|
| Status |
Public on Jun 20, 2017 |
| Title |
DDX21 RIP replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
Kasumi-1 cells stablly expressing V5-tagged AES
|
| Organism |
Homo sapiens |
| Characteristics |
antibody: anti-DDX21 (Novus Biologicals BP100-1781)
|
| Treatment protocol |
1×107 Kasumi-1 cells stably expressing V5-tagged AES were rinsed with ice cold PBS. Cells were resuspended in 1 ml RIP buffer. RIP were performed with Anti-V5 (Abcam, ab9116), anti-DDX21 (Novus Biologicals BP100-1781) or control (Abcam, ab46540G).
|
| Growth protocol |
Kasumi-1 cells stablly expressing V5-tagged AES were cultured in RPMI-1640 medium with 20% of FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol
Sequencing libraries were constructed from total RIP RNA using the TruSeq™ small RNA sample prep kit v2 (Illumina) according to the instructions of the manufacturer. Before sequencing the libraries were size selected to 40-200 insert size.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Data processing |
SnoRNA-seq reads were trimmed using the cutadapt software (version 1.6). Trimmed reads were aligned to human genomes (hg19) with bowtie2 (version 2.2.4).
Specific binding was identified based on peak-calling strategy using the program Piranha. Peaks were called between IgG and RIP sample groups.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include genomic region of the peaks and reads per million values.
|
| |
|
| Submission date |
Apr 22, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Christian Rohde |
| E-mail(s) |
christian.rohde@uni-heidelberg.de
|
| Organization name |
Heidelberg University
|
| Lab |
Molecular Hematology and Oncology
|
| Street address |
Im Neuenheimer Feld 410
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL15456 |
| Series (2) |
| GSE80581 |
Identification of Amino Enhancer of Split (AES) and DDX21 binding snoRNAs by RIP-Seq. |
| GSE80602 |
AML1-ETO induces leukemia via C/D box snoRNA/RNPs. |
|
| Relations |
| BioSample |
SAMN04886221 |
| SRA |
SRX1720744 |
