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Sample GSM6365794 Query DataSets for GSM6365794
Status Public on Jun 07, 2023
Title Group 3 innate lymphoid cell, aged gut ILC3s rep2, scRNAseq
Sample type SRA
 
Source name small intestine
Organism Mus musculus
Characteristics cell type: Group 3 innate lymphoid cell
tissue: small intestine
strain: C57BL/6
age: 18-months-old
Sex: male
Extracted molecule total RNA
Extraction protocol Small intestinal ILC3s were sorted from siLP of aged mice. All samples were uniformly resuscitated and washed twice by PBS (with 0.1% BSA), then the cells were 1 ml stain buffer (with 0.1% BSA) and counted. The viability of cells in all samples was assessed >80%.
Cells for all samples were labeled with sample tags (BD Mouse Single-Cell Multiplexing Kit, USA), counted, and multiplexed, ready for single-cell capture. Single-cell capture and cDNA synthesis were performed by the BD Rhapsody Single-Cell Analysis System (BD, USA), according to the manufacturer's instructions.
scRNA-seq (BD Rhapsody)
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description BD Rhapsody
for multiple sample
sample tag 12
Data processing Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
The FASTQ files were processed using the BD Rhapsody Targeted analysis pipeline v1.9.1 on the Seven Bridges platform (https://www.sevenbridges.com).
First of all, read pairs with low mean base quality scores (less than 20) were removed. The filtered R1 reads were analyzed to identify the cell label sequences and unique molecular identifiers(UMIs). R2 reads were aligned to the mice reference genome(GRCm38) using Bowtie2. Valid reads with the same cell label, the same UMI sequence, and the same gene were collapsed into a single raw molecule. Recursive substation error correction (RSEC) and distribution-based error correction (DBEC) algorithms were applied to correct sequencing and PCR errors of raw UMI counts. The final single-cell expression matrices containing DBEC-adjusted molecules were used for downstream analysis.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Csv files include readcount values for each Sample with different sample tag
 
Submission date Jul 21, 2022
Last update date Jun 07, 2023
Contact name lie wang
E-mail(s) wanglie@zju.edu.cn
Organization name zhejiang universiry
Department immunology
Street address Zijingang Campus, Zhejiang University,Yuhangtang Road 866
City hangzhou
State/province zhejiang
ZIP/Postal code 310058
Country China
 
Platform ID GPL19057
Series (1)
GSE208733 Cxxc finger protein 1 maintains homeostasis and function of intestinal group 3 innate lymphoid cells with aging
Relations
BioSample SAMN29867602
SRA SRX16373325

Supplementary file Size Download File type/resource
GSM6365794_1_Combined_SMK_FKDL202602918-1a_RSEC_MolsPerCell.csv.gz 27.1 Mb (ftp)(http) CSV
GSM6365794_1_SMK_FKDL202602918-1a_Sample_Tag_Calls.csv.gz 76.4 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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