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| Status |
Public on Dec 28, 2022 |
| Title |
iBCG (IBCG)_HTO |
| Sample type |
SRA |
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| Source name |
PBMC
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| Organism |
Homo sapiens |
| Characteristics |
individual: 3 healthy donors
cell type: PBMC
treatment: BCG sub-strain iBCG
hto: C0251_TotalSeqC Antibody Capture (donor 1), C0252_TotalSeqC Antibody Capture (donor 2), C0253_TotalSeqC Antibody Capture (donor 3)
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| Extracted molecule |
protein |
| Extraction protocol |
After co-culture of PBMC with BCG, for 7 days in RPMI complete medium, high viability single-cell suspensions were obtained using the Dead Cell Remove Kit (Miltenyi Biotec), and cells were pooled and resuspended in PBS+0.04% BSA prior to sequencing
[library construction protocol: Low Input] Library was generated according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads to generate partitioned cells (GEMs, Gel beads-in-Emulsion). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscribed to cDNA, incorporating an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriate size fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
[chemistry] SC5P-R2 with sample multiplexing
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| Library strategy |
RNA-Seq |
| Library source |
other |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
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| Description |
IBCG_barcodes.tsv.gz
IBCG_features.tsv.gz
IBCG_matrix.mtx.gz
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| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Sequence read quality was evaluated from FastQC.
Human Total-Seq C Hashtag antibodies [1, 2 and 3] (Biolegend) were used for individual multiplexing
Assembly: GRCh38-2020-A
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)
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| Submission date |
May 16, 2022 |
| Last update date |
Dec 28, 2022 |
| Contact name |
Enrique Vazquez de Luis |
| E-mail(s) |
quiquevzquez@gmail.com
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| Organization name |
CNIC
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| Lab |
Genomics Unit
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| Street address |
Melchor Fernandez Almagro, 3
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| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
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| Platform ID |
GPL30173 |
| Series (1) |
| GSE203098 |
BCG-activation of lymphocytes for the generation of donor-independent innate anti-tumor NK and γδ T cells |
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| Relations |
| BioSample |
SAMN28449421 |
| SRA |
SRX15285514 |
| 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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