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  <Contributor iid="contrib1">
    <Person><First>Evi P.</First><Last>Vlachou</Last></Person>
    <Email>p.vlachou-efstathiou@dkfz.de</Email>
    <Department>D150</Department>
    <Organization>DKFZ</Organization>
    <Address>
      <Line>Im Neuenheimer Feld 280</Line>
      <City>Heidelberg</City>
      <Zip-Code>69120</Zip-Code>
      <Country>Germany</Country>
    </Address>
  </Contributor>

  <Contributor iid="contrib2">
    <Organization>GEO</Organization>
    <Address>
      <City></City>
      <Country>USA</Country>
    </Address>
  </Contributor>

  <Contributor iid="contrib3">
    <Person><First>Evi</First><Middle>P</Middle><Last>Vlachou</Last></Person>
  </Contributor>

  <Contributor iid="contrib4">
    <Person><First>Gianna</First><Last>Triller</Last></Person>
  </Contributor>

  <Contributor iid="contrib5">
    <Person><First>Joseph</First><Middle>P</Middle><Last>Verdi</Last></Person>
  </Contributor>

  <Database iid="GEO">
    <Name>Gene Expression Omnibus (GEO)</Name>
    <Public-ID>GEO</Public-ID>
    <Organization>NCBI NLM NIH</Organization>
    <Web-Link>http://www.ncbi.nlm.nih.gov/geo</Web-Link>
    <Email>geo@ncbi.nlm.nih.gov</Email>
  </Database>

  <Platform iid="GPL19057">
    <Status database="GEO">
      <Submission-Date>2014-08-07</Submission-Date>
      <Release-Date>2014-08-07</Release-Date>
      <Last-Update-Date>2019-03-25</Last-Update-Date>
    </Status>
    <Title>Illumina NextSeq 500 (Mus musculus)</Title>
    <Accession database="GEO">GPL19057</Accession>
    <Technology>high-throughput sequencing</Technology>
    <Distribution>virtual</Distribution>
    <Organism taxid="10090">Mus musculus</Organism>
    <Manufacturer></Manufacturer>
    <Manufacture-Protocol>
    </Manufacture-Protocol>
    <Contact-Ref ref="contrib2" />
  </Platform>

