Blue:RNA-Seq Experiments:09052013: Difference between revisions

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*Achieved good loading efficiency (81/96) but high mortality as indicated by live/dead staining on chip
*Achieved good loading efficiency (81/96) but high mortality as indicated by live/dead staining on chip
*Followed the protocol exactly - including use of spike-in RNA indicated in the protocol rather than those used in our previous experiments
*Followed the protocol exactly - including use of spike-in RNA indicated in the protocol rather than those used in our previous experiments
'''OutCome:'''
*Re-primed incorrectly - broke seal on chip preventing lysis buffer from entering chambers - no cDNA amplification




[[File:Cell_Characterization_Worksheet.docx]]
[[File:Cell_Characterization_Worksheet.docx]]
[[File:Data_Submission_Worksheet.docx]]
[[File:Data_Submission_Worksheet.docx]]
== Sample Attribution ==
Note: d=dead
{| {{table}}
| align="center" style="background:#f0f0f0;"|''''''
| align="center" style="background:#f0f0f0;"|'''1'''
| align="center" style="background:#f0f0f0;"|'''2'''
| align="center" style="background:#f0f0f0;"|'''3'''
| align="center" style="background:#f0f0f0;"|'''4'''
| align="center" style="background:#f0f0f0;"|'''5'''
| align="center" style="background:#f0f0f0;"|'''6'''
| align="center" style="background:#f0f0f0;"|'''7'''
| align="center" style="background:#f0f0f0;"|'''8'''
| align="center" style="background:#f0f0f0;"|'''9'''
| align="center" style="background:#f0f0f0;"|'''10'''
| align="center" style="background:#f0f0f0;"|'''11'''
| align="center" style="background:#f0f0f0;"|'''12'''
|-
| A||1_NPCs_C03||0_NPCs_C02||1d_NPCs_C01||0_NPCs_C49||1d_NPCs_C50||1d_NPCs_C51||1d_NPCs_C06||0_NPCs_C05||1_NPCs_C04||2d_NPCs_C52||0_NPCs_C53||3d_NPCs_C54
|-
| ||||||||||||||||||||||||
|-
| B||1d_NPCs_C09||0_NPCs_C08||0_NPCs_C07||1d_NPCs_C55||1d_NPCs_C56||1d_NPCs_C57||1d_NPCs_C12||1d_NPCs_C11||1d_NPCs_C10||1d_NPCs_C58||0_NPCs_C59||4d_NPCs_C60
|-
| ||||||||||||||||||||||||
|-
| C||1d_NPCs_C15||1d_NPCs_C14||0_NPCs_C13||1_NPCs_C61||0_NPCs_C62||1d_NPCs_C63||1_NPCs_C18||1_NPCs_C17||1_NPCs_C16||1d_NPCs_C64||1d_NPCs_C65||1d_NPCs_C66
|-
| ||||||||||||||||||||||||
|-
| D||1d_NPCs_C21||1d_NPCs_C20||0_NPCs_C19||1_NPCs_C67||1d_NPCs_C68||1d_NPCs_C69||2d_NPCs_C24||1d_NPCs_C23||1d_NPCs_C22||0_NPCs_C70||1d_NPCs_C71||1 + 1d_NPCs_C72
|-
| ||||||||||||||||||||||||
|-
| E||1d_NPCs_C25||3d_NPCs_C26||1_NPCs_C27||0_NPCs_C75||1d_NPCs_C74||0_NPCs_C73||2d_NPCs_C28||2d_NPCs_C29||1d_NPCs_C30||0_NPCs_C78||1d_NPCs_C77||2 + 1d_NPCs_C76
|-
| ||||||||||||||||||||||||
|-
| F||4d_NPCs_C31||1_NPCs_C32||1d_NPCs_C33||1_NPCs_C81||1d_NPCs_C80||2d_NPCs_C79||1d_NPCs_C34||1d_NPCs_C35||3 + 1d_NPCs_C36||1d_NPCs_C84||1_NPCs_C83||1_NPCs_C82
|-
| ||||||||||||||||||||||||
|-
| G||1d_NPCs_C37||0_NPCs_C38||1_NPCs_C39||1d_NPCs_C87||2d_NPCs_C86||1 + 1d_NPCs_C85||1_NPCs_C40||1_NPCs_C41||1d_NPCs_C42||2d_NPCs_C90||1_NPCs_C89||1_NPCs_C88
|-
| ||||||||||||||||||||||||
|-
| H||1d_NPCs_C43||4d_NPCs_C44||1d_NPCs_C45||1d_NPCs_C93||1d_NPCs_C92||4d_NPCs_C91||3d_NPCs_C46||1d_NPCs_C47||1d_NPCs_C48||1d_NPCs_C96||1d_NPCs_C95||1d_NPCs_C94
|-
| ||||||||||||||||||||||||
|-
|
|}

