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GEO help: Mouse over screen elements for information. |
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Status |
Public on Jun 30, 2023 |
Title |
human CD34+ cells, CITE-seq GEX |
Sample type |
SRA |
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Source name |
CD34+ cells
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Organism |
Homo sapiens |
Characteristics |
tissue: CD34+ cells cell type: Hematopoietic stem and progenitor cells treatment: Granulocyte-colony stimulating factor or PBS antibodies/tags: None
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Extracted molecule |
total RNA |
Extraction protocol |
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. 3’ v3.1 GEX libraries were constructed according to 10x Genomics protocol. 3’ v3.1 GEX and ADT libraries were pooled in a 2:1 ratio and sequenced with an Illumina NovaSeq SP flow cell. Target sequencing depth for the GEX libraries was 20,000 read pairs per cell and 5,000 read pairs per cell for the ADT libraries.
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Library strategy |
OTHER |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
10x Genomics GEX
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Data processing |
library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing) Illumina sequencer’s base call files (BCLs) were demultiplexed, for each flow cell directory, into FASTQ files using Cellranger mkfastq with default parameters (v 6.1.2) in NIH Helix/Biowulf High Performance Computation (HPC) system. FASTQ files were then processed using Cellranger Antibody Capture count with default parameters in NIH Helix/Biowulf HPC system. Internally, the software relies on STAR for aligning reads to a pre-build filtered human reference genome relying on GRCh38, while genes are quantified using ENSEMBL genes as gene model. The output of Cellranger is a filtered gene-barcode matrix containing the UMI counts for each gene. Assembly: GRCh38 Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
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Submission date |
Apr 20, 2023 |
Last update date |
Jun 30, 2023 |
Contact name |
Daisuke Araki |
E-mail(s) |
daisuke.araki@nih.gov
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Phone |
301-827-1467
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Organization name |
National Institutes of Health
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Street address |
9000 Rockville Pike
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City |
Bethesda |
State/province |
MD |
ZIP/Postal code |
20892 |
Country |
USA |
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Platform ID |
GPL24676 |
Series (1) |
GSE230182 |
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 |
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Relations |
BioSample |
SAMN34267581 |
SRA |
SRX20026152 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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