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| Status |
Public on Mar 07, 2022 |
| Title |
PBMC-06-4-ADT-S6 |
| Sample type |
SRA |
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| Source name |
peripheral blood mononuclear cells
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| Organism |
Homo sapiens |
| Characteristics |
batchid: PBMC-06
subbatchid: 4
sequencingrunid: S6
librarytype: Antibody Capture
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Libraries of antibody-derived tags (ADT) from feature barcoding antibodies were prepared by repeating size purification on the supernatant obtained from the prior size purification of gene expression cDNA libraries (Step 2.3.d in the manufacturer’s instructions https://assets.ctfassets.net/an68im79xiti/1eX2FPdpeCgnCJtw4fj9Hx/7cb84edaa9eca04b607f9193162994de/CG000204_ChromiumNextGEMSingleCell3_v3.1_Rev_D.pdf), using a 7:8 volumetric ratio of 2.0X SPRIselect reagent (Beckman Coulter, Cat# B23317) to sample. Indexing amplification was performed using Kapa Hifi HotStart ReadyMix (Kapa Biosystems, Cat# KK2601) and TruSeq Small RNA RPI primers (Illumina) with the following thermocycling conditions: (1) 98 °C, 2 min; (2) 15 × (98 °C, 20 sec; 60 °C, 30 sec; 72 °C, 20 sec); (3) 72 °C, 5 min. Size purification was then repeated on amplified libraries using a 5:6 volumetric ratio of 1.2X SPRIselect reagent to sample.
Peripheral blood was collected from each subject in Vacutainer ACD tubes. PBMCs were isolated using a standard Ficoll method and stored in liquid nitrogen.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
PBMC-06-4.barcodes.tsv.gz
PBMC-06-4.features.tsv.gz
PBMC-06-4.matrix.mtx.gz
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| Data processing |
Library strategy: CITE-seq
Raw RNA and ADT fastqs for each Chromium library were respectively aligned to the GRCh38 human genome reference and a reference database of antibody-tag sequences using Cell Ranger 3.1.0
Genome_build: GRCh38
Supplementary_files_format_and_content: CellMetadata_AS_20220103.tsv, CellMetadata_PSA_20220103.tsv: metadata for each barcode (cell type, subject, subject clinical status, whether the cell was identified to be a doublet, etc.); barcodes.tsv.gz: cell barcodes in the sample; features.tsv.gz: Gene and ADT features detected in a sample; matrix.mtx.gz: MTX (MatrixMarket)-formatted read counts in a sample of each feature in the corresponding features.tsv.gz file in each barcode in the corresponding barcodes.tsv.gz file
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| Submission date |
Jan 25, 2022 |
| Last update date |
Mar 07, 2022 |
| Contact name |
Wilson Liao |
| E-mail(s) |
wilson.liao@ucsf.edu
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| Organization name |
University of California, San Francisco
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| Department |
Dermatology
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| Street address |
2340 Sutter St.
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE194315 |
RNA and surface epitope sequencing of single cells involved in spondyloarthritis |
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| Relations |
| BioSample |
SAMN25241903 |
| SRA |
SRX13897052 |
| 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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