count_table: Table of the count table
In EmanuelSoda/ScreenR: Package to Perform High Throughput Biological Screening

count_table

R Documentation

Table of the count table

Description

Table of the count table

Usage

data(count_table)

Format

A data frame with 5323 rows and 15 variables obtained from barcode alignment to the reference library. It is generated from a [Cellecta](https://cellecta.com/) protocol. The samples generated are then sequenced using an RNA-seq protocol. Due to the fact that different shRNAs are sequenced for a gene each barcode has its associated reads. This reads were aligned to the reference library using [bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) and then sorted with [samtools](https://github.com/samtools/samtools). Since this dataset comes from a Chemical Synthetic Lethality experiments the samples treated and combined with the shRNAs knockdown should present a decreased number of reads compared to the controls.

Barcode: It contains an ID that identify each barcode. It can be use to marge the annotation table with the count table. A Barcode is a unique identifier of an shRNA. In a genetic screening multiple slightly different shRNAs perform a knockout of a gene each with its efficacy. For this reason it is important to keep track of each shRNA using a unique barcode.
Time_1: It contains the counts at time zero. This is the first time point at which cells are not treated and not infected.
Time_2: It contains the counts after the cell were washed. At this time point the cells are infected and following the Cellecta protocol are washed with the puromycin.
Time_3_TRT_rep1: It contains the counts for the first replicate of the treated at the first time point. Usually the first time point is 7 day after the puromycin wash.
Time_3_TRT_rep2: It contains the counts for the second replicate of the treated at the first time point. Usually the first time point is 7 day after the puromycin wash.
Time_3_TRT_rep3: It contains the counts for the third replicate of the treated at the first time point. Usually the first time point is 7 day after the puromycin wash.
Time_3_rep1: It contains the counts for the first replicate of the control at the first time point. Usually the first time point is 7 day after the puromycin wash.
Time_3_rep2: It contains the counts for the second replicate of the control at the first time point. Usually the first time point is 7 day after the puromycin wash.
Time_3_rep3: It contains the counts for the third replicate of the control at the first time point. Usually the first time point is 7 day after the puromycin wash.
Time_4_TRT_rep1: It contains the counts for the first replicate of the treated at the second time point. Usually the first time point is 14 day after the puromycin wash.
Time_4_TRT_rep2: It contains the counts for the second replicate of the treated at the second time point. Usually the first time point is 14 day after the puromycin wash.
Time_4_TRT_rep3: It contains the counts for the third replicate of the treated at the second time point. Usually the first time point is 14 day after the puromycin wash.
Time_4_rep1: It contains the counts for the first replicate of the control at the second time point. Usually the first time point is 14 day after the puromycin wash.
Time_4_rep2: It contains the counts for the second replicate of the control at the second time point. Usually the first time point is 14 day after the puromycin wash.
Time_4_rep3: It contains the counts for the third replicate of the control at the second time point. Usually the first time point is 14 day after the puromycin wash.