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Series GSE230182 Query DataSets for GSE230182
Status Public on Jun 30, 2023
Title Cellular Indexing of Transcriptomes and epitopes sequencing (CITE-seq) analysis to investigate the impact of granulocyte-colony stimulating factor on CRISPR/Cas9 gene edited human hematopoietic stem cell function
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Our research has demonstrated that G-CSF impedes engraftment of CRISPR-Cas9 gene edited human hematopoietic stem cells (HSCs) by exacerbating p53-mediated DNA damage response. Results in this study suggest that the potential for G-CSF to exacerbate HSC toxicity mediated by DNA-damaging nucleases should be considered in autologous HSC gene therapy clinical trials.
Overall design Human CD34+ cells edited with Cas9 alone (Cas9 group), Cas9+AAVS1-targeting gRNA (RNP group), or Cas9+AAVS1-targeting gRNA+GSE56 (RNP/GSE56 group) were transplanted into busulfan-conditioned NSG mice, and these mice subsequently received 3 days of PBS or G-CSF. Then, each mouse was euthanized and harvested for bone marrow cells and human CD34+cells were isolated using immunomagnetic beads. These CD34+ cells from a total of 6 mice were individually stained with Total seq B CITE-seq antibodies (CD38, CD45RA, CD90, CD49f) + hashtag oligo antibodies 1-6. Then, FACS sort was used to purify ~2,500 cells from each group, and subsequently pooled for CITE-seq library preparation/sequencing. Seurat was used to demultiplex data into 6 individual groups, and differential gene expression analysis was performed to evaluate the impact of G-CSF within Cas9, RNP and RNP/GSE56 groups.
Contributor(s) Larochelle A, Redekar N, Chen V
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Submission date Apr 20, 2023
Last update date Jun 30, 2023
Contact name Daisuke Araki
Phone 301-827-1467
Organization name National Institutes of Health
Street address 9000 Rockville Pike
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (2)
GSM7191372 human CD34+ cells, CITE-seq GEX
GSM7191373 human CD34+ cells, CITE-seq Surface
BioProject PRJNA957792

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Supplementary file Size Download File type/resource
GSE230182_barcodes.tsv.gz 44.3 Kb (ftp)(http) TSV
GSE230182_features.tsv.gz 325.8 Kb (ftp)(http) TSV
GSE230182_matrix.mtx.gz 123.9 Mb (ftp)(http) MTX
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Processed data are available on Series record

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