|
| Status |
Public on Dec 23, 2019 |
| Title |
Ctrl_3 |
| Sample type |
SRA |
| |
|
| Source name |
A649_control
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
cell type: lung carcinoma epithelial cell line
genotype/variation: control
|
| Treatment protocol |
A549 cells were stably transduced with lentiviral particles encoding small hairpin RNA (shRNA) targeting BCLAF1 or an irrelevant firefly luciferase shRNA.
|
| Growth protocol |
A549 cells were obtained from American Type Culture Collection and were cultured according to the recommended protocols.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For A549 cells, total RNA was extracted with TRIZOL (Ambion) The RNA was further purified with two phenol chloroform treatments and then treated with RQ1 DNase (Promega, Madison, WI, USA) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260 /A280) using Smartspec Plus (BioRad, USA). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.
For each sample, 1 μg of total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (invitrogen) before used for directional RNA-seq library preparation. Purified mRNAs were iron fragmented at 95 ℃ followed by end repair and 5' adaptor ligation. Then reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomizedhexamer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
Ctrl_3-mRNA_raw
|
| Data processing |
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 20 -p 16 --no-discordant. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2 Pvalue <= 0.01 Qvalue <= 0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each sample
|
| |
|
| Submission date |
Dec 22, 2019 |
| Last update date |
Dec 24, 2019 |
| Contact name |
Zhenyi Ma |
| E-mail(s) |
zhyma@tmu.edu.cn
|
| Phone |
86-22-83336533
|
| Organization name |
Tianjin Medical University
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
22 Qixiangtai Road
|
| City |
Tianjin |
| ZIP/Postal code |
300070 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE142508 |
Mediator MED23 induces premature senescence by interacting with BCLAF1 via blocking autophagy flux in lung cancer cells |
|
| Relations |
| BioSample |
SAMN13670859 |
| SRA |
SRX7431054 |
