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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 23, 2019 |
| Title |
PurβKD |
| Sample type |
SRA |
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| Source name |
primary hepatocytes
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| Organism |
Mus musculus |
| Characteristics |
tissue: primary hepatocytes
genotype: pur-beta knockdown
strain: C57BL/6
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| Treatment protocol |
For Purβ-overexpressing experiments, the cells were infected with βgal and Purβ adenoviruses overnight. For Purβ-knocking down experiments, the cells were infected with Scramble and shPurβ1 or shPurβ2 adenoviruses for 30 h.
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| Growth protocol |
Primary hepatocytes were isolated from C57BL/6 mice by liver-perfusion with type II collagenase (Worthington Biochem, Lakewood, NJ) and cultured at 37°C and 5% CO2 in DMEM medium supplemented with 5% FBS.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using TriPure Isolation Reagent (Roche, Mannheim, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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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_GRCm38.96 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_GRCm38.96
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| Submission date |
Sep 02, 2019 |
| Last update date |
Sep 23, 2019 |
| 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 |
GPL24247 |
| Series (1) |
| GSE136728 |
RNA-seq Analysis of mRNA profiles in Purβ-overexpressing and Purβ-knocking down hepatocytes |
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| Relations |
| BioSample |
SAMN12672758 |
| SRA |
SRX6790164 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4056807_PurbetaKD_fpkm.xlsx |
5.7 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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