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| Status |
Public on Nov 23, 2021 |
| Title |
Freeze_disome |
| Sample type |
SRA |
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| Source name |
E. coli culture
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| Organism |
Escherichia coli |
| Characteristics |
treatment: tigecycline, capreomycin
strain: MG1655
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| Extracted molecule |
total RNA |
| Extraction protocol |
MNase footprinting, ribosome pelleting, RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Ribosome Profiling
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| Data processing |
Library strategy: Ribosome profiling
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
rRNA and other non-coding RNA alignment with bowtie2 v2.1.0
Alignment with bowtie2 v2.1.0
Read quantitation using custom scripts
Genome_build: NC_000913.2
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name;2. CDS region (nt) used for read counting;3. read counts
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| Submission date |
Jul 20, 2021 |
| Last update date |
Nov 23, 2021 |
| Contact name |
tomoya fujita |
| E-mail(s) |
[email protected]
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| Organization name |
RIKEN
|
| Department |
Cluster for Pioneering Research
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| Lab |
RNA Systems Biochemistry Laboratory
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| Street address |
2-1, Hirosawa
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| City |
Wako |
| State/province |
Saitama |
| ZIP/Postal code |
3510198 |
| Country |
Japan |
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| Platform ID |
GPL25368 |
| Series (1) |
| GSE180482 |
Bacterial ribosome pause sites surveyed by an integration of ribosome profiling and nascent chain profiling II |
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| Relations |
| BioSample |
SAMN20329788 |
| SRA |
SRX11508267 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5463707_Freeze_disome.txt.gz |
21.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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