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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 23, 2018 |
| Title |
LN229/EGFRvIII/shTRIM24-1# (WGC090200R) |
| Sample type |
SRA |
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| Source name |
GBM cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: GBM cells
genotype/variation: Overexpression of EGFRvIII
treatment: TRIM24 shRNA-#1
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
From purified polyA RNA
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
WGC090200R
Overexpression of EGFRvIII and treatment with a TRIM24 shRNA-#1
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were calculated using a protocol from Trapnell et al., Nat Biotechnol, 2010. In short, A fragment corresponds to a single cDNA molecule, which can be represented by a pair of reads from each end. Exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. FPKM is conceptually analogous to the reads per kilobase per million reads sequenced (RPKM) measure, but it explicitly accommodates sequencing data with one, two, or – if needed for future sequencing platforms – higher numbers of reads from single source molecules.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
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| Submission date |
Feb 27, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Haizhong Feng |
| E-mail(s) |
fenghaizhong@sjtu.edu.cn
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| Phone |
862168383921
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| Organization name |
Shanghai Jiao Tong University
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| Department |
Ren Ji Hospital
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| Street address |
Pujian Road 160
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| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200127 |
| Country |
China |
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| Platform ID |
GPL20795 |
| Series (1) |
| GSE95386 |
TRIM24 is an oncogenic transcriptional co-activator of STAT3 in glioblastoma |
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| Relations |
| SRA |
SRX2591942 |
| BioSample |
SAMN06472262 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2509632_200-R_FPKM.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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