| 1 |
GPL11005 |
Custom NimbleGen A. thaliana ChIP-chip tiling array [HD2.3X] |
711,320 |
INRA - CNRS - UEVE |
2010-10-01 |
NimbleGen |
Arabidopsis thaliana
 |
Tiling Array |
in situ oligonucleotide, Custom NimbleGen A. thaliana ChIP-chip tiling array [HD2.3X], Tiling array HD2.3X. ChIP-chip design of Arabidopsis 7.0 whole genome, with 175 bp spacing. This design is a merge of GPL10911 and GPL10918 (AT7v2) with 3 chambers of 711320 spots on a single slide. |
| 2 |
GPL9893 |
ENS SGDB Trichoderma virens Tv10_Tiling93_1 |
415,372 |
École Normale Supérieure |
2010-01-11 |
Agilent Technologies |
Hypocrea virens
 |
Tiling Array |
in situ oligonucleotide, ENS SGDB Trichoderma virens Tv10_Tiling93_1, Trichoderma virens Tiling array. One probe has been design every 93 base every other strand. The probe design has been done according to T. virens v1.0 genome assembly from the DOE JGI available here: http://genome.jgi-psf.org/Trive1/Trive1.home.html The probe ID is a code to find genome localisation of each probe: Scaffold_Start_Strand. The first number merge to Tv suffix indicates the scaffold number The second number is the start position of the probe The third number is the strand FWD or REV |
| 3 |
GPL10752 |
ENS SGDB Trichoderma atroviride Ta10_Tiling93_1 |
387,105 |
École Normale Supérieure |
2010-08-02 |
Agilent Technologies |
Trichoderma atroviride
 |
Tiling Array |
in situ oligonucleotide, ENS SGDB Trichoderma atroviride Ta10_Tiling93_1, Trichoderma atroviride Tiling array. One probe has been design every 93 base every other strand. The probe design has been done according to T. atroviride v1.0 genome assembly from the DOE JGI available here: http://genome.jgi-psf.org/Triat1/Triat1.home.html The probe ID is a code to find genome localisation of each probe: Scaffold_Start_Strand. The first number merge to Ta suffix indicates the scaffold number The second number is the start position of the probe The third number is the strand FWD or REV |
| 4 |
GPL10911 |
Custom NimbleGen A. thaliana ChIP-chip tiling design AT7v2.1 |
360,718 |
INRA - CNRS - UEVE |
2010-09-14 |
NimbleGen |
Arabidopsis thaliana
|
Tiling Array |
in situ oligonucleotide, Custom NimbleGen A. thaliana ChIP-chip tiling design AT7v2.1, Tiling array AT7v2.1. ChIP-chip design of Arabidopsis 7.0 whole genome, with 165 bp spacing. This design is a refinement of AT7v1 by replacing the existing chrM and chrC probes with a straight tiling of those chromosomes. Probes split between the 2 designs, with every-other probe in each array. |
| 5 |
GPL10918 |
Custom NimbleGen A. thaliana ChIP-chip tiling design AT7v2.2 |
360,718 |
INRA - CNRS - UEVE |
2010-09-15 |
NimbleGen |
Arabidopsis thaliana
|
Tiling Array |
in situ oligonucleotide, Custom NimbleGen A. thaliana ChIP-chip tiling design AT7v2.2, Tiling array AT7v2.2. ChIP-chip design of Arabidopsis 7.0 whole genome, with 165 bp spacing. This design is a refinement of AT7v1 by replacing the existing chrM and chrC probes with a straight tiling of those chromosomes. Probes split between the 2 designs, with every-other probe in each array. |
| 6 |
GPL10919 |
Custom NimbleGen A. thaliana ChIP-chip tiling design AT7v1.1 |
360,718 |
INRA - CNRS - UEVE |
2010-09-15 |
NimbleGen |
Arabidopsis thaliana
|
Tiling Array |
in situ oligonucleotide, Custom NimbleGen A. thaliana ChIP-chip tiling design AT7v1.1, Tiling array NimbleGen AT7v1.1. ChIP-chip design of Arabidopsis 7.0 whole genome, with 165 bp spacing. Array with one chamber but 2 arrays used for one sample (AT7v1.1 and v1.2). |
| 7 |
GPL10920 |
Custom NimbleGen A. thaliana ChIP-chip tiling design AT7v1.2 |
360,718 |
INRA - CNRS - UEVE |
2010-09-15 |
NimbleGen |
Arabidopsis thaliana
|
Tiling Array |
in situ oligonucleotide, Custom NimbleGen A. thaliana ChIP-chip tiling design AT7v1.2, Tiling array NimbleGen AT7v1.2. ChIP-chip design of Arabidopsis 7.0 whole genome, with 165 bp spacing.Array with one chamber but 2 arrays used for one sample (AT7v1.1 and v1.2). |
