|
| Status |
Public on Mar 15, 2023 |
| Title |
HLF_siCo_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
HLF cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HLF cells
treatment: Nonsense
|
| Growth protocol |
Cells were cultured in Dulbecco’s modified eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37°C and 5% CO2 in a humidified incubator.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated 24 hours after transfection using the NucleoSpin RNA II kit (Macherey Nagel, Macherey-Nagel). Only samples with an RNA integrity number (RIN) > 7 were considered for RNA sequencing.
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
Nonsense_3NTC
|
| Data processing |
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
TPM abundance estimates, generated with kallisto quant 0.4.6
Assembly: hg19
Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.
|
| |
|
| Submission date |
Jul 08, 2022 |
| Last update date |
Mar 18, 2023 |
| Contact name |
Carsten Sticht |
| Organization name |
University Heidelberg
|
| Department |
ZMF
|
| Street address |
Theodor-Kutzer-Ufer
|
| City |
Mannheim |
| ZIP/Postal code |
68169 |
| Country |
Germany |
| |
|
| Platform ID |
GPL23227 |
| Series (2) |
| GSE207722 |
YAP/TAZ-dependent expression of lncRNAs [HLF] |
| GSE207724 |
YAP/TAZ-dependent expression of lncRNAs |
|
| Relations |
| BioSample |
SAMN29594716 |
| SRA |
SRX16085221 |
