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Sample GSM7792346 Query DataSets for GSM7792346
Status Public on Jun 12, 2024
Title Tregs, CFA, rep 1
Sample type SRA
 
Source name Lung
Organism Mus musculus
Characteristics tissue: Lung
cell type: regulatory T cells
strain: C57BL/6
treatment: CFA
Extracted molecule total RNA
Extraction protocol Lung tissue were minced and digested with collagenase and DNase, and a single cell suspension was obtained. Mononuclear cells were isolated using a Percoll gradient centrifugation. RBCs were then lysed using a ACK lysis buffer. Tregs from FACS sorted using a FACS Melody cell sorter, and then captured for library generation and sequencing using 10X Chromium single cell capture chip according to the manufacturers protocol.
The single-cell RNAseq libraries were prepared according to manufacturer’s Chromium Single Cell 3ʹ protocol (10X Genomics, document # CG000204). 10,000 FACS sorted Tregs were targeted using the 10x Genomics Chromium Controller for cDNA synthesis and barcoding. cDNA quality and quantity of each sample were assessed using a Bioanalyzer High Sensitivity DNA assay. cDNA was used to begin fragmentation, followed by end-repair, adapter ligation, and sample indexing. Sample libraries were then assessed for proper construction using the same Bioanalyzer assay. Constructed libraries were pooled and quantified using a Quantabio Q cycler, and then denatured and sequenced on an Illumina Novaseq 6000 high-throughput sequencing platform with 28 cycles for the forward read and 91 cycles for the reverse read. Each cell was sequenced to a minimum of 20,000 reads per cell per manufacturer’s recommendations.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing The 10X results were subjected to processing through the Cell Ranger pipeline version 3.1.0 to generate Fastq files.
Fastq files were subsequently aligned using the Cell Ranger Count v7.1.0 pipeline within the 10X Genomics cloud analysis platform (https://www.10xgenomics.com/products/cloud-analysis), employing the Single Cell 3' Gene Expression library type.
Matrices, barcodes and genes were outputed from cloud platform for downstream processing and analysis.
Assembly: Mouse GRCm39 (mm39)
Supplementary files format and content: Tab separated value files and matrix files.
 
Submission date Sep 20, 2023
Last update date Jun 12, 2024
Contact name Booki Min
E-mail(s) booki.min@northwestern.edu
Organization name Northwestern University
Department Microbiology-Immunology
Lab Booki Min
Street address 300 E. Superior Street
City Chicago
State/province IL
ZIP/Postal code 60611
Country USA
 
Platform ID GPL24247
Series (1)
GSE243653 Single cell analysis uncovers striking cellular heterogeneity of lung infiltrating Tregs during steroid-responsive vs. steroid-resistant allergic airway inflammation
Relations
BioSample SAMN37483032
SRA SRX21839852

Supplementary file Size Download File type/resource
GSM7792346_TREG_CFA_S1.barcodes.tsv.gz 41.2 Kb (ftp)(http) TSV
GSM7792346_TREG_CFA_S1.features.tsv.gz 168.2 Kb (ftp)(http) TSV
GSM7792346_TREG_CFA_S1.matrix.mtx.gz 58.8 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA

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