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Sample GSM7310634 Query DataSets for GSM7310634
Status Public on Sep 12, 2023
Title LNCaP_3
Sample type SRA
 
Source name Prostate
Organism Homo sapiens
Characteristics tissue: Prostate
cell line: LNCaP
cell type: Prostate cancer cells
genotype: WT
treatment: DMSO
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 control
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 SAMN35006529
SRA SRX20263092

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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