2024-06-01
ENA first public
ERC000011
ENA-CHECKLIST
UCL
INSDC center name
public
INSDC status
ERS20170129
SRA accession
E-MTAB-11528_2:HCA_LNG13237416
Submitter Id
week
age
ArrayExpress
broker name
not collected
collection date
human
common name
Protocols: Lung tissue for this project was obtained from the MRC-Wellcome Trust Human Developmental Biology Resource (https://www.hdbr.org). The HDBR obtain human embryonic and fetal samples from medical or surgical terminations of pregnancy. We requested lung tissue samples from fetuses aged between 8 and 20 post-conception weeks (pcw). We received whole lungs or lung fragments in refrigerated Hibernate E medium. Any trachea or non-lung tissue was removed by dissection. After removing culture medium from organoids and washing with PBS, 1 ml ice-cold Matrigel Cell Recovery Solution (Corning, 354253) was added per well and incubated for 45 min at 4°C. Organoids were washed with ice-cold PBS, centrifuged at 200 g, 4°C, then utilized in subsequent experiments. For RNA extraction, organoids were lysed in 350 μl RLT buffer and total RNA was extracted using the RNeasy Mini Kit (Qiagen), according to manufacturer’s instructions. RNA yields were measured using Nanodrop 1000. Single-cell gene expression organoid libraries were built using 10X Chromium Single Cell 5' v2 kit. CD45+ cells were thawed and counted, assessing viability using Trypan Blue. Cells were stained using the TotalSeq™- C antibody panel (Biolegend) where possible (some samples were not stained), prior to immediate processing for 10x 5’ single-cell capture using the Chromium Next GEM Single Cell V(D)J Reagent Kit, v 1.1, according to the manufacturer’s protocol. The Chromium Next GEM Single Cell V(D)J Reagent Kit, v 1.1 was used for scRNAseq library construction for unstained samples.  The manufacturer’s protocol (10X Genomics) was followed using individual Chromium i7 Samples Indices. abTCR or BCR enrichment
description
developmental stage
normal
disease
not collected
geographic location (country and/or sea)
IL-1β organoid of human embryo
growth condition
HDBR16389
individual
not applicable
isolate
Homo sapiens
organism
Homo sapiens
organism
lung
organism part
10x 5' v2
protocol
Homo sapiens
scientific_name
male
sex
HCA_LNG13237416
title