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| Status |
Public on Oct 25, 2021 |
| Title |
NK A2 A11 A28 H6 |
| Sample type |
SRA |
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| Source name |
NK A2 A11 A28 H6
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Peripheral Blood
patient id: A2; A11; A28; H6
sample detail: patient A2 #1 d12, patient A11 #3 d13, patient A28 #5 d53, donor H6 #7 healthy
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Frozen Peripheral Blood Mononuclear Cells were thawed and incubated with Fc Blocking Reagent following manufacturer’s instructions. Cells were subsequently incubated with barcoded (hashtagging) and fluorochrome-conjugated antibodies and NK cells were sorted by FACS as live CD3-CD14-CD19-CD45+CD56+ lymphocytes. Sorted cells were then applied to the 10X Genomics platform using the Single Cell 5’ Library & Gel Bead Kit (10x Genomics) following the manufacturer’s instructions. The purified cDNA was amplified using 12 or 13 cycles of PCR and then used for 5’ gene expression (GEX) and cell-surface hashtagging library preparation. Through fragmentation, adapter ligation and index PCR the final libraries were obtained. The quality of single cell 5’ GEX was assessed by Qubit quantification and Bioanalyzer fragment analysis (HS DNA Kit, Agilent).
The sequencing was performed on a NextSeq500 device (Illumina) using High Output v2 Kits (150 cycles) with the recommended sequencing conditions for 5’ GEX and cell-surface hashtagging libraries (read1: 26nt, read2: 98nt, index1: 8nt, index2: n.a.).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
The Cell Ranger Single Cell Software Suite 3.1.1 was used to perform sample demultiplexing, barcode processing, and single cell 5’ gene counting for transcriptome wirh refdata-cellranger-hg19-1.2.0 as reference and expected-cells number of 3000 for each sample; polymorphisms removed.
Genome_build: hg19
Supplementary_files_format_and_content: Barcoded BAM, with Chromium cellular and molecular barcodes for each read, stored as TAG fields; h5: aggregated gene count matrix in hdf5 format. txt: annotation of cellular barcodes with disease state, day after symptom onset or stimulation, if applicable.
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| Submission date |
Sep 17, 2021 |
| Last update date |
Oct 25, 2021 |
| Contact name |
Pawel Durek |
| E-mail(s) |
pawel.durek@drfz.de
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| Organization name |
Deutsches Rheuma-Forschungszentrum
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| Street address |
Charitéplatz 1
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| City |
Berlin |
| ZIP/Postal code |
10117 |
| Country |
Germany |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE184329 |
Untimely TGFβ responses in COVID-19 limit antiviral functions of NK cells |
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| Relations |
| BioSample |
SAMN21468948 |
| SRA |
SRX12219239 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5584154_NK_run1.filtered_feature_bc_matrix.h5 |
15.7 Mb |
(ftp)(http) |
H5 |
| GSM5584154_NK_run1.txt.gz |
32.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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