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| Status |
Public on May 31, 2022 |
| Title |
HSPCs, HLA-DR(+) rep3 |
| Sample type |
SRA |
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| Source name |
peripheral blood
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| Organism |
Homo sapiens |
| Characteristics |
tissue: peripheral blood
cell type: hematopoietic stem progenitor cells
phenotype: HLA-DR(+)
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
HLA-DR(+) HSPCs and HLA-DR(-) HSPCs were isolated by magnetic cell separation and fluorescence-activated cell sorting. SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio USA, San Jose, CA) was used for the construction of sequencing libraries.
cDNA libraries were prepared for sequencing using Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA) and Nextera XT Index Kit v2 set A/B/C/D (Illumina, San Diego, CA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Sample 6
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| Data processing |
Basecalls performed using bcl2fastq2 v2.20
Sequenced reads were mapped to GRCh38 whole genome using DRAGEN Bio-IT Platform (version 3.6.3).
Transcripts per million (TPM) were calculated using DRAGEN Bio-IT Platform (version 3.6.3).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include TPM values and raw counts values for each sample.
Supplementary_files_format_and_content: Matrix table with TPM values and raw gene counts for every gene and every sample
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| Submission date |
Sep 09, 2021 |
| Last update date |
Jun 01, 2022 |
| Contact name |
Noriaki Tsuji |
| Organization name |
Kanazawa University
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| Department |
Hematology
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| Street address |
13-1 Takaramachi
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| City |
Kanazawa |
| ZIP/Postal code |
920-8640 |
| Country |
Japan |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE183768 |
Transcriptome analysis of HLA-DR(+) HSPCs and HLA-DR(-) HSPCs in aplastic anemia patients |
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| Relations |
| BioSample |
SAMN21368256 |
| SRA |
SRX12121263 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5570611_wild_rep3.txt.gz |
634.2 Kb |
(ftp)(http) |
TXT |
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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