title: 20180320.A-Plate_10_N723_S510

description:
fluidigm C1
MF042_S.csv


title: 20180320.A-Plate_10_N724_S506

status: Public on Dec 28 2023

type: SRA

city: Lausanne

first: Yun-Tsan

last: Chang

address: Avenue de Beaumont 29

department: Dermatology

country: Switzerland

institute: CHUV

description:
fluidigm C1
MF042_S.csv

library_source: transcriptomic single cell

data_processing:
The quality control was done using fastQC (v. 0.11.7) and the adaptors and low quality bases having phred quality score less than 20 were trimmed from the ends of the reads using Trim Galore (v. 0.4.4). The T-cell receptors (TCR) were identified using TraCeR and gene expressions were quantified with Kallisto (v. 0.45.0) for cells with an identified T cell receptor as part of the TraCeR workflow. TraCeR was also used to group the cells with identified TCR into groups of clones of different sizes, which all were required to have at least one TCR monomer in common with the other cells in the same clone. The remaining cells with TCR, sharing no identical TCR monomer with each other, were considered as heterogeneous cells. The gene expression data was normalised using Scater (v. 1.10.1) using CPM (counts per million).
Assembly: GRCh37
Supplementary files format and content: Matrix table with counts for every transcript and every cell

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
Capture and processing of single skin and blood T cells was performed using the Fluidigm C1 Autoprep system. Cells were loaded at a concentration of 2,000 cells/µL onto C1 integrated fluidic circuit chips for 5–10-µm cells. All C1 capture sites were microscopically inspected to identify the sites that contained only a single cell. Empty sites and those with multiple cells were excluded from further analysis. External RNA Controls Consortium spike-in RNAs served as a control. The SMARTer® Ultra® Low RNA Kit (Clontech) was used for reverse transcription and cDNA pre-amplification. The single-cell cDNA products from each cell were then used to prepare Illumina sequencing libraries and sequenced as paired-end 150-base reads on the Illumina HiSeq 4000 platform. Quality control was performed using FastQC v. 0.11.7 (Babraham Bioinformatics), and the adaptors and low-quality bases with a Phred quality score <20 were trimmed from the ends of the reads using Trim Galore v. 0.4.4 (Babraham Bioinformatics)
Cells were captured and performed using the Fluidigm C1 Autoprep system. The SMARTer® Ultra® Low RNA Kit (Clontech) was used for reverse transcription and cDNA pre-amplification. The single-cell cDNA products from each cell were then used to prepare Illumina sequencing libraries and sequenced as paired-end 150-base reads on the Illumina HiSeq 4000 platform.

tag: tissue

value: skin

tag: patient diagnosis

value: cutaneous T-cell lymphoma

tag: cell type

value: T cells


title: 20180320.A-Plate_10_N723_S511

description:
fluidigm C1
MF042_S.csv


title: 20180320.A-Plate_10_N723_S507

description:
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MF042_S.csv


title: 20180320.A-Plate_10_N728_S503

description:
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MF042_S.csv


title: 20180320.A-Plate_10_N727_S502

description:
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title: 20180320.A-Plate_10_N726_S507

description:
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MF042_S.csv


title: 20180320.A-Plate_10_N723_S505

description:
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title: 20180320.A-Plate_10_N723_S503

description:
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title: 20180320.A-Plate_10_N723_S502

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description:
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title: 20180320.A-Plate_10_N724_S508

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description:
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description:
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title: 20180320.A-Plate_9_N715_S511

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