title: VHB1-J=7-set4-Cy5

city: Paris

first: Sandrine

last: Imbeaud

address: 15 rue de l'Ecole de Médecine

department: INSERM UMRS1138-EQUIPE 28, Sorbonne Université-Inserm-Université de Paris

institute: Centre de Recherche des Cordeliers

description:
Quality Controls of RNA samples: Concentration and purity of the RNA preparation was checked first by UV-spectrophotometry using the Ultrospec3100 pro (GE Healthcare, USA) and 5-mm cuvettes. The absorbance (A) was measured from 200 nm to 350 nm. A235, A260, A280 and A320 were determined and A260:A280 ratios were calculated. Quality of each total RNA was measured by microfuidic/capillary electrophoresis using RNA 6000 Nano LabChip® kits with an Agilent 2100 Bioanalyzer (Agilent Technologies, USA), and the results assessed by human inspection and with two-user independent classifiers evaluation as described previously [Imbeaud et al., NAR, 2005]. Only samples that reached the anticipated purity and integrity parameters (RIN >= 6; DegFact <= 13) were introduced within the microarray pipeline process.
Quality Controls of  Cy-Dye target labeling: Purity and concentration of each target was checked by UV spectrophotometry, using the Ultrospec3100 pro and 70-mm cuvettes (GE Healthcare). Based on the absorbance measured at 256 nm, 550 nm and 650 nm and considering extinction factor for Cy3- and Cy5-dye respectively of 0.15 and 0.25, the yield of cDNA synthesis and dye incorporation rate were computed. An aliquot (1 µl) of the purified labeling reaction was loaded onto RNA 6000 Nano Labchip® using a Agilent 2100 Bioanalyzer (Agilent Technologies, USA). The chip was prepared according to the manufacturer’s protocol and a mRNA nano assay was run on the chip. The shape and sizes of the Cy-dye targets were compared with the molecular weight markers. Targets with unsatisfactory yield of incorporation (dye incorporation rate < 10; A256:A550 or 650 < 2) and integrity (size < 200 nucleotides) were removed from subsequent analyses. The shape of the Cy-dye probes should present a smeared profile with no clearly identified additional peaks.

hyb_protocol: A mixture of equimolar aliquots (20 pmol) of each labeled target (DATA and REF) was incubated at 95°C for 4 min in the presence of 1.5 µg Oligo-A80 (Eurogentec, USA) and 1 µg human Cot-I DNA® (Invitrogen, USA). Labeled cDNA was then placed onto 11K_VJF-ARRAY slides in a 30 µl hybridization solution (50% formamide, GE Healthcare, USA) and covered by a coverslip. The slides were subsequently hybridized in a humid hybridization cabinet (GE Healthcare, USA) for 16 hr at 42°C. Then the hybridized slides were washed in 1xSSC, 0.2% SDS for 10 min at 55°C, twice in 0.1x SSC, 0.2% SDS for 10 min at 55°C and twice in 0.1x SSC for 1 min at room temperature.

scan_protocol: After washing and drying, the arrays were scanned at 532 nm (PMT 600 V) and 635 nm (PMT 650 V) using a 3rd generation array scanner (GE Healthcare, USA) and independent grayscale images (8 bits, Tiff) were generated for each pair of samples to be compared.

data_processing: Foreground (raw) data - ARMDens - were local background-subtracted (corners between spots - median value) and normalized using a Lowess (locally weighted linear regression) transformation. The following selection criteria were applied: all spots having a mean signal (after background subtraction) less than that of the background and below that of the negative controls in both Cy3 and Cy5 channels were systematically excluded; the data were also filtered to exclude spots flagged as missing or corrupted in one array. We next calculated the expression ratios (DATA/REF) in all analyses; the provided VALUE corresponds to the log, base 2 ratios. Replicate spots on the array (n=2) are considered separately

label_protocol:
Targets were synthesized using 30.0 µg amplified RNA, 1 µl anchored oligo-(dT) for priming (total volume 11 µl, 10 min, 70°C) in presence of 1 µl spike RNA from Lucidea™ Microarray Human Scorecard v1.1 (GE Healthcare, USA). cDNA products were generated using 1 mM of either Cy3- or Cy5-dCTP (GE Healthcare, USA) and 200 units MMLV RNase H- reverse transcriptase (Promega, USA) at 42°C for 2 to 3 hr. After reverse transcription, the RNA was degraded by adding 2 µl of 2.5 N NaOH and incubating at 37°C for 10 min. The reaction was then neutralized by adding 10 µl of 2 M MOPS (free acid) and Cy3- and Cy5-containing targets were purified twice onto QIAquick PCR columns (Qiagen, Germany) according the manufacturer’s instructions with minor modifications. The Cy-dye targets were controlled during quality assessment (purity, size, yield).
Adjusted Cy-dye target yield was calculated to reflect carryover of unlabeled RNA. Thus, certified targets were air-dried in a vacuum centrifuge for 1.5 hr and resuspended in RNase-free water to reach a 10 pmol/µl concentration.

growth_protocol: Cells were maintained in Dulbecco's modified Eagle's medium (DMEM) with GlutaMAX (Invitrogen Ltd., Paisley, UK), supplemented with 10% foetal calf serum (Perbio Sciences, Helsingborg, Sweden), 100 U/ml penicillin, 100 µg/ml streptomycin in a 5% CO2 incubator.

extract_protocol: Total RNA was extracted from monolayer cells in culture at 2/3 confluency using the RNeasy Mini Kit (Qiagen, Hilden, Germany).

treatment_protocol: Cells were treated with 10 nM Dihydrotestosterone (DHT; Sigma #A8380, St Louis, MO) for 7 days before RNA extraction.

tag: VHB1 cells

extract_protocol: see Provider description

tag: human universal reference RNA


title: VHB1-J=7-set2-Cy5

status: Public on Mar 06 2009

type: RNA

country: France

molecule: total RNA

organism: Homo sapiens


title: VHB1-J=7-set4-Cy3


title: EOM-control-R8

city: Philadelphia

first: Thomas

middle: S

last: Postler

state: PA

address: 421 Curie Boulevard

department: Cell and Developmental Biology

country: USA

institute: University of Pennsylvania

description: In general, recommendations by affymetrix were followed, as described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2)

hyb_protocol: As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 72 - 94.

scan_protocol: As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 95 - 97.

data_processing: Fluorescence was recorded using a GCS3000 laser scanner (Affymetrix) and analyzed with GeneChip Operating Software (GCOS) 1.4 (Affymetrix). Average signal intensities of the arrays were scaled to a default Target Signal Value of 150. No normalization procedure was applied.

label: biotin

organism: Rattus norvegicus

source_name: extraocular muscles, dissected, fresh

label_protocol: 1 ug total RNA was transcribed to ss-cDNA using T7-Oligo(dT) Promoter and Superscript II Reverse Transcriptase. Subsequently, the second strand was confected using DNA Polymerase I (E. coli), in combination with RNA digestion by RNase H. Unincorporated nucleotides were removed by cDNA Cleanup Spin Columns. Finally, cDNA was transcribed in vitro to complementary RNA (cRNA) using T7 RNA Polymerase and NTPs mixed with biotinylated nucleotide analog. Proteins and unincorporated nucleotides were removed by cRNA Cleanup Spin Columns.

extract_protocol: RNA was isolated using TRIzol Reagent (Invitrogen) and purified with RNeasy Mini or Micro Kit (Qiagen), as recommended by manufacturers. SUPERase-IN RNase inhibitor (Ambion) was added to samples in final concentration of 1 U/ul. Stored at -80 degC.

treatment_protocol: Untreated control

tag: Strain

value: Sprague-Dawley

tag: Age category

value: adult


title: EOM-control-R7


title: EOM-hyperthyroid-R2

treatment_protocol: 25 ug T3 per 100 g body weight, administered every second day by intraperitoneal injections for six weeks


title: VHB1-J=7-set2-Cy3


title: VHB1-J=7-set3-Cy5


title: EOM-hyperthyroid-R5


title: VHB1-J=7-set1-Cy3


title: The CH10T1/2 cell line transfected with the R150C variant PTHR1 treated with PTHrP

city: toronto

first: benjamin

last: alman

state: ontario

address: 555 university avenue

department: Developmental and stem cell biology

country: Canada

institute: Hospital for Sick Children

description: The CH10T1/2 cell line was stably transfected with either the R150C variant PTHR1 present in enchondromas (Hopyan, S., Gokgoz, N., Poon, R., Gensure, R. C., Yu, C., Cole, W. G., Bell, R. S., Juppner, H., Andrulis, I. L., Wunder, J. S., and Alman, B. A. (2002). A mutant PTH/PTHrP type I receptor in enchondromatosis. Nat Genet 30, 306-310)  or a wild type PTHR1, as previously reported (Mau, E., Whetstone, H., Yu, C., Hopyan, S., Wunder, J. S., and Alman, B. A. (2007). PTHrP regulates growth plate chondrocyte differentiation and proliferation in a Gli3 dependent manner utilizing hedgehog ligand dependent and independent mechanisms. Dev Biol 305, 28-39).  Cells were grown overnight in serum free media and treated with either 10− 7 M PTHrP (Bachem, King of Prussia, Pennsylvania, USA), or carrier alone for one hour.  RNA was isolated from the cells CH10T1/2 cells expressing either the R150C variant PTHR1 or wild type PTHR1.  RNA was converted to double-stranded cDNA using Superscript (Gibco-Invitrogen) with a T7-(dT)24 primer, which was then transcribed to biotinylated complementary RNA (cRNA) by incorporating biotin-CTP and biotin-UTP using Enzo BioArray High Yield RNA labeling kit (Enzo Diagnostics, New York, NY). The cRNA labeling and hybridizations were then performed according to Affymetrix GeneChip Protocol (Affymetrix Inc., Santa Clara, CA). The chips were scanned for fluorescence signal detection. Affymetrix - GeneChip® Mouse Genome 430A 2.0 Array was utilized.  This data is from cells expressing the mutant PTHR1 treated with PTHrP.

data_processing: Expression console software (Affymetrix)

organism: Mus musculus

source_name: The CH10T1/2 cell line transfected with the R150C variant PTHR1 treated for one hour with PTHrP

growth_protocol: Cells were grown overnight in serum free media and treated with either 10-7 M PTHrP (Bachem, King of Prussia, Pennsylvania, USA), or carrier alone for one hour.

