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| Status |
Public on Jan 08, 2024 |
| Title |
Dox_ER_HSCs_01_S4 |
| Sample type |
SRA |
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| Source name |
Hematopoietic
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| Organism |
Mus musculus |
| Characteristics |
tissue: Hematopoietic
cell type: HSC
genotype: ETV6-RUNX1
treatment: Dox food for 2 weeks
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using the Norgen single cell RNA purification kit (51800, Norgen Biotech)
Library preparation was performed using SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (634418, TaKaRa). Library concentration was measured using QuantIT 1X dsDNA HS Assay Kit (Q33232, Thermo Fisher), and quality was assessed on 5200 Fragment Analyzer™ 12-capillary (M3510AA, Agilent) using DNF-930 dsDNA Reagent Kit, 75 bp – 20,000 bp (K0500, Agilent).
The library pool was diluted to a final concentration of 1.25 nM and sequenced on a NovaSeq 6000 System (20012850, Illumina) using NovaSeq 6000 S2 Reagent Kit (2x100 paired end cycles) (20012861, Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Demultiplexing was performed using the bcl2fastq2 software with default settings, and a raw quality control was performed.
Alignment to the Mouse GRCm38 was performed using the HISAT2 software.
Assembly of the alignments into full transcripts and quantification was performed using the StringTie software.
Differentially expressed genes analysis was performed using DESeq2. Gene set enrichment analysis was performed as previously described (Eldeeb et al., 2023; Subramanian et al., 2005).
Assembly: Mouse GRCm38
Supplementary files format and content: Tab-delimited file includes normalized counts (TPM)
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| Submission date |
Jul 26, 2023 |
| Last update date |
Jan 08, 2024 |
| Contact name |
Mohamed Eldeeb |
| E-mail(s) |
mohamed.eldeeb@med.lu.se
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| Organization name |
Lund University
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| Street address |
DMH, BMC B12
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| City |
Lund |
| ZIP/Postal code |
221 84 |
| Country |
Sweden |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE239340 |
ONTOGENY SHAPES THE ABILITY OF ETV6-RUNX1 TO ENHANCE HEMATOPOIETIC STEM CELL SELF-RENEWAL AND DISRUPT EARLY LYMPHOPOIESIS [in vivo] |
| GSE239344 |
ONTOGENY SHAPES THE ABILITY OF ETV6-RUNX1 TO ENHANCE HEMATOPOIETIC STEM CELL SELF-RENEWAL AND DISRUPT EARLY LYMPHOPOIESIS |
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| Relations |
| BioSample |
SAMN36719371 |
| SRA |
SRX21168180 |
| 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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