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Sample GSM3067704 Query DataSets for GSM3067704
Status Public on Nov 28, 2018
Title untreated control 5 (skin)
Sample type SRA
 
Source name primary tumor
Organism Mus musculus
Characteristics age: postnatal 110-140
tissue: Skin
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)
GSE112322 Extrinsic C5a Activation Regulates Squamous Carcinogenesis and Limits Clonal T Cell Responses to Chemotherapy (Skin)
GSE112323 Extrinsic C5a Activation Regulates Squamous Carcinogenesis and Limits Clonal T Cell Responses to Chemotherapy
Relations
BioSample SAMN08795489
SRA SRX3846768

Supplementary file Size Download File type/resource
GSM3067704_TMT5_normClonotypeCounts.txt.gz 2.5 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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