extract_protocol: RNA was extracted using Trisol as per the manufacturer's instructions. RNA was converted to double-stranded cDNA using Superscript (Gibco-Invitrogen) with a T7-(dT)24 primer

treatment_protocol: Cells were grown overnight in serum free media and treated with 10− 7 M PTHrP (Bachem, King of Prussia, Pennsylvania, USA) for one hour.  RNA was isolated from the cells cells

tag: cell line

value: CH10T1/2 fibroblast cell line

tag: agent

value: tranfected with the R150C variant PTHR1 treated for one hour with PTHrP


title: The CH10T1/2 cell line transfected with the R150C variant PTHR1 treated with carrier

description: The CH10T1/2 cell line was stably transfected with either the R150C variant PTHR1 present in enchondromas (Hopyan, S., Gokgoz, N., Poon, R., Gensure, R. C., Yu, C., Cole, W. G., Bell, R. S., Juppner, H., Andrulis, I. L., Wunder, J. S., and Alman, B. A. (2002). A mutant PTH/PTHrP type I receptor in enchondromatosis. Nat Genet 30, 306-310)  or a wild type PTHR1, as previously reported (Mau, E., Whetstone, H., Yu, C., Hopyan, S., Wunder, J. S., and Alman, B. A. (2007). PTHrP regulates growth plate chondrocyte differentiation and proliferation in a Gli3 dependent manner utilizing hedgehog ligand dependent and independent mechanisms. Dev Biol 305, 28-39).  Cells were grown overnight in serum free media and treated with either 10− 7 M PTHrP (Bachem, King of Prussia, Pennsylvania, USA), or carrier alone for one hour.  RNA was isolated from the cells CH10T1/2 cells expressing either the R150C variant PTHR1 or wild type PTHR1.  RNA was converted to double-stranded cDNA using Superscript (Gibco-Invitrogen) with a T7-(dT)24 primer, which was then transcribed to biotinylated complementary RNA (cRNA) by incorporating biotin-CTP and biotin-UTP using Enzo BioArray High Yield RNA labeling kit (Enzo Diagnostics, New York, NY). The cRNA labeling and hybridizations were then performed according to Affymetrix GeneChip Protocol (Affymetrix Inc., Santa Clara, CA). The chips were scanned for fluorescence signal detection. Affymetrix - GeneChip® Mouse Genome 430A 2.0 Array was utilized.  This data is from control cells expressing the mutant PTHR1.

treatment_protocol: Cells were grown overnight in serum free media.  RNA was isolated from the cells at the same time as cells subjected to one hour of PTHrP treatment

value: tranfected with the R150C variant PTHR1 treated with carrier


title: VHB1-J=7-set3-Cy3


title: HCT-116 rep2 expression

city: Stanford

first: Rami

last: Rauch

state: CA

address: 300 Pasteaur Dr

institute: Stanford U

hyb_protocol: Samples were hybridized using manufacturer instructions

scan_protocol: Samples were scanned using manufacturer instructions

data_processing: Array intensities were rank-invariant normalized a

source_name: RNA from HCT116 human cells

label_protocol: Samples were amplified and labeled using standard procedures from the Illumina TotalPrep RNA Kit (Ambion)

extract_protocol: RNA was prepared with Trizol (Invitrogen)

tag: cell type

value: HCT116 human cells


title: VHB1-J=7-set1-Cy5


title: VHB1-J=0-set4-Cy3


title: EOM-hyperthyroid-R3


title: VHB1-J=0-set1-Cy5


title: TA-hyperthyroid-R2

source_name: tibialis anterior, dissected, fresh


title: EOM-hyperthyroid-R1

description: In general, recommendations by Affymetrix were followed, as described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2).


title: VHB1-J=0-set1-Cy3_REP-2.


title: VHB1-J=0-set3-Cy3


title: TA-hyperthyroid-R1


title: VHB1-J=0-set2-Cy5


title: Genomic DNA - 45 day old leaf sample - IR64 wtcheck

type: genomic

city: Los Banos

first: Ramil

middle: Paner

last: Mauleon

state: Laguna

address: IRRI Campus, Pili Drive

department: Crop Research Informatics Laboratory

country: Philippines

institute: International Rice Research Institute

description: Genome hybridization using total DNA from IR64 wildtype

hyb_protocol: Hybridizations were conducted according to Affymetrix standard protocol for eukaryotic target hybridization.  Ten µg of biotinylated fragments were mixed in 200 µl with a final concentration of 0.1 mg/ml sonicated herring sperm DNA in a hybridization buffer with 100 mM 2-N-morpholino-ethane-sulphonic acid (MES), 1 M NaCl, 20 mM EDTA and 0.01% Tween 20, denatured at 99ºC for 5 min and equilibrated at 45ºC for 5 min prior to hybridization.  The hybridization mix was then transferred into the Rice GeneChip® cartridge and hybridized at 45ºC for 16 h.  The hybridized arrays were washed and stained using EukGE-WS2v5_450 protocol with an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: The arrays were scanned twice and the intensities averaged with an Affymetrix GeneChip Scanner 3000 using GCOS 1.4.0.036 software (Affymetrix, Santa Clara, CA).

data_processing:
The "affy" package (R/Bioconductor) was used to extract probe level information and examine diagnostics. Perfect match probe data was scale-normalized to the average of the wild type arrays, using a log2 ratio calculation versus wild type at the probe level.
For arrays with replicates, the average probe level intensity was taken prior to data analysis. Similarly, the wild type average probe level intensity was taken prior to data analysis (note: scale normalization occurs AFTER averaging of the intensity for wild type arrays but BEFORE averaging the replicated mutant arrays (G650 and N1856)).

molecule: genomic DNA

organism: Oryza sativa Indica Group

source_name: 45 day old leaf tissue - wtcheck

label_protocol: Each sample was biotin labeled using the random priming method with BioPrime® Array CGH Genomic Labeling System (Invitrogen, Carlsbad, CA) following the manufacturer's instruction; a total of 3 µg of genomic DNA from each sample was mixed with 40 µl of 2.5X random primer solutions.

growth_protocol: Wildtype samples were grown under greenhouse conditions (standard for rice growth) until 45 days after sowing.

extract_protocol: Genomic DNA was extracted from leaves of 45 day-old greenhouse-grown plants by CTAB extraction and purified by cesium chloride gradient centrifugation.  The genomic DNA samples were assayed and quantified by spectrophotometry.

tag: tissue

value: leaf tissue

tag: genotype

value: IR64 wildtype


title: EOM-control-R11


title: VHB1-J=0-set3-Cy5


title: VHB1-J=0-set1-Cy3


title: VHB1-J=0-set4-Cy5


title: Genomic DNA - 45 day old leaf sample - mutant f1856

description: Genome hybridization using total DNA from f1856

source_name: 45 day old leaf tissue - f1856

growth_protocol: A total of 16 mutant populations were grown under greenhouse conditions (standard for rice growth) until 45 days after sowing.

treatment_protocol: Mutagenesis was induced by treatment of the indica variety IR64 with DEB-treatment, Fast Neutron, or gamma ray (GR) exposure. These mutagenized lines were advanced to M4 or M5 lines prior to DNA extraction by single seed descent

value: IR64 mutant f1856

tag: mutant type

value: fast neutron

extract_protocol: Genomic DNA was extracted from leaves of 45 day-old greenhouse-grown plants by CTAB extraction and purified by cesium chloride gradient centrifugation. The genomic DNA samples were assayed and quantified by spectrophotometry.

value: wildtype


title: Genomic DNA - 45 day old leaf sample - mutant g6989

description: Genome hybridization using total DNA from g6989

source_name: 45 day old leaf tissue - g6989

value: IR64 mutant g6989

value: gamma ray


title: VHB1-J=0-set2-Cy3


title: Genomic DNA - 45 day old leaf sample - mutant f2045

description: Genome hybridization using total DNA from f2045

source_name: 45 day old leaf tissue - f2045

value: IR64 mutant f2045


title: T47D-J=7-set2-Cy5

tag: T47D cells


title: T47D-J=7-set4-Cy5


title: Genomic DNA - 45 day old leaf sample - mutant g7534

description: Genome hybridization using total DNA from g7534

source_name: 45 day old leaf tissue - g7534

value: IR64 mutant g7534


title: Genomic DNA - 45 day old leaf sample - mutant g6728

description: Genome hybridization using total DNA from g6728

source_name: 45 day old leaf tissue - g6728

value: IR64 mutant g6728


title: T47D-J=7-set1-Cy5


title: T47D-J=7-set3-Cy3


title: Genomic DNA - 45 day old leaf sample - mutant g6686

description: Genome hybridization using total DNA from g6686

source_name: 45 day old leaf tissue - g6686

value: IR64 mutant g6686


title: Genomic DNA - 45 day old leaf sample - mutant d2943

description: Genome hybridization using total DNA from d2943

source_name: 45 day old leaf tissue - d2943

value: IR64 mutant d2943

value: DEB


title: Genomic DNA - 45 day old leaf sample - mutant g6489

description: Genome hybridization using total DNA from g6489

source_name: 45 day old leaf tissue - g6489

value: IR64 mutant g6489


title: Genomic DNA - 45 day old leaf sample - mutant g650

description: Genome hybridization using total DNA from g650

source_name: 45 day old leaf tissue - g650

value: IR64 mutant g650


title: Genomic DNA - 45 day old leaf sample - mutant g6485

description: Genome hybridization using total DNA from g6485

source_name: 45 day old leaf tissue - g6485

value: IR64 mutant g6485


title: Genomic DNA - 45 day old leaf sample - mutant g9799

description: Genome hybridization using total DNA from g9799

source_name: 45 day old leaf tissue - g9799

value: IR64 mutant g9799


title: T47D-J=7-set3-Cy5

description:
Quality Controls of RNA samples: Concentration and purity of the RNA preparation was checked first by UV-spectrophotometry using the Ultrospec3100 pro (GE Healthcare, USA) and 5-mm cuvettes. The absorbance (A) was measured from 200 nm to 350 nm. A235, A260, A280 and A320 were determined and A260:A280 ratios were calculated. Quality of each total RNA was measured by microfuidic/capillary electrophoresis using RNA 6000 Nano LabChip® kits with an Agilent 2100 Bioanalyzer (Agilent Technologies, USA), and the results assessed by human inspection and with two-user independent classifiers evaluation as described previously [Imbeaud et al., NAR, 2005]. Only samples that reached the anticipated purity and integrity parameters (RIN >= 6; DegFact <= 13) were introduced within the microarray pipeline process.
Quality Controls of  Cy-Dye target labeling: Purity and concentration of each target was checked by UV spectrophotometry, using the Ultrospec3100 pro and 70-mm cuvettes (GE Healthcare). Based on the absorbance measured at 256 nm, 550 nm and 650 nm and considering extinction factor for Cy3- and Cy5-dye respectively of 0.15 and 0.25, the yield of cDNA synthesis and dye incorporation rate were computed. An aliquot (1 µl) of the purified labeling reaction was loaded onto RNA 6000 Nano Labchip® using a Agilent 2100 Bioanalyzer (Agilent Technologies, USA). The chip was prepared according to the manufacturer’s protocol and a mRNA nano assay was run on the chip. The shape and sizes of the Cy-dye targets were compared with the molecular weight markers. Targets with unsatisfactory yield of incorporation (dye incorporation rate < 10; A256:A550 or 650 < 2) and integrity (size < 200 nucleotides) were removed from subsequent analyses. The shape of the Cy-dye probes should present a smeared profile with no clearly identified additional peaks.


