Mus musculus
Protocols: Cells were grown on 0.1% gelatin-coated plates, using KnockOutTM DMEM supplemented with 10% FBS, 2 mM L-glutamine (Thermo Fisher Scientific, 25030024), 0.1 nM β-mercaptoethanol, 1x NEAA, 1x antibiotic and antimycotic solution and 1 µM retinoic acid (RA; Sigma-Aldrich, R2625) for 4 days. Single-cell suspensions were fixed using the Evercode™ Cell Fixation workflow compatible with the Parse Biosciences Evercode WT Mini scRNA-seq kit. Briefly, freshly isolated cells were washed and incubated with the fixation reagents provided in the Parse Biosciences fixation kit to preserve endogenous RNA profiles and stabilize cellular material. Fixed cells were subsequently washed, counted, and stored under recommended conditions prior to whole-transcriptome split-pool combinatorial barcoding library preparation. Fixed single-cell suspensions were processed using the Parse Biosciences Evercode™ WT Mini scRNA-seq kit. Cells underwent split-pool combinatorial barcoding, in which cells were repeatedly distributed into wells and labeled with unique molecular barcodes. During the first barcoding round, cell-specific barcodes were incorporated and reverse transcription was performed to generate barcoded cDNA from cellular RNA. Subsequent barcoding rounds further labeled cDNA molecules with additional barcode sequences, enabling combinatorial indexing of individual cells. The resulting barcoded cDNA was pooled, amplified, and prepared for next-generation sequencing. Barcoded cDNA was fragmented and processed to generate sequencing-compatible library molecules containing cell-identifying barcode sequences and transcript-derived fragments. Libraries were amplified, purified, and assessed for quality and concentration before sequencing.
ENA first public
2026-07-12
INSDC center name
Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria, Santander, Spain
INSDC status
public
Submitter Id
E-MTAB-17228:Sublibrary_2
broker name
ArrayExpress
cell line
Differentiated mESC
collection date
not collected
common name
house mouse
developmental stage
Differentiated mouse ESC
genotype
pool2
geographic location (country and/or sea)
not collected
i5 forward seq
GGTTGGAC
i7 forward seq
ACTGATAG
isolate
not applicable
organism part
inner cell mass
sample name
E-MTAB-17228:Sublibrary_2
scientific_name
Mus musculus
wells
WT_rep1:A1toA4;WT_rep2:A5toA8;KO_rep1:A9toA12