E-MTAB-14625:d10_CHIR_4days_c
2025-11-14
ENA first public
ERC000011
ENA-CHECKLIST
Max Planck Institute of Molecular Cell Biology and Genetics
INSDC center name
public
INSDC status
ERS22446166
SRA accession
E-MTAB-14625:d10_CHIR_4days_c
Submitter Id
ArrayExpress
broker name
H9-hESC
cell_line
pancreatic cell
cell_type
not collected
collection date
human
common name
CHIR99021 and DMSO
compound treatment
10
day
days in culture
4
day
days of treatment chir
3
day
days of treatment dmso
Protocols: hESC-derived PP-organoids (Gonçalves et al 2021) were dissociated into single cells with TrypLE and snap-frozen for RNA extraction. Total RNA was subjected to a modified version of SMARTseq-2 protocol published by Picelli et al. 2013 (doi: 10.1038/nmeth.2639). In short, total RNA was isolated with RNeasy Micro kit (Qiagen) and eluted in nuclease free water.  mRNA was isolated from on average 450 ng total RNA by poly-dT enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) according to the manufacturer’s instructions. Samples were then directly subjected to the workflow for strand-specific RNA-Seq library preparation (Ultra II Directional RNA Library Prep, NEB). For ligation NEB Next Adapter for Illumina of the NEB Next Multiplex Oligos for Illumina Kit were used. After ligation, adapters were depleted by an XP bead purification (Beckman Coulter) adding the beads solution in a ratio of 0.9:1 to the samples. Unique dual indexing was done during the following PCR enrichment (12 cycles) using amplification primers carrying the same sequence for i7 and i5 index (i5: AAT GAT ACG GCG ACC ACC GAG ATC TAC AC NNNNNNNN ACA TCT TTC CCT ACA CGA CGC TCT TCC GAT CT, i7: CAA GCA GAA GAC GGC ATA CGA GAT NNNNNNNN GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T). After two more XP bead purifications (0.9:1), libraries were quantified using the Fragment Analyzer (Agilent).
description
none
disease
PDX1-P2A-H2B-GFP and NEUROG3-P2A-tagRFP-T-NLS
genotype
not collected
geographic location (country and/or sea)
CHIR_4days
growth condition
not applicable
isolate
Homo sapiens
organism
Homo sapiens
organism
cell line
organism part
embryonic stem cell
progenitor cell type
c
replicate
Homo sapiens
scientific_name
d10_CHIR_4days_c
title