. Data were log2transformed. Day effect was eliminated using standarization with saline samples.

source_name: Mouse striatum

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: day

tag: drug

value: Methamphetamine

tag: phase

value: Drug treatment

tag: tissue

value: striatum

tag: replicate


title: Day: 1; Drug: Saline; Phase: Drug treatment; Replicate: 3

description: microarray name: 5216513049_A

value: Saline


title: Lin minus cKit plus  pure sample 3

description: LinminuscKitplus pure sample

source_name: lineageminusCD117plus pure cell

value: Lin minus cKit plus  pure


title: Day: 12; Drug: Saline; Phase: Drug treatment; Replicate: 3

description: microarray name: 5216513057_C


title: Lin minus cKit minus CX3CR1 plus sample 3

description: LinminuscKitminusCX3CR1plus sample


title: Day: 15; Drug: Saline; Phase: Withdrawal; Replicate: 1

description: microarray name: 5216513049_D

value: Withdrawal


title: Day: 12; Drug: Heroin; Phase: Drug treatment; Replicate: 3

description: microarray name: 5216513049_C

value: Heroin


title: Day: 0; Drug: Naive; Phase: Naive; Replicate: 3

description: microarray name: 5216513057_F

value: Naive


title: Dendritic cell sample 3

description: Dendritic cell sample

source_name: dendritic cell

value: Dendritic cell


title: Day: 15; Drug: Methamphetamine; Phase: Withdrawal; Replicate: 2

description: microarray name: 5216513057_D


title: Day: 6; Drug: Heroin; Phase: Drug treatment; Replicate: 2

description: microarray name: 5216513057_B


title: Day: 0; Drug: Naive; Phase: Naive; Replicate: 2

description: microarray name: 5216513049_F


title: Day: 18; Drug: Heroin; Phase: Withdrawal; Replicate: 3

description: microarray name: 5216513057_E


title: Day: 18; Drug: Methamphetamine; Phase: Withdrawal; Replicate: 3

description: microarray name: 5216513049_E


title: Dendritic cell sample 2

description: Dendritic cell sample


title: Day: 24; Drug: Heroin; Phase: Withdrawal; Replicate: 1

description: microarray name: 5216513030_E


title: Lin minus cKit minus CX3CR1 plus sample 1

description: LinminuscKitminusCX3CR1plus sample


title: Day: 0; Drug: Naive; Phase: Naive; Replicate: 6

description: microarray name: 5216513030_F


title: Day: 15; Drug: Methamphetamine; Phase: Withdrawal; Replicate: 3

description: microarray name: 5216513030_D


title: Dendritic cell sample 1

description: Dendritic cell sample


title: Day: 6; Drug: Methamphetamine; Phase: Drug treatment; Replicate: 2

description: microarray name: 5216513049_B


title: Day: 6; Drug: Heroin; Phase: Drug treatment; Replicate: 3

description: microarray name: 5216513030_B


title: Lin minus cKit plus  pure sample 1

description: LinminuscKitplus pure sample


title: Lin minus cKit plus  pure sample 2

description: LinminuscKitplus pure sample


title: Day: 13; Drug: Saline; Phase: Withdrawal; Replicate: 1

description: microarray name: 5216513030_C


title: Day: 3; Drug: Methamphetamine; Phase: Drug treatment; Replicate: 2

description: microarray name: 5216513030_A


title: Day: 6; Drug: Saline; Phase: Drug treatment; Replicate: 1

description: microarray name: 5216513029_B


title: Day: 0; Drug: Naive; Phase: Naive; Replicate: 1

description: microarray name: 5216513029_F


title: Day: 15; Drug: Saline; Phase: Withdrawal; Replicate: 2

description: microarray name: 5216513026_D


title: Day: 15; Drug: Methamphetamine; Phase: Withdrawal; Replicate: 1

description: microarray name: 5216513028_D


title: Day: 1; Drug: Methamphetamine; Phase: Drug treatment; Replicate: 3

description: microarray name: 5216513028_A


title: Day: 24; Drug: Saline; Phase: Withdrawal; Replicate: 3

description: microarray name: 5216513028_F


title: Day: 12; Drug: Methamphetamine; Phase: Drug treatment; Replicate: 3

description: microarray name: 5216513029_C


title: Day: 6; Drug: Heroin; Phase: Drug treatment; Replicate: 1

description: microarray name: 5216513028_B


title: Day: 1; Drug: Heroin; Phase: Drug treatment; Replicate: 3

description: microarray name: 5216513029_A


title: BDEneuT [AS2]

