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| Status |
Public on Aug 01, 2024 |
| Title |
shControl_rep2 |
| Sample type |
SRA |
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| Source name |
HemSCs
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| Organism |
Homo sapiens |
| Characteristics |
genotype: Control
cell_type: HemSCs
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| Extracted molecule |
total RNA |
| Extraction protocol |
Proliferating regions of IH specimens were minced into pieces and digested with collagenase (Sigma-Aldrich) and Dispase (Gibco). After removal of red blood cells with RBC lysis buffer (Sangon), HemSCs were isolated from cell suspension by anti-CD133 magnetic beads (Miltenyi), and were cultured in vitro on fibronectin-coated (Corning) petri dishes or plates in Endothelial Cell Growth Medium-2 (EGM-2, Lonza, Cat#CC-3162) supplemented with 20% FBS (Gibco). HemSCs between passage 3 to passage 6 were used in this study.
Briefly,mRNA was captured from total RNA with VAHTS mRNA Capture Beads (Vazyme, Cat#N401) for fragmentation into short length nucleotides. First-strand cDNA synthesis was then performed with 1st Strand Enzyme Mix 2, followed by generation of second-strand cDNA with 2nd Strand Enzyme Super Mix. Double-stranded cDNA was then ligated with sequencing adapters, purified and amplified with PCR. After size selection, the RNA-seq libraries were sequenced on Illumina Nova Seq 6000 platform at PE150 mode. Three biological replicates of RNA-seq libraries were prepared for shControl and shKLF2 HemSCs respectively.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
shControl RNA-seq replicate2
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| Data processing |
For analyzing RNA-seq data of shControl and shKLF2 HemSCs, adaptor-trimmed sequencing data were aligned to human reference genome (hg38) with STAR (version 2.7.3a). Mapped reads were then counted with HTSeq (version 0.12.4) to generate counts of RNA-seq libraries, which were further normalized with DESeq2 (version 1.38.1).
Reads matching the forward primer sequence were selected from the total fastq files to ensure an overall high quality of the raw data. The primer sequences were then removed from selected reads, which were then mapped to mm10 reference genome with Bowtie2.
Adaptor sequences in CUT&Tag fastq files were trimmed with trim galore.
Differentially expressed genes (DEGs) were identified with cutoff P value<0.05 and |log2Foldchange|>1.
FPKM values of each sample were counted with rnanorm (https://github.com/genialis/RNAnorm).
Assembly: hg38
Supplementary files format and content: counts (mapped counts)
Supplementary files format and content: csv (FPKM)
Supplementary files format and content: csv (DEGs)
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| Submission date |
Jul 26, 2023 |
| Last update date |
Aug 01, 2024 |
| Contact name |
Qian Bian |
| E-mail(s) |
qianbian@shsmu.edu.cn
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| Phone |
86-21-3845-2656
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| Organization name |
Shanghai Jiao Tong University School of Medicine
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| Department |
Shanghai Institute of Precision Medicine, Ninth People’s Hospital
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| Street address |
Jinzun Road No.115
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| City |
Shanghai |
| ZIP/Postal code |
200011 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE239352 |
Transcription factor KLF2 regulates cell fate decision of stem cells in infantile hemangioma |
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| Relations |
| BioSample |
SAMN36717759 |
| SRA |
SRX21165887 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7663534_shControl_rep2.counts.txt.gz |
231.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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