|
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.
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|
|
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 |