title: Library_1
organism: Mus musculus
description: Protocols: Day 7 differentiated mouse embryonic stem cells are collected as embryonic bodies, washed with PBS, dissociated with TrypLE Express Enzyme for 5 minutes, and Trypsin-EDTA for 3 minutes at 37C in intermittent pipetting. After dissociation, samples are inactivated with PBS+10%FCs, go through a filter (40 um), and spin down 1000rpm for 5 minutes. The samples were washed three times with PBS+10%FCS. Than, 10X Genomics 3' CellPlex Kit Set A (CMO sample multiplexing) protocol followed and continued with  Chromium Next GEM Single Cell 3ʹReagent Kits v3.1. The harvested embryonic bodies were washed three times with PBS, and prewarmed TrypLE was added in a 50 ml falcon tube and placed in a 37°C water bath while shaking with intermittent pipetting for disassociation.  Four minutes later, 3 ml Trypsin/EDTA was added, and the dissociation process continued for at least 7 minutes while visually checking the dissociation of the EB. The disassociation buffer was inactivated with PBS+10%FCS, strained with a 40 µM cell strainer to create a single-cell suspension, washed three times, and stained for cell surface marker staining or prepared for scRNA-seq.   mESCs-Medium: DMEM HyClone™ (cytiva SH30081), 15% - Fetal Bovine Serum (FBS) (Capricorn Scientific FBS-12A, CP18-2152), 1X - MEM Non-Essential Amino Acids Solution (100X) (Gibco 11140-035), 2mM - GlutaMAX™ Supplement (Gibco 35050061), 10mM - HyClone™ HEPES Buffer (cytiva SH30237.01), 1X - Penicillin-Streptomycin (100X) (Sigma-Aldrich P0781), 0.1mM - 2-Mercaptoethanol (50 mM) (Gibco 31350010), 1000U.ml -  ESGRO® Recombinant Mouse LIF Protein 10^7 units/ml (Sigma-Aldrich ESG1107).    Differentiation Medium:  IMDM, GlutaMAX™ Supplement (Gibco 31980048), 15% - FBS (Capricorn Scientific FBS-12A, CP18-2152), 1X - Penicillin-Streptomycin (100X) (Sigma-Aldrich P0781), 0.1 mM - 2-Mercaptoethanol (50 mM) (Gibco 31350010), 50 µg/ml - L-Ascorbic acid (Sigma-Aldrich A5960-25G), 150 μg/mL -Transferrin (Roche 10652202001)  Chromium Next GEM Single Cell 3' Reagent Kits v3.1 protocol has been followed. Chromium Next GEM Single Cell 3' Reagent Kits v3.1 protocol has been followed with dual indexing library construction.
attributes.tag: ENA first public
attributes.value: 2025-08-31
attributes.tag: INSDC center name
attributes.value: Erasmus MC
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-14678:Library_1
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell_line
attributes.value: ESC derived cell line
attributes.tag: cmo id
attributes.value: pool
attributes.tag: collection date
attributes.value: not collected
attributes.tag: common name
attributes.value: house mouse
attributes.tag: developmental stage
attributes.value: embryo stage
attributes.tag: geographic location (country and/or sea)
attributes.value: not collected
attributes.tag: individual
attributes.value: multiplexed pool 5
attributes.tag: isolate
attributes.value: not applicable
attributes.tag: organism part
attributes.value: embryoid body
attributes.tag: sample name
attributes.value: E-MTAB-14678:Library_1
attributes.tag: scientific_name
attributes.value: Mus musculus
attributes.tag: sex
attributes.value: XY
attributes.tag: strain
attributes.value: 129X1/SvJ