2. Cell Specification and Gene Expression Analysis

50 fill-in-the-blank flashcards covering key concepts from the 'Specifying Identity' lecture notes, including in situ hybridization, RNA-seq, and cell fate maps.

In situ hybridization (ISH) involves a labeled nucleic acid probe complementary to target __.

mRNA

The labeled nucleic acid probe in ISH is hybridized to tissue __.

in situ

The label in ISH can be detected using radioactive, enzymatic, or __ tags.

fluorescent

RNA-seq begins by converting a cell's RNA molecules into stable __.

DNA

After converting RNA to DNA, RNA-seq involves __ these DNA molecules.

fragmenting

RNA-seq uses __-throughput sequencing to read the sequence of each fragment.

high

In situ hybridization allows visualization of where particular __ are expressed within tissues.

mRNAs

ISH can determine the __ distribution of mRNA, indicating tissue- and cell-type specificity.

Spatial

Quantitative assessment of expression using ISH involves analyzing signal __.

intensity

ISH can assess regulatory relationships through co-localization with other transcripts or gene __ studies.

knockdown/overexpression

RNA-seq helps in identifying cell types and their gene expression __ during development.

profiles

RNA-seq can be used for reconstructing cell __ pathways.

differentiation

RNA-seq helps in understanding the __ of gene expression changes.

timing

RNA-seq quantifies cellular __ and allele-specific gene expression.

heterogeneity

A fate map is a summary of all of the cell __ data.

lineage

A fate map is often presented as an overlay positioned on top of a diagram of an __.

embryo

The nucleic acid probe used in in situ hybridization is __ to the target mRNA.

complementary

The high-throughput sequencing step in RNA-seq reads the sequence of each __.

fragment

In situ hybridization allows __ of where particular mRNAs are expressed.

visualization

ISH addresses the developmental question of __ of expression.

Time

Relative transcript levels can be assessed using ISH signal __.

intensity

Regulatory relationships can be assessed by ISH through co-localization with other transcripts or gene __ studies.

overexpression

RNA sequencing, or RNA-seq, reveals which genes are expressed in a cell or __.

tissue

Reconstructing cell __ pathways is a key application of RNA-seq.

differentiation

RNA-seq helps understand the __ of gene expression changes.

timing

Allele-specific gene expression and Cellular heterogeneity can be quantified using __-seq.

RNA

A cell fate map summarizes cell __ data.

lineage

Chapter 2 specifies __ as its main topic.

Identity

How in situ hybridization works involves a labeled nucleic acid probe complementary to the target __.

mRNA

Fragmenting DNA molecules is a step in the process of __-seq.

RNA

In situ hybridization is used to visualize where particular mRNAs are expressed within __.

tissues

ISH can address the spatial distribution of expression, referring to __-type specificity.

cell

RNA sequencing reveals which __ are expressed in a cell.

genes

RNA-seq can analyze both bulk and __-cell samples.

single

Understanding the timing of __ expression changes is an RNA-seq application.

gene

Quantifying __ heterogeneity is one of the developmental questions addressed by RNA-seq.

cellular

A fate map is a summary of all cell lineage data, often presented as an __.

overlay