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| Status |
Public on Jan 28, 2022 |
| Title |
5-8F-shHDAC4-2 |
| Sample type |
SRA |
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| Source name |
nasopharyngeal carcinoma cell lines
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| Organism |
Homo sapiens |
| Characteristics |
cell type: nasopharyngeal carcinoma cell lines
passages: 5
cell line: 5-8F
knockdown: shHDAC4
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| Growth protocol |
10% FBS in DMEM
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Libraries were prepared according to Illumina's instructions
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
shHDAC4-2
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo_sapiens.GRCh37 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
DESeq software was used to calculate the RPKM
Genome_build: Alignment was initially to the transcriptome (hg19, GRCh37.72), and then to the genome (hg19, GRCh37). Data in processed data files were from alignment to UCSC hg19.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
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| Submission date |
Jan 28, 2019 |
| Last update date |
Jan 28, 2022 |
| Contact name |
Yi Sang |
| E-mail(s) |
ndsfy001889@ncu.edu.cn
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| Phone |
86-791-8862311
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| Organization name |
Nanchang University
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| Street address |
No.128,Xiangshan North Road
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| City |
Nanchang |
| State/province |
Jiangxi |
| ZIP/Postal code |
330008 |
| Country |
China |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE125744 |
Exploring the downstream genes of HDAC4 |
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| Relations |
| BioSample |
SAMN10830571 |
| SRA |
SRX5299780 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3581397_shHDAC4_5.txt.gz |
329.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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