title: Blood from Stage II (GP2477_WB_142992HP133A11)

city: Stevenage

address: Gunnels Wood Road

institute: GlaxoSmithKline

label_protocol: NuGEN Ovation FLv2 methodology using NuGEN Ovation RNA amplification v2 including C1 spike with Agencourt RNAClean SPIA clean up. FLv2 biotin fragmentation and labelling.

value: blood

value: Stage II

tag: plateid

tag: subject type

value: COPD Subjects

tag: hyb date


title: C.elegans wild type raised in the presence of Cd, rep1

status: Public on Jun 01 2014

type: RNA

city: London

first: Stephen

last: Sturzenbaum

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

country: United Kingdom

institute: King's College London

description: Standard affymetrix recommended quality control parameters were used during entire experiment.

hyb_protocol: 10 μg of Biotin end labeled aRNA (amplified RNA) was fragmented and hybridized to the Affymetrix C. elegans GeneChips as recommended by Affymetrix. The quality & quantity of the aRNA probe preparation was assessed before hybridization using an Agilent 2100 bioanalyzer & Nanodrop-1000 spectrophotometer, receptively.

scan_protocol: Affymetrix GeneChip® Command Console (AGCC) software was used for the control of array washing (GeneChip Fluidics Station-450), data acquisition (Scanner 3000-7G) as well as for the preliminary data analysis.

data_processing:
Preprocessing of microarray raw data including probe-specific background correction, summarization of probe set values, and normalization was carried out using the GCRMA algorithm with CARMAweb 1.4, an R- and Bioconductor-based web service for microarray data analysis (Rainer et al., 2006).
Rainer J, Sanchez-Cabo F, Stocker G, Sturn A, Trajanoski Z (2006). CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis. Nucleic Acids Res 34:W498–W503

label: biotin

molecule: total RNA

organism: Caenorhabditis elegans

source_name: C.elegans Cd exposure

label_protocol: 200 ng of total RNA was subjected to aRNA amplification and Biotin labeling as described in the MessageAmpTM Premier RNA Amplification Kit (Ambion) for microarray analysis. aRNA cleanup was achieved using magnetic beads (Ambion).

extract_protocol: The RNA isolation followed the standard procedures using Trizol reagent (Invitrogen), however modified to include a homogenization step with 0.5 mm glass beads (Sigma) to maximize cell breakage. RNA was subsequently purified using an RNeasy kit (Qiagen) followed by a DNase digestion (Qiagen).

treatment_protocol: Parent population (P0) maintained at 20 ºC on standard nematode growth media (NGM) plates using Escherichia coli OP50 as food source. A synchronous L1 culture was generated by standard bleach prepping and grown to L4 stage. Exposed to 30 µM Cd throughout from hatching to L4 stage.

tag: age

value: larvae (L4)

tag: tissue

value: whole animal

tag: strain

value: N2 (Bristol)

tag: genotype/variation

value: wild type


title: C.elegans MT KO  mtl-1,mtl-2(zs1), raised in the absence of Cd, rep1

source_name: C.elegans MT KO control exposure

growth_protocol: Parent population (P0) maintained at 20 ºC on standard nematode growth media (NGM) plates using Escherichia coli OP50 as food source. A synchronous L1 culture was generated by standard bleach prepping and grown to L4 stage.

value: MT KO mtl-1,mtl-2(zs1)


title: C.elegans MT KO  mtl-1,mtl-2(zs1), raised in the absence of Cd, rep2

treatment_protocol: Parent population (P0) maintained at 20 ºC on standard nematode growth media (NGM) plates using Escherichia coli OP50 as food source. A synchronous L1 culture was generated by standard bleach prepping and grown to L4 stage.


title: C.elegans MT KO  mtl-1,mtl-2(zs1), raised in the absence of Cd, rep3


title: phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 1 Replicate: 1 Passage: 6

city: Chapel Hill

first: Jason

middle: L

last: Stein

state: NC

address: Neuroscience Research Building 8109C, 115 Mason Farm Rd

department: Genetics

country: USA

institute: UNC Chapel Hill

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: Log2 normalization, quantile normalization, and ComBat batch correction

organism: Homo sapiens

source_name: Human fetal tissue

label_protocol: Biotin

growth_protocol: phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2

extract_protocol: phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA).

treatment_protocol: phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin.

tag: donor id

tag: region id

tag: cell type

value: phNPC from Geschwind Lab

tag: differentiation wk

tag: passage

tag: rin

tag: gestation wk

tag: ancestry

value: ASW

tag: Sex

value: M

tag: array batch


title: phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 12 Replicate: 1 Passage: 5

value: MEX


title: C.elegans wild type raised in the presence of Cd, rep3


title: phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 1 Replicate: 1 Passage: 5


title: Blood from Stage I (GP2477_WB_142989HP133A11)

first: steve

middle: matthew

last: fox

department: Statistics

hyb_protocol: Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on GeneChip HG-U133_plus_2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A.

data_processing: The data was analysed with Rosetta Resolver version 5.0

label: Biotin

source_name: blood

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

tag: gender

value: F

tag: gold stage

value: Stage I

tag: plateid

value: Smoker Controls


title: 0.001µg/ml 1 month rep 2

city: Callaghan

first: Belinda

last: Nixon

state: NSW

address: University Drive

country: Australia

institute: University of Newcastle

description: Sample name: 5

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation using BioConductor's lumi package in R statistical software

organism: Mus musculus

source_name: mouse testis following 0.001 µg/ml acrylamide for 1 month

label_protocol: Biotinylated cRNA were prepared with Ambion's Illumina RNA Amplification kit for Illumina arrays

growth_protocol: Adult male Swiss mice were housed under controlled temperature and humidity conditions, 16 h light, 8 h dark, with food and water provided ad libitum. Animals were acclimated for at least 1 month prior to treatment. At each time point, animals were euthanized by CO2 asphyxiation and testes were extracted.

extract_protocol: RNA was extracted from individual testes of acrylamide exposed mice using RNeasy Mini Kit (Qiagen, Chadstone Centre, VIC) according to manufacturers' instructions.

treatment_protocol: Acrylamide drinking water solutions were prepared using research-grade acrylamide obtained from Sigma (≥ 99% purity, A9099) diluted in filtered, deionized water at concentrations 0.001, 0.01, 0.1, 1, and 10 ?g/ml. Drinking water containing acrylamide was prepared fresh on a weekly basis, and was substituted for normal drinking water at the commencement of treatment. Test animals were exposed to acrylamide via the drinking water for a period of 1, 6 or 12 months

value: Swiss

value: Male

tag: age

value: 3-6 months

tag: agent

value: acrylamide

tag: dose

tag: time

value: 1 month

value: testis


title: Blood from Stage II (GP2477_WB_142990HP133A11)

tag: tissue

value: blood

value: Stage II

tag: subject type

value: COPD Subjects

tag: hyb date


title: Blood from Stage II (GP2477_WB_142991HP133A11)


title: NCCIT - EC cell line 102251-05

city: Rotterdam

first: Martin

middle: Anne

last: Rijlaarsdam

address: Wytemaweg 80

department: Pathology

country: Netherlands

institute: Erasmus MC

description: mediastinal germ cell tumor (embryonal carcinoma) (Teshima et al. 1988) replicate 1

hyb_protocol: Per sample, 750 ng of the obtained biotinylated cRNA samples was hybridized onto the Illumina HumanHT-12 v4 (Illumina, Inc., San Diego, CA, U.S.A.). Each BeadChip contains twelve arrays. Hybridization and washing were performed according to the Illumina Manual “Direct Hybridization Assay Guide”.

scan_protocol: Scanning was performed on the Illumina iScan (Illumina, Inc., San Diego, CA, U.S.A.) according to the manufacturer's instructions.

data_processing: Image analysis and extraction of raw expression data was performed with Illumina GenomeStudio v2011.1 (default settings). Further processing was carried out in R using the LUMI package [1]. Following the guidelines presented in [2], robust spline normalization was applied to the log2 transformed intensity values. Probes with pdetection>0.05 in >50% of the samples were excluded from the analysis (n=27,964 out of 47,323).   1. Du, P., W.A. Kibbe, and S.M. Lin, lumi: a pipeline for processing Illumina microarray. Bioinformatics, 2008. 24(13): p. 1547-8.  2. Schmid, R., et al., Comparison of normalization methods for Illumina BeadChip HumanHT-12 v3. BMC Genomics, 2010. 11(1): p. 349.

label_protocol: The Quality control, RNA labeling, hybridization and data extraction were performed at ServiceXS B.V. (Leiden, The Netherlands). RNA concentration was measured using the Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, U.S.A). The RNA quality and integrity was determined using Lab-on-Chip analysis on the Agilent BioAnalyzer (Agilent Technologies Inc., Santa Clara,CA, U.S.A.). Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion, Inc., Austin, TX, U.S.A.) according to the manufacturer’s specifications with an input of 200ng total RNA.

growth_protocol: Cells (wild type) were cultured in DMEM medium (Life Technologies, #31966-021) containing 10% fetal calf serum (FCS, Hyclone) in T75 cm2 flasks to 75-90% confluence. Biological replicates were started as independent cultures at different days and processed similarly.

extract_protocol: Fresh medium was added 24 hours before harvest. Cells were washed once with Hanks balanced Salt Solution (HBSS, Life Technologies, #14175-053), and lysed with 7ml of ice-cold RNA-Bee (TEL-TEST, Inc).

tag: histological_subtype_primary tumor

value: non-seminoma including an embryonal carcinoma component

tag: anatomical localisation

value: mediastinum

tag: cell line

value: NCCIT


title: NAA +AA 1

city: Umeå

first: Simon

middle: R.

last: Law

state: Västerbotten

address: Umeå University

country: Sweden

institute: Umeå Plant Science Centre

hyb_protocol: Following fragmentation, 12.5 µg of the labelled aRNA was hybridised rotating at 60 rpm, 16 hr at 45 °C on GeneChip ATH1 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned individually 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. Additionally, GC RMA normalisation was carried out using Partek Genomics Suite.

organism: Arabidopsis thaliana

source_name: Col:LUC grown on B5 media supplemented with 4.5 µM NAA and treated with AA

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 400 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 40 mg of Col-0 and Attim17-1 Arabidopsis thaliana seeds were surface steralized and plated on B5 media. Stratification was carried out at 4 °C in darkness, followed by long day growth conditions at 100 µE m -2 sec-1 at 22 °C.

extract_protocol: RNA isolation was carried out using the Sigma-Aldrich® Spectrum™ Plant Total RNA Kit.

treatment_protocol: Analyses were carried out using 400 ng total RNA isolated in biological triplicate from Col:LUC seedlings grown on B5 media for 10 days and transferred to fresh plates, containing either B5 media or B5 media supplemented with 4.5 µM NAA for an additional 3 days.Seedlings were treated with 50 µM AA for 3 hours.

