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GEO help: Mouse over screen elements for information. |
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Status |
Public on Sep 27, 2023 |
Title |
Contrl2, replicate 1, scRNAseq |
Sample type |
SRA |
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Source name |
spleen
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Organism |
Mus musculus |
Characteristics |
tissue: spleen cell type: CD3 T treatment: Control
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Extracted molecule |
total RNA |
Extraction protocol |
In each microwell, a magnetic bead was paired with a cell. Each magnetic bead had a unique cell label and multiple molecular labels (unique molecular identifier or UMI) for capturing RNA. When the RNA is released from the captured cells, it can hybridize to the magnetic beads. The magnetic beads were then collected into a 1.5-ml Eppendorf tube for reverse transcription using GEXSCOPER Single-Cell RNA Library Kit to perform cDNA synthesis on single cells. After cDNA synthesis and PCR amplification, Qubit (Thermo, Waltham, MA, USA) was used for cDNA quantification and Fragment Analyzer was used to determine the cDNA fragment size. Following several steps including fragmentation, adapter ligation, purification, PCR amplification, size selection and QC analysis; libraries were constructed before being sequenced with 150 bp paired end reads on Illumina HiSeq X platform.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic single cell |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CeleScope version 1.6.1. Correcting the deviation between samples using Harmony (https://portals.broadinstitute.org/harmony/). Use Seurat to filter data, normalize and standardize data, perform PCA, etc. Assembly: mm9 Supplementary files format and content: *tar: Tar archives include cell barcode file (barcodes.tsv), Feature file (genes.tsv), and Matrix file (matrix.mtx) for each sample.
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Submission date |
Jun 12, 2023 |
Last update date |
Sep 27, 2023 |
Contact name |
Feifei Xiong |
E-mail(s) |
xiongfeifei@sinopharm.com
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Organization name |
Shanghai Institute of Biological Products
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Street address |
350 Anshun Rd,Shanghai
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City |
Shanghai |
ZIP/Postal code |
200052 |
Country |
China |
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Platform ID |
GPL24247 |
Series (1) |
GSE234756 |
An mRNA-based universal vaccine candidate confers improved cross-protection against heterosubtypic influenza viruses in mice |
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Relations |
BioSample |
SAMN35717864 |
SRA |
SRX20663383 |
Supplementary file |
Size |
Download |
File type/resource |
GSM7474275_Contrl-2_matrix.tar.gz |
59.8 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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