title: Malignant Myc B lymphocytes, biological replicate 2

status: Public on Oct 31 2011

type: RNA

city: Tampa

first: John

middle: Lamoine

last: Cleveland

state: FL

address: 12902 USF Magnolia Drive

country: USA

institute: H. Lee Moffitt Cancer Center

description: Gene expression data from EμΜyc mice 4-6 weeks old.

hyb_protocol: Fragmentation/hybridization to MOE430A arrays (Affymetrix) were performed according to Affymetrix protocols.

scan_protocol: Imaging was performed according to standard Affymetrix protocol.

data_processing: The data were analyzed using GeneSpring GX version 11 based on GCRMA analysis default settings.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Malignant Myc B lymphocytes

label_protocol: cRNA was synthesized using the One-Cycle Target Labeling and Control Reagent package (Affymetrix, Inc.).

extract_protocol: B cells were obtained from bone marrow or spleen by MACS using bead conjugated to antibodies against B220 or IgM. RNA was prepared using the RNeasy Kit (Qiagen).

tag: strain background

tag: genotype/variation

value: Eμ-Myc transgenic

tag: age

tag: tissue source

value: bone marrrow or spleen


title: Malignant Myc B lymphocytes, biological replicate 11


title: S3 Replicate 3

city: Worcester

first: Merav

last: Socolovsky

state: MA

address: 364 Plantation Street

department: Pediatrics and Cancer Biology

institute: University of Massachusetts Medical School

hyb_protocol: FS450_0004 (Nugen recommended)

scan_protocol: GeneChip® Scanner 3000

data_processing: Analyses were performed using BRB-ArrayTools developed by Dr. Richard Simon and BRB-ArrayTools Development Team. Microarray suite 5 (MAS5) processed sample data were normalized to the average of 18SRNA (AFFX-18SRNAMur/X00686_M_at), GAPDH (AFFX-GapdhMur/M32599_3_at) and β-actin (1419734_at) expression values.

label: Biotin

source_name: S3 erythroid subset from E13.5 fetal liver

label_protocol: Total RNA was amplified using Nugen Ovation® RNA Amplification System V2 and labeled using NuGEN's Encore™ Biotin Module.

extract_protocol: Total RNA was prepared from cells sorted from each fetal liver subset, using the AllPrep DNA/RNA Micro Kit (Qiagen) with on column DNase treatment.

tag: strain

value: Balb/C

tag: tissue

value: Fetal liver

tag: developmental stage

value: Embryonic day 13.5


title: Malignant Myc B lymphocytes, biological replicate 7


title: Malignant Myc B lymphocytes, biological replicate 9


title: Malignant Myc B lymphocytes, biological replicate 8


title: Malignant Myc B lymphocytes, biological replicate 10


title: S1 Replicate 2

source_name: S1 erythroid subset from E13.5 fetal liver

value: Embryonic day 12.5


title: S3 Replicate 2


title: Malignant Myc B lymphocytes, biological replicate 3


title: Malignant Myc B lymphocytes, biological replicate 13


title: Premalignant Myc B lymphocytes, biological replicate 2

source_name: Myc-expressing B220+ premalignant lymphocytes


title: IM09 vs IM09 ref pool 5

city: Sao Paulo

first: Waleska

middle: Kerllen

last: Martins

state: Sao Paulo

address: Rua Antonio Prudente, 211

country: Brazil

institute: Hospital A.C. Camargo

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

scan_protocol: Hardware: Perkinelmer / Software: ScanArray

data_processing: Lowesss

organism: Homo sapiens

label_protocol: Protocol Cy3/Cy5

extract_protocol: kit Pico Pure RNA Isolation Kit

value: Cutaneous melanoma metastasis

source_name: IM09 ref pool 5

extract_protocol: Trizol

value: 5 human cutaneous melanoma cell lines (SK-MEL 05; 17; 28; 37 and 188)


title: S1 Replicate 3


title: Malignant Myc B lymphocytes, biological replicate 5


title: Malignant Myc B lymphocytes, biological replicate 4


title: Malignant Myc B lymphocytes, biological replicate 12


title: Premalignant Myc B lymphocytes, biological replicate 4


title: Malignant Myc B lymphocytes, biological replicate 1


title: Malignant Myc B lymphocytes, biological replicate 6


title: Wild Type B220+, biological replicate 2

source_name: Wild Type B220+

value: wild type


title: Premalignant Myc B lymphocytes, biological replicate 3


title: Premalignant Myc B lymphocytes, biological replicate 5


title: Premalignant Myc B lymphocytes, biological replicate 1


title: Wild Type B220+, biological replicate 3


title: Wild Type B220+, biological replicate 1


title: Wild Type B220+, biological replicate 4


title: IM09 vs IM09 ref pool 5 dye swap


title: S1 Replicate 1


title: IM07 vs IM07 ref pool 5 dye swap

source_name: IM07 ref pool 5


title: IM98 vs IM98 ref pool 5

source_name: IM98 ref pool 5


title: IM99 vs IM99 ref pool 5 dye swap

source_name: IM99 ref pool 5


title: IM98 vs IM98 ref pool 5 dye swap


title: IM96 vs IM96 ref pool 5

source_name: IM96 ref pool 5


title: IM96 vs IM96 ref pool 5 dye swap


title: IM93 vs IM93 ref pool 5 dye swap

source_name: IM93 ref pool 5


title: IM91 vs IM91 ref pool 5 dye swap

source_name: IM91 ref pool 5

value: Primary cutaneous melanoma - Acral lentiginous


title: IM93 vs IM93 ref pool 5


title: IM95 vs IM95 ref pool 5 dye swap

source_name: IM95 ref pool 5


title: IM99 vs IM99 ref pool 5


title: IM07 vs IM07 ref pool 5


title: IM83 vs IM83 ref pool 5

source_name: IM83  ref pool 5


title: IM91 vs IM91 ref pool 5


title: IM82 vs IM82 ref pool 5

source_name: IM82 ref pool 5


title: IM82 vs IM82 ref pool 5 dye swap


title: IM95 vs IM95 ref pool 5


title: IM83 vs IM83 ref pool 5 dye swap


title: IM79 vs IM79 ref pool 5

source_name: IM79 ref pool 5


title: IM77 vs IM77 ref pool 5

source_name: IM77 ref pool 5


title: IM80 vs IM80 ref pool 5 dye swap

source_name: IM80 ref pool 5


title: IM81 vs IM81 ref pool 5 dye swap

source_name: IM81 ref pool 5


title: IM81 vs IM81 ref pool 5


title: IM80 vs IM80 ref pool 5


title: S3 Replicate 1

source_name: S3 erythroid subset from E13.5 fetal liver


title: IM79 vs IM79 ref pool 5 dye swap


title: IM77 vs IM77 ref pool 5 dye swap


title: IM78 vs IM78 ref pool 5

source_name: IM78 ref pool 5


title: IM73 vs IM73 ref pool 5 dye swap

source_name: IM73 ref pool 5


title: IM78 vs IM78 ref pool 5 dye swap


title: IM72 vs IM72 ref pool 5

value: Primary cutaneous melanoma

source_name: IM72 ref pool 5


title: IM73 vs IM73 ref pool 5


title: IM71 vs IM71 ref pool 5 dye swap

source_name: IM71 ref pool 5

value: Primary cutaneous melanoma - Superficial spreading


title: IM72 vs IM72 ref pool 5 dye swap


title: IM71 vs IM71 ref pool 5


title: IM68 vs IM68 ref pool 5

source_name: IM68 ref pool 5


title: IM69 vs IM69 ref pool 5 dye swap

source_name: IM69 ref pool 5


title: IM64 vs IM64 ref pool 5 dye swap

source_name: IM64 ref pool 5


title: IM63 vs IM63 ref pool 5 dye swap

source_name: IM63 ref pool 5


title: IM64 vs IM64 ref pool 5


title: IM63 vs IM63 ref pool 5


title: IM66 vs IM66 ref pool 5

source_name: IM66 ref pool 5


title: IM61 vs IM61 ref pool 5

source_name: IM61 ref pool 5


title: IM68 vs IM68 ref pool 5 dye swap


title: IM69 vs IM69 ref pool 5


title: IM66 vs IM66 ref pool 5 dye swap


title: IM62 vs IM62 ref pool 5

source_name: IM62 ref pool 5


title: IM62 vs IM62 ref pool 5 dye swap


title: IM59 vs IM59 ref pool 5 dye swap

source_name: IM59 ref pool 5


title: IM60 vs IM60 ref pool 5

source_name: IM60 ref pool 5


title: IM59 vs IM59 ref pool 5


title: IM58 vs IM58 ref pool 5

source_name: IM58 ref pool 5


title: IM54 vs IM54 ref pool 5

value: Primary cutaneous melanoma - Nodular

source_name: IM54 ref pool 5


title: IM53 vs IM53 ref pool 5 dye swap

source_name: IM53 ref pool 5


title: IM60 vs IM60 ref pool 5 dye swap


title: IM55 vs IM55 ref pool 5

source_name: IM55 ref pool 5


title: IM61 vs IM61 ref pool 5 dye swao


title: IM54 vs IM54 ref pool 5 dye swap


title: IM58 vs IM58 ref pool 5 dye swap


title: IM55 vs IM55 ref pool 5 dye swap


title: IM50 vs IM50 ref pool 5

source_name: IM50 ref pool 5


title: IM51 vs IM51 ref pool 5

source_name: IM51 ref pool 5


title: IM50 vs IM50 ref pool 5 dye swap


title: IM51 vs IM51 ref pool 5 dye swap


title: IM53 vs IM53 ref pool 5


title: IM49 vs IM49 ref pool 5 dye swap

source_name: IM49 ref pool 5


title: IM37 vs IM37 ref pool 5

source_name: IM37 ref pool 5


title: IM38 vs IM38 ref pool 5 dye swap

source_name: IM38 ref pool 5


title: IM38 vs IM38 ref pool 5


title: IM49 vs IM49 ref pool 5


title: IM42 vs IM42 ref pool 5

source_name: IM42 ref pool 5


title: IM33 vs IM33 ref pool 5

source_name: IM33 ref pool 5


title: IM37 vs IM37 ref pool 5 dye swap


title: IM20 vs IM20 ref pool 5

source_name: IM20 ref pool 5


title: IM24 vs IM24 ref pool 5 dye swap

source_name: IM24 ref pool 5

value: Primary melanoma - Mucosa


title: IM24 vs IM24 ref pool 5


title: IM14 vs IM14 ref pool 5

source_name: IM14 ref pool 5


title: IM30 vs IM30 ref pool 5

source_name: IM30 ref pool 5


title: IM33 vs IM33 ref pool 5 dye swap


title: IM30 vs IM30 ref pool 5 dye swap


title: IM42 vs IM42 ref pool 5 dye swap


title: IM19 vs IM19 ref pool 5

source_name: IM19 ref pool 5


title: IM129 vs IM129 ref pool 5

source_name: IM129 ref pool 5


title: IM19 vs IM19 ref pool 5 dye swap


title: IM127 vs IM127 ref pool 5

source_name: IM127 ref pool 5


title: IM14 vs IM14 ref pool 5 dye swap


title: IM20 vs IM20 ref pool 5 dye swap


title: IM127 vs IM127 ref pool 5 dye swap


title: IM129 vs IM129 ref pool 5 dye swap


title: IM126 vs IM126 ref pool 5

source_name: IM126 ref pool 5


title: IM119 vs IM119 ref pool 5

value: Primary cutaneous melanoma - without classification

source_name: IM119 ref pool 5


title: IM118 vs IM118 ref pool 5 dye swap

source_name: IM118 ref pool 5


title: IM118 vs IM118 ref pool 5


title: IM119 vs IM119 ref pool 5 dye swap


title: IM112 vs IM112 ref pool 5

source_name: IM122 ref pool 5


title: IM126 vs IM126 ref pool 5 dye swap


title: IM117 vs IM117 ref pool 5

source_name: IM117 ref pool 5


title: IM113 vs IM113 ref pool 5 dye swap

source_name: IM113 ref pool 5


title: IM116 vs IM116 ref pool 5

source_name: IM116 ref pool 5


title: IM111 vs IM111 ref pool 5

source_name: IM111 ref pool 5


title: IM110 vs IM110 ref pool 5

source_name: IM110 ref pool 5


title: IM112 vs IM112 ref pool 5 dye swap

source_name: IM112 ref pool 5


title: IM117 vs IM117 ref pool 5 dye swap


title: IM113 vs IM113 ref pool 5


title: IM110 vs IM110 ref pool 5 dye swap


title: IM116 vs IM116 ref pool 5 dye swap


title: IM115 vs IM115 ref pool 5 dye swap

source_name: IM115 ref pool 5


title: IM109 vs IM109 ref pool 5

source_name: IM109 ref pool 5


title: IM111 vs IM111 ref pool 5 dye swap


title: IM115 vs IM115 ref pool 5


title: IM108 vs IM108 ref pool 5

source_name: IM108 ref pool 5


title: IM108 vs IM108 ref pool 5 dye swap


title: IM106 vs IM106 ref pool 5 dye swap

source_name: IM106 ref pool 5


title: IM107 vs IM107 ref pool 5 dye swap

source_name: IM107 ref pool 5


title: IM107 vs IM107 ref pool 5


title: IM109 vs IM109 ref pool 5 dye swap


title: IM106 vs IM106 ref pool 5


title: IP Spo14_rep1

type: genomic

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description: IP of Spo14-LytA. Replicate 1. Filter V5R2-L1-22.