tag: ecotype

tag: treatment


title: C.elegans wild type raised in the presence of Cd, rep2

value: larvae (L4)

value: whole animal

tag: strain

value: N2 (Bristol)

tag: genotype/variation

value: wild type


title: Blood from Stage II (GP2477_WB_142984HP133A11)

tag: gender

value: M


title: Blood from Stage III (GP2477_WB_142988HP133A11)

tag: gold stage

value: Stage III


title: Blood from Stage II (GP2477_WB_142986HP133A11)

tag: plateid


title: Obese B, rep6

city: Daegu

first: Seo

last: Yu-Ri

address: 1370, Sankyuk-Dong, Buk-gu

country: South Korea

institute: uree

description:
replicate 6
OB6

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each mouse-6 expression bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA). Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual.

scan_protocol: Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions. Array data export processing and analysis was performed Illumina GenomeStudio v2009.2 (Gene Expression Module v1.5.4).

data_processing: The quality of hybridization and overall chip performance were monitored by visual inspection of both internal quality control checks and the raw scanned data. Raw data were extracted using the software provided by the manufacturer(Illumina GenomeStudio v2009.2 (Gene Expression Module v1.5.4)).

source_name: Human PBMC

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions. Briefly, 550 ng of total RNA was reverse-transcribed to cDNA using a T7 oligo(dT) primer. Second-strand cDNA was synthesized, in vitro transcribed, and labeled with biotin-NTP. After purification, the cRNA was quantified using the ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA).

extract_protocol: Total RNA was extracted from the PBMC using TRIZOL reagent (Invitrogen Life Technologies, NY) according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: PBMCs were separated from 8 mL of whole blood mixed with heparin by centrifugation over a Ficoll-Paque (Pharmacia, Uppsala, Sweden) density gradient at 3000 rpm for 30 minutes at room temperature. The separated PBMCs were washed 3 times in 5 mL of Hank’s Balanced Salt Solution (HBSS) (Sigma-Aldrich, St. Louis, MO) and then PBMCs were lysed in 1 ml of TRIZOL reagent (Invitrogen Life Technologies, Grand Island, NY). Lysates were frozen at -70°C until RNA purification.

value: male

tag: age

value: 45 years

value: peripheral blood mononuclear cell

tag: phenotype

value: obese


title: NAA -AA 3

source_name: Col:LUC grown on B5 media supplemented with 4.5 µM NAA and untreated


title: NAA +AA 2

value: B5 media supplemented with 4.5 µM NAA and treated with AA


title: TCam-2 - SE cell line 102251-02

description: testicular seminoma (Mizuno et al, 1993, de Jong et al,2008) replicate 2

source_name: testicular seminoma

value: seminoma

value: testis


title: NCCIT - EC cell line 102251-06

description: mediastinal germ cell tumor (embryonal carcinoma) (Teshima et al. 1988) replicate 2


title: Blood from Stage III (GP2477_WB_142987HP133A11)

value: blood

value: COPD Subjects


title: TCam-2 - SE cell line 102251-01

description: testicular seminoma (Mizuno et al, 1993, de Jong et al,2008) replicate 1


title: Obese B, rep7

description:
replicate 7
OB7

value: 53 years


title: C.elegans wild type raised in the absence of Cd, rep2

source_name: C.elegans control exposure


title: NAA +AA 3


title: NAA -AA 2

value: B5 media supplemented with 4.5 µM NAA and untreated


title: NAA -AA 1


title: Blood from Stage I (GP2477_WB_142983HP133A11)

value: Stage I

value: Non-smoker Controls


title: Obese B, rep5

description:
replicate 5
OB5

value: 42 years


title: Obese B, rep4

description:
replicate 4
OB4

value: 23 years


title: C.elegans wild type raised in the absence of Cd, rep3

value: larvae (L4)

value: whole animal

value: N2 (Bristol)

value: wild type


title: Blood from Stage III (GP2477_WB_142982HP133A11)

value: M

value: Stage III


title: C.elegans wild type raised in the absence of Cd, rep1


title: Obese B, rep3

description:
replicate 3
OB3

value: male

value: 26 years

value: peripheral blood mononuclear cell

value: obese


title: Blood from Stage III (GP2477_WB_142980HP133A11)

value: blood

value: F

value: COPD Subjects


title: B5 -AA 3

source_name: Col:LUC grown on B5 media and untreated

value: B5 media and untreated


title: Blood from Stage III (GP2477_WB_142979HP133A11)


title: B5 +AA 3

source_name: Col:LUC grown on B5 media and treated with AA

value: B5 media and treated with AA


title: Obese B, rep2

description:
replicate 2
OB2

value: 25 years


title: B5 +AA 1


title: Blood from Stage II (GP2477_WB_142977HP133A11)

value: Stage II


title: Blood from Stage I (GP2477_WB_142981HP133A11)

value: Stage I

value: Non-smoker Controls


title: B5 -AA 2


title: Blood from Stage I (GP2477_WB_142978HP133A11)

value: Smoker Controls


title: Obese A, rep8

description:
replicate 8
OA8

value: 52 years


title: Obese A, rep9

description:
replicate 9
OA9

value: 58 years


title: Obese B, rep1

description:
replicate 1
OB1

value: 23 years


title: Obese A, rep6

description:
replicate 6
OA6

value: male

value: 43 years


title: PLC_CIS_DOX_Terence Lee_090713_U133_MAS5

city: Hong Kong

first: Kin Wah

last: Lee

address: 21 Sassoon Road

country: China

institute: The University of Hong Kong

description: Gene Expression

hyb_protocol: Service by The University of Hong Kong (HKU) Genome Research Centre (protocol attached)

data_processing: The data were analyzed with MAS5 using Affymetrix default analysis settings and global scaling as normalization method

source_name: chemoresistant (cisplatin and doxorubicin) hepatospheres

growth_protocol: PLC/PRF/5 HCC cells were grown as spheroids and treated with cisplatin and doxorubicin combination. Differentiated counterparts were generated by addition of FBS in the spheroids and allowed to attached.

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

value: HCC

tag: protocol

value: HCC grown as spheroids and treated with cisplatin and doxorubicin combination


title: C.elegans MT KO  mtl-1,mtl-2(zs1) raised in the presence of Cd, rep2

source_name: C.elegans MT KO Cd exposure

value: larvae (L4)

value: whole animal

value: N2 (Bristol)

value: MT KO mtl-1,mtl-2(zs1)


title: Obese A, rep4

description:
replicate 4
OA4

value: 27 years

value: peripheral blood mononuclear cell

value: obese


title: Blood from Stage III (GP2477_WB_142975HP133A11)

value: blood

value: F

value: Stage III

value: COPD Subjects


title: B5 +AA 2

value: B5 media and treated with AA


title: Wild type (Col-0) inflorescence, moderate drought-treated, day 10, replicate 1

city: University Park

first: Zhao

last: SU

state: PA

address: 354 N. Frear

department: Biology

institute: The Penn State University

description: Gene expression data from Arabidopsis unopen flower buds sampled 10 days later from drought-treated plant

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: The data were analyzed by using robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) with the R/Bioconductor package affy. and then converted to logarithm base 2.

source_name: Arabidopsis inflorescence sampled 10 days later from moderate drought-treated plant

label_protocol: Standard Affymetrix protocol.

growth_protocol: Seeds were directly sown into pots containing 100g soil mixture of Metro-Mix 360 soil (Sun Gro Horticulture Canada Ltd) and Turface profile greens grade (Profile Products LLC) in 3:2 ratio by volume, with a maximum water-holding capacity of 100g (defined as 100% soil moisture). Seeds were stratified in a cold room for 2 d at 4 ℃ in the dark. After stratification, the pots with seeds were transferred into a Conviron growth chamber (Conviron Inc), which was set at our normal conditions (22 ℃, 16h day/8h night photoperied, ~300 μmol m-2 s-1 photon flux, 60% humidity) until just after flowering (bolting) when some of the plants were subjected to moderate drought stress.

extract_protocol: Total RNA was isolated from unopened flower buds using RNeasy columns following instructions from the manufacturer (Qiagen, Valencia, CA, USA).

treatment_protocol: Arabidopsis were well-watered until after just bolting (after 24 days growth with the main stem about 1 cm high) when moderate drought treatment was started by withholding water (defined as day 0 for moderate drought treatment). The relative soil moisture content decreased rapidly and, after about 48 hours the relative soil moisture content was near 50 % of the soil water capacity (collecting M3 sample at day 3(72 h after withholding water). The soil water condition was maintained by daily watering until almost all the fruits were mature and ready to harvest (about 50 days). For well-watered (control) plants, 90% of the soil water capacity was maintained until tissue harvest or after seed maturation (pots were weighed and watered twice per day). Unopened floral buds samples were collected at day 0, 3, 4, 5, 10.

value: Unopen flower buds

tag: cultivar

value: at day 34 after seed germination


title: Obese A, rep3

description:
replicate 3
OA3

value: male

value: 24 years

tag: tissue


title: Obese A, rep7

description:
replicate 7
OA7

value: 42 years


title: Obese A, rep10

description:
replicate 10
OA10

value: 56 years


title: Obese A, rep5

description:
replicate 5
OA5

value: 49 years


title: mutated 3

city: Boston

first: Aldo

last: Roccaro

state: MA

address: 450 Brookline Av

institute: Dana-Farber Cancer Institute

description: Gene expression data from mutated cells

hyb_protocol: The cRNA is hybridized to a microarray chip. The bound cRNA is stained with fluorescent streptavidin

scan_protocol: The microarray chip is then scanned using a laser, and the positions and intensities of the fluorescent emissions are captured. These measurements provide the basis of subsequent biostatistical analysis.

data_processing: The data were analyzed using d-Chip software.

