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Series GSE155683 Query DataSets for GSE155683
Status Public on Apr 19, 2021
Title A single cell atlas of human cornea that defines its development, limbal progenitor cells and their interactions with the immune cell
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary To study the development and composition of human ocular surface, we performed single cell (sc) RNA-Seq at key embryonic, fetal and adult stages and generated the first atlas of the corneal and conjunctival cell types from development to adulthood. The conjunctival epithelium is the first to be specified in the epithelial layer , followed by the corneal epithelium and the establishment of proliferative epithelial progenitors, which predate the formation of limbal niche by a few weeks. Bioinformatic comparison of adult cell clusters identified GPHA2,a novel cell-surface marker for quiescent limbal stem cells (qLSCs), whose function is to maintain qLSCs self-renewal. Combining scRNA- and ATAC-Seq analysis, we identified multiple upstream regulators for qLSCs and transit amplifying (TA) cells and demonstrated a close interaction between the immune cells and epithelial stem and progenitor cells in the cornea. Single cell RNA-Seq analysis indicated loss of qLSCs and acquisition of proliferative limbal epithelial progenitor markers during limbal epithelial cell expansion: this phenomenon was independent of culture method used. Extending the single cell analyses to Keratoconus, we were able to reveal activation of collagenase in the corneal stroma and a reduced pool of TA cells in the corneal epithelium as two key mechanistic changes underlying the disease phenotype. Our scRNA-Seq data comparisons of developing and adult cornea and conjunctiva provide a unique resource for defining pathways/genes that could lead to improvement in ex vivo expansion methods for cell based replacement therapies and better understanding and treatment of ocular surface disorders.
 
Overall design scRNA-Seq and scATAC-Seq of 17 human developing cornea/conjunctiva (10-21 post-conception weeks), 4 adult cornea/conjunctiva and 8 human cornea-scleral rings
 
Contributor(s) Collin J, Queen R, Zerti D, Moyse N, Bojic S, Molina MM, Reynold G, Yang C, Hussain R, Coxhead JM, Lisgo S, Henderson D, Joseph A, Rooney P, Ghosh S, Connon C, Haniffa M, Figueiredo F, Armstrong L, Lako M
Citation(s) 33865984
Submission date Aug 04, 2020
Last update date Jul 26, 2021
Contact name Majlinda Lako
Organization name Newcastle University
Department Institute of Genetic Medicine and Institute for Ageing
Street address International Centre for Life, Central Parkway
City Newcastle Upon Tyne
ZIP/Postal code NE1 3 BZ
Country United Kingdom
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (32)
GSM4710450 RNA-Seq Dev Cor/Conj 10PCW 14615
GSM4710451 RNA-Seq Dev Cor/Conj 10PCW 14849
GSM4710452 RNA-Seq Dev Cor/Conj 12PCW 14823
Relations
BioProject PRJNA655218
SRA SRP275814

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE155683_additional1.csv.gz 9.2 Mb (ftp)(http) CSV
GSE155683_additional2.csv.gz 17.6 Mb (ftp)(http) CSV
GSE155683_additional3.csv.gz 42.7 Mb (ftp)(http) CSV
GSE155683_counts_10PCW.txt.gz 2.1 Mb (ftp)(http) TXT
GSE155683_counts_12PCW.txt.gz 50.9 Mb (ftp)(http) TXT
GSE155683_counts_13PCW.txt.gz 24.0 Mb (ftp)(http) TXT
GSE155683_counts_14PCW.txt.gz 32.4 Mb (ftp)(http) TXT
GSE155683_counts_16PCW.txt.gz 32.2 Mb (ftp)(http) TXT
GSE155683_counts_17_18PCW.txt.gz 21.1 Mb (ftp)(http) TXT
GSE155683_counts_20_21PCW.txt.gz 56.2 Mb (ftp)(http) TXT
GSE155683_counts_adult_cornea.txt.gz 60.5 Mb (ftp)(http) TXT
GSE155683_peaks.csv.gz 125.3 Mb (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record

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