title: naive B cells from normal human tonsils

source_name: aRNA, naive BC


title: Hepa1-6, Mock, 24h

status: Public on Mar 04 2009

type: RNA

city: Boston

first: Julja

last: Burchard

state: MA

address: 33 Avenue Louis Pasteur

department: Computational & Systems Biology

country: USA

institute: Merck & Co., Inc.

description:
conditions: Hepa1-6, 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.

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.

molecule: total RNA

organism: Mus musculus

source_name: Hepa1-6 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.

tag: cell line


title: AEx, biological rep6

status: Public on Mar 03 2009

city: Pittsburgh

first: Kazuhisa

last: Konishi

state: PA

address: 1212 Kaufmann Building  3471 Fifth Ave

department: Pulmonry, Allergy, and Critical Care Medicine

institute: University of Pittsburgh

description: Lung tissue samples obtained from the University of Pittsburgh Health Sciences Tissue Bank. Gene expression data from a lung with usual interstitial pneumonia.

hyb_protocol: Following fragmentation, 1.5 ug of cRNA were hybridized for 17 hr at 65C on Agilent 4x44k Whole Human Genome Array. Arrays were washed according to the manufacturer's protocol.

scan_protocol: Agilent Scanner protocol

data_processing: Agilent Feature Extraction

organism: Homo sapiens

source_name: Lung tissue with acute exacerbations of idiopathic pulmonary fibrosis (IPF-AEx), biological rep6

label_protocol: Cy3 labeled cRNA were prepared according to the standard Agilent protocol from 500ng total RNA.

extract_protocol: Trizol extraction of total RNA followed by RNeasy cleanup was performed according to the manufacturers' instructions.

tag: Tissue from a patient with pathological diagnosis of usual interstitial pneumonia with diffuse alveolar damage.


title: AEx, biological rep7

source_name: Lung tissue with acute exacerbations of idiopathic pulmonary fibrosis (IPF-AEx), biological rep7


title: AEx, biological rep8

source_name: Lung tissue with acute exacerbations of idiopathic pulmonary fibrosis (IPF-AEx), biological rep8


title: GFPshVsMLL5sh1 R (biological replicate 2)

city: Hyderabad

first: Jyotsna

last: Dhawan

state: Andhra pradesh

address: Uppal road

department: Cell Biology

country: India

institute: Centre for cellular and Molecular Biology

description: Expression profile of differentially expressed genes in MLL5 knock down C2C12 cells

hyb_protocol: Purified Cy3,Cy5 Labelled cDNA was incubated on the NIA15K5  chip at 42 degree celsius for 16hr.washed with 1XSSC+0.2%SDS for 5 min then second wash with 0.1XSSC+0.2%SDS for 5 min and third wash with 0.1XSSC for 5 min and dried the chip by spinning briefly.

scan_protocol: Scanned using  Molecular Dynamics scanner using excitation wavelengths of 543nm and 663nm.

data_processing: LOWESS normalized, TIGR MIDAS, background subtracted VALUE data obtained from log2 of processed Experimental signal/processed reference signal.

source_name: C2C12 cell line transfected with MLL5sh RNA

label_protocol: 20 micrograms of RNA is taken for labelling with Cy3/Cy5 dyes. Reverse transcription was performed to make cDNA (1hr 30 min at 42 degrees celsius using SuperScript II from Invitrogen). Unincorporated nucleotides were removed using Millipore Spin columns.

growth_protocol: Grown in Dulbecco's modified Eagle medium supplemented with 20% Fetal calf serum

extract_protocol: RNA was isolated using Trizol Invitrogen)

treatment_protocol: Synchronized cells in G0 and reactivated to enter cell cycle by replating and grown for 24hrs to get synchronized S phase cells

tag: genotype

value: transfected with MLL5sh RNA

tag: cell type

value: myoblast

tag: growth protocol

value: S phase enriched

source_name: C2C12 cell line transfected with GFPsh RNA

value: transfected with GFPsh RNA


title: Hepa1-6, Mock, 48h

description:
conditions: Hepa1-6, 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: AEx, biological rep5

source_name: Lung tissue with acute exacerbations of idiopathic pulmonary fibrosis (IPF-AEx), biological rep5


title: GFPshVsMLL5sh1 F (biological replicate 1)


title: AEx, biological rep4

source_name: Lung tissue with acute exacerbations of idiopathic pulmonary fibrosis (IPF-AEx), biological rep4


title: AEx, biological rep2

source_name: Lung tissue with acute exacerbations of idiopathic pulmonary fibrosis (IPF-AEx), biological rep2


title: FOM173/Nic-rep2

city: Philadelphia

first: Gao

last: Zhang

address: 3601 SPRUCE ST

department: Molecular and Cellular Oncogenesis Program

institute: Wistar Institute

description: human melanocyte transfected with Notch replicate 2

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was preprocessed by BeadStudio. It was normalized.

source_name: human melanocyte

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

value: neonatal melanocytes


title: AEx, biological rep1

source_name: Lung tissue with acute exacerbations of idiopathic pulmonary fibrosis (IPF-AEx), biological rep1


title: AEx, biological rep3

source_name: Lung tissue with acute exacerbations of idiopathic pulmonary fibrosis (IPF-AEx), biological rep3


title: FOM173/Nic-rep1

description: human melanocyte transfected with Notch replicate 1


title: FOM173-rep1

description: human melanocyte replicate 1


title: normal prostate, patient 80 (Sty)

type: genomic

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: normal prostate, patient 80 (Sty)

hyb_protocol: The amplified, fragmented and biotinylated DNA were hybridized to 250K Sty1 or Nsp1 chips at 49oC for 16 hours.

