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Platform GPL18980 Query DataSets for GPL18980
Status Public on Dec 31, 2014
Title Agilent-031243 Clostridium perfringens pangenome
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Clostridium perfringens
Manufacturer Agilent Technologies
Manufacture protocol see manufacturer's web site at http://www.agilent.com/
 
Description TIFN C1056 project. Contains probes for ATCC13124, SM101, strain 13; incomplete: ATCC3626, F4969, JGS1495, JGS1721, JGS1987, NCTC8239; plasmids: pBCNF5603, pCP13, pCP8533etx, pCPF4969, pCPF5603, pCW3, pSM101A, pSM101B

Arrays of this design have barcodes that begin with 16031243 or 2531243.

Orientation:
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.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

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.

The scan files were dissected into the 4 slide regions which generates a data file for each hybridization
 
Submission date Jul 21, 2014
Last update date Dec 31, 2014
Contact name Yinghua Xiao
E-mail(s) yinghua.xiao@wur.nl
Organization name Wageningen University
Street address Bornse Weilanden 9
City Wageningen
ZIP/Postal code 6700AA
Country Netherlands
 
Samples (13) GSM1440542, GSM1440543, GSM1440544, GSM1440545, GSM1440546, GSM1440547 
Series (1)
GSE59616 Genome-wide transcriptional profiling of Clostridium perfringens SM101 during sporulation

Data table header descriptions
ID Agilent feature number
COL Column
ROW Row
NAME NAME
SPOT_ID Spot identifier
CONTROL_TYPE Control type
CHROMOSOMAL_LOCATION Chromosomal Location
SEQUENCE Sequence

Data table
ID COL ROW NAME SPOT_ID CONTROL_TYPE CHROMOSOMAL_LOCATION SEQUENCE
1 266 170 GE_BrightCorner GE_BrightCorner pos
2 266 168 DarkCorner DarkCorner pos
3 266 166 DarkCorner DarkCorner pos
4 266 164 DarkCorner DarkCorner pos
5 266 162 DarkCorner DarkCorner pos
6 266 160 DarkCorner DarkCorner pos
7 266 158 DarkCorner DarkCorner pos
8 266 156 DarkCorner DarkCorner pos
9 266 154 DarkCorner DarkCorner pos
10 266 152 DarkCorner DarkCorner pos
11 266 150 DarkCorner DarkCorner pos
12 266 148 Strain13__-_CPE1169_201-260 Strain13__-_CPE1169_201-260 FALSE unmapped CTTCATTGCAGATAGAAAACAACTTAAAGTTGGAACTTTTGTACTTGTTTTAGTAGTAGG
13 266 146 cluster_1009_1_20-79 cluster_1009_1_20-79 FALSE unmapped AGTGATGAATTAAAGATTTATTTAGAAAAAACAGAGAATATAGGTGCTATTCAAATGTTT
14 266 144 cluster_1991_7_26-82 cluster_1991_7_26-82 FALSE unmapped TAGATAGTAAAATAGGTGATGAAACAACTGTAGGACCATTTGCTTATGTTAGACCAG
15 266 142 SM101__CPR_0932_6-64 SM101__CPR_0932_6-64 FALSE unmapped TGATTGCACTGATGAAAAATTAAAACTAGAGTATGCACGTGTATATATATTACCTCAAA
16 266 140 pSM101B__CPR_B0010_27-84 pSM101B__CPR_B0010_27-84 FALSE unmapped GATAAACTATATAGATAATGTTCATAGTAACAGTAAAGGGTGGATAACCAGGAGCGTT
17 266 138 cluster_101_4_1-59 cluster_101_4_1-59 FALSE unmapped TCTATAGCTTATGGAGAAAAATTAGGTCTTGTTTATGGACCTCATTCTAGAGGTATTTC
18 266 136 cluster_672_2_4-63 cluster_672_2_4-63 FALSE unmapped CTTACCTCTGCAAAGATACTATTAATCATCGCGCCTCTATCTCAGTTATTCACTTTATAT
19 266 134 cluster_1179_6_7-61 cluster_1179_6_7-61 FALSE unmapped GGAACAATGTCAGGAAATCCAATAGTAATGAGTGCAGGACTTGCAACAGTTAAAA
20 266 132 Strain13__-_CPE0260_175-233 Strain13__-_CPE0260_175-233 FALSE unmapped ATTGTTAGAGCTTTAGAAAATCCATTAAAGCTTATCGTATCCTTTGTTGGAATATATTC

Total number of rows: 45220

Table truncated, full table size 5861 Kbytes.




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

Supplementary file Size Download File type/resource
GPL18980_probe_to_locus_Agilent-031243.txt.gz 281.5 Kb (ftp)(http) TXT

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