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Sample GSM8473785

Query DataSets for GSM8473785

Status

Public on Aug 25, 2024

Title

ID12167967, Ecoli, GuaBi, 1h

Sample type

SRA

Source name

bacterial cell

Organism

Escherichia coli

Characteristics

cell type: bacterial cell
treatment: GuaBi
timepoint: 1h

Extracted molecule

total RNA

Extraction protocol

RNA was extracted using RNeasy spin columns (Qiagen) according to the manufacturer’s protocol.
RNA-seq library generation was continued using the Truseq RNA Library Prep Kit v2 (Illumina) starting at the “Elute, Prime, Fragment” step and was completed according to the manufacturer’s protocol.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 4000

Description

ID12167967
Ecoli_counts.txt
Ecoli_metadata_samples.txt
Ecoli_metadata_genes.txt

Data processing

Ribosomal RNA contamination was removed from the fastq sequence files and reads were filtered for quality, keeping only reads where at least 70% of the cycles had Q scores Ñ23.
Single-end 50 bp reads were aligned to the E. coli K12 MG1655 and A. baumannii ATCC19606 genome using GSNAP version 2013-11-01 with the following parameters: -M 2 -n 10 -B 2 -i 1 --pairmax-dna=1000 --terminal-threshold=1000 --gmap-mode=none --clip-overlap.
Uniquely mapped reads were used to obtain read counts and RPKMs per gene.
Assembly: ASM73714v1 (Abaumannii) and ASM584v2 (Ecoli K-12)
Supplementary files format and content: Tab-delimited text files include raw counts for each Sample, column metadata (samples), and row metadata (genes)

Submission date

Aug 20, 2024

Last update date

Aug 25, 2024

Contact name

Yutian Peng

Organization name

Genentech Inc.

Street address

340 Point San Bruno

City

South San Francisco