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Platform GPL3767 Query DataSets for GPL3767
Status Public on May 22, 2006
Title Zebrafish 44K oligo promoter array_Slide 2 of 2
Technology type spotted oligonucleotide
Distribution custom-commercial
Organism Danio rerio
Manufacturer Agilent Technology
Manufacture protocol as described in www.agilent.com
Support glass
Coating aminosilane
 
Description Microarrays were designed as described below and manufactured by Agilent Technologies (www.agilent.com). Further information on design can be found at http://jura.wi.mit.edu/bioc/gbell/zfish_chip/.

The Whitehead zebrafish promoter chipsets were designed for large-scale chromatin immunoprecipitation using microarrays (ChIP chips). The chipsets represent the promoters of about 11,000 transcriptional units derived using transcript sequences from Refseq, Ensembl, Vega, ZGC, and the Zon Lab. The 2-chipset represents proximal promoters (-1500 nt to +500 nt from the transciptional start site [tss]) on two microarrays of the same density. Probes are spaced an average of 250 nt apart.
 
Submission date May 15, 2006
Last update date May 22, 2006
Contact name Elizabeth Herbolsheimer
E-mail(s) herbolsheimer@wi.mit.edu
Organization name Whitehead Institute
Lab Young Lab
Street address 9 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02140
Country USA
 
Samples (3) GSM109326, GSM109328, GSM109330
Series (1)
GSE4863 Zebrafish promoter microarrays identify actively transcribed embryonic genes

Data table header descriptions
ID
MetaColumn placement on array MetaColumn
MetaRow Placement on array MetaRow
Column Placement on array Column
Row Placement on array Row
GB_RANGE ACCESSION.VERSION[start..end]
SPOT_ID spot identifier
Reporter Identifier Probe Indentifier
Reporter Name Probe name
Reporter Biosequence Type intergenic or genic
Reporter Biosequence Polymer Type DNA
Reporter BioSequence [Actual Sequence] Sequence
Reporter Group [role] Probe is identified as Experimental or Control
Reporter Control Type Type of Control

