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Platform GPL3352 Query DataSets for GPL3352
Status Public on Oct 24, 2006
Title FHCRC DMEL 4.2 Tiling 1 of 3
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Drosophila melanogaster
Manufacturer NimbleGen Systems Inc.
Manufacture protocol http://www.nimblegen.com/products/chip/index.html
 
Description Fly tiling array using NimbleGen platform (DesignID=2347), chip 1 of 3. FlyBase release 4.2. All of Chr 3R with isothermal oligos averaging 50bp. Dense tiling of Chr 2L proximal, Chr X proximal and distal, first part of Chr 4, and Bithorax complex (BXC1).
 
Web link http://www.nimblegen.com
Contributor(s) Henikoff S, Mito Y
Submission date Jan 11, 2006
Last update date Oct 24, 2006
Contact name Jorja Henikoff
E-mail(s) jorja@fhcrc.org
Phone 206-667-4850
Organization name Fred Hutchinson Cancer Research Center
Department Basic Sciences
Lab Henikoff
Street address 1100 Fairview AV N, A1-162
City Seattle
State/province WA
ZIP/Postal code 98109-1024
Country USA
 
Samples (3) GSM93208, GSM93209, GSM143928
Series (2)
GSE4091 Histone turnover mediates epigenetic processes in Drosophila S2 cells
GSE6234 Histone turnover marks the boundaries of cis-regulatory domains

Data table header descriptions
ID NimbleGen PROBE_DESIGN_ID
CONTAINER Probes are arranged in sets in different containers
DESIGN_NOTE Comment field for data analysis
SELECTION_CRITERIA Information about how the probe was selected
SEQ_ID NimbleGen sequence identifier
SEQUENCE DNA sequence synthesized on the array
MISMATCH Number of mismatches in the PROBE_SEQUENCE. Generally 0 (for the perfect match probe) or 2 (for the corresponding mismatch probe)
MATCH_INDEX Integer number that ties probe pairs together
FEATURE_ID Unique number used to tie together multiple features that compose a feature cell
ROW_NUM Y coordinate of the feature within the CONTAINER holding the feature
COL_NUM X coordinate of the feature within the CONTAINer holding the feature
PROBE_CLASS Experimental or Control
PROBE_ID NimbleGen probe identifier
POSITION Position of the probe within the parent sequence
DESIGN_ID NimbleGen identifier for the desing
X Absolute X coordinate of the feature on the array
Y Absolute Y coordinate of the feature on the array

