|
| Status |
Public on Nov 18, 2020 |
| Title |
HTR-8_KD_rep4-3 |
| Sample type |
SRA |
| |
|
| Source name |
HTR-8_KD
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: placental cell line HTR-8/Svneo
treatment: Plagl1 siRNA
genotype: PLAGL1 knockdown
|
| Treatment protocol |
Cells were seeded at 15 x 10Âe4 cells/well in a 6-well plate and grown for 48 hours before transfecting. Transfections were carried out with the Lipofectamine RNAiMAX Transfection Reagent (Fisher Scientific 13778150) and with PLAGL1 siRNA(ThermoFisher Scientific 4392420) or a negative control(ThermoFisher Scientific 4390843). We performed a media change 24 hours after transfection.
|
| Growth protocol |
HTR-8/SVneo cells were cultured in RPMI-1640 (ATCC 30-2001) with 5% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted 48 hours after transfection using the Qiagen Mini RNA kit
Libraries were prepared using the NEBNext Ultra II Directional library prep kit, unique dual index plate, and poly(A) mRNA magnetic isolation module, following manufacturer’s protocol
Samples were run on the HiSeq 3000, across three lanes using single-end 50bp reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
aligned to the hg19 genome using HISAT2 (v2.1.0; default paraeters)
transcript abundance was calculated using htseq-count from the HTseq package.
Genome_build: hg19
Supplementary_files_format_and_content: Files contain the number of reads aligning to each gene
|
| |
|
| Submission date |
Jul 16, 2020 |
| Last update date |
May 05, 2021 |
| Contact name |
Geetu Tuteja |
| Organization name |
Iowa State University
|
| Department |
Genetics, Development and Cell Biology
|
| Street address |
2106 Molecular Biology Building
|
| City |
Ames |
| State/province |
IA |
| ZIP/Postal code |
50011 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE154577 |
A potential role for PLAGL1 in the regulation of blood vessel development |
|
| Relations |
| BioSample |
SAMN15558332 |
| SRA |
SRX8746290 |