source_name: BCWM1 mutated

label_protocol: RNA of interest is converted into cDNA, then amplified and labeled with biotinylated nucleotides by in vitro transcription to produce biotinylated cRNA

extract_protocol: RNA was isolated using RNeasy kit (Qiagen)

value: mutated


title: mutated 1

description: Gene expression data from mutated cells


title: Obese A, rep2

description:
replicate 2
OA2

value: 22 years


title: Wild type (Col-0) inflorescence, moderate drought-treated, day 3, replicate 2

description: Gene expression data from Arabidopsis unopen flower buds sampled 3 days later from drought-treated plant

source_name: Arabidopsis inflorescence sampled 3 days later from moderate drought-treated plant

value: at day 27 after seed germination


title: parental 1

description: Gene expression data from parental cells

source_name: BCWM1 parenatal

value: parenatal


title: Wild type (Col-0) inflorescence, moderate drought-treated, day 4, replicate 1

description: Gene expression data from Arabidopsis unopen flower buds sampled 4 days later from drought-treated plant

source_name: Arabidopsis inflorescence sampled 4 days later from moderate drought-treated plant

value: at day 28 after seed germination


title: PLC_Adherent_Terence Lee_090713_U133_MAS5

description: Gene Expression

scan_protocol: Service by The University of Hong Kong (HKU) Genome Research Centre (protocol attached)

source_name: differentiated HCC cells

value: HCC

value: differentiated HCC cells


title: Wild type (Col-0) inflorescence, moderate drought-treated, day 4, replicate 2


title: parental 3


title: mutated 2

description: Gene expression data from mutated cells


title: Normal weight, rep6

description:
replicate 6
N6

value: 53 years

value: peripheral blood mononuclear cell

value: normal weigth


title: parental 2


title: Wild type (Col-0) inflorescence, moderate drought-treated, day 10, replicate 2

value: Unopen flower buds


title: Wild type (Col-0) inflorescence, moderate drought-treated, day 5, replicate 1

description: Gene expression data from Arabidopsis unopen flower buds sampled 5 days later from drought-treated plant

source_name: Arabidopsis inflorescence sampled 5 days later from moderate drought-treated plant

value: at day 29 after seed germination


title: Wild type (Col-0) inflorescence, moderate drought-treated, day 3, replicate 1


title: Wild type (Col-0) inflorescence, well-watered, day 0, replicate 2 [C02]

description: Gene expression data from Arabidopsis unopen flower buds sampled from well-watered control

source_name: Arabidopsis inflorescence sampled from well-watered control

value: at day 24 after seed germination


title: Obese A, rep1

description:
replicate 1
OA1

value: male

value: 23 years

value: obese


title: Col-0 plants under 4 days salt treatment, rep3

city: Postdam

first: Salma

last: Balazadeh

address: Am Muehlenberg 1

department: Stitt

country: Germany

institute: MPIMP

hyb_protocol: Hybridizaton was done according to the Affymetrix Expression Analysis Technical Manual; the wash followed the protocol EukGE-WS2v4_450 for Rice Genome Arrays.  Technical Manual used the wash protocol EukGE-WS2v4_450 for Rice  Affymetrix Expression Analysis Technical Manual and the wash protocol EukGE-WS2v4_450 for RiceGenome Arrays Genome Arrays

scan_protocol: Scanning was done using the Gene Chip Operating System (GCOS) scanner.

data_processing: Raw data (CEL files) obtained from RNA hybridisation experiments were normalized with the affyPLM package from the Bioconductor software project (Gentleman et al., 2004) using the GCRMA that uses GC content of probes in normalization with RMA (Robust Multiple array Average) and  gives one value for each probe set instead of keeping probe level information (Wu et al., 2004). The transcriptional changes were determined by subtracting the normalized signal intensity of the control samples from that of induced samples.

source_name: Col-0 whole rosette salt condition

label_protocol: Labeling was done using biotinylated UTP (Bio-11-UTP) according to the MessageAmp™ II aRNA Amplification protocol (Life Technologies).  >  > protocol from Life Technologies  place during washing of array. Streptavidin was used to label (along with anti-streptavidin antibody) the bound Bio-11-UTP according to the MessageAmp™ II aRNA Amplification Bio-11-UTP and allowed for detection during array scanning. This is based on the Affymetrix Expression Analysis Technical Manual.  protocol from Life Technologies  MessageAmp™ II aRNA Amplification protocol from Life Technologies

growth_protocol: Arabidopsis thaliana (L.) Heynh. (Col-0 ecotype) were surface sterilized. Plants were grown in a hydroponic system in a climate chamber at an 8-h light (150 µmol m-2 sec-1 20°C, 60%  RH)/16-h dark (16°C, 75% RH) cycle. The medium used was essentially as described by Loque et al. (2003). Six plants were grown in each hydroponic box and the growth medium was replaced with fresh, autoclaved solution every seventh day to limit the growth of microorganisms and supply enough nutrients for normal plant growth.

extract_protocol: Total RNA extraction from control and salt treated plants was done using  RNAeasy Plant mini kit from Qiagen.

treatment_protocol: 150 mM NaCl was supplied to the liquid medium and maintained for 4 days

value: 4 days salt treatment

value: rosette

value: wild type Col-0

value: 28 days old


title: Normal weight, rep5

description:
replicate 5
N5

source_name: Human PBMC

value: 40 years


title: Col-0 plants under 4 days salt treatment, rep2


title: Wild type (Col-0) inflorescence, well-watered, day 0, replicate 1 [C01]


title: Huh7-NTC-MAS5

description: gene expression

hyb_protocol: Service by The University of Hong Kong (HKU) Genome Research Centre

growth_protocol: HCC cell line Huh7 cells with or without CD47 repressed using lentiviral-based approach

tag: cell type


title: Normal weight, rep2

description:
replicate 2
N2

value: 21 years


title: Wild type (Col-0) inflorescence, moderate drought-treated, day 5, replicate 2


title: Normal weight, rep4

description:
replicate 4
N4

value: 43 years


title: Col-0 plants under 4 days salt treatment, rep1


title: Normal weight, rep1

description:
replicate 1
N1

value: 20 years


title: Col-0 plants under control conditions, rep3

source_name: Col-0 whole rosette control condition

value: control


title: Normal weight, rep3

description:
replicate 3
N3

value: 22 years

value: peripheral blood mononuclear cell


title: MeWo cells treated with DMSO

city: New York

first: Nora

last: Pencheva

state: NY

address: 1230 York Avenue, Box 194

institute: Nora Pencheva

hyb_protocol: per manufacturer's instruction

scan_protocol: per manufacturer's instruction

data_processing:
Data were quantile-normalized and processed using the lumi package
Values indicate the average probe hybrydization signal. The GW3965 signal was normalized by multiplying by the ratio of the median DMSO signal/ median GW3965 signal
Non-normalized values indicate the average probe hybrydization signal. Normalized values are quantile-normalized

source_name: human melanoma cells treated with DMSO for 48 hours

label_protocol: The RNA was biotin-labeled using the TargetAmp-Nano Labeling Kit for Ilumina Expression BeadChip

growth_protocol: Cells were grown in DMEM-based media supplemented with 10% FBS, 1% L-glutamine, 1% Sodium Pyruvate, and 1% Pen/Strep

extract_protocol: RNA was extracted using the Norgen RNA extraction kit

treatment_protocol: Cells were treated with DMSO or GW3965 at 1 micromolar for 48 hours

value: lymph node melanoma metastasis

tag: Sex

value: 78 years old


title: N114 mimic negative control-3

city: Los Angeles

first: Mete

last: Civelek

state: CA

address: 675 Charles E. Young Dr. S. MRL 3220

department: Medicine

institute: University of California Los Angeles

description: Replicate 3

hyb_protocol: Illumina Whole-Genome Gene Expression Direct Hybridization Assay (Catalogue Number BD-901-1003)

scan_protocol: Illumina iScan System with default settings

data_processing: probes were removed due to (i) lack of mapping to any genomic or transcriptomic location, (ii) mapping to multiple genomic or transcriptomic locations, and (iii) presence of single nucleotide polymorphisms in the probe sequence that may affect hybridization efficiency using the methodology developed by Barbosa-Morais et al. (PMID:19923232). The remaining 15,044 probes were processed using non-parametric background correction followed by quantile normalization with both control and expression probes utilizing the neqc function in the limma package (R v2.13.0) (PMID:20929874).

source_name: aortic endothelial cells

label_protocol: Ambion TotalPrep -96 RNA Amplification kit (Catalogue Number 4393543)

growth_protocol: Human Aortic Endothelial Cell (HAEC) were isolated from aortic explants of heart transplant donors of anonymous origin through the UCLA transplant program and grown to confluence in 100 mm dishes in MCBD-131C complete medium (Vec Technologies, Rensselar NY).

extract_protocol: Total RNA was isolated from the cells using Qiagen miRNeasy kit according to manufacturer’s instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 9.0 were used for transcriptional profiling.

treatment_protocol: miRNA overexpression experiments were performed using Dharmacon miRDIAN miRNA mimics (miR-21-3p: C-301023-01-0005, miR-27a-5p: C-301028-01-0005, negative control: CN-001000-01-05) at 1nM concentration for 24 hours. All transfections were performed with  Invitrogen Lipofectamine 2000 according to manufacturer's instructions

tag: human donor

value: Donor 2

value: 1 nM miRIDIAN negative control (Catalog Number:CN-001000-01-05)

value: aortic endothelial cells


title: Col-0 plants under control conditions, rep2


title: NSC34 cells subjected to shTardbp knockdown 4

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

institute: University of Sheffield

description:
P48
NSC34 cells subjected to shTardbp knockdown.

hyb_protocol: Hybridized to GeneChip Mouse Exon 1.0 ST Arrays, washed and stained using the Affymetrix GeneChip Hybridization, Wash and Stain Kit and an Affymetrix Fluidics Station 450.

scan_protocol: Scanned on an Affymetrix® GeneChip Scanner 3000 according to manufacturer's protocols.

data_processing: The Partek Genomics Suite was used to normalize (by GC RMA) and then analyse the microarray data following Affymetrix guidelines. Core probesets only were used.

source_name: cultured NSC34 cells, shTardbp knockdown

label_protocol: The Ambion WT Expression Kit was used to amplify the RNA and convert it to cDNA. The cDNA was then fragmented and biotin-labelled using the Affymetrix GeneChip WT Terminal Labelling Kit.

growth_protocol: NSC34 cells were transfected using lipofectamine 2000 with Tardbp-specific short hairpin (sh) RNA and two control shRNAs using the pSUPERIOR (oligoengine) vector and stable clones isolated following puromycin selection. The hairpin targeted the Tardbp sequence TCTAAGCAAAGCCCCAGACGAGCCT. Oligonucleotides were annealed and ligated into the vector using the BglII and HindIII sites and the constructs generated were verified by sequencing. NSC34 control lines were established using GFP-shRNA and Renilla-shRNA (henceforth shGFP and shLuciferase) constructs.

extract_protocol: RNA was extracted from the cells using the Qiagen RNeasy Mini Kit (Qiagen).

value: shTardbp knockdown


title: Myd88mutant_Mm_4d_3

city: Leiden

first: Annemarie

middle: H.

last: Meijer

address: Einsteinweg 55

department: Animal Sciences and Health

institute: Institute of Biology, Leiden University

description: Biological replicate 3 of 3: mutant embryos M.marinum infected 4d

hyb_protocol: The dual colour hybridization of the microarray chips was performed at the Microarray Department (MAD) of the University of Amsterdam (Amsterdam, The Netherlands) using the standard Agilent protocol.

scan_protocol: The arrays were scanned with DNA Microarray Scanner G2565CA from Agilent Technologies. The arrays were scanned twice with 10% PMT and 100% PMT laser power.

data_processing: Microarray data was processed from raw data image files with Feature Extraction Software 9.5.3.1 (Agilent Technologies). The XDR function was used to extend the dynamic range. Processed data were subsequently imported into Rosetta Resolver 7.0 (Rosetta Biosoftware, Seattle, Washington) and subjected to default ratio error modelling. The Agilent Feature Extraction files contain the final log ratio data. The algorithms that were used to normalize the feature signal and calculate the log ratios are described in the Reference Guide for Agilent Feature Extraction Software v9.5. The standard settings as described for the GE2-v5_95 protocol in the Reference Guide were used. In order to calculate the normalized signal, the Rank Consistency Probes method was used and the Linear&LOWESSDyeNormFactor (= DyeNormalSignal/(BGSubSignal x LinearDyeNormFactor) was calculated as described on page 231 of the Reference Guide. The dye normalized signal was calculated as follows (page 232): DyeNormSignal = BGSubSignal x DyeNormFactor. The log10 ratio was subsequently calculated as follows (page 232): LogRatio = Log(rProcessedSignal/gProcessedSignal), where rProcessedSignal and gProcessedSignal are signals post dye normalization and post surrogate processing in the red and green channels, respectively. The surrogate values are calculated and used as the lowest limit of detection to replace the dye normalized signal when either the mean feature signal is less than the background signal or not significant when compared to the background signal, or when the mean signal is less than its background standard deviation (page 226).

organism: Danio rerio

label_protocol: Amino Allyl modified aRNA was synthesized in one amplification round from 1 ug of total RNA using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion). Subsequently, 6 ug of Amino Allyl modified aRNA was used for coupling of monoreactive Cy3 or Cy5 dye (GE Healthcare) and column purified.