title: Genomic DNA - 45 day old leaf sample - mutant g6603

description: Genome hybridization using total DNA from g6603

source_name: 45 day old leaf tissue - g6603

value: leaf tissue

value: IR64 mutant g6603


title: T47D-J=7-set1-Cy3


title: T47D-J=7-set2-Cy3


title: T47D-J=0-set3-Cy3


title: T47D-J=0-set3-Cy5


title: T47D-J=0-set2-Cy5


title: T47D-J=0-set4-Cy5


title: Genomic DNA - 45 day old leaf sample - mutant d1137

description: Genome hybridization using total DNA from d1137

source_name: 45 day old leaf tissue - d1137

value: IR64 mutant d1137


title: Genomic DNA - 45 day old leaf sample - mutant d256

description: Genome hybridization using total DNA from d256

source_name: 45 day old leaf tissue - d256

value: IR64 mutant d256


title: T47D-J=0-set1-Cy5


title: Genomic DNA - 45 day old leaf sample - mutant g282

description: Genome hybridization using total DNA from g282

source_name: 45 day old leaf tissue - g282

value: IR64 mutant g282

value: wildtype


title: T47D-J=0-set2-Cy3


title: T47D-J=0-set1-Cy3


title: T47D-J=0-set4-Cy3


title: Genomic DNA - 45 day old leaf sample - mutant d1

description: Genome hybridization using total DNA from d1

source_name: 45 day old leaf tissue - d1

value: IR64 mutant d1


title: MB231-J=7-set1-Cy3

tag: MDA-MB231 cells


title: MB231-J=7-set4-Cy5


title: MB231-J=7-set2-Cy5


title: MB231-J=7-set1-Cy5


title: MB231-J=7-set4-Cy3


title: MB231-J=7-set2-Cy3


title: MB231-J=7-set3-Cy5


title: MB231-J=0-set1-Cy3_REP-2


title: MB231-J=0-set2-Cy5


title: MB231-J=0-set1-Cy5


title: MB231-J=0-set4-Cy5


title: MB231-J=0-set4-Cy3


title: MB231-J=0-set3-Cy3


title: MB231-J=0-set2-Cy3


title: MB231-J=0-set3-Cy5


title: MCF7-J=0-set2-Cy3

tag: MCF7 cells


title: MB231-J=0-set1-Cy3


title: Chimp_Chimp_PR00738_Clint

city: Seattle

first: Tomas

last: Marques-Bonet

state: WA

address: 1705 NE Pacific St,

department: Genome Sciences

institute: University of Washington

description: Performed by NimbleGen following company specifications.

data_processing: Normalization was performed using NimbleScan 2.4. Normalized log2 Cy3/Cy5.

organism: Pan troglodytes

extract_protocol: Coriell

tag: DNA from Chimpanzee PR00738

tag: DNA from Chimpanzee Clint


title: Orang_Orang_AG06105_Susie

hyb_protocol: Performed by NimbleGen following company specifications.

organism: Pongo abelii

tag: DNA from Orangutan AG06105

tag: DNA from Orangutan Susie


title: Orang_Orang_Puti_Susie

scan_protocol: Performed by NimbleGen following company specifications.

tag: DNA from Orangutan Puti


title: Orang_Gorilla_Susie_Bahati

label_protocol: Performed by NimbleGen following company specifications.

organism: Gorilla gorilla

tag: DNA from Gorilla Bahati


title: Orang_Orang_PPY9_Susie

tag: DNA from Orangutan PPY9


title: Chimp_Chimp_PR01009_Clint

tag: DNA from Chimpanzee PR01009


title: Orang_Orang_AG12256_Susie

tag: DNA from Orangutan AG12256


title: Gorilla_Orang_Bahati_Susie


title: Orang_Orang_AG05252_Susie

organism: Pongo pygmaeus pygmaeus

tag: DNA from Orangutan AG05252


title: Chimp_Chimp_PR00238_Clint

tag: DNA from Chimpanzee PR00238


title: Chimp_Chimp_PR00496_Clint

tag: DNA from Chimpanzee PR00496


title: Chimp_Chimp_PR00226_Clint

tag: DNA from Chimpanzee PR00226


title: Orang_Human_AG05252_NA15510

tag: DNA from Human NA15510


title: Human_Human_NA12878_NA15510

tag: DNA from Human NA12878


title: Human_Human_NA19129_NA15510

tag: DNA from Human NA19129


title: Orang_Orang_Tengku_Susie

tag: DNA from Orangutan Tengku


title: MCF7-J=0-set4-Cy5_REP-2

tag: MCF7 cells

tag: human universal reference RNA


title: MCF7-J=0-set4-Cy3


title: Orang_Orang_Hati_Susie

tag: DNA from Orangutan Hati


title: Chimp_Chimp_Logan_Clint

tag: DNA from Chimpanzee Logan

tag: DNA from Chimpanzee Clint


title: Human_Human_NA19240_NA15510

tag: DNA from Human NA19240


title: Human_Chimp_NA18507_Clint

tag: DNA from Human NA18507


title: MCF7-J=0-set4-Cy3_REP-2


title: MCF7-J=0-set4-Cy3_REP-3


title: Orang_Orang_PPY6_Susie

tag: DNA from Orangutan PPY6

tag: DNA from Orangutan Susie


title: MCF7-J=0-set4-Cy5


title: MCF7-J=0-set3-Cy5


title: C-terminal truncated STAT5Δ750_160

city: Rehovot

first: Tali

last: Eilon

address: Rehovot

country: Israel

institute: The Volcani Center

description: Gene expression data from mammary tumor

hyb_protocol: Hybridization was performed according to Affymetrix's protocol to Affymetrix GeneChip® Mouse Genome 430A 2.0 array.

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

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.

source_name: Mammary tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mammary tumors were derived from transgenic mice carrying one of two Stat5 variants on a FVB/N background.

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

treatment_protocol: Tumors were excised and snap-frozen for RNA isolation.

tag: genotype

value: C-terminal truncated STAT5Δ750

tag: tissue

value: mammary tumor

tag: strain

value: FVB/N background

tag: disease state

value: tumor


title: MCF7-J=0-set3-Cy3


title: MCF7-J=0-set2-Cy5


title: Human_Human_NA18956_NA15510

tag: DNA from Human NA18956

tag: DNA from Human NA15510


title: Human_Human_NA12156_NA15510

tag: DNA from Human NA12156


title: C-terminal truncated STAT5Δ750_178

description: Gene expression data from mammary tumor


title: MCF7-J=0-set1-Cy5_REP-2


title: Human_Human_NA18555_NA15510

tag: DNA from Human NA18555


title: C-terminal truncated STAT5Δ750_174

description: Gene expression data from mammary tumor


title: C-terminal truncated STAT5Δ750_165

description: Gene expression data from mammary tumor


title: MCF7-J=0-set1-Cy5

tag: MCF7 cells


title: MCF7-J=0-set1-Cy3_REP-2

tag: human universal reference RNA


title: C-terminal truncated STAT5Δ750_254

description: Gene expression data from mammary tumor


title: C-terminal truncated STAT5Δ750_92

description: Gene expression data from mammary tumor


title: MCF7-J=0-set1-Cy3


title: Human_Human_NA18517_NA15510

tag: DNA from Human NA18517


title: Chimp_Chimp_PR01097_Clint

tag: DNA from Chimpanzee PR01097


title: Macaque_Human_ID17573_NA15510

organism: Macaca mulatta

tag: DNA from Macaque ID17573


title: Constitutively active STAT5ca_177

description: Gene expression data from mammary tumor

value: Constitutively active STAT5


title: MCF7-J=7-set2-Cy3


title: MCF7-J=7-set4-Cy3


title: Constitutively active STAT5ca_171

description: Gene expression data from mammary tumor


title: Human_Human_NA18507_NA15510


title: SF_RRE2_5408cipR_5408wt_LBlog_E_7DE1306

city: Irvine

first: Michael

last: McClelland

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description: biological replicate, Date of Scan Tue May 06 11:24:29 2008

hyb_protocol: overnight hyb on Corning UltraGAPS slides at 42°C in 25% formamide / 5xSSC / 0.1% BSA

scan_protocol: Axon 4100A scanner, image acquisition with GenePix software, spot quantification using Quantarray 3.0 software, adaptive quantification, protocol STv7S_01_051201

data_processing: normalized based on total signal for each channel, background subtracted VALUE data obtained from log of normalized background subtracted ch1/ch2 signal.

organism: Salmonella enterica subsp. enterica serovar Enteritidis

source_name: Enteriditis 5408 cipR LB log

label_protocol: incorporation of Cy3-dCTP with Superscript RT and random hexamers

extract_protocol: RiboPureTM-Yeast (Ambion) kit

tag: isolate

value: Salmonella Enteritidis 5408

value: cipR mutant

source_name: Enteriditis 5408 wt LB log

label_protocol: incorporation of Cy5-dCTP using Klenow enzyme and random hexamers

