Editing BioMicroCenter:HTLR TEST HTLR TEST (section)

= LOW INPUT RNA-SEQ (Eukaryotic)=
== Cv2 ==
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  ! style="text-align: center; width: 150px;" | Parameter
  ! style="text-align: center; width: 300px;" | General requirements
  ! style="text-align: center; width: 300px;" | [[BioMicroCenter:HTLR_TEST_HTLR_TEST#RNA_Pre-load_Submissions|Pre-load requirements]]
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  | style="text-align: center; height: 2em;" | SAMPLE INPUT
  | colspan="2" style="text-align: center; height: 2em;" | Single cells or [[BioMicroCenter:RIN|intact]] low RNA input
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  | style="text-align: center; height: 2em;" | RANGE OF INPUT
  | style="text-align: center; height: 2em;" | 10pg - 250pg<br>(Or as available for single cells)
  | style="text-align: center; height: 2em;" | Single cells pre-arrayed across plate or [[BioMicroCenter:HTLR_TEST_HTLR_TEST#Normalization|normalized]] RNA
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  | style="text-align: center; height: 2em;" | SUBMISSION VOLUME
  | style="text-align: center; height: 2em;" | &ge;5&micro;L nuclease free water
  | style="text-align: center; height: 2em;" | Single cell or RNA in 1&micro;L nuclease free water
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  | style="text-align: center; height: 2em;" | UNIT
  | colspan="2" style="text-align: center; height: 2em;" | 24 samples <BR> 96 samples
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  | style="text-align: center; height: 2em;" | PLATE SETUP
  | style="text-align: center; height: 2em;" | Samples should be arrayed by column in a 96-well full-skirt plate (Axygen)
  | style="text-align: center; height: 2em;" | Samples arrayed by column in [[BioMicroCenter:HTLR_TEST_HTLR_TEST#Quadrant_Layout|1st quadrant]] of 384-well hard-shell plate (BioRad)
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  | style="text-align: center; height: 2em;" | SEQUENCING RECOMMENDATIONS
  | colspan="2" style="text-align: center; height: 2em;" | All platforms
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  | style="text-align: center; height: 2em;" | INDEX AVAILABILITY
  | colspan="2" style="text-align: center; height: 2em;" | Up to 384 [[BioMicroCenter:HTLR_TEST_HTLR_TEST#Unique_versus_Combinatorial_Dual_Indexing|Unique Dual Indexes]] (w/ Nextera Flex) <br> 384 [[BioMicroCenter:HTLR_TEST_HTLR_TEST#Unique_versus_Combinatorial_Dual_Indexing|Combinatorial Dual Indexes]]
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  | style="text-align: center; height: 2em;" | INCLUDED
  | colspan="2" style="text-align: center; height: 2em;" |cDNA generation of poly(A) RNA <br>cDNA amplification<br>Spot check of cDNA<br>Library preparation (Nextera Flex or XT)<br>Spot check of final libraries  
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  | style="text-align: center; height: 2em;" | ADDITIONAL SERVICES AVAILABLE
  | style="text-align: center; height: 2em;" | Sample QC <BR> Sample cleaning <BR> Sample arraying <BR> Sample re-prep
  | style="text-align: center; height: 2em;" | [[BioMicroCenter:HTLR_TEST_HTLR_TEST#RNA_Pre-load_Submissions|N/A]]
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  | style="text-align: center; height: 2em;" | SUBMISSION FORM
  | colspan="2" style="text-align: center; height: 2em;" | MIT - [https://mit.ilabsolutions.com/service_item/new/3381?spt_id=3863 ilabs] <BR> External - [[BioMicroCenter:Forms|form]]
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  | style="text-align: center; height: 2em;" | PRICING
  | colspan="2" style="text-align: center; height: 2em;" | [[BioMicroCenter:Pricing#ILLUMINA_LIBRARY_-_RNA|LINK]]
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<br>
:Our Cv2 prep is a "home-brew" version of Clontech's SMART-Seq kits which generates cDNA of full length transcripts from low inputs of RNA (i.e. single cell, dilute RNA sample). This workflow plugs into either our HTL [[BioMicroCenter:HTLD_TEST_HTLD_TEST#Nextera_Flex|Nextera Flex]] or [[BioMicroCenter:HTLD_TEST_HTLD_TEST#Nextera_XT|XT]] preps where the cDNA is tagmented and indexed.<br>
