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Sample GSM2861521

Query DataSets for GSM2861521

Status

Public on May 03, 2018

Title

R88A_1

Sample type

SRA

Source name

RbpA R88A_cell extract

Organism

Mycolicibacterium smegmatis

Characteristics

strain: csm314
genotype/variation: RbpA R88A
growth phase: log phase growth

Growth protocol

Each strain was grown to OD600 = 0.4 - 0.6 by inoculating LB media supplemented with 0.5% dextrose, 0.5% glycerol, 0.05% Tween-80 and 40μg/ml kanamycin from a glycerol stock.

Extracted molecule

total RNA

Extraction protocol

Thirty milliliters of culture from each strain was pelleted by centrifugation, resuspended in Trizol and lysed by bead beating. RNA was choloform extracted, isoproponal precipitated and resuspended in water. RNA integrity and concentration were measured with an Agilent Bioanalyzer.
RNA libraries were prepared using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Description

run_2000_s_4_withindex_sequence.txt_TTGCCCC

Data processing

cDNA libraries were pooled and sequenced in a single Illumina HiSeq2000 Rapid Run flow cell lane.
Sequencing reads were de-multiplexed and converted to FASTQ format by Illumina bcl2fastq script.
STAR aligner was used to trim the adapter sequences from the raw reads and align to M. smegmatis mc2155 reference genome.
SAM files generated from the alignment were converted to BAM files using SAMTools and aligned reads were counted per genome feature using R BioConductor package Subread featureCounts function.
R BioConductor DESeq2 was used to analyze differential expression between the strains.
Genome_build: NC_008596
Supplementary_files_format_and_content: DESeq2 differential expression analysis comparing R79A, R88A and 72-111 against WT is shown in separate tabs labeled a. R79A, b. R88A, and c. 72-111. For each tab, column 1 includes the name of each genomic feature, column 2 is the base mean value of the six samples including 3 replicates of the mutant and 3 replicates of the WT, column 3 is the log2 fold change of mutant relative to WT, column 4 is the log fold change standard error (lfcse), column 5 is the Wald statistic, column 6 is the p-value and column 7 is the adjusted p-value.

Submission date

Nov 19, 2017

Last update date

May 15, 2019

Contact name

Christina L Stallings

E-mail(s)

[email protected]

Organization name

Washington University in St Louis

Street address

660 S. Euclid Avenue