README Microbiome Metadata copy.txt

README.txt

This includes information about the selection_exp1_mapping.csv file for specialist (potato aphid) portion of the selection experiment. This mapping file is used to generate a phyloseq object that can be analyzed in R.

*** Note: The file "selection_exp1_mappingV2.csv" was made during data analysis/visualization and has slighted changed the Selection & Block variables for more straightforward analysis & visualization. G0 Bulk samples (6 total) have renamed Selection = Starter;  Block # is identified. Negative controls renames as well Selection = NoM +A, NoM -A and NoIns; New "Treatment" Variable created ***


*SampleID is the ID that was submitted to UMN Genomics Core for sequencing. This should correspond with the file names that you receive.

*Type refers to whether the sample was collected from the rhizosphere or the bulk soil that was used to inoculate the following generation.

*Control refers to whether samples were DNA negative controls (blanks/water) or soil DNA extractions from experimental samples. Use in pre-processing for identifying contamintants. y = blank/negative control, n = sample

*Generation refers to 1, 2, 4 and 6 generations of the selection experiment (we chose not to sequence all six generations). G0 is also included as bulk soil samples only-- these were samples taken from the initial mixture of field soils that were used to inoculate each block (soil was mixed separately for each of six blocks).

*Block refers to blocks 1, 3, 5, and 6 that were the most interesting in the overall experiment. 'A' simply refers to "aphids" (in this case, potato aphids). We did not sequence any 'B' samples (tobacco hornworm).

*Selection refers to high, low, random, and no microbiome selection lines. H, L, and R were selected using the number of aphids at the end of each generation. No microbiome control samples (in which soil was sterilized in the steamer) are included for generations 1, 4, and 6 (no microbiome controls were not collected for Generation 2) - "A" or "NoM +A" = NoM w/ insect added; "Ins" or "NoM -A" = NoM w/ no insect. In Generations 2, 4, and 6, there were two no insect control included within each selection line within each block; however, these were their own separate block in Generation 1 (these are specified as "NoIns" under the Selection column). Extraction Blanks are indicated with "NA".

*Treatment ***only in V2**Same as Selection except Rhizosphere samples Reps 11&12 (No insect controls) are designated as NoIns.H, NoIns.L, NoIns.R for Generations 2,4,6 (b/c No Insect controls were included in each Block)

*Rep refers to the replicate number. Replicates 1-3 of the rhizospheres were the three selected plants used to inoculate the next generation. Replicates 10-12 of the rhizospheres indicate no insect control plants that were included within each selection line and block.

*Microbiome_added refers to whether or not the microbiome was live or not when added to the soil. "Yes" indicates that live soil was added to inoculate that generation. "No" indicates that the soil was sterilized.

*Insect_added refers to whether or not aphids were added to the plants. "Added" indicates that aphids were added to the plants. "CONTROL" indicates that aphids were not added to the plants.

*Extracted_Soil_Weight specifies the exact weight of the soil that was added to the plate prior to DNA extraction. Whenever possible, weights between 0.17-0.26g were used. Samples that had less than 0.17g were still included for sequencing but may be lower quality.
	README.txt

	This includes information about the selection_exp1_mapping.csv file for specialist (potato aphid) portion of the selection experiment. This mapping file is used to generate a phyloseq object that can be analyzed in R.

	* Note: The file "selection_exp1_mappingV2.csv" was made during data analysis/visualization and has slighted changed the Selection & Block variables for more straightforward analysis & visualization. G0 Bulk samples (6 total) have renamed Selection = Starter; Block # is identified. Negative controls renames as well Selection = NoM +A, NoM -A and NoIns; New "Treatment" Variable created *


	*SampleID is the ID that was submitted to UMN Genomics Core for sequencing. This should correspond with the file names that you receive.

	*Type refers to whether the sample was collected from the rhizosphere or the bulk soil that was used to inoculate the following generation.

	*Control refers to whether samples were DNA negative controls (blanks/water) or soil DNA extractions from experimental samples. Use in pre-processing for identifying contamintants. y = blank/negative control, n = sample

	*Generation refers to 1, 2, 4 and 6 generations of the selection experiment (we chose not to sequence all six generations). G0 is also included as bulk soil samples only-- these were samples taken from the initial mixture of field soils that were used to inoculate each block (soil was mixed separately for each of six blocks).

	*Block refers to blocks 1, 3, 5, and 6 that were the most interesting in the overall experiment. 'A' simply refers to "aphids" (in this case, potato aphids). We did not sequence any 'B' samples (tobacco hornworm).

	*Selection refers to high, low, random, and no microbiome selection lines. H, L, and R were selected using the number of aphids at the end of each generation. No microbiome control samples (in which soil was sterilized in the steamer) are included for generations 1, 4, and 6 (no microbiome controls were not collected for Generation 2) - "A" or "NoM +A" = NoM w/ insect added; "Ins" or "NoM -A" = NoM w/ no insect. In Generations 2, 4, and 6, there were two no insect control included within each selection line within each block; however, these were their own separate block in Generation 1 (these are specified as "NoIns" under the Selection column). Extraction Blanks are indicated with "NA".

	Treatment only in V2Same as Selection except Rhizosphere samples Reps 11&12 (No insect controls) are designated as NoIns.H, NoIns.L, NoIns.R for Generations 2,4,6 (b/c No Insect controls were included in each Block)

	*Rep refers to the replicate number. Replicates 1-3 of the rhizospheres were the three selected plants used to inoculate the next generation. Replicates 10-12 of the rhizospheres indicate no insect control plants that were included within each selection line and block.

	*Microbiome_added refers to whether or not the microbiome was live or not when added to the soil. "Yes" indicates that live soil was added to inoculate that generation. "No" indicates that the soil was sterilized.

	*Insect_added refers to whether or not aphids were added to the plants. "Added" indicates that aphids were added to the plants. "CONTROL" indicates that aphids were not added to the plants.

	*Extracted_Soil_Weight specifies the exact weight of the soil that was added to the plate prior to DNA extraction. Whenever possible, weights between 0.17-0.26g were used. Samples that had less than 0.17g were still included for sequencing but may be lower quality.