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| Status |
Public on Nov 23, 2021 |
| Title |
tRNA_Seq RNC1 |
| Sample type |
SRA |
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| Source name |
tRNA_RNC1
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| Organism |
Escherichia coli |
| Characteristics |
strain: MG1655
|
| Extracted molecule |
total RNA |
| Extraction protocol |
MNase footprinting, ribosome pelleting, RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification (for ribosome profiling) or deacylation reaction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification (for tRNA-seq)
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
tRNA-seq
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| Data processing |
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 |
Nov 02, 2020 |
| Last update date |
Nov 23, 2021 |
| Contact name |
tomoya fujita |
| E-mail(s) |
tomoya.fujita.at.riken@gmail.com
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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 |
GPL21433 |
| Series (1) |
| GSE160623 |
Bacterial ribosome pause sites surveyed by an integration of ribosome profiling and nascent chain profiling |
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| Relations |
| BioSample |
SAMN16623552 |
| SRA |
SRX9417096 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4876111_tRNA_RNC1.txt.gz |
490 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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