| 8 |
GPL10759 |
ENS SGDB Trichoderma reesei Tr20_Tiling93_1 |
359,089 |
École Normale Supérieure |
2010-08-04 |
Agilent Technologies |
Hypocrea jecorina
 |
Tiling Array |
in situ oligonucleotide, ENS SGDB Trichoderma reesei Tr20_Tiling93_1, Trichoderma reesei Tiling array. One probe has been design every 93 base every other strand. The probe design has been done according to T. reesei v2.0 genome assembly from the DOE JGI available here: http://genome.jgi-psf.org/Trire2/Trire2.home.html The probe ID is a code to find genome localisation of each probe: Scaffold_Start_Strand. The first number merge to Tr suffix indicates the scaffold number The second number is the start position of the probe The third number is the strand FWD or REV |
| 9 |
GPL9076 |
ENS SGDB Trichoderma reesei Tr20_Tiling140_1 240k oligo array |
238,588 |
École Normale Supérieure |
2009-08-21 |
Agilent Technologies |
Hypocrea jecorina
|
Tiling Array |
in situ oligonucleotide, ENS SGDB Trichoderma reesei Tr20_Tiling140_1 240k oligo array, Trichoderma reesei Tiling array. One probe has been design every 140 base every other strand. The probe design has been done according to T. reesei v2.0 genome assembly from the DOE JGI available here: http://genome.jgi-psf.org/Trire2/Trire2.home.html The probe ID is a code to fing genome localisation of each probe: Scaffold_Start_Strand The first number indicate the scaffold number The second number is the start position of the probe The third number is the strand FWD or REV |
| 10 |
GPL10772 |
URGV Arabidopsis thaliana CHROMO4_2 array |
21,800 |
INRA - CNRS - UEVE |
2010-08-10 |
URGV |
Arabidopsis thaliana
|
Tiling Array |
spotted DNA/cDNA, URGV Arabidopsis thaliana CHROMO4_2 array, The entire TIGR4 Arabidopsis thaliana ec. Col chromosome 4 assembly was used to design a genomic tiling microarray. This ~18.6 Mb sequence represented on the microarray starts downstream of the nucleolar organizing region (NOR) comprising the 5’ terminus of the chromosome. Notably, it contains several megabases of pericentromeric heterochromatin. In the microarray design, annotation was intentionally ignored, thus ensuring that repeated and unique sequences were equally represented. PCR primer pairs were selected using the Primer3 software. Probe selection was first accomplished by BLASTN analysis of sequential 100-bp windows of sequence along chromosome 4 against the whole genome to discriminate between unique and repeated DNA. Whenever a window gave at least one hit with 85% identity elsewhere in the genome, that window was marked as repeated, or unique otherwise. This information was then used to define repeated and unique segments of at least 300bp along the chromosome, as follows. Repeat segments were composed of successive repeat windows, possibly interrupted by series of contiguous unique windows spanning less than 300bp in each case. Conversely, unique segments were composed of successive unique windows, never interrupted by more than 300bp of contiguous repeat windows. Series of alternate unique and repeated windows were treated as repeat segments. Within each repeated or unique segment, PCR primer pairs were then selected using the Primer3 software and a routine that ensured maximum coverage of the segment and limited overlap between successive probes. Briefly, primer pairs were designed from both ends of the segment, considering sequential 1.2 kb windows, amplicon sizes ranging from 850 bp to 1.2 kb (optimum 1 kb) and primers (19-23 nt each, optimum 21 nt, 40-60% GC) with similar melting temperatures in the 57°CÂÂ63°C range (optimum 60°C). Each new 1.2 kb window was positioned 50 bp within the end of the preceding amplicon. Successive amplicons could therefore overlap by up to 50 bp or be