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Sample GSM6574589 Query DataSets for GSM6574589
Status Public on May 09, 2023
Title HM1-shControl-3
Sample type SRA
 
Source name HM1 cells
Organism Mus musculus
Characteristics tissue: cell line
cell line: HM1
cell type: murine ovarian cancer cell
genotype: wild type
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
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
 
Data processing Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp ).
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
The expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited txt files include TPM values for each sample.
 
Submission date Sep 12, 2022
Last update date May 11, 2023
Contact name Haiou Liu
E-mail(s) liuhaiou@fudan.edu.cn
Phone +8613916273769
Organization name Fudan University
Street address No.128, Shengyang road, Yangpu distinct, Shanghai, P. R. China.
City Shanghai
ZIP/Postal code 200000
Country China
 
Platform ID GPL24247
Series (1)
GSE213219 Tumor-intrinsic ST3GAL3 Activity Blunts Anti-tumor Immune and Drives Immunotherapy Resistance
Relations
BioSample SAMN30813966
SRA SRX17538792

Supplementary file Size Download File type/resource
GSM6574589_HM1-shControl-3.txt.gz 1.2 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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