hyb_protocol: Hybridization Solution was: 5X SSC, 5X Denhardt’s, 0.5% SDS and 100 µg herring sperm DNA/ml.The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 3X10exp6 dpm/mL of radioactive sample and hybridized for 44h. Washing conditions were: 1h at 65ºC for 20 min in 2X SSC, 0.1% SDS, and twice at 65ºC for 30 min in 0.2XSSC, 0.1% SDS.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times. Filters were stripped by pouring 3X150 ml boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane. The first time, the stripping buffer was immediately changed while after the second and third washes the filters were left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter or re-scanned with the Phosphorimager.

data_processing: Raw image quantization background subtracted.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: IP of Spo14-LytA

label_protocol: Ligation Mediated PCR (Ren B. et al. 2000) was used for DNA amplification. Briefly,the DNA was blunted by T4 phage DNA polymerase. The reaction was allowed to proceed for 20 minutes at 12°C. After phenol/chloroform/isoamylic alcohol extraction, DNA was ethanol-precipitated and ligated in a final volume of 50 μl with annealed linkers oJW102 and oJW103 (1.5 μM of each primer). The reaction was carried out overnight at 16°C and ligated DNA was precipitated and resuspended in 25 μl milliQ water. The ligated DNA was amplified by PCR. The PCR  program was 2 minutes at 95°C and 33 cycles of 30 s at 95°C, 30 s at 55°C and 2 minutes at 72°C. The DNA was precipitated overnight and resuspended in 50 μl of milliQ water. The LMPCR product was used as a template for the radioactive labeling reaction. The reaction mixture contained 5-15 μL of amplified DNA in 50 μl (1× DNApol buffer, 2 mM MgCl2, 0.2 mM dATP, dTTP and dGTP, 25 μM dCTP, 1 μM oJW102, 0.8 μCi α-33P-dCTP and 5 U DNApol). The mix was denatured for 5 minutes at 95°C, annealed 5 minutes at 50°C and was amplified during 30 minutes at 72°C. The reaction product was purified through a ProbeQuant G-50 column to remove unincorporated 33P-dCTP and oligonucleotides.

growth_protocol: Exponential growth in YPD

extract_protocol: 50 mL of cells were cross-linked by adding formaldehyde to a final concentration of 1% for 15 minutes at room temperature, and the cross-link was quenched by adding glycine to a final concentration of 125 mM. Cell were washed 4 times with 30 mL ice-cold TBS buffer (20mM Tris-HCl, 140 mM NaCl, pH 7.5) and frozen. Cells were thawed on ice and resuspended in 300 μl lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM PMSF (Phenylmethylsulfonyl fluoride), 1 mM benzamidine and 1 pill of protease inhibitor cocktail (Roche Diagnostics, Mannheim, Germany) dissolved in every 50 ml of buffer). The equivalent of 0.3 ml of frozen glass beads (425-600 mm; Sigma-Aldrich, St Louis, MO, USA) was added to the cellular suspension and cells were lysed at 4°C for 12 minutes of vortexing at maximum power. Lysis buffer (300 μl) was added and the extract was transferred to a new tube. Sonication of DNA was performed to obtain DNA fragments between 200 and 500 bp, with an average size of 350 bp. Chromatin was sonicated on ice-cold water, with 5 pulses of 30 s at High output (200W) in a Bioruptor (Diagenode SA, Liège, Belgium). Cell debris was removed by centrifugation at 12,000 rpm at 4°C for 5 minutes. An aliquot of 10 μl of this whole cell extract (WCE) was kept as positive control.

tag: matalfa his3d1 leu2d0 lys2d0 ura3d0 spo14lyta

value: :Km


title: IM103 vs IM103 ref pool 5 dye swap

source_name: IM103 ref pool 5


title: IM100 vs IM100 ref pool 5

source_name: IM100 ref pool 5


title: IM101 vs IM101 ref pool 5 dye swap

source_name: IM101 ref pool 5


title: IM105 vs IM105 ref pool 5 dye swap

source_name: IM105 ref pool 5


title: IM105 vs IM105 ref pool 5


title: IM100 vs IM100 ref pool 5 dye swap


title: IM103 vs IM103 ref pool 5


title: IP Mvp1_rep2

description: IP of Mvp1-LytA. Replicate 2. Filter V5R2-L1-21.

source_name: IP of Mvp1-LytA

tag: matalfa his3d1 leu2d0 lys2d0 ura3d0 mvp1lyta


title: IM101 vs IM101 ref pool 5


title: IP Spo14_rep2

description: IP of Spo14-LytA. Replicate 2. Filter V5R2-L1-20.


title: GH887 vs GH887 ref pool 5

value: GH887 - primary cutaneous melanoma - without classification

source_name: GH887 ref pool 5


title: IP Mvp1_rep1

description: IP of Mvp1-LytA. Replicate 1. Filter V5R2-L1-20.


title: GH887 vs GH887 ref pool 5 dye swap


title: Hemo vs. whole 2

city: Baltimore

first: George

last: Dimopoulos

state: MD

address: 615 N. Wolfe Street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

description: Agilent

hyb_protocol: Agilent

scan_protocol: GenePix

organism: Anopheles gambiae

source_name: hemocyte

label_protocol: Agilent

extract_protocol: Qiagen

tag: cell type

value: hemocytes

source_name: mosquito

value: whole adult female mosquito


title: Dengue Virus-Infected Cell Responses R3

scan_protocol: GenePix Axon

data_processing: GenePix

organism: Aedes aegypti

source_name: Dengue-virus-infected cells

extract_protocol: QIAGEN

treatment_protocol: Dengue virus infection.

tag: cell line

tag: treatment

value: dengue virus infection

source_name: Naive cells

treatment_protocol: Naive Cells

value: mock infection


title: Hemo vs. whole 3

description: Agilent


title: Hemo E coli vs. hemo unchallenged C

description: Agilent

source_name: Hemo E coli

value: E. coli

source_name: hemo unchallenged

value: unchallenged


title: RNA_UNR IP5_dye swap

city: Barcelona

first: Francesco

middle: Mattia

last: Mancuso

address: C/ Dr. Aiguader, 88

institute: CRG (Centre for Genomic Regulation)

description:
216
Biological replicate 3 of 3. Dye swap. Cytoplasmic RNA associated with the RNA binding protein UNR in Female vs. in Male

hyb_protocol: Microarrays were hybridized at the CRG Genomics Facility following the Corning protocol for UltraGaps slides.

scan_protocol: Microarrays were scanned using the Agilent scanner and the images were processed with GenePix image analysis software v6.0.

data_processing: GPR files were analyzed with Limma package from BioConductor (Gentleman et al., 2004; Genome Biol 5, R80; Smyth, 2004; Statistical Applications in Genetics and Molecular Biology 3, Article 3) using the same criteria. Data was background corrected with the normexp method and normalized with OLIN (Futschik and Crompton, 2005; Bioinformatics 21, 1724-1726). Spots not fulfilling the quality thresholds (based on spot size, foreground versus background signals, saturation, coincidence between differently calculated ratio measures and R2 of regression ratio) were eliminated from further analysis

molecule: cytoplasmic RNA

organism: Drosophila melanogaster

source_name: UNR_IP with Cytoplasmic extracts from male adult flies

label_protocol: Probes were generated using the pico version of the ExpressArt mRNA Amplification Kit (Artus) following the manufacturer's instructions.

extract_protocol: Cytoplasmic extracts were prepared from adult flies as described in Wilhelm et al.(2000) J. Cell. Biol. 148:427-440, and used to immunoprecipitate UNR as described in Abaza et al. (2006) Genes Dev 20: 380-389. RNA was isolated from the immunoprecipitate using TRizol.

tag: gender

value: Male

source_name: UNR_IP with Cytoplasmic extracts from female adult flies

value: Female


title: Heat-Inactivated Dengue Virus-Exposed Cell Responses R1

source_name: Heat-inactivated dengue virus-exposed cells

treatment_protocol: Heat-inactivated dengue virus infection.

value: heat-inactivated dengue virus infection


title: Dengue Virus-Infected Cell Responses R1


title: RNA_UNR IP5_direct

description:
215
Biological replicate 3 of 3. Cytoplasmic RNA associated with the RNA binding protein UNR in Male vs. in Female


title: Dengue Virus-Infected Cell Responses R2


title: Heat-Inactivated Dengue Virus-Exposed Cell Responses R3


title: Hemo m luteus vs. hemo unchallenged C

description: Agilent

source_name: Hemo m luteus

value: M. luteus


title: LPA_L_88

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

country: Germany

institute: Leibniz Institute for Farm Animal Biology (FBN)

description:
Gene expression data from liver of pig breed Pix(DLxDE).
trait 1: Fat area [cm2] = fat area on M. longissimus dorsi at 13th/14th rib
trait 2: Drip loss (%) percentage of weight loss of M. longissimus dorsi samples collected at 24 hours post mortem that was weighted, suspended in a plastic bag, held at 4 °C for 48 h, and thereafter re-weighed

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42C on Affymetrix GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500.

organism: Sus scrofa

source_name: liver taken at slaughter, mean end weight of 110 kg

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

tag: breed

value: commercial pig of crosbred Pix(DLxDE).

tag: trait 1 (see description below)

tag: trait 2 (see description below)

value: liver


title: RNA_UNR IP3_direct

description:
200
Biological replicate 2 of 3. Cytoplasmic RNA associated with the RNA binding protein UNR in Male vs. in Female


title: LPA_L_93


title: RNA_UNR IP1_dye swap

description:
199
Biological replicate 1 of 3. Dye swap. Cytoplasmic RNA associated with the RNA binding protein UNR in Female vs. in Male


title: Heat-Inactivated Dengue Virus-Exposed Cell Responses R2


title: LPA_L_759


title: LPA_L_81


title: LPA_L_82


title: LPA_L_73


title: RNA_UNR IP3_dye swap

description:
214
Biological replicate 2 of 3. Dye swap. Cytoplasmic RNA associated with the RNA binding protein UNR in Female vs. in Male


title: timepoint 38 vs timepoint 39 #2

city: Haren

first: EJ

last: Blom

address: Kerklaan 30

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

description: data 38 vs 39.slide #2 ratio

hyb_protocol: The labeled cDNA was hybridized to oligonucleotide microarrays (Lulko et al., 2007) in Ambion Slidehyb #1 buffer (Ambion Europe Ltd) at 45°C for 16-18 h. After hybridization, slides were washed for 5 min at 37°C in 2x SSC with 0.5% SDS, 2x 5 min at 37°C in 1x SSC with 0.25% SDS and 1 min at 37°C in 1x SSC with 0.1% SDS, and then dried by centrifugation (2 min, 2000 rpm). SSC = 150 mM NaCl, 15 mM trisodium citrate.

scan_protocol: The microarrays were scanned with a GenePix Autoloader 4200AL confocal laser scanner (Molecular Devices Ltd). Determination of the individual intensities of each spot was done with ArrayPro 4.5 (Media Cybernetics Inc., Silver Spring, Md., USA) with a local corners background correction method.

