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| Status |
Public on May 27, 2021 |
| Title |
JCYL008E |
| Sample type |
SRA |
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| Source name |
Xylose_feeding_4h
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: Engineered SR8U containing xylose-utilizing and xylodextrin-degrading pathway
growth condition: Anaerobically
carbon source: Xylodextrins
xylose feeding condition: 4 h with xylose feeding
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RiboPure Yeast kit (Ambion, Austin, TX, USA), according to manufacturer's instructions, except cells were disrupted by bead-beating 3 times for 30 sec, with a 30 sec pause between runs.
4 µg of total RNA were used to prepare the multiplexing libraries with barcodes following the standard instructions of the Illumina TruSeq RNA Sample Prep Kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
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| Data processing |
Illumina Casava_v1.8.0 software used for basecalling. Sequenced reads were trimmed for adaptor sequence.
Sequence reads were assembled and analyzed in CLC Genomics Workbench 7.0 (CLC Bio, Aarhus, Denmark). The Saccharomyces cerevisiae S288C genome was downloaded from RefSeq at the NCBI (sequence assembly version R64-1-1, http://www.ncbi.nlm.nih.gov/assembly/GCF_000146045.2/) including 16 chromosomes and the mitochondrial genome. The genes for XYL1 (xylose reductase gene), XYL2 (xylitol dehydrogenase gene), and XKS1 (xylulose kinase gene) from Scheffersomyces stipitis, as well as cdt-2 (coding for cellodextrin transporter 2), gh43-2 (coding for β-xylosidase) and gh43-7 (coding for a xylosyl-xylitol-specific β-xylosidase) from N. crassa were manually annotated and combined with the S. cerevisiae S288C genome as the reference. Expression values were normalized by calculating the reads per kilobase of mRNA exon per million mapped reads (RPKM), and further normalized using the option of “By totals”.
Genome_build: R64; Saccharomyces cerevisiae S288C
Supplementary_files_format_and_content: Excel file includes RPKM values for all the samples.
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| Submission date |
Jun 02, 2015 |
| Last update date |
May 27, 2021 |
| Contact name |
Yuping Lin |
| E-mail(s) |
lin_yp@tib.cas.cn
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| Organization name |
Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences
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| Street address |
32 West 7th Avenue, Tianjin Airport Economic Area
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| City |
Tianjin |
| State/province |
Tianjin |
| ZIP/Postal code |
300308 |
| Country |
China |
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| Platform ID |
GPL9377 |
| Series (1) |
| GSE69448 |
Impact of xylose feeding on transcriptome profiles of anaerobically fed-batch xylodextrins consumption in Saccharomyces cerevisiae |
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| Relations |
| BioSample |
SAMN03754707 |
| SRA |
SRX1045480 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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