ERC000011
ENA-CHECKLIST
2022-08-18T00:13:25Z
ENA-FIRST-PUBLIC
2022-08-18T00:13:25Z
ENA-LAST-UPDATE
SAMEA110472588
External Id
ETH Zurich, DBSSE
INSDC center name
2022-08-18T00:13:25Z
INSDC first public
2022-08-18T00:13:25Z
INSDC last update
public
INSDC status
ERS12570608
SRA accession
E-MTAB-11998:DAY11_ATAC
Submitter Id
ArrayExpress
broker name
mixed Hoik1; H9; Wibj2 and 409B2
cell_line
mixed fibroblast and embryonic stem cell
cell_type
human
common name
Protocols: We collected these single cell suspensions from an EB time point (day 4), the time points of neuronal induction (day 7, 9 and 11) and after embedding in matrigel and starting the neuronal differentiation process (day 12, 16, 18, 21, 26, 31 and 61). Multiple organoids of each line were pooled together to obtain a sufficient number of cells. For time points just after matrigel embedding, matrigel was dissolved in Cell Recovery Solution (Corning, 354253)​​ for 15 min at 4°C. Organoids were cut in halves and washed three times with HBSS without Ca2+/Mg2+ (STEMCELL technologies, 37250). Single cell suspensions were acquired by dissociation of the organoids with a papain-based dissociation (Miltenyi Biotec, 130-092-628). Each sample was divided into a sample to be processed for scRNAseq and a sample for scATACseq, cryopreserved in Cryostor CS10, moved to -80C in a MrFrosty before moving to liquid nitrogen storage the next day. They were kept in liquid nitrogen until processesing. The cryopreserved single cell suspensions of each time point were thawed by warming up the cryo for 1-2 minutes in a water bath at 37℃ and directly centrifuged in 10ml prewarmed DMEM with 10% FBS. Cells were washed twice with PBS + 5% BSA and filtered through a 40µm cell strainer (Flomi). Nuclei were isolated according to the protocol provided by 10x genomics (Demonstrated protocol CG000169 Rev D) using the low input protocol and a lysis time of 3 min. Cerebral organoids were generated from four different stem cell lines (H9, 409B2, Wibj2, Hoik1) simultaneously using a whole brain organoid differentiation protocol (Lancaster et al. 2013; https://doi.org/10.1038/nprot.2014.158). Single cell ATACseq libraries were generated with the Chromium Single Cell ATAC V1 Library & Gel Bead Kit. Nuclei encapsulation and library preparation were performed according to the manufacturer's protocol. Single cell ATACseq libraries were generated with the Chromium Single Cell ATAC V1 Library & Gel Bead Kit. Nuclei encapsulation and library preparation were performed according to the manufacturer's protocol.
description
mixed adult and embryo
developmental stage
normal
disease
wild type genotype
genotype
Homo sapiens
organism
Homo sapiens
organism
mixed skin and inner cell mass
organism part
Homo sapiens
scientific_name
DAY11_ATAC
title