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| Status |
Public on Jan 12, 2021 |
| Title |
rep2 ribo-seq araP |
| Sample type |
SRA |
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| Source name |
Long Term Evolution Experiment
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| Organism |
Escherichia coli |
| Characteristics |
strain: REL607
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| Treatment protocol |
No treatments were applied to the samples.
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| Growth protocol |
Bacteria were grown in the DM25 medium supplemented with 4g/L of glucose.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected via vacuum filtration, flash frozen in liquid nitrogen, ground to a fine powder with frozen lysis buffer, then allowed to thaw to complete lysis. Lysis buffer contained 20 mM Tris pH 8, 10 mM MgCl2, 100 mM NH4Cl, 5 mM CaCl2, 1 mM chloramphenicol, 0.1% v/v sodium deoxycholate, 0.4% v/v Triton X-100, 100 U/mL DNase I, 1 uL/mL SUPERase-In (Thermo Fisher Scientific AM2694)
Each sample produced a matched set of RNA-seq and ribo-seq fragments which were size selected to a range of 18-50nt. These were ligated with a 5' linker (containing a 4nt UMI) and a 3' linker (containing a 5nt UMI and a 5nt sample barcode). rRNA depletion was completed with the Illumina Ribo-Zero rRNA Depletion Kit for bacteria.
RNA-seq and ribo-seq in E. coli cell lines from the Long Term Evolution Experiment
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Library strategy: Ribo-seq
adapter removal performed with cutadapt v2.8
demultiplexing using the fastX toolkit script fastx_barcode_splitter.pl
deduplication with the BBtools script dedupe.sh
removal of UMIs and barcodes with cutadapt v2.8
in silico rRNA depletion with hisat2 v2.1.0
transcript quantification with kallisto v0.46.2
alignment with hisat2 v2.1.0
Genome_build: Each cell lines individual genome was determined in Tenaillon et al 2016
Supplementary_files_format_and_content: A single csv file contains the counts and TPMs for each of the samples. These are not the original counts and TPMs. Counts were first rounded, and new TPMs were calculated from rounded counts. Analysis was based on rounded counts and the TPMs generated from them.
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| Submission date |
Jan 05, 2021 |
| Last update date |
Jan 12, 2021 |
| Contact name |
Premal Shah |
| Organization name |
Rutgers University
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| Department |
Genetics
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| Street address |
145 Bevier Rd
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| City |
Piscataway |
| State/province |
NJ |
| ZIP/Postal code |
08854 |
| Country |
USA |
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| Platform ID |
GPL21222 |
| Series (1) |
| GSE164308 |
Landscape of transcriptional and translational changes over 22 years of bacterial adaptation |
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| Relations |
| BioSample |
SAMN17218787 |
| SRA |
SRX9786610 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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