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| Status |
Public on May 12, 2018 |
| Title |
Rend-ylbF_StaphHG003 |
| Sample type |
SRA |
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| Source name |
Bacteria
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| Organism |
Staphylococcus aureus |
| Characteristics |
strain: subspecies HG003
media: TSB
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| Growth protocol |
Overnight cultures were diluted to OD590 0.003 in 25 mL fresh media. The culture was kept in a 125 mL flask at 37C with aeration (180 rpm) until OD590 reached 0.5.
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| Extracted molecule |
total RNA |
| Extraction protocol |
5 mL of cell culture was added to 5 mL of cold (-30C) methanol, mixed by inversion and spun down at 3000 rcf for 10 min at 4C. The supernatant was decanted and the cell pellet frozen at -80C. RNA was extracted using Trizol (ThermoFisher) and cleaned up and DNase treated using RNAeasy kit (QIAGEN). Ribosomal RNA was depleted using the MICROBExpress kit (Thermo Fisher). The resulting RNA was fragmented for 90 s at 95C using RNA fragmentation reagents (Thermo Fisher, AM 8740). Fragments in the 15 to 45 nt range were selected, dephosphorylated at the 3’ end and ligated to a 5’ adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
mRNA
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| Data processing |
Sequence reads were trimmed for adaptor sequences.
Trimmed reads were aligned to NC_000964.3 using Bowtie v1.2.1.1 with options -v 1 -k 1. To deal with non-template addition during reverse transcription, reads with a mismatch at their 5' end had their 5' end re-assigned to the immediate next downstream position.The 5' and 3' ends of mapped reads between 15 and 45 nt in sizes were added separately at genomic positions to generate the wig file (thus leading to 4 wig files: 3’ forward, 3’ reverse, 5’ forward, 5’ reverse). Peaks shadows were removed as described in the publication.
genome build: NC_007795.1
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| Submission date |
Dec 19, 2017 |
| Last update date |
May 13, 2018 |
| Contact name |
Aaron James DeLoughery |
| E-mail(s) |
adelough@mit.edu
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| Organization name |
Massachusetts Institute of Technology
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| Department |
Biology
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| Lab |
Gene-Wei Li
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| Street address |
31 Ames St
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
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| Platform ID |
GPL17452 |
| Series (1) |
| GSE108295 |
Maturation of polycistronic mRNA by RNase Y and its associated Y-complex in Gram-positive bacteria |
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| Relations |
| BioSample |
SAMN08204525 |
| SRA |
SRX3485058 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2895022_160721-6723_ylbF_StaphHG003_3_f.wig.gz |
1.5 Mb |
(ftp)(http) |
WIG |
| GSM2895022_160721-6723_ylbF_StaphHG003_3_r.wig.gz |
1.5 Mb |
(ftp)(http) |
WIG |
| GSM2895022_160721-6723_ylbF_StaphHG003_5_f.wig.gz |
1.5 Mb |
(ftp)(http) |
WIG |
| GSM2895022_160721-6723_ylbF_StaphHG003_5_r.wig.gz |
1.4 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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