Week 10 Flashcards

1
Q

How to make a non-homologous end rejoining (NHEJ)?

A

Double DNA break leads to gene inactivation –> miRNA site inactivation.
Can lead to frameshift.

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2
Q

What is base editing?

A

Deaminating and replacing specific base. Efficient and not often naturally repaired.

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3
Q

Whole genome library screening

A

Guide RNA mixed with cas9. Cut and inactivate gene. In each cell, only 1 specific gene will be inactivated. If crucial, cell dies.

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4
Q

Transcriptomics disadvantages

A

Need to design primer specific for each qPCR (quantitative pcr)

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5
Q

How microarray works?

A

CDNA probes attached to wells —> hybridise w control and non-control cells

But limited by probe making

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6
Q

Next generation sequencing

A

Incorporate cDNA into sequence of full cell. Primers are oligonucleotide based and laser detects their incorporation. Lysis —> library

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7
Q

Why use single nucleotide sequencing?

A

Bulk can mask cellular heterogeneity —> averaging artifacts

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8
Q

Split pool/ combinational in situ barcoding sequencing

A

Fix many cells into single well then split to analyse.

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9
Q

Nanodroplet sequencing method

A

Cell encapsulated into droplet —> lyse —> mRNA bind to oligoDT probes —> RNA hybridisation —> reverse transcription

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10
Q

Batch effect causes

A

Technical variability, changes in sample/processing, library prep/sequencing tech

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11
Q

Biological variability

A

Patient, environment, evolution

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12
Q

Validation methods

A

Antibody immunostaining
Mass spectrometry
Transgene knockout

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13
Q

Pseudotemporal ordering

A

Look at cells and infer a “life trajectory”. Can see them as “fake timepoints” at the same time.

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14
Q

Cell atlasing

A

Take tissue apart and look at markers. Can know processes of tissues

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15
Q

Comparative analysis in single cell RNA sequencing (scRNQseq)?

A

Can identify if a subpopulation of rnas are associated with disease

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16
Q

ATACseq

A

Assay for transposase accessible chromatin

Transposase —> adaptor in freed regions —> primers —> sequence and align to genome —> find silent genes!