|
| Status |
Public on Nov 15, 2020 |
| Title |
Tnfaip2-/- EBs with PA/PC treatment rep2 [KO_EB_PAPC_2] |
| Sample type |
SRA |
| |
|
| Source name |
embryoid bodies
|
| Organism |
Mus musculus |
| Characteristics |
age: E14
cell type: embryonic stem cells
genotype: Tnfaip2-/-
agent: palmitic acid (PA) and palmitoyl-L-carnitine (PC) treatment
|
| Treatment protocol |
3.75 × 10,000 ES cells/ml were re-suspended and rows of 27μl drops (1000 cells per drop) on the up-turned inner surface of the lid of the 10cm tissue culture dish were made and incubated at 37°C for 3 days to form EBs. The EBs (at day 0) were plated onto 0.1% gelatin coated tissue culture dishes to initiate in vitro differentiation by incubating for another 3 days at 37°C MEF medium containing 15% KnockOut™ D-MEM supplemented with Knockout Serum Replacement, L-glutamine, penicillin/streptomycin, nonessential amino acids. For the rescue experiments (samples KO_EB_PAPC_1,2,3), the EBs were supplemented with 8μM each of palmitic acid (PA) and palmitoyl-L-carnitine (PC). After 3 days of in vitro differentiation the EBs were harvested.
|
| Growth protocol |
ES cells were plated on gelatin-coated plates and cultured using mouse ES cell medium containing 15% KnockOut™ D-MEM supplemented with Knockout Serum Replacement, L-glutamine, penicillin/streptomycin, nonessential amino acids, β-mercaptoethanol, and 1,000 U/ml Leukemia Inhibitory Factor.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from embryoid bodies using the Masterpure RNA Purification Kit (Epicentre) as per manufacturer’s instruction.
Library preparation was done using Illumina’s TruSeq RNA v2 library preparation kit following the manufacturer’s description.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
KO_EB_PAPC_2
palmitic acid (PA) and palmitoyl-L-carnitine (PC) treatment
|
| Data processing |
Reads were extracted in FastQ format using Illumina’s bcl2fastq v2.20.0.422. Read mapping was done with STAR (version 2.7.2b, parameters: --alignIntronMax 100000 --outSJfilterReads --outSAMmultNmax Unique --outFilterMismatchNoverLmax 0.04) to the mouse reference genome (GRCm38) with the Ensembl gene annotation (release 99). Read counting was performed with FeatureCounts (version 1.6.5, multi-mapping or multi-overlapping reads were not counted, stranded mode was set to “–s 2”).
Genome_build: GRCm38
Supplementary_files_format_and_content: csv file containing read counts per gene over all samples
|
| |
|
| Submission date |
Apr 16, 2020 |
| Last update date |
Nov 15, 2020 |
| Contact name |
Philipp Koch |
| Organization name |
Leibniz Institute on Aging - Fritz Lipmann Institute
|
| Department |
Core Facility Life Science Computing
|
| Street address |
Beutenbergstraße 11
|
| City |
Jena |
| ZIP/Postal code |
07745 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE134302 |
Tnfaip2/Exoc3 driven lipid metabolism is essential for stem cell differentiation & organ homeostasis |
| GSE148758 |
Tnfaip2/Exoc3 driven lipid metabolism is essential for stem cell differentiation & organ homeostasis [Mus musculus, 2] |
|
| Relations |
| BioSample |
SAMN14604370 |
| SRA |
SRX8121687 |
