SRX112037 G.hirsutum_Capture_Pilot_1 SRP009879 Cotton_Sequence_Capture_Pilot A total of four regions on a single 454 PTP plate were used to generate sequence capture data for this pilot experiment. Region 1 was composed entirely of TX2094. TX2094 fragments were captured using a custom Nimblegen Sequence Array containing DNA probes targeting 534 genes. The library was independently made using the traditional WGS kit from Roche. After capture, the library fragments were amplified (LM-PCR). We titered the number of LM-PCR cycles needed by 1st amplifying a test sample (30 ul) and sampling the amount of amplified product every 5 cycles on a Lonza Electorphoresis system to avoid over-amplification. SRS282764 Region_1 WGS_Maxxa_library WGS GENOMIC other 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX Titanium SRX112038 G.hirsutum_Capture_Pilot_2 SRP009879 Cotton_Sequence_Capture_Pilot A total of four regions on a single 454 PTP plate were used to generate sequence capture data for this pilot experiment. Region 2 was composed entirely of a mixture of Maxxa (MID1) and TX2094 (MID2) in a 75:25 mix. Two WGS libraries were constructed by Roche methods from Maxxa and TX2094 DNA. The libraries were independently prepared, subjected to sequence capture and subsequent ligation-mediated PCR to generate sufficient quantities of the captured fragments for sequencing. The samples were captured using custom Nimblegen Sequence Capture Microarrays. The samples were mixed together after LM-PCR for sequencing. SRS282765 Region_2 Capture_libraries_of_Maxxa_TX2094 WGS GENOMIC other 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX Titanium SRX112039 G.hirsutum_Capture_Pilot_3 SRP009879 Cotton_Sequence_Capture_Pilot A total of four regions on a single 454 PTP plate were used to generate sequence capture data for this pilot experiment. Region 3 was composed entirely of Maxxa Acala. The fragments of the library was independently captured using a custom Nimblegen Sequence Array containing DNA probes targeting 534 genes. The library was independently made using the traditional WGS kit from Roche. After capture, the library fragments were amplified (LM-PCR). We titered the number of LM-PCR cycles needed by 1st amplifying a test sample (30 ul) and sampling the amount of amplified product every 5 cycles on a Lonza Electorphoresis system to avoid over-amplification. SRS282766 Region_3 Capture_libraries_Maxxa_TX2094 WGS GENOMIC other 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX Titanium SRX112040 Region_4 SRP009879 Cotton_Sequence_Capture_Pilot A total of four regions on a single 454 PTP plate were used to generate sequence capture data for this pilot experiment. Region 4 was composed of a mixture of Maxxa (MID1) and TX2094 (MID2) in 50:50 molar amounts prior to a common emPCR pool to prepare a single 'library' for sequencing. The fragments of both libraries were independently captured using a custom Nimblegen Sequence Array containing DNA probes targeting 534 genes. Each library was independently made using the traditional WGS kit from Roche. After capture, the library fragments were amplified (LM-PCR). We titered the number of LM-PCR cycles needed for each library by 1st amplifying a test sample (30 ul) and sampling the amount of amplified product every 5 cycles on a Lonza Electorphoresis system to avoid over-amplification. SRS282767 Region_4 Capture_libraries_Maxxa_TX2094 WGS GENOMIC other 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX Titanium SRX112052 G.hisrustum_Capture_4 SRP009879 Cotton_Sequence_Capture_Pilot A total of four regions on a 0.5 454 PTP plate were used to generate sequence capture data for this pilot experiment. This means, 1/8 of a plate was used to sequence the captured products. Capture 2 was composed of a mixture of Maxxa (MID1) and TX2094 (MID2) in 50:50 molar amounts prior to a common emPCR pool to prepare a single 'library' for sequencing. The fragments of both libraries were independently captured using a custom Mycroarray Capture Beads containing DNA probes targeting 534 genes. The samples were independently captured on Mycroarray beads containing probes targeting 534 genes of the cotton exome. The capture followed the recommended protocols from Mycroarray. The samples were amplified after capture using the adapter sequences (LM-PCR). The number of PCR cycles for LM-PCR was empirically determined using a test PCR sample (30 ul) and evaluation of amplificed products of every 5-cycle increment on a Lonza gel. SRS282771 Mycroarray_Capture_4 WGS libraries of Maxxa and TX2094 WGS GENOMIC other 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX Titanium SRX112053 G.hirsustum_Capture_3 SRP009879 Cotton_Sequence_Capture_Pilot A total of four regions on a 0.5 454 PTP plate were used to generate sequence capture data for this pilot experiment. This means, 1/8 of a plate was used to sequence the captured products. Capture 3 was composed entirely of Maxxa. The fragments of the libraries were independently captured using a custom Mycroarray Capture Beads containing DNA probes targeting 534 genes. The sample was independently captured on Mycroarray beads containing probes targeting 534 genes of the cotton exome. The capture followed the recommended protocols from Mycroarray. The samples were amplified after capture using the adapter sequences (LM-PCR). The number of PCR cycles for LM-PCR was empirically determined using a test PCR sample (30 ul) and evaluation of amplificed products of every 5-cycle increment on a Lonza gel. SRS282770 Mycroarray_Capture_3 WGS Maxxa Library WGS GENOMIC other 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX Titanium SRX112054 G.hirsustum_Capture_2 SRP009879 Cotton_Sequence_Capture_Pilot A total of four regions on a 0.5 454 PTP plate were used to generate sequence capture data for this pilot experiment. This means, 1/8 of a plate was used to sequence the captured products. Capture 2 was composed of a mixture of Maxxa (MID1) and TX2094 (MID2) in 75:25 molar amounts prior to a common emPCR pool to prepare a single 'library' for sequencing. The fragments of both libraries were independently captured using a custom Mycroarray Capture Beads containing DNA probes targeting 534 genes. The samples were independently captured on Mycroarray beads containing probes targeting 534 genes of the cotton exome. The capture followed the recommended protocols from Mycroarray. The samples were amplified after capture using the adapter sequences (LM-PCR). The number of PCR cycles for LM-PCR was empirically determined using a test PCR sample (30 ul) and evaluation of amplificed products of every 5-cycle increment on a Lonza gel. SRS282769 Mycroarray_Capture_2 WGS libraries of Maxxa and TX2094 WGS GENOMIC other 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX Titanium SRX112055 G.hirsustum_Capture_1 SRP009879 Cotton_Sequence_Capture_Pilot A total of four regions on a 0.5 454 PTP plate were used to generate sequence capture data for this pilot experiment. This means, 1/8 of a plate was used to sequence the captured products. Capture 1 was composed entirely of TX2094. The sample was captured on Mycroarray beads containing probes targeting 534 genes of the cotton exome. The capture followed the recommended protocols from Mycroarray. The samples were amplified after capture using the adapter sequences (LM-PCR). The number of PCR cycles for LM-PCR was empirically determined using a test PCR sample (30 ul) and evaluation of amplificed products of every 5-cycle increment on a Lonza gel. SRS282768 Mycroarray_Capture_1 WGS TX2094 library WGS GENOMIC other 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX Titanium