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| Status |
Public on Jan 16, 2024 |
| Title |
Eosinophils__P51 |
| Sample type |
SRA |
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| Source name |
peripheral blood cells
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| Organism |
Homo sapiens |
| Characteristics |
tissue: peripheral blood cells
cell type: Eosinophils
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| Extracted molecule |
total RNA |
| Extraction protocol |
The fractional blood derivatives as well as the whole blood samples were directly lysed in Qiazol. For RNA isolation the miRNeasy Serum/Plasma mini kit was combined with minElute columns.
Dual indexed sRNA libraries with unique molecular identifiers (UMIs) adaptors were generated using the QIAseq miRNA Library Kit.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
NextSeq 2000 |
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| Data processing |
Raw sequence reads were adapter trimmed and depleted of PCR duplicates based on the UMIs.
Only sequences that had at least one read in at least three samples per blood component type and that were longer than 17 nucleotides were kept.
For 25 cellular fractions (4.6% of derivatives, 25/539) the purification process did not meet the prespecified quality standard (purity > 70% as determined by flow cytometry). These samples were excluded from further analyses. See 'quality filter for processed data'
As additional quality control, the normalized data of the blood component samples was converted to a two-dimensional T-distributed Stochastic Neighbor Embedding (t-SNE) space. When plotting the two embedding vectors against each other, four samples did not cluster with the samples of the same blood component type (0.8% of derivatives, 4/514) and were excluded from further analysis. See 'quality filter for processed data'
The pre-processed sRNA sequences were annotated using the annotation pipelines unitas and SPORTS. In case of multi-assignments, the annotation was prioritized in the following manner: miRNA > tRNA > rRNA > YRNA > snoRNA > lncRNA > snRNA > piRNA.
Assembly: hg38
Supplementary files format and content: csv files including log2-transformed RPM values per small RNA name for all blood component samples (1 file) and for all whole blood samples (1 file)
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| Submission date |
Feb 22, 2023 |
| Last update date |
Jan 16, 2024 |
| Contact name |
Bruno Steinkraus |
| E-mail(s) |
publication@hb-dx.com
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| Phone |
062219143350
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| Organization name |
HUMMINGBIRD DIAGNOSTICS GMBH
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| Street address |
Im Neuenheimer Feld 583
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| City |
Heidelberg |
| State/province |
Baden-Württemberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
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| Platform ID |
GPL30173 |
| Series (1) |
| GSE225872 |
miR-Blood - a small RNA sequencing atlas of purified human blood components |
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| Relations |
| BioSample |
SAMN33418720 |
| SRA |
SRX19476438 |
| 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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