value: wt


title: SF_RRE2_5408cipR_5408wt_LBlog_F_7DE1307

description: biological replicate, Date of Scan Tue May 06 11:37:17 2008


title: MCF7-J=7-set1-Cy3


title: Constitutively active STAT5ca_169

description: Gene expression data from mammary tumor


title: SF_RRE2_104cipR_104wt_LBlog_F_7DE1304

description: biological replicate, Date of Scan Wed Apr 16 14:33:01 2008

source_name: Enteriditis 104 cipR LB log

value: Salmonella Enteritidis 104

source_name: Enteriditis 104 wt LB log


title: MCF7-J=7-set2-Cy5


title: SF_RRE2_5408cipR_5408wt_LBlog_D_7DE1305

description: biological replicate, Date of Scan Tue May 06 10:56:13 2008


title: Bonobo_Human_LB501_NA15510

organism: Pan paniscus

tag: DNA from Bonobo LB501


title: MCF7-J=7-set3-Cy3


title: Constitutively active STAT5ca_213

description: Gene expression data from mammary tumor


title: SF_RRE2_104cipR_104wt_LBlog_E_7DE1303

description: biological replicate, Date of Scan Wed Apr 16 14:25:28 2008


title: Gorilla_Human_Makari_NA15510

tag: DNA from Gorilla Makari


title: Orang_Human_Susie_NA15510

tag: DNA from Orangutan Susie


title: Constitutively active STAT5ca_124

description: Gene expression data from mammary tumor

tag: genotype


title: SF_RRE2_104cipR_104wt_LBlog_D_7DE1302

description: biological replicate, Date of Scan Wed Apr 16 14:17:08 2008


title: Constitutively active STAT5ca_159

description: Gene expression data from mammary tumor

tag: tissue


title: SF_RRE2_5408cipR_5408wt_LBlog_C_7DE1151

description: biological replicate, Date of Scan Fri Feb 29 11:35:44 2008


title: Human_Macaque_NA15510_ID17573


title: MCF7-J=7-set3-Cy5


title: Human_Orang_NA15510_Susie


title: Human_Gorilla_NA15510_Makari


title: SF_RRE2_5408cipR_5408wt_LBlog_B_7DE1150

description: biological replicate, Date of Scan Fri Feb 29 11:28:44 2008


title: Gorilla_Human_Kowali_NA15510

tag: DNA from Gorilla Kowali


title: Mammary gland_4

description: Gene expression data from mammary gland

source_name: Mammary gland

value: Mammary gland_4

value: mammary gland

tag: strain

tag: disease state

value: normal


title: Mammary gland_6

description: Gene expression data from mammary gland

value: Mammary gland_6


title: MCF7-J=7-set4-Cy5


title: Bonobo_Human_LB502_NA15510

tag: DNA from Bonobo LB502

tag: DNA from Human NA15510


title: Mammary gland_1

description: Gene expression data from mammary gland


title: Constitutively active STAT5ca_123

description: Gene expression data from mammary tumor


title: MCF7-J=7-set4-Cy3_REP-2


title: MCF7-J=7-set4-Cy5_REP-2


title: Gorilla_Human_Bahati_NA15510

tag: DNA from Gorilla Bahati


title: Human_Gorilla_NA15510_Bahati


title: SF_RRE2_104cipR_104wt_LBlog_C_7DE1149

description: biological replicate, Date of Scan Fri Feb 29 11:19:30 2008


title: MCF7-J=7-set1-Cy5

description: Quality Controls of RNA samples: Concentration and purity of the RNA preparation was checked first by UV-spectrophotometry using the Ultrospec3100 pro (GE Healthcare, USA) and 5-mm cuvettes. The absorbance (A) was measured from 200 nm to 350 nm. A235, A260, A280 and A320 were determined and A260:A280 ratios were calculated. Quality of each total RNA was measured by microfuidic/capillary electrophoresis using RNA 6000 Nano LabChip® kits with an Agilent 2100 Bioanalyzer (Agilent Technologies, USA), and the results assessed by human inspection and with two-user independent classifiers evaluation as described previously [Imbeaud et al., NAR, 2005]. Only samples that reached the anticipated purity and integrity parameters (RIN >= 6; DegFact <= 13) were introduced within the microarray pipeline process.Quality Controls of  Cy-Dye target labeling: Purity and concentration of each target was checked by UV spectrophotometry, using the Ultrospec3100 pro and 70-mm cuvettes (GE Healthcare). Based on the absorbance measured at 256 nm, 550 nm and 650 nm and considering extinction factor for Cy3- and Cy5-dye respectively of 0.15 and 0.25, the yield of cDNA synthesis and dye incorporation rate were computed. An aliquot (1 µl) of the purified labeling reaction was loaded onto RNA 6000 Nano Labchip® using a Agilent 2100 Bioanalyzer (Agilent Technologies, USA). The chip was prepared according to the manufacturer’s protocol and a mRNA nano assay was run on the chip. The shape and sizes of the Cy-dye targets were compared with the molecular weight markers. Targets with unsatisfactory yield of incorporation (dye incorporation rate < 10; A256:A550 or 650 < 2) and integrity (size < 200 nucleotides) were removed from subsequent analyses. The shape of the Cy-dye probes should present a smeared profile with no clearly identified additional peaks.

label_protocol:
Targets were synthesized using 30.0 µg amplified RNA, 1 µl anchored oligo-(dT) for priming (total volume 11 µl, 10 min, 70°C) in presence of 1 µl spike RNA from Lucidea™ Microarray Human Scorecard v1.1 (GE Healthcare, USA). cDNA products were generated using 1 mM of either Cy3- or Cy5-dCTP (GE Healthcare, USA) and 200 units MMLV RNase H- reverse transcriptase (Promega, USA) at 42°C for 2 to 3 hr. After reverse transcription, the RNA was degraded by adding 2 µl of 2.5 N NaOH and incubating at 37°C for 10 min. The reaction was then neutralized by adding 10 µl of 2 M MOPS (free acid) and Cy3- and Cy5-containing targets were purified twice onto QIAquick PCR columns (Qiagen, Germany) according the manufacturer’s instructions with minor modifications. The Cy-dye targets were controlled during quality assessment (purity, size, yield).
Adjusted Cy-dye target yield was calculated to reflect carryover of unlabeled RNA. Thus, certified targets were air-dried in a vacuum centrifuge for 1.5 hr and resuspended in RNase-free water to reach a 10 pmol/µl concentration

tag: MCF7 cells


title: SF_RRE2_104cipR_104wt_LBlog_B_7DE1148

description: biological replicate, Date of Scan Fri Feb 29 11:12:34 2008


title: Human_Gorilla_NA15510_Kowali


title: SF_RRE2_5408cipR_5408wt_LBlog_A_7DE1140

description: biological replicate, Date of Scan Tue Feb 26 14:56:26 2008


title: LIF_rep3_Cy3

status: Public on Mar 05 2009

first: Brig

last: Mecham

address: 1100 Fairview Ave N

description: Gene Expression in LIF

hyb_protocol: 825ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) and 825ng of Cy5-labelled cRNA (specific activity >10.0 pmol Cy5/ug cRNA) were combined and fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) and Agilent Whole Genome Mouse Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by compressed nitrogen (N2) gun.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Red and both Green PMT and Red PMT arer set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE2-v5_95 and Grid: 014868_D_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: R1 mESC

label_protocol: Cyanine-3 (Cy3) and Cyanine-5 (Cy5) labeled cRNA was prepared from 0.5 ug RNA using the Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: mESC in DMEM, 15% serum replacer, glutamax, pen/strep, NEAA, pyruvate (Invitrogen) and mercaptoethanol (Sigma), grown on gelatin (Sigma) at 37C in 5% CO2

extract_protocol: RNA extraction utilized the Rneasy Minikit (Qiagen) following manufacturer's protocol.  The RNA was treated with Dnase and given to the Center for Array Technologies for quantitation and purity analysis.

treatment_protocol: Independent quadruplicate: groupA in LIF (Chemicon) without feeders, groupB in 0.2mM sodium butyrate (without LIF) for 15 passages

tag: cell type

value: mouse embryo stem cells

tag: cell line


title: SF_RRE2_104cipR_104wt_LBlog_A_7DE1141

description: biological replicate, Date of Scan Tue Feb 26 15:04:14 2008


title: Condition_Media_rep2_Cy5

description: Gene Expression in Conditioned Media

source_name: BG02 hESC

growth_protocol: hESC in DMEM/F12, 20% serum replacer, glutamax, pen/strep, NEAA, pyruvate (Invitrogen) and mercaptoethanol (Sigma), grown on Matrigel (BD) at 37C in 5% CO2

treatment_protocol: Independent triplicate: groupA in conditioned medium (CM) 31 passages and groupB in 0.2mM sodium butyrate for 20 passages

value: human embryonic stem cells


title: LIF_rep1_Cy3

description: Gene Expression in LIF


title: Butyrate_rep4_Cy5

description: Gene Expression after exposure to Butyrate


title: Condition_Media_rep3_Cy5

description: Gene Expression in Conditioned Media


title: Butyrate_rep2_Cy5


title: Butyrate_rep3_Cy3


title: Chimp_Human_PR00238_NA15510

tag: DNA from Chimpanzee PR00238


title: LIF_rep2_Cy3

description: Gene Expression in LIF


title: Butyrate_rep3_Cy5


title: Butyrate_rep1_Cy5


title: Condition_Media_rep1_Cy5

description: Gene Expression in Conditioned Media


title: Butyrate_rep1_Cy3


title: Butyrate_rep2_Cy3


title: LIF_rep4_Cy3

description: Gene Expression in LIF


title: Fog2flox/delta; alpha MHC Cre biological replicate 3

city: Boston

first: Sek Won

last: Kong

state: MA

address: 300 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

description: Aberrant transcriptional regulation contributes to the pathogenesis of both congenital and adult forms of heart disease. While the transcriptional regulator FOG2 is known to be essential for heart morphogenesis and coronary development, its tissue specific function has not been previously investigated. Additionally, little is known about the role of FOG2 in the adult heart. Here we use spatiotemporally regulated inactivation of Fog2 to delineate its function both in embryo and adult heart. Early cardiomyocyte-restricted loss of Fog2 recapitulated the cardiac and coronary defects of the Fog2 germline knockouts. Later cardiomyocyte-restricted loss of Fog2 (Fog2MC) did not result in defects in cardiac structure or coronary vessel formation. However, Fog2MC adult mice had severely depressed ventricular function and died at 8-14 weeks. Fog2MC adult hearts displayed a paucity of coronary vessels. This was associated with myocardial hypoxia, increased cardiomyocyte apoptosis, and cardiac fibrosis. Induced inactivation of Fog2 in adult heart resulted in similar phenotype, as did ablation of FOG2 interaction with the transcription factor GATA4. Loss of FOG2 or FOG2-GATA4 interaction altered expression of a panel of angiogenesis-related genes. Collectively, our data indicated that FOG2 regulates adult heart function and coronary angiogenesis.

hyb_protocol: Affymetrix standard protocol was used.

scan_protocol: Affymetrix standard protocol was used.

data_processing: Affymetrix PLIER algorithm

label: Biotin

source_name: Murine Heart Apex

label_protocol: Affymetrix standard protocol was used.

growth_protocol: Mice, 6-7 wks old, male.

extract_protocol: Trizol then Rneasy

treatment_protocol: MHCaCre induced knockout of Fog2flox.

tag: treatment

value: alpha MHC Cre

tag: age

value: 6-7 wks old

tag: gender

value: male

value: heart


title: Fog2flox/delta; alpha MHC Cre biological replicate 2


title: Chimp_Chimp_PR01105_Clint

tag: DNA from Chimpanzee PR01105

tag: DNA from Chimpanzee Clint


title: Fog2flox/delta; alpha MHC Cre biological replicate 1

tag: genotype


title: Human_Bonobo_NA15510_LB502


title: Condition_Media_rep3_Cy3

description: Gene Expression in Conditioned Media

source_name: H1 hESC

treatment_protocol: Independent triplicate: groupA in conditioned medium (CM) 9 passages, groupB in 0.2mM sodium butyrate for 6 passages, groupC removed from 4 passages in butyrate back into CM for 3 more passages


title: Butyrate_rep3_Cy3


title: Foxp2wt/wt_strKi2_E16.5d_m_run5_litter18_rep1

city: Leipzig

first: Mehmet

last: Somel

address: Deutscher Platz 6

department: Evolutionary Genetics

country: Germany

institute: Max Planck Institute for Evolutionary Anthropology

description: Gene expression data from the striatum of a E16.5 days old wild-type mouse, belonging to strain Ki2

hyb_protocol: Embryonic samples were processed in two batches, adult samples in one batch, and the young animals in three batches. For the young animals, all probes were labelled together but hybridised in three different runs. Hybridization to Affymetrix MG-430 2.0 GeneChip arrays was carried out following standard Affymetrix protocols.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneChip Scanner 3000.

data_processing: Affymetrix microarray image data were collected with Affymetrix GeneChip Operating Software version 1.1 using default parameters. For summarizing the expression data, we used custom chip definition files (CDF) based on Ensembl gene annotation rather than the standard Affymetrix annotation (customCDF v. 10; see Dai et al., PMID: 16284200). We used the R Bioconductor 'affy' software package for further data analysis (Gautier et al., PMID: 14960456). Signal intensities were calculated with the 'rma' function using default parameters, including quantile normalization and log2 transformation. Detection p-values were calculated with the 'mas5calls' function.

source_name: Mus musculus striatum, genotype:Foxp2wt/wt, strain:Ki2, age:E16.5days

label_protocol: Biotinylated cRNA were prepared from 3.5 micrograms (embryonic striatum), 3.3 micrograms (adult striatum) and 1microgram (young animals) of total RNA following standard Affymetrix protocols.

