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| Status |
Public on Jul 28, 2020 |
| Title |
INS-1 832/13 cells: NIKKA |
| Sample type |
SRA |
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| Source name |
INS-1 832/13 cells
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: INS-1 832/13 cells
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| Extracted molecule |
total RNA |
| Extraction protocol |
Not provided
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Ensemble_GRCm38.90 whole genome using tophat2 with parameters -p 8 -N 2 --read-edit-dist 2
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then F PKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. F PKM, expected number of Fragment s 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 ( Tr apnell, Cole, et al., 2010 )
Genome_build: Ensemble_GRCm38.90
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| Submission date |
Apr 22, 2019 |
| Last update date |
Jul 29, 2020 |
| Contact name |
Zheng Chen |
| E-mail(s) |
chenzheng@hit.edu.cn
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| Phone |
+8645186402029
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| Organization name |
Harbin Institute of Technology
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| Street address |
92 Xidazhijie Harbin Institute of Technology
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| City |
Harbin |
| State/province |
Heilongjiang |
| ZIP/Postal code |
150001 |
| Country |
China |
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| Platform ID |
GPL24688 |
| Series (1) |
| GSE130121 |
RNA-seq analysis of mRNA profiles in β-Gal-overexpressing, NIK-overexpressing, and NIK(KA)-overexpressing INS-1 832/13 cells |
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| Relations |
| BioSample |
SAMN11475753 |
| SRA |
SRX5717523 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3732430_NIK_KA_fpkm.xlsx |
872.9 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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