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts).

extract_protocol: Single embryos for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C. Embryos were homogenized in 1 ml of TRIZOL® Reagent (Invitrogen) and subsequently total RNA was extracted according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro-injected into the caudal vein with 200 CFU of M. marinum Mma20 bacteria suspended in PBS/2%PVP or mock-injected with PBS/2%PVP as a control. At 5 days post fertilization (4 d post infection) three single embryos per treatment group were snap-frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent.

tag: sample type

value: The CR (common reference) was a mixture of all RNA samples from this microarray study.

value: embryo

value: MyD88 mutant; injected with M. marinum into the caudal vein at 28 hpf; RNA isolated at 4d post injection

tag: genotype

value: MyD88 mutant


title: Control NSC34 cells treated with shLuciferase 2

description:
C14
Control NSC34 cells treated with shLuciferase.

source_name: cultured NSC34 cells, shLuciferase

tag: cell line

value: shLuciferase


title: N114 mimic negative control-2

description: Replicate 2

tag: treatment


title: Control NSC34 cells treated with shLuciferase 4

description:
P28
Control NSC34 cells treated with shLuciferase.


title: NSC34 cells subjected to shTardbp knockdown 2

description:
P59
NSC34 cells subjected to shTardbp knockdown.


title: NSC34 cells subjected to shTardbp knockdown 1

description:
P32
NSC34 cells subjected to shTardbp knockdown.


title: MeWo cells treated with GW3965

source_name: human melanoma cells treated with GW3965 for 48 hours

value: male


title: Control NSC34 cells treated with shLuciferase 1

description:
C13
Control NSC34 cells treated with shLuciferase.


title: Col-0 plants under control conditions, rep1

value: rosette

tag: ecotype

value: wild type Col-0

value: 28 days old


title: Control NSC34 cells treated with shGFP 5

description:
C11
Control NSC34 cells treated with shGFP.

source_name: cultured NSC34 cells, shGFP

value: shGFP


title: N114 27a-5p mimic- 3

description: Replicate 3

value: 1 nM miRIDIAN miR-27a-5p (Catalog Number:C-301028-01-0005)


title: Control NSC34 cells treated with shGFP 3

description:
C3
Control NSC34 cells treated with shGFP.


title: Huh7-CD47-knockdown-MAS5

description: gene expression

scan_protocol: Service by The University of Hong Kong (HKU) Genome Research Centre

value: HCC


title: NSC34 cells subjected to shTardbp knockdown 3

description:
P99
NSC34 cells subjected to shTardbp knockdown.


title: Wildtype_PVP_4d_1

description: Biological replicate 1 of 3: control embryos PVP control 4d

value: Wildtype; mock-injected with buffer into the caudal vein at 28 hpf; RNA isolated at 4d post injection

value: wild type


title: N114 mimic negative control-1

description: Replicate 1

value: Donor 2

value: 1 nM miRIDIAN negative control (Catalog Number:CN-001000-01-05)


title: Myd88mutant_Mm_4d_1

description: Biological replicate 1 of 3: mutant embryos M.marinum infected 4d

value: injected with M. marinum into the caudal vein at 28 hpf


title: Wildtype_Mm_4d_2

description: Biological replicate 2 of 3: control embryos M.marinum infected 4d

value: The CR (common reference) was a mixture of all RNA samples from this microarray study.

value: Wildtype; injected with M. marinum into the caudal vein at 28 hpf; RNA isolated at 4d post injection


title: Myd88mutant_PVP_4d_3

description: Biological replicate 3 of 3: mutant embryos PVP control 4d

value: embryo

value: MyD88 mutant; mock-injected with buffer into the caudal vein at 28 hpf; RNA isolated at 4d post injection


title: N114 27a-5p mimic- 1

description: Replicate 1

value: aortic endothelial cells


title: Myd88mutant_PVP_4d_2

description: Biological replicate 2 of 3: mutant embryos PVP control 4d

value: mock-injected with buffer into the caudal vein at 28 hpf

value: MyD88 mutant


title: Control NSC34 cells treated with shGFP 2

description:
C2
Control NSC34 cells treated with shGFP.


title: N114 21-3p mimic -3

description: Replicate 3

value: 1 nM miRIDIAN miR-21-3p (Catalog Number:C-301023-01-0005)


title: Switched_56h

city: Providence

first: M. Pilar

last: Gil

state: Rhode Island

address: 75 Waterman St

institute: Brown University

description: Gene expression data from 40d. old female flies switched from control to restricted food

hyb_protocol: Preparation of biotynilated cRNA and hybridization to the Drosophila2 array were performed as described by the manufacturer (Affymetrix).

scan_protocol: Stained arrays were scanned using an Affymetrix 3000 G7 scanner. Data acquisition was carried out at Brown University.

data_processing: The data was PVAC filtered, quantile normalized and summarized using Robust Multichip Analysis (RMA) to obtain expression scores in the log2 scale.

organism: Drosophila melanogaster

source_name: Switched from CF to RF, 56 hours after switch

extract_protocol: Total head and thorax RNA was isolated from at least 75 females using Trizol (Invitrogen) and further purified using RNeasy columns (QIAGEN).

value: head and thorax

value: Canton-S

value: females

value: 40 days


title: N114 27a-5p mimic- 2

description: Replicate 2

value: 1 nM miRIDIAN miR-27a-5p (Catalog Number:C-301028-01-0005)


title: N114 21-3p mimic -2

description: Replicate 2


title: B5 -AA 1

source_name: Col:LUC grown on B5 media and untreated

value: B5 media and untreated


title: Switched_48h

source_name: Switched from CF to RF, 48 hours after switch

label_protocol: Preparation of biotynilated cRNA and hybridization to the Drosophila2 array were performed as described by the manufacturer (Affymetrix).


title: N114 21-3p mimic -1

description: Replicate 1

value: Donor 2


title: Wildtype_Mm_4d_3

description: Biological replicate 3 of 3: control embryos M.marinum infected 4d

value: wild type


title: Switched_40h

source_name: Switched from CF to RF, 40 hours after switch


title: Control NSC34 cells treated with shGFP 1

description:
C1
Control NSC34 cells treated with shGFP.

value: shGFP


title: Switched_24h

source_name: Switched from CF to RF, 24 hours after switch


title: Switched_32h

source_name: Switched from CF to RF, 32 hours after switch


title: U134 mimic negative control-2

description: Replicate 2

value: Donor 1

value: 1 nM miRIDIAN negative control (Catalog Number:CN-001000-01-05)


title: U134 mimic negative control-1

description: Replicate 1


title: U134 mimic negative control-3

description: Replicate 3


title: NB33

type: genomic

city: Cologne

first: Jessica

last: Theissen

state: NRW

address: Kerpener Straße 62

department: Department of Pediatric Oncology and Hematology

institute: University of Cologne

description: Agilent-012750 Human Genome CGH Microarray 44A (G4410A)

hyb_protocol: Labelled DNA were hybridized to oligonucleotide microarrays (Agilent Technologies) following the manufacture's instructions ("Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol”, v. 5.0 (Agilent Technologies). Briefly, fluorescent-labeled reference and tumor DNA (3 ug each) were mixed with 50 ug of human Cot-1 DNA (Invitrogen Life Technologies) and control targets (Agilent Technologies). Slides were hybridized in SureHyb gasket (Agilent Technologies) placed in rotisserie (20 RPM rotation speed) in hybridization oven at 65°C for 40 hrs. After hybridization, the slides were washed with Oligo aCGH Wash Buffer 1(Agilent Technologies) at room temperature for 5 min, with Oligo aCGH Wash Buffer 2 (Agilent Technologies) at 37°C for 1 min, with the Stabilization solution (Agilent) for 1 minute at room temperature, then dried immediately by rinsing slides into Drying solution (Agilent) for 30 seconds.

scan_protocol: Arrays were scanned by using an Agilent G2567AA Scanner follwowing the manufacturer's protocol (Agilent Technologies).

data_processing: The scanned TIFF images were loaded into the Feature Extraction (v9.5 Agilent technologies), Feature Extraction files were analyzed by CGH Analytics Software (v. 3.5.14 Agilent Technologies). The circular binary segmentation algorithm was applied. Ref: PMID:  17234643

molecule: genomic DNA

source_name: Tumor DNA

label_protocol: We followed the "Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol”, v. 5.0 (Agilent Technologies). Briefly, 2 ug of sample and reference genomic DNAs (for reference were used Human Genomic DNA: male Cat G1471, female Cat G1521, Promega, Madison, WI) were separately digested with AluI/RsaI restriction enzyme mix (Promega). Fragmented DNA was labeled by direct enzymatic incorporation of fluorescent tags. Genomic DNA was labeled with Cy3-dUTP or Cy5-dUTP (Perkin Elmer) using the Random-Primed Bioprime DNA Labeling kit (Invitrogen Life Technologies). Briefly, 50 ul reaction mix containing dATP, dGTP and dTTP (120 ueach), dUTP (60 uM) and Cy3-dUTP (60 uM) or Cy5-dUTP (60 uM) was incubated with Klenow Fragment (40 units) at 37°C for 2 hrs. Unincorporated nucleotides were removed on Microcon YM-30 filters (Millipore) according to the manufacturer’s protocol. Dye incorporations of post-labeling products were measured by NanoDrop 1000 (ThermoScientific) and the parameters that predicted successful hybridization were a minimum Cy3 incorporation of 0.5 pmol/ul and Cy5 incorporation of 0.3 pmol/ul.

