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Status |
Public on Dec 12, 2022 |
Title |
mESC Day4_HMG20A KO RNA_Rep1 |
Sample type |
SRA |
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Source name |
mES V6.5
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Organism |
Mus musculus |
Characteristics |
cell line: mES V6.5 cell type: embryonic stem cell genotype: Hmg20A knock out treatment: Cardiomyocyte differentiation
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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.
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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.
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
RNA-seq
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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
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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 |
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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 |
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Relations |
BioSample |
SAMN28088288 |
SRA |
SRX15148536 |