data_processing: Expression levels were processed and normalized (Lowess method) with MicroPrep (van Hijum et al., 2003). The median expression level was calculated for all genes based on the expression values from all six measurements for each timepoint. To facilitate the analysis of intensity levels of genes for each time point we divided the median intensity for each gene by the averaged intensity of all genes for each timepoint, which was followed by a natural log transformation. Normalized intensity of each signal (Cy3, Cy5) is given as well as the log2 ratio. The additional processed data file available on the Series record (TimepointProcessedData.txt) contains the natural log transformed median expression level all genes based on the expression values from all six measurements for each timepoint.

organism: Bacillus subtilis

source_name: timepoint 38

label_protocol: cDNA was synthesized with the Superscript III Reverse Transcriptase kit (Invitrogen) using 10 μg of total RNA as template and 360 U of SuperscriptTM III RT and purified with the Cyscribe GFX purification kit (Amersham Biosciences). The purified cDNA was labeled with Cy3- or Cy5-monoreactive dye and purified again with the Cyscribe GFX purification kit.

growth_protocol: Wild-type Bacillus subtilis 168 (trpC2; Anagnostopoulos and Spizizen, 1961) was grown in TY medium (10 g/L trypton, 5 g/L yeast extract, 5 g/L NaCl) in batch mode at 37°C in a 16 L fermentor using a working volume of 12 L. Cultures were aerated at 40 L/min and 400 rpm. The pH and oxygen levels were monitored, but were allowed to fluctuate during the batch culture incubation period.  To prevent foaming, 0.3% antifoam A (SIGMA) was added on an as-needed basis. Cultures were inoculated to an OD600 of approximately 0.01 from synchronized exponentially grown pre-cultures grown at 37°C in TY and frozen in 10% glycerol (Lulko et al., 2007). Growth was monitored by measurement of the OD at 600 nm. As soon as the culture reached an OD600 of 0.1 (typically after around 75 min.), samples were taken every 10 minutes for optical density measurements and RNA isolation. In total 40 timepoints were sampled.  Cells were harvested by centrifugation (14.000 rpm, 4°C, 1 min.) and the pellet was immediately frozen in liquid nitrogen and stored at -80°C.

extract_protocol: RNA was isolated with the High Pure RNA Isolation Kit (Roche Applied Science) according to the manufacturer's instuctions. RNA quantity and quality were assessed with a Nano Drop ND-1000 spectrophotometer (NanoDrop Technologies) and an Agilent Bioanalyzer 2100 with RNA 6000 LabChips (Agilent Technologies Netherlands BV).

value: strain 168

source_name: timepoint 39


title: LPA_L_83


title: Hemo vs. whole

description: Agilent


title: RNA_UNR IP1_direct

description:
198
Biological replicate 1 of 3. Cytoplasmic RNA associated with the RNA binding protein UNR in Male vs. in Female


title: LPA_L_708


title: LPA_L_713


title: timepoint 38 vs timepoint 39 #1

description: data 38 vs 39.slide #1 ratio


title: LPA_L_728


title: timepoint 37 vs timepoint 40 #1

description: data 37 vs 40.slide #1 ratio

source_name: timepoint 37

source_name: timepoint 40


title: timepoint 37 vs timepoint 40 #2

description: data 37 vs 40.slide #2 ratio


title: LPA_L_86


title: LPA_L_71


title: LPA_L_707


title: LPA_L_77


title: LPA_L_705


title: LPA_L_80


title: LPA_L_72


title: LPA_L_704


title: LPA_L_695


title: timepoint 36 vs timepoint 36 #2

description: data 36 vs 37.slide #2 ratio

source_name: timepoint 36


title: LPA_L_635


title: LPA_L_627


title: LPA_L_624


title: timepoint 37 vs timepoint 38 #2

description: data 37 vs 38.slide #2 ratio


title: LPA_L_594


title: LPA_L_596


title: LPA_L_63


title: LPA_L_628


title: timepoint 35 vs timepoint 36 #2

description: data 35 vs 36.slide #2 ratio

source_name: timepoint 35


title: LPA_L_629


title: timepoint 35 vs timepoint 36 #1

description: data 35 vs 36.slide #1 ratio


title: timepoint 35 vs timepoint 38 #1

description: data 35 vs 38.slide #1 ratio


title: LPA_L_70


title: LPA_L_604


title: timepoint 36 vs timepoint 37 #1

description: data 36 vs 37.slide #1 ratio


title: timepoint 37 vs timepoint 38 #1

description: data 37 vs 38.slide #1 ratio


title: timepoint 34 vs timepoint 35 #1

description: data 34 vs 35.slide #1 ratio

source_name: timepoint 34


title: LPA_L_622


title: timepoint 35 vs timepoint 38 #2

description: data 35 vs 38.slide #2 ratio


title: timepoint 34 vs timepoint 35 #2

description: data 34 vs 35.slide #2 ratio


title: LPA_L_687


title: LPA_L_626


title: LPA_L_580


title: LPA_L_568


title: timepoint 39 vs timepoint 40 #2

description: data 39 vs 40.slide #2 ratio


title: LPA_L_557


title: LPA_L_587


title: LPA_L_545


title: LPA_L_550


title: LPA_L_559


title: LPA_L_571


title: timepoint 39 vs timepoint 40 #1

description: data 39 vs 40.slide #1 ratio


title: timepoint 33 vs timepoint 34 #1

description: data 33 vs 34.slide #1 ratio

source_name: timepoint 33


title: LPA_L_538


title: LPA_L_543


title: LPA_L_546


title: timepoint 32 vs timepoint 33 #2

description: data 32 vs 33.slide #2 ratio

source_name: timepoint 32


title: LPA_L_52


title: timepoint 33 vs timepoint 34 #2

description: data 33 vs 34.slide #2 ratio


title: LPA_L_49


title: LPA_L_542


title: timepoint 32 vs timepoint 33 #1

description: data 32 vs 33.slide #1 ratio


title: LPA_L_51


title: LPA_L_510


title: timepoint 31 vs timepoint 34 #2

description: data 31 vs 34.slide #2 ratio

source_name: timepoint 31


title: LPA_L_530


title: timepoint 31 vs timepoint 34 #1

description: data 31 vs 34.slide #1 ratio


title: LPA_L_484


title: timepoint 31 vs timepoint 32 #2

description: data 31 vs 32.slide #2 ratio


title: LPA_L_485


title: LPA_L_489


title: LPA_L_474


title: LPA_L_428


title: LPA_L_48


title: LPA_L_476


title: LPA_L_482


title: LPA_L_426


title: timepoint 29 vs timepoint 32 #2

description: data 29 vs 32.slide #2 ratio

source_name: timepoint 29


title: timepoint 30 vs timepoint 31 #1

description: data 30 vs 31.slide #1 ratio

source_name: timepoint 30


title: LPA_L_418


title: LPA_L_423


title: LPA_L_42


title: timepoint 29 vs timepoint 30 #1

description: data 29 vs 30.slide #1 ratio


title: timepoint 29 vs timepoint 30 #2

description: data 29 vs 30.slide #2 ratio


title: LPA_L_409


title: LPA_L_415


title: LPA_L_405


title: LPA_L_403


title: LPA_L_392


title: LPA_L_38


title: LPA_L_413


title: LPA_L_386


title: timepoint 29 vs timepoint 32 #1

description: data 29 vs 32.slide #1 ratio


title: timepoint 28 vs timepoint 29 #1

description: data 28 vs 29.slide #1 ratio

source_name: timepoint 28


title: LPA_L_388


title: LPA_L_391


title: timepoint 28 vs timepoint 29 #2

description: data 28 vs 29.slide #2 ratio


title: timepoint 31 vs timepoint 32 #1

description: data 31 vs 32.slide #1 ratio


title: timepoint 30 vs timepoint 31 #2

description: data 30 vs 31.slide #2 ratio


title: timepoint 27 vs timepoint 30 #2

description: data 27 vs 30.slide #2 ratio

source_name: timepoint 27


title: LPA_L_424


title: LPA_L_376


title: LPA_L_380


title: timepoint 33 vs timepoint 36 #2

description: data 33 vs 36.slide #2 ratio


title: timepoint 27 vs timepoint 30 #1

description: data 27 vs 30.slide #1 ratio


title: LPA_L_360


title: LPA_L_361


title: LPA_L_378


title: timepoint 25 vs timepoint 28 #1

description: data 25 vs 28.slide #1 ratio

source_name: timepoint 25


title: LPA_L_335


title: timepoint 26 vs timepoint 27 #2

description: data 26 vs 27.slide #2 ratio

source_name: timepoint 26


title: LPA_L_353

source_name: liver taken at slaughter, mean end weight of 110 kg


title: timepoint 25 vs timepoint 26 #2

description: data 25 vs 26.slide #2 ratio


title: timepoint 26 vs timepoint 27 #1

description: data 26 vs 27.slide #1 ratio


title: timepoint 25 vs timepoint 28 #2

description: data 25 vs 28.slide #2 ratio


title: LPA_L_325


title: LPA_L_346


title: LPA_L_326


title: LPA_L_307


title: LPA_L_305


title: LPA_L_328


title: LPA_L_322


title: LPA_L_343


title: LPA_L_315


title: LPA_L_333


title: LPA_L_309


title: timepoint 23 vs timepoint 26 #1

description: data 23 vs 26.slide #1 ratio

source_name: timepoint 23


title: timepoint 22 vs timepoint 23 #2

description: data 22 vs 23.slide #2 ratio

source_name: timepoint 22


title: timepoint 23 vs timepoint 26 #2

description: data 23 vs 26.slide #2 ratio


title: LPA_L_232


title: timepoint 24 vs timepoint 25 #2

description: data 24 vs 25.slide #2 ratio

source_name: timepoint 24


title: timepoint 25 vs timepoint 26 #1

description: data 25 vs 26.slide #1 ratio


title: timepoint 24 vs timepoint 25 #1

description: data 24 vs 25.slide #1 ratio


title: LPA_L_240


title: LPA_L_233


title: LPA_L_225


title: timepoint 23 vs timepoint 24 #2

description: data 23 vs 24.slide #2 ratio


title: timepoint 23 vs timepoint 24 #1

description: data 23 vs 24.slide #1 ratio


title: LPA_L_241


title: LPA_L_306


title: LPA_L_36


title: timepoint 33 vs timepoint 36 #1

description: data 33 vs 36.slide #1 ratio


title: LPA_L_230


title: LPA_L_229


title: LPA_L_227


title: LPA_L_267


title: LPA_L_223


title: LPA_L_221


title: LPA_L_222


title: LPA_L_247


title: LPA_L_29


title: timepoint 21 vs timepoint 22 #2

description: data 21 vs 22.slide #2 ratio

source_name: timepoint 21


title: timepoint 27 vs timepoint 28 #2

description: data 27 vs 28.slide #2 ratio


title: timepoint 21 vs timepoint 22 #1

description: data 21 vs 22.slide #1 ratio


title: timepoint 27 vs timepoint 28 #1

description: data 27 vs 28.slide #1 ratio


title: LPA_L_210


title: LPA_L_215


title: timepoint 19 vs timepoint 22 #2

description: data 19 vs 22.slide #2 ratio

source_name: timepoint 19


title: LPA_L_207


title: LPA_L_20


title: LPA_L_214


title: LPA_L_194


title: LPA_L_216


title: LPA_L_208


title: timepoint 19 vs timepoint 22 #1

description: data 19 vs 22.slide #1 ratio


title: LPA_L_224


title: timepoint 22 vs timepoint 23 #1

description: data 22 vs 23.slide #1 ratio


title: LPA_L_204


title: LPA_L_195


title: LPA_L_193


title: Uninf Bf Hemo vs. Pla Hemo 24hr B

description: Agilent

source_name: Uninf Bf Hemo

value: uninfected

tag: time

source_name: Pla Hemo 24hr

value: Plasmodium berghei


title: timepoint 21 vs timepoint 24 #1

description: data 21 vs 24.slide #1 ratio


title: LPA_L_192


title: timepoint 19 vs timepoint 20 #2

description: data 19 vs 20.slide #2 ratio

source_name: timepoint 20


title: timepoint 21 vs timepoint 24 #2

description: data 21 vs 24.slide #2 ratio


title: Uninf Bf Hemo vs. Pla Hemo 24hr A

description: Agilent


title: LPA_L_218


title: Uninf Bf Hemo vs. Pla Hemo 19d C

description: Agilent

source_name: Pla Hemo 19d


title: LPA_L_200


title: Uninf Bf Hemo vs. Pla Hemo 24hr C

description: Agilent


title: timepoint 19 vs timepoint 20 #1

description: data 19 vs 20.slide #1 ratio


title: Uninf Bf Hemo vs. Pla Hemo 19d B

description: Agilent


title: LPA_L_19


title: sample B1

city: La Jolla

first: Elizabeth

middle: Ann

last: Winzeler

state: CA

address: 9500 Gilman Drive 0741

department: Pediatrics

institute: University of California San Diego

hyb_protocol: The samples were hybridized to the microarrays overnight at 45°C in Affymetrix buffers, washed, and scanned using a modified protocol with wash temperatures of 23°C to account for the high AT content of P. falciparum (Supplementary File 6 from this publication) (Dharia et al. 2009).

