Strand Determination and Antisense Transcription
|
A. Number of transfrags Transfragsa |
No. transfrags |
Base pair coverage |
|
||
|---|---|---|---|---|---|
| cDNA (1 of 2) | 3747 | 496,537 | |||
| + strand (1 of 2) | 1392 | 159,778 | |||
| - strand (1 of 2)
|
1112
|
130,966
|
|
||
| B. Characterization based on annotations | |||||
| Base pair coverage
|
|||||
| Overlapping data setsb
|
Total known, mRNA, ESTc transfrags
|
Total novel transfrags
|
|
||
| + strand | 15,440 | 8277 | |||
| - strand | 41,283 | 8529 | |||
| Totals
|
56,723
|
16,806
|
|
||
| C. Antisense transcription | |||||
| Base pair coverage | |||||
| Overlapping data setsb
|
Total known, mRNA, ESTc transfrags
|
|
|
||
| + strand | 1948 | ||||
| - strand | 4187 | ||||
| Percent of antisense detectedd
|
10.8%
|
|
|
||
| D. Novel transcriptione | |||||
| Base pair coverage
|
|||||
| Overlapping data setsb
|
Total novel intronic transfrags
|
Same strand
|
Antisense
|
||
| + strand | 2596 | 1506 | 1090 | ||
| - strand | 2672 | 1071 | 1601 | ||
| Percent of novel transcription
|
|
48.9%
|
51.1%
|
||
-
↵a Transfrags cDNA (1 of 2) = A375 and Jurkat cDNA data combined into a nonoverlapping map. + strand (1 of 2) = A375 and Jurkat (+) strand specific data combined into a nonoverlapping map. - strand (1 of 2) = A375 and Jurkat (-) strand specific data combined into a nonoverlapping map.
-
↵b A set of transfrags that overlap between the cDNA and RNA direct-labeling assays was generated. The resulting set was then compared to the indicated annotations for each chromosome and strand.
-
↵c Only ESTs of confident strandedness were used, where strandedness evidence comes from splicing and/or having a polyadenylation site, possibly with associated signal.
-
↵d Percent base-pair coverage in B that is antisense to the annotations.
-
↵e Distribution of the base-pair coverage of the novel intronic transfrags based on the strand of the overlapping annotation.
