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Status |
Public on Apr 22, 2024 |
Title |
S. pombe, Set1_del, rep3 |
Sample type |
SRA |
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Source name |
Schizosaccharomyces strains
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Organism |
Schizosaccharomyces pombe |
Characteristics |
genotype: Set1 knockdown
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted using Trizol reagent kit.The RNA libraries of RNA-Seq were enriched for mRNA using Oligo (dT), reverse transcribed to cDNA, after PCR amplification, and then sequenced. The RNA libraries of RNA-Seq were enriched for mRNA using Oligo (dT), following manufacturer's protocols.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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Description |
WT-vs-set1_del.all.annot.txt WT-vs-set1_del.filter.annot.txt
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Data processing |
First, the descending raw reads was quality-controlled using the fastp clean reads were aligned to the ribosome database of this species using the short reads alignment tool bowtie2[2], the reads on the upper ribosomes were removed without mismatch allowed, and the retained unmapped reads was used for subsequent transcriptome analysis. Using the HISAT2 software, a reference genome-based alignment analysis was performed. Based on the alignment results of the HISAT2, we reconstructed the transcripts using the Stringtie and calculated the expression levels of all the genes in each sample using the RSEM Input data for gene differential expression analysis are the reads count data obtained from gene expression level analysis and were analyzed using DESeq2[6] software Using the STRING protein interaction database (http://string-db.org). Assembly: Ensembl_release45 Supplementary files format and content: Each txt file corresponds to the information of one sample, with a total of two tables, namely all gene expression and significant gene expression.
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Submission date |
Sep 02, 2022 |
Last update date |
Apr 22, 2024 |
Contact name |
冯 刚 |
E-mail(s) |
fengg@njnu.edu.cn
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Organization name |
南京师范大学
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Street address |
江苏省南京市仙林街道南京师范大学
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City |
南京 |
ZIP/Postal code |
210000 |
Country |
China |
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Platform ID |
GPL17225 |
Series (1) |
GSE212629 |
Differential expression analysis of mutated genes at different loci of H2B |
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Relations |
BioSample |
SAMN30654711 |
SRA |
SRX17415058 |
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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