data_processing:
Briefly for polymorphism detection, using a sliding window of three overlapping probes we scanned for sets probes that had significantly lower hybridization when compared to the reference indicative of a polymorphism as determined by z-test using a p-value cutoff of 1´10-5 and a reference 3D7 hybridization. Gene copy number variation scanning was performed by calculating the log2 ratio of the mean intensity for probes to a gene divided by the mean intensity of the probes for a reference 3D7 hybridization as previously described (Dharia et al. 2009).
Files can be directly visualized with PfGenominator software (http://www.scripps.edu/cb/winzeler/software/download/PftilingAnalysis_v2_0.zip)

organism: Plasmodium falciparum

source_name: Genomic DNA from Dd2-B1 strain - resistant to GNF452 compound

label_protocol: Fifteen micrograms of genomic DNA from each isolate and 2.5 ng each of Bio B, Bio C, Bio D, and Cre Affymetrix control plasmids (Affymetrix Inc., Santa Clara, CA, USA) were fragmented with DNaseI and end-labeled with biotin (Winzeler et al. 1998).

growth_protocol: 3D7 (MRA-151) was obtained from the Malaria Research and Reference Reagent Resource Center (MR4; American Type Culture Collection, Manassas, VA, USA). 3D7 and Dd2 P. falciparum patient isolates were propagated in human erythrocytes as previously described (Trager and Jenson 1978) with media for 3D7 containing 5% human serum and 1.2% GIBCO™ AlbuMAX II (Invitrogen) while the media for patient isolates contained 10% human serum.

extract_protocol: Genomic DNA was isolated by standard phenol-chloroform extraction.


title: sample A1

scan_protocol: The samples were hybridized to the microarrays overnight at 45°C in Affymetrix buffers, washed, and scanned using a modified protocol with wash temperatures of 23°C to account for the high AT content of P. falciparum (Supplementary File 6 from this publication) (Dharia et al. 2009).

source_name: Genomic DNA from 3D7-A1 strain - resistant to Pf-5069 compound


title: LPA_L_191


title: sample B3

source_name: Genomic DNA from Dd2-B3 strain - resistant to GNF452 compound


title: sample B2

source_name: Genomic DNA from Dd2-B2 strain - resistant to GNF452 compound


title: 3D7 reference for sample A1

source_name: Genomic DNA from 3D7 reference


title: Dd2 reference for samples B1-3

source_name: Genomic DNA from Dd2 reference


title: Uninf Bf Hemo vs. Pla Hemo 19d A

description: Agilent


title: timepoint 17 vs timepoint 18 #2

description: data 17 vs 18.slide #2 ratio

source_name: timepoint 17

source_name: timepoint 18


title: timepoint 17 vs timepoint 20 #1

description: data 17 vs 20.slide #1 ratio


title: LPA_L_188

source_name: liver taken at slaughter, mean end weight of 110 kg


title: timepoint 18 vs timepoint 19 #2

description: data 18 vs 19.slide #2 ratio


title: timepoint 17 vs timepoint 20 #2

description: data 17 vs 20.slide #2 ratio


title: timepoint 18 vs timepoint 19 #1

description: data 18 vs 19.slide #1 ratio


title: LPA_L_180


title: LPA_L_184


title: timepoint 16 vs timepoint 17 #2

description: data 16 vs 17.slide #2 ratio

source_name: timepoint 16


title: LPA_L_186


title: timepoint 17 vs timepoint 18 #1

description: data 17 vs 18.slide #1 ratio


title: LPA_L_185


title: timepoint 15 vs timepoint 18 #2

description: data 15 vs 18.slide #2 ratio

source_name: timepoint 15


title: LPA_L_16


title: timepoint 15 vs timepoint 18 #1

description: data 15 vs 18.slide #1 ratio


title: timepoint 16 vs timepoint 17 #1

description: data 16 vs 17.slide #1 ratio


title: LPA_L_176


title: timepoint 15 vs timepoint 16 #2

description: data 15 vs 16.slide #2 ratio


title: LPA_L_115


title: timepoint 15 vs timepoint 16 #1

description: data 15 vs 16.slide #1 ratio


title: LPA_L_171


title: timepoint 20 vs timepoint 21 #2

description: data 20 vs 21.slide #2 ratio

source_name: timepoint 21


title: timepoint 14 vs timepoint 15 #2

description: data 14 vs 15.slide #2 ratio

source_name: timepoint 14


title: timepoint 14 vs timepoint 15 #1

description: data 14 vs 15.slide #1 ratio


title: LPA_L_1115


title: LPA_L_1112


title: timepoint 20 vs timepoint 21 #1

description: data 20 vs 21.slide #1 ratio


title: LPA_L_1114


title: timepoint 13 vs timepoint 14 #2

description: data 13 vs 14.slide #2 ratio

source_name: timepoint 13


title: LPA_L_1117


title: LPA_L_1106


title: timepoint 13 vs timepoint 14 #1

description: data 13 vs 14.slide #1 ratio


title: HepG2_GC1_rep3

city: Houston

first: Paul

last: Webb

state: Texas

department: Diabetes Research Center

institute: Methodist Hospital Reseach Institute

description: HepG2 10nM GC1

hyb_protocol: The biotinylated cRNAs were purified and the quality and integrity analyzed by NanoDrop 1000 (Thermo) and Bioanalyzer (Agilent), respectively. Prior to array hybridization, Biotin-cRNA was fragmented by Magnesium-potassium at 94C to generate 35-200 nucleotides cRNA fragments.

scan_protocol: GeneChips were scanned using Affymetrix gcs3000.

data_processing: CEL files were read into R/Bioconductor using the Affy/affyPLM package (Bolstad et al 2003) and RMA (robust multi-array average) intensity in log2 scale was generated for each probe set.

source_name: HepG2 cells treated with 10nM GC1 for 24 hrs

label_protocol: Biotin-labeled cRNAs were generated from total RNA by using MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Ambion, TX), incubation time for all in vitro transcription reactions was 14 hours at 37C.

growth_protocol: HepG2 cells were grown in Dulbecco's modified Eagle's medium (DMEM)-H21 supplemented with 10% fetal bovine serum (FBS), 100 U/mL of penicillin, 0.1 g/L of streptomycin and 4 mmol/L glutamine, under 95% air and 5% CO2 at 37C.

extract_protocol: RNA was isolated with acid guanidinium thiocyanate/phenol/chloroform (Chomczynski and Sacchi 1987) by employing TRIZOL® Reagent (Invitrogen, CA) following manufacture’s instruction.RNA integrity was analyzed by Bioanalyzer (Agilent Technologies, Santa Clara, CA) applying Agilent RNA 6000 Nano kit (Agilent).  Only samples with 28S/18S rRNA ratio = or  ≥ than 1.8 were used.

treatment_protocol: For the gene expression analysis cells were grown to approximately 60-70% confluence, washed with PBS three times and incubated with DMEM supplemented with 10% TH-depleted serum and treated with vehicle or 10nM ligand (T3 or GC-1).

value: hepatoma cells


title: LPA_L_1099


title: HepG2_GC1_rep2

description: HepG2 10nM GC1


title: LPA_L_109


title: LPA_L_1109


title: HepG2_GC1_rep1

description: HepG2 10nM GC1


title: timepoint 11 vs timepoint 14 #2

description: data 11 vs 14.slide #2 ratio

source_name: timepoint 11


title: HepG2_T3_rep3

description: HepG2 10nM T3

source_name: HepG2 cells treated with 10nM T3 for 24 hrs


title: timepoint 12 vs timepoint 13 #1

description: data 12 vs 13.slide #1 ratio

source_name: timepoint 12


title: timepoint 11 vs timepoint 14 #1

description: data 11 vs 14.slide #1 ratio


title: HepG2_control_rep_3

description: HepG2 control

source_name: HepG2 cells treated with vehicle for 24 hrs


title: LPA_L_1092


title: LPA_L_1088


title: HGA_9

city: Aurora

first: Andrew

middle: M

last: Donson

state: CO

institute: CU Anschutz Medical Campus

description: Gene expression data from surgical tumor sample of high grade astrocytoma

hyb_protocol: Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.

data_processing: Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 20,722 genes.

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

extract_protocol:
Tumor samples were snap frozen in liquid nitrogen or transferred to RNAlater immediately after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500).
RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

value: brain tumor (high grade astrocytoma)

tag: genotype

tag: survival (months)


title: LPA_L_1085


title: HepG2_T3_rep2

description: HepG2 10nM T3


title: timepoint 11 vs timepoint 12 #2

description: data 11 vs 12.slide #2 ratio


title: HGA_13


title: HepG2_T3_rep1

description: HepG2 10nM T3


title: LPA_L_108


title: HepG2_control_rep_2

description: HepG2 control


title: LPA_L_1075


title: timepoint 10 vs timepoint 11 #1

description: data 10 vs 11.slide #1 ratio

source_name: timepoint 10


title: timepoint 11 vs timepoint 12 #1

description: data 11 vs 12.slide #1 ratio


title: timepoint 10 vs timepoint 11 #2

description: data 10 vs 11.slide #2 ratio


title: timepoint 12 vs timepoint 13 #2

description: data 12 vs 13.slide #2 ratio


title: LPA_L_1074


title: LPA_L_1080


title: hypothyroid_GC1_rep_4

description:
5613754058_F
hypothyroid mouse GC1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol on the BeadArray Reader

data_processing: Unmodified data obtained from GenomeStudio was background-subtracted and quantile-normalized using the lumi package within R. Only probes aligning to a single gene in the mouse genome as defined by Ensembl, had their signal values background corrected and quantile normalized using lumi.

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep-96 RNA amplificatio kit.

growth_protocol: 12h light-dark cycle, standard rodent chow and water ad libitum

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

treatment_protocol: oral gavage

value: male

tag: age

value: 9 months


title: hypothyroid_GC1_rep_3

description:
5613754058_E
hypothyroid mouse GC1


title: LPA_L_1068


title: timepoint 8 vs timepoint 9 #2

description: data 8 vs 9.slide #2 ratio

source_name: timepoint 8

source_name: timepoint 9


title: hypothyroid_T3_rep_1

description:
5613754020_E
hypothyroid mouse T3


title: hypothyroid_T3_rep_2

description:
5613754020_F
hypothyroid mouse T3


title: hypothyroid_GC1_rep_2

description:
5613754058_D
hypothyroid mouse GC1


title: timepoint 9 vs timepoint 12 #2

description: data 9 vs 12.slide #2 ratio


title: timepoint 9 vs timepoint 10 #1

description: data 9 vs 10.slide #1 ratio


title: timepoint 9 vs timepoint 10 #2

description: data 9 vs 10.slide #2 ratio


title: LPA_L_104


title: LPA_L_1066


title: timepoint 7 vs timepoint 10 #1

description: data 7 vs 10.slide #1 ratio

source_name: timepoint 7


title: GB-associated stromal cells 2

city: Rennes

first: Amandine

last: Etcheverry

address: 2 rue Henri Le Guilloux

country: France

institute: CNRS UMR 6290 - IGDR

description:
GASCs 2
Agilent Feature Extraction file:
251485048385_SLOT01_S01_GE1_105_Dec08_1_1.txt

hyb_protocol: Hybridizations were performed following the manufacturer's recommendations (protocol version 5.7)

