|
| Status |
Public on Mar 17, 2021 |
| Title |
RNase III (DG3K) |
| Sample type |
SRA |
| |
|
| Source name |
NTREA-2 D1
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: testicular embryonal carcinoma cell line
cell line: NTREA-2 D1
treatment: RNase III
|
| Treatment protocol |
Extracted DNA was subjected to mock or enzymatic treatments (RNase H1, RNase III, RNase T1, or RNase T1+RNase III) prior to immunoprecipitation with the S9.6 antibody.
|
| Growth protocol |
NTERA-2 D1 cells were obtained from ATCC and grown in high-glucose Dulbecco’s Modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin / streptomycin. Cells were seeded 1-2 days prior to experiments and were grown to 40-60% confluency
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
sDRIP-seq: Genomic DNA was gently extracted using salt/ethanol percipitation, sonicated, and immunoprecipitated with S9.6 antibody.
sDRIP-seq: Enriched R-loop fragments were subjected to second strand synthesis using dUTP instead of dTTP for strand-specific library construction. Illumina TruSeq Single adapter was ligated and the cDNA and amplified as per standard Illumina TruSeq Single end protocol.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Library strategy: sDRIP-seq
Raw fastq reads were trimmed with fastq-mcf v2.4.4 and mappved with bowtie2 v2.2.6 (sDRIP-seq).
sDRIP-seq peaks were called using Macs v2.2.5 with default parameters except for --nomodel. We then merged peaks from all samples. HTseq-count v0.11.2 was then used to count the total number of reads in each merged peak.
Gencode v19 APPRIS gene annotation was used for our analysis, prioritizing highest principal isoform. DESeq2 was used to call differentially expressed regions.
Genome_build: hg19
Supplementary_files_format_and_content: sDRIP-seq bedGraph files were generated using bedtools genomecov and converted into bigWig using wigToBigWig; scores indicate tag per million (x30).
|
| |
|
| Submission date |
Dec 11, 2019 |
| Last update date |
Mar 20, 2021 |
| Contact name |
Frederic Chedin |
| E-mail(s) |
[email protected]
|
| Organization name |
UC Davis
|
| Department |
MCB
|
| Lab |
Chedin
|
| Street address |
1 Shields Avenue
|
| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE141833 |
Recognition of cellular RNAs by the S9.6 antibody creates pervasive artifacts when imaging RNA:DNA hybrids |
|
| Relations |
| BioSample |
SAMN13541106 |
| SRA |
SRX7347902 |
