Systems and methods for quality control in single cell processing

Abstract

Provided are systems and methods for analyzing a single cell application or experiment. A set of control beads may be introduced to a biological sample and subjected to the single cell application. The control beads may be configured to mimic analytes in the biological sample, such as a cell or other analyte, and comprise one or more known sequences. The one or more known sequences may be identified to analyze the single cell application.

1 - 30 . (canceled) 
     
     
         31 . A kit for analyzing a cellular sample comprising analyte carriers, comprising:
 a. a set of control beads, wherein at least a subset of said set of control beads comprises (i) identical nucleic acid molecules each comprising a known nucleic acid sequence, and (ii) has a characteristic corresponding to within 70% deviation from an average value of said characteristic of said analyte carriers; and   b. an index comprising said known nucleic acid sequence.   
     
     
         32 . The kit of  claim 31 , wherein said characteristic is selected from a group consisting of size, shape, density, conductivity, hardness, deformability, and hydrophobicity. 
     
     
         33 . The kit of  claim 31 , wherein said index comprises a concentration of said known nucleic acid sequence. 
     
     
         34 . The kit of  claim 31 , wherein a subset of said set of control beads comprises additional identical nucleic acid molecules that are different than said identical nucleic acid molecules, each of which additional nucleic acid molecules comprises an additional known nucleic acid sequence. 
     
     
         35 . The kit of  claim 33 , wherein said index comprises said additional known nucleic acid sequence. 
     
     
         36 . The kit of  claim 33 , wherein said index comprises a concentration of said additional known nucleic acid sequence. 
     
     
         37 . The kit of  claim 31 , wherein said known nucleic acid sequence and said additional known nucleic acid sequence vary in length. 
     
     
         38 . The kit of  claim 31 , wherein said known nucleic acid sequence and said additional known nucleic acid sequence vary in concentration. 
     
     
         39 . The kit of  claim 31 , wherein said known nucleic acid sequence and said additional known nucleic acid sequence vary in GC content. 
     
     
         40 . The kit of  claim 31 , wherein said set of control beads comprises a first subset of control beads and a second subset of control beads. 
     
     
         41 . The kit of  claim 31 , wherein said first subset of control beads comprises a first set of nucleic acid molecules comprising a first set of known sequences, and said second subset of control beads comprises a second set of nucleic acid molecules comprising a second set of known sequences. 
     
     
         42 . The kit of  claim 41 , wherein said first set of known sequences comprises 96 different known sequences and said second set of known sequences comprises 96 different known sequences. 
     
     
         43 . The kit of  claim 41 , wherein said 96 different known sequences of said first set of known sequences are different then said 96 different known sequences of said second set of known sequences. 
     
     
         44 . The kit of  claim 40 , wherein said first subset of control beads and said second subset of control beads are present in a ratio of at least 1:0.001. 
     
     
         45 . The kit of  claim 44 , wherein said ratio is at most 1:0.001. 
     
     
         46 . The kit of  claim 44 , wherein said ratio is about 1:2. 
     
     
         47 . The kit of  claim 31 , further comprising reagents and buffers for sample preparation for a sequencing assay. 
     
     
         48 . The kit of  claim 31 , wherein said kit comprises at least 2 sets of control beads. 
     
     
         49 . The kit of  claim 31 , wherein said kit comprises at most 50 sets of control beads.