  <Sample iid="GSM6102635">
    <Status database="GEO">
      <Submission-Date>2022-05-03</Submission-Date>
      <Release-Date>2023-05-17</Release-Date>
      <Last-Update-Date>2023-05-17</Last-Update-Date>
    </Status>
    <Title>mouse 1</Title>
    <Accession database="GEO">GSM6102635</Accession>
    <Type>SRA</Type>
    <Channel-Count>1</Channel-Count>
    <Channel position="1">
      <Source>spleen</Source>
      <Organism taxid="10090">Mus musculus</Organism>
      <Characteristics tag="cell type">
B cells
      </Characteristics>
      <Characteristics tag="tissue">
spleen
      </Characteristics>
      <Characteristics tag="strain">
C57BL/6J
      </Characteristics>
      <Characteristics tag="age">
24-26 weeks
      </Characteristics>
      <Molecule>total RNA</Molecule>
      <Extract-Protocol>
Spleens were collected  in cold RPMI buffer (usually 10 ml),  and with the use of a 2 ml syringe plunger, spleens were mashed through a 40 µm Nylon cell strainer which is put in a small Petri dish. Cells are spun down (1400 rpm, 7 min, 4 °C) and resuspend in 10% FCS/DMSO to freeze the cells at -80°C. Normally 200 µl of a 10 ml spleen suspension are used for one FACS staining or around 600.000 cells.
Single-cell RNA sequencing was performed following the SMART-seq 2.5 library preparation protocol as described in Picelli et al. (Picelli et al., 2014), and modified by the DKFZ scOpenLab in Bioquant, Heidelberg. Plate preparation was assisted by the BRAVO Agilent and Mosquito LV liquid handling platforms. Quality control was performed on the TapeStation provided by Agilent Technology, using a D5000 Tape.  Single cell library preparation was performed using the Nextera XT DNA SMP Prep Kit (96 SMP). DNA was cleaned-up using a magnetic size selection. The samples were finally quantified and assessed on a D1000 TapeStation.
Smartseq2.5 scRNA-seq, 75 bps, Single-end
      </Extract-Protocol>
    </Channel>
    <Description>
Smartseq2
    </Description>
    <Data-Processing>
Adapter (Nextera transposase sequence) and quality trimming (Phred score cutoff of 20, overlap of 3 bp) was performed with the TrimGalore version: 0.6.4_dev (Cutadapt version: 1.18) (Krueger, 2015), keeping the sequencing reads with a length of at least 36 bps.
Genome reference-based alignment was performed using the slice-aware STAR alignment tool with the default parameters with Release M25 (GENCODE-GRCm38.p6) of the mouse genome. The reference genome was indexed with a bp overhang of 100-1.
The generated bam files were sorted using Samtools based on the chromosome coordinates. Unmapped reads, PCR duplicates, and reads with an alignment p.score &lt;20 were removed by filtering the sorted bam files.
The count matrices with only the exonic sequences were generated using the summarizeOverlaps function of the GenomicAlignments package (1.30 version - (Lawrence et al., 2013)). Gene annotation was performed with the makeTxDbFromGFF function of the GenomicFeatures package (1.46.1), the AnnotationDbi 1.52.0 and the org.Mm.eg.db 3.12.0 package.
Assembly: mm10
Supplementary files format and content: Column-separated values files
    </Data-Processing>
    <Platform-Ref ref="GPL19057" />
    <Library-Strategy>RNA-Seq</Library-Strategy>
    <Library-Source>transcriptomic</Library-Source>
    <Library-Selection>cDNA</Library-Selection>
    <Instrument-Model>
      <Predefined>Illumina NextSeq 500</Predefined>
    </Instrument-Model>
    <Contact-Ref ref="contrib1" />
    <Supplementary-Data type="TSV">
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6102nnn/GSM6102635/suppl/GSM6102635_count_matrix_m1.tsv.gz
    </Supplementary-Data>
    <Supplementary-Data type="TSV">
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6102nnn/GSM6102635/suppl/GSM6102635_metadata_m1.tsv.gz
    </Supplementary-Data>
    <Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN28072602" />
  </Sample>