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters

source_name: brain

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 350 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Before cell isolation, we removed meninges and visible blood vessels from the biopsy specimens, which were then minced and mechanically dissociated in Dulbecco’s modified Eagles’ medium (DMEM) (Lonza, Verviers, Belgium). Aliquots of the resulting suspension corresponding to samples before culture were stored at -80°C for further analysis by real-time quantitative PCR (Q-PCR) and flow cytometry analysis of DNA. The remainder of the suspension was used to seed T80 flasks (Nunc, Dominique Dutsher, Brumath, France) containing DMEM supplemented with 10% human AB serum (HABS) (EFS, Lyon, France) and 1% antibiotics (Sigma-Aldrich, Saint Quentin Fallavier, France). Cells were grown at 37°C in a humidified incubator, under an atmosphere containing 5% CO2, and the medium was changed twice weekly. Primary cultures were used under passage 10.

extract_protocol: Total RNA was isolated using NucleoSpin RNAII Kit (Macherey-Nagel)

tag: disease state

value: Glioblastoma (GB)

value: stromal cell


title: GB-associated stromal cells 3

description:
GASCs 3
Agilent Feature Extraction file:
251485048430_SLOT01_S01_GE1_105_Dec08_1_3.txt


title: hypothyroid_T3_rep_3

description:
5613754058_A
hypothyroid mouse T3

tag: strain


title: timepoint 7 vs timepoint 10 #2

description: data 7 vs 10.slide #2 ratio


title: timepoint 8 vs timepoint 9 #1

description: data 8 vs 9.slide #1 ratio


title: GB-associated stromal cells 4

description:
GASCs 4
Agilent Feature Extraction file:
251485048431_SLOT04_S01_GE1_105_Dec08_1_3.txt


title: hypothyroid_GC1_rep_1

description:
5613754058_C
hypothyroid mouse GC1

tag: tissue


title: hypothyroid_ctrl_rep_4

description:
5613754020_D
hypothyroid mouse control


title: HepG2_control_rep_1

description: HepG2 control


title: timepoint 9 vs timepoint 12 #1

description: data 9 vs 12.slide #1 ratio


title: GB-associated stromal cells 1

description:
GASCs 1
Agilent Feature Extraction file:
251485048375_SLOT03_S01_GE1_105_Dec08_1_2.txt


title: hypothyroid_ctrl_rep_3

description:
5613754020_C
hypothyroid mouse control


title: timepoint 13 vs timepoint 16 #2

description: data 13 vs 16.slide #2 ratio


title: hypothyroid_ctrl_rep_1

description:
5613754020_A
hypothyroid mouse control


title: hypothyroid_ctrl_rep_2

description:
5613754020_B
hypothyroid mouse control


title: control stroma cells 1

description:
control cells 1
Agilent Feature Extraction file:
251485048385_SLOT01_S01_GE1_105_Dec08_1_4.txt

value: control


title: euthyroid_T3_rep_1

description:
4818387008_F
euthyroid mouse T3


title: timepoint 7 vs timepoint 8 #2

description: data 7 vs 8.slide #2 ratio


title: control stroma cells 3

description:
control cells 3
Agilent Feature Extraction file:
251485048431_SLOT04_S01_GE1_105_Dec08_1_2.txt


title: timepoint 7 vs timepoint 8 #1

description: data 7 vs 8.slide #1 ratio


title: euthyroid_T3_rep_5

description:
4818387020_A
euthyroid mouse T3


title: timepoint 13 vs timepoint 16 #1

description: data 13 vs 16.slide #1 ratio


title: timepoint 5 vs timepoint 8 #2

description: data 5 vs 8.slide #2 ratio

source_name: timepoint 5


title: euthyroid_GC1_rep_4

description:
4818387005_B
euthyroid mouse GC1


title: euthyroid_GC1_rep_3

description:
4818387032_B
euthyroid mouse GC1


title: euthyroid_GC1_rep_5

description:
4818387020_B
euthyroid mouse GC1


title: control stroma cells 2

description:
control cells 2
Agilent Feature Extraction file:
251485048386_SLOT02_S01_GE1_105_Dec08_1_1.txt


title: Retina U2 STZ

city: Irvine

first: Stefanie

middle: J

last: Kirwin

address: 18655 Teller Ave

department: Biological Sciences

institute: Allergan, Inc.

description: Retina U2

hyb_protocol: 2 µg of purified cRNA was fragmented to uniform size and applied to Agilent Whole Rat Genome microarrays in hybridization buffer. All fragmented samples were visualized on the Agilent Bioanalyzer to verify complete fragmentation to ~0.1 kb size before the sample was applied to the array.  Arrays were hybridized at 65° C for 17 hrs. in a shaking incubator and washed at 37° C for 1 min.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2565 Microarray Scanner at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) using protocol GE1-v5_91_0806 and Grid: 014879_D_20060807

organism: Rattus norvegicus

label_protocol: Cyanine-3-CTP cRNA was prepared by linear amplification of the Poly(A)+ RNA population within the total RNA sample. <1 µg of total RNA was reverse transcribed after priming with a DNA oligonucleotide containing the T7 RNA polymerase promoter 5’ to a d(T)24 sequence.  After second-strand cDNA synthesis and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase in the presence of Cy3-CTP.  The quantity and quality of the cRNA was assayed by spectrophotometry and on the Agilent Bioanalyzer.

extract_protocol: RNA isolation was performed using RiboPure RNA isolation (Ambion) according to the manufacturer's instructions.

treatment_protocol: Male Long Evans rats were rendered diabetic by intraperitoneal injection of 65 mg/kg bodyweight streptozotocin (STZ) in 0.09 M citrate buffer pH 4.8.  Age matched control rats were injected with buffer only. Rats with blood glucose levels above 250 mg/dl after 48h were deemed diabetic. Those that remained normoglycemic after STZ treatment were used as normoglycemic STZ controls. One retina each from three individual rats was removed, immediately transferred to RNAlater (Ambion, Austin, TX), and the pooled sample incubated overnight at 4 °C. Excess RNAlater was then removed and the samples stored at -70 °C.

value: Long Evans

value: retina

value: STZ

tag: diabetes status

value: hyperglycemic

tag: days post-stz injection


title: Retina_Xb STZ-non-c

value: normoglycemic


title: euthyroid_T3_rep_4

description:
4818387005_A
euthyroid mouse T3


title: euthyroid_T3_rep_3

description:
4818387032_A
euthyroid mouse T3


title: timepoint 6 vs timepoint 7 #2

description: data 6 vs 7.slide #2 ratio

source_name: timepoint 6


title: timepoint 5 vs timepoint 8 #1

description: data 5 vs 8.slide #1 ratio


title: Retina X (775) STZ-non-c

description: Retina X (775)


title: timepoint 6 vs timepoint 7 #1

description: data 6 vs 7.slide #1 ratio


title: Retina U3 STZ

description: Retina U3


title: Retina S3 Control

description: Retina S3


title: GBM_12


title: Retina S2 Control

description: Retina S2


title: timepoint 3 vs timepoint 6 #2

description: data 3 vs 6.slide #2 ratio

source_name: timepoint 3


title: euthyroid_T3_rep_2

description:
4818387006_A
euthyroid mouse T3


title: euthyroid_GC1_rep_1

description:
4818387006_B
euthyroid mouse GC1


title: SW480 cells, biological rep3

city: Guangzhou

first: Jianming

last: Li

address: Guangzhou North Road

country: China

institute: Southern Medical University

description: Gene expression data

hyb_protocol: Following fragmentation, The biotinylated cRNA were fragmented at 94℃ for 35 min and hybridized to human Genome U133 Plus 2.0 gene chip array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000.

data_processing: The hybridization data were analyzed using GeneChip Operating software (GCOS 1.4). The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of GCOS 1.4. A global scaling procedure was performed to normalize the different arrays using dChip software.

source_name: colorectal cancer cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5–10 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum and 100 U/ml penicillin/streptomycin. All cell lines were maintained in humidified chamber with 5% CO2 at 37°C.

extract_protocol: Total RNA was isolated with RNeasy Mini Kit (Qiagen, Chatswort, CA)

treatment_protocol: A subpopulation named as M5 with enhanced metastatic abilities to liver was isolated by in vivo selection of SW480 cells

tag: parent cell

tag: relatively low metastatic abilities to liver


title: euthyroid_ctrl_rep_4

description:
4818387008_D
euthyroid mouse control


title: M5 cells, biological rep2

description: Gene expression data

tag: A subpopulation named as M5 with enhanced metastatic abilities to liver

tag: enhanced metastatic abilities to liver


title: Retina Q1_LE M d7 Treated Ctrl STZ-non-c

description: Retina Q1_LE M d7 Treated Ctrl

tag: treatment

tag: gender


title: M5 cells, biological rep1

description: Gene expression data


title: euthyroid_GC1_rep_2

description:
4818387006_C
euthyroid mouse GC1


title: Retina P1 Control

description: Retina P1


title: Retina S1 Control

description: Retina S1


title: Retina U1 STZ

description: Retina U1


title: timepoint 3 vs timepoint 6 #1

description: data 3 vs 6.slide #1 ratio


title: euthyroid_ctrl_rep_5

description:
4818387008_E
euthyroid mouse control


title: Retina P3 Control

description: Retina P3


title: Retina O3 STZ

description: Retina O3


title: euthyroid_ctrl_rep_3

description:
4818387008_C
euthyroid mouse control


title: euthyroid_ctrl_rep_2

description:
4818387008_B
euthyroid mouse control


title: timepoint 5 vs timepoint 6 #2

description: data 5 vs 6.slide #2 ratio


title: M5 cells, biological rep3

description: Gene expression data


title: timepoint 5 vs timepoint 6 #1

description: data 5 vs 6.slide #1 ratio


title: Retina P2 Control

description: Retina P2


title: timepoint 1 vs timepoint 4 #2

description: data 1 vs 4.slide #2 ratio

source_name: timepoint 1

source_name: timepoint 4


title: SNRK_3

city: Chicago

first: Amy

last: Rines

state: IL

address: 303 E. Chicago Ave.  Tarry 14-735

institute: Northwestern University

description: replicate 3

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed using the Bioconductor lumi package to conduct variance stabilization and robust spline normalization.

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

growth_protocol: HEK293 cells were grown in ATCC MEM media supplemented with 10% FBS, 0.01% sodium pyruvate, 100 units/mL penicillin, and 100 μg/mL streptomycin

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent 2100 Bioanalyser.

treatment_protocol: HEK293 were transfected with human SNRK-pEGFPN3 or pEGFPN3 using Lipofectamine with Plus Reagent at a Lipofectamine:DNA ratio of 2:1, then incubated for 48 hours prior to RNA exraction

tag: cell line

tag: genotype/variation

value: tranfected with SNRK-pEGFPN3


title: timepoint 4 vs timepoint 5 #1

description: data 4 vs 5.slide #1 ratio


title: timepoint 1 vs timepoint 4 #1

description: data 1 vs 4.slide #1 ratio


title: timepoint 4 vs timepoint 5 #2

description: data 4 vs 5.slide #2 ratio


title: Retina O2 STZ

description: Retina O2


title: euthyroid_ctrl_rep_1

description:
4818387008_A
euthyroid mouse control

value: liver


title: SNRK_2

description: replicate 2


title: Retina H2 Control

description: Retina H2


title: timepoint 3 vs timepoint 4 #2

description: data 3 vs 4.slide #2 ratio

value: strain 168


title: timepoint 3 vs timepoint 4 #1

description: data 3 vs 4.slide #1 ratio


title: Retina H1 Control

description: Retina H1


title: Retina O1 STZ

description: Retina O1


title: SNRK_1

description: replicate 1


title: SW480 cells, biological rep2

description: Gene expression data


title: Retina H3 Control

description: Retina H3


title: GFP_3

description: replicate 3

value: tranfected with pEGFPN3


title: Splenic_CD11b+_dendritic_cells_RBPJnull_Esam(lo)

city: New York

first: Boris

last: Reizis

state: NY

department: Microbiology and Immunology

institute: Columbia University Medical Center

hyb_protocol: Samples were hybridized to microarrays in GeneChip Hybridization Oven 640 (Affymetrix) at 45C for 16 hours, and microarrays were washed in GeneChip Fluidics station 450 (Affymetrix).

scan_protocol: Microarrays were scanned using GeneChip 3000 7G scanner (Affymetrix) using Command Console as a scanning software.

data_processing: Data were processed using Expression Console software of the scanner and normalized using RMA algorithm.

