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| Status |
Public on Jul 01, 2016 |
| Title |
H2-26-act |
| Sample type |
SRA |
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| Source name |
mycelium
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| Organism |
Streptomyces albus |
| Characteristics |
strain: J074
cosmid: H2-26-act
id_in_files: Lanact
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| Growth protocol |
S. albus H2-26-act and S. albus H2-26 were inoculated in TSB medium and cultivated at 28 °C and 180 rpm for 24 hours. Obtained precultures were reinoculated into SG production medium. The strains were cultivated for 3 days at 28 °C and 180 rpm until the onset of secondary metabolite production.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Mycelium was harvested by centrifugation.
Briefly, ribosomal RNA depletion of isolated total RNA was performed with a Ribo-Zero Bacteria kit from Epicentre (Madison, WI, USA). The rRNA-depleted RNA was fragmented with RNase III, and 5′PPP structures were removed using RNA 5′ polyphosphatase (Epicentre). Next, RNA fragments were poly(A)-tailed using poly(A) polymerase. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and M-MLV reverse transcriptase. The resulting cDNA was amplified and purified, and fragments in the length range of 250 – 500 bp were sequenced on an Illumina HiSeq 2000 machine (San Diego, CA, USA) with 100 bp read length.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
H2_vs_Lanact_pval.csv
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| Data processing |
Basecalling: Illumina CASAVA1.8
Preprocessing: prinseq-lite.pl -min_len 20 -trim_tail_left 4 -trim_tail_right 4 -trim_ns_left 1 -trim_ns_right 1 -trim_qual_left 20 -trim_qual_right 20 -trim_qual_type mean -trim_qual_window 3
Mapping: novoalign 3.00.04, -r Random -H
Computational rRNA depletion: reads mapping within any of the 7 rRNA clusters were discarded.
Genome_build: NC_020990.1, with appended 200 bps of Ns, followed by the H2-26-act cosmid
Supplementary_files_format_and_content: Tab-delimited files with raw read counts and a matrix (CSV) file with DESeq normalized values and processing results.
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| Submission date |
Jun 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Bogdan Tokovenko |
| Organization name |
Helmholtz Institute for Pharmaceutical Research Saarland
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| Street address |
Campus C2.3
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| City |
Saarbrücken |
| ZIP/Postal code |
66123 |
| Country |
Germany |
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| Platform ID |
GPL21996 |
| Series (1) |
| GSE83137 |
Generation of new compounds through unbalanced transcription of landomycin A cluster |
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| Relations |
| BioSample |
SAMN05217705 |
| SRA |
SRX1832744 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2194179_NG-7363_VB1408_CAAAAG_lib42520_2329_1_1_good_norRNA_counts.txt.gz |
65.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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