|
| Status |
Public on Dec 21, 2019 |
| Title |
HELA_WT1 |
| Sample type |
SRA |
| |
|
| Source name |
HeLa cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
genotype: wt
sequencing: single-end
|
| Growth protocol |
HeLa cells were cultured in DMEM (Sigma) supplemented with 10% fetal calf serum (Biochrom) and 50 µg/ml gentamycine (PAA).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from HeLa cells in biological quadruplicates using the nucleospin triprep kit (Macherey-Nagel).
Smart-seq2 (Picelli et al. 2013) from 5ng of RNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
base-calls were performed with Illumina bcl2fastq
demultiplexing was done using the assignRG package
cDNA reads were mapped to the hg19 genome assembly using NGM (v.4.12) Sedlazeck et al. 2013 and minimum sequence identity of 0.9
reads were assigned to gene features using the Rsubread package Liao et al. 2014
Genome_build: hg19
Supplementary_files_format_and_content: .txt gene-wise read-counts per sample
|
| |
|
| Submission date |
Dec 17, 2015 |
| Last update date |
Dec 21, 2019 |
| Contact name |
Martha Smets |
| E-mail(s) |
smets@bio.lmu.de
|
| Organization name |
Ludwig-Maximilians University Munich
|
| Department |
Department Biology II
|
| Street address |
Großhaderner Str. 2
|
| City |
Martinsried |
| ZIP/Postal code |
82152 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18460 |
| Series (1) |
| GSE76129 |
ZNF599 and DNMT3A coordinately control nuclear envelope organization by repression of SUN4 expression |
|
| Relations |
| BioSample |
SAMN04349623 |
| SRA |
SRX1490515 |