source_name: Splenic CD11b+ dendritic cells, Esam(lo) subset, RBPJ-deficient

label_protocol: Samples were amplified using Ambion WT expression kit (Ambion) and labeled using GeneChip WT Terminal Labeling and Controls Kit (Affymetrix) according to manufacturer's instructions

extract_protocol: Total RNA was isolated using RNeasy columns (Qiagen)

value: RBPJflox/flox CD11c-Cre Cx3cr1-GFP

tag: organ

value: spleen

tag: cell population

value: CD11c(high) CD11b+ Esam(lo) GFP(hi)


title: A549-VC

city: Nagoya

first: Osada

last: Hirotaka

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

country: Japan

institute: Aichi Cancer Center Research Institute

hyb_protocol: see miRNA Labeling and Microarray Hybricization Protocol Version 0.1 (Agilent Technologies)

scan_protocol: Human miRNA Microarray was scanned using an Agilent DNA microarray scanner (G2505B, Agilent Technologies). Images were quantified using Agilent Feature Extraction Software.

data_processing: Raw data was normalized by a 75 percentile shift.

source_name: vector control in A549

extract_protocol: Total RNA was extracted using the miRNeasy Mini kit (Qiagen).


title: SW480 cells, biological rep1

description: Gene expression data


title: Splenic_CD11b+_dendritic_cells_control_Esam(lo)

source_name: Splenic CD11b+ dendritic cells, Esam(lo) subset, control


title: timepoint 2 vs timepoint 1 #2

description: data 2 vs 1.slide #2 ratio

source_name: timepoint 2


title: A549_premiR-375_96h

hyb_protocol: Cy5-sample cRNA and Cy3-sample cRNA were generated and hybridized to a Whole Human Genome oligo DNA microarray kit (Agilent Technologies) with 41000 distinct probes.

scan_protocol: Whole Human Genome oligo DNA microarray with 41000 distinct probes was scanned using an Agilent DNA microarray scanner (G2505B, Agilent Technologies). Images were quantified using Agilent Feature Extraction Software.

data_processing: LOWESS normalized, background subtracted VALUE data obtained from ratio of processed Red signal/processed Green signal using Agilent Feature Extraction Software (version A.7.5.1).

source_name: trasfected with premiR-375 in A549

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen, Valencia, CA), followed by treatment with DNase I. Double-stranded cDNA was synthesized from 500 ng of total RNA using MMLV-RT and poly dT primer incorporating the T7 promoter.

tag: transfection time

source_name: trasfected with premiR-NC in A549


title: timepoint 2 vs timepoint 3 #2

description: data 2 vs 3.slide #2 ratio


title: A549_premiR-375_48h

label_protocol: Cy5-sample cRNA and Cy3-sample cRNA were generated and hybridized to a Whole Human Genome oligo DNA microarray kit (Agilent Technologies) with 41000 distinct probes.


title: GFP_2

description: replicate 2


title: Retina G3 STZ

description: Retina G3

value: male


title: timepoint 2 vs timepoint 1 #1

description: data 2 vs 1.slide #1 ratio


title: 3A-25 clone 1-1

city: Jerusalem

first: Amir

last: Eden

address: Givat Ram

department: Cell & Developmental Biology

country: Israel

institute: Hebrew University

description: DNA methylation profiling of WI-38 fibroblasts

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

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

data_processing: GenomeStudio v2009.1 Methylation (M) module 1.1.1

label: Cy5, Cy3

source_name: Cultured WI-38 fibroblasts

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using standard techniques and purified using Qiagen DNeasy Kit according to standard instructions

tag: cell type

value: fibroblasts

tag: sample type

value: subclone derived passage 25 of clone 3 by subcloning passage 25 cells.p16 is silenced and partially methylated


title: Retina G2 STZ

description: Retina G2

tag: strain


title: timepoint 1 vs timepoint 2 #2

description: data 1 vs 2.slide #2 ratio


title: A549_premiR-375_12h


title: timepoint 2 vs timepoint 3 #1

description: data 2 vs 3.slide #1 ratio


title: timepoint 1 vs timepoint 2 #1

description: data 1 vs 2.slide #1 ratio


title: Retina G1 STZ

description: Retina G1

tag: tissue


title: 3B-26 clone 1

value: subclone derived passage 26 of clone 3 by subcloning passage 26 cells. p16 is silenced and partially methylated


title: A549-ASH1

source_name: infected with ASH1-lentivirus in A549

label_protocol: see miRNA Labeling and Microarray Hybricization Protocol Version 0.1 (Agilent Technologies)


title: A549_premiR-375_24h


title: WI-38 7-2

value: subclone derived from passage 33 WI-38 hTert immortalized. Has silencesd and methylated p16


title: GFP_1

description: replicate 1


title: WI-38 Clone 3

value: subclone derived from tert hTert immortalized pool (p18h pool) experesses p16 and not methylated


title: HealthyControl_N9

status: Public on Oct 30 2011

city: Navi Mumbai

first: Manoj

middle: Balkrishna

last: Mahimkar

state: Maharashtra

address: Sector-22, Owe Village, Kharghar Node

country: India

institute: Cancer Research Institute, Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre

description: Gene expression of normal oral cavity tissue

hyb_protocol: 1650ng of cy3 labeled samples were fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent's Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1)

data_processing: The normalization was done using GeneSpring GX 11 Software. Recommended Percentile Shift Normalization and samples normalized with respect to control samples. Significant genes up and down regulated showing one fold and above among the groups was identified. Differentially regulated genes were clustered using hierarchical clustering to identify significant expression patterns.

source_name: Oral Normal Tissue

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

extract_protocol: RNA was prepared using the Qiagen RNeasy mini kit (Qiagen GmbH, Hilden) following the manufacturer's recommendations. RNA was quantified using NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Freshly collected oral tissues from oral cancer patients and healthy donors were kept at -80°C till RNA was extracted.

value: Oral Cavity - normal

tag: age

value: Male

tag: site

value: Oral Cavity

tag: stage


title: WI-38 primary culture

value: WI-38 primary culture passage 18


title: Splenic_CD11b+_dendritic_cells_control_Esam(hi)

source_name: Splenic CD11b+ dendritic cells, Esam(hi) subset, control

value: CD11c(high) CD11b+ Esam(hi) GFP(lo)


title: HealthyControl_N8

value: Female


title: HealthyControl_N6


title: HealthyControl_NP

description: Gene expression of pooled normal tissue from oral cavity

value: Pooled RNA

value: Pooled RNA (5 Males + 4 Females)


title: LSK WT CONTROL REP2

city: MADRID

first: Lorena

last: Arranz

address: MELCHOR FERNANDEZ ALMAGRO

department: CARDIOVASCULAR DEVELOPMENT AND REPAIR

institute: CNIC

hyb_protocol: Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of labeled extract used: ~190-250 ng. Volume: 40 uL, Temperature: 65C, Duration: 40 hours.

scan_protocol: Scanned on an G2505C DNA microarray scanner (Agilent). Images were quantified using Agilent Feature Extraction Software (ver. 10.7).

data_processing: Hybridized microarray images were analyzed and backgound subtracted with Agilent FeatureExtraction (FE) Software. Raw data was subsequently normalized with GeneSpring software.  Threshold raw signals to 1, Log base2 transformation, Global intra-array normalization (normalization of the distribution of the overall expression level of all genes for each sample, which is assumed to be constant): Shift to 75.0 percentile, Baseline Transformation: the value per-gene in each sample is centered by subtracting the median for that same gene in all samples. The term ''raw'' signal values refer to the linear data after thresholding and summarization. ''Normalization'' comprises log transformation, intra-array quantile normalization (to 75th percentile of all measurements from the same array) and per-gene transformation (signal from each probe in the array to the median of the corresponding signals across all arrays).  [More details on the analysis are provided as Series supplementary files: analysis.pdf & analysis_result.xls]

source_name: LSK WT CONTROL

label_protocol: Amount of nucleic acid labeled: 250ng. Commercial Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis. ULS Labeling for Blood, Cells, Tissues or FFPE (with a High Throughput option) version 3.2 kit was used. Recommendations from Sigma-Aldrich for the integration of TransPlex WTA with the Agilent microarray workflow were followed, such as the omission of Cot-1 DNA. Briefly, cDNA is non-enzymatically labeled with ULS technology (Kreatech), in which a platinum dye complexed with Cy3 fluorophore couples preferentially with guanine molecules of the sample. Labeled samples are purified with gel filtration columns.

extract_protocol: Total RNA fraction. RNA Integrity Numbers were in the range 9.1 to 10.0 when assayed by Lab-chip technology on an Agilent 2100 Bioanalyzer. Available RNA amounts in the range of 3-27 ng were subjected to a preliminary amplification step with a TransPlex Whole Transcriptome Amplification WTA2 kit (Sigma-Aldrich). Optimal cycle number was set at 17, by proceeding 2–3 cycles beyond the amplification “plateau” as observed with real-time qPCR.

tag: strain background

value: control wild type mice

value: LSK cells


title: LSK WT CONTROL REP1


title: HealthyControl_N4


title: LSK WT CONTROL REP3


title: LSK BMI1-KO REP2

source_name: LSK BMI1-KO

value: Bmi1 cKO mice


title: Patient_OC1418

description: Gene expression of oral cancer tissue

source_name: Oral Tumor Tissue

value: Oral Tumor


title: Patient_OC1367

description: Gene expression of oral cancer tissue


title: Patient_OC1501

description: Gene expression of oral cancer tissue


title: Patient_OC1496

description: Gene expression of oral cancer tissue


title: Patient_OC1508

description: Gene expression of oral cancer tissue


title: Patient_OC1331

description: Gene expression of oral cancer tissue


title: Impaired 5

city: Hershey

first: Penn State

last: COM

state: PA

address: 500 University Drive

department: Genome Sciences Facility

institute: Penn State College of Medicine

description:
5022655028_J
Replicate 5 of 7.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization in GenomeStudio v1.0.6.

source_name: hippocampus, cognitively impaired

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep kit for Illumina arrays.  Cy3-Streptavidin was incorporated during the Wash and Block protocol as a fluor for scanning.

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

value: Fischer 344 x Brown Norway (F1)

value: hippocampus

value: synaptosomes

value: 28 months

tag: group

value: aged cognitively impaired


title: Patient_OC1663

description: Gene expression of oral cancer tissue


title: Patient_OC1667

description: Gene expression of oral cancer tissue


title: Patient_OC1426

description: Gene expression of oral cancer tissue


title: Impaired 7

description:
5022655028_L
Replicate 7 of 7.


title: Impaired 6

description:
5022655028_K
Replicate 6 of 7.


title: Patient_OC1726

description: Gene expression of oral cancer tissue


title: Patient_OC1507

description: Gene expression of oral cancer tissue


title: Patient_OC1665

description: Gene expression of oral cancer tissue


title: Patient_OC1664

description: Gene expression of oral cancer tissue


title: Patient_OC1405

description: Gene expression of oral cancer tissue


title: LSK BMI1-KO REP1


title: Patient_OC1662

description: Gene expression of oral cancer tissue


title: Patient_OC1750

description: Gene expression of oral cancer tissue


title: Impaired 4

description:
5022655028_I
Replicate 4 of 7.


title: Patient_OC1371

description: Gene expression of oral cancer tissue


title: Patient_OC1658

description: Gene expression of oral cancer tissue


title: Patient_OC1718

description: Gene expression of oral cancer tissue


title: Impaired 2

description:
5022655028_E
Replicate 2 of 7.


title: Patient_OC1649

description: Gene expression of oral cancer tissue


title: Patient_OC1645

description: Gene expression of oral cancer tissue


title: 6hrs light replica 1

city: Trieste

first: Diana

middle: Eva

last: Bedolla Orozco

address: Via Bonomea 265

department: Neurobiology

country: Italy

institute: International School for Advanced Studies - SISSA

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

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

data_processing: R/Bioconductor

source_name: retinas collected at 1pm from rats kept all night in dark and then exposed to 3 hours of 1000 lux light

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

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

treatment_protocol: 3 or 6 hours of light exposure (1000 Lux).

value: retina

value: Long-Evans


title: Patient_OC1653

description: Gene expression of oral cancer tissue

value: Male

value: Oral Cavity


title: Patient_OC1656

description: Gene expression of oral cancer tissue


title: Impaired 1

description:
5022655028_C
Replicate 1 of 7.


title: Intact 6

description:
5022655028_A
Replicate 1 of 5.

source_name: hippocampus, cognitively intact

value: aged cognitively intact


title: Patient_OC1644

description: Gene expression of oral cancer tissue

value: Female


title: Intact 12

description:
5022655028_G
Replicate 5 of 5.


