High-Throughput Sequencing Will Metamorphose the Analysis of Thyroid Hormone Receptor Function During Amphibian Development - Current Topics in Developmental Biology - page 288

A

0 206,775 413,550 620,325 827,100 1,033,875

1,002,818 1,007,318 1,011,817 1,016,317 1,020,816 1,025,316

RefSeq_genes

XenBase_genes

Probesets

RXT002 TF CTRL

800
600
400
200

0

1,003,000 1,005,200 1,007,400 1,009,600 1,011,800 1,014,000 1,016,200 1,018,400 1,020,600 1,022,800 1,025,000

RXT001 TF +T3

800
600
400
200
0

1,003,000 1,005,200 1,007,400 1,009,600 1,011,800 1,014,000 1,016,200 1,018,400 1,020,600 1,022,800 1,025,000

B

0 885,256 1,770,513 2,655,769 3,541,026 4,426,282

1,201,440 1,387,132 1,572,824 1,758,516 1,944,208 2,129,900

TR b

RefSeq_genes

XenBase_genes

Probesets

RXT002 TF CTRL

110
83
55
28
0

1,200,000 1,293,000 1,386,000 1,479,000 1,572,000 1,665,000 1,758,000 1,851,000 1,944,000 2,037,000 2,130,000

RXT001 TF +T3

110
83
55
28
0

1,200,000 1,293,000 1,386,000 1,479,000 1,572,000 1,665,000 1,758,000 1,851,000 1,944,000 2,037,000 2,130,000

Figure 10.5 RNA-Seq is less limited than microarrays for quantitative measures of gene
expression. (A) Genome view of the THb/ZIP locus. The first two tracks represent
the RefSeq and XenBase gene models. The second track represents the (curated) prob-
esets from the commercially available

Affymetrix microarray, with which the
expression level of THb/ZIP appears induced 2.8 fold. The last two tracks correspond to
the RNA-Seq profiles before and after T 3 treatment, respectively. In this case, the
induction level is fivefolds, which fits better with RT-qPCR data. (B) Genome view
of the TR b locus. The tracks are the same as in A. No probeset is associated to the
TR b gene (on the right-hand side of the panel), as opposed to other genes (left-hand
side). Thus, the Affymetrix microarray cannot monitor the expression of a key regulator
of metamorphosis.

X. tropicalis