|
| Status |
Public on Nov 28, 2018 |
| Title |
untreated control 5 (blood) |
| Sample type |
SRA |
| |
|
| Source name |
peripheral blood mononuclear cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Blood
age: postnatal 110-140
genotype: FvB wild type
|
| Treatment protocol |
PMX-53 was resuspended in water and administered at 1.0 mg/kg/day via subcutaneous implantation via Alzet pump on day 40 when SCCs reached ~50 mm3. Paclitaxel was injected intravenously at 12 mg/kg every 4 days for a total of 3 injections per cycle
|
| Growth protocol |
Mice were maintained in standard conditions
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Dneasy Blood and tissue kit from Qiagen was used to isolate DNA from whole tumor and PBMC lysates
2-step PCR was used to construct libraries for Illumina NextSeq platform
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
PEAR (v.0.9.6) is used to combine paired-end sequences
Synthetic template sequences are extracted using custom script
Reads are aligned to TCR sequences and clonotypes are assembled using MiXCR (v2.1.9)
Clonotype counts are normalized using scaling factors based on synthetic templates
repseqio.v1.2:10090 (9a1b61eb20896bbb44a5d38d9359107b)
Supplementary_files_format_and_content: tab-delimited text files containing information on each clonotype: raw counts/frequency, normalized counts/frequency, V, D, J identity, CDR3 sequence, etc.
|
| |
|
| Submission date |
Mar 26, 2018 |
| Last update date |
Jan 30, 2020 |
| Contact name |
Lisa Coussens |
| E-mail(s) |
coussenl@ohsu.edu
|
| Organization name |
OHSU
|
| Street address |
SW Sam Jackson Park Rd
|
| City |
Portland |
| State/province |
Oregon |
| ZIP/Postal code |
97239 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE112321 |
Extrinsic C5a Activation Regulates Squamous Carcinogenesis and Limits Clonal T Cell Responses to Chemotherapy (Blood) |
| GSE112323 |
Extrinsic C5a Activation Regulates Squamous Carcinogenesis and Limits Clonal T Cell Responses to Chemotherapy |
|
| Relations |
| BioSample |
SAMN08795446 |
| SRA |
SRX3846716 |