extract_protocol: Genomic DNA was isolated using the DNA-Isolation Kit (Gentra) according to the manufacturer's protocol. A pool of normal male or female DNA (Promega) was used as reference.

value: male

tag: age at diagnosis (days)

tag: tumor stage

value: neuroblastoma

source_name: Promega Reference DNA

value: M


title: Myd88mutant_Mm_4d_2

description: Biological replicate 2 of 3: mutant embryos M.marinum infected 4d

value: The CR (common reference) was a mixture of all RNA samples from this microarray study.

value: embryo

value: MyD88 mutant; injected with M. marinum into the caudal vein at 28 hpf; RNA isolated at 4d post injection


title: Wildtype_PVP_4d_3

description: Biological replicate 3 of 3: control embryos PVP control 4d

value: Wildtype; mock-injected with buffer into the caudal vein at 28 hpf; RNA isolated at 4d post injection


title: Wildtype_Mm_4d_1

description: Biological replicate 1 of 3: control embryos M.marinum infected 4d

value: Wildtype; injected with M. marinum into the caudal vein at 28 hpf; RNA isolated at 4d post injection


title: Switched_72h

source_name: Switched from CF to RF, 72 hours after switch

value: head and thorax

value: Canton-S

value: females


title: Wildtype_PVP_4d_2

description: Biological replicate 2 of 3: control embryos PVP control 4d

value: mock-injected with buffer into the caudal vein at 28 hpf


title: Myd88mutant_PVP_4d_1

description: Biological replicate 1 of 3: mutant embryos PVP control 4d

value: MyD88 mutant; mock-injected with buffer into the caudal vein at 28 hpf; RNA isolated at 4d post injection

value: MyD88 mutant


title: U134 27a-5p mimic- 3

description: Replicate 3

value: 1 nM miRIDIAN miR-27a-5p (Catalog Number:C-301028-01-0005)

value: aortic endothelial cells


title: U134 27a-5p mimic- 1

description: Replicate 1

value: Donor 1


title: Switched_18h

source_name: Switched from CF to RF, 18 hours after switch

value: 40 days


title: U134 21-3p mimic -2

description: Replicate 2

value: 1 nM miRIDIAN miR-21-3p (Catalog Number:C-301023-01-0005)


title: U134 27a-5p mimic- 2

description: Replicate 2


title: Switched_6h

source_name: Switched from CF to RF, 6 hours after switch


title: Switched_8h

source_name: Switched from CF to RF, 8 hours after switch


title: NB31

value: male

value: neuroblastoma

value: M


title: Switched_12h

source_name: Switched from CF to RF, 12 hours after switch


title: NB28

value: female

value: F


title: U134 21-3p mimic -3

description: Replicate 3

source_name: aortic endothelial cells


title: NB30


title: Switched_2h

source_name: Switched from CF to RF, 2 hours after switch


title: U134 21-3p mimic -1

description: Replicate 1


title: NB32


title: NB29


title: Switched_4h

source_name: Switched from CF to RF, 4 hours after switch


title: NB27


title: Array-CGH analysis: FC9

city: Stockholm

first: Johanna

last: Winberg

address: CMM L8:02, Karolinska University Hospital

department: Molecular Medicine and Surgery

institute: Karolinska Institutet

hyb_protocol: Corresponding labelled patient and reference samples were pooled and 5 µl CotDNA, 11 µl blocking buffer and 55 µl hybridization buffer from the Oligo aCGH/CHp-on chip hybridization kit (Agilent Technologies).Denaturation was performed at 95⁰ for 5 mins followed by pre-hybridization at 37⁰ for 45 min. 100 µl per sample were dispensed in each well on a 4x180K oligonucleotide array glass slide and a gasket slide added to close. The glass was hybridized for 24 hours in 65⁰ in a rotation oven. After 24 hours, each glass was put in wash solution B1 (Agilent Technologies) for 5 min followed by 1 min in 37⁰ wash solution B2 (Agilent Technologies) and subsequently air-dried and stored in a light-proof box.

scan_protocol: The glasses were scanned on a DNA Microarray Scanner from Agilent Technologies with 3 µm resolution.

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

source_name: genomic DNA from lung

label_protocol: 1.1 µg of genomic patient and control DNA (Promega) was diluted in water to a total volume of 19 µl. 20 µl of primer buffer (CGH labelling kit for oligo arrays, Enzo Life Sciences) was added on ice. The samples were incubated at 99⁰ for 10 min and then placed on ice for 5 mins. 10 µl of Cy3 or Cy5 were added to each sample and subsequently 1 µl of Klenow polymerase was added. The samples were incubated at 37⁰ for 13.5 hours and then heated to 65⁰ for 10 mins before cooling to 4⁰. Purification of labelled samples was performed by adding 250 µl of PB buffer to a spin column and adding 50 µl of labelled sample (the total volume). The samples were centrifuged at 14000 rpm for 1 min, and the flow-through discarded. 750 µl of PE wash buffer was added to each column, and the samples centrifuged at 14000 rpm for 1 min. The flow-through was discarded and the samples centrifuged once more at 14000 rpm for 1 min. DNA was eluated with 22 µl TE buffer and incubated at 2 min in room temperature before centrifugation at 14000 rpm for 1 min. Concentration of labelled DNA was measured using NanoDrop.

extract_protocol: Genomic DNA was isolated from either peripheral blood or tissue samples according to standard procedures. For fetal cases, DNA was isolated from routinely preserved fresh frozen heart, liver, lung, or spleen tissue using the Gentra Puregene Blood Kit (QIAGEN Sciences, Maryland, USA) in combination with Proteinase K (Finnzymes, Espoo, Finland) with slight modifications to the manufacturer’s protocol.

treatment_protocol: No cell culture was performed.

value: lung

source_name: DNA pooled from blood 10 healthy individuals

value: Blood


title: Restricted_72h

description: Gene expression data from 40d. old female flies passed in restricted food

source_name: Restricted food, 72 hours after switch

value: head and thorax

value: Canton-S


title: Restricted_56h

source_name: Restricted food, 56 hours after switch

value: females


title: Array-CGH analysis: FC10

source_name: genomic DNA from liver

value: liver


title: MDA-MB-231_siScramble_rep.2

city: Oviedo

first: Jorge

last: de la Rosa

address: Avda. Jose Maria Richard

country: Spain

institute: Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA)

description: MDA-MB-231-siScr (2)

data_processing:
The array probe summaries were calculated in BeadStudio and quantile normalised. Using limma (R-package), a linear model fit was applied and the top differentially expressed genes were tabulated for each contrast using the method of Benjamini and Hochberg to correct the p-values.
Non-normalized signal intensity values are shown in the non-normalized matrix (linked as a supplementary file on the Series record); whereas in the data table below, quantile normalized values are depicted. No error model was applied in any case.

source_name: Mock-treated MDA-MB-231

label_protocol: Biotinylated cRNA were prepared with using the Illumina TotalPrep-96 RNA Amplification kit (Ambion, UK), according to the manufacturers instructions.

extract_protocol: Total RNA was extracted using the TRIzol reagent (Invitrogen) and  an RNeasy kit (Qiagen).

tag: cell line origin

value: Breast cancer

tag: genotype/variation

value: control


title: NB26


title: NB25


title: Restricted_32h

source_name: Restricted food, 32 hours after switch

tag: age


title: MDA-MB-231_siScramble_rep.1

description: MDA-MB-231-siScr (1)


title: A549_siScramble_rep.2

description: A549-siScr (2)

source_name: Mock-treated A549

value: Lung cancer


title: MDA-MB-231_siZMPSTE24_rep.2

description: MDA-MB-231-siZMPSTE24 (2)

source_name: siZMPSTE24-treated MDA-MB-231

value: ZMPSTE24 silencing


title: Array-CGH analysis: FC8

source_name: genomic DNA from heart

value: heart


title: MDA-MB-231_siZMPSTE24_rep.1

description: MDA-MB-231-siZMPSTE24 (1)


title: Array-CGH analysis: FC4


title: Restricted_48h

source_name: Restricted food, 48 hours after switch

value: 40 days


title: Restricted_40h

source_name: Restricted food, 40 hours after switch


title: NB22

description: Agilent-014698 Human Genome CGH Microarray 105A (G4412A)

source_name: Tumor DNA

value: male

tag: age at diagnosis

source_name: Promega Reference DNA


title: Restricted_24h

source_name: Restricted food, 24 hours after switch


title: Array-CGH analysis: FC11


title: A549_siScramble_rep.1

description: A549-siScr (1)


title: Restricted_18h

source_name: Restricted food, 18 hours after switch


title: Restricted_8h

source_name: Restricted food, 8 hours after switch


title: Restricted_12h

source_name: Restricted food, 12 hours after switch


title: NB23

value: neuroblastoma


title: NB24

value: M


title: Array-CGH analysis: FC6

source_name: genomic DNA from lung

source_name: DNA pooled from blood 10 healthy individuals


title: A549_siZMPSTE24_rep.1

description: A549-siZMPSTE24 (1)

source_name: siZMPSTE24-treated A549


title: Array-CGH analysis: FC7

source_name: genomic DNA from spleen

value: spleen


title: NB20

value: female

value: F


title: NB18


title: NB21


title: NB19


title: Array-CGH analysis: FC3

value: Blood


title: NB17


title: Restricted_6h

source_name: Restricted food, 6 hours after switch

value: head and thorax


title: Array-CGH analysis: FC2


title: SCC-2_siScramble_rep.1

description: SCC-2-siScr (1)

source_name: Mock-treated SCC-2

value: Oral cancer


title: Array-CGH analysis: FC1

source_name: genomic DNA from liver


title: SCC-2_siScramble_rep.2

description: SCC-2-siScr (2)


title: SCC-2_siZMPSTE24_rep.2

description: SCC-2-siZMPSTE24 (2)

source_name: siZMPSTE24-treated SCC-2


title: Restricted_0h

source_name: Restricted food, time of switch

value: Canton-S

value: females


title: Restricted_2h

source_name: Restricted food, 2 hours after switch


title: NB14


title: SCC-2_siZMPSTE24_rep.1

description: SCC-2-siZMPSTE24 (1)


title: SCC-40_siScramble_rep.2

description: SCC-40-siScr (2)

source_name: Mock-treated SCC-40


title: Restricted_4h

source_name: Restricted food, 4 hours after switch


title: Control_72h

description: Gene expression data from 40d. old female flies passed in control food

source_name: Control food, 72 hours after switch


title: Array-CGH analysis: V16

source_name: genomic DNA from blood

value: blood


title: NB13

source_name: Tumor DNA

source_name: Promega Reference DNA


title: Array-CGH analysis: V17


title: A549_siZMPSTE24_rep.2

description: A549-siZMPSTE24 (2)


title: Array-CGH analysis: V20


title: Control_56h

source_name: Control food, 56 hours after switch


title: NB16


title: SCC-40_siZMPSTE24_rep.2

description: SCC-40-siZMPSTE24 (2)

source_name: siZMPSTE24-treated SCC-40


title: SCC-40_siScramble_rep.1

description: SCC-40-siScr (1)

value: control


title: NB15


title: NB12


title: SCC-40_siZMPSTE24_rep.1

description: SCC-40-siZMPSTE24 (1)


title: Array-CGH analysis: V9

source_name: DNA pooled from blood 10 healthy individuals


title: Array-CGH analysis: V13


title: Array-CGH analysis: V12


title: Array-CGH analysis: V14


title: NB11


title: Control_40h

source_name: Control food, 40 hours after switch


title: Control_32h

source_name: Control food, 32 hours after switch


title: Test (insulin) experiment

city: BERN

first: Brigitte M.

