|
| Status |
Public on May 27, 2019 |
| Title |
SLIT2_1 |
| Sample type |
SRA |
| |
|
| Source name |
HTR-8/Svneo cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HTR8/SVneo
cell type: trophoblast
tissue: placenta
treatment: silenced with siRNA of SLIT2
|
| Treatment protocol |
The transfection with siRNA was done either with 30-40 nM siRNA pair or 30-40 nM siRNA universal negative control and using approximately 70 000 cells and duoble transfection. The first transfection was done in suspension (30 nM siRNA) and the second transfection in adherent cells (40mM).
|
| Growth protocol |
The HTR-8/Svneo cells were cultured in RPMI 1640 medium supplemented with 10 % fetal bovine serum, 100 U/ml penicillin and 100 mg/ml streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated by RNeasy Micro Kit
Library preparation was done according to Illumina TruSeq® Stranded mRNA Sample Preparation Guide (part # 15031047)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
sequencing was done in 1 lane
|
| Data processing |
The base calling was done using bcl2fastq (v. 2.17)
Read alignment was done using star (2.5.2b) to hg38 human genome reference
Genewise read counts were calculated using subread (v1.5.1)
Genome_build: Human GRCh38
Supplementary_files_format_and_content: files are tab delimited text files containing the genewise read counts for each sample
|
| |
|
| Submission date |
Aug 27, 2018 |
| Last update date |
May 27, 2019 |
| Contact name |
Antti Haapalainen |
| E-mail(s) |
antti.haapalainen@oulu.fi
|
| Organization name |
University of Oulu
|
| Department |
CRC
|
| Lab |
Pediatrics
|
| Street address |
Aapistie 5A
|
| City |
Oulu |
| ZIP/Postal code |
90220 |
| Country |
Finland |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE119101 |
Functional role of SLIT2 and ROBO1 in trophoblasts |
|
| Relations |
| BioSample |
SAMN09924820 |
| SRA |
SRX4615331 |
