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Sample GSM3976435 Query DataSets for GSM3976435
Status Public on Jul 25, 2019
Title M198_M-3-25-16
Sample type SRA
 
Source name Islets, pLN
Organism Mus musculus
Characteristics strain/background: NOD/ShiltJ
tissue: mixed sample (non-demultiplexed)
tetramer: 13-21
age in weeks: 7
mouse number: No Mouse Number
Extracted molecule total RNA
Extraction protocol Protocol is detailed in Holt et al. (PMID 29224077). In short, cells stained with tetramer were single cell sorted into single wells that contained lysis buffer from the SuperScript Vilo Master Mix kit. Isolated total RNA was reverse transcribed, pre-amplified and then, utilizing the Fluidigm AccessArray, the TCRalpha and TCRbeta chains for each individual cell were barcoded and amplified again. Then samples were sent to TSRI Genomics Core for library preparation.
Detailed in Holt et al.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina MiSeq
 
Description Sheet number: Sheet12-032516_TRAC_and_TRBC.xlsx
processed data file: ALL_T1D_TCRA_TCRB_Master_List_Ms.xlsx
Data processing Post sequencing, adapter trimming was performed by TrimGalore v0.4.1 (F Krueger - A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files (2015): https://github.com/FelixKrueger/TrimGalore). FLASH was used to pair end reads (FLASH: Fast length adjustment of short reads to improve genome assemblies. T. Magoc and S. Salzberg. Bioinformatics 27:21 (2011), 2957-63.)
Cd-hit was used for upstream analysis (Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences (2006) Bioinformatics, v22(13), pages 1658-9.). After counts were generated, sequences with the highest counts and greatest alignment were run through the International Immunogenetics information system (IMGT) ("IMGT®, the international ImMunoGeneTics information system® http://www.imgt.org). Further data analysis utilized a custom R script.
Genome_build: hg19
Supplementary_files_format_and_content: All alpha and beta chains returned from IMGT were placed into a single Excel file. This file has the barcode information of the alpha or beta chain for each single cell as well as metadata. Each "Sheet" in this file is a sorted 96 well plate; thus, by sheet, the alpha and beta chains of a TCR from a single cell can be reassembled. Not all T cells had an alpha and a beta chain that amplified, thus some cells have only one or the other.
 
Submission date Jul 25, 2019
Last update date Jul 27, 2019
Contact name Luc Teyton
E-mail(s) lteyton@scripps.edu
Organization name TSRI
Lab Teyton Lab
Street address 10550 North Torrey Pines Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platform ID GPL16417
Series (2)
GSE134883 The Position Beta57 of IAg7 Controls the Early Anti-Insulin Response and Onset of Diabetes in NOD mice to Link MHC and Disease [sequencing]
GSE134885 The Position Beta57 of IAg7 Controls the Early Anti-Insulin Response and Onset of Diabetes in NOD mice to Link MHC and Disease
Relations
BioSample SAMN12364065
SRA SRX6592016

Supplementary file Size Download File type/resource
GSM3976435_Sheet12-032516_TRAC_and_TRBC.xlsx 56.1 Kb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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