|
| Status |
Public on Apr 30, 2019 |
| Title |
CS1AN_un |
| Sample type |
SRA |
| |
|
| Source name |
fibroblast cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: CS1AN
stress: control
|
| Treatment protocol |
12J/m2 UV-C irradiation
|
| Growth protocol |
culture in complete DMEM + 10% FBS + 1% Amp/Strep
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Culture medium was removed and total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
FastQC was conducted for Quality control (QC) of RNA-seq reads
Trimming was performed by seqtk for known Illumina TruSeq adapter sequences, poor reads, and ribosomal RNA reads
Trimmed reads were mapped to the Homo Sapiens reference genome by the Hisat 2(version:2.0.4)
String Tie(version:1.3.0) was performed for each gene count from trimmed reads
Gene counts were normalized by trimmed mean of M-values, and fragments per kilobase of transcript per million mapped reads (FPKM) in Perl script
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Apr 29, 2019 |
| Last update date |
Apr 30, 2019 |
| Contact name |
Yuming Wang |
| E-mail(s) |
[email protected]
|
| Phone |
008602037103555
|
| Organization name |
Guangzhou medical university
|
| Department |
School of Basic Medical Science
|
| Street address |
Room 512, Anatomy Building
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
511436 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE130444 |
Transcriptome profiles in MRC5 and CS1AN cell lines upon UV irradiation |
|
| Relations |
| BioSample |
SAMN11526850 |
| SRA |
SRX5764712 |
