|
| Status |
Public on Dec 08, 2017 |
| Title |
Qki5_CLIP1-3 |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic brain
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: CD1
genotype/variation: wild-type
tissue: brain
developmental stage: E14.5
|
| Treatment protocol |
Brain tissue was UV irradiated and subjected to Qki5-CLIP.
Partial RNase digestion, RNA linker ligation and PCR amplification.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qki5 bound fragments were ligated to a degenerate 3' linker to discriminate derivative tags from 3 different brains.
HITS-CLIP
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Qki5_CLIP1, Qki5_CLIP2, Qki5_CLIP3
|
| Data processing |
Library strategy: HITS-CLIP
Collapsing of exact sequences.
Stripping of degenerate linker (barcode:First 5nt; ends with a C and next 9nt degenerate linker ends with a C) .
Alignment with Bowtie
to have Bed and wiggle file.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Bed file, bedGraph file
|
| |
|
| Submission date |
Aug 29, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Masato Yano |
| E-mail(s) |
myano@med.niigata-u.ac.jp
|
| Organization name |
Niigata University
|
| Department |
Division of Neurobiology and Anatomy
|
| Street address |
757, Ichibancho, Asahimachidori, Chuo-ku, Niigata-shi,
|
| City |
Niigata |
| ZIP/Postal code |
950-0907 |
| Country |
Japan |
| |
|
| Platform ID |
GPL16417 |
| Series (2) |
| GSE103247 |
Qki5 CLIP in E14.5 mouse brain |
| GSE103248 |
RNAseq in control and shQk KD mouse neural stem cells, and Qki5 CLIP in E14.5 mouse brain |
|
| Relations |
| BioSample |
SAMN07571968 |
| SRA |
SRX3144865 |
