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| Status |
Public on May 24, 2023 |
| Title |
CT26 sh1_1 |
| Sample type |
SRA |
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| Source name |
CT26
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| Organism |
Mus musculus |
| Characteristics |
cell line: CT26
cell type: colorectal cancer
genotype: Phf8 knockdown
treatment: CT26 Phf8 sh1 tumor tissues
time: Day 18 after CT26 Phf8 sh1 cells injection
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit 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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| Data processing |
Quality control; Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome; We selected Hisat2 as the mapping tool; Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level; featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.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.
Assembly: mm10 (CT26) and hg38 (PANC28)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
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| Submission date |
Aug 17, 2022 |
| Last update date |
May 24, 2023 |
| Contact name |
Yanan Liu |
| E-mail(s) |
Lyn19950902@outlook.com
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| Organization name |
East China Normal University
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| Department |
School of Life Sciences
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| Street address |
500 Dongchuan Road, Minhang District, Shanghai, China
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| City |
China |
| ZIP/Postal code |
200241 |
| Country |
China |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE211474 |
PHF8 enables immune evasion by silencing endogenous retroelements [RNA-Seq] |
| GSE212779 |
PHF8 enables immune evasion by silencing endogenous retroelements |
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| Relations |
| BioSample |
SAMN30371710 |
| SRA |
SRX17119651 |
| 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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