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Distribute PCR reactions file
The distribute PCR reactions j5 output file is a CSV file that contains information resulting from designing thermocycler block annealing temperature gradients for the set of PCR reactions contained within a j5 assembly file, and optimally arranging the PCR reactions on the block with respect to the designed gradient. The first line in the file is a header line that just serves to identify the downstream automation task selected (e.g. "Distribute PCR Reactions"), as well as the version of j5 used to generate the assembly (e.g. "v0.1alpha") and the date that the assembly was designed (e.g. "3/23/2011").

Here is an example first line header:


If any problems are encountered when inputting the downstream automation parameters file, or if more than six source plates are utilized (no PR-PR configuration files output), j5 will place the resulting warning messages immediately following the first line header.

(Split) PCR Reactions subsection:
displays how the (Split) PCR reactions will be arranged on the resulting multi-well plates.

Index column fields:
A sequential order of the PCR reactions, starting with "1", arranged from lowest to highest optimal annealing temperature.

TEMPLATE_PLATE column fields:
The name of the multi-well plate serving as the source of the PCR template for this row's PCR reaction.

TEMPLATE_WELL column fields:
The name of the well (e.g. "A01") containing the PCR template for this row's PCR reaction.

TEMPLATE_VOLUME column fields:
The volume (in uL) of the PCR template to be used for this row's PCR reaction.

PRIMER1_PLATE column fields:
The name of the multi-well plate serving as the source of the forward primer for this row's PCR reaction.

PRIMER1_WELL column fields:
The name of the well (e.g. "A01") containing the forward primer for this row's PCR reaction.

PRIMER1_VOLUME column fields:
The volume (in uL) of the forward primer to be used for this row's PCR reaction.

PRIMER2_PLATE column fields:
The name of the multi-well plate serving as the source of the reverse primer for this row's PCR reaction. Note that this column will not be present in Distribute Split and Pool PCR Reaction designs.

PRIMER2_WELL column fields:
The name of the well (e.g. "A01") containing the reverse primer for this row's PCR reaction. Note that this column will not be present in Distribute Split and Pool PCR Reaction designs.

PRIMER2_VOLUME column fields:
The volume (in uL) of the reverse primer to be used for this row's PCR reaction. Note that this column will not be present in Distribute Split and Pool PCR Reaction designs.

PCR_MIX_PLATE column fields:
The name of the multi-well plate serving as the source of the PCR master mix for this row's PCR reaction.

PCR_MIX_WELL column fields:
The name of the well (e.g. "A01") containing the PCR master mix for this row's PCR reaction.

PCR_MIX_VOLUME column fields:
The volume (in uL) of the PCR master mix to be used for this row's PCR reaction.

OUTPUT_PLATE column fields:
The name of the multi-well PCR plate serving as the destination for this row's (split) PCR reaction.

OUTPUT_WELL column fields:
The name of the well (e.g. "A01") serving as the destination for this row's (split) PCR reaction.

REACTION_NUMBER column fields:
The number corresponding to the PCR Reaction ID Number in the input j5 assembly file for this (split) PCR row's reaction.

OPTIMAL_ANNEALING_TEMP column fields:
The optimal annealing temperature (in degrees C) for this row's PCR reaction. This is calculated as 2 degrees C above the minimum 3'-only Tm of the forward and reverse primers for this row's (split) PCR reaction, as specified in the input j5 assembly file.

THERMOCYCLER_BLOCK column fields:
The thermocycler block assigned to this row's (split) PCR reaction. Note that the zone numbering starts with "0".

THERMOCYCLER_ZONE column fields:
The thermocycler zone assigned to this row's (split) PCR reaction. Note that the zone numbering starts with "0".

THERMOCYCLER_ZONE_ANNEALING_TEMP column fields:
The designed annealing temperature (in degrees C) for the thermocycler zone selected for this row's (split) PCR reaction.

EXPECTED_SIZE column fields:
The anticipated size (in bp) for the product of this row's (split) PCR reaction.

Here is an example regular PCR Reactions subsection (stylized for clarity; click to see an enlarged version):


Here is an example split PCR Reactions subsection (stylized for clarity; click to see an enlarged version):


Thermocycler Blocks subsection:
displays the designed annealing temperature zone gradients for each of the thermocycler blocks.

BLOCK_ID column fields:
The thermocycler block assigned to this row's PCR reaction. Note that the zone numbering starts with "0".

BLOCK_ZONE column fields:
The thermocycler zone assigned to this row's PCR reaction. Note that the zone numbering starts with "0".

BLOCK_ZONE_ANNEALING_TEMP column fields:
The designed annealing temperature (in degrees C) for the thermocycler zone selected for this row's PCR reaction.

Here is an example Thermocycler Blocks subsection (stylized for clarity; click to see an enlarged version):

Here is the actual Regular Distribute PCR reactions (myassemblyfilelist_condensed_distribute_pcr.csv);

Pool PCR Reactions subsection:
displays how the (Split) PCR reactions will be arranged on the resulting multi-well plates.

Index column fields:
A sequential order of the PCR reactions, starting with "1", arranged from lowest to highest optimal annealing temperature.

FORWARD_SPLIT_PLATE column fields:
The name of the multi-well plate serving as the source of the forward split PCR reaction for this row's pooled PCR reaction.

FORWARD_SPLIT_WELL column fields:
The name of the well (e.g. "A01") containing the forward split PCR reaction for this row's pooled PCR reaction.

FORWARD_SPLIT_VOLUME column fields:
The volume (in uL) of the forward split PCR reaction to be used for this row's pooled PCR reaction.

REVERSE_SPLIT_PLATE column fields:
The name of the multi-well plate serving as the source of the reverse split PCR reaction for this row's pooled PCR reaction.

REVERSE_SPLIT_WELL column fields:
The name of the well (e.g. "A01") containing the reverse split PCR reaction for this row's pooled PCR reaction.

REVERSE_SPLIT_VOLUME column fields:
The volume (in uL) of the reverse split PCR reaction to be used for this row's pooled PCR reaction.

OUTPUT_PLATE column fields:
The name of the multi-well PCR plate serving as the destination for this row's PCR reaction.

OUTPUT_WELL column fields:
The name of the well (e.g. "A01") serving as the destination for this row's PCR reaction.

REACTION_NUMBER column fields:
The number corresponding to the PCR Reaction ID Number in the input j5 assembly file for this PCR row's reaction.

OPTIMAL_ANNEALING_TEMP column fields:
The optimal annealing temperature (in degrees C) for this row's PCR reaction. This is calculated as 2 degrees C above the minimum full-length Tm of the forward and reverse primers for this row's PCR reaction, as specified in the input j5 assembly file.

THERMOCYCLER_BLOCK column fields:
The thermocycler block assigned to this row's pooled PCR reaction. Note that the zone numbering starts with "0".

THERMOCYCLER_ZONE column fields:
The thermocycler zone assigned to this row's pooled PCR reaction. Note that the zone numbering starts with "0".

THERMOCYCLER_ZONE_ANNEALING_TEMP column fields:
The designed annealing temperature (in degrees C) for the thermocycler zone selected for this row's pooled PCR reaction.

EXPECTED_SIZE column fields:
The anticipated size (in bp) for the product of this row's pooled PCR reaction.

Here is an example Pooled PCR Reactions subsection (stylized for clarity; click to see an enlarged version):

Here is the actual Distribute Split and Pool PCR Reactions (myassemblyfilelist_condensed_distribute_pcr_pool.csv):