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| Status |
Public on Oct 18, 2024 |
| Title |
MIP_SE_SA_acid_rep3_half_spia |
| Sample type |
SRA |
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| Source name |
bacterial culture
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| Organisms |
Staphylococcus aureus; Staphylococcus epidermidis |
| Characteristics |
tissue: bacterial culture
strain se: Tu3298
strain se: USA300
seqeuncing appraoch: Molecular Loop (MIP)
experimental batch: batch 2
treatment rrna: no ribo-depletion
treatment spia: half SPIA
treatment media: Acid
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| Treatment protocol |
S. aureus and S. epidermidis were grown in TSB, TSB pH 4.8 or on reconstructed human epidermidis for bulk and targted RNA-seq with and without ribo-depletion and/or SPIA.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using RNeasy 96 QIAcube HT kit (Qiagen, Hilden, Germany) according to the manufacturer’s directions. Samples were eluted in nuclease-free water (Qiagen, Hilden, Germany) and frozen at -80°C until sequencing preparation.
The sequencing libraries were prepared with NEBNext rRNA Depletion Kit v2 (New England Biolabs, Ipswich, MA) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) following the manufacturer’s directions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
SE + SA 50:50 mix (10ng each)_BR3_Acidic stress culture_1/2 SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx
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| Data processing |
quality control with FastQCv0.12.1
adapter removal with Cutadatv4.4 (bulk, SPE) and seqtkv1.2-r122 (MIP)
alignment with BWA-MEMv0.7.12-r1188
read extraction and filtering with bamtoolsv2.5.2 (MAPQ >30, NM<4)
count tables generated with SAMtoolsv0.7.17-r1188
Assembly: GCF_017329165.1 (Sa M2872), GCF_006094375.1 (Se ATCC 14990), GCF_002993865.1 (Sa USA300)
Supplementary files format and content: Supp_Table_06_Bulk_data_expdb.xlsx: table of bulk RNA-seq samples mapped to Se Tu3298 and Sa USA300, data sheets include raw counts, CPMs, TPMs, and log transformations.
Supplementary files format and content: Supp_Table_05_Bulk_data_refdb.xlsx: table of bulk RNA-seq samples mapped to Se ATCC 14990 and Sa M2872, data sheets include raw counts, CPMs, TPMs, and log transformations.
Supplementary files format and content: Supp_Table_08_MIP_data_expdb.xlsx: table of MIP RNA-seq samples mapped to Se Tu3298 and Sa USA300, data sheets include probe and CDS raw counts, CPMs, TPMs, and log transformations.
Supplementary files format and content: Supp_Table_07_MIP_data_refdb.xlsx: table of MIP RNA-seq samples mapped to Se ATCC 14990 and Sa M2872, data sheets include probe and CDS raw counts, CPMs, TPMs, and log transformations.
Supplementary files format and content: Supp_Table_10_SPE_data_expdb.xlsx: table of SPE RNA-seq samples mapped to Se Tu3298 and Sa USA300, data sheets include probe and CDS raw counts, CPMs, TPMs, and log transformations.
Supplementary files format and content: Supp_Table_09_SPE_data_refdb.xlsx: table of SPE RNA-seq samples mapped to Se ATCC 14990 and Sa M2872, data sheets include probe and CDS raw counts, CPMs, TPMs, and log transformations.
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| Submission date |
Oct 10, 2024 |
| Last update date |
Oct 18, 2024 |
| Contact name |
Mark Adams |
| E-mail(s) |
[email protected]
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| Organization name |
The Jackson Laboratory
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| Street address |
10 Discovery Drive
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| City |
Farmington |
| State/province |
CT |
| ZIP/Postal code |
06032 |
| Country |
USA |
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| Platform ID |
GPL34976 |
| Series (1) |
| GSE279187 |
TEAL-seq (Targeted Expression Analysis Sequencing) of S. aureus and S. epidermidis in TSB and skin-relevent conditions |
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| Relations |
| BioSample |
SAMN44240596 |
| SRA |
SRX26345121 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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