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czbiohub-sf / tabula-sapiens

Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens
BSD 3-Clause "New" or "Revised" License
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3/2/20 Meeting #12

Closed aopisco closed 3 years ago

aopisco commented 4 years ago

Recap from last week

@YtheRookie gave a summary of last meeting (#10)

aopisco commented 4 years ago

Acinar cells tjat express Cpa1 and Ifgn

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olgabot commented 4 years ago

Last time: https://github.com/czbiohub/tabula-sapiens/issues/10

aopisco commented 4 years ago

@YtheRookie grouped cells in rogue cells and proper pancreas

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aopisco commented 4 years ago
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aopisco commented 4 years ago

Working hypothesis biological

  1. Floating acinar cells 1.1. Is it technical? 1.2. We cannot tell any transcriptomic differences 1.3. These cells are almost all 10X 1.4. Calculate the percentage of floating cells in each organ and get confidence estimates for the amount of cells and likelihood of capture in the tissues

To do

  1. Apoptosis signature 1.1. Collect apoptosis signature gene list

  2. Get pancreatic disease samples 2.1. Best control is acinar cell carcinoma (ACC) 2.2. Chronic pancreatitis sample is also a good control

olgabot commented 4 years ago

Is it known whether the patient had Klebsiella pneumonia?

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aopisco commented 4 years ago

Working hypothesis technical

  1. 10X mix-up 1.1. Chip loading 1.1.1. We cleared this by looking at the order

  2. Sequence alignment 2.1. We cleared this by realigning

  3. NovaSeq barcode hooping 3.1. If the sequencer is causing the contamination this shouldn't happen if we run the samples in separate

laurabob commented 4 years ago

Working hypothesis technical ... Awaiting data from re-sequencing of two 10X blood sequencing libraries on NextSeq