scan_protocol: Genechips were washed and stained according to the Affymetrix protocol GenomeWideSNP5v1_450.  Washed and stained chips were scanned using the Affymetrix 3000 GeneChip scanner.

data_processing: Affymetrix CEL and CHP files were processed using dChip (with Invariant Set normalization and “Average” modeling).

label: biotin

molecule: genomic DNA

source_name: normal prostate

label_protocol: 250 ng of high quality genomic DNA were digested with either Sty1 or Nsp1 according to the Genome-wide Human SNP Sty/Nsp 5.0 assay protocol (Affymetrix Inc, Santa Clara, CA).

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

tag: normal prostate


title: normal prostate, patient 96 (Nsp)

description: normal prostate, patient 96 (Nsp)


title: normal prostate, patient 80 (Nsp)

description: normal prostate, patient 80 (Nsp)


title: normal prostate, patient 167 (Sty)

description: normal prostate, patient 167 (Sty)


title: prostate tumor, patient 96 (Sty)

description: prostate tumor, patient 96 (Sty)

source_name: prostate cancer

tag: prostate cancer


title: prostate tumor, patient 80 (Sty)

description: prostate tumor, patient 80 (Sty)


title: prostate tumor, patient 80 (Nsp)

description: prostate tumor, patient 80 (Nsp)


title: normal prostate, patient 167 (Nsp)

description: normal prostate, patient 167 (Nsp)


title: normal prostate, patient 154 (Nsp)

description: normal prostate, patient 154 (Nsp)


title: normal prostate, patient 96 (Sty)

description: normal prostate, patient 96 (Sty)


title: prostate tumor, patient 167 (Nsp)

description: prostate tumor, patient 167 (Nsp)


title: prostate tumor, patient 167 (Sty)

description: prostate tumor, patient 167 (Sty)


title: prostate tumor, patient 96 (Nsp)

description: prostate tumor, patient 96 (Nsp)


title: normal prostate, patient 140 (Nsp)

description: normal prostate, patient 140 (Nsp)


title: prostate tumor, patient 140 (Nsp)

description: prostate tumor, patient 140 (Nsp)


title: prostate tumor, patient 140 (Sty)

description: prostate tumor, patient 140 (Sty)


title: prostate tumor, patient 154 (Sty)

description: prostate tumor, patient 154 (Sty)


title: normal prostate, patient 154 (Sty)

description: normal prostate, patient 154 (Sty)


title: prostate tumor, patient 138 (Sty)

description: prostate tumor, patient 138 (Sty)


title: prostate tumor, patient 154 (Nsp)

description: prostate tumor, patient 154 (Nsp)


title: normal prostate, patient 138 (Nsp)

description: normal prostate, patient 138 (Nsp)


title: normal prostate, patient 138 (Sty)

description: normal prostate, patient 138 (Sty)


title: prostate tumor, patient 138 (Nsp)

description: prostate tumor, patient 138 (Nsp)


title: normal prostate, patient 137 (Nsp)

description: normal prostate, patient 137 (Nsp)


title: normal prostate, patient 140 (Sty)

description: normal prostate, patient 140 (Sty)


title: prostate tumor, patient 137 (Nsp)

description: prostate tumor, patient 137 (Nsp)


title: prostate tumor, patient 137 (Sty)

description: prostate tumor, patient 137 (Sty)


title: normal prostate, patient 137 (Sty)

description: normal prostate, patient 137 (Sty)


title: normal prostate, patient 128 (Nsp)

description: normal prostate, patient 128 (Nsp)


title: prostate tumor, patient 128 (Nsp)

description: prostate tumor, patient 128 (Nsp)


title: normal prostate, patient 128 (Sty)

description: normal prostate, patient 128 (Sty)


title: FOM173-rep2

description: human melanocyte replicate 2


title: normal prostate, patient 122 (Nsp)

description: normal prostate, patient 122 (Nsp)


title: prostate tumor, patient 128 (Sty)

description: prostate tumor, patient 128 (Sty)


title: normal prostate, patient 115 (Sty)

description: normal prostate, patient 115 (Sty)


title: prostate tumor, patient 115 (Sty)

description: prostate tumor, patient 115 (Sty)


title: prostate tumor, patient 110 (Sty)

description: prostate tumor, patient 110 (Sty)


title: prostate tumor, patient 122 (Nsp)

description: prostate tumor, patient 122 (Nsp)


title: normal prostate, patient 115 (Nsp)

description: normal prostate, patient 115 (Nsp)


title: normal prostate, patient 122 (Sty)

description: normal prostate, patient 122 (Sty)


title: normal prostate, patient 75 (Nsp)

description: normal prostate, patient 75 (Nsp)


title: normal prostate, patient 75 (Sty)

description: normal prostate, patient 75 (Sty)


title: normal prostate, patient 60 (Nsp)

description: normal prostate, patient 60 (Nsp)


title: prostate tumor, patient 110 (Nsp)

description: prostate tumor, patient 110 (Nsp)