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

value: BDEneu (high grade malignant)

value: Fischer 344

tag: gender

value: male


title: Day: 18; Drug: Heroin; Phase: Withdrawal; Replicate: 2

description: microarray name: 5216513028_E


title: Day: 15; Drug: Heroin; Phase: Withdrawal; Replicate: 1

description: microarray name: 5216513029_D


title: Day: 6; Drug: Saline; Phase: Drug treatment; Replicate: 2

description: microarray name: 5216513025_B


title: Day: 18; Drug: Saline; Phase: Withdrawal; Replicate: 2

description: microarray name: 5216513029_E


title: Day: 0; Drug: Naive; Phase: Naive; Replicate: 4

description: microarray name: 5216513025_F


title: Day: 13; Drug: Heroin; Phase: Withdrawal; Replicate: 1

description: microarray name: 5216513026_C


title: Day: 0; Drug: Naive; Phase: Naive; Replicate: 5

description: microarray name: 5216513026_F


title: Day: 3; Drug: Heroin; Phase: Drug treatment; Replicate: 1

description: microarray name: 5216513025_A


title: Day: 12; Drug: Saline; Phase: Drug treatment; Replicate: 2

description: microarray name: 5216513028_C


title: Day: 18; Drug: Saline; Phase: Withdrawal; Replicate: 3

description: microarray name: 5216513025_E


title: Day: 13; Drug: Saline; Phase: Withdrawal; Replicate: 3

description: microarray name: 5216513023_D


title: Day: 15; Drug: Heroin; Phase: Withdrawal; Replicate: 2

description: microarray name: 5216513025_D


title: Day: 6; Drug: Methamphetamine; Phase: Drug treatment; Replicate: 3

description: microarray name: 5216513026_B


title: Day: 13; Drug: Methamphetamine; Phase: Withdrawal; Replicate: 1

description: microarray name: 5216513025_C


title: Day: 18; Drug: Methamphetamine; Phase: Withdrawal; Replicate: 2

description: microarray name: 5216513023_E


title: Day: 6; Drug: Methamphetamine; Phase: Drug treatment; Replicate: 1

description: microarray name: 5216513023_B


title: Day: 12; Drug: Heroin; Phase: Drug treatment; Replicate: 2

description: microarray name: 5216513023_C


title: Day: 24; Drug: Methamphetamine; Phase: Withdrawal; Replicate: 1

description: microarray name: 5216513026_E


title: Day: 24; Drug: Heroin; Phase: Withdrawal; Replicate: 3

description: microarray name: 5216513023_F


title: Day: 3; Drug: Saline; Phase: Drug treatment; Replicate: 1

description: microarray name: 5216513026_A


title: KO2

city: Berlin

first: Alexandra

last: Klaus

state: Berlin

department: Signal Transduction, Invasion and Metastasis of Epithelial Cells

institute: MDC (Max Delbrück Center)

data_processing: The data have been normalized using the BeadStudio Gene Expression Module v3.3.7, and quantile normalization without background correction. Not or low expressed transcripts have been removed by a minimum Illumina detection p-value < 0.05. The data filtering resulted in 14,788 of 25,697 probes.

source_name: KO_embryonic heart

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplif Kit

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

tag: strain background

value: C57/BL6;129Ola mixed

value: MesP1-cre:RBPJlox/lox (KO)

tag: age

tag: developmental stage

value: embryonic heart


title: DKOhet2

source_name: DKOhet_embryonic heart


title: Day: 1; Drug: Saline; Phase: Drug treatment; Replicate: 2

description: microarray name: 5216513023_A


title: KO3


title: Day: 18; Drug: Saline; Phase: Withdrawal; Replicate: 1

description: microarray name: 5216513011_E


title: Day: 13; Drug: Heroin; Phase: Withdrawal; Replicate: 3

description: microarray name: 5216513011_D


title: DKOhet1


title: DKO4

source_name: DKO_embryonic heart

value: MesP1-cre:RBPJlox/lox//Axin2-/- (DKO)


title: hetDKO2

source_name: hetDKO_embryonic heart

value: MesP1-cre:RBPJlox/+//Axin2-/- (hetDKO)


title: Day: 12; Drug: Methamphetamine; Phase: Drug treatment; Replicate: 2

description: microarray name: 5216513011_C

value: Methamphetamine


title: Day: 18; Drug: Heroin; Phase: Withdrawal; Replicate: 1

description: microarray name: 5216513010_E


title: KO1


title: DKO3


title: hetDKO1


title: Day: 12; Drug: Saline; Phase: Drug treatment; Replicate: 1

description: microarray name: 5216513010_C

value: Drug treatment


title: control4

source_name: control_embryonic heart

value: wild type (control)


