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Sample GSM7845934 Query DataSets for GSM7845934
Status Public on Oct 17, 2023
Title midgut
Sample type SRA
 
Source name midgut
Organism Aedes aegypti
Characteristics tissue: midgut
strain: Higg's White Eye
age: 7-day-old
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
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 10x Genomics
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
 
Submission date Oct 17, 2023
Last update date Oct 17, 2023
Contact name Alexander W.E. Franz
E-mail(s) franza@missouri.edu
Organization name University of Missouri
Department Department of Veterinary Pathology
Street address 303 Connaway Hall
City columbia
State/province MO
ZIP/Postal code 65211
Country USA
 
Platform ID GPL28657
Series (1)
GSE245622 A cell atlas of the adult Aedes aegypti midgut revealed by single nucleus RNA-Seq
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 SelectorHelp
Raw data are available in SRA

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