|
| Status |
Public on Jul 08, 2017 |
| Title |
KD_Ino80_replicate2 |
| Sample type |
SRA |
| |
|
| Source name |
ESC cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: ESC cells
cell type: ESC cells
|
| Treatment protocol |
Cells were transfected with siRNA following the protocol of Lipofectamine RNAiMAX Transfection Reagent. 72 hours post transfection, cells were harvested for experiments
|
| Growth protocol |
Cells were transfected with siRNA following the protocol of Lipofectamine RNAiMAX Transfection Reagent. 72 hours post transfection, cells were harvested for experiments
E14 cells were grown on feeder-free tissue culture plates (0.5% gelatin treated before use) in ESC media: knockout DMEM supplemented with 15% fetal bovine serum, leukemia inhibiting factor, L-glutamine, non-essential amino acids, penicillin/streptomycin and 2-mercaptoethanol. Cells were passaged at least twice before treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted using TRIzol Reagent, followed by DNaseI treatment and a second round of TRIzol extraction.
For RNA-seq, total RNA was extracted using TRIzol Reagent, followed by DNaseI treatment and a second round of TRIzol extraction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Total RNA (RiboMinus)
Ino80KD_vs_ctr_antisense_ratio.txt.gz
Ino80KD_vs_ctr_sense_ratio.txt.gz
Sample 100
|
| Data processing |
For mouse RNA-seq
Fastq files were used to map reads to mouse genome(mm9) with TopHat v2.0.8
Use SAMMate to caclutate RPKM using accepted bam file from Tophat
Mapped reads were counted and used to calculate the metagene profile for mutant and control
log2 ratio of mutant vs control was used for metagene profile
genome build: mm9
|
| |
|
| Submission date |
Jun 08, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Siavash K Kurdistani |
| E-mail(s) |
Skurdistani@mednet.ucla.edu
|
| Organization name |
UCLA
|
| Department |
Biological Chemistry
|
| Lab |
Kurdistani
|
| Street address |
615 Charles E Young Dr South
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE95633 |
MINC Regulates Pervasive Transcription in Yeast and Mammals |
|
| Relations |
| BioSample |
SAMN07204567 |
| SRA |
SRX2894815 |
