|
| Status |
Public on Jul 30, 2019 |
| Title |
MBC7_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
breast cancer
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: patient derived xenograft cells
disease: derived from metastatic mammary adenocarcinoma
subtype: TRIPLE NEGATIVE SUBTYPE
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells isolated from PDXs and normal breast tissues were used for total RNA extraction with Zymo Research kit (cat# 1055) according to manufacturer protocol
libraries were constructed using Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) starting from at least 200 ng of total RNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
MBC7_1
|
| Data processing |
Demultiplexing of reads from superpools into separate pools was performed with bcl2fastq.
Reads were aligned to the homo sapiens genome build hg19 using tophat (v2.0.8), which uses Bowtie (2.1.0) and Samtools (v0.1.18) using default parameters and --transcriptome H. sapiens index, UCSC hg19 gtf.
Raw read counts were summarised using HTSeq (v0.5.3p9), then normalized for library size differences using estimateSizeFactors function from DESeq package (v1.10.1).
Differential expression of genes was calculated with the same R package, using three biological replicas for each PDX against non three pathologic tissue samples
Genome_build: hg19
Supplementary_files_format_and_content: A Excel worksheet file with normalized read counts for all samples
|
| |
|
| Submission date |
Apr 10, 2019 |
| Last update date |
Jul 30, 2019 |
| Contact name |
Marine Melixetian |
| E-mail(s) |
[email protected]
|
| Organization name |
European Institute of Oncology
|
| Street address |
via Adamello 16
|
| City |
Milano |
| ZIP/Postal code |
20141 |
| Country |
Italy |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE129563 |
Couple transcriptome and genomic data obtained from the PDXs to identify pathways linking oncogenic alterations |
|
| Relations |
| BioSample |
SAMN11382593 |
| SRA |
SRX5661275 |