title: hetDKO3


title: Day: 24; Drug: Saline; Phase: Withdrawal; Replicate: 2

description: microarray name: 5216513010_F

value: Saline

value: striatum


title: DKO1


title: Day: 3; Drug: Saline; Phase: Drug treatment; Replicate: 3

description: microarray name: 5216513011_B


title: Day: 13; Drug: Methamphetamine; Phase: Withdrawal; Replicate: 3

description: microarray name: 5216513010_D

value: Withdrawal


title: Day: 24; Drug: Methamphetamine; Phase: Withdrawal; Replicate: 3

description: microarray name: 5216513011_F


title: Day: 24; Drug: Heroin; Phase: Withdrawal; Replicate: 2

description: microarray name: 5184013029_F

value: Heroin


title: control3


title: Day: 1; Drug: Heroin; Phase: Drug treatment; Replicate: 2

description: microarray name: 5216513011_A


title: Day: 3; Drug: Heroin; Phase: Drug treatment; Replicate: 3

description: microarray name: 5216513010_B


title: Day: 1; Drug: Methamphetamine; Phase: Drug treatment; Replicate: 2

description: microarray name: 5216513010_A


title: DKO2


title: control2


title: Day: 18; Drug: Methamphetamine; Phase: Withdrawal; Replicate: 1

description: microarray name: 5184013029_E


title: control1


title: Day: 12; Drug: Heroin; Phase: Drug treatment; Replicate: 1

description: microarray name: 5184013029_C


title: Day: 3; Drug: Saline; Phase: Drug treatment; Replicate: 2

description: microarray name: 5184013028_B


title: IL-1β treated (2ng/ml for 36 h) 2

city: Delhi

first: Malabika

address: Mall Road

country: India

institute: Institute of Genomics and Integrative Biology

description: IL-1b treated Rep2

hyb_protocol: Standard Illumina hybridization protocol on WG-6_V3 chip

data_processing: The data were normalised using average normalisation with Illumina bead studio software v 3.3.7 and significant genes were with differential scores ≥±13.

label: botin

source_name: Human epithelial pancreas

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

growth_protocol: Human epithelial pancreatic cell line Mia Paca-2 were cultured in DMEM high glucose supplemented with 10% FBS

extract_protocol: RNA was isolated using 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.

treatment_protocol: Mia Paca-2 cells were treated in the presence and absence of IL-1β with the concentration of 2ng/ml for 36 hours

tag: cell line

value: Mia Paca-2

tag: treatment

value: IL-1β treated (2ng/ml for 36 h)


title: Untreated Control 2

description: Control Rep2

value: Untreated Control


title: Day: 12; Drug: Methamphetamine; Phase: Drug treatment; Replicate: 1

description: microarray name: 5184013028_C


title: HDAC9_3

city: Philadelphia

first: Wayne

middle: W

last: Hancock

state: PA

address: 916B ARC, 3615 Civic Ctr Blvd

institute: CHOP/UPenn

hyb_protocol: 10 microgram of labeled aRNA was fragmented, and 6.5 microgram of the fragmented aRNA was hybridized to the Affymetrix Mouse 430A_2 chips.  Hybridization conditions were 16hrs at 45C.

scan_protocol: The chips were washed using Fluidics protocol midiEuk2v3_450 on an Affymetrix GeneChip Fluidics Station 450 and scanned on an Affymetrix Genechip Scanner.

data_processing: Microarray experiments were performed using whole-mouse-genome oligoarrays (Mouse430A_2, Affymetrix). Array data were analyzed using MAYDAY (Version 2.12). Array data were subjected to robust multi-array average (RMA) normalization. Normalized data were used for calculating fold changes of up- and down-regulated genes using Student's T-test. Data underwent z-score transformation for display.

source_name: Regulatory T-cells CD4+CD25+

label_protocol: 100ng of totalRNA was labeled using Ambion's MessageAmp Premier RNA Amplification Kit (PN:4383452)

extract_protocol: Total RNA was isolated using Rneasy (Quiagen). RNA integrity and quantity was analyzed using a DU640 (Beckman-Coulter).

tag: genotype


title: Day: 1; Drug: Heroin; Phase: Drug treatment; Replicate: 1

description: microarray name: 5184013028_A


title: Day: 15; Drug: Saline; Phase: Withdrawal; Replicate: 3

description: microarray name: 5184013028_E


title: Day: 13; Drug: Methamphetamine; Phase: Withdrawal; Replicate: 2

description: microarray name: 5184013017_D


title: Day: 15; Drug: Heroin; Phase: Withdrawal; Replicate: 3

description: microarray name: 5184013017_E


title: Day: 13; Drug: Saline; Phase: Withdrawal; Replicate: 2

description: microarray name: 5184013029_D


title: Day: 24; Drug: Methamphetamine; Phase: Withdrawal; Replicate: 2

description: microarray name: 5184013028_F


title: Wild type_3

value: Wild type


title: Wild type_1


title: Day: 1; Drug: Saline; Phase: Drug treatment; Replicate: 1

description: microarray name: 5184013029_A


title: IL-1β treated (2ng/ml for 36 h) 1

description: IL-1b treated Rep1


title: Wild type_2


title: HDAC9_1


title: HDAC9_2


title: Untreated Control 1

description: Control Rep1


title: Day: 3; Drug: Methamphetamine; Phase: Drug treatment; Replicate: 3

description: microarray name: 5184013029_B


title: Day: 6; Drug: Saline; Phase: Drug treatment; Replicate: 3

description: microarray name: 5184013017_C


title: Day: 3; Drug: Heroin; Phase: Drug treatment; Replicate: 2

description: microarray name: 5184013017_B


title: Day: 13; Drug: Heroin; Phase: Withdrawal; Replicate: 2

description: microarray name: 5184013028_D


title: Day: 24; Drug: Saline; Phase: Withdrawal; Replicate: 1

description: microarray name: 5184013017_F


title: M537-preNC

city: Torrance

first: Tsai-Der

last: Chuang

state: California

address: 1124 WEST CARSON STREET

department: OB-GYN

institute: LA Biomed at UCLA medical center

description: replicate 1

data_processing: The expression values were background-subtracted, globally normalized (BeadStudio version 1.5.1.3, Illumina)

source_name: Primary MSMC

growth_protocol: Small portions of leiomyoma and matched myometrium from untreated patients were used for isolation of MSMC and LSMC as previously described in detail (Chegini, Ma et al., 2002). The isolated MSMC and LSMC were cultured in DMEM supplemented with 10% FBS until reaching confluence (Chegini, Ma et al., 2002). All supplies for isolation and culturing of these cells were purchased from Sigma-Aldrich (St. Louis, MO), Invitrogen (Carlsbad, CA) and Fisher Scientific (Atlanta, GA).

