|
| Status |
Public on Aug 07, 2021 |
| Title |
999-124 (SID-30) |
| Sample type |
SRA |
| |
|
| Source name |
FFPE fixed biopsy of melanoma
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: melanoma
tissue: lymph node
melanoma stage, ajcc 6th edition: 3C
prognosis: poor prognosis
|
| Treatment protocol |
na
|
| Growth protocol |
na
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
HTG EdgeSeq Immuno-Oncology Panel (Tucson, Arizona)
Tumor samples were processed by adding HTG Lysis Buffer to lyse and/or permeabilize the RNA available to subsequently bind to corresponding target-specific Nuclease Protection Probes (NPPs). The lysed samples was transferred to a 96-well micro-titer plate. Target capture was done by adding NPPs to the lysed samples to hybridize to the target mRNA. Then S1 nuclease was added to digest non-hybridized miRNA and excess NPPs, leaving target mRNA/NPP duplexes. S1 digestion was terminated by heat denaturation of S1 enzyme. The processed samples were used as template to set up PCR reactions with primer tags. These tags share common sequences that are complementary to 5’-end and 3’-end “wing” sequences of the probes and common adaptors required for cluster generation for deep sequencing. The library was prepared using HTG EdgeSeq PCR processing. Following library preparation, it was quantified using HTG EdgeSeq KAPA Library Quantification for Illumina Sequencing. All samples and controls were quantified in triplicate.
HTG EdgeSeq KAPA Library Quantification/Calculator
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina bcl2fastq is used for generation of FASQ files
HTG EdgeSeq Parser software (version10196100F) is used for alignment to a priori defined target sequences. Requirements include %Q30 >= 85%, %PF >= 75%, and 180 < CD < 290
Post-sequencing quality control using statistical process controls on negative control probes (see supplementary file for samples removed by QC).
Supplementary_files_format_and_content: Comma separated values file of raw mRNA count values with samples as columns and mRNA targets as rows.
|
| |
|
| Submission date |
Aug 05, 2021 |
| Last update date |
Aug 07, 2021 |
| Contact name |
Dominic LaRoche |
| E-mail(s) |
dlaroche@htgmolecular.com
|
| Organization name |
HTG Molecular Diagnostics
|
| Street address |
3430 E. Global Loop
|
| City |
Tucson |
| State/province |
AZ |
| ZIP/Postal code |
85706 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE181525 |
Associations of immune cell homing gene signatures and infiltrates of lymphocyte subsets in human melanomas: discordance with CD163+ myeloid cell infiltrates |
|
| Relations |
| BioSample |
SAMN20593644 |
| SRA |
SRX11657326 |