title: prostate tumor, patient 60 (Nsp)

description: prostate tumor, patient 60 (Nsp)


title: prostate tumor, patient 115 (Nsp)

description: prostate tumor, patient 115 (Nsp)


title: normal prostate, patient 60 (Sty)

description: normal prostate, patient 60 (Sty)


title: prostate tumor, patient 75 (Nsp)

description: prostate tumor, patient 75 (Nsp)


title: prostate tumor, patient 60 (Sty)

description: prostate tumor, patient 60 (Sty)


title: prostate tumor, patient 75 (Sty)

description: prostate tumor, patient 75 (Sty)


title: normal prostate, patient 110 (Nsp)

description: normal prostate, patient 110 (Nsp)


title: prostate tumor, patient 58 (Sty)

description: prostate tumor, patient 58 (Sty)


title: normal prostate, patient 52 (Sty)

description: normal prostate, patient 52 (Sty)


title: normal prostate, patient 58 (Sty)

description: normal prostate, patient 58 (Sty)


title: prostate tumor, patient 58 (Nsp)

description: prostate tumor, patient 58 (Nsp)


title: normal prostate, patient 110 (Sty)

description: normal prostate, patient 110 (Sty)


title: normal prostate, patient 45 (Sty)

description: normal prostate, patient 45 (Sty)


title: prostate tumor, patient 122 (Sty)

description: prostate tumor, patient 122 (Sty)


title: prostate tumor, patient 52 (Sty)

description: prostate tumor, patient 52 (Sty)


title: normal prostate, patient 58 (Nsp)

description: normal prostate, patient 58 (Nsp)


title: normal prostate, patient 52 (Nsp)

description: normal prostate, patient 52 (Nsp)


title: prostate tumor, patient 31 (Sty)

description: prostate tumor, patient 31 (Sty)


title: normal prostate, patient 31 (Sty)

description: normal prostate, patient 31 (Sty)


title: prostate tumor, patient 45 (Sty)

description: prostate tumor, patient 45 (Sty)


title: normal prostate, patient 25 (Sty)

description: normal prostate, patient 25 (Sty)


title: prostate tumor, patient 27 (Sty)

description: prostate tumor, patient 27 (Sty)


title: normal prostate, patient 27 (Sty)

description: normal prostate, patient 27 (Sty)


title: normal prostate, patient 24 (Sty)

description: normal prostate, patient 24 (Sty)


title: normal prostate, patient 45 (Nsp)

description: normal prostate, patient 45 (Nsp)


title: prostate tumor, patient 31 (Nsp)

description: prostate tumor, patient 31 (Nsp)


title: prostate tumor, patient 45 (Nsp)

description: prostate tumor, patient 45 (Nsp)


title: prostate tumor, patient 25 (Sty)

description: prostate tumor, patient 25 (Sty)


title: prostate tumor, patient 24 (Sty)

description: prostate tumor, patient 24 (Sty)


title: Foxp2wt/wt_strKo_21d_f_run3_litter10

status: Public on Mar 02 2009

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 21 days old wild-type mouse, belonging to strain Ko

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:Ko, age:21days

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).

tag: strain

value: Ko - a knock-out or wild-type mouse from crosses between Foxp2wt/ko and C57BL/6J animals

tag: age

tag: sex

value: female

tag: run (microarray batch)

tag: litter

tag: biological replicate

tag: tissue

value: striatum (brain)


title: prostate tumor, patient 27 (Nsp)

description: prostate tumor, patient 27 (Nsp)


title: Foxp2wt/wt_strKo_21d_m_run2_litter10

value: male


title: Foxp2wt/wt_strKo_18d_m_run1_litter12

description: Gene expression data from the striatum of a 18 days old wild-type mouse, belonging to strain Ko

source_name: Mus musculus striatum, genotype:Foxp2wt/wt, strain:Ko, age:18days


title: Foxp2wt/wt_strKo_18d_f_run2_litter12


title: normal prostate, patient 31 (Nsp)

description: normal prostate, patient 31 (Nsp)


title: Foxp2wt/wt_strKo_15d_m_run3_litter11

description: Gene expression data from the striatum of a 15 days old wild-type mouse, belonging to strain Ko

source_name: Mus musculus striatum, genotype:Foxp2wt/wt, strain:Ko, age:15days


title: normal prostate, patient 27 (Nsp)

description: normal prostate, patient 27 (Nsp)


title: Foxp2wt/wt_strKo_15d_f_run1_litter8


title: Foxp2wt/ko_strKo_18d_m_run3_litter12

description: Gene expression data from the striatum of a 18 days old mouse with one Foxp2 allele knocked-out (Foxp2wt/ko), belonging to strain Ko

source_name: Mus musculus striatum, genotype:Foxp2wt/ko, strain:Ko, age:18days


title: Foxp2wt/ko_strKo_21d_f_run2_litter10

description: Gene expression data from the striatum of a 21 days old mouse with one Foxp2 allele knocked-out (Foxp2wt/ko), belonging to strain Ko

source_name: Mus musculus striatum, genotype:Foxp2wt/ko, strain:Ko, age:21days


title: Foxp2wt/ko_strKo_21d_m_run3_litter10


title: Foxp2wt/ko_strKo_18d_f_run2_litter12


title: Foxp2wt/ko_strKo_21d_f_run1_litter12


title: Foxp2wt/ko_strKo_21d_f_run3_litter10


title: prostate tumor, patient 24 (Nsp)

