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| Status |
Public on Jul 04, 2023 |
| Title |
2C_P14_WT_LCMV |
| Sample type |
SRA |
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| Source name |
spleen
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| Organism |
Mus musculus |
| Characteristics |
tissue: spleen
cell type: splenocytes
genotype: P14 wt
treatment: adoptive T cell transfer, LCMV infection
barcode umi_r2: GACTACCAcagtggtatcaacgcagagNNNNNNNNNNNNNNNN
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from splenocytes or CD8+ T cells (Qiagen, 74106), reverse transcribed (500ng), and uracil-DNA glycosylase-treated (NEB). TCR sequences were amplified in PCR I (2 μl cDNA) and II (3 μl PCR I) using two TCR specific Primers for the 3'region and UMI SmartN oligos and bardode primers for the 5'region (IDT, Table S7).
After agarose gel separation, 400-800 bp long PCR II fragments were barcoded with Illumina NEBNext Multiplex Oligos in PCR III (NEB, E7645L). The R2 fastq files start with an 8 bp barcode + 19bp adapter + 16bp Unique Molecular Identifier (UMI).
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
splenocytes, P14 wt mice after LCMV infection
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| Data processing |
Sequences were processed with Molecular Identifier Groups-Based Error Correction (MIGEC) program v1.2.9
The steps performed included: which included demultiplexing, UMI clustering, filtering, V(D)J junction and CDR3 region extraction, and clonotype assembly
The final CDR3 sequences were obtained by the FilterCdrBlastResults which filter for hot-spot PCR and NGS errors.
Assembly: mm10
Supplementary files format and content: tab-delimited text files with CDR3 sequences
Library strategy: TCR-seq
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| Submission date |
Feb 17, 2023 |
| Last update date |
Jul 04, 2023 |
| Contact name |
Gianni Monaco |
| E-mail(s) |
mongianni1@gmail.com
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| Organization name |
Freiburg Medical Center
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| Street address |
Breisacher Straße
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| City |
Freiburg |
| ZIP/Postal code |
79106 |
| Country |
Germany |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE225534 |
Gene Editing of Hematopoietic Stem Cells Restores T Cell Response in a Familial Hemophagocytic Lymphohistiocytosis Model [TCR] |
| GSE225541 |
Gene Editing of Hematopoietic Stem Cells Restores T Cell Response in a Familial Hemophagocytic Lymphohistiocytosis Model |
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| Relations |
| BioSample |
SAMN33339309 |
| SRA |
SRX19402540 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7049979_2C_P14_WT_LCMV_cdrblast.txt.gz |
114.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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