Data table
ID CONTAINER DESIGN_NOTE SELECTION_CRITERIA SEQ_ID SEQUENCE MISMATCH MATCH_INDEX FEATURE_ID ROW_NUM COL_NUM PROBE_CLASS PROBE_ID POSITION DESIGN_ID X Y
2433_0001_0001 CONTROL 0 chr4dense chr4_1_1281640 CCACGAGTTGTCTCGCTGCTCAAAGGGCCAGATAAGGACAAGTGTGAGCC 0 39465334 39465334 1 1 experimental CHR4dense chr4P614177 614177 2433 1 1
2433_0004_0001 NGS_CONTROLS upper left fiducial bright FIDUCIAL_UPPER_LEFT TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 0 2000187 37331612 1 4 fiducial CPK6 0 2433 4 1
2433_0006_0001 NGS_CONTROLS upper left fiducial bright FIDUCIAL_UPPER_LEFT TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 0 2000197 37331622 1 6 fiducial CPK6 0 2433 6 1
2433_0008_0001 NGS_CONTROLS upper left fiducial bright FIDUCIAL_UPPER_LEFT TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 0 2000198 37331623 1 8 fiducial CPK6 0 2433 8 1
2433_0010_0001 NGS_CONTROLS upper left fiducial bright FIDUCIAL_UPPER_LEFT TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 0 2000199 37331624 1 10 fiducial CPK6 0 2433 10 1
2433_0012_0001 NGS_CONTROLS upper left fiducial bright FIDUCIAL_UPPER_LEFT TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 0 2000200 37331625 1 12 fiducial CPK6 0 2433 12 1
2433_0014_0001 NGS_CONTROLS upper left fiducial bright FIDUCIAL_UPPER_LEFT TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 0 2000201 37331626 1 14 fiducial CPK6 0 2433 14 1
2433_0016_0001 NGS_CONTROLS upper left fiducial bright FIDUCIAL_UPPER_LEFT TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 0 2000202 37331627 1 16 fiducial CPK6 0 2433 16 1
2433_0018_0001 NGS_CONTROLS upper left fiducial bright FIDUCIAL_UPPER_LEFT TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 0 2000203 37331628 1 18 fiducial CPK6 0 2433 18 1
2433_0020_0001 NGS_CONTROLS upper left fiducial bright FIDUCIAL_UPPER_LEFT TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 0 2000204 37331629 1 20 fiducial CPK6 0 2433 20 1
2433_0022_0001 NGS_CONTROLS upper left fiducial bright FIDUCIAL_UPPER_LEFT TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 0 2000205 37331630 1 22 fiducial CPK6 0 2433 22 1
2433_0025_0001 ISOTHERMAL target_tm:76.00;probe_tm:75.61 cluster:38788;probe:01 CHR3R AAGAGGGTATTTTATGCGAAAAATGTGCTTTCAGGCATGTGAAGTTATAGTTTGCTCTGC 0 38947249 38947249 1 25 experimental CHR3R00P005100166 5100166 2433 25 1
2433_0027_0001 ISOTHERMAL target_tm:76.00;probe_tm:75.57 cluster:89051;probe:01 CHR3R AGGCATATTAGGGATAACTGCAACACAGCAGACACACACACACACA 0 38962715 38962715 1 27 experimental CHR3R00P011545442 11545442 2433 27 1
2433_0029_0001 ISOTHERMAL target_tm:76.00;probe_tm:75.91 cluster:200035;probe:01 CHR3R TTTGTGCCGTCATTACGTCATTGTCAGGCTAAAATTGGTCTAAAAATAGCCCAACAC 0 39009533 39009533 1 29 experimental CHR3R00P025612924 25612924 2433 29 1
2433_0031_0001 CONTROL 0 Xprox chrX_20730000_21377940 AAAAATGTGTATTTTCTAAAATTCTGTCAGCCATCTCAATTTCATCTTGT 0 39271518 39271518 1 31 experimental CHRXP20760980 20760980 2433 31 1
2433_0033_0001 ISOTHERMAL target_tm:76.00;probe_tm:75.39 cluster:49379;probe:01 CHR3R ACACAGATGGAGGAAATCGTTTTCCTATGAAAAACTACTTAGTCCAAATGGAGGC 0 39095256 39095256 1 33 experimental CHR3R00P006444862 6444862 2433 33 1
2433_0035_0001 ISOTHERMAL target_tm:76.00;probe_tm:75.45 cluster:155644;probe:01 CHR3R CTTTAAAGGTTAGGGCGTACTTTACTACCCAGTACTTAGTGGGGAGT 0 39060086 39060086 1 35 experimental CHR3R00P020123797 20123797 2433 35 1
2433_0037_0001 CONTROL 0 chr4dense chr4_1_1281640 TGGTCCCATGTCTAGACAGGATGCTACTGAAGTTTTGATGAACGAACGCG 0 39442186 39442186 1 37 experimental CHR4dense chr4P230817 230817 2433 37 1
2433_0039_0001 ISOTHERMAL target_tm:76.00;probe_tm:76.61 cluster:36729;probe:01 CHR3R ACCGGACTCTCGGGCACAAAGCATAGCATTATTATGGTGATCACC 0 39019007 39019007 1 39 experimental CHR3R00P004822552 4822552 2433 39 1
2433_0041_0001 ISOTHERMAL target_tm:76.00;probe_tm:75.57 cluster:83186;probe:01 CHR3R TCACAAGCGTACGCTGCTCGCAGTTTGCTCTTCATGCTTATATGAA 0 38984428 38984428 1 41 experimental CHR3R00P010798423 10798423 2433 41 1

Total number of rows: 391015

Table truncated, full table size 77002 Kbytes.




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