description: prostate tumor, patient 24 (Nsp)


title: Foxp2wt/ko_strKo_15d_f_run1_litter8

description: Gene expression data from the striatum of a 15 days old mouse with one Foxp2 allele knocked-out (Foxp2wt/ko), belonging to strain Ko

source_name: Mus musculus striatum, genotype:Foxp2wt/ko, strain:Ko, age:15days


title: Foxp2wt/ko_strKo_15d_f_run3_litter8


title: Foxp2wt/ko_strKo_18d_m_run2_litter7


title: prostate tumor, patient 25 (Nsp)

description: prostate tumor, patient 25 (Nsp)


title: Foxp2wt/wt_strKi_21d_m_run1_litter2

description: Gene expression data from the striatum of a 21 days old wild-type mouse, belonging to strain Ki

source_name: Mus musculus striatum, genotype:Foxp2wt/wt, strain:Ki, age:21days

value: Ki - a knock-in or wild-type mouse from crosses of Foxp2wt/hum animals (clone no. 5H11)


title: Foxp2wt/ko_strKo_15d_m_run2_litter9


title: Foxp2wt/wt_strKi_18d_m_run3_litter1

description: Gene expression data from the striatum of a 18 days old wild-type mouse, belonging to strain Ki

source_name: Mus musculus striatum, genotype:Foxp2wt/wt, strain:Ki, age:18days


title: Foxp2wt/ko_strKo_15d_m_run1_litter10


title: Foxp2wt/wt_strKi_21d_f_run2_litter2


title: prostate tumor, patient 52 (Nsp)

description: prostate tumor, patient 52 (Nsp)


title: Foxp2wt/wt_strKi_18d_f_run3_litter1


title: Foxp2wt/wt_strKi_15d_m_run2_litter5

description: Gene expression data from the striatum of a 15 days old wild-type mouse, belonging to strain Ki

source_name: Mus musculus striatum, genotype:Foxp2wt/wt, strain:Ki, age:15days


title: Foxp2wt/wt_strKi_15d_f_run1_litter6


title: Foxp2hum/hum_strKi_21d_m_run3_litter2

description: Gene expression data from the striatum of a 21 days old mouse homozygous for the human Foxp2 allele (Foxp2hum/hum), belonging to strain Ki

source_name: Mus musculus striatum, genotype:Foxp2hum/hum, strain:Ki, age:21days


title: Foxp2hum/hum_strKi_18d_m_run2_litter1

description: Gene expression data from the striatum of a 18 days old mouse homozygous for the human Foxp2 allele (Foxp2hum/hum), belonging to strain Ki

source_name: Mus musculus striatum, genotype:Foxp2hum/hum, strain:Ki, age:18days


title: Foxp2hum/hum_strKi_15d_m_run3_litter6

description: Gene expression data from the striatum of a 15 days old mouse homozygous for the human Foxp2 allele (Foxp2hum/hum), belonging to strain Ki

source_name: Mus musculus striatum, genotype:Foxp2hum/hum, strain:Ki, age:15days


title: Foxp2hum/hum_strKi_21d_f_run1_litter2


title: Foxp2hum/hum_strKi_18d_m_run1_litter4


title: Foxp2hum/hum_strKi_15d_m_run1_litter6


title: Foxp2hum/hum_strKi_15d_f_run3_litter5


title: Foxp2hum/hum_strKi_18d_f_run2_litter4


title: Yeast_freeze_2day_rep1

status: Public on Feb 28 2009

city: Tsukuba

first: Jun

last: Shima

state: Ibaraki

address: 2-1-12 Kannondai

country: Japan

institute: National Food Research Institute

description: Statistical analysis after data acquisition and normalization of expression data were performed using GeneSpring ver.7.3.1 (Agilent Technologies, Palo Alto, CA, USA) based on the gene expression data from two independent experiments. After data transformation to GeneSpring, per-chip normalization to the 50th percentile was performed, and per-gene normalization to the control samples (non freeze sample: 0h) was applied to the per-chip normalized data.

hyb_protocol: At 45degree for 16h.

scan_protocol: GeneChip scanner

data_processing: GeneChip operating system (GCOS)

label: The biotinyated RNA

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: Yeast, freeze, 2day

label_protocol: Accoding to the Affymetrix user's mannual.

extract_protocol: Poly A RNA was enriched from total RNA with Oligotex dT30.

treatment_protocol: The strain was grown at 30 oC until log growth phase (OD600=1) in YPD medium. Cells were harvested by centrifugation, washed in distilled water, and suspended in equal volume of distilled water. Then an aliquot of 5 ml was taken from the cell cultures and used as the control without freezing (0 h). The remaining cell cultures were divided into 5 ml and frozen at –30 °C for 24 h or 48 h. The frozen cell cultures were then thawed at 30 °C in water bath for 10 min.


title: Foxp2hum/hum_strKi_15d_f_run2_litter5


title: Foxp2hum/hum_strKi_21d_f_run3_litter3


title: Yeast_freeze_1day_rep2

source_name: Yeast, freeze, 1day


title: Yeast_freeze_2day_rep2

hyb_protocol: At 45degree for 16h

label_protocol: Accoding to the Affymetrix user's mannual

extract_protocol: RNA was extracted from the yeast cells using the hot phenol method. Poly(A)+ RNA was enriched from total RNA by using an Oligotex dt30 (Super) mRNA purification kit (Takara Bio, Ohtsu, Japan).


