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| Status |
Public on Jul 27, 2023 |
| Title |
PNK006, rep 2 |
| Sample type |
SRA |
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| Source name |
PNK006
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| Organism |
Escherichia coli |
| Characteristics |
cell line: PNK006
cell type: UPEC
genotype: Group A
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| Extracted molecule |
total RNA |
| Extraction protocol |
Once grown, cells were collected by centrifugation at maximum speed for 10 minutes at 4 degrees Celsius. Media was decanted and pellets frozen overnight a -80 degrees Celsius. The next day, pellets were thawed on ice and 700 microliters of buffer RLT added. Buffered cells are mechanically lysed using a bead beater set the highest setting for 45 five seconds a cycle for three cycles with a 5 minute rest between cycles. During the rest, the cells are stored on ice. Once lysed, a Qiagen RNeasy mini kit was used to collect RNA. Contaminating DNA was removed though RNase-free DNase digestion of at least 10 micrograms of RNA determined by nanodrop. To remove the DNase and concentrate the RNA, a GeneJet RNA isolation and concentration kit was used.
Lexogen RiboCop rRNA depletion kit for Bacteria followed by Illumina Truseq Stranded mRNA library prep kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
High Output 75bp
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| Data processing |
We performed pan-genome analysis of 34 E. coli strains gene annotation by Roary with default parameter setting.
Kallisto was used to estimate the read counts on transcripts for each library by using all transcripts from 34 E. coli strains.
We quantified gene expression at group level by using gene groups defined from Roary and summing estimated read counts from all transcripts clustered into this group.
Assembly: All transcripts from 34 E. coli strains grouped by Roary.
Supplementary files format and content: A matrix of estimated read counts per group per sample.
Supplementary files format and content: A matrix of estimated TPM (transcript per million transcripts) per group per sample.
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| Submission date |
Jun 27, 2023 |
| Last update date |
Jul 27, 2023 |
| Contact name |
Zhenyu Xuan |
| E-mail(s) |
zhenyu.xuan@utdallas.edu
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| Phone |
972-883-2518
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| Organization name |
UT Dallas
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| Street address |
800 West Campbell
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| City |
Richardson |
| State/province |
TX |
| ZIP/Postal code |
75080 |
| Country |
USA |
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| Platform ID |
GPL21222 |
| Series (1) |
| GSE235964 |
The distinct transcriptome of virulence-associated phylogenetic group B2 Escherichia coli |
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| Relations |
| BioSample |
SAMN36002253 |
| SRA |
SRX20793925 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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