growth_protocol: The two nucleotide substitutions that occurred during human evolution are both located in exon seven of the FOXP2 gene. We introduced these two substitutions into the orthologous exon of the mouse Foxp2 gene by homologous recombination in embryonic stem (ES) cells derived from C57BL/6 mice, thus generating mice carrying the Foxp2hum allele. Mice carrying the Foxp2hum allele were generated by Ozgene (Bentley, Australia) from two C57BL/6 ES cell clones that had integrated the vector via homologous recombination. Whereas the first line (clone 5H10) was used for initial analyses, the second one (clone 5H11) was used for testing the reproducibility of the results from the first line. To this end, some mice were generated that carried a Foxp2hum allele in which the Neomycin resistance cassette had been removed by crossings with a FLPe deleter strain (Jackson Laboratory, Stock Number 003800; C57BL/6J) followed by removal of the FLPe transgene by crossings. Mice carrying the Foxp2ko allele were generated by crossing chimeric mice (clone 5H11) to a B6 Cre deleter strain (Ozgene, Bentley, Australia) and subsequent crosses to remove the Cre transgene. Mice were bred at the MPI-EVA facility under standard conditions. We picked individuals so that genotypes were balanced as much as possible for sex, litter and run in the three different “strains.”

extract_protocol: For RNA isolation, the tissue was transferred to 1ml of TRIZol reagent (Invitrogen) and immediately homogenized using a teflon pestle (cylindrical) in a 2ml glass homogenizer on a Schütt homgenplus homogenizer (Schütt Labortechnik, Göttingen, Germany). RNA and genomic DNA were isolated according to the TRIZol protocol with addition of 250µg Glycogen (Roche Diagnostics, Mannheim, Germany) to 1ml of homogenate. DNA was used to confirm genotypes and RNA was further purified using the MiniElute kit (Qiagen, Valencia, California, USA). High and equal quality RNA was ensured on an Agilent 2100 Bioanalyzer system (Foster City, California, USA).

treatment_protocol: Embryos (E16.5) were dissected and briefly washed in ice-cold dissection buffer (15mM HEPES (hemisodium salt, Research Organics, Cleveland, Ohio, USA), 30mM glucose (Sigma-Aldrich, Steinheim, Germany ), 1x Hanks balanced Salt solution (without Calcium, Magnesium, Phenol Red, Sodium Bicarbonate; Invitrogen, Carlsbad, California, USA) and 1.34 mM NaHCO3 (Sigma-Aldrich); sterile filtered). The brain of each embryo was then removed, dissected under a stereomicroscope in RNAlater (Ambion, Austin, Texas, USA) and stored in RNAlater until all brains of the litter had been prepared. For preparation of the striatum, the cerebellum was removed, the brain cut into the two hemispheres and the striatum (i.e. caudate nucleus, putamen and pallidum) was prepared from each hemisphere according to (Schambra et al., 1992). The striata of both hemispheres were combined and stored in RNAlater at -20° until further use. Tailbuds of the embryos were used for genotyping and sex determination. A second batch of embryos was prepared in a similar fashion. Striatal tissue from adult females was prepared in a similar fashion. All embryonic and adult samples were derived from crosses of Foxp2wt/hum animals (5C10 line). Striatal samples from young animals P15, P18 and P21) were prepared slightly different in that brains were cut in ice-cold PBS by a custom-build razorblade holder that allowed making 2 mm thick coronal sections. 2-3 slices were used to obtain striatal biopsy punches each 2 mm in diameter, which were then frozen in liquid nitrogen. We picked individuals so that genotypes were balanced as much as possible for sex, litter and run in the two different “strains” (“Ki” for pups from crosses of Foxp2wt/hum animals (5H11 line with the Neomycin cassette removed(Foxp2hum?neo)) and “Ko” for pups from crosses of Foxp2wt/ko and C57BL/6J animals).

value: Ki2 - a knock-in or wild-type mouse from crosses of Foxp2wt/hum animals (clone no. 5H10)

tag: sex

tag: run (microarray batch)

tag: litter

tag: biological replicate

tag: tissue

value: striatum (brain)


title: Foxp2wt/wt_strKi2_E16.5d_m_run5_litter16_rep1

tag: strain


title: Foxp2wt/wt_strKi2_E16.5d_m_run5_litter17_rep1


title: Butyrate_rep2_Cy3


title: Foxp2wt/wt_strKi2_E16.5d_m_run5_litter17_rep2


title: Foxp2wt/wt_strKi2_E16.5d_m_run4_litter19_rep1


title: Fog2flox/delta; no Cre biological replicate 2

value: no Cre


title: Fog2flox/delta; no Cre biological replicate 3


title: Fog2flox/delta; no Cre biological replicate 1


title: Foxp2wt/wt_strKi2_E16.5d_m_run4_litter19_rep2


title: Butyrate_rep1_Cy3


title: Condition_Media_rep2_Cy3

description: Gene Expression in Conditioned Media


title: Human_Chimp_NA15510_PR00238

description: Performed by NimbleGen following company specifications.

tag: DNA from Human NA15510


title: Chimp_Human_Katie_NA15510

tag: DNA from Chimpanzee Katie


title: Foxp2wt/wt_strKi2_E16.5d_f_run5_litter16_rep2

value: female


title: Foxp2wt/wt_strKi2_E16.5d_f_run5_litter18_rep1


title: Condition_Media_rep1_Cy3

description: Gene Expression in Conditioned Media

tag: cell type


title: ReConditioned_Media_rep3_Cy5

description: Gene Expression in Butyrate followed by reconditioned media

tag: cell line


title: Foxp2wt/wt_strKi2_E16.5d_f_run5_litter16_rep1


title: Human_Chimp_NA15510_Clint


title: Butyrate_rep3_Cy5


title: ReConditioned_Media_rep1_Cy5


title: Foxp2wt/wt_strKi2_E16.5d_f_run4_litter21_rep1


title: Foxp2wt/wt_strKi2_95d_f_run6_litter13_rep1

description: Gene expression data from the striatum of a 95 days old wild-type mouse, belonging to strain Ki2

source_name: Mus musculus striatum, genotype:Foxp2wt/wt, strain:Ki2, age:95days


title: Foxp2wt/wt_strKi2_95d_f_run6_litter25_rep1


title: Foxp2wt/wt_strKi2_E16.5d_f_run4_litter15_rep1


title: Foxp2hum/hum_strKi2_E16.5d_m_run5_litter18_rep1

description: Gene expression data from the striatum of a E16.5 days old mouse homozygous for the human Foxp2 allele (Foxp2hum/hum), belonging to strain Ki2

source_name: Mus musculus striatum, genotype:Foxp2hum/hum, strain:Ki2, age:E16.5days


title: Foxp2wt/wt_strKi2_95d_f_run6_litter24_rep1


title: Chimp_Human_Clint_NA15510


title: Foxp2wt/wt_strKi2_95d_f_run6_litter25_rep2


title: Human_Chimp_NA15510_Katie


title: Foxp2wt/wt_strKi2_95d_f_run6_litter20_rep1


title: ReConditioned_Media_rep2_Cy5


title: Foxp2hum/hum_strKi2_E16.5d_m_run5_litter17_rep3


title: Foxp2hum/hum_strKi2_E16.5d_m_run5_litter17_rep2


title: Butyrate_rep1_Cy5


title: Foxp2hum/hum_strKi2_E16.5d_m_run5_litter16_rep1


title: Butyrate_rep2_Cy5


title: Foxp2hum/hum_strKi2_E16.5d_m_run5_litter17_rep1


title: Foxp2hum/hum_strKi2_E16.5d_f_run4_litter23_rep3


title: Foxp2hum/hum_strKi2_E16.5d_f_run5_litter16_rep2


title: Foxp2hum/hum_strKi2_E16.5d_f_run5_litter16_rep1


title: Foxp2hum/hum_strKi2_E16.5d_f_run4_litter22_rep1


title: Foxp2hum/hum_strKi2_E16.5d_f_run4_litter23_rep2


title: Foxp2hum/hum_strKi2_E16.5d_f_run4_litter21_rep1


title: Foxp2hum/hum_strKi2_95d_f_run6_litter26_rep1

description: Gene expression data from the striatum of a 95 days old mouse homozygous for the human Foxp2 allele (Foxp2hum/hum), belonging to strain Ki2

source_name: Mus musculus striatum, genotype:Foxp2hum/hum, strain:Ki2, age:95days


title: Foxp2hum/hum_strKi2_95d_f_run6_litter26_rep2


title: Foxp2hum/hum_strKi2_E16.5d_f_run4_litter22_rep2


title: Foxp2hum/hum_strKi2_E16.5d_f_run4_litter23_rep1


title: Foxp2hum/hum_strKi2_95d_f_run6_litter25_rep1


title: Foxp2hum/hum_strKi2_95d_f_run6_litter25_rep2


title: Foxp2hum/hum_strKi2_95d_f_run6_litter20_rep1


title: Malting_kilned_Morex_rep2

city: Fort Collins

first: Nora

middle: L

last: Lapitan

state: CO

address: Plant Science Bldg

department: Soil and Crop Sciences

institute: Colorado State University

description: Probe synthesis, labeling and hybridization were perfomed according to manufacturer's protocols (Affymetrix, Santa Clara, CA) at the  VBI Microarray Core Facility, Blacksburg, VA.

hyb_protocol: 10 µg labeled, fragmented cRNA was hybridized at 45°C with rotation for 16 h in an Affymetrix GeneChio Hybridization Oven 320 on Affymetrix Barley1 GeneChip arrays. The arrays were washed and stained using streptavidin phycoerythrin on an Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Different quality control checks were performed including inspection of hybridized images, boxplots and histograms of log2(PM) values, examination of hybridization and PolyA controls.  Based on the results of the quality control screening, some chips were discarded from the analysis.  Twenty-two arrays were retained for further analysis, with two replications per cultivar per time point, with the exception of Harrington day 1, where one of the replicates was discarded. Data analysis was carried out using Bioconductor in R (Gentleman et al. 2004).  Data preprocessing and summarization were performed using Robust Multichip Average (RMA) (Irizarry et al. 2003).

organism: Hordeum vulgare

source_name: Barley seed kilned, Morex

label_protocol: The BioArray High-Yield RNA Transcript labeling kit (Enzo Diagnostics) was used to synthesize biotin-labeled cRNA from template cDNA by in vitro transcription.

growth_protocol: Fifty to 100 g seeds of each variety were micro-malted at Busch Agricultural Resources, LLC, Fort Collins, CO. The micromalting conditions were as follows: steeping at 12°C for 37 h, germination at 12°C for 5 h, 17°C for 65 h, 18°C for 23 h, and kilning stages consisting of  55°C for 10 h, 60°C for 4 h, 68°C for 3 h, 80°C for 2 h and 90°C for 3 h.

extract_protocol: Frozen barley malt was ground and incubated with RNA purification reagent from Invitrogen (Carlsbad, CA) at room temperature for 10 minutes. Total RNA was extracted using Qiagen RNeasy Plant Mini Kit with RNase Free/DNase (Qiagen, Valencia, CA) following the manufacturer's instructions.

treatment_protocol: Samples were frozen in liquid nitrogen and stored at -80°C until use.

