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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 25, 2024 |
| Title |
B cells, spleen, TFEB-KO, rep2 |
| Sample type |
SRA |
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| Source name |
spleen
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: spleen
cell type: CD19+ (B cells)
genotype: TFEB fl/fl Mb1-Cre +/-
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Spleen were passed through 40µm cell strainer to generate single-cell suspensions. Subsequently, ells were were sorted according to indicated marker, pelleted by centrifugation, subsequently resuspended in TRIzol reagent (Invitrogen) and stored at -80°C. Total RNA was purified from sorted cells using the TRIzol protocol (Invitrogen)extracted with
RNA-seq libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) with minor modifications in ligation and amplification (protocol from Schattling, B., Engler, J.B., Volkmann, C. et al. Bassoon proteinopathy drives neurodegeneration in multiple sclerosis. Nat Neurosci 22, 887–896 (2019). https://doi.org/10.1038/s41593-019-0385-4)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
54B
salmon_raw_counts.tsv
kallisto_normalized_abundances.tsv
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| Data processing |
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20.0.422
salmon version 1.10.1 was used for selective alignment and transcript-level quantification with the parameters -l A --validateMappings
kallisto.v0.48.0 was used for quasi-mapping and transcript-level quantification with 100 bootstrap samples
Assembly: Ensembl GRCm39 version 109
Supplementary files format and content: tab-delimited text file includes raw counts generated with salmon for each sample per column
Supplementary files format and content: tab-delimited text file includes normalized transcript abundances generated with kallisto
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| Submission date |
Jul 19, 2023 |
| Last update date |
Jun 25, 2024 |
| Contact name |
Gabriela Salinas |
| E-mail(s) |
Gabriela.Salinas-Riester@medizin.uni-goettingen.de
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| Organization name |
Universitaetsmedizin Goettingen
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| Department |
Department of Pathology
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| Lab |
NGS Integrative Genomics
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| Street address |
Kreuzbergring 57
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| City |
Goettingen |
| State/province |
Lower-Saxony |
| ZIP/Postal code |
37075 |
| Country |
Germany |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE237799 |
The influence of TFEB on gene expression in primary murine germinal center and non-germinal center B cells |
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| Relations |
| BioSample |
SAMN36620611 |
| SRA |
SRX21081713 |
| 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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