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Platform GPL17005 Query DataSets for GPL17005
Status Public on Dec 21, 2013
Title Agilent-032722 Halobacterium sp. NRC-1 Tiling V2 030521
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Halobacterium salinarum NRC-1
Manufacturer Agilent Technologies
Manufacture protocol see manufacturer's web site at http://www.agilent.com/
 
Description Arrays of this design have barcodes that begin with 16032722 or 2532722.
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.
Halobacterium sp. NRC-1 Whole genome tiling Array. 60 bp tiles with 24 bp spacing. Includes 227 probes for ncRNAs selected from Next-Gen sequencing plus 10 probes for non-Halo random sequences that can be used for spike-in controls
Orientation:
Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).
The ID column represents the Agilent Feature Extraction feature number.
To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.
 
Submission date Apr 11, 2013
Last update date Dec 21, 2013
Contact name Nicolas Pinel
E-mail(s) pinel.n@gmail.com
Organization name Institute for Systems Biology
Street address 401 Terry Ave N
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Samples (52) GSM1121334, GSM1121335, GSM1121336, GSM1121337, GSM1121338, GSM1121339 
Series (4)
GSE45988 H. salinarum NRC-1 vs VNG2099C knockout
GSE53544 RNA expression data from Halobacterium NRC-1 in varied extracellular salinity conditions
GSE61975 Evolution of Context Dependent Regulation by Expansion of Feast/Famine Regulatory Proteins [expression]

Data table header descriptions
ID Agilent feature number
SPOT_ID Spot identifier
CONTROL_TYPE Control type
REFSEQ RefSeqAccession
GB_ACC GenBankAccession
ACCESSION_STRING Accession String
CHROMOSOMAL_LOCATION Chromosomal Location
SEQUENCE Sequence
RANGE_GB
RANGE_START
RANGE_END

Data table
ID SPOT_ID CONTROL_TYPE REFSEQ GB_ACC ACCESSION_STRING CHROMOSOMAL_LOCATION SEQUENCE RANGE_GB RANGE_START RANGE_END
(+)E1A_r60_1 (+)E1A_r60_1 pos
(+)E1A_r60_3 (+)E1A_r60_3 pos
(+)E1A_r60_a104 (+)E1A_r60_a104 pos
(+)E1A_r60_a107 (+)E1A_r60_a107 pos
(+)E1A_r60_a135 (+)E1A_r60_a135 pos
(+)E1A_r60_a20 (+)E1A_r60_a20 pos
(+)E1A_r60_a22 (+)E1A_r60_a22 pos
(+)E1A_r60_a97 (+)E1A_r60_a97 pos
(+)E1A_r60_n11 (+)E1A_r60_n11 pos
(+)E1A_r60_n9 (+)E1A_r60_n9 pos
3xSLv1 3xSLv1 neg
DCP_1_0 DCP_1_0 pos
DCP_1_1 DCP_1_1 pos
DCP_1_11 DCP_1_11 pos
DCP_1_2 DCP_1_2 pos
DCP_1_4 DCP_1_4 pos
DCP_1_7 DCP_1_7 pos
DCP_20_0 DCP_20_0 pos
DCP_20_1 DCP_20_1 pos
DCP_20_3 DCP_20_3 pos

Total number of rows: 61533

Table truncated, full table size 11139 Kbytes.




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

Supplementary file Size Download File type/resource
GPL17005_Agilent-032722_Halobacterium_sp_NRC-1_Tiling_V2.txt.gz 2.7 Mb (ftp)(http) TXT

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