|
| Status |
Public on May 08, 2024 |
| Title |
Control |
| Sample type |
SRA |
| |
|
| Source name |
Fetal Kidney
|
| Organism |
Homo sapiens |
| Characteristics |
genotype: HMGN5_GFP_knockin
plasmid transfected: non_induced
cell line: Flp-In T-REx 293
|
| Treatment protocol |
3 conditions were used 70-80% confluent HMGN5-FlpIn cell line were induced 24h with (1µg/µl Doxycycline); 24h HMGN5 knock-down (40 nM of a SmartPool siRNA) and non-treated control cells (70% confluent 10cm culture dish per replicate)
|
| Growth protocol |
HMGN5-FlpIn cell lines were cultured in low glucose DMEM GlutaMAX™ supplemented with 10% Tetracycline-Free FBS (Biochrom), 100 µg/ml Hygromycin and 10 μg/ml Blasticidin, at 37°C and 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with the NucleoSpin RNA Kit (MACHEREY-NAGEL)
Libraries were prepared using TruSeq RNA Sample Preparation Kit v2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw sequencing reads were trimmed by removing Illumina adapters sequences and low-quality bases
pre-processing steps were performed using the SAMtools or BEDtools packages
Trimmed reads were mapped using STAR software
The number of reads per transcript was counted using HTSeq (v0.11.2)
The differentially expressed genes (DEGs) were estimated using DEseq2 package from R (v3.1.2)
Genome_build: hg19
Supplementary_files_format_and_content: .txt files containing normalised counts and differential expression analysis data (DESeq2)
|
| |
|
| Submission date |
Feb 03, 2021 |
| Last update date |
May 08, 2024 |
| Contact name |
Gino Nardocci |
| E-mail(s) |
gnardo@gmail.com
|
| Organization name |
Universidad de los Andes
|
| Street address |
Av. Mons. Álvaro del Portillo 12.455
|
| City |
Santiago |
| ZIP/Postal code |
7620001 |
| Country |
Chile |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE166091 |
HMGN5, an RNA and Nucleosome binding protein required for chromatin de-condensation and gene activation [RNA-seq] |
| GSE166103 |
HMGN5, an RNA and Nucleosome binding protein required for chromatin de-condensation and gene activation |
|
| Relations |
| BioSample |
SAMN17769420 |
| SRA |
SRX10012801 |
