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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 30, 2022 |
| Title |
Lung-C |
| Sample type |
SRA |
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| Source name |
Porcine extraintestinal pathogenic Escherichia coli (ExPEC)
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| Organism |
Escherichia coli PCN033 |
| Characteristics |
infection: mouse infection with a transposon mutagenesis library
library type: output
bacteria recovered from: Lung
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Bacterial genomic DNA of input libraries and output libraries recovered from mouse brain, spleen, and lung were extracted from using E.Z.N.A.® Bacterial DNA Kit (Omega Bio-Tek, USA)
The genomic DNA was subjected to fragmentation, end repair, and 3' end dA-tailing. The Illumina universal adaptors were added using the TIANSeq Quick Connect Module (Cat# NG303, TIANGEN Biotech, China) which was then purified using Magic DNA Select Beads (Cat# M3022, Magic Bio, China). Primer pair F-/R- was used in the first round PCR amplification for enrichment of the DNA region flaking the transposon. The PCR product was purified and used as the template for the second round amplification using P5/7 primer pair, and the amplification product was purified which was used to construct Illumina sequencing library by using Magic DNA Select Beads (Cat# M3022, Magic Bio, China). The DNA library was sequenced using an Illumina Novaseq sequencer.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Library strategy: TraDIS
The clean sequencing reads obtained above were aligned to the ExPEC PCN033 (GenBank: CP006632.1) genome using BWA (mem algorithm)
The resulting bam files were sorted by using Sambamba (default parameter) to exclude redundant sequences
DEseq2 was used to compare the change in the total number of insertion reads for each gene between the input and output libraries
Genome_build: CP006632
Supplementary_files_format_and_content: The total number of insertion reads for each gene between the input and output libraries
Supplementary_files_format_and_content: Matrix of changes in the number of reads per gene
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| Submission date |
Feb 21, 2022 |
| Last update date |
Apr 30, 2022 |
| Contact name |
Yin Fan |
| E-mail(s) |
yinfan@webmail.hzau.edu.cn
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| Phone |
15927566709
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| Organization name |
Huazhong Agricultural University
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| Street address |
Shizishan street
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| City |
WuHan |
| State/province |
HuBei |
| ZIP/Postal code |
430070 |
| Country |
China |
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| Platform ID |
GPL31960 |
| Series (1) |
| GSE197084 |
Genome-wide identification of genes critical for in vivo fitness of porcine extraintestinal pathogenic Escherichia coli by using transposon-directed insertion site sequencing |
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| Relations |
| BioSample |
SAMN26135200 |
| SRA |
SRX14238322 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5908225_Lung-GroupC_L4_20_F_insert_site_reads_counts_F.txt.gz |
122.9 Kb |
(ftp)(http) |
TXT |
| GSM5908225_Lung-GroupC_L4_20_R_insert_site_reads_counts_R.txt.gz |
30.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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