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| Status |
Public on Apr 08, 2024 |
| Title |
uncultured, scRNAseq |
| Sample type |
SRA |
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| Source name |
cord blood
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| Organism |
Homo sapiens |
| Characteristics |
tissue: cord blood
cell type: HSPC
genotype: CB_d0
treatment: uncultured
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| Growth protocol |
Human HSPCs were cultured in serum-free conditions with StemSpan SFEM II (StemCell Technologies, 9655) supplemented with 1% Pen/Strep, 1% L-glutamine, human FLT3-L (100 ng/mL, human TPO (50 ng/mL), human SCF (100 ng/mL) (Thermofisher Scientific15140122, 25030081 PHC9411, PHC9513, and PHC2113), human low-density lipoprotein (10 μg/mL), SR1 (500 nM) and UM171 (35 nM) (StemCell Technologies 2698, 72352, and 72914). Cells were cultured at 37 °C and 5% CO2, re-plated as necessary to maintain a cell density of ≤ 1x10^6/mL, and half media changes were performed every other day.
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| Extracted molecule |
total RNA |
| Extraction protocol |
CB HSPCs were sorted after thawing (7AAD- CD34+ CD38- CD90+) and sequenced (uncultured) or transduced with control (empty vector, EV), MYCT1 OE, or MYCT1 KD and sorted again (7AAD- CD34+ CD38- CD90+ GFP+) 72 hours after transduction. Cells were sorted into PBS 0.04% Ultrapure BSA (Thermofisher Scientific AM2616) using a BD FACS Aria cell sorter.
A Chromium single cell instrument (10x genomics) was used for the generation of single-cell gel beads in emulsion. In brief, single-cell suspension of cells in 0.4% BSA-PBS were added to each channel on the 10X chip. Cells were partitioned with Gel Beads into emulsion in the Chromium instrument where cell lysis and barcoded reverse transcription of RNA occurred following amplification. scRNA-seq libraries were prepared by using the Chromium single-cell 3′ library and gel bead kit v3 (10x Genomics).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
CB_d0
10x Genomics
aggregatedAll_barcodes.tsv.gz
aggregatedAll_features.tsv.gz
aggregatedAll_matrix.mtx.gz
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| Data processing |
Sequencing was performed on the Illumina NovaSeq 6000 system.
Sequence data was mapped to the human reference genome (refdata-cellranger-GRCh38-1.2.0) using cellranger count.
Assembly: GRCh38
Supplementary files format and content: Annotated sequence data that contain cell barcodes (tsv), features (tsv) and gene expression matrix (mtx). Processed data files for the aggregated data of all samples is also provided (“aggregatedAll_”).
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| Submission date |
May 11, 2023 |
| Last update date |
Apr 08, 2024 |
| Contact name |
Júlia Aguadé-Gorgorió |
| Organization name |
University of California Los Angeles
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| Department |
Molecular, Cell and Developmental Biology
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| Lab |
Mikkola lab
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| Street address |
615 Charles E Young Drive South
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| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE232361 |
MYCT1 Controls Environmental Sensing in human Hematopoietic Stem Cells [scRNA-seq] |
| GSE232362 |
MYCT1 Controls Environmental Sensing in human Hematopoietic Stem Cells. |
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| Relations |
| BioSample |
SAMN35052797 |
| SRA |
SRX20302721 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7329389_CB_d0_seq1_barcodes.tsv.gz |
66.4 Kb |
(ftp)(http) |
TSV |
| GSM7329389_CB_d0_seq1_features.tsv.gz |
311.3 Kb |
(ftp)(http) |
TSV |
| GSM7329389_CB_d0_seq1_matrix.mtx.gz |
52.9 Mb |
(ftp)(http) |
MTX |
| GSM7329389_CB_d0_seq2_barcodes.tsv.gz |
65.7 Kb |
(ftp)(http) |
TSV |
| GSM7329389_CB_d0_seq2_features.tsv.gz |
311.3 Kb |
(ftp)(http) |
TSV |
| GSM7329389_CB_d0_seq2_matrix.mtx.gz |
42.6 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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