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Sample GSM3358030 Query DataSets for GSM3358030
Status Public on May 27, 2019
Title SLIT2_3
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
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
BioSample SAMN09924827
SRA SRX4615333

Supplementary file Size Download File type/resource
GSM3358030_170036_II_3_S3_L001.txt.gz 2.6 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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