|
| Status |
Public on Dec 30, 2016 |
| Title |
ZNFKD_exp2 |
| Sample type |
SRA |
| |
|
| Source name |
Daoy cell line
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: brain/cerebellum
cell type: cerebellar medulloblastoma
cell line: Daoy
genotype/variation: ZNF423 knockdown
|
| Treatment protocol |
Daoy cells were cultured in DMEM supplemented with 10% fetal bovine serum. Daoy cells were flow sorted after infected with virus for 5days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. mRNA were purified with Dynabeads® mRNA Purification Kit (Cat#61006).
RNA libraries were prepared for sequencing using strand specific dUTP protocols.(nature methods 2010, 7(9): 709-715)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample 5
|
| Data processing |
Illumina CASAVA-1.8.2 software used for basecalling.
Reads were aligned to the hg19 genome assembly using STAR version 2.3.1f with parameters --genomeDir hg19 –runThreadN 8 …
Reads of genes were counted using HOMER software (Mol Cell 2010, 38(4):576-589) followed analysis with edgeR package in R
for bedGraph file, reads were mapped to hg19 using STAR 2.3.1f, and the bed files were made based on the mapping information with HOMER software command “makeTagDirectory” with -flip option and followed by “makeUCSCfile”.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph file reports Total Tags
|
| |
|
| Submission date |
Jul 18, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Bruce Hamilton |
| E-mail(s) |
bah@ucsd.edu
|
| Phone |
8588222298
|
| Organization name |
UC San Diego
|
| Department |
Medicine
|
| Lab |
CMM
|
| Street address |
9500 Gilman Dr.
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE59598 |
mRNA expression in human DAOY cells |
|
| Relations |
| BioSample |
SAMN02927662 |
| SRA |
SRX657421 |
