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Sample GSM7060171 Query DataSets for GSM7060171
Status Public on Feb 23, 2024
Title RBE cells, sh#HSDL2 3
Sample type SRA
 
Source name human bile duct
Organism Homo sapiens
Characteristics tissue: human bile duct
cell line: RBE
cell type: cholangiocarcinoma cell
genotype: HSDL4 knockdown
treatment: routine culture
Treatment protocol routine culture
Growth protocol RBE cholangiocarcinoma cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃
Extracted molecule total RNA
Extraction protocol RNA was extracted using trizol reagent. 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using RNA-Seq Library Preparation Protocol(DNBSEQ) following manufacturer's protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model BGISEQ-500
 
Data processing The sequencing data was filtered with SOAPnuke(v1.5.2)
After obtaining the clean reads, we used HISAT2(v2.0.4) to align the clean reads to the reference genome sequence
clean reads were compared to reference gene sequences using Bowtie2(v2.2.5)
then the expression level of gene was calculated by RSEM(v1.2.12),differential expression analysis was performed using DESeq2(v1.4.5)
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited text files files include fpkm, tpm,read count values for each Sample
 
Submission date Feb 23, 2023
Last update date Feb 23, 2024
Contact name Shuoshuo Ma
Organization name The First Affiliated Hospital of Bengbu Medical College
Street address NO. 287, Changhuai Road, Longzihu district, Bengbu 233000, Anhui, China;
City Bengbu
State/province Anhui
ZIP/Postal code 23300
Country China
 
Platform ID GPL23227
Series (1)
GSE225900 Knockdown of HSDL2 promotes the progression of cholangiocarcinoma and inhibits ferroptosis through STAT3/P53 pathway
Relations
BioSample SAMN33422392
SRA SRX19481855

Supplementary file Size Download File type/resource
GSM7060171_SH3.txt.gz 715.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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