Abstract: A phenol-free method for isolating a nucleic acid from a sample is provided, said method comprising the following steps: a) adding a precipitation buffer to a sample to prepare an acidic precipitation mixture wherein said precipitation buffer comprises a metal cation precipitant and a buffering agent, has a pH value of 4.0 or less and does not comprise an organic solvent selected from aprotic polar solvents and protic solvents and wherein the acidic precipitation mixture comprises the metal cation precipitant in a concentration of less than 200 mM and precipitating proteins; b) separating the precipitate from the supernatant, wherein the supernatant comprises small RNA having a length of less than 200 nt and large RNA having a length of at least 1000 nt; and c) isolating a nucleic acid from the supernatant. The present method allows to avoid the use of organic solvents during protein precipitation. Also provided is a precipitation buffer.

Abstract: A phenol-free method for isolating a nucleic acid from a sample is provided, said method comprising the following steps: a) adding a precipitation buffer to a sample to prepare an acidic precipitation mixture wherein said precipitation buffer comprises a metal cation precipitant and a buffering agent, has a pH value of 4.0 or less and does not comprise an organic solvent selected from aprotic polar solvents and protic solvents and wherein the acidic precipitation mixture comprises the metal cation precipitant in a concentration of less than 200 mM and precipitating proteins; b) separating the precipitate from the supernatant, wherein the supernatant comprises small RNA having a length of less than 200 nt and large RNA having a length of at least 1000 nt; and c) isolating a nucleic acid from the supernatant. The present method allows to avoid the use of organic solvents during protein precipitation. Also provided is a precipitation buffer.

Abstract: A method is provided for enriching extracellular DNA from a biological sample comprising extracellular DNA and extracellular vesicles, wherein the method comprises: (a) preparing a binding mixture comprising—the biological sample, —a solid phase comprising anion exchange groups, —an acidic binding buffer comprising a buffering agent, and binding extracellular DNA to the solid phase comprising anion exchange groups; (b) separating the solid phase with the bound extracellular DNA from the remaining binding mixture, wherein the remaining binding mixture comprises extracellular vesicles. The method may furthermore comprise processing the remaining binding mixture to enrich one or more biological targets of interest therefrom, wherein processing may comprise (c) enriching as biological targets extracellular vesicles and/or extracellular RNA from the remaining binding mixture.

Abstract: The present invention pertains to methods and kits for enriching extracellular nucleic acids such as vesicular RNA from a sample comprising extracellular vesicles. Accordingly to the methods an acidic binding mixture is prepared comprising the sample and anion exchange particles and binding extracellular vesicles to the anion exchange particles. After separating the anion exchange particles comprising the bound extracellular vesicles from the remaining mixture, bound extracellular vesicles are lysing the in the presence of at least one detergent and released RNA is bound to the anion exchange particles. The anion exchange particles with the bound RNA from the lysate are then eluted.

Abstract: The present invention pertains to a method for isolating a target nucleic acid including small target nucleic acids from a sample, said method comprising at least the following steps a) binding at least a portion of the target nucleic acid including small target nucleic acids to a nucleic acid binding solid phase comprised in a column by passing the sample through said column, b) performing an enzymatic and/or chemical treatment on the nucleic acid binding solid phase while the target nucleic acid is bound to said solid phase, c) collecting at least a portion of the small target nucleic acids released from the solid phase during said treatment of step b) as flow-through, d) contacting said flow-through which comprises small target nucleic acids mixed with a recovery solution with a nucleic acid binding solid phase for binding the contained small target nucleic acids to said nucleic acid binding solid phase, e) optionally performing an elution.

Abstract: The present invention pertains inter alia to a method for isolating poly(A) nucleic acids having a single stranded poly(A) stretch from a nucleic acid containing sample comprising: (a) providing a hybridization composition comprising: i) a nucleic acid containing sample; ii) a hybridization solution comprising: aa. a sodium salt; bb. a quaternary ammonium salt; wherein the components of the hybridization solution can be added as single solution to the sample or may be added separately in any order to the sample; iii) a capture probe capable of hybridizing to the poly(A) stretch of the poly(A) nucleic acids; and incubating said hybridization composition under conditions to form nucleic acid-hybrids between the poly(A) nucleic acids and the capture probe; (b) separating the formed hybrids from the remaining sample. The method is in particular suitable for efficiently isolating poly(A) RNA from various samples while avoiding carry-over of unwanted non-poly(A) nucleic acids such as rRNA.

