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Project Documentation & Protocols: Maize Gene Discovery Project: ESTs: Reports

Contents: Index | Libraries | Reports | Assembly | Annotation | Unigene | Search | Ordering | Protocols | FAQs

Maize EST Requests - Response Time

The data below shows our final report on response time for sending out maize EST clones requested through ZmDB. Our goal was to distribute clones the majority of clones within three weeks of a request while maintaining production sequencing.

Beginning in the third year of the Maize Gene Discovery Project unigene consolidation sets selected from finished EST projects were prepared. These selected Maize Gene Discovery clones are now distributed by Texas A&M University GENEfinder Genomic Resources. Stanford distributes clones only while an EST project is in active production sequencing, i.e. in March 2002 projects 952 and 953. Project 952 will enter its consolidation phase in April 2002, and clones from this project should be available from GENEfinder in June 2002. With each new EST consolidation we pick both new unique clone types and find substitutes for poorly growing or very short existing Unigene clones.

The data below shows the response time for sending out maize EST clones requested through ZmDb. Note that Maize Gene Discovery clones are now distributed by Texas A&M University GENEfinder Genomic Resources. Stanford distributes clones only while an EST project is in active production sequencing.

Response Time Report, October 2000

Days to Fill Pct Filled Clones
<11 days 0% 0
11-20 days 27% 4
21+ days 73% 11
Open 0% 0

Summary of Response Times

EST clone response time

Last Updated on 2/23/01
by John Fernandes
Email:


Overlap Between EST Projects -- August 16, 1999

Summary of Overlap

A major surprise has been the low overlap between and among the four large EST projects we have completed. With more than 5,000 entries each, leaf primordia and 10 day developing kernels have only 4% overlap between the "singlets" and "contigs" of each project. Similarly each project shows low overlap with the immature ear and root libraries.

We do not increase the fraction of overlap between libraries when we include the ~10% "reverse sequencing" information from each library. We hypothesized that examining the 3' ends of cDNAs would result in much higher levels of overlap. If the 3' ends of cDNAs are distinct, the corresponding genes are likely to be distinct.

The low percentage overlap we have found so far could reflect:

  1. with only ~25,000 ESTs, we are still in the "good news" part of the sampling,
  2. by using libraries prepared from very immature organs, we have minimized the overlap,
  3. we have many very long inserts and even with ~500+ base ESTs from the 5' end we are unlikely to form many contigs,
  4. there is only a small core of a few hundred genes that are expressed ubiquitously in corn,
  5. your idea here.

For more information on example library overlaps, see the upcoming paper by Fernandes, et. al. in the March 2002 issue of Plant Physiology.

Shown below are the comparisons between pairs of projects performed by John Fernandes.  All of the EST sequences from the two libraries were assembled using phrap (minimum overlap = 40).  The percentages of how many sequences that only assembled with other sequences in the same project (or did not assemble at all) are shown in the larger pie.   The percentages of how many sequences assembled with sequences of other projects are shown in the smaller pie breakout.

Project 1 Project 2
486 leaf primordia  605  immature ear
486 leaf primordia 606 10 day developing kernel
605 immature ear 606 10 day developing kernel
603 desiccation stress seedling root 614 seven day seedling root

Explanation of Legend Codes

SS -> C   Two singlets from different libraries assembled into a contig.
SC -> C   A singlet from 1 library assembled with a contig from another.
CC -> C   Two contigs from different libraries assembled

Graphs Representing EST Overlap

ChartObject August 4th - Inserts Comparison - 614/603
Compare 614 (seedling root) and 603 (stressed root)

ChartObject July - Inserts Comparison - 486/606
Compare 486 (leaf primordia) and 606 (immature ear)

ChartObject July - Inserts Comparison - 605/606
Compare 605 (10 day kernel) and 606 (immature ear)

ChartObject July - Inserts Comparison - 605/486
Compare 605 (10 day kernel) and 486 (leaf primordia)

Last Updated on 8/6/99
by John Fernandes
Email:


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