 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 25, 2019 |
| Title |
M134-080515 |
| Sample type |
SRA |
| |
|
| Source name |
Islets
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: NOD/ShiltJ
tissue: Islets
tetramer: mixed sample (non-demultiplexed)
age in weeks: 9
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: Sheet10_TRAC_080515.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 |
SAMN12364067 |
| SRA |
SRX6592014 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3976433_Sheet10_TRAC_080515.xlsx |
81.2 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