extract_protocol: Total RNA was extracted from MSMC and LSMC using Trizol (Invitrogen). The quantity and quality of the isolated RNAs was determined using ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE)

treatment_protocol: MSMC, LSMC were seeded at a cell density of 3.5 x 104/well in 6-well plates and at sub-confluence transfected with 50nM of pre-miR-200c or pre-miR negative (preNC) (Applied Biosystems) for 96 hrs using PureFection transfection reagent (System Biosciences, Inc., Mountain View, CA) according to the manufacturer’s protocol.

value: Primary cell isolated from normal myometrium tissue

value: 48 years old

tag: race

value: african-american

value: women

tag: transfection

value: pre-miR negative


title: L537-preNC

description: replicate 1

source_name: Primary LSMC

value: Primary cell isolated from leiomyoma tissue


title: Day: 1; Drug: Methamphetamine; Phase: Drug treatment; Replicate: 1

description: microarray name: 5184013017_A

tag: strain

value: Methamphetamine


title: L537-pre200c

description: replicate 1


title: M537-pre200c

description: replicate 1


title: wild_type_OSE

city: Houston

first: JoAnne

last: Richards

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: gene expression data

hyb_protocol: cRNA were hybridized on GeneChip Mouse Genome 430 2.0 Array using Hybridization Oven 640. The GeneChip® Fluidics Station 450 automates the delivery, timing and temperature control of reagents for staining and washing of the probe arrays.

scan_protocol: GeneChips were scanned using GeneArray™ Scanner 3000 and quantified with Affymetrix GCOS 1.4.

data_processing: The data were analyzed using affy package from Bioconductor with RMA method.

source_name: Ovarian surface epithelia cells from wild type mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

growth_protocol: Animals were housed under a 16-h light/8-h dark schedule in the Center for Comparative Medicine at Baylor College of Medicine and provided food and water ad libitum.

extract_protocol: Total RNA extraction by RNeasy Mini Kit (Qiagen, Valencia, CA)

treatment_protocol: Animals were treated in accordance with the NIH Guide for the Care and Use of Laboratory Animals, as approved by the Animal Care and Use Committee at Baylor College of Medicine.

value: ovarian surface epithelia cells

value: wild type

value: 3 month


title: 502L pre-200c

description: replicate 1

value: 37 years old

value: caucasian


title: 502L pre-NC

description: replicate 1


title: P53_Pten_Kras_OSE

description: gene expression data

source_name: Ovarian surface epithelia cells from P53;Pten;Kras;Amhr2-Cre mice

value: Trp53 fl/fl;Ptentm1Hwu/ Ptentm1Hwu;Krastm4Tyj/ Krastm4Tyj ; Amhr2-cre (P53;Pten;Kras;A-cre)


title: Pten_Kras_OSE

description: gene expression data

source_name: Ovarian surface epithelia cells from Pten;Kras;Amhr2-Cre mice

value: Ptentm1Hwu/ Ptentm1Hwu;Krastm4Tyj/ Krastm4Tyj ; Amhr2-cre (Pten;Kras;A-cre)


title: 502M pre-200c

description: replicate 1


title: 502M pre-NC

description: replicate 1


title: WT MEFs, passage 5, rep2

city: Charlotesville

first: David

last: Wotton

department: Biochemistry and Molecular Genetics

institute: University of Virginia

description: Gene expression data from wild type passage 5 MEFs

hyb_protocol: Standard Affymetrix hybridization protocol with Mouse430_2.0 chips

data_processing: All data was normlaized using the GCRMA algorithm. Linear Models for Microarray Data (LIMMA) was run using a linear model fit by robust M-estimation allowing for a small proportion of outliers.  Empirical Bayes statistics for Differential Expressions was used to rank differentially expressed genes, using a Bonferroni  adjusted p-values

source_name: Primary wild type MEFs at passage 5

label_protocol: Biotinylated cRNA was prepared using Affymetrix IVT 3' Express from 5 ug total RNA.

growth_protocol: MEFs were isolated from 13.5 day mouse embryos, and cultured in DMEM supplemented with 10% Fetal Bovine Serum. For 3T3 growth MEFs were seeded at 3x105 cells per 10cm plate, trypsinized after three days, counted with a hemacytometer, and re-seeded at the same density.

extract_protocol: RNA was isolated and purified using Absolutely RNA kit (Stratagene), according to the manufacturer's instructions.

treatment_protocol: RNA was harvested at passage 3 or passage 5. No treatments.

