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Sample GSM6725439 Query DataSets for GSM6725439
Status Public on Apr 12, 2023
Title PCP_1
Sample type SRA
 
Source name Brain tumor tissue
Organism Homo sapiens
Characteristics tissue: Brain tumor tissue
cell type: tumor tissue
genotype: PCP
Growth protocol To test whether high content of lipids was originated from ACP cells, the ACP tissues (n=5), PCP tissues (n=4) and PA (n=3) tissues were prepared and sequenced.
Extracted molecule total RNA
Extraction protocol A total amount of 1 μg RNA per sample was used as input material for RNA sample preparations
Sequencing libraries were generated using NEB Next® Ultra RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Sequencing libraries were generated using NEB Next® Ultra RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations, and index codes were added to attribute sequences to each sample
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated
Feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Next, FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Assembly: Hisat2 v2.0.5
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
 
Submission date Nov 10, 2022
Last update date Apr 12, 2023
Contact name Yi Liu
E-mail(s) liuyi818@smu.edu.cn
Organization name Nanfang Hospital of Southern Medical University
Street address Guangzhou Dadao Bei Street 1838
City Guangzhou
ZIP/Postal code 510515
Country China
 
Platform ID GPL24676
Series (2)
GSE217717 The characteristic of cholesterol metabolism-related gene expression in ACP, PCP and PA
GSE217719 Cholesterol metabolism-related gene expression in ACP, PCP and PA; htNSC senescence process due to ACP cystic fluid
Relations
BioSample SAMN31683306
SRA SRX18230992

Supplementary file Size Download File type/resource
GSM6725439_PCP_1.txt.gz 380.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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