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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 23, 2020 |
| Title |
INFDC_2 |
| Sample type |
SRA |
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| Source name |
Human breast cancer iLN mononuclear phagocytes
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Breast cancer iLN
donor: 2
cell type: CD11c+HLADR+CD1a-CD1c+CD14+ cells
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Tumor-draining lymph nodes (tdLN) and primary tumors were collected in CO2 independent medium (Gibco) within few hours after the primary surgery. Tissue were cut into small fragments and submitted to enzymatic digestion using 0.1 mg/ml of Liberase TL (Roche) and 0.1 mg/ml of DNase (Roche) for 30 min. Cells were filtered on 40-μm cell strainer (BD), washed using CO2 independent medium (Gibco) containing 0.4g/ml of human albumin and resuspended for cell counting.
T and B lymphocytes, NK cells, erythrocytes and myelomonocytic cells were depleted using monoclonal antibodies against: CD3, CD19, CD56, CD235a and CD15, respectively. Subsequently, cell suspensions were stained for 30 min with antibody-conjugated as the following: HLA-DR, CD11c, CD14, CD1c, CD304, CD1a, CD206, CD141. Around 1,000 cells of each DC subset were sorted by flow cytometry using BD FACS ARIA II cell sorter, (purity > 98%). Cells were centrifuged and lysed with TCL buffer (Qiagen) containing 1% of beta-mercaptoethanol before storage at -80°C. RNA were extracted and isolated using the Single Cell RNA purification kit (Norgen) according to the manufacturer’s instructions and the RNA integrity number was evaluated with an Agilent RNA 6000 pico kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
PG_iLN_HTSeqCounts.csv
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| Data processing |
Transcriptomic data were aligned using STAR (version 2.5.0a) on hg19 and RefSeq gene annotation. Sequencing read coverage per gene was determined using HTSeq (version 0.6.1p1) using these parameters: --stranded no --idattr gene_id --mode intersection-nonempty --format bam --type exon (all others are the default parameters).
Genome_build: hg19
Supplementary_files_format_and_content: Comma-separated value file with raw data values for each sample
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| Submission date |
May 22, 2020 |
| Last update date |
May 23, 2020 |
| Contact name |
Kristine Vaivode |
| E-mail(s) |
kristine.vaivode@kcl.ac.uk
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| Phone |
02078486907
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| Organization name |
King's College London
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| Department |
Centre for Inflammation Biology and Cancer Immunology
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| Lab |
Dr Pierre Guermonprez lab
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| Street address |
CIBCI, First Floor, New Hunt's House, Great Maze Pond
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| City |
London |
| ZIP/Postal code |
SE1 1UL |
| Country |
United Kingdom |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE151072 |
Transcriptional and functional analysis of CD1c+ human dendritic cells identifies a CD163+ subset priming CD8+CD103+ T cells [Breast_iLN] |
| GSE151095 |
Transcriptional and functional analysis of CD1c+ human dendritic cells identifies a CD163+ subset priming CD8+CD103+ T cells |
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| Relations |
| BioSample |
SAMN14999207 |
| SRA |
SRX8383025 |
| 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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