Data table
ID MetaColumn MetaRow Column Row GB_RANGE SPOT_ID Reporter Identifier Reporter Name Reporter Biosequence Type Reporter Biosequence Polymer Type Reporter BioSequence [Actual Sequence] Reporter Group [role] Reporter Control Type
1 1 1 430 103 --BrightCorner_Pro25G_T10_Pro25G Pro25G_T10_Pro25G BrightCorner intergenic DNA ATCATCGTAGCTGGTCAGTGTATCCTTTTTTTTTTATCATCGTAGCTGGTCAGTGTATCC Control control_biosequence
2 1 1 430 102 --BrightCorner_Pro25G_T10_Pro25G Pro25G_T10_Pro25G BrightCorner intergenic DNA ATCATCGTAGCTGGTCAGTGTATCCTTTTTTTTTTATCATCGTAGCTGGTCAGTGTATCC Control control_biosequence
3 1 1 430 101 --3xSLv1 (-)3xSLv1 3xSLv1 intergenic DNA GCTAGCGAAAGCTAGCTTTTCGATCGGAAACGATCGTTTTCCAGTGACGAAAGTCACTGG Control control_biosequence
4 1 1 430 100 NC_007115.1[8299601-8299661] WH_07_P0060909 chr4:8299601-8299661 intergenic DNA ATAGTTTCACAGGTGCGATTAATAATTTGTCTTTAATTGTATATATTCCCCCTTCTTTAG Experimental null
5 1 1 430 99 chrUn:19520004-19519944_WGS supercontig that mapped to FPC contigs, unknown chromosome WH_07_P0050678 chrUn:19520004-19519944 intergenic DNA GCCAGCATCATTGCATTGACAAACATACACGTAAGCTGGTTATGCCCAGAACACATGAGG Experimental null
6 1 1 430 98 NC_007116.1[38199913-38199973] WH_07_P0067569 chr5:38199913-38199973 intergenic DNA ATAGAAATTATAATCATAACCGCTCACCCGAGCTATTCCCTCTCTTATTGTTGCAGTGTC Experimental null
7 1 1 430 97 chrNA:227407957-227408017_WGS contig that could not be related to any FPC contig WH_07_P0078407 chrNA:227407957-227408017 intergenic DNA TGTTTTAAAGGGGCATACACATCTGCATTGCTCTTAAAATGTTGAAGAAAGTAAGCTCAT Experimental null
8 1 1 430 96 NC_007116.1[21232891-21232951] WH_07_P0066809 chr5:21232891-21232951 intergenic DNA AAGGTACGGTTAAAACTAGATACTCTACATCACAGTAAGCATAAGTTGGACAAAGCTTTT Experimental null
9 1 1 430 95 NC_007120.1[32119804-32119864] WH_07_P0065203 chr9:32119804-32119864 intergenic DNA TAGTTATTGGACTAGAATCAAGTCAAGTAAGTTCTCTAAGTAATCTCAAAGTAAGAAATG Experimental null
10 1 1 430 94 chrNA:35611477-35611417_WGS contig that could not be related to any FPC contig WH_07_P0070238 chrNA:35611477-35611417 intergenic DNA GAGTCTCTGGATCTCATCTATAATTGGTTTATAACAGCTGTCTCTTTCAGCCTTTCCTGC Experimental null
11 1 1 430 93 chrUn:50230764-50230704_WGS supercontig that mapped to FPC contigs, unknown chromosome WH_07_P0052074 chrUn:50230764-50230704 intergenic DNA AATCATTTCATTTTAATTTTGGATATACCGTTACTATTGCTTTAACGCTCATTAGTGGAG Experimental null
12 1 1 430 92 chrNA:40599708-40599648_WGS contig that could not be related to any FPC contig WH_07_P0070438 chrNA:40599708-40599648 intergenic DNA ATCAGTTAAAGTTCATCTCAAATCATTATTAGATAAACACTCGGGGAGTCGAGTCATGTC Experimental null
13 1 1 430 91 --3xSLv1 (-)3xSLv1 3xSLv1 intergenic DNA GCTAGCGAAAGCTAGCTTTTCGATCGGAAACGATCGTTTTCCAGTGACGAAAGTCACTGG Control control_biosequence
14 1 1 430 90 NC_007113.1[12186747-12186807] WH_07_P0047471 chr2:12186747-12186807 intergenic DNA AACGTGCATTTCGCCAGCTCCATCTCATTTATTCTGGTTTTGTAATTATTTGGGATCCTT Experimental null
15 1 1 430 89 NC_007116.1[40971371-40971311] WH_07_P0067818 chr5:40971371-40971311 intergenic DNA TTTCCGTTTGTGAGCCCCCGCGCGCCCCACACAGGAAGACTGCGGTTGTTTCATATACAG Experimental null
16 1 1 430 88 WH_07_P8000557_Gene_desert_5-39 WH_07_P8000557 Gene_desert_5-39 intergenic DNA TAATCAAGATTTTAGGCCAAATGGCCCAGCCCTATTTGAAGTCAAAATCATTAGTCAAAA Experimental null
17 1 1 430 87 NC_007113.1[40726050-40726110] WH_07_P0049061 chr2:40726050-40726110 intergenic DNA ACAATACTCTTTGACACAAAAAAACTATCTTTCAGCTATTCAATGTTTTAATATGATGTT Experimental null
18 1 1 430 86 chrNA:227237000-227236940_WGS contig that could not be related to any FPC contig WH_07_P0078400 chrNA:227237000-227236940 intergenic DNA AGTATTCCCAGTGCATCTTTTAGGACGACATCCACTTCTTCCCACGTTTCCCGCTCTGCT Experimental null
19 1 1 430 85 NC_007114.1[26570052-26570112] WH_07_P0043703 chr3:26570052-26570112 intergenic DNA AGTGCTCAGTGTGGCTTGACGACACATAAACTGGGCCATACGCTCGGTGTTTGCCAAAAC Experimental null
20 1 1 430 84 chrUn:161187278-161187218_WGS supercontig that mapped to FPC contigs, unknown chromosome WH_07_P0056182 chrUn:161187278-161187218 intergenic DNA AGGCAAAAGCAAAGGGCAGGAGAACGTGTCGAGTTCTCTCCTCAGCAGCCTGGAAAATGA Experimental null

Total number of rows: 44290

Table truncated, full table size 8785 Kbytes.




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