tag: Genotype

value: Morex


title: Foxp2hum/hum_strKi2_95d_f_run6_litter14_rep1


title: Calcineurin Tg, biological replicate 4 (Luminex)

description: mircroRNA profile from isolated cardiac myocytes

hyb_protocol: Denatured targets were hybridized to beads coupled with capture probes for miRNAs.

scan_protocol: After binding to streptavidin-phycoerythrin (SAPE), the beads went through a flow cytometer that has two lasers and is capable of detecting both the bead identity and fluorescence intensity on each bead (Luminex).

data_processing: Preprocessed as described in Lu et al. (http://www.broad.mit.edu/mpr/publications/projects/microRNA/Supplementary_Notes.pdf)

source_name: Cardiomyocytes dissociated by retrograde collagenase perfusion

label_protocol: 18 to 26-nucleotide (nt) small RNAs were purified by denaturing PAGE (polyacrylamide gel electrophoresis) from total RNAs extracted from cells. Small RNAs underwent two steps of adaptor ligation  utilizing both the 5’-phosphate and 3’-hydroxl groups, each followed by a denaturing purification. Ligation products were reverse-transcribed (RT) and PCR amplified using a common set of primers, with biotinylation on the sense primer.

extract_protocol: Total RNAs are prepared with Trizol (Invitrogen, 15596-018). Add 200ul chloroform per 1ml of Trizol. After 5mins on ice, spin for 10 mins at high speed in a cooled centrifuge (at least 3000rpm for 15ml tube). Take the supernatant to a new tube, measure the volume while transferring. Precipitate with same volume of 100% isopropanol in -20 for 30mins or store in -80.   Spin down the pellet at high speed in a cooled centrifuge. Wash pellet once with 80% ethanol and air dry the pellet. Add appropriate amount of DEPC-H2O to dissolve the pellet.   Measure RNA concentration with OD260.

value: Calcineurin-transgenic mice


title: Malting_kilned_Morex_rep1


title: Foxp2wt/wt_strKi2_E16.5d_m_run4_litter21_rep1


title: Malting_day4_Morex_rep2

description: Probe synthesis, labeling and hybridization were perfomed according to manufacturer's protocols (Affymetrix, Santa Clara, CA) at the  UCI Microarray Core Facility, Irvine, CA.

source_name: Barley seed day 4 germination, Morex


title: BMDCs_NPs_24h_2

city: Kagoshima

first: Takayuki

last: Hamasaki

state: Kagoshima

address: 8-35-1 Sakuragaoka

department: Graduate School of Medical and Dental Sciences

country: Japan

institute: Kagoshima University

description: Gene expression after 24hr in gamma-PGA-NPs-treated mouse bone marrow derived dendritic cells

hyb_protocol: The cRNA was fragmented and hybridized to Agilent whole mouse genome oligonucleotide microarray (4 × 44K slide format) at 37 ºC for 17 hours.

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 9.1.3.1 (Agilent) using default parameters (protocol GE1-v5_91_0806 and Grid: 014868_D_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: bone marrow derived dendritic cells

label_protocol: RNA (500 ng) was converted to cDNA with Molony murine leukemia virus RT and T7 promoter primer. The cDNA was transcribed and amplified with T7 RNA polymerase to produce the cRNA labeled with cyanine 3. The cyanine 3-labeled cRNA was purified with RNeasy and examined for its concentration and labeling quality by a spectrophotometer.

growth_protocol: Femurs and tibias were removed from mice and purified from the surrounding muscle tissues. Both ends of the bones were cut with scissors, and the marrow was flushed with PBS using a syringe with a 26-gauge needle. The suspension was passed through a 50-mm cell strainer. Bone marrow cells (2.5 × 10^6 cells/10 ml) were suspended in RPMI 1640 medium supplemented with 10 % heat-inactivated fetal bovine serum, 100 U/ml penicillin G, 100 µg/ml streptomycin, 2-mercaptoethanol, and 20 ng/ml recombinant GM-CSF (PeproTech) and placed into a Petri dish (InaOptica). Fresh culture medium was added to the dish on day 3. On day 7, non-adherent or loosely adherent cells were harvested and used as immature DCs.

extract_protocol: Total RNA was extracted from the cells with RNeasy (Qiagen). The quality of the total RNA was examined by 2100 Bioanalyzer (Agilent).

treatment_protocol: Immature DCs (1 × 10^6 cells/ml) were incubated with either 300 µg/ml γ-PGA NPsA. The cultures were incubated for 6, 12 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: 6 - 8 weeks


title: Malting_steeped_Morex_rep2

source_name: Barley seed steeped, Morex


title: BMDCs_NPs_24h_3


title: BMDCs_NPs_12h_3

description: Gene expression after 12hr in gamma-PGA-NPs-treated mouse bone marrow derived dendritic cells


title: BMDCs_NPs_24h_1


title: BMDCs_NPs_12h_2


title: BMDCs_NPs_12h_1


title: Malting_steeped_Morex_rep1


title: Malting_day1_Morex_rep2

source_name: Barley seed day 1 germination, Morex


title: BMDCs_NPs_6h_3

description: Gene expression after 6hr in gamma-PGA-NPs-treated mouse bone marrow derived dendritic cells


title: Calcineurin Tg, biological replicate 3 (Luminex)


title: BMDCs_NPs_6h_2


title: Calcineurin Tg, biological replicate 2 (Luminex)


title: Calcineurin Tg, biological replicate 1 (Luminex)


title: BMDCs_NPs_0h_3

description: Gene expression after 0hr in gamma-PGA-NPs-treated mouse bone marrow derived dendritic cells


title: NTg, biological replicate 5 (Luminex)

value: Nontransgenic control mice


title: Malting_day4_Harrington_rep4

source_name: Barley seed day 4 germination, Harrington

value: Harrington


title: NTg, biological replicate 3 (Luminex)


title: Malting_day4_Morex_rep1


title: BMDCs_NPs_6h_1


title: BMDCs_NPs_0h_1


title: NTg, biological replicate 2 (Luminex)


title: Malting_day1_Morex_rep1


title: BMDCs_NPs_0h_2


title: NTg, biological replicate 1 (Luminex)


title: Malting_day1_Harrington_rep1

source_name: Barley seed day 1 germination, Harrington


title: NTg, biological replicate 4 (Luminex)


title: BMDCs_g-PGA_ 6h_2

description: Gene expression after 6hr in PBS-treated mouse bone marrow derived dendritic cells

treatment_protocol: Immature DCs (1 × 10^6 cells/ml) were incubated with either 300 µg/ml γ-PGA NPs, 1 µg/ml LPS, or 300 µg/ml unparticulate γ-PGA. The cultures were incubated for 6 hours at 37 ºC in a humidified incubator with 5% CO2.


title: BMDCs_g-PGA_ 6h_3


title: Malting_day4_Harrington_rep2


title: BMDCs_g-PGA_ 6h_1


title: Malting_day1_Merit_rep1

source_name: Barley seed day 1 germination, Merit

value: Merit


title: BMDCs_LPS_ 6h_2


title: Malting_day1_Legacy_rep4

source_name: Barley seed day 1 germination, Legacy

value: Legacy


title: Malting_day1_Legacy_rep2


title: BMDCs_LPS_ 6h_1


title: Malting_day1_Merit_rep3


title: BMDCs_g-PGA-NPs_ 6h_3


title: Control_dryseed_Morex_rep1

source_name: Barley seed ungerminated, Morex, Control


title: BMDCs_g-PGA-NPs_ 6h_2


title: NPC_CNE2 (250K_Sty2_SNP Array)

city: Guangzhou

first: Zhong-Xi

last: Huang

address: Tonghe

department: Cancer Institute

country: China

institute: Southern Medical University

description: copy number variation analysis

hyb_protocol: Affymetrix standard procedure

scan_protocol: Microarray scanning and data acquisition was carried out at GeneTech Biotechnology Limited Company (Shanghai, China) using Affymetrix-recommended equipment and procedures.

data_processing: The same type of data of 45 Chinese samples from the HapMap project was used as normal control. Data was analyzed using GCOS (GeneChip operating software, Ver.1.4), GTYPE (GeneChip Genotyping Analysis Software, Ver.4.1), and CNAT (chromosome copy number analysis tool, Ver.4.0, BRLMM algorithm).

source_name: Nasopharyngeal carcinoma cell line CNE2

label_protocol: Affymetrix standard procedure

growth_protocol: Cells were grown in RPMI-1640 medium (Hyclone, Logan, UT) supplemented with 10% fetal calf serum (ExCell, Shanghai, China) and 1% L-glutamine. Cells were cultured at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol: Affymetrix standard procedure

value: nasopharyngeal carcinoma cell line CNE2


title: 300-800 nt nascent strands, hyb2

city: Madrid

first: Ramon

last: Diaz-Uriarte

state: Madrid

address: Melchor Fernandez Almagro 3

department: Structural Biology and Biocomputing Programme

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

description: 300-800 nt nascent strands, hyb2

hyb_protocol: The labelled DNA was denatured at 95º C for 3 minutes, transferred to ice, mixed with 100 μl H20 and 250 μl 2x Hybridisation buffer (Agilent) and loaded onto a fresh array slide placed into a Agilent SureHyb chamber base.  The chamber was sealed and slides hybridised at 65º C for 40 h at 10 rpm.  Prior to scanning the slides were washed 5 minutes at room temperature in Wash Buffer 1 and then 5 minutes at room temperature in Wash Buffer 2 (OGT).

scan_protocol: All labelled samples were sent to Oxford Gene Technology facilities (OGT, Oxford, UK), using the Agilent platform and protocols for the hybridisation and scanning of the arrays. Data was scanned at 100% and 50% PMT and the 100% PMT data feature extracted using local background and spatial detrending to account for differences in hybridisation intensities across the array. Poor quality features were discarded, as were those with very high signal intensities, following standard Agilent protocols.

data_processing: Raw datasets from each experiment were loess normalised to remove signal intensity-dependent bias using GeneSpringX software (Agilent).

source_name: embryonic stem cells, nascent strands

label_protocol: The DNA samples hybridised in the arrays were labelled as described on the protocol published by Agilent (Agilent_Technologies, 2005). Briefly, each sample (nascent strands or control) resuspended in 21 μl H2O was mixed with 20 μl of 2.5x Random primer buffer (BioPrime DNA Labeling System, Invitrogen) and incubated at 95º C for 5 minutes. This mix was transferred immediately to ice and the following reagents added: dNTPs (2 mM each of dATP, dGTP and dTTP and 0.5 mM dCTP), 3.75 μl Cy 3-dCTP or Cy 5-dCTP (Amersham), and 20 U Klenow enzyme.  The reactions were incubated at 37ºC for 3 hours, an extra 10 U Klenow enzyme added and then incubated for further 2 hours.  Corresponding nascent strands and control samples were pooled, diluted in 400 μl of TE pH 8.0 and purified on a MicroCon YM-30 filter column (Millipore) to remove the unincorporated label, following manufacturer’s instructions.  The labelled DNA was transferred to a fresh 1.5 ml tube and brought to a final volume of 150 μl with nuclease-free water and stored in the dark at -20ºC until hybridisation.

