|
| Status |
Public on May 29, 2023 |
| Title |
safb/2 dko clone 4, embyonic stemm cell, safb/2 dko bio rep #1 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic Stem Cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Embryonic Stem Cells
strain: CAST/B6 Male Rosa26-RMCE
cell type: embryonic stem cells
genotype: safb/2 dko
treatment: 3 Days Doxycycline induction
|
| Growth protocol |
RMCE embryonic Stem Cells were maintained in DMEM supplemented with 15% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
immunoprecipitated RNA was prepared with Zymo Clean and Concentrator
KAPA RNA Hyperprep Kit with RiboErase, 9uL of IP +1uL ERCC rna spike in sequenced
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
rip_dko_ezh2_negative_scaled.wig
rip_dko_ezh2_positive_scaled.wig
prc2_ezh2peaks_fc
|
| Data processing |
reads were aligned to genome using star/2.5.4b
filtered for reads that passed quality score q30
used subread featureCounts with manually curated peak files to assign sequence reads to features
Assembly: mm10
Supplementary files format and content: wig
Supplementary files format and content: excel file of processed data
|
| |
|
| Submission date |
Mar 21, 2023 |
| Last update date |
May 29, 2023 |
| Contact name |
Joseph Mauro Calabrese |
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Pharmacology
|
| Lab |
Calabrese
|
| Street address |
120 Mason Farm Road
|
| City |
Chapel Hill |
| State/province |
North Carolina |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE227892 |
A monoclonal antibody raised against human EZH2 cross-reacts with the RNA-binding protein SAFB [RIP-seq] |
| GSE227893 |
A monoclonal antibody raised against human EZH2 cross-reacts with the RNA-binding protein SAFB |
|
| Relations |
| BioSample |
SAMN33847036 |
| SRA |
SRX19744014 |