title: Yeast_freeze_1day_rep1


title: normal prostate, patient 25 (Nsp)

description: normal prostate, patient 25 (Nsp)


title: Yeast_freeze_0day_rep2

source_name: Yeast, freeze, 0day


title: Yeast_freeze_0day_rep1


title: Sample_ETS1

status: Public on Feb 16 2009

city: Chicago

first: monika

last: stankiewicz

state: IL

address: 303 E. Superior St. Lurie Bldg 5-250

department: Hematology/Oncology

institute: Northwestern University

hyb_protocol: The samples were hybridized to the Illumina Mouse Ref8v1.1 Expression Beadchip Array following manufacturers instructions.

data_processing: The data was preprocessed by Bioconductor lumi package (version 1.7.18). It was vst transformed and quantile normalized.

extract_protocol: Cells from the fourth replating were collected from methylcellulose and RNAs for gene expression profiling were isolated with the Qiagen RNeasy Plus mini kit.

tag: Sample ETS1


title: Sample_Fli3

tag: Sample FLI3


title: Sample_ETS2

tag: Sample ETS2


title: Sample_Fli2

tag: Sample FLI2


title: Sample_ERG2

tag: Sample ERG2


title: Sample_ETS3

tag: Sample ETS3


title: Sample_ERG3

tag: Sample ERG3


title: 251486814895_A01

status: Public on Feb 05 2009

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: Phagocytosis represents a mechanism used by macrophages to remove pathogens and cellular debris. Recent evidence suggested that amino acid or glucose deprivation may cause an increase in phagocytosis of heat-inactivated Escherichia coli and Staphylococcus aureus by macrophages, but not the uptake of platelets, apoptotic cells or beads. Increased phagocytosis of bacteria could be blocked by phagocytosis inhibitors and depended on p38 MAP kinase activity. To examine potentially important downstream pathways linked to EBSS-induced starvation and p38 MAP kinase activation, a full genome microarray representing over 41,000 mouse genes or transcripts was probed with cDNA isolated from J774A.1 macrophages that were treated with EBSS, EBSS supplemented with the p38 inhibitor SB202190 or control medium supplemented with 10% fetal bovine serum.

hyb_protocol: For Cy3 14pmol and for Cy5 10 pmol incorporated dye was fragmented and resuspended in 55ul hybridization solution (Agilent).  The arrays were hybridized in microarray hybridization chambers (Agilent) overnight at 65ºC, rpm=10 for 17 hours.

scan_protocol: After washing the slides were scanned with a DNA microarray scanner (Agilent) using the `extended dynamic range' and images were processed with the Feature Extraction Software version 9.5 (Agilent).

data_processing: Log-ratio of the Agilent processed signal values (i.e., feature gProcessedSignal for the Cy3 signal and rProcessedSignal for the Cy5 signal from Agilent Feature Extraction v9.5.3.1) were used for the data analysis.  In case of multiple probes for the same Agilent ID, log-ratios were averaged.

label_protocol: Probes were prepared from 1 µg total RNA using the Low RNA input Fluorescent Linear Amplification Kit for dual color (Agilent) and the Cy5 CTP of Amersham. Probes were verified for amplification yield and incorporation efficiency by measuring the RNA concentration at 280 nm, Cy5 incorporation at 650 nm using a Nanodrop.

extract_protocol: Total RNA was prepared from cultured cells using the Absolutely RNA Miniprep Kit (Stratagene, La Jolla, CA). All RNA samples were treated with RNase-free DNase I. RNA quality was verified on an Agilent 2100 Bioanalyser using the RNA 6000 Nano LabChip kit (Agilent Technologies, Palo Alto, CA).

tag: J774A.1 cells incubated in RPMI 1640 medium supplemented with 10% fetal bovine serum for 6 hours

label_protocol: Probes were prepared from 1 µg total RNA using the Low RNA input Fluorescent Linear Amplification Kit for dual color (Agilent) and the Cy5 CTP of Amersham. Probes were verified for amplification yield and incorporation efficiency by measuring the RNA concentration at 280 nm, Cy3 incorporation at 550 nm using a Nanodrop.

tag: J774A.1 cells incubated in Earle’s Balanced Salt Solution (EBSS) for 6 hours


title: PLC/PRF/5, APOB-Hs4, 10nM, 48h

status: Public on Feb 01 2009

description:
PLC/PRF/5, APOB-Hs4, 10nM, 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.

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 45oC 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.

