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Series GSE235708 Query DataSets for GSE235708
Status Public on Jun 30, 2023
Title In vitro differentiated CD56-positive ILC transcriptional profiling via scRNA-seq
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary The innate cytotoxic Natural Killer (NK) cells emerged during hematopoiesis through a linear model of human NK development, yet how in vitro model of NK differentiation recapitulates in vivo process is largely under-explored. Here, we established that NK cell trajectory in vitro can be divided into 4 stages by sequential acquisition of CD161, CD56 and CD94 in which CD56 bifurcation can separate Stage 3a (CD56-) as ILC-precursor that can further give rise to stage 3b (CD56+) and stage 4 (CD94+). Re-plating results together with clonal tracing between S3b, S4 and ILC3 subsets supported a diverging developmental point between NK and ILC3 lineages occurs at the S3a stage and accompanied by the loss of the ILC3 potential as NK cell maturation progress from S3b toward S4. Single-cell transcriptomic and RNA-velocity connected the NK cytotoxic trajectory with a coordinated network of transcription factors (TFs) that are highly compatible with primary NK cell gene program.
 
Overall design CD56-positive ILC generated from in vitro differentiation culture after 4 weeks, further undegone column-purification for Lineage-postive cells removal. Purifed CD56-positive ILC cells are subjected to transcriptomic profiling via single-cell RNA sequencing with 10X Genomics platform.
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Authors state:
raw FASTQ files cannot be uploaded due to compliance with GDPR guildlines for human samples.
 
Contributor(s) Vo DN, Sitnicka E
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Submission date Jun 23, 2023
Last update date Jun 30, 2023
Contact name Dang Nghiem Vo
E-mail(s) dang_nghiem.vo@med.lu.se
Phone (+46) 729720931
Organization name Lund University
Department Department of Laboratory Medicine
Lab Ewa Sitnicka Lab
Street address B12 Biomedical Center, Klinikgatan 26
City LUND
ZIP/Postal code 22242
Country Sweden
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (1)
GSM7508264 CD56 ILC, in vitro, week 4, scRNAseq
Relations
BioProject PRJNA986935

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Supplementary file Size Download File type/resource
GSE235708_RAW.tar 89.6 Mb (http)(custom) TAR (of MTX, TXT)
Raw data not provided for this record
Processed data provided as supplementary file

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