|
| Status |
Public on Jan 04, 2023 |
| Title |
NIID1 cortex |
| Sample type |
SRA |
| |
|
| Source name |
Cerebral Cortex
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Cerebral Cortex
disease/model: NIID
|
| Treatment protocol |
No treatment.
|
| Growth protocol |
Human neural progenitor cells were cultured in neural progenitor media from Stem cell (Cat.05833).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Samples for RNA-seq were extracted with Trizol and quick RNA kit.
An amount of 1ug total RNA per sample was processed for library preparation using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations. Libraries were sequenced on a HiSeq with a read length configuration of 150 PE, targeting 100M total reads per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
NIID_Ctx1
MmCtx_NIIDvCTL.txt
|
| Data processing |
All total reads were mapped to hg38/mm9 by TopHat2 with default parameter followed by gene expression quantification and differential expression analysis using Cuffdiff.
The alternative splicing events, including SE, IR, MXE, A3SS and A5SS, were reported by rMATS.
Genome_build: hg38 (GRCh38), mm9 (MGSCv37)
Supplementary_files_format_and_content: txt and csv files include FPKM.
|
| |
|
| Submission date |
Aug 26, 2021 |
| Last update date |
Jan 04, 2023 |
| Contact name |
Ziyi Li |
| E-mail(s) |
zli16@mdanderson.org
|
| Organization name |
MD Anderson Cancer Center
|
| Street address |
1400 Pressler Street
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
770030 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE182878 |
GGC repeat expansion within NOTCH2NLC causes behavioral deficits and neurodegeneration through misregulated alternative splicing |
|
| Relations |
| BioSample |
SAMN21008734 |
| SRA |
SRX11929834 |
