|
| Status |
Public on Apr 16, 2024 |
| Title |
#2 iAM-1 D9, P10, untransduced, n=1 |
| Sample type |
SRA |
| |
|
| Source name |
iAM-1 cells
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: wistar
transduction: untransduced
|
| Treatment protocol |
During the differentiation phase no doxycyclin was added to the culture medium. Lentiviral vectors containing the shRNA constructs were added shortly after the the initiation of differentiation
|
| Growth protocol |
iAM-1 cells were cultured in Advanced DMEM/F-12 (Thermo Fisher Scientific, cat# 12634010) supplemented with 2% FBS and 1⨯ GlutaMAX Supplement (Thermo Fisher Scientific).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was collected using the RNeasy Mini Kit. The quality of the RNA samples designated for RNA-Seq was confirmed using the Advanced Analytical Fragment Analyzer.
cDNA was generated from total RNA samples with RNA integrity numbers of 10 using the NEBNext Ultra Directional RNA library preparation method including polyA enrichment (New England Biolabs, cat# E7760S/L). Sequencing was performed on a NovaSeq 6000 system (Illumina, San Diego, CA). For each sample at least 40 million 150-bp paired-end reads were obtained.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
104528-001-002
|
| Data processing |
Read counting was performed in the DESeq2 software package (version 2-1.14) and in parallel normalized using depth normalization (counts per million, CPM) as well as length normalization (transcript per million, TPM).
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for the pooled samples of every gene
|
| |
|
| Submission date |
Oct 26, 2021 |
| Last update date |
Apr 16, 2024 |
| Contact name |
Pim van Gorp |
| E-mail(s) |
p.r.r.van_gorp@lumc.nl
|
| Organization name |
Leiden University Medical Center
|
| Department |
Experimental Cardiology
|
| Street address |
Albinusdreef 2
|
| City |
Leiden |
| State/province |
Zuid-Holland |
| ZIP/Postal code |
2333ZA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL25947 |
| Series (1) |
| GSE186626 |
RNA sequencing in iAM-1 differentiated cells and RnSbk2 knockdown |
|
| Relations |
| BioSample |
SAMN22581366 |
| SRA |
SRX12780612 |
