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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 21, 2023 |
| Title |
Control-BoneMarrow-2 |
| Sample type |
SRA |
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| Source name |
Eosinophil
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| Organism |
Mus musculus |
| Characteristics |
cell type: Eosinophil
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from the samples was extracted using the RNeasy Plus Mini Kit (74134, Qiagen, Hilden Germany), following the manufacturer’s instructions. The quantity and quality of the purified total RNA was assessed using a Thermo Fisher Scientific Qubit 3.0 fluorometer with the Qubit RNA BR Assay Kit (Q10211, Thermo Fisher Scientific, distributed by LuBioScience GmbH, Lucerne, Switzerland) and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer RNA Kit (DNF-471, Agilent Technologies, Santa Clara, USA), respectively.
Sequencing libraries were constructed using an illumina TruSeq Stranded mRNA Library Prep kit (20020595, illumina, San Diego, USA) in combination with TruSeq RNA UD Indexes (20022371, illumina) according to illumina’s guidelines. The cDNA libraries were evaluated using a Thermo Fisher Scientific Qubit 3.0 fluorometer with the Qubit dsDNA HS Assay Kit (Q32854, Thermo Fisher Scientific) and an Agilent Fragment Analyzer (Agilent) with an HS NGS Fragment Kit (DNF-474, Agilent), respectively.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Data processing |
The quality of the RNA-seq data was assessed usingfastqc v. 0.11.9.
The reads were mapped to the reference genome using HISAT2 v. 2.2.1
FeatureCounts v. 2.0.1was used to count the number of reads overlapping with each gene as specified in the genome annotation (Mus_musculus.GRCm39.104)
Subsequent data analysis was performed in R v. 4.1.0. The Bioconductor package DESeq2 v. 1.32.0 was used to analyze differentially expressed genes with default parameters.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count reads for each gene for each sample
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| Submission date |
Oct 11, 2023 |
| Last update date |
Nov 21, 2023 |
| Contact name |
Aref Hosseini |
| Organization name |
Institute of Pharmacology
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| Street address |
Inselspital, INO-F
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| City |
Bern |
| State/province |
Switzerland |
| ZIP/Postal code |
3010 |
| Country |
Switzerland |
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| Platform ID |
GPL21493 |
| Series (1) |
| GSE245134 |
Genome-wide expression analysis in Control and Atg5-deficient eosinophils. |
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| Relations |
| BioSample |
SAMN37776390 |
| SRA |
SRX22066187 |
| 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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