last: FREY

state: BERN

address: Freiburgstrasse 15

department: Nephrology hypertension

country: Switzerland

institute: DKF

description: performed in triplicate

data_processing:
Beta-2-microglobulin was used as housekeeping gene.
fold-change.txt supplementary file reports test/control (i.e., Insulin/control) ratios.

label: SYBR® Green

source_name: HT-29 cell line

label_protocol: Total RNA (1μg) was used as template to synthesize cDNA with the RT2 First Strand kit (SABiosciences). The PCR cycle condition was as follows: 95°C for 10min, followed by 40 cycles of 95°C for 15 s, 60°C for 60s. At the end of PCR cycling steps, data for each sample were displayed as a melting curve.

growth_protocol: HT-29 cells were cultured at the density of 600000 cells per well in 6 well plate in DMEM high glucose, 10% serum for 48h.

extract_protocol: Total RNA was isolated using SV Total RNA Isolation System from Promega

treatment_protocol: Cells were serum starved for 24h and then treated with 10-7M of insulin for an additional 24h.

value: HT-29 cell line

value: colonic cell line

value: Insulin 10-7M

tag: treatment duration

value: 24h in serum deprived media


title: NB10


title: Control experiment

description: performed in triplicate


title: Array-CGH analysis: V11


title: Control_18h

source_name: Control food, 18 hours after switch

value: 40 days


title: Array-CGH analysis: V10


title: NB9

value: neuroblastoma


title: Control_48h

source_name: Control food, 48 hours after switch


title: Array-CGH analysis: V7


title: Array-CGH analysis: V8


title: Exercise [35 days]

city: Porto Alegre

first: Nidiane

middle: Carla

last: Martinelli

state: Rio Grande do Sul

address: AV ALEGRETE, 414/202

department: Cardiology Division at Hospital de Clínicas de Porto Alegre

country: Brazil

institute: Federal University of Rio Grande do Sul

description: This sample is representative sample consisted of a pool from 4 animals within the same group

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.  Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].  A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.  t-Test is performed between “control” and “test” sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.  All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

source_name: Left Ventricule

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 4 to 8 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy3 dye staining.

extract_protocol: microRNA extracted using miRNeasy mini kit (Qiagen) following manufacturer's instructions

treatment_protocol: Stored in RNA later solution (Qiagen)

value: Left Ventricule

tag: strain

value: Balb/c

tag: gender

value: Male

value: Adult; 8 weeks old

tag: group

value: Exercise 35 days

tag: type of exercise

value: Voluntary; running wheels


title: NB8

tag: Sex

value: female

tag: tissue

value: F


title: NB6


title: NB7


title: Control_6h

source_name: Control food, 6 hours after switch

value: head and thorax

tag: genotype

value: Canton-S

value: females


title: Control_24h

source_name: Control food, 24 hours after switch


title: Exercise [7 days]

value: Exercise 7 days


title: Sedentary [35 days]

value: Sedentary 35 days


title: Sedentary [7 days]

value: Sedentary 7 days


title: Control_4h

source_name: Control food, 4 hours after switch


title: Control_8h

source_name: Control food, 8 hours after switch


title: Array-CGH analysis: V5

source_name: genomic DNA from intestine

value: intestine

value: Blood


title: Array-CGH analysis: V6

source_name: genomic DNA from blood

value: blood


title: Array-CGH analysis: V4


title: NB3

source_name: Tumor DNA

value: male

value: neuroblastoma

value: M


title: NB4

source_name: Promega Reference DNA


title: Control_0h

source_name: Control food, time of switch

value: 40 days


title: NB1


title: NB2


title: Array-CGH analysis: V3


title: NB5


title: Control_2h

source_name: Control food, 2 hours after switch


title: SCYL1 esiRNA transfected cells, biological rep1

status: Public on May 15 2014

city: Regensburg

first: Julia

middle: C

last: Engelmann

address: Josef-Engert-Str. 9

department: Statistical Bioinformatics

institute: University of Regensburg

description: Gene expression data from esiRNA transfected cells

hyb_protocol: 3.8 μg of fragmented and labeled sense-strand cDNA were hybridized for 16 h at 45°C on GeneChip Human Gene 2.0 ST microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (performed at an Affymetrix Service Provider and Core Facility, “KFB - Center of Excellence for Fluorescent Bioanalytics” (Regensburg, Germany; www.kfb-regensburg.de).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G (performed at an Affymetrix Service Provider and Core Facility, “KFB - Center of Excellence for Fluorescent Bioanalytics” (Regensburg, Germany; www.kfb-regensburg.de).

data_processing: The raw intensities of the CEL files were normalized with RMA.

source_name: SCYL1 esiRNA transfected cells

label_protocol: The Ambion WT Expression Kit Protocol was used for the preparation of biotinylated sense-strand cDNA from 300ng of total RNA, followed by fragmentation and labeling according to the Affymetrix GeneChip WT Terminal Labeling and Hybridization User Manual (performed at an Affymetrix Service Provider and Core Facility, “KFB - Center of Excellence for Fluorescent Bioanalytics” (Regensburg, Germany; www.kfb-regensburg.de).

growth_protocol: Cells were grown under standard conditions in DMEM 10% FBS

extract_protocol: Total RNA extraction was performed 48h after transfection according to the manufacturer's instructions (Nucleospin RNA, Machery Nagel).

treatment_protocol: Cells were transfected with 3nM siRNA/ siPool or mock transfected with Lipofectamine RNAiMax according to the manufacturers protocol

tag: cell line

tag: transfection

value: RNAseIII generated mixture of dsRNAs (esiRNAs)


title: SCYL1 siPool 60 transfected cells, biological rep2

description: Gene expression data from siPool 60 transfected cells

source_name: SCYL1 siPool 60 transfected cells

value: single siRNA targeting human SCYL1 in combination with 59 other siRNAs


title: mock transfected cells, biological rep1

description: Gene expression data from mock transfected cells

source_name: mock transfected cells

value: mock


title: SCYL1 esiRNA transfected cells, biological rep3


title: SCYL1 siPool 60 transfected cells, biological rep3


title: SCYL1 esiRNA transfected cells, biological rep2


title: SCYL1 siPool 60 transfected cells, biological rep1


title: Array-CGH analysis: V2

source_name: DNA pooled from blood 10 healthy individuals


title: Control_12h

source_name: Control food, 12 hours after switch


title: mock transfected cells, biological rep2


title: Array-CGH analysis: V1


title: SCYL1 siPool 15 transfected cells, biological rep1

description: Gene expression data from siPool 15 transfected cells

hyb_protocol: 3.8 μg of fragmented and labeled sense-strand cDNA were hybridized for 16 h at 45°C on GeneChip Human Gene 1.0 ST microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (performed at KfB, Kompetenzzentrum für fluoreszente Bioanalytik, Regensburg, Germany).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G (performed at KfB, Kompetenzzentrum für fluoreszente Bioanalytik, Regensburg, Germany).

data_processing: The intensities of the CEL files were normalized with the VSN algorithm (Huber, 2002) and summarized to expression levels based on ensembl transcript identifiers using median polish and the chip description file from BrainArray version 16 (Dai, 2005)

source_name: SCYL1 siPool 15 transfected cells

label_protocol: The Ambion WT Expression Kit Protocol was used for the preparation of biotinylated sense-strand cDNA from 300ng of total RNA, followed by fragmentation and labeling according to the Affymetrix GeneChip WT Terminal Labeling and Hybridization User Manual (performed at KfB, Kompetenzzentrum für fluoreszente Bioanalytik, Regensburg, Germany).

value: Hela

value: single siRNA targeting human SCYL1 in combination with 14 other siRNAs


title: SCYL1-siRNA transfected cells, biological rep3

description: Gene expression data from single siRNA transfected cells

source_name: SCYL1-siRNA transfected cells

value: single siRNA targeting human SCYL1


title: vehicle control mice, hippocampus, biological replicate 15

status: Public on May 12 2014

city: Richmond

first: Michael

last: Miles

state: VA

department: Pharmacology and Toxicology

institute: Virginia Commonwealth Univ.

description:
SCID_Veh_15
Gene expression data from SCID mice treated with saline vehicle during contextual fear conditioning.
Hippocampus, control saline treated orally x 3 days, tissue harvested 1 hour after consolidation test, 17 hours after last saline treatment.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430A 2.0 microarrays. GeneChips were washed, and stained with streptavidin-phycoerythrin (Molecular Probes, Eugene, OR), in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 (Affymetrix).

data_processing: Affymetrix Expression Console software was used to generate both MAS 5.0 and RMA probe set data. Differential expression was additionally measured using S-scores produced from the CEL files by the sscore package within the R statistical framework, and biological reproducibility of gene expression differences were identified by a one-class SAM (Statistical Analysis of Microarrays).

source_name: hippocampus, control saline treated, 1 hr after fear consolidation test

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip 3' IVT Express Kit, 2008, Affymetrix).

extract_protocol: Hippocampal tissue was dissected from single mice and Stat-60 extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol:
SCID mice were FTY720 treated (1 mg/kg orally in saline) x 3 days or control saline treated orally x 3 days.
Mice were subjected to the contextual fear conditioning paradigm and were sacrificed 1 hour after consolidation test (17 hours after last FTY720 or saline treatment).

value: SCID

value: 12 weeks

value: brain, hippocampus

tag: treatment

value: saline vehicle control


title: vehicle control mice, hippocampus, biological replicate 13

description:
SCID_Veh_13
Gene expression data from SCID mice treated with saline vehicle during contextual fear conditioning.
Hippocampus, control saline treated orally x 3 days, tissue harvested 1 hour after consolidation test, 17 hours after last saline treatment.


title: vehicle control mice, hippocampus, biological replicate 14

description:
SCID_Veh_14
Gene expression data from SCID mice treated with saline vehicle during contextual fear conditioning.
Hippocampus, control saline treated orally x 3 days, tissue harvested 1 hour after consolidation test, 17 hours after last saline treatment.


