|
| Status |
Public on Dec 15, 2019 |
| Title |
OLN93 Sox10-deficient (Sox10ko) cells, clone B |
| Sample type |
SRA |
| |
|
| Source name |
OLN93 cell line, Crispr/Cas9-mediated Sox10 inactivation
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell line: OLN93
cell type: Oligodendrocytes cell line
genotype/variation: Sox10-deficient
|
| Treatment protocol |
The genome of OLN93 cells was edited using Crispr/Cas9 to inactivate the Sox10 gene.
|
| Growth protocol |
OLN93 cells were kept in DMEM medium with 10% FCS and PenStrep and split every 96 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini Kit according to QIAGEN protocol.
RNA libraries were prepared for sequencing using Illumina Stranded mRNA Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
OLN93_Sox10ko_2
RNAseq data from OLN93 cells (Sox10ko).
processed data file: OLN93_Sox10_ko_CrisprCas_vs_ctrl.xlsx
|
| Data processing |
Sequencing data were pooled using the Illumina HiSeq 2500 platform and converted into fastq files.
Reads from rRNA, tRNA, mt-rRNA and mt-tRNA were purged from demultiplexed reads.
Reads were aligned to rn5 reference genome using STAR (version 2.5.1.b).
Unique maps were generated using HTSeq count relating to Ensembl gene identifier version 75.
Statistical analysis of raw data was done with DESeq2 by R version 1.8.1.
Genome_build: rn5 (Rnor_5.0)
Supplementary_files_format_and_content: *_rn5_htseq-count.tabular.txt: Tab-delimited text files
Supplementary_files_format_and_content: OLN93_Sox10_ko_CrisprCas_vs_ctrl.txt: Tab-delimited text file
|
| |
|
| Submission date |
Aug 29, 2019 |
| Last update date |
Dec 16, 2019 |
| Contact name |
Michael Wegner |
| Organization name |
Friedrich-Alexander Universität Erlangen-Nürnberg
|
| Department |
Institut of Biochemistry
|
| Lab |
Michael Wegner
|
| Street address |
Fahrstr. 17
|
| City |
Erlangen |
| State/province |
Bavaria |
| ZIP/Postal code |
91054 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE136659 |
Determination of Sox10-regulated genes in the oligodendroglial precursor cell line OLN93 |
|
| Relations |
| BioSample |
SAMN12660083 |
| SRA |
SRX6772536 |