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).

source_name: PLC/PRF/5 cells

tag: cell line


title: 251486814895_A02

tag: J774A.1 cells incubated in Earle’s Balanced Salt Solution (EBSS) for 6 hours in the presence of the p38 inhibitor SB202190 (10 µM)


title: 251486814895_A03

hyb_protocol: For Cy3 14pmol and for Cy5 10 pmol incorporated dye was fragmented and resuspended in 55 ul hybridization solution (Agilent).  The arrays were hybridized in microarray hybridization chambers (Agilent) overnight at 65ºC, rpm=10 for 17 hours.


title: Sample_ETS4

tag: Sample ETS4


title: normal prostate, patient 24 (Nsp)

description: normal prostate, patient 24 (Nsp)

source_name: normal prostate

tag: normal prostate


title: Sample_Fli4

tag: Sample FLI4


title: Sample_Fli1

tag: Sample FLI1


title: PLC/PRF/5, APOB-Hs3, 10nM, 48h

description:
PLC/PRF/5, APOB-Hs3, 10nM, 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, APOB-Hs4, 10nM, 6h

description:
PLC/PRF/5, APOB-Hs4, 10nM, 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.


title: PLC/PRF/5, APOB-Hs1, 10nM, 6h

description:
PLC/PRF/5, APOB-Hs1, 10nM, 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.


title: PLC/PRF/5, Apob-Mm2, 10nM, 6h

description:
PLC/PRF/5, Apob-Mm2, 10nM, 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.


title: PLC/PRF/5, APOB-Hs2, 10nM, 6h

description:
PLC/PRF/5, APOB-Hs2, 10nM, 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.


title: PLC/PRF/5, APOB-Hs3, 10nM, 6h

description:
PLC/PRF/5, APOB-Hs3, 10nM, 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.


title: PLC/PRF/5, APOB-Hs4, 10nM, 12h

description:
PLC/PRF/5, APOB-Hs4, 10nM, 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: PLC/PRF/5, APOB-Hs2, 10nM, 12h

description:
PLC/PRF/5, APOB-Hs2, 10nM, 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: PLC/PRF/5, APOB-Hs2, 10nM, 48h

description:
PLC/PRF/5, APOB-Hs2, 10nM, 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, APOB-Hs1, 10nM, 48h

description:
PLC/PRF/5, APOB-Hs1, 10nM, 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, RAD18, 10nM, 6h

description:
PLC/PRF/5, RAD18, 10nM, 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.


title: PLC/PRF/5, APOB-Hs1, 10nM, 12h

description:
PLC/PRF/5, APOB-Hs1, 10nM, 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: PLC/PRF/5, Apob-Mm2, 10nM, 12h

description:
PLC/PRF/5, Apob-Mm2, 10nM, 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: PLC/PRF/5, APOB-Hs3, 10nM, 12h

description:
PLC/PRF/5, APOB-Hs3, 10nM, 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: PLC/PRF/5, Apob-Mm2, 10nM, 48h

description:
PLC/PRF/5, Apob-Mm2, 10nM, 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, Apob-Mm1, 10nM, 12h

description:
PLC/PRF/5, Apob-Mm1, 10nM, 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: PLC/PRF/5, Apob-Mm1, 10nM, 6h

description:
PLC/PRF/5, Apob-Mm1, 10nM, 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.


title: Foxp2wt/ko_strKo_21d_m_run1_litter7.10

description: Gene expression data from the striatum of a 21 days old mouse with one Foxp2 allele knocked-out (Foxp2wt/ko), belonging to strain Ko

tag: genotype

tag: strain

tag: age

tag: sex

tag: run (microarray batch)

tag: litter

value: pool of two individuals from litters 7 and 10

tag: biological replicate


title: PLC/PRF/5, Apob-Mm1, 10nM, 48h

description:
PLC/PRF/5, Apob-Mm1, 10nM, 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, Apob-Mm2, 10nM, 6h

description:
HUH7, Apob-Mm2, 10nM, 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: HUH7, APOB-Hs2, 10nM, 6h

description:
HUH7, APOB-Hs2, 10nM, 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.


title: HUH7, APOB-Hs4, 10nM, 6h

description:
HUH7, APOB-Hs4, 10nM, 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.


title: HUH7, APOB-Hs3, 10nM, 6h

description:
HUH7, APOB-Hs3, 10nM, 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.


title: HUH7, RAD18, 10nM, 6h

description:
HUH7, RAD18, 10nM, 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.


title: HUH7, RAD18, 10nM, 12h

description:
HUH7, RAD18, 10nM, 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: HUH7, APOB-Hs1, 10nM, 6h

description:
HUH7, APOB-Hs1, 10nM, 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.


title: HUH7, Apob-Mm1, 10nM, 12h

description:
HUH7, Apob-Mm1, 10nM, 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: HUH7, APOB-Hs2, 10nM, 12h

description:
HUH7, APOB-Hs2, 10nM, 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: HUH7, APOB-Hs4, 10nM, 24h

description:
HUH7, APOB-Hs4, 10nM, 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: HUH7, Apob-Mm1, 10nM, 6h

description:
HUH7, Apob-Mm1, 10nM, 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.


title: HUH7, APOB-Hs1, 10nM, 12h

description:
HUH7, APOB-Hs1, 10nM, 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: PLC/PRF/5, RAD18, 10nM, 12h

description:
PLC/PRF/5, RAD18, 10nM, 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: HUH7, APOB-Hs2, 10nM, 24h

description:
HUH7, APOB-Hs2, 10nM, 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: HUH7, Apob-Mm2, 10nM, 12h

description:
HUH7, Apob-Mm2, 10nM, 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: HUH7, APOB-Hs4, 10nM, 12h

description:
HUH7, APOB-Hs4, 10nM, 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: HUH7, APOB-Hs3, 10nM, 24h

description:
HUH7, APOB-Hs3, 10nM, 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: HUH7, APOB-Hs1, 10nM, 24h

description:
HUH7, APOB-Hs1, 10nM, 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: HUH7, RAD18, 10nM, 24h