title: Patient 3 ART PG_PCB_024

status: Public on May 06 2014

city: Barcelona

first: Mireia

last: Arnedo

state: Other

address: Casanovas, 143. CELLEX, A41

department: AIDS Unit

institute: Institut Investigacions Biomediques Agusti Pi i Sunyer (IDIBAPS)

description:
PG_PCB_024
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards. Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNA.

data_processing: SDS software (Applied Biosystems) was used to collect data. Threshhold intensities were set, visually and individually confirmed, and standardized with RQ Manager (Applied Biosystems). Data were processed using StatMiner Software (Integromics), global mean normalization and Tmev Software

label: FAM

source_name: PBMC

label_protocol: 100ng total RNA per sample was reverse-trasncribed using Megaplex primers, set A (Applied Biosystems). cDNA was pre-amplified for twelve cycles with Megaplex Pre-Amp primers, set A (Applied Biosystems), then diluted to 100ul. Manufacturer's protocol was followed throughout.

extract_protocol: Peripheral blood mononuclear cells (PBMC) were isolated from fresh blood using a standard Ficoll protocol. Total RNA was extracted from ten million PBMCs using the miRvana isolation kit (Ambion) per the manufacturer's protocol. RNA was eluted in 100ul nuclease-free water.

tag: individual

value: Patient 3

tag: infection status

value: HIV-1 ART treated

value: ART

tag: cell type

value: PBMC


title: Patient 8 ART PG_PCB_029

description:
PG_PCB_029
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards. Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNA.

value: Patient 8


title: Patient 6 ART PG_PCB_027

description:
PG_PCB_027
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards. Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNA.

value: Patient 6


title: Patient 5 ART PG_PCB_026

description:
PG_PCB_026
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards. Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNA.

value: Patient 5


title: FTY720 mice, hippocampus, biological replicate 5

description:
SCID_FTY_5
Gene expression data from SCID mice treated with FTY720 during contextual fear conditioning.
Hippocampus, FTY720 treated (1 mg/kg orally in saline) x 3 days, tissue harvested 1 hour after consolidation test, 17 hours after last FTY720 treatment.

source_name: hippocampus, FTY720 treated, 1 hr after fear consolidation test

value: male


title: mock transfected cells, biological rep2


value: single siRNA targeting human SCYL1 in combination with 59 other siRNAs


title: FTY720 mice, hippocampus, biological replicate 1

description:
SCID_FTY_1
Gene expression data from SCID mice treated with FTY720 during contextual fear conditioning.
Hippocampus, FTY720 treated (1 mg/kg orally in saline) x 3 days, tissue harvested 1 hour after consolidation test, 17 hours after last FTY720 treatment.


title: SCYL1-siRNA transfected cells, biological rep1


title: mock transfected cells, biological rep3

value: mock


title: SCYL1-siRNA transfected cells, biological rep2

value: Hela


title: FTY720 mice, hippocampus, biological replicate 4

description:
SCID_FTY_4
Gene expression data from SCID mice treated with FTY720 during contextual fear conditioning.
Hippocampus, FTY720 treated (1 mg/kg orally in saline) x 3 days, tissue harvested 1 hour after consolidation test, 17 hours after last FTY720 treatment.


title: FTY720 mice, hippocampus, biological replicate 6

description:
SCID_FTY_6
Gene expression data from SCID mice treated with FTY720 during contextual fear conditioning.
Hippocampus, FTY720 treated (1 mg/kg orally in saline) x 3 days, tissue harvested 1 hour after consolidation test, 17 hours after last FTY720 treatment.


title: vehicle control mice, hippocampus, biological replicate 16

description:
SCID_Veh_16
Gene expression data from SCID mice treated with saline vehicle during contextual fear conditioning.
Hippocampus, control saline treated orally x 3 days, tissue harvested 1 hour after consolidation test, 17 hours after last saline treatment.


title: mock transfected cells, biological rep3


title: mock transfected cells, biological rep1


title: Patient 2 ART PG_PCB_023

description:
PG_PCB_023
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards. Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNA.

value: Patient 2


title: SCYL1 siPool 15 transfected cells, biological rep3

value: single siRNA targeting human SCYL1 in combination with 14 other siRNAs


title: Patient 7 ART PG_PCB_028

description:
PG_PCB_028
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards. Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNA.

value: Patient 7


title: SCYL1 siPool 15 transfected cells, biological rep2


title: Patient 4 ART PG_PCB_025

description:
PG_PCB_025
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards. Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNA.

value: Patient 4


title: Patient 1 ART PG_PCB_022

description:
PG_PCB_022
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards. Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNA.

value: Patient 1


title: Patient 6 EC PG_PCB_019

description:
PG_PCB_019
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards. Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNA.

value: HIV-1 Elite Controller

value: no ART


title: Patient 7 EC PG_PCB_020

description:
PG_PCB_020
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards. Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNA.


title: Patient 8 EC PG_PCB_021

description:
PG_PCB_021
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards. Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNA.


title: Patient 5 EC PG_PCB_018

description:
PG_PCB_018
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards. Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNA.


title: Patient 2 EC PG_PCB_015

description:
PG_PCB_015
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards. Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNA.


title: Patient 4 EC PG_PCB_017

description:
PG_PCB_017
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards. Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNA.


title: Patient 8 VP PG_PCB_013

description:
PG_PCB_013
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards. Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNA.

value: HIV-1 viremic


title: Patient 3 VP PG_PCB_008

description:
PG_PCB_008
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards. Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNA.

value: Patient 3


title: Patient 6 VP PG_PCB_011

description:
PG_PCB_011
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards. Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNA.

value: PBMC


title: Patient 5 VP PG_PCB_010

description:
PG_PCB_010
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards. Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNA.


title: Patient 4 VP PG_PCB_009

description:
PG_PCB_009
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards. Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNA.


title: Patient 1 EC PG_PCB_014

description:
PG_PCB_014
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards. Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNA.


title: Patient 2 VP PG_PCB_007

description:
PG_PCB_007
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards. Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNA.


title: Patient 5 HIVneg PG_PCB_005

description:
PG_PCB_005
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards. Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNA.

value: HIV negative


title: Patient 4 HIVneg PG_PCB_004

description:
PG_PCB_004
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards. Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNA.


title: Patient 1 HIVneg PG_PCB_001

description:
PG_PCB_001
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards. Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNA.


title: Patient 2 HIVneg PG_PCB_002

description:
PG_PCB_002
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards. Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNA.


title: Patient 3 HIVneg PG_PCB_003

description:
PG_PCB_003
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards. Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNA.


title: Patient 3 EC PG_PCB_016

description:
PG_PCB_016
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards. Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNA.


title: Patient 7 VP PG_PCB_012

description:
PG_PCB_012
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards. Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNA.


title: 89_CD14_Normalpair4_normal_MZ

status: Public on Apr 09 2014

city: London

first: Robert

last: Lowe

address: 4 Newark Street

department: Blizard Institute

institute: QMUL

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina Protocol

data_processing:
The raw Beta scores were normalized using standard quantile normalization algorithms that are available from https://github.com/dasmoth/metharray-scripts
The raw_data.txt file cotnains Unmethylated (Signal_A) and methylated (Signal_B) signal intensities

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from all samples using Qiagen DNeasy Kit according to standard instructions. Magnetic separation was performed according to the manufacturers specifications (MACS, Miltenyi Biotec).

value: female

value: normal monozygotic (MZ)

tag: age (yrs)

value: purified CD14+ monocytes

tag: pair id


title: 88_CD14_Normalpair3_normal_MZ

value: male


title: 2_CD14_T1Dpair102_T1D

value: Type 1 Diabetes (T1D)


title: 94_CD14_Normalpair6_normal_MZ


title: 6_CD14_T1Dpair102_unaffected

value: unaffected


title: 7_CD14_T1Dpair103_unaffected


title: 97_CD14_Normalpair8_normal_MZ


title: 100_CD14_Normalpair9_normal_MZ


title: 96_CD14_Normalpair7_normal_MZ


title: 99_CD14_Normalpair9_normal_MZ


title: 5_CD14_T1Dpair101_unaffected


title: 3_CD14_T1Dpair103_T1D


title: 85_CD14_Normalpair2_normal_MZ


title: 98_CD14_Normalpair8_normal_MZ


title: 4_CD14_T1Dpair104_T1D


title: 92_CD14_Normalpair5_normal_MZ


title: 8_CD14_T1Dpair104_unaffected


title: 84_CD14_Normalpair1_normal_MZ


title: 91_CD14_Normalpair5_normal_MZ


title: 86_CD14_Normalpair2_normal_MZ


title: 1_CD14_T1Dpair101_T1D


title: Muscle_old_control_936

city: Berlin

first: Jens

last: Fielitz

address: Augustenburger Platz 1

department: Cardiology

institute: Charité Universitätsmedizin Berlin

hyb_protocol: Fluidic station 450 protocol FS450_0001

scan_protocol: Scanning was performed using the the AFFYMETRIX GeneChip Scanner 3000 7G and the Affymetrix Genechip Command Console 2.0.0.1029

data_processing:
Date were quantile normalized using Partek Genomic Suite 6.5, RMA background correction and pre background adjustment for GC content
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: not applicable

source_name: skeletal muscle, orthopedic control

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

extract_protocol: Total RNA extracted with Trizol.

value: IPmnsCIM

tag: age

tag: disease

value: orthopedic control

tag: critical illness myopathy

value: skeletal muscle


title: 82_CD14_T1Dpair14_T1D

tag: gender


title: 87_CD14_Normalpair3_normal_MZ


title: 81_CD14_T1Dpair14_unaffected


title: 90_CD14_Normalpair4_normal_MZ


title: 95_CD14_Normalpair7_normal_MZ


title: 83_CD14_Normalpair1_normal_MZ


title: 93_CD14_Normalpair6_normal_MZ


title: Patient 1 VP PG_PCB_006

description:
PG_PCB_006
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards. Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNA.


