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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 19, 2021 |
| Title |
PB_day4_1: Plasmablasts day 4 after immunization |
| Sample type |
SRA |
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| Source name |
Splenic B cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: Igh B1-8hi/+
cell preparation: Ex vivo, FACS-sorted from spleens
cell sorting strategy: Igκ- CD4- CD8- F4/80- CD3- Ter119 -CD11c- CD45.1+ CD19+ Igλ+ TACI+ CD138+
cell type: Splenic B cells
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single cell lysis kit
NEBNext Ultra II
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
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| Data processing |
Sequence reads that passed the Illumina quality filtering were considered for alignment. Reads were aligned to the mouse transcriptome (genome assembly version of July 2007 NCBI37/mm9) using RNA STAR (Dobin et al., 2012) (usegalaxy.eu; Galaxy Version 2.7.8a (Afgan et al., 2018)). The calculation of RNA expression values was all based on the RefSeq database, which was downloaded from UCSC on January 10th, 2014. The annotation of immunoglobulin and T cell receptor genes was incorporated from the Ensembl release 67 (Cunningham et al., 2015). Genes with overlapping exons were flagged and double entries (i.e. exactly the same gene at two different genomic locations) were renamed. Genes with several transcripts were merged to consensus-genes consisting of a union of all underlying exons using the fuge software (I. Tamir, unpublished), which resulted in 25,726 gene models. The data sets were analyzed using the R package DESeq2 version 1.2.10 (Love et al, 2014). Sample normalizations and dispersion estimations were conducted using the default DESeq2 settings. Transcripts per million (TPM) were calculated from RNA-seq data, as described (Wagner et al, 2012).
Genome_build: MM9
Supplementary_files_format_and_content: Excel table with TPM values for all samples, see ‘data processing step’ for details.
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| Submission date |
May 24, 2021 |
| Last update date |
Aug 19, 2021 |
| Contact name |
Taras Kreslavsky |
| E-mail(s) |
taras.kreslavskiy@ki.se
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| Phone |
+46761124813
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| Organization name |
Karolinska Institutet
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| Department |
Department of Medicine, Solna (MedS)
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| Lab |
Taras Kreslavsky
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| Street address |
Nks Bioclinicum, J7:30, Visionsgatan 4
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| City |
Solna |
| ZIP/Postal code |
171 64 |
| Country |
Sweden |
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| Platform ID |
GPL30172 |
| Series (1) |
| GSE175427 |
Limited access to antigen drives the generation of early B cell memory while restraining the plasmablast response |
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| Relations |
| BioSample |
SAMN19317270 |
| SRA |
SRX10971560 |
| 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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