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Sample GSM4318466 Query DataSets for GSM4318466
Status Public on Feb 18, 2023
Title H2BL.2
Sample type SRA
 
Source name Liver cancer cells
Organism Homo sapiens
Characteristics cell line: SMMC-7721
overexpression: HIST1H2BL
Growth protocol Cell lines were cultured in DMEM supplemented with 10% FBS, at 37℃ with 5% CO2.
Extracted molecule total RNA
Extraction protocol Culture medium was removed and the cells were washed by PBS twice. Total RNA was extracted by RNAiso (Takara). 1μg total RNA was used for the construction of libraries.
Libraries was constructed using TruSeq RNA Sample Prep Kit v2 for Illumina.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
 
Data processing Illumina Casava software used for basecalling.
Sequenced reads were mapped to hg19 transcripts genome using hisat2 v2.1.0 with default parameters, and then filtered by samtools v1.9 with parameters -f 3 -F 256 to reserve paired and primary aligment reads
Reads count for genes were counted by featureCounts v1.6.1 with parameter -p, and then were normalized by the size of the library and removed the batch effect using R packages for futher analysis.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include gene reads count values.
 
Submission date Feb 18, 2020
Last update date Feb 18, 2023
Contact name Dade Song
E-mail(s) dsucifer@gmail.com
Phone 17521689979
Organization name Advanced Institute of Qingdao,Tongji University
Street address No.1239,Siping Road
City Shanghai
ZIP/Postal code 200000
Country China
 
Platform ID GPL9115
Series (1)
GSE145448 Nucleotide variation in histone H2BL promotes cell proliferation by upregulating c-Myc
Relations
BioSample SAMN14124578
SRA SRX7739062

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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