|
| Status |
Public on Jan 25, 2019 |
| Title |
TMZ_HOTAIR-KO2 replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
RNA-seq of TMZ-treated HOTAIR regulatory element KO glioma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U251
cell type: glioma
genotype: HOTAIR regulatory element KO
|
| Treatment protocol |
TMZ-treated groups were 1mM TMZ treated for 72h,and DMSO-treated groups were control groups for the same conditions
|
| Growth protocol |
U251 cell line was cultured in DMEM supplemented with 10% fetal bovine serum (FBS)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Eastep® Super Total RNA Extraction Kit following the manufacturer’s instruction. Then, ribosomal RNA was deleted from 5 μg of total extracted RNA using the Ribo-Zero Gold Kit, using Illumina HiSeq-4000.
RNA, Capture Hi-C libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
RNA-seq of TMZ-treated HOTAIR regulatory element KO glioma cell line
|
| Data processing |
Clean reads of RNA-seq were mapped to hg19 using HISAT2(2.1.0)
Expression levels of all genes were counted and expression profile matrix was constructed with HTSeq (0.9.1)
Differential expression analysis was calculated in R using DESeq2(1.18.1), with p value < 0.05 and fold change > 2 or < 1/2
Clean reads of Capture Hi-C were cut into two pieces in the DpnII sites
All the reads were mapped to hg19 with Bowtie2(2.3.1)
Report all the reads that contains the Bait sequence
Genome_build: hg19
Supplementary_files_format_and_content: Text files include genes counts values, Capture Hi-C signal peaks for each Sample
|
| |
|
| Submission date |
Jan 24, 2019 |
| Last update date |
Jan 25, 2019 |
| Contact name |
Bohan Chen |
| E-mail(s) |
bhchen1@sina.cn
|
| Organization name |
Nankai University
|
| Street address |
NO.94 Weijin Road
|
| City |
Tianjin |
| ZIP/Postal code |
300071 |
| Country |
China |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE125629 |
A HOTAIR regulatory element modulates glioma cell sensitivity to temozolomide through long-range regulation of multiple target genes |
|
| Relations |
| BioSample |
SAMN10790521 |
| SRA |
SRX5280578 |
