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Sample GSM5657977 Query DataSets for GSM5657977
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
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
BioSample SAMN22581366
SRA SRX12780612

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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