description:
HUH7, RAD18, 10nM, 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: tdb 72h

city: Munich

first: Joerg

last: Mages

address: Trogerstrasse 30

department: Institute of Medical Microbiology, Immunology and Hygiene

institute: Technical University Munich

description: macrophages from wt mice, not stimulated

hyb_protocol: Affymetrix standard procedure

scan_protocol: Affymetrix standard procedure; Affymetrix Scanner 3000 7G

data_processing: rma background correction and normalization. Linear values

label: biotin, PE

source_name: Macrophages

label_protocol: Biotinylated cRNA were processed using the GeneChip Expression 3’ Amplification One-Cycle Target Labeling Kit starting with 1 microg total RNA according to the manufactorers recommendations

growth_protocol: Macrophages were differentiated from bone marrow cells in cDMEM containing 10 % L-cell conditioned medium for 6 days and prestimulated with 10 ng/ml interferon gamma for 3h

extract_protocol: Qiagen RNeasy Mini Kit

treatment_protocol: cells were incubated for 72h with 20 µg/ml TDB

tag: 72h, TDB


title: HUH7, Apob-Mm1, 10nM, 24h

description:
HUH7, Apob-Mm1, 10nM, 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: tdb 48h

treatment_protocol: cells were incubated for 48h with 20 µg/ml TDB

tag: 48h, TDB


title: HUH7, Apob-Mm2, 10nM, 24h

description:
HUH7, Apob-Mm2, 10nM, 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: tdb 8h

treatment_protocol: cells were incubated for 8h with 20 µg/ml TDB

tag: 8h, TDB


title: tdb 24h

treatment_protocol: cells were incubated for 24h with 20 µg/ml TDB

tag: 24h, TDB


title: cpg 48h

treatment_protocol: cells were incubated for 48h with 1 µM CpG

tag: 48h, CpG


title: cpg 72h

treatment_protocol: cells were incubated for 72h with 1 µM CpG

tag: 72h, CpG


title: cpg 24h

treatment_protocol: cells were incubated for 24h with 1 µM CpG

tag: 24h, CpG


title: HUH7, APOB-Hs2, 10nM, 48h

description:
HUH7, APOB-Hs2, 10nM, 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.

tag: cell line


title: HUH7, APOB-Hs1, 10nM, 48h

description:
HUH7, APOB-Hs1, 10nM, 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, APOB-Hs4, 10nM, 48h

description:
HUH7, APOB-Hs4, 10nM, 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: control 24h

treatment_protocol: control cells incubated for 24h without stimulus

tag: 24h, not stimulated


title: cpg 8h

treatment_protocol: cells were incubated for 8h with 1 µM CpG

tag: 8h, CpG


title: HUH7, APOB-Hs3, 10nM, 48h

description:
HUH7, APOB-Hs3, 10nM, 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, Apob-Mm2, 10nM, 48h

description:
HUH7, Apob-Mm2, 10nM, 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: Foxp2hum/hum_strKi_18d_f_run1_litter1

description: Gene expression data from the striatum of a 18 days old mouse homozygous for the human Foxp2 allele (Foxp2hum/hum), belonging to strain Ki

tag: genotype

tag: tissue


title: Wild Type (Aromatase KO) Meibomian_Male 1

first: David

middle: A

last: Sullivan

address: 20 Staniford Street

institute: Schepens Eye Research Institute

description: Meibomian gland gene expression in male wild type (aromatase knockout) mice.

hyb_protocol: Following fragmentation, 20 microg of cRNA were hybridized for 18 hr at 45C on a Affymetrix GeneChip Mouse Expression Array 430A using a Affymetrix hybridization oven. GeneChips were washed and stained with streptavidin-Alexa 647 and washed again using a Model 450 Fluidics station and Affymetrix GeneChip Operating Software (GCOS) .

scan_protocol: GeneChips were scanned with a Affymetrix Model 7000 scanner running GCOS v1.3 software.

data_processing: Data were analyzed with GCOS software using the default settings.  No normalization was performed.

source_name: Meibomian glands from male wild type mice ( glands pooled from 5-8 mice)

label_protocol: Biotinylated cRNA were prepared according to the standard Codelink protocol from 2 microg total RNA using a CodeLink Expression Assay Reagent Kit.

extract_protocol: RNA was purified with Trizol and RNAqueous spin columns following the manufacturer's instructions.

tag: Meibomian glands from male wild type mice (glands pooled from 5-8 mice)


title: Wild Type (Aromatase KO) Meibomian_Male 3


title: Wild Type (Aromatase KO) Meibomian_Female 1

description: Meibomian gland gene expression in female wild type (aromatase knockout) mice.

scan_protocol: GeneChips were scanned with a Affymetrix Model 7000 scanner running GCOS v1.3 software. Bioarrays were scanned with a ScanArray Express HT scanner using ScanArray Express software.