value: primary MEFs

value: C57BL/6J x 129Sv/J

tag: passage number


title: WT MEFs, passage 5, rep3

tag: cell type


title: WT MEFs, passage 3, rep2

description: Gene expression data from wild type passage 3 MEFs

source_name: Primary wild type MEFs at passage 3


title: WT MEFs, passage 5, rep1


title: WT MEFs, passage 3, rep3


title: Tgif1 null MEFs, passage 3, rep2

description: Gene expression data from Tgif1 null passage 3 MEFs

source_name: Primary MEFs lacking Tgif1 at passage 3

value: Tgif1 -/-


title: Tgif1 null MEFs, passage 3, rep3


title: AL(2.0% glucose)

city: Liverpool

first: Daniel

last: Wuttke

state: Meyerside

address: Crownstreet

department: Department of Functional and Comparative Genomics

institute: University of Liverpool

description: Gene expression data from budding yeast on dietary restriction media.

hyb_protocol: RNA samples were processed and hybridized with GeneChip Yeast genome 2.0 arrays (Affymetrix Inc., Santa Clara, CA) by Expression Analysis (Durham, NC).

scan_protocol: see standard Affymetrix protocol

data_processing: The hybridization signals were normalized and analyzed with the Affy statistical algorithms by Expression Analysis.

organism: Saccharomyces cerevisiae

source_name: Budding yeast cells on AL media (unrestricted)

label_protocol: see standard Affymetrix protocol

growth_protocol: Wild-type yeast cells (BY4742) were inoculated into AL or DR liquid media and incubated overnight on a shaker. These seed cultures were then inoculated into fresh media to an initial OD600 of 0.01. Cells were grown at 30 degree Celsius for 12 hours. The final OD600 of cultures were 0.85 - 0.99.

extract_protocol: Three OD600 units of cells were collected and lysed with zymolyase. Total RNA was isolated using the Qiagen RNeasy mini kit according to the manufacturer’s protocol. Total RNA obtained was between 60 to 100 microgram.

treatment_protocol: Cells were inoculated into AL or DR liquid media (AL: yeast extract (1%) peptone plus (2%) D-glucose; DR: yeast extract (1%) peptone plus (0.5%) D-glucose).

value: wild-type (Mat alpha; his3Delta1; leu2Delta0; lys2Delta0; ura3Delta0)

tag: diet

value: unrestricted


title: Rat hepatocellular carcinoma cell line L2

city: Kamiyoga, Setagaya-ku

first: Kumiko

last: Ogawa

state: Tokyo

department: Pathology

institute: National Institute of Health Sciences

hyb_protocol: After the fragmentation of 10 µg cRNA incubated at 94 ˚C for 20 minutes, hybridization is performed in a temperature-controlled shaking incubator for 18–24 h at 37 ˚C. After the hybridization, the slide is washed with 0.75× TNT in the bioarray rack at 46 °C for exactly 1 hr, and incubated in Cy5-Streptavidin working solution for 30 min at room temperature. The slide is washed four times with 1× TNT (5 minutes each wash), and rinsed in 0.1× SSC/0.05% TweenTM for 30 seconds. The slide is dried up with centrifuge.

scan_protocol: The slide is scanned with ArrayWoRx Biochip Reader using manufacturer recommended settings.

data_processing:
The resulting images were processed through the CodeLink Expression Analysis v4.1 software which automatically grids and quantifies each feature while assigning spot quality metrics.
Data processing Raw values represent the final number of the spot after background is subtracted out. Normalized values represent median global normalization method, i.e. raw intensity/median intensity of all spots on the array.

source_name: Rat HCC L2

label_protocol: 2 µg of total RNA was processed following GE Healthcare's CodeLink(TM) iExpress Expression Assay Reagent Kit protocol. Biotin-labeled cRNA was prepared by linear amplification of the Poly(A)+ RNA population within the total RNA sample.

extract_protocol: Total RNA is extracted with ISOGEN according to the manufacturers instructions.

treatment_protocol: This rat hepatocellular carcinoma cell line is established from F344 rat treated with N-nitrosomorpholine and diethylnitrosamine (Ogawa et al., International Journal of Cancer, Vol. 91, pages 797–802, 2001.).

value: male

value: 31 weeks old

value: Liver tumor


title: WT MEFs, passage 3, rep1


title: Tgif1 null MEFs, passage 3, rep1


title: DR(0.5% glucose)

source_name: Budding yeast cells on DR media (restricted)

value: restricted


title: T cell non-activated in micro g rep3

city: San Francisco

first: Tammy

middle: T

last: Chang

address: 513 Parnassus Ave., HSW 1601

department: Surgery

institute: University of California, San Francisco

hyb_protocol: 10ug of biotinylated aRNA was hybridized on to the Human U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA) through the UCSF Gladstone Institute Genomics Core.  The arrays were stained using a Fluidics Station 400 (Affymetrix).

scan_protocol: Gene arrays were scaned using a GeneArray Scanner (Affymetrix).

