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Platform GPL2678 Query DataSets for GPL2678
Status Public on Sep 11, 2005
Title Tiling design for D. melanogaster
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 All of Chr 4, 2L, pericentric regions on 2, first 2MB on X and part of 2R. Based on FlyBase release 3.2.2. One 60mer per 100 bases.
 
Web link http://www.nimblegen.com
Contributor(s) Henikoff S, van Steensel B
Submission date Jul 27, 2005
Last update date Sep 11, 2005
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 (15) GSM66596, GSM66597, GSM66599, GSM66601, GSM66602, GSM66603 
Series (5)
GSE3031 Genome-scale profiling of histone H3.3 replacement patterns in Drosophila S2 cells
GSE4564 Genome-wide profiling of PRC1 and PRC2 Polycomb chromatin binding in Drosophila
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 prob 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
1883_0004_0001 NGS_CONTROLS upper left fiducial bright FIDUCIAL_UPPER_LEFT TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNNNNNNNNNN 0 2000187 36543017 1 4 fiducial CPK6 0 1883 4 1
1883_0006_0001 NGS_CONTROLS upper left fiducial bright FIDUCIAL_UPPER_LEFT TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNNNNNNNNNN 0 2000197 36543027 1 6 fiducial CPK6 0 1883 6 1
1883_0008_0001 NGS_CONTROLS upper left fiducial bright FIDUCIAL_UPPER_LEFT TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNNNNNNNNNN 0 2000198 36543028 1 8 fiducial CPK6 0 1883 8 1
1883_0010_0001 NGS_CONTROLS upper left fiducial bright FIDUCIAL_UPPER_LEFT TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNNNNNNNNNN 0 2000199 36543029 1 10 fiducial CPK6 0 1883 10 1
1883_0012_0001 NGS_CONTROLS upper left fiducial bright FIDUCIAL_UPPER_LEFT TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNNNNNNNNNN 0 2000200 36543030 1 12 fiducial CPK6 0 1883 12 1
1883_0014_0001 NGS_CONTROLS upper left fiducial bright FIDUCIAL_UPPER_LEFT TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNNNNNNNNNN 0 2000201 36543031 1 14 fiducial CPK6 0 1883 14 1
1883_0016_0001 NGS_CONTROLS upper left fiducial bright FIDUCIAL_UPPER_LEFT TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNNNNNNNNNN 0 2000202 36543032 1 16 fiducial CPK6 0 1883 16 1
1883_0018_0001 NGS_CONTROLS upper left fiducial bright FIDUCIAL_UPPER_LEFT TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNNNNNNNNNN 0 2000203 36543033 1 18 fiducial CPK6 0 1883 18 1
1883_0020_0001 NGS_CONTROLS upper left fiducial bright FIDUCIAL_UPPER_LEFT TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNNNNNNNNNN 0 2000204 36543034 1 20 fiducial CPK6 0 1883 20 1
1883_0022_0001 NGS_CONTROLS upper left fiducial bright FIDUCIAL_UPPER_LEFT TGAGTTGTTTGATAGGATTATTCATAGAGGTCATTACAGCGAGAGGAANNNNNNNNNNNNNNNNN 0 2000205 36543035 1 22 fiducial CPK6 0 1883 22 1
1883_0025_0001 CHR2L 0 2L 2L RELEASE:3 LENGTH:22217931BP ASSEMBLED 2L CHR CTGCTACGTTTACGTCGATGACGTCATCATCTTTTCGGAAGATGAAAACGACCATGTCAA 0 42589941 42589941 1 25 experimental DMEL00P000032583 3247485 1883 25 1
1883_0027_0001 CHR2L 0 2L 2L RELEASE:3 LENGTH:22217931BP ASSEMBLED 2L CHR ATGATAAATGGCACTATTTATTTAAATCAAGCGACCCGCGGAGACCTCCAAAACAAACAC 0 42513015 42513015 1 27 experimental DMEL00P000054790 5469677 1883 27 1
1883_0029_0001 CHR2L 0 2L 2L RELEASE:3 LENGTH:22217931BP ASSEMBLED 2L CHR TTAATCAATATCACGCATAGGCATATAAAAAGTTCAGTTTAACTTTAGTTTGTTTTATTC 0 42581810 42581810 1 29 experimental DMEL00P000067429 6734142 1883 29 1
1883_0031_0001 CHR2R 0 2R 2R.3 ASSEMBLED 23-11-2001 CGCCACAATCCGCTGCCGTATCTGCTCAAGGATCGGATGACCGGCCGACCCACCCGCACC 0 43797556 43797556 1 31 experimental DMEL00P000308685 8663080 1883 31 1
1883_0033_0001 CHR2H 0 GADFLY|SEG:2R_WGS3_CENTROMERE_EXTENSION|GB|2R_WGS3 ATTTGAAAAAGGAGGGAAAATATCGCATCCTTGCTGATTATTGAGCGCTTTTCCATTATT 0 42913027 42913027 1 33 experimental DMEL00P000467790 48556 1883 33 1
1883_0035_0001 CHR2R 0 2R 2R.3 ASSEMBLED 23-11-2001 AAACTATAAATTTGGCATTGTGCTGAGCGATGATTAGCATATATGTGGAAATGTTCGGGG 0 43799554 43799554 1 35 experimental DMEL00P000251805 2972093 1883 35 1
1883_0037_0001 CHR2L 0 2L 2L RELEASE:3 LENGTH:22217931BP ASSEMBLED 2L CHR CCGTCTTCATTTCAGGCTTTGTATCGGACTTGATTTCAGACTTCAGTTCAGACTTCTTTT 0 42586854 42586854 1 37 experimental DMEL00P000186552 18653434 1883 37 1
1883_0039_0001 CHR2R 0 2R 2R.3 ASSEMBLED 23-11-2001 CCAACTGCTACTTCAACCAGGCCATTGCCGACGATATCCAGCTCAGCGATATTGAAGAAC 0 43734425 43734425 1 39 experimental DMEL00P000243775 2168702 1883 39 1
1883_0041_0001 CHR2R 0 2R 2R.3 ASSEMBLED 23-11-2001 ACTTTTTATATATTTATAATTTTGTAAATTTTTTTTTATGATTTAACTATATATCTTTGG 0 43749630 43749630 1 41 experimental DMEL00P000280702 5863241 1883 41 1

Total number of rows: 390919

Table truncated, full table size 78344 Kbytes.




Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp

Supplementary file Size Download File type/resource
GPL2678_probe_locations.txt.gz 4.0 Mb (ftp)(http) TXT

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