title: Intact 8

description:
5022655028_B
Replicate 2 of 5.


title: Patient_OC1652

description: Gene expression of oral cancer tissue


title: Patient_OC1666

description: Gene expression of oral cancer tissue


title: Patient_OC1651

description: Gene expression of oral cancer tissue


title: 3hrs light replica 2

source_name: retinas collected at 10am from rats kept all night in dark and then exposed to 3 hours of 1000 lux light


title: 6hrs dark replica 1

source_name: retinas collected at 1pm from rats kept all night in dark

value: 1pm from rats kept all night in dark


title: 6hrs light replica 2

value: 1pm from rats kept all night in dark and then exposed to 3 hours of 1000 lux light


title: 6hrs dark replica 2


title: Intact 9

description:
5022655028_D
Replicate 3 of 5.


title: 3hrs light replica 1

value: 10am from rats kept all night in dark and then exposed to 3 hours of 1000 lux light


title: 3hrs light replica 3


title: Intact 11

description:
5022655028_F
Replicate 4 of 5.


title: 6hrs dark replica 3


title: Adult 9

description:
5022655003_I
Replicate 5 of 5.

source_name: hippocampus, adult

value: 12 months

value: adult


title: 3hrs dark replica 3

source_name: retinas collected at 10am from rats kept all night in dark

value: 10am from rats kept all night in dark


title: 6hrs light replica 3


title: Impaired 3

description:
5022655028_H
Replicate 3 of 7.

value: Fischer 344 x Brown Norway (F1)


title: 3hrs dark replica 2


title: t0 replica 3

source_name: retinas collected at 7am from rats kept all night in dark

value: 7am from rats kept all night in dark


title: Adult 6

description:
5022655003_G
Replicate 3 of 5.

value: hippocampus

value: synaptosomes


title: Adult 5

description:
5022655003_F
Replicate 2 of 5.


title: t0 replica 1


title: Prolin_rep1

city: Wuerzburg

first: Patrick

last: Olbermann

address: Josef-Schneider-Strasse 2

department: Research Center for Infectious diseases research

institute: University of Wuerzburg

hyb_protocol: Hybridisation was carried by the manufacturer (febit) out using labelled cRNA

scan_protocol: Scanning was done using Geniom® RT analyzer

data_processing: Data processing was done using Geniom® RT analyzer software, background correction lead to flagging of spots not reaching pre processing criteria vsn normalization was used for signal normalization, replicate spots spots were processed for combined mean intensities

label: biotin/ streptavidin-phycoerythrin

organism: Aspergillus fumigatus

source_name: mycelium

label_protocol: SAPE-labelling was done according to febit Protocol 019 by the manufacturer of the microarray, weak signals were enhanced using consectuvie signal enhancement technology (see febit Protocol 010)

growth_protocol: A. fumigatus liquid media shifts were performed according to ref. (Narendja et al.,  2002) with minor modifications: 200 ml minimal medium base with 5 mM ammonium  tartrate was inoculated with 108 freshly harvested, 5 day old A. fumigatus ATCC 46645  conidia and grown at 37°C and 150 rpm for 16 hours. This pre-culture was then harvested,  washed liberally with sterile saline and divided into mycelial masses of equal size on a sterile  surface. The portions were then added to 100 ml of minimal medium base without nitrogen  source. After addition of 1% glucose, flasks were  incubated for 20 min at 37°C. Thereafter, one of the following sterile nitrogen sources was  added: ammonium tartrate to a final concentration of 5 mM,  1 g  proline suspended in 2 ml minimal medium base, or 0.5 g BSA (Albumin Fraktion V, Roth),  suspended in 15 ml minimal medium base. The cultures were incubated for 60  Minutes, then harvested.

extract_protocol: Total RNA was extracted using Trizol® (Invitrogen)

treatment_protocol: Cultures were  harvested by filtering through Miracloth, snap frozen in liquid nitrogen, and ground using a cooled mortar to obtain a fine powder.


title: NO3_rep2


title: Adult 8

description:
5022655003_H
Replicate 4 of 5.


title: 3hrs dark replica 1


title: BSA_rep1


title: t0 replica 2


title: BSA_rep2


title: 5-hmC-mediated epigenetic dynamics (P7.1) [mRNA]

city: Atlanta

first: Keith

middle: E

last: Szulwach

state: GA

address: 615 Michael Street, Whitehead Suite 301

department: Human Genetics

institute: Emory University

description:
P7.1
P7.1_(MoEx-1_0-st-v1).CEL
5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging

hyb_protocol: Hybridization performed according to Affymetrix P/N 701880 Rev.5

scan_protocol: Washing, staining, and scanning performed according to Affymetrix P/N 702731 Rev 3

data_processing:
CEL intensity files were processed by RMA using Affymetrix Power Tools, distributed through AltAnalyze6, using core probes with DABG p-values <0.05, and a raw expression threshold of 70
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoGene-1_0-st-v1.na28.mm9.transcript.csv

source_name: C57/BL6 Cerebellum

label_protocol: Biotinylated sense strand cDNA was generated with the GeneChip WT Terminal Labeling Kit according to Affymetrix P/N 701880 Rev.5

extract_protocol: Total RNA from mouse brain tissues was isolated with TRIzol. Quantity and quality were determined by Agilent 2100 bioanalyzer RNA Nano assay. Prior to cDNA synthesis, ribosomal RNAs (rRNA) were removed form 1ug total RNA using the RiboMinus Transcriptome Isolation Kit (Invitrogen, Cat# K1550-01) and rRNA-reduced total RNA was cleaned with IVT cRNA Clean Up Kit (Affymetrix, P/N900547). Removal of rRNA from the total RNA was confirmed by Agilent Bioanalyzer 2100 mRNA Nano assay.


title: NH4_rep1


title: Adult 4

description:
5022655003_E
Replicate 1 of 5.


title: Prolin_rep2


title: 5-hmC-mediated epigenetic dynamics (P7.3) [mRNA]

description:
P7.3
P7.3_(MoEx-1_0-st-v1).CEL
5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging


title: HCEC

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

institute: National Center for Child Health and Development

description: Gene expression data from primary human corneal endothelial cells

hyb_protocol: Biotinylated cRNA was hybridized with a probe array for 16h at 45C, and the hybridized biotinylated cRNA was stained with streptavidin-PE.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner (Palo Alto).

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

source_name: Primary human corneal endothelial cells

label_protocol: Biotin-labelled.

growth_protocol: The corneal piece, which was grossly normal with no pathological lesions, was cut 1.5 mm from the corneal limbus, avoiding contamination of the trabecular meshwork tissue. HCEC with Descemet's membrane were stripped from the posterior surface of the corneal tissue with sterile surgical forceps under a dissecting microscope. They were cut into 2 pieces and cultured in a cell culture dish covered with Type IV collagen in a growth medium (GM); Dulbecco's modified Eagle's medium (DMEM)/Nutrient mixture F12 (1:1) with high glucose supplemented with 10% fetal bovine serum, insulin-transferrin-selenium and MEM-NEAA (Gibco, Auckland, NZ).

extract_protocol: Total RNA was extracted from 2 x 10E6 cultured HCEC using the RNeasy Plus mini-kitH (Qiagen, Germantown/Gaithersburg, MA) according to the manufacturer's instructions and quantified by absorption at 260 nm.

treatment_protocol: Lentiviral vector plasmids, CSII-CMV-cyclin D1 and -CDK4R24C were constructed by recombination using the Gateway system (Invitrogen, Carlsbad, CA).The recombinant retrovirus vector plasmids, pCLXSN-16E6E7 encoding HPV16 E6/E7 (16E6E7) was produced. Stably transduced cells with an expanded life span were designated transduced human corneal endothelial cell by E6/E7 (THCEC (E6/E7) ) and transduced human corneal endothelial cell by Cdk4R24C/cyclinD1 (THCEH (Cyclin) ).

value: Cornea

value: corneal endothelial

value: non-transduced (primary)


title: 5-hmC-mediated epigenetic dynamics (6wk.1) [mRNA]

description:
6wk.1
6wk.1_(MoEx-1_0-st-v1).CEL
5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging


title: THCEH (cyclin)

description: Gene expression data from human corneal endothelial cells transduced by Cdk4R24C/CyclinD1

source_name: Transduced human corneal endothelial cells

value: transduced by Cdk4R24C/CyclinD1


title: 5-hmC-mediated epigenetic dynamics (P7.2) [mRNA]

description:
P7.2
P7.2_(MoEx-1_0-st-v1).CEL
5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging


title: 5-hmC-mediated epigenetic dynamics (6wk.3) [mRNA]

description:
6wk.3
6wk.3_(MoEx-1_0-st-v1).CEL
5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging


title: NH4_rep2


title: 5-hmC-mediated epigenetic dynamics (6wk.2) [mRNA]

description:
6wk.2
6wk.2_(MoEx-1_0-st-v1).CEL
5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging


title: NO3_rep1


title: T3_Ei_LG_48hrs_(Eh_Eia520620F_Ei), biological replicate 3

status: Public on Oct 29 2011

city: Shnjuku

first: Ghulam

last: Jeelani

department: Parasitology

institute: National Institute of Infectious Diseases

description: Gene expression data from Entamoeba invadens cell harvested at 48hrs when cultured in 47% LG media

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Eh_Eia520620F_Ei Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned with an Affymetrix GeneChip Scanner 3000

data_processing: Raw probe intensities were generated by the GeneChip Operating Software (GCOS) and GeneTitan Instrument. Resulting expression values were analyzed by Genespring GX 10.0.2 to identify differentially expressed genes.

organism: Entamoeba invadens

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: wild type Entmoeba invadens was grown in 47% LG media.

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

tag: amoeba

value: wild-type

value: cultured in 47% LG media

tag: time point


title: THCEC (E6/E7)

description: Gene expression data from human corneal endothelial cells transduced by human papillomavirus type E6/E7


title: T2_Ei_LG_120hrs_(Eh_Eia520620F_Ei), biological replicate 2

description: Gene expression data from Entamoeba invadens cell harvested at 120hrs when cultured in 47% LG media

tag: treatment


title: T1_Ei_LG_120hrs_(Eh_Eia520620F_Ei), biological replicate 1


title: T2_Ei_LG_48hrs_(Eh_Eia520620F_Ei), biological replicate 2


title: T3_Ei_LG_120hrs_(Eh_Eia520620F_Ei), biological replicate 3


title: T2_Ei_LG_24hrs_(Eh_Eia520620F_Ei), biological replicate 2

description: Gene expression data from Entamoeba invadens cell harvested at 24hrs when cultured in 47% LG media


title: T2_Ei_LG_2hrs_(Eh_Eia520620F_Ei), biological replicate 2

description: Gene expression data from Entamoeba invadens cell harvested at 2hrs when cultured in 47% LG media


title: T1_Ei_LG_2hrs_(Eh_Eia520620F_Ei), biological replicate 1


title: T3_Ei_LG_24hrs_(Eh_Eia520620F_Ei), biological replicate 3


title: T1_Ei_LG_48hrs_(Eh_Eia520620F_Ei), biological replicate 1


title: T3_Ei_LG_2hrs_(Eh_Eia520620F_Ei), biological replicate 3


title: T2_Ei_LG_8hrs_(Eh_Eia520620F_Ei), biological replicate 2

description: Gene expression data from Entamoeba invadens cell harvested at 8hrs when cultured in 47% LG media


title: T1_Ei_LG_30min_(Eh_Eia520620F_Ei), biological replicate 1

description: Gene expression data from Entamoeba invadens cell harvested at 30min when cultured in 47% LG media


title: T2_Ei_LG_0hrs_(Eh_Eia520620F_Ei), biological replicate 2

description: Gene expression data from Entamoeba invadens cell harvested at 0hrs when cultured in 47% LG media


title: T2_Ei_LG_30min_(Eh_Eia520620F_Ei), biological replicate 2


title: T3_Ei_LG_8hrs_(Eh_Eia520620F_Ei), biological replicate 3


title: T3_Ei_LG_0hrs_(Eh_Eia520620F_Ei), biological replicate 3


title: T1_Ei_LG_8hrs_(Eh_Eia520620F_Ei), biological replicate 1


title: iCell_10 μM_72 h_rep2

city: Silver Spring

first: Xiugong

last: Gao

address: 503 Robert Grant Ave

institute: Walter Reed Army Institute of Research

description:
iCell_10 uM_72h_2
gene expression data of iCell human cardiomyocytes exposed to 10 μM VX 72 h after exposure

hyb_protocol: Hybridization was carried out using the Affymetrix GeneChip Hybridization, Wash, and Stain Kit following the manufacturer’s protocols.

