|
| Status |
Public on Nov 07, 2019 |
| Title |
ATAC-WT-1 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: BDF1
cell type: derived ESC
genotype/variation: wild type
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples were lysed in lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2 and 0.15%NP-40) for 10 min on ice to prepare the nuclei. Immediately after lysis, nuclei were spun at 500g for 5 min to remove the supernatant.
Nuclei were then incubated with the Tn5 transposome and tagmentation buffer at 37 °C for 30 min (Vazyme Biotech). After the tagmentation, the stop buffer was added directly into the reaction to end the tagmentation. PCR was performed to amplify the library for 15 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; following by 72 °C 5 min. After the PCR reaction, libraries from 200bp to 700bp were purified from gel extraction before sequencing.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
processed data file: GSE127790_WT-ATAC.bw
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to mm9 reference genome using bowtie2 (v 2.2.9) command with default parameters.
MACS14 (v 1.4.2) with default parameters was used for peak finding with parameter --nomodel --shiftsize 25.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig file were generated using MACS2(v 2.0.10) pileup function.
|
| |
|
| Submission date |
May 30, 2019 |
| Last update date |
Nov 07, 2019 |
| Contact name |
You Wu |
| E-mail(s) |
wuyou@tongji.edu.cn
|
| Organization name |
tongji university
|
| Department |
school of life science and technology
|
| Street address |
1239 siping road
|
| City |
shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE127790 |
Nuclear exosome targeting complex core factor Zcchc8 regulates the degradation of LINE1 RNA in early embryos and embryonic stem cells |
|
| Relations |
| BioSample |
SAMN11896026 |
| SRA |
SRX5936435 |