Latest revision as of 16:31, 11 October 2013

Fluidigm C1 Small Chip Beta Test[edit]

  • Tested NPCs on the small 5-10um chip
  • First run on 09-04-2013 produced too few viable cells for loading and resulted in only 10 captured - therefore, reprimed the chip and stored overnight for re-loading
  • Second run on 09-05-2013 involved E13.5 neural progenitors sorted as PI negative
  • Achieved good loading efficiency (81/96) but high mortality as indicated by live/dead staining on chip
  • Followed the protocol exactly - including use of spike-in RNA indicated in the protocol rather than those used in our previous experiments

OutCome:

  • Re-primed incorrectly - broke seal on chip preventing lysis buffer from entering chambers - no cDNA amplification


File:Cell Characterization Worksheet.docx

File:Data Submission Worksheet.docx

Sample Attribution[edit]

Note: d=dead


' 1 2 3 4 5 6 7 8 9 10 11 12
A 1_NPCs_C03 0_NPCs_C02 1d_NPCs_C01 0_NPCs_C49 1d_NPCs_C50 1d_NPCs_C51 1d_NPCs_C06 0_NPCs_C05 1_NPCs_C04 2d_NPCs_C52 0_NPCs_C53 3d_NPCs_C54
B 1d_NPCs_C09 0_NPCs_C08 0_NPCs_C07 1d_NPCs_C55 1d_NPCs_C56 1d_NPCs_C57 1d_NPCs_C12 1d_NPCs_C11 1d_NPCs_C10 1d_NPCs_C58 0_NPCs_C59 4d_NPCs_C60
C 1d_NPCs_C15 1d_NPCs_C14 0_NPCs_C13 1_NPCs_C61 0_NPCs_C62 1d_NPCs_C63 1_NPCs_C18 1_NPCs_C17 1_NPCs_C16 1d_NPCs_C64 1d_NPCs_C65 1d_NPCs_C66
D 1d_NPCs_C21 1d_NPCs_C20 0_NPCs_C19 1_NPCs_C67 1d_NPCs_C68 1d_NPCs_C69 2d_NPCs_C24 1d_NPCs_C23 1d_NPCs_C22 0_NPCs_C70 1d_NPCs_C71 1 + 1d_NPCs_C72
E 1d_NPCs_C25 3d_NPCs_C26 1_NPCs_C27 0_NPCs_C75 1d_NPCs_C74 0_NPCs_C73 2d_NPCs_C28 2d_NPCs_C29 1d_NPCs_C30 0_NPCs_C78 1d_NPCs_C77 2 + 1d_NPCs_C76
F 4d_NPCs_C31 1_NPCs_C32 1d_NPCs_C33 1_NPCs_C81 1d_NPCs_C80 2d_NPCs_C79 1d_NPCs_C34 1d_NPCs_C35 3 + 1d_NPCs_C36 1d_NPCs_C84 1_NPCs_C83 1_NPCs_C82
G 1d_NPCs_C37 0_NPCs_C38 1_NPCs_C39 1d_NPCs_C87 2d_NPCs_C86 1 + 1d_NPCs_C85 1_NPCs_C40 1_NPCs_C41 1d_NPCs_C42 2d_NPCs_C90 1_NPCs_C89 1_NPCs_C88
H 1d_NPCs_C43 4d_NPCs_C44 1d_NPCs_C45 1d_NPCs_C93 1d_NPCs_C92 4d_NPCs_C91 3d_NPCs_C46 1d_NPCs_C47 1d_NPCs_C48 1d_NPCs_C96 1d_NPCs_C95 1d_NPCs_C94