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| Status |
Public on Oct 16, 2024 |
| Title |
PD-L1 positive D11 |
| Sample type |
SRA |
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| Source name |
lung
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| Organism |
Mus musculus |
| Characteristics |
tissue: lung
cell type: Neutrophils
genotype: C57Bl/6 WT
treatment: IAV infected
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| Treatment protocol |
C57Bl/6j mice were intranasally infected with 150pfu of a virulent strain of influenza A virus (H3N2/A/Scotland/74)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Freshly collected lungs were harvested and single cell suspension of immune cells was performed. Cell suspensions were labelled with antibodies and neutrophils were purified using a flow cytometry-based sorting (FACS Melody, BD Biosciences) as live CD45+ SiglecF- CD11b+ Ly6G+ PD-L1+/-. Cells were collected in low binding tubes containing PBS pH 7.2 supplemented with 0.04% BSA (Mg2+/Ca2+ EDTA free).
Libraries were performed according to the manufacter’s instructions (Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 Dual Index). Briefly, Gel Beads-in-emulsion (GEM) were generated by combining barcoded gel beads, partitioning oil and the Master Mix containing neutrophils onto a Chromium NextGEM Chip G. After GEM generation, gel beads were dissolved and partitioned cells were lysed before reverse transcription (RT) to obtain barcoded, full-length cDNA from poly-adenylated mRNA (primers contained an Illumina TruSeq Read 1, a 10x Barcode, a Unique Molecular Identifier UMI and poly(dT) sequence). The pooled barcoded cDNA was then cleaned up with Silane magnetic beads to purify the first-strand cDNA and amplified via PCR to generate sufficient mass for library construction. SPRIselect reagent was used to optimize the cDNA fragment size. During the library construction, Illumina TruSeq Read 2 primer, i7 and i5 sample indexes and paired-end constructs with P5 and P7 sequences were added via End Repair, A-tailing, Adaptor Ligation and PCR. The final step was sequencing using an Illumina NovaSeq 6000.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10X genomics
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| Data processing |
The demultiplexing, barcoded processing , genes counting were made using Cellranger 7.1.0
Assembly: mm10
Supplementary files format and content: tab-separated values and matrix files
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| Submission date |
Jun 04, 2024 |
| Last update date |
Oct 16, 2024 |
| Contact name |
Guy Ilango |
| E-mail(s) |
guy.ilango@univ-tours.fr
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| Organization name |
University of Tours
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| Lab |
Centre d'Etude des Pathologies Respiratoires
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| Street address |
10, boulevard Tonnellé
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| City |
Tours |
| ZIP/Postal code |
37000 |
| Country |
France |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE269075 |
Gene expression profiles of PD-L1 positive and PD-L1 negative lung neutrophils from Influenza A virus infected mice |
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| Relations |
| BioSample |
SAMN41675456 |
| SRA |
SRX24802739 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8305925_PDL1pos_filtered_feature_bc_matrix.tar.gz |
9.2 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
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