scan_protocol: The chips were scanned using an Affymetrix GeneChip Instrument System and the image (.DAT) files were processed using the Affymetrix GeneChip Operating Software (GCOS) to generate cell intensity (.CEL) files.

data_processing: The data were averaged and normalized in Partek Genomics Suite 6.5 (Partek, St. Louis, MO) using the robust multiarray analysis (RMA) algorithm.

label_protocol: ~0.1 μg of total RNA were labeled using the Affymetrix (Santa Clara, CA) GeneChip 3’ IVT Express Kit following the manufacturer’s protocol.

growth_protocol: Human iCell cardiomyocytes were seeded in 6-well plates in media formulated by the manufacturer (Cellular Dynamics International, Madison, WI) and cultured at 37 °C under humidified 5% CO2 for 48 h before VX exposure.

extract_protocol: Total RNA was isolated using the RNeasy Plus Mini Kit from Qiagen (Valencia, CA) following the manufacturer’s protocol, including an on-column DNase digestion.

treatment_protocol: VX was added to cell culture at the specified concentrations and maintained for 1 h. Then VX was removed and the culture was washed 3X with fresh medium. The culture was then maintained at 37 °C with 5% CO2 until the indicated time points.

value: iCell cardiomyocytes derived from WA09 human embryonic stem cells


title: T1_Ei_LG_0hrs_(Eh_Eia520620F_Ei), biological replicate 1


title: iCell_10 μM_72 h_rep3

description:
iCell_10 uM_72h_3
gene expression data of iCell human cardiomyocytes exposed to 10 μM VX 72 h after exposure


title: iCell_10 μM_24 h_rep4

description:
iCell_10 uM_24h_4
gene expression data of iCell human cardiomyocytes exposed to 10 μM VX 24 h after exposure


title: T1_Ei_LG_24hrs_(Eh_Eia520620F_Ei), biological replicate 1


title: iCell_10 μM_72 h_rep4

description:
iCell_10 uM_72h_4
gene expression data of iCell human cardiomyocytes exposed to 10 μM VX 72 h after exposure


title: iCell_10 μM_72 h_rep1

description:
iCell_10 uM_72h_1
gene expression data of iCell human cardiomyocytes exposed to 10 μM VX 72 h after exposure


title: iCell_10 μM_24 h_rep1

description:
iCell_10 uM_24h_1
gene expression data of iCell human cardiomyocytes exposed to 10 μM VX 24 h after exposure


title: T3_Ei_LG_30min_(Eh_Eia520620F_Ei), biological replicate 3


title: iCell_10 μM_24 h_rep3

description:
iCell_10 uM_24h_3
gene expression data of iCell human cardiomyocytes exposed to 10 μM VX 24 h after exposure


title: iCell_10 μM_6 h_rep3

description:
iCell_10 uM_6h_3
gene expression data of iCell human cardiomyocytes exposed to 10 μM VX 6 h after exposure


title: iCell_0.1 μM_72 h_rep4

description:
iCell_0.1 uM_72h_4
gene expression data of iCell human cardiomyocytes exposed to 0.1 μM VX 72 h after exposure


title: iCell_10 μM_6 h_rep2

description:
iCell_10 uM_6h_2
gene expression data of iCell human cardiomyocytes exposed to 10 μM VX 6 h after exposure


title: iCell_0.1 μM_72 h_rep3

description:
iCell_0.1 uM_72h_3
gene expression data of iCell human cardiomyocytes exposed to 0.1 μM VX 72 h after exposure


title: iCell_10 μM_6 h_rep1

description:
iCell_10 uM_6h_1
gene expression data of iCell human cardiomyocytes exposed to 10 μM VX 6 h after exposure


title: iCell_10 μM_6 h_rep4

description:
iCell_10 uM_6h_4
gene expression data of iCell human cardiomyocytes exposed to 10 μM VX 6 h after exposure


title: iCell_control_72 h_rep4

description:
iCell_0 uM_72h_4
gene expression data of iCell human cardiomyocytes not exposed to VX at 72 h


title: iCell_0.1 μM_24 h_rep4

description:
iCell_0.1 uM_24h_4
gene expression data of iCell human cardiomyocytes exposed to 0.1 μM VX 24 h after exposure


title: iCell_0.1 μM_6 h_rep4

description:
iCell_0.1 uM_6h_4
gene expression data of iCell human cardiomyocytes exposed to 0.1 μM VX 6 h after exposure


title: iCell_0.1 μM_72 h_rep1

description:
iCell_0.1 uM_72h_1
gene expression data of iCell human cardiomyocytes exposed to 0.1 μM VX 72 h after exposure


title: iCell_0.1 μM_24 h_rep2

description:
iCell_0.1 uM_24h_2
gene expression data of iCell human cardiomyocytes exposed to 0.1 μM VX 24 h after exposure


title: iCell_control_24 h_rep2

description:
iCell_0 uM_24h_2
gene expression data of iCell human cardiomyocytes not exposed to VX at 24 h


title: iCell_0.1 μM_6 h_rep3

description:
iCell_0.1 uM_6h_3
gene expression data of iCell human cardiomyocytes exposed to 0.1 μM VX 6 h after exposure


title: iCell_control_6 h_rep3

description:
iCell_0 uM_6h_3
gene expression data of iCell human cardiomyocytes not exposed to VX at 6 h


title: iCell_control_24 h_rep4

description:
iCell_0 uM_24h_4
gene expression data of iCell human cardiomyocytes not exposed to VX at 24 h


title: iCell_control_24 h_rep1

description:
iCell_0 uM_24h_1
gene expression data of iCell human cardiomyocytes not exposed to VX at 24 h


title: iCell_control_0 h_rep4

description:
iCell_0 uM_0h_4
gene expression data of iCell human cardiomyocytes not exposed to VX at the beginning of experiment


title: iCell_control_72 h_rep1

description:
iCell_0 uM_72h_1
gene expression data of iCell human cardiomyocytes not exposed to VX at 72 h


title: iCell_control_0 h_rep1

description:
iCell_0 uM_0h_1
gene expression data of iCell human cardiomyocytes not exposed to VX at the beginning of experiment


title: iCell_0.1 μM_24 h_rep1

description:
iCell_0.1 uM_24h_1
gene expression data of iCell human cardiomyocytes exposed to 0.1 μM VX 24 h after exposure


title: iCell_0.1 μM_24 h_rep3

description:
iCell_0.1 uM_24h_3
gene expression data of iCell human cardiomyocytes exposed to 0.1 μM VX 24 h after exposure


title: iCell_control_72 h_rep3

description:
iCell_0 uM_72h_3
gene expression data of iCell human cardiomyocytes not exposed to VX at 72 h


title: iCell_0.1 μM_6 h_rep1

description:
iCell_0.1 uM_6h_1
gene expression data of iCell human cardiomyocytes exposed to 0.1 μM VX 6 h after exposure


title: LCL MZ 49b

city: Brisbane

first: Joseph

last: Powell

state: Qld

address: St lucia

department: Queensland Brain Institute

country: Australia

institute: University of Queensland

description: Whole blood samples were collected from MZ twin pairs and processed within 24 hours of collection

hyb_protocol: Expression profiles were generated by hybridising 750ng of cRNA to Illumina HumanHT-12 v3.0 Beadchip according to Illumina whole-genome gene expression direct hybridization assay guide (Illumina Inc, San Diego, USA). Briefly, 500 ng of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridised to an Illumina whole genome expression chip, HumanHT-12 v3.0 for 18 h at 58oC.

scan_protocol: Beadchips were then washed and stained and subsequently scanned to obtain fluorescence intensities using an Illumina Bead Array Reader (BAR). A Latin square design was used to randomise the samples on the chips and chip positions.

data_processing:
Relative expression values were generated for each transcript using Illumina Genome Studio software (Illumina Inc., San Diego). To minimise the influence of overall signal levels, which may reflect RNA quantity and quality rather than a true biological difference between individuals, the following standardisation procedures were used. Background noise detected from negative control beads was subtracted from raw expression values for each transcript. Data were then filtered for gene transcripts that were present in at least 50% of samples at p < 0.05 according to the global-error threshold calculated by Genome Studio’s cross-gene error model. To prevent the introduction of bias between the LCL and WB samples, the raw microarray data from both tissue samples were quantile normalised together. Adjusted expression levels for each transcript were transformed using a quantile transformation to achieve a stabilized variance distribution across average expression levels.
Non-normalised data have just background subtraction from the raw signals. Normalised data has been filtered for  genes significantly expressed in greater than 50% of samples. Values have then been quantile normalized.

source_name: Whole blood was collected directly into ACD (Acid Citrate Dextrose) vacuum tube. Mononucleated cells were isolated using a ficoll gradient and LCL established by Epstein-Barr virus transformation of lymphocytes and stored in liquid nitrogen.

label_protocol: standard Illumina protocol

extract_protocol: Whole blood was collected directly into ACD (Acid Citrate Dextrose) vacuum tube. Mononucleated cells were isolated using a ficoll gradient and LCL established by Epstein-Barr virus transformation of lymphocyte and stored in liquid nitrogen. For RNA isolation, established cell lines were regrown under tightly controlled growth conditions in the same batch of RPMI 1640 media with 10% FCS and antibiotics, to limit the cell culture effects on RNA preparation. Total RNA was extracted from samples using Qiagen RNeasy Midi-Kits (QIAGEN, Valencia, CA), when cells were in log phase growth.

value: Lymphoblastoid Cell Line

tag: twin


title: iCell_control_72 h_rep2

description:
iCell_0 uM_72h_2
gene expression data of iCell human cardiomyocytes not exposed to VX at 72 h


title: iCell_control_6 h_rep4

description:
iCell_0 uM_6h_4
gene expression data of iCell human cardiomyocytes not exposed to VX at 6 h


title: iCell_control_0 h_rep3

description:
iCell_0 uM_0h_3
gene expression data of iCell human cardiomyocytes not exposed to VX at the beginning of experiment


title: iCell_control_6 h_rep2

description:
iCell_0 uM_6h_2
gene expression data of iCell human cardiomyocytes not exposed to VX at 6 h


title: iCell_control_0 h_rep2

description:
iCell_0 uM_0h_2
gene expression data of iCell human cardiomyocytes not exposed to VX at the beginning of experiment


title: iCell_0.1 μM_72 h_rep2

description:
iCell_0.1 uM_72h_2
gene expression data of iCell human cardiomyocytes exposed to 0.1 μM VX 72 h after exposure


title: iCell_control_24 h_rep3

description:
iCell_0 uM_24h_3
gene expression data of iCell human cardiomyocytes not exposed to VX at 24 h


title: LCL MZ 48a


title: LCL MZ 48b


title: iCell_0.1 μM_6 h_rep2

description:
iCell_0.1 uM_6h_2
gene expression data of iCell human cardiomyocytes exposed to 0.1 μM VX 6 h after exposure


title: iCell_control_6 h_rep1

description:
iCell_0 uM_6h_1
gene expression data of iCell human cardiomyocytes not exposed to VX at 6 h


title: LCL MZ 49a


title: LCL MZ 47a


title: LCL MZ 46a


title: LCL MZ 40a


title: LCL MZ 39a


title: LCL MZ 38a


title: LCL MZ 43b


title: LCL MZ 45b


title: LCL MZ 46b


title: LCL MZ 44b


title: LCL MZ 47b


title: LCL MZ 37a


title: LCL MZ 41a


title: LCL MZ 42b


title: LCL MZ 39b


title: LCL MZ 45a


title: LCL MZ 41b


title: LCL MZ 40b


title: LCL MZ 44a


title: LCL MZ 43a


title: LCL MZ 37b


title: LCL MZ 42a


title: LCL MZ 38b


title: LCL MZ 36a


title: LCL MZ 36b


title: LCL MZ 35b


title: LCL MZ 35a


title: LCL MZ 33b


title: LCL MZ 34a


title: LCL MZ 32b


title: LCL MZ 33a


title: LCL MZ 31b


title: LCL MZ 32a