|
| Status |
Public on Nov 22, 2022 |
| Title |
4C, testis part of ovotestis |
| Sample type |
SRA |
| |
|
| Source name |
Adult testis part
|
| Organism |
Talpa occidentalis |
| Characteristics |
tissue: Adult testis part
genotype: wildtype
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Embryonic tissues were dissociated with trypsin, filtered through a cell strainer to obtain a single cell suspension and subsequently fixed in 2% formaldehyde.
4C-seq libraries were prepared according to standard protocols. For the first digestion NlaIII was used, and for the second digestion DpnII was used. A total of 1.6 mg of each library was amplified by PCR for the viewpoint in the promoter of Sall1
The libraries were sequenced using Illumina HiSeq technology according to standard procedures
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw reads were pre-processed and mapped to the reference genome (talOcc4) using BWA. Finally, reads were summarized and normalized by coverage (RPM) for each fragment generated by neighboring restriction enzyme sites. The viewpoint and its flanking fragments (1.5 kb upstream and downstream) were removed for data visualization and a window of 10 fragments was used to smoothen the data.
Assembly: talOcc4
Supplementary files format and content: bedgraph
Library strategy: 4C
|
| |
|
| Submission date |
Nov 21, 2022 |
| Last update date |
Nov 22, 2022 |
| Contact name |
Francisca Martinez Real |
| E-mail(s) |
martinez@molgen.mpg.de
|
| Organization name |
Max Planck Institute for Molecular Genetics
|
| Street address |
Ihnestrasse 73
|
| City |
Berlin |
| ZIP/Postal code |
D-14195 |
| Country |
Germany |
| |
|
| Platform ID |
GPL25619 |
| Series (2) |
| GSE218437 |
Co-option of the transcription factor SALL1 in mole ovotestis formation [4C] |
| GSE219025 |
Co-option of the transcription factor SALL1 in mole ovotestis formation |
|
| Relations |
| BioSample |
SAMN31814902 |
| SRA |
SRX18327299 |
