|
| Status |
Public on May 31, 2023 |
| Title |
T_IM_12 [RNA-Seq] |
| Sample type |
SRA |
| |
|
| Source name |
tumor
|
| Organism |
Mus musculus |
| Characteristics |
genotype: IMP1/MYCN, CRE +
tumor type: neuroblastoma tumor
batch run: run3
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Transgenic tumors and murine organs were dissected and shock-frozen on dry ice. Approximately 30 mg of frozen tissue was lysed in 600 µl RLT lysis buffer (Qiagen) containing β-mercaptoethanol. Tumors were homogenized with Zirconium Oxide beads and Precellys 24 homogenizer (berting technologies). Lysates were subjected to the Qiagen AllPrep DNA/RNA/Protein Kit protocol, with the exception, that precipitated protein was solubilized in 5% SDS solution.
For RNA-seq library preparation of transgenic mouse tumor samples, 2 µg of total RNA served as input for polyA(+)-RNA enriched and strand-specific library preparation, performed by Novogene (Hong Kong)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
T_IM_12
|
| Data processing |
Sequenced strand specific paired-end reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 2.8) with parameters -q 20 -O 7 -m 20 –trim-n
Trimmed reads were mapped against the human genome (UCSC mm39) using HiSat2 (v 2.1.0) with parameters -q --rna-strandness RF --dta -k 5
Secondary alignments were filtered out using samtools (v 1.10)
Mapped reads were summarized using featureCounts (v 2.0.0) with parameterst -p -s 2 -T 6 -M -t exon -g gene_id and Ensembl gene annotations (GRCm 39.105)
Raw counts were corrected for batch effects using ComBat-seq from R package sva (version 3.46.0)
Differential gene expression was assessed using R/edgeR (v 3.40) using TMM normalization
Assembly: mm38
Supplementary files format and content: Comma-separated text file including FPKM, log2 fold change and false discovery rate values
|
| |
|
| Submission date |
Dec 28, 2022 |
| Last update date |
May 31, 2023 |
| Contact name |
Danny Misiak |
| E-mail(s) |
danny.misiak@medizin.uni-halle.de
|
| Phone |
+49345573962
|
| Organization name |
Martin Luther University Halle-Wittenberg
|
| Department |
Molecular Cell Biology
|
| Lab |
Hüttelmaier Lab
|
| Street address |
Kurt-Mothes-Str. 3a
|
| City |
Halle (Saale) |
| ZIP/Postal code |
06120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE181580 |
IGF2BP1 induces neuroblastoma via a druggable feedforward loop with MYCN promoting 17q oncogene expression [mouse RNA-seq] |
| GSE181582 |
IGF2BP1 induces neuroblastoma via a druggable feedforward loop with MYCN promoting 17q oncogene expression |
|
| Relations |
| BioSample |
SAMN32471441 |
| SRA |
SRX18865195 |
