|
| Status |
Public on Mar 05, 2021 |
| Title |
RNA-seq of mES total RNA after non-targeting shRNA replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
murine embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6 (female) x 129/S (male)
cell type: mES
shRNA: Non-targeting
|
| Extracted molecule |
total RNA |
| Extraction protocol |
ES cells (V6.5) were infected with lentivirus carrying either Non-targeting shRNA or Cnot10 shRNA in the presence of 8 ug/ml of polybrene. 24 hours later, ES cells were selected with 2 ug/ml of puromycin for additional 48 hours and then were grown one passage off feeders for 30 min before harvesting. Total RNA was isolated with the RNeasy (74106 Qiagen) kit, treated with DNase I (M0303L NEB), and re-purified with RNeasy. For total RNA-seq analyses, 2.5 µg of total RNA was depleted of ribosomal RNA with the Ribo-Zero kit from Epicentre (#RZH1046). Ribosomal RNA-depleted samples were used for library preparation with the TruSeq RNA Sample Prep Kit (FC-122-1001 Illumina) for next-generation sequencing.
TruSeq RNA Sample Prep Kit (FC-122-1001 Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file: ES_Cnot10.xlsx
|
| Data processing |
We first evaluated each RNA-seq data quality using FastQC (version 0.11.8) and confirmed that all datasets are qualified for following analysis. The RNA-seq reads were aligned to mouse reference genome (mm10/GRCm38) using HISAT2 (version 2.1.0). The mouse reference genome sequence was downloaded from ENSEMBL (Mus Musculus GRCm38/mm10). Then we used featureCounts (version 2.0.0) to count reads or read pairs for each protein-coding gene annotated in GENCODE (vM23)34.
Genome_build: UCSC mm10 (GRCm38)
Supplementary_files_format_and_content: *.bw: bigWig files
Supplementary_files_format_and_content: ES_Cnot10.xlsx: Excel file
|
| |
|
| Submission date |
Mar 06, 2020 |
| Last update date |
Mar 06, 2021 |
| Contact name |
Xiaoxu Liu |
| E-mail(s) |
liuxiaoxu1010@126.com
|
| Organization name |
Southeast University
|
| Department |
Institute of Life Sciences
|
| Lab |
the Key Laboratory of Developmental Genes and Human Disease
|
| Street address |
2 Sipailou
|
| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210018 |
| Country |
China |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE146511 |
Functional characterization of RNF219 |
|
| Relations |
| BioSample |
SAMN14313877 |
| SRA |
SRX7860277 |
