|
| Status |
Public on Dec 01, 2018 |
| Title |
932S |
| Sample type |
SRA |
| |
|
| Source name |
IDH1WT tumor line (RAS glioma)
|
| Organism |
Mus musculus |
| Characteristics |
tissue: cell line derived from tumor
idh genotype: IDH wildtype
mouse genotype: N::TVA; Cdkn2alox/lox
cell type: Cell line derived from brain tumor
background strain: C57Bl/6, 129, and FVB/n
|
| Growth protocol |
DMEM, 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Qiagen DNeasy DNA extraction kit.
Genomic DNA was processed with the Agilent SureSelect XT Mouse Methyl-Seq Enrichment System capture kit following manufacturer’s recommendations.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
IDH1WT tumor line (RAS glioma)
14323X6_932S
|
| Data processing |
Paired reads were aligned to the genome with Novocraft Novoalign v3.7.1 with options -b 2 -t 360 -h 120 -r random.
Reads were de-duplicated with Picard MarkDuplicates v2.9.0.
Alignments were processed with USeq (v9.0.8) NovoalignBisulfiteParser. Point data was filtered for CpG contexts using USeq ParsePointDataContexts. Base fraction CpG methylation tracks were generated with USeq BisStat with a minimum read coverage of 10.
Genome_build: mm10
Supplementary_files_format_and_content: tar bundle of bar.zip point data representing Converted and NonConverted CpG observations from NovoalignBisulfiteParser.
Supplementary_files_format_and_content: bigWig file representation of the fraction methylation at CpG sites
Supplementary_files_format_and_content: bed file of the covered regions with a mean depth of 10 bp across samples used in differential methylation analysis
|
| |
|
| Submission date |
Dec 01, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Sheri Holmen |
| E-mail(s) |
sheri.holmen@hci.utah.edu
|
| Phone |
801-213-4237
|
| Organization name |
University of Utah
|
| Department |
Surgery
|
| Street address |
2000 Circle of Hope Dr.
|
| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84112 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE107614 |
Mutant IDH1 promotes glioma formation in vivo [Bisulfite-seq] |
| GSE107616 |
Mutant IDH1 promotes glioma formation in vivo |
|
| Relations |
| BioSample |
SAMN08120329 |
| SRA |
SRX3437638 |
