|
| Status |
Public on May 08, 2020 |
| Title |
HGFDFN168 |
| Sample type |
SRA |
| |
|
| Source name |
skin
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: fibroblasts
disease status: control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using TRIzol (Invitrogen) and following the manufacturer’s instructions. Total RNA was then purified with the RNA Clean & Concentrator-5 kit (Zymo Research) and reverse-transcribed using SuperScript III reverse transcriptase (Invitrogen), again following the manufacturer’s instructions.
Sequencing libraries were prepared using 1µg of DNAse-treated total RNA in the first step of the TruSeq RNA Sample Preparation v2 protocol (Illumina, Part# 15026495 Rev. A) as recommended by the manufacturer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming and quality filtering: Trimmomatic 0.39
Transcriptome mapping: Tophat 2.0.6
computation of count data: htseq.py
Genome_build: hg19
Supplementary_files_format_and_content: count table containing the count values for all genes in all samples
|
| |
|
| Submission date |
May 08, 2020 |
| Last update date |
May 09, 2020 |
| Contact name |
Guenter Raddatz |
| Organization name |
German Center for Cancer Research
|
| Street address |
Im Neuenheimer Feld 580
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE150137 |
Epigenetic deregulation of lamina-associated domains in Hutchinson-Gilford Progeria Syndrome (RNA-Seq) |
| GSE150138 |
Epigenetic deregulation of lamina-associated domains in Hutchinson-Gilford Progeria Syndrome |
|
| Relations |
| BioSample |
SAMN14856594 |
| SRA |
SRX8294573 |
