|
| Status |
Public on May 01, 2023 |
| Title |
TET1 homozygous loss of function mutant replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
TET1 homozygous loss of function mutant, primary human glioblastoma culture
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: adult brain
tumor: Glioblastoma (Grade IV)
derived culture: G523NS
genotype/variation: TET1 homozygous loss of function mutant
|
| Treatment protocol |
Untreated
|
| Growth protocol |
Cells were grown adherently on laminin-coated tissue culture plates in neural stem cell media containing EGF and FGF
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed on the plate using RLT buffer (Qiagen) and total RNA was extracted using the Qiagen Rneasy kit with on-column Dnase digestion
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
TET1N1-B
|
| Data processing |
FASTQ files were aligned to the hg19 genome and sorted using STAR v2.4.2a in two-pass mode with the following redefined parameters: --sjdbOverhang 47, --genomeChrBinNbits 18, --genomeSAsparseD 2
Read groups were added to the aligned and coordinate-sorted BAM files using picard v1.9.1
QC of BAM files were checked using RNA-SeQC v1.1.8
Read counts were generated from the bam files using HTSeq v0.6.1 with the following redefined parameters: --stranded=reverse, --type=exon, --idattr=gene_id, --mode=union
Annotation file was based on the Gencode v19 GTF file
Genome_build: hg19
Supplementary_files_format_and_content: Read counts by clone_EnsemblID.txt file contains log2 normalized read counts by gene
|
| |
|
| Submission date |
Aug 01, 2017 |
| Last update date |
May 01, 2023 |
| Contact name |
Fiona J Coutinho |
| E-mail(s) |
fiona.coutinho@sickkids.ca
|
| Organization name |
The Hospital for Sick Children
|
| Department |
Developmental and Stem Cell Biology
|
| Lab |
Dr. Peter Dirks
|
| Street address |
686 Bay Street, PGCRL 16-9801
|
| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
M5G 0A4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE102136 |
Single Copy Loss of Tet1 disrupts neural stem cell differentiation and enhances GBM aggressiveness |
|
| Relations |
| BioSample |
SAMN07436167 |
| SRA |
SRX3053986 |
