|
| Status |
Public on Sep 17, 2020 |
| Title |
U87_DPF3CM_3 RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
U87
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U87
genotype/variation: DPF3-over-expressed
treatment: U87 cells transfer plasmid containing DPF3 gene and treated with 0.5mM 8-cpt-cAMP and 1nM MS275 for 48hr.
|
| Treatment protocol |
U87 cells were treated with bulk control/combination of 0.5mM 8-cpt-cAMP and 1nM MS275 for 48 hours. Total RNA was extracted from 1×10^6 cells with TRIzol Reagent (Thermo Fisher Scientific) and was sent for RNA sequencing
|
| Growth protocol |
The cells were cultured according to the guideline of ATCC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cultured cell lines. Beads containing oligo (dT) were used to isolate poly(A) mRNA from total RNA. Purified mRNA was then fragmented in fragmentation buffer. Using these short fragments as templates, random hexamer-primers ere used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized using buffer, dNTPs, RNase H and DNA polymerase I. Short double-stranded cDNA fragments were purified with a QIAquick PCR extraction kit (vendor) and eluted with EB buffer for end repair and the addition of an ‘A’ base. Next, the short fragments were ligated to Illumina sequencing adaptors. DNA fragments of a selected size were gel-purified and amplified by PCR. The amplified library was sequenced using Illumina HiSeq 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
We use Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample QC:RNA concentration, RIN value,28S/18S and the fragment length distribution.
We use internal software SOAPnuke to filter reads
We use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step.
We mapped clean reads to reference using Bowtie2 and then calculate gene expression level with RSEM
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Sep 16, 2020 |
| Last update date |
Sep 20, 2020 |
| Contact name |
liu xincheng |
| E-mail(s) |
chaoyanglxc123@gmail.com
|
| Organization name |
sysu
|
| Street address |
zhongshan Road 74
|
| City |
GuangZhou |
| ZIP/Postal code |
515100 |
| Country |
China |
| |
|
| Platform ID |
GPL23227 |
| Series (1) |
| GSE158065 |
RNAseq of U87/over-expressed DPF3 U87 treated with bulk control/0.5mM 8-cpt-cAMP combination with 1nM MS275 for 48hrs |
|
| Relations |
| BioSample |
SAMN16182254 |
| SRA |
SRX9134875 |
