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| 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
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| 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.
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| 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.
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| Contributor(s) |
Vo DN, Sitnicka E |
| Citation(s) |
38484189 |
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| Submission date |
Jun 23, 2023 |
| Last update date |
Jun 28, 2024 |
| Contact name |
Dang Nghiem Vo |
| E-mail(s) |
dang_nghiem.vo@med.lu.se
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| Phone |
(+46) 729720931
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| Organization name |
Lund University
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| Department |
Department of Laboratory Medicine
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| Lab |
Ewa Sitnicka Lab
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| Street address |
B12 Biomedical Center, Klinikgatan 26
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| City |
LUND |
| ZIP/Postal code |
22242 |
| Country |
Sweden |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (1) |
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| Relations |
| BioProject |
PRJNA986935 |
| 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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