  <Sample iid="GSM6102636">
    <Status database="GEO">
      <Submission-Date>2022-05-03</Submission-Date>
      <Release-Date>2023-05-17</Release-Date>
      <Last-Update-Date>2023-05-17</Last-Update-Date>
    </Status>
    <Title>mouse 6</Title>
    <Accession database="GEO">GSM6102636</Accession>
    <Type>SRA</Type>
    <Channel-Count>1</Channel-Count>
    <Channel position="1">
      <Source>spleen</Source>
      <Organism taxid="10090">Mus musculus</Organism>
      <Characteristics tag="cell type">
B cells
      </Characteristics>
      <Characteristics tag="tissue">
spleen
      </Characteristics>
      <Characteristics tag="strain">
C57BL/6J
      </Characteristics>
      <Characteristics tag="age">
24-26 weeks
      </Characteristics>
      <Molecule>total RNA</Molecule>
      <Extract-Protocol>
Spleens were collected  in cold RPMI buffer (usually 10 ml),  and with the use of a 2 ml syringe plunger, spleens were mashed through a 40 µm Nylon cell strainer which is put in a small Petri dish. Cells are spun down (1400 rpm, 7 min, 4 °C) and resuspend in 10% FCS/DMSO to freeze the cells at -80°C. Normally 200 µl of a 10 ml spleen suspension are used for one FACS staining or around 600.000 cells.
Single-cell RNA sequencing was performed following the SMART-seq 2.5 library preparation protocol as described in Picelli et al. (Picelli et al., 2014), and modified by the DKFZ scOpenLab in Bioquant, Heidelberg. Plate preparation was assisted by the BRAVO Agilent and Mosquito LV liquid handling platforms. Quality control was performed on the TapeStation provided by Agilent Technology, using a D5000 Tape.  Single cell library preparation was performed using the Nextera XT DNA SMP Prep Kit (96 SMP). DNA was cleaned-up using a magnetic size selection. The samples were finally quantified and assessed on a D1000 TapeStation.
Smartseq2.5 scRNA-seq, 75 bps, Single-end
      </Extract-Protocol>
    </Channel>
    <Description>
Smartseq2
    </Description>
    <Data-Processing>
Adapter (Nextera transposase sequence) and quality trimming (Phred score cutoff of 20, overlap of 3 bp) was performed with the TrimGalore version: 0.6.4_dev (Cutadapt version: 1.18) (Krueger, 2015), keeping the sequencing reads with a length of at least 36 bps.
Genome reference-based alignment was performed using the slice-aware STAR alignment tool with the default parameters with Release M25 (GENCODE-GRCm38.p6) of the mouse genome. The reference genome was indexed with a bp overhang of 100-1.
The generated bam files were sorted using Samtools based on the chromosome coordinates. Unmapped reads, PCR duplicates, and reads with an alignment p.score &lt;20 were removed by filtering the sorted bam files.
The count matrices with only the exonic sequences were generated using the summarizeOverlaps function of the GenomicAlignments package (1.30 version - (Lawrence et al., 2013)). Gene annotation was performed with the makeTxDbFromGFF function of the GenomicFeatures package (1.46.1), the AnnotationDbi 1.52.0 and the org.Mm.eg.db 3.12.0 package.
Assembly: mm10
Supplementary files format and content: Column-separated values files
    </Data-Processing>
    <Platform-Ref ref="GPL19057" />
    <Library-Strategy>RNA-Seq</Library-Strategy>
    <Library-Source>transcriptomic</Library-Source>
    <Library-Selection>cDNA</Library-Selection>
    <Instrument-Model>
      <Predefined>Illumina NextSeq 500</Predefined>
    </Instrument-Model>
    <Contact-Ref ref="contrib1" />
    <Supplementary-Data type="TSV">
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6102nnn/GSM6102636/suppl/GSM6102636_count_matrix_m6.tsv.gz
    </Supplementary-Data>
    <Supplementary-Data type="TSV">
ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM6102nnn/GSM6102636/suppl/GSM6102636_metadata_m6.tsv.gz
    </Supplementary-Data>
    <Relation type="BioSample" target="https://www.ncbi.nlm.nih.gov/biosample/SAMN28072601" />
  </Sample>

  <Series iid="GSE202173">
    <Status database="GEO">
      <Submission-Date>2022-05-03</Submission-Date>
      <Release-Date>2023-05-17</Release-Date>
      <Last-Update-Date>2023-05-19</Last-Update-Date>
    </Status>
    <Title>Gene expression profile at single cell level of splenic antigen specific memory B-cells after immunization with the Fentanyl-VAST vaccine platform</Title>
    <Accession database="GEO">GSE202173</Accession>
    <Pubmed-ID>36719797</Pubmed-ID>
    <Summary>
Antigen specific memory B cells are considered as a homogeneous population. Here, we wanted to isolate antigen-specific memory cells from mice in order to both characterize the response to the immunization regimine and identify high-affinity candidate BCRs for expression. For this, we used single cell RNA sequencing (scRNA-seq) to describe the diversity of anti-fentanyl B cells elicited by a fentanyl-immunization platform and identify the different markers for each subbpopulation. We use this appoach to select the switched memory B cell, study their BCR repertoir and identify the BCR sequences from the most potent memory B cells.
    </Summary>
    <Overall-Design>
Fentanyl specific B cells from mice spleens were isolated by Fluorescence-activated cell sorting (FACS) according to several markers and their specificity for fentanyl and analyzed using scRNAseq.

**Please note that raw data is not provided due to proprietary concerns regarding the raw sequences**
    </Overall-Design>
    <Type>Expression profiling by high throughput sequencing</Type>
    <Contributor-Ref ref="contrib3" position="1" />
    <Contributor-Ref ref="contrib4" position="2" />
    <Contributor-Ref ref="contrib5" position="3" />
    <Contact-Ref ref="contrib1" />
    <Sample-Ref ref="GSM6102635" />
    <Sample-Ref ref="GSM6102636" />
    <Supplementary-Data type="TAR">
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE202nnn/GSE202173/suppl/GSE202173_RAW.tar
    </Supplementary-Data>
    <Relation type="BioProject" target="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA834835" />
  </Series>

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