Library Tables

Assigned Ids: Sequences can be identified by Stanford ID, dbEST ID, GenBank Accession and GenBank Gi number. Stanford ID is composed of the PlateWell number and a suffix indicating whether the sequence was a forward or reverse reaction ('x' or 'y', respectively) and whether the plate was sequenced multiple times. If there is no information for the dbEST ID and GenBank Accession variables, this sequence was not submitted to either database because it was too short. A 75-base pair sequence is provided for these short sequences in the downloadable form of this table.

Sequence length: It gives the number of bases in the sequence submitted to GenBank after trimming vector and low quality sequence.

Do Not Print information: If DNP is indicated, this sequence was identified by Stanford as problematic (short) or redundant. The reason for assignment of this code is indicated in the Note column*. For the 605 Library only, sequences identified with DNP were not removed from the library prior to printing and WERE PRINTED on the 605 microarrays. Sequences identified with DNP were removed from the 606 and 614 libraries prior to printing. *Note that for the 605 Library, Stanford asked us to omit 8 whole plates even though they provided us with data for these plates. The plates are 605030, 036, 040, 067, 069, 086, 087, and 094-some data are provided for these plates since they are part of the library, but they were not printed on the Microarrays.

PCR Product size and quality: PCR products were amplified in two separate reactions. Each product was analyzed separately by gel electrophoresis. Size (estimated to the nearest 100 base pairs) and product quality from both gels is provided (quality codes: d=double band, m=multiple bands, f=faint band, np=no product, dnp=do not print code, we did not analyze all sequences in these plates because we were asked by Stanford to omit them). If two numbers are provided (one in the size and one in the quality columns) then there were two bands of equal intensity on the gel.

Array Identification: Each Microarray is identified by EST Project number, array format used, and replicate printing. Every time we change the format we use to print an EST library, we assign it a new format number. Each batch of 100 slides printed is designated by a unique number. For example, Microarray 605.04.01 was made from the 605 EST library and has a different format than the 605.03 microarrays. Slides from the 605.04.01 came from the first printing of 100 slides.

EST Contig: We assemble all maize ESTs to minimize redundancy. EST assemblies generate two classes of tentative genes: TUS = tentative unique singlets, only one EST is in the unit; TUC = tentative unique contigs, two or more ESTs are in the contig. For the singlets, the composing EST clone is chosen. For the contigs, which were assembled from multiple EST sequences, a consensus sequence is drawn. For more information about our assembly strategy, please visit the EST assembly page. The contig information will be updated frequently (every 3-4 months).