|
| Status |
Public on May 01, 2018 |
| Title |
U87_tumor_TW_681_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Brain
genotype: TWIST1 Wild
|
| Growth protocol |
U87MG glioma cells with WT TWIST1 and CRISPR mediated TWIST1 deletion were maintaned in DMEM supplemented with 10% Fetal bovine Essence (VWR). Cells plated at 1.2 x10^6 in 60 mm plate were harvested 48h later. Same cells were injected in the brain of nude mice. Animals were sucrificed after when clinical manifestation is detected. Animals were perfuced with PBS and tumors were collected under fluorescent dissecting microscope.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Harvested cells were lysed in Trizol reagent. Tumor fragments ground in liquid nitrogen were lysed in Trizol reagent. RNAesy kit was used to extract RNA
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina CASAVA v1.8.2 software was used for basescalling.
Fragment reads were mapped to the UCSC mouse genome (hg38) using Tophat2.
Raw counts for each gene were obtained by HTSeq2, and we also obatined the FPKMs (Fragments Per Kilobase of transcript per Million mapped reads) of raw counts using Cufflinks and scaled via the median of the genomic means for each gene across all libraries as described (Anders and Huber, 2010 [PMID 20979621]).
Adjusted p values for each gene were obtained by Deseq 2.
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Tab-delimited text file includes rawcounts for each Sample.
|
| |
|
| Submission date |
Oct 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
LEI HUANG |
| E-mail(s) |
hleicug@gmail.com
|
| Phone |
7134411019
|
| Organization name |
Houston Methodist Research Institute
|
| Department |
Systems medicine and Bioengineering
|
| Lab |
SMAB
|
| Street address |
6565 Fannin ST, B5-041
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE106159 |
Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and TWIST1 knock out U87 xenograft mice transcriptomes |
|
| Relations |
| BioSample |
SAMN07834382 |
| SRA |
SRX3326313 |
