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Status |
Public on Oct 17, 2023 |
Title |
midgut |
Sample type |
SRA |
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Source name |
midgut
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Organism |
Aedes aegypti |
Characteristics |
tissue: midgut strain: Higg's White Eye age: 7-day-old
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Extracted molecule |
total RNA |
Extraction protocol |
Around 30 midguts were dissected from 7-day old blood-fed femaleAe. aegyptiat 24h (h) post-blood meal (pbm) or from sugar-fed females.Single nuclei were extracted from dissected midguts using the Nuclei PURE Prep nuclei isolation kit (Sigma-Aldrich, St. Louis, MO, USA). Library was performed according to the manufacter’s instructions (single cell 3’ protocol, 10x Genomics). single cell 3’ protocol, 10x Genomics
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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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Description |
10x Genomics
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Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) The analysis was performed with R package Seurat 3.1 Three data sets were integrated in to one, the single nuclei with over 500 & less than 6,500 genes were used for analysis, cells were clustered at resolution of 1. Uniform manifold approximation and projection (UMAP) was used to reduce the data dimensionality to visualize single-nucleus data. Assembly: AaegL5.2_pre_mRNA Supplementary files format and content: Tab-separated values files and matrix files
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Submission date |
Oct 17, 2023 |
Last update date |
Oct 17, 2023 |
Contact name |
Alexander W.E. Franz |
E-mail(s) |
franza@missouri.edu
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Organization name |
University of Missouri
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Department |
Department of Veterinary Pathology
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Street address |
303 Connaway Hall
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City |
columbia |
State/province |
MO |
ZIP/Postal code |
65211 |
Country |
USA |
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Platform ID |
GPL28657 |
Series (1) |
GSE245622 |
A cell atlas of the adult Aedes aegypti midgut revealed by single nucleus RNA-Seq |
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Relations |
BioSample |
SAMN37863421 |
SRA |
SRX22118346 |
Supplementary file |
Size |
Download |
File type/resource |
GSM7845934_barcodes1.tsv.gz |
20.0 Mb |
(ftp)(http) |
TSV |
GSM7845934_features1.tsv.gz |
132.4 Kb |
(ftp)(http) |
TSV |
GSM7845934_matrix1.mtx.gz |
150.9 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
Raw data are available in SRA |
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