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| Status |
Public on Jan 24, 2020 |
| Title |
cca_stat_1 |
| Sample type |
SRA |
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| Source name |
E. coli CA244 cca K.O.
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| Organism |
Escherichia coli |
| Characteristics |
growth phase: stationary phase
genotype: cca KO
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| Growth protocol |
Cells were grown in LB-medium at 37°C and 250rpm
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by Hot Phenol or TriZol extraction, tRNA was PAGE-purified
3'-adapter ligation, alkaline fragmentation, 5'-adapter ligation, reverse transcription, PCR
3'-terminus RNAseq
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Read trimming with fastx-toolkit (0.0.13.2; quality threshold: 20)
Adapter cutting with cutadapt (1.2.1; minimal overlap: 1 nt)
Mapping against 10 nt upstream of CCA, sequences from genomic tRNA database (Escherichia coli K12)
Genome_build: tRNAscan-SE 1.3 Analysis of Escherichia coli K12 (http://gtrnadb2009.ucsc.edu/Esch_coli_K12/)
Supplementary_files_format_and_content: txt-file containing mapping sequences and raw reads for different tRNA sub-populations (CCA, CC, C, -, others)
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| Submission date |
Feb 01, 2019 |
| Last update date |
Jan 24, 2020 |
| Contact name |
Andreas Czech |
| E-mail(s) |
andreas.czech@posteo.de
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| Organization name |
University of Hamburg
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| Street address |
Martin-Luther-King-Platz 6
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| City |
Hamburg |
| ZIP/Postal code |
20146 |
| Country |
Germany |
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| Platform ID |
GPL14548 |
| Series (1) |
| GSE126019 |
NGS of 3'-termini of tRNA from E. coli |
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| Relations |
| BioSample |
SAMN10862782 |
| SRA |
SRX5325618 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3588860_cca_stat_1_tRNA_counts_NR2_10nt.txt.gz |
1.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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