|
| Status |
Public on Aug 29, 2019 |
| Title |
NCCIT_CDDP_RNA |
| Sample type |
SRA |
| |
|
| Source name |
germ cell tumor cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: NCCIT
cell type: nonseminoma
condition: CDDP-resistant
|
| Extracted molecule |
total RNA |
| Extraction protocol |
DNeasy Mini Kit (Qiagen), and RecoverAll Total Nucleic Acid Isolation Kit (ThermoFisher Scientific), Rneasy Mini Kit (Qiagen)
SureSelectXT Human All Exon V5+UTR kit (Agilent Technologies) and SureSelectXT RNA Reagent Kit (Agilent Technologies)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
cell line
deseq_counts_gene_annot.tsv
sample name:
NCCIT100
|
| Data processing |
Variant calling:
alignment bwa mem (0.7.10-r789)
picard-tools FixMateInformation (picard tools version 1.113)
picard-tools SortSam
picard-tools MarkDuplicates
samtools mpileup (version 0.1.19-96b5f2294a)
VarScan.v2.4.0 mpileup2cns, readcounts
SnpSift, snpEff
R pipeline to merge and annotate vcf file to create csv report
Copy-Number Variation:
CNVkit etal/cnvkit docker image was used - version 0.9.1
Gene Expression Analysis:
alignment bowtie2 version 2.2.5
DESeq2 (1.14.1)
Genome_build: Hg19
Supplementary_files_format_and_content: *coding.csv: annotated variants calls
Supplementary_files_format_and_content: *call.cns: Copy-number variations call
Supplementary_files_format_and_content: deseq_counts_gene_annot.tsv: deseq annotated gene counts
|
| |
|
| Submission date |
Aug 28, 2019 |
| Last update date |
Sep 10, 2019 |
| Contact name |
Jan Stuchly |
| Organization name |
Charles University in Prague, 2nd Faculty of Medicne
|
| Department |
Department of Paediatric Hematology/Oncology
|
| Street address |
V Uvalu 84
|
| City |
Prague |
| ZIP/Postal code |
15006 |
| Country |
Czech Republic |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE136560 |
Molecular basis of cisplatin resistance in testicular germ cell tumors |
|
| Relations |
| BioSample |
SAMN12647571 |
| SRA |
SRX6777784 |