growth_protocol: The mouse embryonic stem cell line PGK12.1 was grown as described in Penny GD, Kay GF, Sheardown SA, Rastan S, Brockdorff N (1996; Requirement for Xist in X chromosome inactivation. Nature 379: 131-137). Mouse embryonic fibroblasts (MEFs) were derived from 12.5 dpc CD1 embryos and grown in F12 Nutrient Mixture (Ham) medium supplemented with 10% FCS, 1x105 U/ml penicillin, 100 mg/ml streptomycin, 2 mM L- lutamine, 1x non-essential amino acids, and 50 M beta-mercaptoethanol (Invitrogen). NIH/3T3 cells were cultivated as recommended in the ATCC.

extract_protocol: Genomic DNA isolation and nascent strands fractionation was performed as described in Gómez M, Antequera F (2008; Overreplication of short DNA regions during S phase in human cells. Genes & Development 22: 375-385)

treatment_protocol: No treatment was applied

value: female pluripotent cells

tag: dna type

value: nascent strands

source_name: embryonic stem cells

value: total DNA


title: 300-800 nt nascent strands, hyb1

description: 300-800 nt nascent strands, hyb1


title: BMDCs_g-PGA-NPs_ 6h_1

tag: age


title: NPC_CNE1 (250K_Sty2_SNP Array)

description: copy number variation analysis

source_name: Nasopharyngeal carcinoma cell line CNE1

value: nasopharyngeal carcinoma cell line CNE1


title: 100-600 nt nascent strands, hyb2

description: 100-600 nt nascent strands, hyb2


title: NPC_6-10B (250K_Sty2_SNP Array)

description: copy number variation analysis

source_name: Nasopharyngeal carcinoma cell line 6-10B

value: nasopharyngeal carcinoma cell line 6-10B


title: Malting_day4_Merit_rep4

source_name: Barley seed day 4 germination, Merit


title: Malting_day4_Legacy_rep 2

source_name: Barley seed day 4 germination, Legacy


title: Malting_day4_Merit_rep2


title: BMDCs_PBS_ 6h_2

tag: gender


title: BMDCs_PBS_ 6h_3


title: NP_NP69 (250K_Sty2_SNP Array)

description: copy number variation analysis

source_name: immortalized nasopharyngeal epithelial cell line NP69

growth_protocol: Cells were grown in defined-KSFM medium supplemented with EGF (Invitrogen, Carlsbad, CA). Cells were cultured at 37°C in a humidified atmosphere of 5% CO2.

value: immortalized nasopharyngeal epithelial cell line Np69


title: NPC_5-8F (250K_Sty2_SNP Array)

description: copy number variation analysis

source_name: Nasopharyngeal carcinoma cell line 5-8F

value: nasopharyngeal carcinoma cell line 5-8F


title: Malting_day4_Legacy_rep 3


title: Malting_day4_Merit_rep3


title: NPC_HONE1 (250K_Sty2_SNP Array)

description: copy number variation analysis

source_name: Nasopharyngeal carcinoma cell line HONE1

value: nasopharyngeal carcinoma cell line HONE1


title: 100-600 nt nascent strands, hyb1

description: 100-600 nt nascent strands, hyb1


title: BMDCs_PBS_ 6h_1

source_name: bone marrow derived dendritic cells

value: female


title: gastric cancer patient31 censored in prospective phase

status: Public on Mar 04 2009

city: Suita

first: ATSUSHI

last: TAKENO

state: Osaka

address: 2-2, Yamadaoka

department: Surgery

institute: Osaka university

hyb_protocol: Hybridized for 16 h at 42 °C. Hybridization buffer and washing protocol was followed by the protocol supplied by Hitachi Software Engineering Co., Ltd. (DNA Chip Research Inc. / AceGene website)

scan_protocol: ScanArray HT (PerkinElmer Japan Co., Ltd.) was used for scanning. Array images were analyzed with DNASIS Array V2.6(Hitachi Software Engineering Co., Ltd.).

data_processing: In each sample, intensity values for both channels (Cy5 and Cy3) were independently transformed using a quantile equalization method, yielding pairs of normalized values of non-exponential scale. We enforced the normalized values to follow an independent hypothetical standard normal distribution, keeping only the rank within a sample and a chennel. The abundance of transcription for each probe was then defined by subtracting the value of Cy5 from that of Cy3, which are free from dye-sensor bias and can be treated just like the log ratio of Cy5 and Cy3.

source_name: 15 Total RNAs mixture from normal gastric mucosa labeled with Cyanine-3 (green).

label_protocol: Amino Allyl aRNA was synthesized by Amino Allyl MessageAmp aRNA Amplification Kit (Ambion).CyeDye coupling and fragmentation were performed using the protocol supplied by Hitachi Software Engineering Co., Ltd. (DNA Chip Research Inc. / AceGene website)

extract_protocol: Total RNA was purified from the clinical samples utilizing TRIzol reagent (Invitrogen, San Diego, CA) using the protocol supplied by the manufacturer.

treatment_protocol: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -85°C until RNA extraction.

value: mixture of normal gastric mucosa

value: primary gastric cancer

tag: phenotype

value: gastric cancer with no recurrence


title: gastric cancer patient27 censored in prospective phase


title: gastric cancer patient33 censored in prospective phase


title: gastric cancer patient29 censored in prospective phase


title: gastric cancer patient25 censored in prospective phase


title: gastric cancer patient26 censored in prospective phase


title: gastric cancer patient21 censored in prospective phase


title: gastric cancer patient23 censored in prospective phase


title: gastric cancer patient32 censored in prospective phase


title: gastric cancer patient30 censored in prospective phase


title: gastric cancer patient20 censored in prospective phase


title: gastric cancer patient14 censored in prospective phase


title: gastric cancer patient18 censored in prospective phase


title: gastric cancer patient22 censored in prospective phase


title: gastric cancer patient17 censored in prospective phase


title: gastric cancer patient24 censored in prospective phase


title: gastric cancer patient19 censored in prospective phase


title: gastric cancer patient15 censored in prospective phase


title: BMDCs_LPS_ 6h_3

value: 6 - 8 weeks


title: gastric cancer patient16 censored in prospective phase


title: gastric cancer patient13 censored in prospective phase


title: gastric cancer patient10 censored in prospective phase


title: gastric cancer patient8 censored in prospective phase


title: gastric cancer patient11 censored in prospective phase


title: gastric cancer patient4 censored in prospective phase


title: gastric cancer patient9 censored in prospective phase


title: gastric cancer patient6 censored in prospective phase


title: gastric cancer patient12 censored in prospective phase


title: gastric cancer patient5 censored in prospective phase


title: gastric cancer patient7 censored in prospective phase


title: gastric cancer patient3 censored in prospective phase


title: gastric cancer patient2 censored in prospective phase


title: gastric cancer patient15 with peritoneal relapse in prospective phase

source_name: gastric cancer patient with peritoneal relapse in prospective phase


title: gastric cancer patient11 with peritoneal relapse in prospective phase


title: gastric cancer patient10 with peritoneal relapse in prospective phase


title: gastric cancer patient12 with peritoneal relapse in prospective phase


title: gastric cancer patient14 with peritoneal relapse in prospective phase


title: gastric cancer patient8 with peritoneal relapse in prospective phase


title: gastric cancer patient1 censored in prospective phase


title: RVI079

city: London

first: Patricia

middle: Jean

last: Hunter

address: 30 Guilford Street

department: Rheumatology

country: United Kingdom

institute: UCL Institute of Child Health

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Affymetrix GeneChip Human U133 2.0 array. GeneChips were washed and stained on the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000.

data_processing: Data was normalised using MAS5.0.

source_name: Synovial fluid mononuclear cells

label_protocol: RNA was coverted to cDNA (Roche) using an oligod(T) primer and converted to cRNA using In Vitro Triscription labelling kit (Affymetrix).

extract_protocol: Cell were thawed and RNA was extracted using Qiagen Rneasy

treatment_protocol: Synovial fluid was aspirated from patients' knees. Mononuclear cells were isolated using density centrifugation with Lymphoprep. Cells were preserved in liquid nitrogen

tag: outcome at one year

value: persistent

value: Synovial fluid mononuclear cells


title: RVI085


title: gastric cancer patient13 with peritoneal relapse in prospective phase


title: gastric cancer patient9 with peritoneal relapse in prospective phase


title: PA47


title: PA291

value: extended


title: PA174


title: gastric cancer patient4 with peritoneal relapse in prospective phase


title: gastric cancer patient7 with peritoneal relapse in prospective phase


title: RVI037


title: gastric cancer patient2 with peritoneal relapse in prospective phase


title: gastric cancer patient37 with relapse free in prospective phase

source_name: gastric cancer patient with relapse free in prospective phase


title: gastric cancer patient6 with peritoneal relapse in prospective phase


title: gastric cancer patient5 with peritoneal relapse in prospective phase


title: gastric cancer patient3 with peritoneal relapse in prospective phase


title: PA281


title: gastric cancer patient1 with peritoneal relapse in prospective phase


title: gastric cancer patient34 with relapse free in prospective phase


title: gastric cancer patient35 with relapse free in prospective phase


title: gastric cancer patient36 with relapse free in prospective phase


title: gastric cancer patient32 with relapse free in prospective phase


title: PA124


title: PA206


title: gastric cancer patient30 with relapse free in prospective phase


title: gastric cancer patient31 with relapse free in prospective phase


title: gastric cancer patient27 with relapse free in prospective phase


title: gastric cancer patient25 with relapse free in prospective phase


title: gastric cancer patient28 with relapse free in prospective phase


title: gastric cancer patient29 with relapse free in prospective phase


title: gastric cancer patient26 with relapse free in prospective phase


title: gastric cancer patient24 with relapse free in prospective phase


title: gastric cancer patient23 with relapse free in prospective phase


title: gastric cancer patient13 with relapse free in prospective phase


title: gastric cancer patient19 with relapse free in prospective phase


title: gastric cancer patient21 with relapse free in prospective phase


title: gastric cancer patient10 with relapse free in prospective phase


title: gastric cancer patient9 with relapse free in prospective phase


title: gastric cancer patient11 with relapse free in prospective phase


title: gastric cancer patient22 with relapse free in prospective phase


title: gastric cancer patient18 with relapse free in prospective phase


title: gastric cancer patient20 with relapse free in prospective phase


title: gastric cancer patient15 with relapse free in prospective phase


title: gastric cancer patient17 with relapse free in prospective phase


title: gastric cancer patient12 with relapse free in prospective phase


title: gastric cancer patient14 with relapse free in prospective phase


title: gastric cancer patient16 with relapse free in prospective phase


title: gastric cancer patient8 with relapse free in prospective phase


title: gastric cancer patient7 with relapse free in prospective phase


title: gastric cancer patient6 with relapse free in prospective phase


title: gastric cancer patient5 with relapse free in prospective phase


title: gastric cancer patient4 with relapse free in prospective phase


title: gastric cancer patient2 with relapse free in prospective phase


title: gastric cancer patient3 with relapse free in prospective phase


title: gastric cancer patient10 with peritoneal relapse in retrospective phase

source_name: gastric cancer patient with peritoneal relapse in retrospective phase


title: gastric cancer patient13 with peritoneal relapse in retrospective phase


title: gastric cancer patient17 with peritoneal relapse in retrospective phase


title: gastric cancer patient16 with peritoneal relapse in retrospective phase


title: gastric cancer patient15 with peritoneal relapse in retrospective phase


title: gastric cancer patient1 with relapse free in prospective phase


title: gastric cancer patient14 with peritoneal relapse in retrospective phase


title: gastric cancer patient11 with peritoneal relapse in retrospective phase


title: gastric cancer patient8 with peritoneal relapse in retrospective phase


title: gastric cancer patient18 with peritoneal relapse in retrospective phase


title: FACS sorted cells enriched for hematopoietic stem cells (HSC) from BM donor 24_9

city: Oslo

first: June

middle: Helen

last: Myklebust

address: Montebello

department: Immunology

country: Norway

institute: The National Hospital

hyb_protocol: Samples were hybridized to the arrays as described in Alizadeh A. et al, Nature 403(6769):503-11.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a Axon GenePix Scanner (Axon Instruments) and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software.

