|
| Status |
Public on Sep 30, 2020 |
| Title |
Enterocyte_Mid_M1 |
| Sample type |
SRA |
| |
|
| Source name |
enterocytes isolated from jejunum
|
| Organism |
Mus musculus |
| Characteristics |
cell type: enterocytes
cell markers: Cd73/Nt5e mid
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells and nuclei were lysed with mild buffers. After blunting of DSBs and BLISS adapter ligation, DNA was extracted using DNA extraction buffer and proteinase K, followed by phenol/chloroform extraction and ethanol precipitation.
After DNA sonication, genomic DSB ends were amplified with in vitro transcription, after which generated RNA was subjected to an Illumina small RNA-like library preparation protocol (similar to the one described for BLISS in Yan et al, Nature Communications 2017).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Library strategy: sBLISS-seq
Reads with the correct structure at the start (8 nt UMI and 8 nt sample barcode) were extracted using scan_for_matches
Reads were mapped to the reference genome (GRCh37/Ensembl v75 for human and GRCm38/Ensembl V90 for mouse) using BWA-MEM. Only reads with mapping quality scores greater than or equal to 60 were retained.
PCR duplicates were filtered out by searching for proximal reads with at most two mismatches in the UMI sequence.
BED files were generated, containing a list of double-strand break (DSB) end genomic locations associated with the number of unique UMIs identified.
To overcome a base mismatch between BAM and BED files, for reads mapping to the - strand the DSB location is shifted -1 nt.
Genome_build: GRCh37/Ensembl v75 for human, GRCm38/Ensembl v90 for mouse
Supplementary_files_format_and_content: BED files containing a list of detected DSB end locations and the associated number of UMIs detected there
|
| |
|
| Submission date |
Feb 20, 2020 |
| Last update date |
Oct 01, 2020 |
| Contact name |
Federico Agostini |
| E-mail(s) |
agostini.federico@gmail.com
|
| Organization name |
Science for Life Laboratories
|
| Street address |
Tomtebodavägen 23a
|
| City |
Solna |
| State/province |
Stockholm |
| ZIP/Postal code |
171 65 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE145598 |
Genome-wide detection of DNA double-strand breaks by in-suspension BLISS |
|
| Relations |
| BioSample |
SAMN14144196 |
| SRA |
SRX7756508 |