data_processing: Microarray data were analyzed using the GeneSpring GX 11.0.2 software (Silicon Genetics, Redwood City, CA) and the GC-RMA algorithm. The background normalization was set to the average level of expression in mg non-activated T cells.  Statistical analysis was performed using one-way ANOVA and the Benjamini-Hochberg multiple testing correction with p<0.05.  Post-hoc Tukey analysis was performed to identify genes significantly differentially regulated between 1g and mg activated samples.  Significant genes were further filtered for a 2-fold or greater difference in expression between 1g and mg activated samples.

source_name: T cells, non-activated, micro g

label_protocol: RNA was amplified and biotinylated using the MessageAmp II-Biotin Enhanced Kit per manufacturer’s instructions (Ambion, Austin, TX).

growth_protocol: Human T cells were resuspended into RPMI 1640 with 10% FCS and loaded at 7x106 cells/chamber into the spaceflight hardware, LYCIS.

extract_protocol: RNA was isolated using RNeasy Mini kit (QIAGEN, Valencia, CA) according to the manufacturer’s protocol.

treatment_protocol: Experimental units were launched into space and placed into the KUBIK facility onboard the International Space Station.   The 1g units were placed in the central centrifuge positions and centrifuged with an applied 1g force.  The mg units were place in the static positions for continued mg exposure.  After 30 minutes of pre-incubation, mg non-activated units were fixed by addition of RNALater (QIAGEN, Valencia, CA), removed from the incubator, and stored in 4°C.  The mg and 1g activated units were injected with final concentration 10mg/ml Con A and 4mg/ml anti-CD28.  These cassettes were replaced into KUBIK on either the centrifuge or static positions and activated for 1.5 hours.  Activation was stopped with the addition of RNALater and the units were then moved to 4°C storage.  All units were returned to Earth for analysis.

value: Non-activated

tag: gravity

value: micro g

value: T cell


title: T cell non-activated in micro g rep2


title: Rat hepatocellular carcinoma cell line N1

source_name: Rat HCC N1


title: Rat hepatocellular carcinoma cell line C6

source_name: Rat HCC C6


title: T cell non-activated in micro g rep1


title: Rat hepatocellular carcinoma cell line C5F

source_name: Rat HCC C5F

value: 31 weeks


title: 10336_Relapse_Ascites

city: Melbourne

first: Prof David

last: Bowtell PhD.

state: VIC

address: Locked Bag 1 A' Beckett St

department: Research Division

country: Australia

institute: PeterMacCallum Cancer Centre

description: Tumour tissue collected at primary surgery

hyb_protocol: Protocol per manufacturer's protocol

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner

data_processing: Raw CEL files were normalized using methods available in R package "aroma.affymetrix". Systematic biases including allelic-crosstalk and fragment length biases were removed using the methods available in this package. The resultant values were log2 transformed to obtain the normalized values.

label_protocol: Protocol per manufacturer's protocol

growth_protocol: Frozen tissues were sectioned on a cryostat and lysed immediately

extract_protocol: Genomic DNA was isolated using the Qiagen Dneasy kit

value: Female

value: Tumour


title: 11242_Right_Ovary


title: T cell activated in 1g rep3

source_name: T cells, activated, 1g, 1.5h

value: Activated with 10mg/ml Con A and 4mg/ml anti-CD2 in 1 g


title: Control liver

source_name: Control rat liver tissue

value: SD

value: 50 weeks

value: Liver


title: T cell activated in 1g rep2


title: 10335_Primary_Ovarian


title: 10336_Primary_Ovarian


title: 10335_Relapse_Ascites


title: 11276_Relapse_Ascites


title: 11424_Relapse_Ascites


title: 11313_Relapse_Ascites


title: 11242_Left_Ovary


title: 11313_Primary_Ovarian

description: Tumour tissue collected at relapse


title: 11242_Pouch_of_Douglas


title: 11424_Primary_Ovarian

description: Tumour tissue collected at relapse


title: 18-81 miR-125b #2

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

hyb_protocol: Agilent : 825.0 ng at 65 degree C during 17 hours.

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature Extraction data processing.

label_protocol: Agilent Low RNA Input QuickAmp kit. No amplification.

extract_protocol: miRNeasy kit (Qiagen). 0.2 ug. RIN number: 9.

treatment_protocol: Chemically synthesized miRNA duplexes, called pre-miR-125b and miR-Neg, were purchased from Ambion. The cells were transfected with pre-miRNA at a final concentration of 10 nM using Lipofectamin RNAi MAX (Invitrogen) according to the manufacturer's instructions. The medium was replaced 8 hours after transfection. RNA samples were harvested at 48 hours post-transfection.