:This method uses oligo-d(T) priming to selectively process polyadenylated RNA which is then amplified by an initial round of PCR, making this prep ideal low-input high quality RNA or single cells. Due to the nature method, submissions should be coordinated with BMC to schedule sample drop-off of up to 384 samples to begin processing immediately in order to reduce possible loss/degradation of sample. <br>
[[Image:Cv2_BMC.png|center|350px]]
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== ZapR ==
{|
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  {| class="wikitable" border=1
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  ! style="text-align: center; width: 150px;" | Parameter
  ! style="text-align: center; width: 300px" | General requirements
  ! style="text-align: center; width: 300px" | [[BioMicroCenter:HTLR_TEST_HTLR_TEST#RNA_Pre-load_Submissions|Pre-load requirements]]
  |-
  | style="text-align: center; height: 2em;" | SAMPLE INPUT
  | colspan="2" style="text-align: center; height: 2em;" | [[BioMicroCenter:RIN|Degraded]] low RNA input
  |-
  | style="text-align: center; height: 2em;" | RANGE OF INPUT
  | style="text-align: center; height: 2em;" | 250pg - 10ng
  | style="text-align: center; height: 2em;" | [[BioMicroCenter:HTLR_TEST_HTLR_TEST#Normalization|Normalized]] sample<br>(&ge; 750 pg/&micro;L strongly recommended)
  |-
  | style="text-align: center; height: 2em;" | SUBMISSION VOLUME
  | style="text-align: center; height: 2em;" | &ge; 5&micro;L nuclease free water
  | style="text-align: center; height: 2em;" | 1.5&micro;L nuclease free water
  |-
  | style="text-align: center; height: 2em;" | UNIT
  | colspan="2" style="text-align: center; height: 2em;" | 24 samples <BR> 96 samples
  |-
  | style="text-align: center; height: 2em;" | PLATE SETUP
  | style="text-align: center; height: 2em;" | Samples should be arrayed by column in a 96-well full-skirt plate (Axygen)
  | style="text-align: center; height: 2em;" | Samples arrayed by column in [[BioMicroCenter:HTLR_TEST_HTLR_TEST#Quadrant_Layout|1st quadrant]] of 384-well hard-shell plate (BioRad)
  |-
  | style="text-align: center; height: 2em;" | SEQUENCING RECOMMENDATIONS
  | colspan="2" style="text-align: center; height: 2em;" | All platforms
  |-
  | style="text-align: center; height: 2em;" | INDEX AVAILABILITY
  | colspan="2" style="text-align: center; height: 2em;" |16 [[BioMicroCenter:HTLR_TEST_HTLR_TEST#Unique_versus_Combinatorial_Dual_Indexing|Unique Dual Indexes]] <br> 96 [[BioMicroCenter:HTLR_TEST_HTLR_TEST#Unique_versus_Combinatorial_Dual_Indexing|Combinatorial Dual Indexes]]
  |-
  | style="text-align: center; height: 2em;" | INCLUDED
  | colspan="2" style="text-align: center; height: 2em;" | cDNA synthesis<br>cDNA amplification<br>cDNA selection<br>Library preparation<br>Spot check of final libraries
  |-
  | style="text-align: center; height: 2em;" | ADDITIONAL SERVICES AVAILABLE
  | style="text-align: center; height: 2em;" | Sample QC <BR> Sample cleaning <BR> Sample arraying <BR> Sample re-prep
  | style="text-align: center; height: 2em;" | [[BioMicroCenter:HTLR_TEST_HTLR_TEST#RNA_Pre-load_Submissions|N/A]]
  |-
  | style="text-align: center; height: 2em;" | SUBMISSION FORM
  | colspan="2" style="text-align: center; height: 2em;" | MIT - [https://mit.ilabsolutions.com/service_item/new/3381?spt_id=3863 ilabs] <BR> External - [[BioMicroCenter:Forms|form]]
  |-
  | style="text-align: center; height: 2em;" | PRICING
  | colspan="2" style="text-align: center; height: 2em;" | [[BioMicroCenter:Pricing#ILLUMINA_LIBRARY_-_RNA|LINK]]
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:SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (ZapR) is used for library preparation of low input degraded RNA samples by generating and amplifying cDNA from total RNA, after which the ribosomal cDNA is depleted through targeted enzymatic degradation using ZapR probes while keeping all other cDNA for library preparation. This method is typically used for low concentration RNA samples of poor quality ([[BioMicroCenter:RIN|RIN]]<7 or [[BioMicroCenter:RIN|DV200]]<60%). We have miniaturized the ZapR method to 1/10th the original reaction volume on the Mosquito HV. This method is capable of handling inputs ranging from 250pg to 10ng (or 50ng for FFPE) however, performance for a given sample input is dependent on the quality of the sample itself. Due to the design of the ZapR probes, this method is only available for Human samples.
[[Image:ZapR_BMC.gif|center|250px]]
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