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Platform GPL3354 Query DataSets for GPL3354
Status Public on Oct 24, 2006
Title FHCRC DMEL 4.2 Tiling 3 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 3 of 3. FlyBase release 4.2. All of Chr 2L, Chr 3L and Chr 4 with isothermal oligos averaging 50bp. Dense tiling of second 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 (5) GSM93212, GSM93213, GSM143923, GSM143926, GSM143927
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
1883_0001_0001 CHR2R 0 2R 2R.3 ASSEMBLED 23-11-2001 TCTAGCTCCCGACACCCCACTCACTGTTCTCATCCCCAATCCCCATCACCCACCGTTTCT 0 43759081 43759081 1 1 experimental DMEL00P000244094 2200602 1883 1 1
ID CONTAINER DESIGN_NOTE SELECTION_CRITERIA SEQ_ID PROBE_SEQUENCE MISMATCH MATCH_INDEX FEATURE_ID ROW_NUM COL_NUM PROBE_CLASS PROBE_ID POSITION DESIGN_ID X Y
2435_0001_0001 ISOTHERMAL target_tm:76.00;probe_tm:77.52 cluster:157416;probe:01 CHR2L TATCCTGCACTGGTTCTGGTGAGCTTACGTGCTGCTTCAGAGAAG 0 39611837 39611837 1 1 experimental CHR2L00P020650191 20650191 2435 1 1
2435_0004_0001 NGS_CONTROLS upper left fiducial bright FIDUCIAL_UPPER_LEFT TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 0 2000187 37331612 1 4 fiducial CPK6 0 2435 4 1
2435_0006_0001 NGS_CONTROLS upper left fiducial bright FIDUCIAL_UPPER_LEFT TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 0 2000197 37331622 1 6 fiducial CPK6 0 2435 6 1
2435_0008_0001 NGS_CONTROLS upper left fiducial bright FIDUCIAL_UPPER_LEFT TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 0 2000198 37331623 1 8 fiducial CPK6 0 2435 8 1
2435_0010_0001 NGS_CONTROLS upper left fiducial bright FIDUCIAL_UPPER_LEFT TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 0 2000199 37331624 1 10 fiducial CPK6 0 2435 10 1
2435_0012_0001 NGS_CONTROLS upper left fiducial bright FIDUCIAL_UPPER_LEFT TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 0 2000200 37331625 1 12 fiducial CPK6 0 2435 12 1
2435_0014_0001 NGS_CONTROLS upper left fiducial bright FIDUCIAL_UPPER_LEFT TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 0 2000201 37331626 1 14 fiducial CPK6 0 2435 14 1
2435_0016_0001 NGS_CONTROLS upper left fiducial bright FIDUCIAL_UPPER_LEFT TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 0 2000202 37331627 1 16 fiducial CPK6 0 2435 16 1
2435_0018_0001 NGS_CONTROLS upper left fiducial bright FIDUCIAL_UPPER_LEFT TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 0 2000203 37331628 1 18 fiducial CPK6 0 2435 18 1
2435_0020_0001 NGS_CONTROLS upper left fiducial bright FIDUCIAL_UPPER_LEFT TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 0 2000204 37331629 1 20 fiducial CPK6 0 2435 20 1
2435_0022_0001 NGS_CONTROLS upper left fiducial bright FIDUCIAL_UPPER_LEFT TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNN 0 2000205 37331630 1 22 fiducial CPK6 0 2435 22 1
2435_0025_0001 ISOTHERMAL target_tm:76.00;probe_tm:75.60 cluster:102133;probe:01 CHR3L TAATAACAAAACCACCTCGACCACTAGTGGTCAATTCCCATTAAATTCCCCCA 0 39369337 39369337 1 25 experimental CHR3L00P013223697 13223697 2435 25 1
2435_0027_0001 ISOTHERMAL target_tm:76.00;probe_tm:75.60 cluster:140795;probe:01 CHR2L TTTAATTAAAGCTTCAACGGTAGCAATGCCAAGGGGGTGTGGGTTGAAATTGT 0 39595216 39595216 1 27 experimental CHR2L00P018515961 18515961 2435 27 1
2435_0029_0001 ISOTHERMAL target_tm:76.00;probe_tm:75.39 cluster:103911;probe:01 CHR2L GCGCAAAGTTTCTGGCTCTGCTCTTGACTTGATTTTCTTTTAATTTTTTCCCGAC 0 39558332 39558332 1 29 experimental CHR2L00P013413381 13413381 2435 29 1
2435_0031_0001 ISOTHERMAL target_tm:76.00;probe_tm:77.52 cluster:16054;probe:01 CHR3L GATAGTGTTGTTGCCTTCCAACAGGCACGTCAAAGAGTCTGCTCC 0 39283258 39283258 1 31 experimental CHR3L00P001946457 1946457 2435 31 1
2435_0033_0001 ISOTHERMAL target_tm:76.00;probe_tm:75.52 cluster:81137;probe:01 CHR3L TTGTTGTCAACTGCAATTGAAATCATTATGACAAAGTCAACAATGAGGTTCTACACCCCTC 0 39348341 39348341 1 33 experimental CHR3L00P010356933 10356933 2435 33 1
2435_0035_0001 ISOTHERMAL target_tm:76.00;probe_tm:75.81 cluster:85472;probe:01 CHR3L ATACAGTAGCTCAAAACAACGGCGATAAAAACAAACAAATGTCAGGCTGCAATTGTGG 0 39352676 39352676 1 35 experimental CHR3L00P010970862 10970862 2435 35 1
2435_0037_0001 ISOTHERMAL target_tm:76.00;probe_tm:75.52 cluster:178397;probe:01 CHR3L ATTATATCCATGAGGTTACGGTTTTGTGTTTCCAAAACAGCCATATACTGATCAGATCTGC 0 39445601 39445601 1 37 experimental CHR3L00P023539052 23539052 2435 37 1

Total number of rows: 391017

Table truncated, full table size 81991 Kbytes.




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