|
| Status |
Public on Jul 01, 2022 |
| Title |
KDM1A KO hESC derived with CRISPR-Cas9 Bulk RNAseq HiSeq 4000 1297 |
| Sample type |
SRA |
| |
|
| Source name |
hESC H1
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: KDM1A KO hESC derived with CRISPR-Cas9
rna identifier: 1297
name in the manuscript: KDM1A KO Clone #1
|
| Treatment protocol |
hESC-derived cardiomyocytes were cultered on Vitronectin (VTN-N) coated plates in presence of differentiation medium and RNA extraction was performed around 15-18 of differentiation when the monolayer started beating
|
| Growth protocol |
hESCs H1 were grown on Vitronectin-coated plates in presence of E8 medium, dissociated using Accutase and differentiated into cardiomyocytes using the The PSC Cardiomyocyte Differentiation Kit (Thermo Fisher Scientific) according to the Manufacturer ‘s instruction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For bulk RNA-Seq libraries the RNA has been extracted using the Qiagen RNeasy Mini Kit according to manufacturer’s instructions
Bulk RNA libraries were generated using the human mRNA TruSeq Stranded library preparation KIT from Illumina.
Bulk RNA-Sequencing was performed using HiSeq4000 and Novaseq 6000 SP1 systems (Illumina) with 150 bp paired-end sequencing method
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
KDM1A KO hESC derived with CRISPR-Cas9 Bulk RNAseq HiSeq 4000
Bulk RNAseq HiSeq 4000
|
| Data processing |
Bulk RNA-Seq data validation, pairing and FastQC quality control was followed by trimming using BBDuk by setting a minimum read length of 35 bp and a minimum Phred-quality score of 25. After trimming quality control, high quality reads were mapped against the reference genome (GrCh38 release 91) using the STAR end-to-end alignment method and gene expression quantification performed with featureCounts. Data normalization was performed with the Trimmed Mean of M-values (TMM) method
The pre-processing of single cell RNA-Seq data that includes the identification of cell barcodes and the steps of UMI detection, extraction and processing was performed using UMI-tools 1.0.1. Read quality control (QC) analyses and filtering of high-quality reads, were executed using FastQC and BBDuk with default options of minimum size 35 bp and minimum quality score 25 to perform adapter and quality trimming. To align the filtered reads to a human genome reference (GrCh38 release 91) STAR 2.7.3a was used, while FeatureCounts 1.6.3 package was used to assign reads to genes.
Genome_build: GrCh38 release 91
|
| |
|
| Submission date |
Dec 01, 2021 |
| Last update date |
Jul 01, 2022 |
| Contact name |
Antonio Adamo |
| E-mail(s) |
antonio.adamo@kaust.edu.sa
|
| Organization name |
King Abdullah University of Science and Technology, KAUST
|
| Department |
Biological and Environmental Science and Engineering Division, BESE
|
| Lab |
Stem cells and diseases, STEMD
|
| Street address |
4700 KAUST, Thuwal
|
| City |
Jeddah |
| State/province |
Not in US |
| ZIP/Postal code |
23955-6900 |
| Country |
Saudi Arabia |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE189944 |
Fine-tuned KDM1A alternative splicing regulates human cardiomyogenesis through an enzymatic-independent mechanism |
|
| Relations |
| BioSample |
SAMN23551650 |
| SRA |
SRX13273868 |