title: 74_CD14_T1Dpair10_T1D


title: 78_CD14_T1Dpair12_T1D


title: 79_CD14_T1Dpair13_unaffected


title: 80_CD14_T1Dpair13_T1D


title: 75_CD14_T1Dpair11_unaffected


title: 71_CD14_T1Dpair8_unaffected


title: 70_CD14_T1Dpair7_T1D


title: 77_CD14_T1Dpair12_unaffected


title: 65_CD14_T1Dpair5_unaffected


title: 73_CD14_T1Dpair10_unaffected


title: 57_CD14_T1Dpair1_unaffected


title: 76_CD14_T1Dpair11_T1D


title: 56_CD4_Normalpair9_normal_MZ


title: 72_CD14_T1Dpair8_T1D


title: 63_CD14_T1Dpair4_unaffected


title: 68_CD14_T1Dpair6_T1D


title: 52_CD4_Normalpair7_normal_MZ


title: 59_CD14_T1Dpair2_unaffected


title: 53_CD4_Normalpair8_normal_MZ


title: 58_CD14_T1Dpair1_T1D


title: 62_CD14_T1Dpair3_T1D


title: 64_CD14_T1Dpair4_T1D


title: 51_CD4_Normalpair7_normal_MZ


title: 55_CD4_Normalpair9_normal_MZ


title: 61_CD14_T1Dpair3_unaffected


title: 54_CD4_Normalpair8_normal_MZ


title: 66_CD14_T1Dpair5_T1D


title: 67_CD14_T1Dpair6_unaffected


title: 69_CD14_T1Dpair7_unaffected


title: 60_CD14_T1Dpair2_T1D


title: 50_CD4_Normalpair6_normal_MZ


title: 47_CD4_Normalpair5_normal_MZ


title: 49_CD4_Normalpair6_normal_MZ


title: 48_CD4_Normalpair5_normal_MZ


title: 46_CD4_Normalpair4_normal_MZ


title: 45_CD4_Normalpair4_normal_MZ


title: 39_CD4_Normalpair1_normal_MZ


title: 42_CD4_Normalpair2_normal_MZ


title: 38_CD4_T1Dpair17_T1D


title: 44_CD4_Normalpair3_normal_MZ


title: 43_CD4_Normalpair3_normal_MZ


title: 33_CD4_T1Dpair14_unaffected


title: 40_CD4_Normalpair1_normal_MZ


title: 41_CD4_Normalpair2_normal_MZ


title: 37_CD4_T1Dpair17_unaffected


title: 35_CD4_T1Dpair16_unaffected


title: 34_CD4_T1Dpair14_T1D


title: 30_CD4_T1Dpair12_T1D


title: 26_CD4_T1Dpair10_T1D


title: 13_CD4_T1Dpair3_unaffected


title: 36_CD4_T1Dpair16_T1D


title: 32_CD4_T1Dpair13_T1D


title: 31_CD4_T1Dpair13_unaffected


title: 19_CD4_T1Dpair6_unaffected


title: 22_CD4_T1Dpair7_T1D


title: 16_CD4_T1Dpair4_T1D


title: 28_CD4_T1Dpair11_T1D


title: 27_CD4_T1Dpair11_unaffected


title: 25_CD4_T1Dpair10_unaffected


title: 21_CD4_T1Dpair7_unaffected


title: 20_CD4_T1Dpair6_T1D


title: 15_CD4_T1Dpair4_unaffected


title: 24_CD4_T1Dpair8_T1D


title: 18_CD4_T1Dpair5_T1D


title: 14_CD4_T1Dpair3_T1D


title: 9_CD4_T1Dpair1_unaffected


title: 10_CD4_T1Dpair1_T1D


title: AFT011 rep1

status: Public on Mar 14 2014

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

description:
AFT011-1
Gene expression from FL non-supportive stromal clone.

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene from Affymetrix. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix).

data_processing: The data were RMA normalized and analysed with Partek Genomic Suite.

source_name: FL stromal clone

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Following the GeneChip whole transcript (WT) Sense Target labelling assay kit Affymetrix).

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

treatment_protocol: Stromal cells were cultured on 0.1% gelatin coated 12 well plates at 33°C. At confluency, culture medium was removed and cultures were washed in PBS 1X and total RNA was extracted.

tag: strain/background

value: FL

value: embryonic day 14.5

tag: hspc support

value: non-supportive


title: 11_CD4_T1Dpair2_unaffected


title: 14F1-1 rep3

description:
14F1-1-3
Gene expression from BM supportive stromal clone.

source_name: BM stromal clone

treatment_protocol: Stromal cells were cultured on 0.1% gelatin coated 12 well plates at 37°C. At confluency, culture medium was removed and cultures were washed in PBS 1X and total RNA was extracted.

value: BALB/c

value: BM

value: adult

value: supportive


title: 23_CD4_T1Dpair8_unaffected


title: AFT011 rep3

description:
AFT011-3
Gene expression from FL non-supportive stromal clone.


title: BFC012+KLS rep1

status: Public on Mar 01 2014

description: Gene expression from FL non-supportive stromal clone. Cultured in the presence of BM KLS cells.

treatment_protocol: AFT024 and BFC012 stromal cells, cultured in the presence or in the absence of BM c-ki+Sca1+Lin- (KLS) cells, were purified by cell sorting after 4 days of culture on the basis of absence of CD45 expression and total RNA was extracted.

tag: culture condition

value: presence of BM KLS cells


title: AM30-3F4- rep1

description:
AM30-3F4-1
Gene expression from AGM supportive stromal clone.

source_name: AGM stromal clone

tag: tissue

value: AGM

value: embryonic day 11


title: AFT024+KLS rep2

description: Gene expression from FL supportive stromal clone. Cultured in the presence of BM KLS cells.


title: AFT011 rep2

description:
AFT011-2
Gene expression from FL non-supportive stromal clone.


title: AM14-1C4 rep3

description:
AM14-1C4-3
Gene expression from AGM supportive stromal clone.


title: 14F1-1 rep2

description:
14F1-1-2
Gene expression from BM supportive stromal clone.


title: AM14-1C4 rep2

description:
AM14-1C4-2
Gene expression from AGM supportive stromal clone.


title: 12_CD4_T1Dpair2_T1D

value: female


title: 17_CD4_T1Dpair5_unaffected


title: 29_CD4_T1Dpair12_unaffected

value: male


title: 14F1-1 rep1

description:
14F1-1-1
Gene expression from BM supportive stromal clone.

treatment_protocol:
Stromal cells were cultured on 0.1% gelatin coated 12 well plates at 37°C. At confluency, culture medium was removed and cultures were washed in PBS 1X and total RNA was extracted.
Stromal cells were cultured on 0.1% gelatin coated 12 well plates at 37°C. At confluency, culture medium was removed and cultures were washed in PBS 1X and total RNA was extracted.


title: AFT024+KLS rep3


title: 2012 rep1

description:
2012-1
Gene expression from FL supportive stromal clone.


title: AM30-3F4 rep2

description:
AM30-3F4-2
Gene expression from AGM supportive stromal clone.


title: 2012 rep3

description:
2012-3
Gene expression from FL supportive stromal clone.


title: AM30-3F4 rep3

description:
AM30-3F4-3
Gene expression from AGM supportive stromal clone.


title: AM14-1C4 rep1

description:
AM14-1C4-1
Gene expression from AGM supportive stromal clone.


title: 2012 rep2

description:
2012-2
Gene expression from FL supportive stromal clone.


title: BFC012+KLS rep3


title: BFC012+KLS rep2


title: BFC012-KLS rep3

description: Gene expression from FL non-supportive stromal clone. Cultured in the absence of BM KLS cells.

value: absence of BM KLS cells


title: AFT024+KLS rep1


title: AFT024-KLS rep3

description: Gene expression from FL supportive stromal clone. Cultured in the absence of BM KLS cells.


title: BFC012-KLS rep2


title: AFT024-KLS rep2


title: OP9 rep1

description: Gene expression from fetal calvaria supportive stromal line

source_name: Fetal calvaria stromal line

value: Fetal calvaria

value: Fetal


title: BFC_3

description: Gene expression from FL non-supportive stromal clone.


title: AFT024-KLS rep1


title: AFT024 rep3

description: Gene expression from FL supportive stromal clone.


title: BFC012 rep2


title: BFC012 rep3


title: BFC_1


title: AFT024 rep1


title: OP9 rep3


title: UG26.3B5 rep1

description: Gene expression from AGM less-supportive stromal clone.

value: less-supportive


title: BMC9 rep 2

description: Gene expression from BM supportive stromal clone.


title: BMC10 rep1

description: Gene expression from BM less-supportive stromal clone.


title: UG26.1B6 rep2

description: Gene expression from AGM supportive stromal clone.


title: BMC10 rep2


title: UG26.3B5 rep3


title: BFC012 rep1


title: BMC9 rep3


title: BFC012-KLS rep1


title: OP9 rep2


title: BFC_2


title: UG26.3B5 rep2


title: BMC9 rep1


title: AFT024 rep2


title: BMC10 rep3


title: UG26.1B6 rep3


title: 15556T

status: Public on Feb 19 2014

city: Bethesda

first: Aaron

last: Schetter

state: MD

address: 37 Convent Drive, Building 37, Room 3050

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

description: Gene expression data from colon tumor and adjacent noncancerous tissue

hyb_protocol: Following fragmentation  cRNA were hybridized using a Affymetrix U133A arrays according to manufacterer's specifications

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

data_processing: The data were imported and normalized using Partek.  Arrays were in two batches and the batch correction function of Partek was used to normalize that difference away.

source_name: Colon tissue from patient with colon cancer

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

tag: microarray batch

value: B

tag: rs5995355 genotype

value: GG

value: Tumor


title: UG26.1B6 rep1


title: 15556N

value: adjacent nontumor


title: 15527T


title: 15527N


title: 15430T


title: 15313T

value: AA


title: 15313N


title: 15149T


title: 15021N

value: AG


title: 14915T


title: 15430N


title: 14915N


title: 15059N


title: 14559T


title: 15363T


title: 15363N


title: 15149N


title: 15059T


title: 14559N


title: 14273N


title: 14467N


title: 14467T


title: 14273T


title: 14554N


title: 13799N


title: 13822T


title: 13799T


title: 14554T


title: 13736T


title: 14070T


title: 14070N


title: 13701N


title: 13736N


title: 13547 N

value: A


title: 12892 T


title: 13687T


title: 13201 N


title: 13687N


title: 13701T


title: 13201 T


title: 13273 N


title: 12861 N


title: 13547 T


title: 12874 N


title: 13273 T


title: 12892 N


title: 12861 T


title: 12792 T


title: 12814 T


title: 12724 T


title: 12742 T


title: 12742 N


title: 12633 N


title: 12663 T


title: 12740 N


title: 12663 N


title: 12462 N


title: 12464 T


title: 12464 N


title: 12724 N


title: 12740 T


title: 12385-T


title: 12417 T


title: 12417 N


title: 12294 N


title: 12375 T


title: 12385 T


title: 12450 T


title: 12462 T


title: 12298 T


title: 12294 T


title: 12158 N


title: 12447 T


title: 12298 N


title: 12158 T


title: 12447 N


title: 12139 T


title: 12169 N


title: 12146 N


title: 12124 T


title: 12076 N


title: 12146 T


title: 12139 N


title: 12051 T


title: 11873 N


title: 12124 N


title: 11873 T


title: 11918 T


title: 11437 N


title: 11731 N


title: 11731 T


title: 11918 N


title: 12051 N


title: 11716 N


title: 11303 N


title: 11642 N


title: 11157 T


title: 11437 T


title: 11716 T