|
| Status |
Public on Jun 01, 2022 |
| Title |
GV stage oocytes, Input_2 |
| Sample type |
SRA |
| |
|
| Source name |
GV stage oocytes
|
| Organism |
Bos taurus |
| Characteristics |
developmental stage: GV stage
cell type: oocytes
ip antibody: none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIZOL, ThermoFisher
NEXTflex Small RNA-Seq Kit V3
small RNA sequencing, NextSeq 500 75bp single-end
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
small RNAs
|
| Data processing |
FASTQ to FASTA conversion (NGS TOOLBOX)
adapter trimming (NGS TOOLBOX)
size filtering 18-36nt (NGS TOOLBOX)
collapsing (NGS TOOLBOX)
filtering of low complexity reads (NGS TOOLBOX)
mapping with SeqWrap (custom Perl script that uses SeqMap to find best alignments with up to 1 internal mismatch and up to 2 non-template 3' bases)
sequence annotation with unitas v.1.5.3
Genome_build: bosTau7
Supplementary_files_format_and_content: Tab-delimited table (plain text file) containing sequences of mapped small RNAs, abundance and annotation (small RNA class)
|
| |
|
| Submission date |
Jun 04, 2019 |
| Last update date |
Jun 01, 2022 |
| Contact name |
David Rosenkranz |
| E-mail(s) |
rosenkranz@uni-mainz.de
|
| Organization name |
Johannes Gutenberg-University Mainz
|
| Department |
Institute of Anthropology
|
| Street address |
Anselm-Franz-von-Bentzel-Weg 7
|
| City |
Mainz |
| ZIP/Postal code |
55099 |
| Country |
Germany |
| |
|
| Platform ID |
GPL23055 |
| Series (1) |
| GSE132158 |
PIWIL3 forms a complex with TDRKH in mammalian oocytes |
|
| Relations |
| BioSample |
SAMN11955621 |
| SRA |
SRX5970459 |