source_name: Meibomian glands from female wild type mice ( glands pooled from 5-8 mice)

tag: Meibomian glands from female wild type mice (glands pooled from 5-8 mice)


title: Wild Type (Aromatase KO) Meibomian_Female 3


title: Aromatase KO Meibomian_Male 2

description: Meibomian gland gene expression in male aromatase knockout mice

source_name: Meibomian glands from male aromatase knockout mice ( glands pooled from 5-8 mice)

label_protocol: Biotinylated cRNA were prepared according to the standard Codelink protocol from 2 microg total RNA using a CodeLink Expression Assay Reagent Kit

tag: Meibomian glands from male aromatase knockout mice (glands pooled from 5-8 mice)


title: Aromatase KO Meibomian_Female 3

description: Meibomian gland gene expression in female aromatase knockout mice

source_name: Meibomian glands from female aromatase knockout mice ( glands pooled from 5-8 mice)

tag: Meibomian glands from female aromatase knockout mice (glands pooled from 5-8 mice)


title: Wild Type (Aromatase KO) Meibomian_Female 2


title: Aromatase KO Meibomian_Female 2


title: Aromatase KO Meibomian_Female 1

description: Meibomian gland gene expression in female aromatase knockout mice.


title: Wild Type (Aromatase KO) Lacrimal_Male 3

description: Lacrimal gland gene expression in male wild type (aromatase knockout) mice.

source_name: Lacrimal glands from male wild type mice ( glands pooled from 5-8 mice)

tag: Lacrimal glands from male wild type mice (glands pooled from 5-8 mice)


title: Aromatase KO Meibomian_Male 3


title: Wild Type (Aromatase KO) Lacrimal_Male 1


title: Aromatase KO Meibomian_Male 1


title: Wild Type (Aromatase KO) Lacrimal_Male 2


title: HUH7, RAD18, 10nM, 48h

description:
HUH7, RAD18, 10nM, 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, Apob-Mm1, 10nM, 48h

description:
HUH7, Apob-Mm1, 10nM, 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: Wild Type (Aromatase KO) Lacrimal_Female 3

description: Lacrimal gland gene expression in female wild type (aromatase knockout) mice.

source_name: Lacrimal glands from female wild type mice ( glands pooled from 5-8 mice)

tag: Lacrimal glands from female wild type mice (glands pooled from 5-8 mice)


title: control 48h

description: macrophages from wt mice, not stimulated

treatment_protocol: control cells incubated for 48h without stimulus

tag: 48h, not stimulated


title: Wild Type (Aromatase KO) Lacrimal_Female 2


title: Wild Type (Aromatase KO) Lacrimal_Female 1


title: Aromatase KO Lacrimal_Male 3

description: Lacrimal gland gene expression in male aromatase knockout mice

source_name: Lacrimal glands from male aromatase knockout mice ( glands pooled from 5-8 mice)

tag: Lacrimal glands from male aromatase knockout mice (glands pooled from 5-8 mice)


title: Aromatase KO Lacrimal_Female 3

description: Lacrimal gland gene expression in female aromatase knockout mice

source_name: Lacrimal glands from female aromatase knockout mice ( glands pooled from 5-8 mice)

tag: Lacrimal glands from female aromatase knockout mice (glands pooled from 5-8 mice)


title: Aromatase KO Lacrimal_Male 2


title: Aromatase KO Lacrimal_Male 1


title: Aromatase KO Lacrimal_Female 2


title: Female MRL/lpr Lacrimal Gland_Testosterone-3

description: Lacrimal gland gene expression from female MRL/lpr mice treated with testosterone for 18 days.

source_name: Lacrimal glands from testosterone treated female MRL/lpr mice ( glands pooled from 6 mice).

tag: Lacrimal glands from testosterone treated female MRL/lpr mice (glands pooled from 6 mice).


title: Female NOD Lacrimal Gland_Placebo-2

description: Lacrimal gland gene expression from female NOD mice treated with placebo for 21 days.

source_name: Lacrimal glands from placebo treated female NOD ( glands pooled from 2-4 mice).

tag: Lacrimal glands from placebo treated female NOD (glands pooled from 2-4 mice).


title: Female NOD Lacrimal Gland_Placebo-3


title: Female NOD Lacrimal Gland_Testosterone-3

description: Lacrimal gland gene expression from female NOD mice treated with testosterone for 21 days.

data_processing: Data were analyzed with GCOS software using the default settings. No normalization was performed.

source_name: Lacrimal glands from testosterone treated female NOD mice ( glands pooled from 2-4 mice).

tag: Lacrimal glands from testosterone treated female NOD mice (glands pooled from 2-4 mice).


title: Female MRL/lpr Lacrimal Gland_Testosterone-2


title: Female NOD Lacrimal Gland_Testosterone-1


title: Female NOD Lacrimal Gland_Placebo-1


title: Female MRL/lpr Lacrimal Gland_Testosterone-1


title: Female MRL/lpr Lacrimal Gland_Placebo-3

description: Lacrimal gland gene expression from female MRL/lpr mice treated with placebo for 18 days.

source_name: Lacrimal glands from placebo treated female MRL/lpr mice ( glands pooled from 6 mice).

tag: Lacrimal glands from placebo treated female MRL/lpr mice (glands pooled from 6 mice).


title: Female MRL/lpr Lacrimal Gland_Placebo-2


title: Female NOD Lacrimal Gland_Testosterone-2


title: Female MRL/lpr Lacrimal Gland_Placebo-1


title: Male NOD Lacrimal Gland_Male-1

description: Lacrimal gland gene expression in male NOD mice.

source_name: Lacrimal glands from male NOD mice ( glands pooled from 5-8 mice)

tag: Lacrimal glands from male NOD mice (glands pooled from 5-8 mice)