|
| Status |
Public on Sep 12, 2023 |
| Title |
LNCaP_5_0_Era_1 |
| Sample type |
SRA |
| |
|
| Source name |
Prostate
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Prostate
cell line: LNCaP
cell type: Prostate cancer cells
genotype: WT
treatment: 5μmol/Lerastin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
treatment
LNCaP_group_gene_fpkm.txt
|
| Data processing |
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
May 09, 2023 |
| Last update date |
Sep 12, 2023 |
| Contact name |
周 青鸟 |
| E-mail(s) |
ebirdie123@126.com
|
| Phone |
18077161397
|
| Organization name |
Guangxi Medical University
|
| Street address |
shaungyonglu street num 22
|
| City |
nan ning |
| ZIP/Postal code |
530021 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE232034 |
RNA-seq Analysis of Prostate Cancer Cell Under Erastin Exposure |
|
| Relations |
| BioSample |
SAMN35006528 |
| SRA |
SRX20263093 |