Abstract: A phenol-free method for isolating a nucleic acid from a sample is provided, said method comprising the following steps: a) adding a precipitation buffer to a sample to prepare an acidic precipitation mixture wherein said precipitation buffer comprises a metal cation precipitant and a buffering agent, has a pH value of 4.0 or less and does not comprise an organic solvent selected from aprotic polar solvents and protic solvents and wherein the acidic precipitation mixture comprises the metal cation precipitant in a concentration of less than 200 mM and precipitating proteins; b) separating the precipitate from the supernatant, wherein the supernatant comprises small RNA having a length of less than 200 nt and large RNA having a length of at least 1000 nt; and c) isolating a nucleic acid from the supernatant. The present method allows to avoid the use of organic solvents during protein precipitation. Also provided is a precipitation buffer.

Abstract: The present invention provides a method for isolating RNA including small RNA having a size of 200 nt or less from a sample, comprising the following steps: a) providing a composition comprising RNA and a chaotropic agent; b) adding alcohol; c) incubating the mixture for at least 2 min; d) adding additional alcohol to the mixture to adjust the overall alcohol concentration in the mixture to ?50%; e) binding RNA contained in the mixture to a nucleic acid binding solid phase; f) optionally washing the bound RNA; g) optionally eluting RNA from the solid phase. Due to the step-wise addition of alcohol, the overall RNA yield and the yield of small RNA is improved.

Abstract: The present invention relates to a set of biomarkers, microarrays that provide for detection thereof, an expression signature comprising 16 genes or a subset thereof, and the use thereof in determining the regulation status of IL-6/STAT3 signaling pathway in a cell sample or subject, as well as compositions for the detection thereof. The regulation status of IL-6/STAT3 signaling pathway in a cell sample or subject may be assayed based on the level of expression of one or more of these genes. The methods and compositions provided herein may be used to evaluate IL-6/STAT3 pathway regulation status in a sample; classify a cell sample as having a deregulated or regulated IL-6/STAT3 signaling pathway; determine whether an agent modulates the IL-6/STAT3 signaling pathway; predict the response of a subject to an agent that modulates the IL-6/STAT3 signaling pathway; assign treatment to a subject; and/or evaluate the pharmacodynamic effects of therapies designed to regulate IL-6/STAT3 pathway signaling.

Abstract: The present invention pertains inter alia to a method for isolating poly(A) nucleic acids having a single stranded poly(A) stretch from a nucleic acid containing sample comprising: (a) providing a hybridization composition comprising: i) a nucleic acid containing sample; ii) a hybridization solution comprising: aa. a sodium salt; bb. a quaternary ammonium salt; wherein the components of the hybridization solution can be added as single solution to the sample or may be added separately in any order to the sample; iii) a capture probe capable of hybridizing to the poly(A) stretch of the poly(A) nucleic acids; and incubating said hybridization composition under conditions to form nucleic acid-hybrids between the poly(A) nucleic acids and the capture probe; (b) separating the formed hybrids from the remaining sample. The method is in particular suitable for efficiently isolating poly(A) RNA from various samples while avoiding carry-over of unwanted non-poly(A) nucleic acids such as rRNA.

