 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 22, 2020 |
| Title |
MC38 B+ replicate3 |
| Sample type |
SRA |
| |
|
| Source name |
CD8 tumor infiltrating lymphocytes
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: CD8 TILs from MC38
replicate: 3
biotin: biotin+
|
| Treatment protocol |
Biotin+ and Biotin- CD8 TILs from murine E0771 and MC38 tumor were collected by FACS. Then TILs were cultured in T cell medium containing 100 IU/mL IL2 for 24 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted from 10000 cells per sample using PicopureTM RNA isolation kit (Qiagen RNase-Free DNase set were used to digest trace DNA).
TCRbeta library was prepared by SMART filter process (iRepertoire). Details please see: https://irepertoire.com/technology/
Illumina MiSeq v2
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Library strategy: TCR-seq
Our data processing is a proprietary process in which reads are trimmed for quality, paired and stitched, then subjected to mapping to a build of the IMGT database for V-, D-, J-, and C-gene references.
With TCR data, following mapping and the identification of CDR3s via conserved motifs, additional filtering steps include the removal of chimeric sequences, sequences that likely contain PCR and/or sequencing error, and then a collapse of reads based on sequence identity (which forms the Frequency or Copy numbers seen in iRweb).
With TCR data, reads that have a frequency of 1 following collapse are removed.
The FASTQ files have not been trimmed nor stitched. The FASTA files have only been trimmed for quality, overlapped, and stitched. Each sample will have a R1 and R2 (FASTQ) and a FASTA formatted, trimmed and stitched read (3 files per sample).
Genome_build: We do not use a genome build per se, but use sequences pulled from the IMGT database
Supplementary_files_format_and_content: cvs files compressed in zip file contains TCRbeta sequences and their frequencies of each sample and statistic analysis
|
| |
|
| Submission date |
Jul 16, 2020 |
| Last update date |
Oct 22, 2020 |
| Contact name |
Peng Wu |
| E-mail(s) |
[email protected]
|
| Phone |
8587847626
|
| Organization name |
Scripps Research
|
| Department |
Molecular Medicine
|
| Lab |
Wu Lab
|
| Street address |
10550 North Torrey Pines Road
|
| City |
San Diego |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL16417 |
| Series (2) |
| GSE154604 |
Detecting Tumor Specific Antigen-Reactive T cells from Tumor Infiltrating Lymphocytes via Interaction Dependent Fucosyl-biotinylation [TCR-seq] |
| GSE154605 |
Detecting Tumor Antigen-Specific T Cells via Interaction-Dependent Fucosyl-Biotinylation |
|
| Relations |
| BioSample |
SAMN15564094 |
| SRA |
SRX8752324 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4675537_131084_0_CDR3Length.csv.gz |
174 b |
(ftp)(http) |
CSV |
| GSM4675537_131084_0_Naddition.csv.gz |
117 b |
(ftp)(http) |
CSV |
| GSM4675537_131084_1_CDR3Length.csv.gz |
178 b |
(ftp)(http) |
CSV |
| GSM4675537_131084_1_Naddition.csv.gz |
116 b |
(ftp)(http) |
CSV |
| GSM4675537_131084_CDR3_list_1.csv.gz |
2.2 Kb |
(ftp)(http) |
CSV |
| GSM4675537_131084_CDR3_list_2.csv.gz |
3.1 Kb |
(ftp)(http) |
CSV |
| GSM4675537_131084_CDRs.csv.gz |
3.1 Kb |
(ftp)(http) |
CSV |
| GSM4675537_131084_J_0_trim.csv.gz |
103 b |
(ftp)(http) |
CSV |
| GSM4675537_131084_J_0_usage.csv.gz |
123 b |
(ftp)(http) |
CSV |
| GSM4675537_131084_J_1_trim.csv.gz |
103 b |
(ftp)(http) |
CSV |
| GSM4675537_131084_J_1_usage.csv.gz |
125 b |
(ftp)(http) |
CSV |
| GSM4675537_131084_V_0_trim.csv.gz |
102 b |
(ftp)(http) |
CSV |
| GSM4675537_131084_V_0_usage.csv.gz |
164 b |
(ftp)(http) |
CSV |
| GSM4675537_131084_V_1_trim.csv.gz |
101 b |
(ftp)(http) |
CSV |
| GSM4675537_131084_V_1_usage.csv.gz |
170 b |
(ftp)(http) |
CSV |
| GSM4675537_131084_pep.csv.gz |
25.9 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