data_processing: After background correction and removal of flagged values, data was normalized based on a global median normalization factor, and log base 2 (Cy5/Cy3) expression ratios were calculated to produce the values given in the data table.

source_name: reference RNA pool

label_protocol: Total RNA from the reference pool was labeled with Cy3 dUTP in a first strand cDNA reaction.

extract_protocol: A reference pool was created from total RNA isolated from nine different lymphoma cell lines (RNA control pool prepared at NIH) using TRIzol extraction.

tag: cell lines

value: Raji, Jurkat, L428, OCI-Ly3, OCI-Ly8, OCI-Ly1, SUDHL5, SUDHL6, and WSU1

source_name: aRNA, HSC_24_9

label_protocol: Antisense RNA (5 ug) from an experimental sample was labeled with Cy5 dUTP in a first strand cDNA reaction.

extract_protocol: Total RNA was extracted from 10,000 - 80,000 cells of each of the sorted cellular population (naive BC, centroblasts, centrocytes, memory B) with Absolutely RNA® Microprep Kit (Stratagene) followed by 2 rounds of linear amplification:  in a 10 ul reverse transcription reaction, total RNA was transcribed by priming with a dT/T7-primer. Second strand synthesis was initiated by RNase digestion. The purified double stranded cDNA served as the template for the first round of in vitro aRNA transcription (MEGAscript® T7 Kit, Ambion Inc.). For the subsequent round of amplification, the first strand cDNA was primed with random hexamers. The synthesis of the second strand was initiated by annealing a dT/T7-primer to the aRNA:cDNA heteroduplex with partially digested aRNA. After purification, a second round of in vitro transcription was performed. The quality of the aRNA was always detected by the Agilent 2100 bioanalyzer.

value: bone marrow


title: gastric cancer patient12 with peritoneal relapse in retrospective phase


title: gastric cancer patient7 with peritoneal relapse in retrospective phase


title: gastric cancer patient3 with peritoneal relapse in retrospective phase


title: gastric cancer patient1 with peritoneal relapse in retrospective phase


title: gastric cancer patient38 with relapse free in retrospective phase

source_name: gastric cancer patient with relapse free in retrospective phase


title: gastric cancer patient5 with peritoneal relapse in retrospective phase


title: gastric cancer patient4 with peritoneal relapse in retrospective phase


title: FACS sorted cells enriched for hematopoietic stem cells (HSC) from BM donor 9_1

source_name: aRNA, HSC_9_1


title: gastric cancer patient6 with peritoneal relapse in retrospective phase


title: gastric cancer patient2 with peritoneal relapse in retrospective phase


title: FACS sorted cells enriched for hematopoietic stem cells (HSC) from BM donor 9_10

source_name: aRNA, HSC_9_10


title: gastric cancer patient9 with peritoneal relapse in retrospective phase


title: FACS sorted cells enriched for hematopoietic stem cells (HSC) from BM donor 3_5b

source_name: aRNA, HSC_3_5b


title: gastric cancer patient37 with relapse free in retrospective phase


title: gastric cancer patient36 with relapse free in retrospective phase


title: gastric cancer patient35 with relapse free in retrospective phase


title: FACS sorted precursor B cells (preB) from BM donor 23_10

source_name: aRNA, preB_23_10


title: FACS sorted cells enriched for hematopoietic stem cells (HSC) from BM donor 3_5a

source_name: aRNA, HSC_3_5a


title: FACS sorted precursor B cells (preB) from BM donor 25_9

source_name: aRNA, preB_25_9


title: FACS sorted precursor B cells (preB) from BM donor 12_2

source_name: aRNA, preB_12_2


title: FACS sorted cells enriched for hematopoietic stem cells (HSC) from BM donor 15_10

source_name: aRNA, HSC_15_10


title: FACS sorted precursor B cells (preB) from BM donor 3_11

source_name: aRNA, preB_3_11


title: FACS sorted precursor B cells (preB) from BM donor 27_1

source_name: aRNA, preB_27_1


title: gastric cancer patient34 with relapse free in retrospective phase

source_name: 15 Total RNAs mixture from normal gastric mucosa labeled with Cyanine-3 (green).


title: gastric cancer patient30 with relapse free in retrospective phase


title: gastric cancer patient32 with relapse free in retrospective phase


title: FACS sorted precursor B cells (preB) from BM donor 10_2

source_name: aRNA, preB_10_2


title: FACS sorted progenitor B cells (proB) from BM donor 15_10

source_name: aRNA, proB_15_10


title: gastric cancer patient33 with relapse free in retrospective phase


title: gastric cancer patient31 with relapse free in retrospective phase


title: FACS sorted progenitor B cells (proB) from BM donor 25_9

source_name: aRNA, proB_25_9


title: gastric cancer patient29 with relapse free in retrospective phase


title: gastric cancer patient27 with relapse free in retrospective phase


title: gastric cancer patient28 with relapse free in retrospective phase


title: gastric cancer patient26 with relapse free in retrospective phase


title: FACS sorted progenitor B cells (proB) from BM donor 23_10

source_name: reference RNA pool

source_name: aRNA, proB_23_10


title: FACS sorted progenitor B cells (proB) from BM donor 12_2

source_name: aRNA, proB_12_2


title: FACS sorted progenitor B cells (proB) from BM donor 3_11

source_name: aRNA, proB_3_11


title: gastric cancer patient22 with relapse free in retrospective phase

source_name: gastric cancer patient with relapse free in retrospective phase


title: gastric cancer patient23 with relapse free in retrospective phase


title: FACS sorted Common lymphoid cells (CLP) from BM donor 10_2

source_name: aRNA, CLP_10_2


title: FACS sorted Common lymphoid cells (CLP) from BM donor 12_2

source_name: aRNA, CLP_12_2


title: gastric cancer patient19 with relapse free in retrospective phase


title: gastric cancer patient24 with relapse free in retrospective phase


title: FACS sorted progenitor B cells (proB) from BM donor 27_1

source_name: aRNA, proB_27_1


title: gastric cancer patient16 with relapse free in retrospective phase


title: gastric cancer patient21 with relapse free in retrospective phase


title: gastric cancer patient15 with relapse free in retrospective phase


title: gastric cancer patient20 with relapse free in retrospective phase


title: gastric cancer patient18 with relapse free in retrospective phase


title: PLC/PRF/5, Mock, 6h

first: Julja

last: Burchard

address: 33 Avenue Louis Pasteur

department: Computational & Systems Biology

institute: Merck & Co., Inc.

description:
conditions: PLC/PRF/5, Mock, 6h
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques.  Arrays are hybridized for 18 hours at 45?C with vigorous mixing.   Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed.  Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were loaded into the Rosetta Resolver? system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260).  Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value.  The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1111).

label: Biotin is incorporated during the amplification.  This binds a streptavidin-conjugated phycoerythrin during the post-hybridization staining process that provides the measurable signal.

source_name: PLC/PRF/5 cells

label_protocol: The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin.  After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.  The labeled molecules are biotinylated-cRNA.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation.  Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.


title: PLC/PRF/5, Mock, 48h

description:
conditions: PLC/PRF/5, Mock, 48h
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.


title: PLC/PRF/5, Mock, 12h

description:
conditions: PLC/PRF/5, Mock, 12h
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.


title: FACS sorted Common lymphoid cells (CLP) from BM donor 25_9

source_name: aRNA, CLP_25_9


title: gastric cancer patient17 with relapse free in retrospective phase


title: HUH7, Mock, 6h

description:
conditions: HUH7, Mock, 6h
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.

source_name: HUH7 cells


title: gastric cancer patient14 with relapse free in retrospective phase


title: gastric cancer patient13 with relapse free in retrospective phase


title: FACS sorted Common lymphoid cells (CLP) from BM donor 21_4

source_name: aRNA, CLP_21_4


title: gastric cancer patient11 with relapse free in retrospective phase


title: FACS sorted Common lymphoid cells (CLP) from BM donor 3_2

source_name: aRNA, CLP_3_2


title: gastric cancer patient12 with relapse free in retrospective phase

source_name: 15 Total RNAs mixture from normal gastric mucosa labeled with Cyanine-3 (green).


title: HUH7, Mock, 12h

description:
conditions: HUH7, Mock, 12h
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.


title: FACS sorted Common lymphoid cells (CLP) from BM donor 3_11

source_name: aRNA, CLP_9_1


title: gastric cancer patient8 with relapse free in retrospective phase


title: FACS sorted Immature B cells from BM donor 3_11

source_name: aRNA, immature B_3_11


title: gastric cancer patient6 with relapse free in retrospective phase


title: gastric cancer patient4 with relapse free in retrospective phase


title: gastric cancer patient10 with relapse free in retrospective phase


title: FACS sorted Immature B cells from BM donor 25_9

source_name: aRNA, immature B_25_9


title: gastric cancer patient9 with relapse free in retrospective phase


title: gastric cancer patient7 with relapse free in retrospective phase


title: gastric cancer patient5 with relapse free in retrospective phase


title: gastric cancer patient2 with relapse free in retrospective phase


title: HUH7, Mock, 48h

description:
conditions: HUH7, Mock, 48h
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.


title: HUH7, Mock, 24h

description:
conditions: HUH7, Mock, 24h
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.


title: gastric cancer patient3 with relapse free in retrospective phase


title: gastric cancer patient1 with relapse free in retrospective phase


title: FACS sorted Immature B cells from BM donor 15_10

source_name: reference RNA pool

source_name: aRNA, immature B_15_10


title: FACS sorted Immature B cells from BM donor 24_9

source_name: aRNA, immature B_24_9


title: gastric cancer patient25 with relapse free in retrospective phase


title: Hepa1-6, Mock, 6h

description:
conditions: Hepa1-6, Mock, 6h
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.

source_name: Hepa1-6 cells


title: centroblasts from normal  human tonsils

source_name: aRNA, CB

value: tonsil


title: Hepa1-6, Mock, 12h

description:
conditions: Hepa1-6, Mock, 12h
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.


title: centrocytes from normal human tonsils

source_name: aRNA, CC


title: FACS sorted Immature B cells from BM donor 12_2

source_name: aRNA, immature B_12_2


title: FACS sorted Immature B cells from BM donor 27_1

source_name: aRNA,  immature B_27_1


title: memory B cells from normal human tonsils

source_name: aRNA, memory BC