Containers for agitation of liquid samples and methods of use thereof

1. A method of lysing cells in a liquid sample, said method comprising:

(a) providing liquid in a container comprising: (i) an interior chamber with a central axis, (ii) a top comprising an opening, and (iii) a substantially circular cross section or a substantially polygonal cross section, wherein the surface of said interior chamber comprises one or more substantially linear protrusions substantially parallel to said central axis, and wherein said liquid comprises rigid particles and cells; and

(b) agitating said liquid in said container,

wherein said agitation is of a sufficient force and duration to lyse said cells.

2. The method of claim 1 , wherein the substantially linear protrusions have a length substantially parallel to said central axis, a depth substantially parallel to the radius of said substantially circular or polygonal cross section, and a width substantially perpendicular to said radius, wherein said depth increases from top to bottom of the substantially linear protrusions and said width increases from top to bottom of the substantially linear protrusions, and wherein the depth of the substantially linear protrusions is greater than 10% of the radius at some point along the length of the substantially linear protrusions.

3. The method of claim 2 , wherein said container comprises a substantially polygonal cross section having a radius, wherein said radius is the distance from said central axis to a corner point, and wherein the surface of said interior chamber additionally comprises one or more substantially linear protrusions substantially parallel to said central axis.

4. The method of claim 2 , wherein said container comprises a substantially polygonal cross section having a radius, wherein said radius is the distance from said central axis to a corner point, and wherein said substantially polygonal cross section is substantially triangular, quadrilateral, pentagonal, hexagonal, heptagonal, octagonal, nonagonal, decagonal, or dodecagonal.

5. The method of claim 1 , wherein said interior chamber comprises 2 to 6 substantially linear protrusions.

6. The method of claim 1 , wherein said rigid particles have a diameter of between 0.1 mm to 1 mm.

7. A method of detecting the presence of a target nucleic acid in a whole blood sample, the method comprising:

(a) providing an extract produced by: (a1) lysing the red blood cells in a whole blood sample from a subject, (a2) centrifuging the sample to form a supernatant and a pellet, (a3) discarding some or all of the supernatant, and (a4) resuspending the pellet to form an extract, wherein the extract comprises one or more additional cells;

(b) lysing said additional cells in said extract, said lysing of said additional cells comprising (b1) combining the extract with rigid particles to form a mixture in a container comprising: (i) an interior chamber with a central axis, (ii) a top comprising an opening, and (iii) a substantially circular cross section or a substantially polygonal cross section, wherein the surface of said interior chamber comprises one or more substantially linear protrusions substantially parallel to said central axis; and (b2) agitating the mixture at a sufficient force and duration to lyse said additional cells, thereby forming a lysate;

(c) providing the lysate of step (b) in a detection tube and amplifying nucleic acids therein to form an amplified lysate solution comprising from 40% (w/w) to 95% (w/w) the target nucleic acid and from 5% (w/w) to 60% (w/w) nontarget nucleic acid; and

(d) detecting the amplified target nucleic acid.

8. The method of claim 7 , wherein the substantially linear protrusions have a length substantially parallel to said central axis, a depth substantially parallel to the radius of said substantially circular or polygonal cross section, and a width substantially perpendicular to said radius, wherein said depth increases from top to bottom of the substantially linear protrusions and said width increases from top to bottom of the substantially linear protrusions, and wherein the depth of the substantially linear protrusions is greater than 10% of the radius at some point along the length of the substantially linear protrusions.

9. The method of claim 8 , wherein said container comprises a substantially polygonal cross section having a radius, wherein said radius is the distance from said central axis to a corner point, and wherein the surface of said interior chamber additionally comprises one or more substantially linear protrusions substantially parallel to said central axis.

10. The method of claim 9 , wherein said container comprises a substantially polygonal cross section having a radius, wherein said radius is the distance from said central axis to a corner point, and wherein said substantially polygonal cross section is substantially triangular, quadrilateral, pentagonal, hexagonal, heptagonal, octagonal, nonagonal, decagonal, or dodecagonal.

11. The method of claim 7 , wherein said interior chamber comprises 2 to 6 substantially linear protrusions.

12. The method of claim 7 , wherein said rigid particles have a diameter of between 0.1 mm to 1 mm.

13. A method of amplifying a target nucleic acid in a whole blood sample, the method comprising:

(a) providing an extract produced by: (a1) lysing the red blood cells in a whole blood sample from a subject, (a2) centrifuging the sample to form a supernatant and a pellet, (a3) discarding some or all of the supernatant, and (a4) resuspending the pellet to form an extract, wherein the extract comprises one or more additional cells;

(b) lysing said additional cells in said extract, said lysing of said additional cells comprising: (b1) combining the extract with rigid particles to form a mixture in a container comprising: (i) an interior chamber with a central axis, (ii) a top comprising an opening, and (iii) a substantially circular cross section or a substantially polygonal cross section, wherein the surface of said interior chamber comprises one or more substantially linear protrusions substantially parallel to said central axis; and (b2) agitating the mixture at a sufficient force and duration to lyse said additional cells, thereby forming a lysate; and

(c) providing the lysate of step (b) in a detection tube and amplifying nucleic acids therein to form an amplified lysate solution comprising from 40% (w/w) to 95% (w/w) the target nucleic acid and from 5% (w/w) to 60% (w/w) nontarget nucleic acid.

14. The method of claim 13 , wherein the substantially linear protrusions have a length substantially parallel to said central axis, a depth substantially parallel to the radius of said substantially circular or polygonal cross section, and a width substantially perpendicular to said radius, wherein said depth increases from top to bottom of the substantially linear protrusions and said width increases from top to bottom of the substantially linear protrusions, and wherein the depth of the substantially linear protrusions is greater than 10% of the radius at some point along the length of the substantially linear protrusions.

15. The method of claim 14 , wherein said container comprises a substantially polygonal cross section having a radius, wherein said radius is the distance from said central axis to a corner point, and wherein the surface of said interior chamber additionally comprises one or more substantially linear protrusions substantially parallel to said central axis.

16. The method of claim 14 , wherein said container comprises a substantially polygonal cross section having a radius, wherein said radius is the distance from said central axis to a corner point, and wherein said substantially polygonal cross section is substantially triangular, quadrilateral, pentagonal, hexagonal, heptagonal, octagonal, nonagonal, decagonal, or dodecagonal.

17. The method of claim 13 , wherein said interior chamber comprises 2 to 6 substantially linear protrusions.

18. The method of claim 13 , wherein said rigid particles have a diameter of between 0.1 mm to 1 mm.