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| Status |
Public on Feb 22, 2021 |
| Title |
ET3HSC |
| Sample type |
SRA |
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| Source name |
hematopoietic stem cells (HSCs)
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| Organism |
Homo sapiens |
| Characteristics |
sample type: essential thrombocythemia patient
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| Treatment protocol |
no treatment
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| Growth protocol |
patient samples
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
BMMNCs were stained with a lineage-marker cocktail (biotinylated anti-CD2, -CD3, -CD11b, -CD14, -CD15, -CD16, -CD19, -CD56, -CD123, and -CD235a) and subsequently magnetically labeled with Anti-Biotin MicroBeads (Miltenyi Biotec). Lineage-negative stem and progenitor cells (Lin- cells) were obtained by depleting the magnetically-labeled cells after passing through LS columns (Miltenyi Biotec). Lin- cells were stained with antibodies of PE-cy7-conjugated anti-CD38 (BD Biosciences), APC-conjugated anti-CD34 (BD Biosciences), Percp-cy5-conjugated anti-CD45RA (BD Biosciences) and APC-cy7-conjugated anti-CD123 (BD Biosciences). HSCs (CD34+CD38-CD45RA-CD123-) and MEPs (CD34+CD38+CD45RA-CD123-) were sorted with an Aria III instrument (BD Biosciences)
Briefly, cells were lysed in lysis buffer (Novogene), and the direct first-strand cDNA was synthesized from polyA-selected RNA with a SMARTer® Ultra Low RNA Kit for Illumina® Sequencing (Clontech) (Cat. #. 634888). cDNAs were purified using AMPure XP beads, followed by LD-PCR, to yield the full-length first-strand cDNA. Double-stranded cDNA was synthesized and amplified with an Advantage® 2 PCR kit. After generating the sequencing libraries using the NEBNext® UltraTM DNA Library Prep Kit for Illumina® (NEB, USA)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
shilabsubmit_gene_count_matrix.csv
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| Data processing |
remove low-quality reads and adapters by trimmomatic
aligning by hisat2
mark and remove duplicates by Picard
quantification by stringtie
Genome_build: hg38(gencode v27)
Supplementary_files_format_and_content: csv
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| Submission date |
Mar 05, 2018 |
| Last update date |
Feb 22, 2021 |
| Contact name |
Coral Tong |
| Organization name |
Institute of Hematology & Blood Disease Hospital
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| Street address |
288 Nanjing Rd, Heping
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| City |
Tianjin |
| ZIP/Postal code |
300020 |
| Country |
China |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE111410 |
Hematopoietic Stem Cell Heterogeneity in JAK2 V617F+ Essential Thrombocythemia |
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| Relations |
| BioSample |
SAMN08636087 |
| SRA |
SRX3765292 |
| 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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