Abstract: The present invention provides a method of preparing a target RNA depleted composition from an initial RNA containing composition, comprising a) contacting the initial RNA containing composition with one or more groups of probe molecules, wherein a group of probe molecules has the following characteristics: i) the group comprises two or more different probe molecules having a length of 100 nt or less; ii) the probe molecules comprised in said group are complementary to a target region of a target RNA; iii) when hybridized to said target region, the two or more different probe molecules are located adjacent to each other in the formed double-stranded hybrid; and generating a double-stranded hybrid between the target RNA and the probe molecules; b) capturing the double-stranded hybrid by using a binding agent which binds the double-stranded hybrid, thereby forming a hybrid/binding agent complex; c) separating the hybrid/binding agent complexes from the composition, thereby providing a target RNA depleted compos

Abstract: The present invention provides a method for isolating RNA including small RNA having a size of 200 nt or less from a sample, comprising the following steps: a) providing a composition comprising RNA and a chaotropic agent; b) adding alcohol; c) incubating the mixture for at least 2 min; d) adding additional alcohol to the mixture to adjust the overall alcohol concentration in the mixture to ?50%; e) binding RNA contained in the mixture to a nucleic acid binding solid phase; f) optionally washing the bound RNA; g) optionally eluting RNA from the solid phase. Due to the step-wise addition of alcohol, the overall RNA yield and the yield of small RNA is improved.

Abstract: The present invention relates to a set of biomarkers, microarrays that provide for detection thereof, an expression signature comprising 16 genes or a subset thereof, and the use thereof in determining the regulation status of IL-6/STAT3 signaling pathway in a cell sample or subject, as well as compositions for the detection thereof. The regulation status of IL-6/STAT3 signaling pathway in a cell sample or subject may be assayed based on the level of expression of one or more of these genes. The methods and compositions provided herein may be used to evaluate IL-6/STAT3 pathway regulation status in a sample; classify a cell sample as having a deregulated or regulated IL-6/STAT3 signaling pathway; determine whether an agent modulates the IL-6/STAT3 signaling pathway; predict the response of a subject to an agent that modulates the IL-6/STAT3 signaling pathway; assign treatment to a subject; and/or evaluate the pharmacodynamic effects of therapies designed to regulate IL-6/STAT3 pathway signaling.

Abstract: The present invention relates to a method for processing a wax-embedded biological sample, the use of poly(organosiloxane)s for liquefying the embedding medium of a wax-embedded biological sample and a kit for processing a wax-embedded biological sample.

Abstract: The present invention relates to a method for processing a wax-embedded biological sample, the use of poly(organosiloxane)s for liquefying the embedding medium of a wax-embedded biological sample and a kit for processing a wax-embedded biological sample.

Abstract: The present invention relates to the use of reagent for permanently inactivating nucleases wherein the reagent comprises an oxidizing agent, a protein denaturant and optionally a pH adjustor and to a method for permanently inactivating nucleases using said reagent.

Abstract: The present invention relates to a method for concentrating one or more target compounds in a liquid sample, a device for carrying out this method and a kit for processing a biological sample comprising such a device.

Abstract: The present invention pertains to a method for isolating a target nucleic acid including small target nucleic acids from a sample, said method comprising at least the following steps a) binding at least a portion of the target nucleic acid including small target nucleic acids to a nucleic acid binding solid phase comprised in a column by passing the sample through said column, b) performing an enzymatic and/or chemical treatment on the nucleic acid binding solid phase while the target nucleic acid is bound to said solid phase, c) collecting at least a portion of the small target nucleic acids released from the solid phase during said treatment of step b) as flow-through, d) contacting said flow-through which comprises small target nucleic acids mixed with a recovery solution with a nucleic acid binding solid phase for binding the contained small target nucleic acids to said nucleic acid binding solid phase, e) optionally performing an elution.

Abstract: The present invention relates to the use of reagent for permanently inactivating nucleases wherein the reagent comprises an oxidizing agent, a protein denaturant and optionally a pH adjustor and to a method for permanently inactivating nucleases using said reagent.

Abstract: The present invention relates to a method for treating a fixed biological sample, comprising the steps of the method: i) provision of a fixed biological sample, ii) contacting the fixed biological sample with an aqueous solution comprising at least one nucleophilic reagent, and iii) heating the biological sample contacted with the aqueous solution. The invention also relates to the biological sample obtainable by this method, to the use of a nucleophilic reagent for the treatment of a fixed biological sample, to a kit for isolating a biomolecule from a fixed biological sample, to the use of this kit, and to a method for the treatment of a disease.