tag: origin

value: pre-B cell

value: pre-B cell transformed by Abelson-murine leukemia virus (A-MuLV)

tag: miRNA transfection


title: T cell activated in micro g rep2

source_name: T cells, activated, micro g, 1.5h

value: Activated with 10mg/ml Con A and 4mg/ml anti-CD2 in microgravity


title: 18-81 miR-Neg #2

value: miR-Neg


title: T cell activated in 1g rep1


title: 11276_Primary_Ovarian

description: Tumour tissue collected at relapse

tag: tissue


title: 11360_Primary_Ovarian

description: Tumour tissue collected at relapse

tag: gender


title: 11242_Omentum

source_name: Omentum


title: T cell activated in micro g rep3


title: T cell activated in micro g rep1


title: 70Z/3 miR-125b #2

value: pre-B lymphoblast

tag: disease state

value: leukemia


title: 11503_Relapse_Ascites


title: 11995_Primary_Ovarian

description: Tumour tissue collected at relapse


title: H226 Spheroid, biological rep3

city: Bethesda

first: Mitchell

last: Ho

state: MD

address: 37 Convent Drive, MSC 4264

department: Laboratory of Molecular Biology

institute: National Cancer Institute, NIH

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol (see complete protocol descriptions: http://www.affymetrix.com/support/technical/manual/expression_manual.affx) on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: H226 Spheroid

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (see complete protocol descriptions: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (see complete protocol descriptions: http://www.affymetrix.com/support/technical/manual/expression_manual.affx)     http://www.affymetrix.com/support/technical/manual/expression_manual.affx)   Biotinylated cRNA was prepared according to the standard Affymetrix protocol (see complete protocol descriptions: http://www.affymetrix.com/support/technical/manual/expression_manual.affx)

growth_protocol: The human mesothelioma cell line NCI-H226 was maintained as adherent monolayer cultures in RPMI 1640 medium supplemented with 10% fetal bovine serum, L-glutamine, pyruvate, nonessential amino acids, and penicillin-streptomycin and incubated in 5% CO2 with balance of air at 37°C.

extract_protocol: Total RNA was prepared using RNeasy Plus Mini Kit according to the manufacturer’s instructions (Qiagen, Valencia, CA)

treatment_protocol: A 96-well Greiner suspension culture plate was coated with 50 µL of 5 mg/mL of poly-HEMA (poly-2-hydroxyethyl methacrylate) in 95% ethanol and evaporated with lid on at room temperature for 72 hours. Each well contained 10,000 cells for one spheroid. The plate was then centrifuged at 1000 rpm for 10 minutes to initiate cell-cell interaction and incubated at 37°C, 5% CO2 for 24 hours. The spheroids are stable for 48–72 hours and can be easily transferred using a regular pipette without dissociating.

value: Mesothelioma

tag: culture type

value: Spheroid


title: H226 Spheroid, biological rep2


title: 15001_Primary_Ovarian

description: Tumour tissue collected at relapse


title: 11360_Relapse_Ascites


title: 11503_Primary_Ovarian

description: Tumour tissue collected at relapse


title: 70Z/3 miR-Neg #1

source_name: 70Z/3, miR-Neg


title: 18-81 miR-125b #1


title: 15001_Relapse_Ascites


title: 18-81 miR-Neg #1


title: H226 Monolayer, biological rep1

source_name: H226 Monolayer

value: Monolayer


title: 15002_Primary_Ovarian

description: Tumour tissue collected at relapse


title: H226 Monolayer, biological rep2


title: 15002_Relapse_Ascites


title: 11995_Relapse_Ascites


title: 11709_Primary_Ovarian

description: Tumour tissue collected at relapse


title: 11709_Relapse_Ascites


title: 70Z/3 miR-125b #1


title: MA-104 SARS CoV DeltaE 65hpi rep2

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

institute: CNB, CSIC

description: Gene expression data from MA-104 cells infected with SARS-CoV-DeltaE and collected at 65hpi

hyb_protocol: Following fragmentation, 10 µg of biotinylated cRNA were hybridized to Affymetrix GeneChips (Human Genome U133 plus 2.0) at 45ºC during 16 hours. Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino)ethanesulfonic acid, 1 M Na+, 20mM of EDTA and 0,01% tween-20

scan_protocol: The arrays were stained with streptavidin-ficoeritrin and read at 1.56 μm in a GeneChip Scanner 3000 7G System (Affymetrix, Santa Clara, CA)

data_processing: GeneChip intensities were background-corrected, normalized and sumarized by RMA method, using the “Affy” package from Bioconductor.

organism: Chlorocebus aethiops

source_name: MA-104 cells, infected with SARS-CoV-DeltaE, 65hpi

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

growth_protocol: Subconfluent monolayers (90% confluency) of Vero E6 and MA-104 cells were infected at multiplicity of infection (moi) of 0.01 or 2 with the viruses rSARS-CoV-ΔE, and rSARS-CoV or rSARS-CoV-MA15-ΔE and rSARS-CoV-MA15. Culture supernatants were collected at different hours post-infection (hpi) and virus titer was determined as previously described.

extract_protocol: Total RNA was prepared using the RNeasy Mini Kit (Qiagen) according to the manufacturer´s instructions. RNA was quantified and the RNA quality was assessed with a 2100 Bioanalyzer (Agilent Technologies).

