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| Status |
Public on May 23, 2020 |
| Title |
CD103pos_Tcells_2 |
| Sample type |
SRA |
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| Source name |
Naïve blood CD8+ T cells
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| Organism |
Homo sapiens |
| Characteristics |
tissue: In vitro differentiated cells
donor: 2
cell type: CXCR3+ CD103+ CD8+ T
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| Treatment protocol |
Blood Monocytes, DC2 and DC3 were stimulated ex vivo with a TLR agonist cocktail (LPS, Poly I:C, R848) for 16h.
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| Growth protocol |
Naïve CD8+ T cells from healthy blood donor were cocultured, for 5 days, with mismatched DC3 from healthy blood donor in presence of superantigen (Cytostim).
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were FACS sorted in in 1.5ml Eppendorf tubes (100-1000 cells/tube) containing Trizol
RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA). RNA library preparations, sequencing reactions, and initial bioinformatics analysis were conducted at GENEWIZ, LLC. (South Plainfield, NJ, USA). The SMART-Seq v4 Ultra Low Input Kit for Sequencing was used for full-length cDNA synthesis and amplification (Clontech, Mountain View, CA) as per manufacturer’s protocol. Illumina Nextera XT library was used for library preparation. Briefly, cDNA was fragmented, and adaptor was added using Transposase, followed by limited-cycle PCR to enrich and add index to the cDNA fragments. Final libraries were analyzed on the Agilent TapeStation for library sizing and quantified using the Qubit dsDNA HS Assay Kit and by qPCR using the KAPA Library Quantification Kit. The sequencing libraries were multiplexed and clustered on four lanes of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Paired End (PE) configuration.
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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_Bulk_Blood_raw_counts.csv
CD103pos-d2
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| Data processing |
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the the human reference genome using STAR aligner (v2.5.3a).
Raw read counts matrix made also with STAR (using the parameter --quantMode GeneCounts).
The read counts matrix was imported in Rstudio Version 1.2.5033 with R version 3.6.1.
Dataset was processed using DESeq2 R package (version 1.24.0) functions.
Genome_build: hg38
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) |
| GSE151073 |
Transcriptional comparison of in vitro and in vivo generated human dendritic cells |
| 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 |
SAMN14999225 |
| SRA |
SRX8383072 |
| 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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