title: DmelWhiteLab2003Jul30_r40
status: Public on Jan 07 2005
contact.city: Cambridge
contact.first: Scott
contact.middle: A
contact.last: Rifkin
contact.state: MA
contact.address: 16 Divinity Ave
contact.department: OEB
contact.country: USA
contact.web_link: http://kim.bio.upenn.edu/~scott/
contact.institute: Harvard University
contact.phone: 617-496-5540
organism: Drosophila melanogaster
description: PCR fragment spotted array with 95% of the genes in D. melanogaster BDGP release 4.0	Array has 8 rows of 4 blocks each, numbered 1-32 starting in the upper left and ending in the lower right.  16 pins used to print.  Each KP is only spotted once.
  KP# annotation file	files used:	isPcr:  http://www.soe.ucsc.edu/~kent/src/ options -out=bed -maxSize=1500 accessed: 22 Dec 04
  D. mel. euchromatin release 4:  ftp://ftp.fruitfly.org/pub/download/compressed/na_euchromatin_genomic_dmel_RELEASE4.FASTA.gz accessed: 22 Dec 04
  D. mel. .gff annotation files by chromosome:  ftp://flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-[CHR]-r4.0.gff.gz accessed 22 Dec 04
  D. mel. .fasta transcript and gene files:  ftp://flybase.net/genomes/Drosophila_melanogaster/current/fasta/dmel-all-[transcript/gene]-r4.0.fasta.gz accessed 22 Dec 04
  Heterochromatin from release hetr32b:  ftp://flybase.net/genomes/Drosophila_melanogaster/current_hetchr/ accessed 28 Dec 04
  Used dmel-all-chromosome.hetr32b.fasta and similar files as above
  r4.0 euchromatin extends into heterochromatin.  However, genes.gff files don't seem to yet.  So some KPs may have multiple chromosomes listed e.g. 2h,2R but are still good.
  Gene calls are based first on transcripts (isPcr.transcript file).  So if a probe hits an intron in gene A on the + strand and transcript in gene B on the - strand, it will call it for gene B
  If it hits no transcripts but it hits a gene, it calls it for that gene (this is slightly inconsistent in how complete we regard the annotation)
  In PCR_results field, I don't have the data for the KPST genes so I filled these in with 1MB (1 maybe) except for KPST3 (dpp) which apparently did not work.  Note that KPST8 is GFP.
  Note also that for some genes the PCR_results says 2 or more bands, but it is flagged good.  For these, there were 2 or more hits in the same transcript in the genome, so we'd expect multiple bands.
  Fields should be self-explanatory except SPOT_GROUP.  These are KPs which hit the same transcript with one catch:  singletons are left alone.
  If KP1, KP2, KP3, KP4, and KP5 are probes and T1-5 are transcripts of a gene ('{' means contained in) and KP1{T1,T5 KP2{T2, KP3{T2,T3 , KP4{T3,T4, KP5{T2 then:
  The spot groups will be [KP1], [KP2,KP5], [KP3,KP4]
  Keywords = spotted, PCR product, Drosophila melanogaster