tag: infection

value: SARS CoV DeltaE

tag: induce ifnβ

value: YES

tag: hours post infection

value: 65 hpi


title: H226 Spheroid, biological rep1

tag: cell line


title: H226 Monolayer, biological rep3


title: MA-104 SARS CoV 65hpi rep3

description: Gene expression data from MA-104 cells infected with SARS-CoV (WT) and collected at 65hpi

source_name: MA-104 cells, infected with SARS-CoV (WT), 65hpi

value: SARS CoV


title: 70Z/3 miR-Neg #2


title: MA-104 SARS CoV 65hpi rep2


title: MA-104 SARS CoV DeltaE 65hpi rep1


title: MA-104 Mock infected 0hpi rep3

description: Gene expression data from MA-104 cells mock-infected and collected at 0hpi

source_name: MA-104 cells, mock-infected, 0hpi

value: Mock infected

value: 0 hpi


title: MA-104 SARS CoV 65hpi rep1


title: MA-104 SARS CoV DeltaE 65hpi rep3


title: MA-104 Mock infected 0hpi rep1


title: MA-104 SARS CoV DeltaE 24hpi rep3

description: Gene expression data from MA-104 cells infected with SARS-CoV-DeltaE and collected at 24hpi

source_name: MA-104 cells, infected with SARS-CoV-DeltaE, 24hpi

value: 24 hpi


title: 15003_Relapse_Ascites

value: Female

value: Tumour


title: MA-104 Mock infected 0hpi rep2


title: Sample 34 vs 42, heavy polysomes vs heavy polysomes, reverse labeling slide A

city: Leicester

first: Kate

middle: Marie

last: Dudek

address: Hodgkin Building, Lancaster Road

department: Genomics Group

institute: MRC Toxicology Unit

hyb_protocol: Samples combined (cy-3 labelled and cy-5 labelled). 4 µg tRNA and 40 µl Genisphere 2x enhanced hybridisation buffer added. Samples denatured at 95°C for 5 minutes and then incubated at 42°C. Complete MEEBO array is split over 2 slides (part A and part B), therefore, sample split and equal volume added to each slide. Slides hybridised for 16 hours at 42°C using Genetix hybridisation chamber. Following hybridisation slides were washed sequentially: wash 1: 1X SSC, 0.03% SDS for 5 minutes, wash 2: 0.2X SSC for 3 minutes, wash 3: 0.05X SSC for 3 minutes.

scan_protocol: Slides scanned on a 4200 Axon scanner and data acquired using GenePix Pro v.6.0.

data_processing: Result files were LOWESS normalised and tested for statistical significance using a two-labelled T test. Forward and reverse reactions were combined and each mRNA had a normalised log 2 value, indicative of fold change. The data for each of the 4 sub pools (monosome, light polysome, medium polysome and heavy polysome) was combined into one data matrix file so that the  normalised log 2 values could be analysed across the gradient.

source_name: Fractionated liver RNA, treated with 1120mg/kg of FP014SC for 15 days.

label_protocol: Equal amounts of RNA from each sub-pool were precipitated with 10 µl 3M NaOAc pH 5.2 and 275 µl 100% ethanol at -20°C overnight. Following centrifugation (12000xg, 10 minutes, 4°C) pellets were washed twice with 75% ethanol and resuspended in 10 µl water. We used a direct labelling technique to conjugate the reverse transcribed cDNA to cy dyes. The precipitated RNA was first primed with 8 µg/ul oligo dT25N2 and 1 µl 10 nM/µl random pentadecamers at 70°C for 8 minutes, then reverse transcribed and labelled at 50°C for 2 hours in the presence of dNTPs, Superscript III and Cy-3/Cy-5. The cDNA was hydrolysed through addition of 0.5M EDTA and 3M NaOH (70°C for 10 minutes) and then purified using Microcon YM-30 columns.

growth_protocol: Male Wistar rats, 209-248g, 8-10 weeks old. 12 hour light/dark cycle. Food and water provided ad libitum, 24 hours a day.

extract_protocol: Liver samples were lysed (15 mM Tris-HCl (pH 8.0), 300 mM NaCl and 15 mM MgCl2, plus inhibitors (1 mg/ml heparin 100 µg/ml cycloheximide and 80 U RNAsin)), added  to a 10-50% sucrose gradient and ultracentrifuged at 182,000x g for 2 hours. The gradient was aliquotted into 16 1ml fractions and added to Tri reagent (Sigma). RNA was extracted as per the manufacturer's instructions and then sub-pooled into fractions corresponding to monosomes, light polysomes, medium polysomes and heavy polysomes.

treatment_protocol: Rats were randomly assigned to groups on the basis of body weight. Dosing was performed intra-gastricallly by gavage. Treated rats received 2 x 560mg/kg of test compound per day for 15 days, controls received vehicle-only; in a dose volume of 10ml/kg. 20 hours after the final administration rats were sacrificed under chloroform anaesthesia and exsanguinated. Liver and kidneys were taken for analysis.

tag: treatment

value: Male

value: Wistar

value: Liver

tag: fraction sub-pool

value: Heavy polysomes

source_name: Fractionated liver RNA, treated with vehicle-only.

value: treated with vehicle-only.


title: MA-104 SARS CoV DeltaE 24hpi rep2


title: Sample 34 vs 42, heavy polysomes vs heavy polysomes, forward labeling slide A

tag: strain

value: treated with 1120mg/kg of FP014SC for 15 days.