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| Status |
Public on May 22, 2021 |
| Title |
fnr40%-3 |
| Sample type |
SRA |
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| Source name |
bacteria
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| Organism |
Komagataeibacter xylinus |
| Characteristics |
strain: CGMCC 2955
genotype/variation: FNR
oxygen %: 40
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was used as input material for the RNA sample preparations. For prokaryotic samples, mRNA was purified from total RNA using probes to remove rRNA. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. And in the DNA polymerase I system, use dUTP to replace the dNTP of dTTP as the raw material to synthesize the second strand of cDNA. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. Then USER Enzyme was used to degrade the second strand of cDNA containing U, In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
gene_fpkm.xls
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| Data processing |
Illumina Casava1.8 software used for basecalling.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then 2 FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels .
Genome_build: CP024644.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
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| Submission date |
May 21, 2021 |
| Last update date |
May 24, 2021 |
| Contact name |
Lixuejing huanglonghui zhongcheng |
| E-mail(s) |
lixuejing1010@126.com
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| Phone |
18522519961
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| Organization name |
Tianjin University of Science and Technology
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| Street address |
13th Street, Binhai New Area, Tianjin City
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| City |
Tianjin |
| ZIP/Postal code |
300450 |
| Country |
China |
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| Platform ID |
GPL30182 |
| Series (1) |
| GSE174847 |
Effects of FNR, Arca and oxygen on the synthesis of bacterial cellulose |
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| Relations |
| BioSample |
SAMN19299813 |
| SRA |
SRX10957129 |
| 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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