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| Status |
Public on Nov 08, 2021 |
| Title |
LM.wt.7 |
| Sample type |
SRA |
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| Source name |
KL25HL splenocytes
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| Organism |
Mus musculus |
| Characteristics |
cell type: KL25HL B cells
treatment: LM immunization on d-9
genotype: C57BL/6
ID: 7
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| Treatment protocol |
On day -9, recipient mice were pre-immunized with either LM61 (mice 1-4) or control (LM, mice 5-8)). Another group of wt recipients (mice 9-12) and IFNAR-/- recipients (mice 13-16) were not pre-immunized. On day 0, all mice received KL25HL B cells by adoptive transfer and were challenged with LCMV. Mice 9-12 additionally were given SM CD4 T cells on day -1 by adoptive transfer. On day 4, KL25HL B cells (CD45.1+B220+CD138-) were purified by FACS-sorting and were subject to RNAseq.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
KL25HL B cells (CD45.1+ B220+CD138-) were FACS sorted on day 4 days directly into Trizole LS; RNA was extracted using the Direct-Zol RNA Microprep Kit, Zymo Research
Library preparation was performed, starting from 100ng total RNA, using the TruSeq Stranded mRNA Library Prep Kit High Throughput (Cat# RS-122-2103, Illumina, San Diego, CA, USA) and the TruSeq RNA CD Index Plate (Cat# 20019792, Illumina). 15 cycles of PCR were performed. Libraries were quality-checked on the Fragment Analyzer (Advanced Analytical, Ames, IA, USA) using the Standard Sensitivity NGS Fragment Analysis Kit (Cat# DNF-473, Advanced Analytical). Samples were pooled to equal molarity and sequenced using single-reads 76 bases on an Illumina NextSeq 500.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
d0 KL25HL B cell transfer and LCMV infection, analysis d4 pi
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| Data processing |
Reads were aligned to the mouse genome (UCSC version mm10) with STAR (version 2.5.2a) using the multi-map settings '-outFilterMultimapNmax 10 --outSAMmultNmax 1'.
Mapped reads were assigned to genes based on the UCSC refGene annotation (downloaded 2015-12-18) using the function qCount of the R/Bioconductor package QuasR (R version 3.4.0, Bioconductor version 3.5).
Genes with zero counts were removed resulting in n=18824 genes.
Genome_build: mm10
Supplementary_files_format_and_content: counts.tsv.gz; gzipped tab-separated values text file with columns: 1. Entrez gene id, 2. gene symbol, 3. gene name, 4. gene length (exon-union model), 5. - 20. counts per sample
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| Submission date |
Oct 28, 2020 |
| Last update date |
Nov 18, 2021 |
| Contact name |
DBM Bioinformatics Core Facility |
| Phone |
+41612073541
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| Organization name |
University of Basel
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| Department |
Departement of Biomedicine
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| Street address |
Hebelstrasse 20
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| City |
Basel |
| State/province |
BS |
| ZIP/Postal code |
4053 |
| Country |
Switzerland |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE160294 |
Vaccine-elicited CD4 T cells prevent the deletion of antiviral B cells in chronic infection |
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| Relations |
| BioSample |
SAMN16580542 |
| SRA |
SRX9386701 |
| 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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