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Sample GSM6103006 Query DataSets for GSM6103006
Status Public on Dec 12, 2022
Title mESC Day2_HMG20A KO RNA_Rep1
Sample type SRA
 
Source name mES V6.5
Organism Mus musculus
Characteristics cell line: mES V6.5
cell type: embryonic stem cell
genotype: Hmg20A knock out
treatment: Cardiomyocyte differentiation
Treatment protocol On differentiation day 0, naïve wild type and Hmg20a KO mESCs (2i+LIF) were adapted to primed state in differentiation media (DMEM, Sigma) supplemented with 10% FCS, 2 mM L-glutamine, 1% nonessential amino acids, 0.1 mM β-mercaptoethanol, 1000 U/mL leukemia inhibitory factor (LIF) for 2 days. Hanging drops containing 1000 cells were prepared in 25 µl of differentiation media (without LIF) supplemented with 50 µg/ml vitamin C. On differentiation day 6 (4 days in suspension), each droplet containing one EB was carefully transferred onto a 0.1%-gelatin-coated 24-well plate.
Growth protocol mESCs were cultured on 0.1%-gelatin-coated 6-well plates in N2B27 medium supplemented with 50 μM β-mercaptoethanol, 2 mM L-glutamine, 0.1% Sodium bicarbonate, 0.11% bovine serum albumin fraction V, 1000 units/ml recombinant mouse leukemia inhibitory factor (LIF), 1 µM PD0325901 (MEK inhibitor) and 3 µM CHIR99021 (GSK3 inhibitor). Every two days, cells were passaged at a density of 1.4x105 cells/well.
Extracted molecule polyA RNA
Extraction protocol At indicated timepoints of differentiation total RNA was harvested using Rneasy mini columns with on-column Dnase digestion (QUIAGEN)
Performed by NOVOGENE using TruSeq® Stranded Total RNA LT-Ribo-Zero Gold kit (Illumina RS-122–2301/2) or others.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description RNA-seq
Data processing Paired end raw FASTQ files were quality and adaptor trimmed using trimGalore v.1.18
Alignment of the trimmed FASTQ files against the mm9 genome build was performed using hisat2 v.2.2.1 with “--min-intronlen 30 --max-intronlen 3000” parameters
Based on the BAM files and the mouse mm9 GTF read counts per gene for each sample were calculated using the summarizedOverlaps function of the GenomicAlignments R package
The resulting read counts were normalized using DESeq2 v.1.28.1.
DESeq2 was used for the identification of differentially expressed genes
Assembly: mm9
Supplementary files format and content: CSV of raw sequencing counts per gene
 
Submission date May 04, 2022
Last update date Dec 12, 2022
Contact name Marek Bartkuhn
E-mail(s) marek.bartkuhn@gen.bio.uni-giessen.de
Organization name Justus-Liebig-University Giessen
Department Biomedical Informatics and Systems Medicine
Street address Aulweg 132
City Giessen
State/province Hessen
ZIP/Postal code 35392
Country Germany
 
Platform ID GPL24247
Series (2)
GSE202198 The H2A.Z.1/PWWP2A/NuRD-associated protein HMG20A controls early head and heart developmental transcription programs [RNA_CM_AH]
GSE202199 The H2A.Z.1/PWWP2A/NuRD-associated protein HMG20A controls early head and heart developmental transcription programs
Relations
BioSample SAMN28088282
SRA SRX15148542

Supplementary file Size Download File type/resource
GSM6103006_KO_pr_1.csv.gz 104.3 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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