separated by up to 250 bp. When no primer pair was found in a given window, window size was increased to 1.4 kb, and if still unsuccessful, amplicons were finally designed using the forward and reverse primers of the upstream and downstream amplicons, respectively. When the last (central) window of a segment was less than 1.2kb but more than 300bp, primer pair selection was carried out by considering the actual size of that window plus 50bp on either side. Using this approach, 21,405 amplicons were designed with an average size of ~950bp. An additional 356 amplicons were designed that cover 36 genes of interest and neighboring sequences located on the other 4 chromosomes. Most amplicons were produced using BAC clones as templates, and all amplicons were verified by gel electropheresis. |
| 11 |
GPL10892 |
Chromochip Arabidopsis thaliana 21.7K CHROMO4_1 |
21,768 |
INRA - CNRS - UEVE |
2010-09-08 |
Chromochip |
Arabidopsis thaliana
|
Tiling Array |
spotted DNA/cDNA, Chromochip Arabidopsis thaliana 21.7K CHROMO4_1, The entire TIGR4 Arabidopsis thaliana ec. Col chromosome 4 assembly was used to design a genomic tiling microarray. This ~18.6 Mb sequence represented on the microarray starts downstream of the nucleolar organizing region (NOR) comprising the 5’ terminus of the chromosome. Notably, it contains several megabases of pericentromeric heterochromatin. In the microarray design, annotation was intentionally ignored, thus ensuring that repeated and unique sequences were equally represented. PCR primer pairs were selected using the Primer3 software. Probe selection was first accomplished by BLASTN analysis of sequential 100-bp windows of sequence along chromosome 4 against the whole genome to discriminate between unique and repeated DNA. Whenever a window gave at least one hit with 85% identity elsewhere in the genome, that window was marked as repeated, or unique otherwise. This information was then used to define repeated and unique segments of at least 300bp along the chromosome, as follows. Repeat segments were composed of successive repeat windows, possibly interrupted by series of contiguous unique windows spanning less than 300bp in each case. Conversely, unique segments were composed of successive unique windows, never interrupted by more than 300bp of contiguous repeat windows. Series of alternate unique and repeated windows were treated as repeat segments. Within each repeated or unique segment, PCR primer pairs were then selected using the Primer3 software and a routine that ensured maximum coverage of the segment and limited overlap between successive probes. Briefly, primer pairs were designed from both ends of the segment, considering sequential 1.2 kb windows, amplicon sizes ranging from 850 bp to 1.2 kb (optimum 1 kb) and primers (19-23 nt each, optimum 21 nt, 40-60% GC) with similar melting temperatures in the 57°CÂÂ63°C range (optimum 60°C). Each new 1.2 kb window was positioned 50 bp within the end of the preceding amplicon. Successive amplicons could therefore overlap by up to 50 bp or be separated by up to 250 bp. When no primer pair was found in a given window, window size was increased to 1.4 kb, and if still unsuccessful, amplicons were finally designed using the forward and reverse primers of the upstream and downstream amplicons, respectively. When the last (central) window of a segment was less than 1.2kb but more than 300bp, primer pair selection was carried out by considering the actual size of that window plus 50bp on either side. Using this approach, 21,405 amplicons were designed with an average size of ~950bp. An additional 356 amplicons were designed that cover 36 genes of interest and neighboring sequences located on the other 4 chromosomes. Most amplicons were produced using BAC clones as templates, and all amplicons were verified by gel electropheresis. |
|