|
| Status |
Public on Jan 10, 2022 |
| Title |
SK-N-Be2C TWIST1_KO, Xenograft 3 [TBegT3] |
| Sample type |
SRA |
| |
|
| Source name |
SK-N-Be2C TWIST1_KO Xenograft
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
cell-line: SK-N-Be2C
genotype: TWIST1-KO
sample type: Tumor from Xenograft
|
| Growth protocol |
SK-N-Be2c either WT or TWIST1_KO cells have been cultured at the density of 2x10^5 cells/ml in DMEM containing 1% P/S and 10% FBS. SK-N-Be2c -derived xenograft have been obtained upon orthotopical injection of 5x10^5 cells in the left adrenal gland of mice. Xenograft have been grown since their size reached 1000 mm3.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from cell lines and tumors was extracted using RNeasy or miRNeasy mini kit (Qiagen, Hilden, Germany), respectively according to manufacturer instructions. RNA was quantified using Qubit Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was verified using the Agilent 2100 Bioanalyzer system (Agilent Technologies).
RNAseq was performed at the iGE3 Genomics platform (University of Geneva). The total RNA ribo-zero gold kit from Illumina was used for the library preparation with 1 µg or 500 ng of total RNA as input for cells (n=3 biological replicates/group) and tumors (n=4/group), respectively. Library molarity and quality were assessed with the Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies). Libraries were pooled at 2 nM and loaded for clustering on 1.5 lanes for cells and 1.5 lanes for tumors of a Single-read Illumina Flow cell. Reads of 100 bases were generated using the TruSeq SBS chemistry on an Illumina HiSeq 4000 sequencer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
fastq files were mapped with STAR version 2.5.2b on both the Human genome version Hg19 and the Mouse genome version Mm10, simultaneously. The following options were changed from the default parameters: --outSAMmultNmax 50; --outFilterMatchNminOverLread 0.4; --quantMode TranscriptomeSAM.
Transcriptome annotations in gtf format for both organisms were downloaded from the gencode website (https://www.gencodegenes.org/). Reads mapped on either the Human or the Mouse transcriptome were then parsed and split in one file per organism with an in-house perl script. Reads with matches on both Human and Mouse were discarded from the Mouse file. Per-gene quantification was then calculated independently for each organism using rsem version 1.3.0.
Mouse and Human data were analyzed independently, but following the same protocol. Genes with a log2 (rpkm) value above 1 in at least one sample were kept
Differential analysis was performed using the raw data counts in DESeq2 package version 1.26.0. For each comparison, the cutoffs for fold-change and adjusted p-values to call differentially transcribed genes were set to 1 and 0.05, respectively
Genome_build: Hg19/Mm10
Supplementary_files_format_and_content: The two supplemental tab-delimited text files Hs_GeneMat_raw_counts.txt and Mm_GeneMat_raw_counts.txt contain the rsem raw counts for Homo sapiens and Mus musculus.
|
| |
|
| Submission date |
Nov 03, 2020 |
| Last update date |
Jan 10, 2022 |
| Contact name |
Nicolo Riggi |
| Organization name |
CHUV
|
| Department |
Département de Pathologie Expérimentale
|
| Lab |
Institut universitaire de pathologie
|
| Street address |
Bugnon 25
|
| City |
Lausanne |
| State/province |
VD |
| ZIP/Postal code |
1011 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL25431 |
| Series (1) |
| GSE160765 |
TWIST1 expression is associated with high-risk neuroblastoma and promotes primary and metastatic tumor growth |
|
| Relations |
| BioSample |
SAMN16651485 |
| SRA |
SRX9426792 |
