|
| Status |
Public on Jun 21, 2022 |
| Title |
KC_Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
U87-MG cells
|
| Organism |
Homo sapiens |
| Characteristics |
genotype: KO
treatment: None
|
| Treatment protocol |
Cells were treated with 500 ng/ml recombinant SEMA3A proteins for 6 hours.
|
| Growth protocol |
Cells were cultured in DMEM supplemented with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted by TRIzol (Thermo Fisher Scientific) from U87-MG cells with or without SEMA3s treatment.
The resulting RNA was then used to prepare libraries using Illumina TruSeq Stranded mRNA Library Prep Kit Set A (Illumina, RS- 122-2101) or Set B (Illumina, RS-122-2102).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina Casava1.8 software was used for basecalling.
Reads were aligned to the hg19 reference genome using STAR 2.4.2a with default parameters.
Only uniquely mapped reads were kept for further analysis.
FPKM values for each gene were computed using cufflinks v2.2.1 with default parameters according to Gencode human annotation release 24.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values
|
| |
|
| Submission date |
Oct 30, 2019 |
| Last update date |
Jun 21, 2022 |
| Contact name |
Yunjiang Qiu |
| Organization name |
University of California, San Diego
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE139630 |
Semaphorin activates Hippo signaling to control cell growth |
|
| Relations |
| BioSample |
SAMN13162468 |
| SRA |
SRX7077132 |
