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Status |
Public on May 21, 2024 |
Title |
E. coli strain AP, engineered strain, rep 1 |
Sample type |
SRA |
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Source name |
bacteria
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Organism |
Escherichia coli str. K-12 substr. MG1655 |
Characteristics |
cell type: bacteria
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Treatment protocol |
Cells were harvested after 12 h of IPTG induction by quick centrifugation at 4℃, 12,000 rpm for 1 min, and immediately frozen in liquid nitrogen.
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Growth protocol |
The A (CF) and AP (pcnBi) strains were cultivated in modified M9 medium at 30℃ and inducted by IPTG when OD600 reached about 1.
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted using the RiboPure™ Bacteria Kit (Invitrogen, USA) following the manufacturer’s recommendations. RNA quality was checked using the DNF-471 Standard Sensitivity RNA Analysis Kit (Agilent, USA) and running on Fragment Analyzer (Agilent, USA). RNA sample was treated with DNase-I to remove DNA and was subjected to TIANSeq rRNA Depletion Kit (G- Bacteria) (TIANGEN, China) to remove rRNA. Sequencing libraries were constructed using the Optimal Dual-mode mRNA Library Prep Kit (BGI, China) following the manufacturer’s instructions. Circularization was performed using the MGIEasy Circularization Kit (MGI, China) and the product was quantitated using the Qubit® ssDNA Assay Kit (Invitrogen, USA). The libraries were then prepared using the MGISEQ-2000RS High-throughput Sequencing Set (FCL PE100) (MGI, China) and sequenced via the DNBSEQ-G400 platform (BGI, China) according to the manufacturer’s instructions.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
DNBSEQ-G400 |
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Data processing |
The sequencing data was filtered with SOAPnuke (v1.5.6) by removing reads containing sequencing adapter, reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20% and reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com). HISAT2 (v2.1.0) was applied to align the clean reads to the reference genome. Bowtie2 (v2.3.4.3) was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included. Expression level of gene was calculated by RSEM (v1.3.1). Essentially, differential expression analysis was performed using the DESeq2 (v1.4.5) with Q value <= 0.05. KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value <= 0.05). Assembly: GCF_000005845.2_ASM584v2 Supplementary files format and content: Excel file-gene expression (fpkm, read, log2 fold change, and q-value)
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Submission date |
May 16, 2024 |
Last update date |
May 21, 2024 |
Contact name |
Lixia Fang |
E-mail(s) |
lxfang@tju.edu.cn
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Organization name |
Tianjin University
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Street address |
135 Yaguan Road, Jinnan District
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City |
Tianjin |
ZIP/Postal code |
300350 |
Country |
China |
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Platform ID |
GPL34485 |
Series (1) |
GSE267710 |
Genome-scale CRISPRi screen identifies pcnB repression conferring improved physiology for overproduction of free fatty acids in Escherichia coli |
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Relations |
BioSample |
SAMN41426573 |
SRA |
SRX24584870 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
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