|
| Status |
Public on Jul 29, 2016 |
| Title |
mESC_unstranded_RNASeq |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Embryonic stem cells
genotype: wild type
library type: Illumina Truseq unstranded library
|
| Growth protocol |
mES cells were cultured in regular media containing 15% FBS, 1% PEN/STREP, 1% glutamine, 1% NEAA, and LIF. For mES cell maintenance, dishes were coated with 0.2% gelatin and irradiated CF1 mouse embryonic fibroblasts were plated as a confluent layer of feeder cells. mES cells were seeded at a density of 50,000 cells/6-well plate and were split every 2-3 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from mES cells was extracted using an RNeasy kit (Qiagen, USA). Polyadenylated RNA was isolated using Oligo dT beads (Invitrogen, USA).
Illumina Truseq stranded and unstranded mRNA library prep kits (Illuminca, USA) were used for deep sequencing library preparation from 6ug of total RNA according to the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.8 sotfware used for basecalling.
To check RNA-seq data quality, RNA-seq reads were mapped to the mm9 genome assembly using Bowtie (version 1.0.0) with default parameters.
We calculate mismatch rates across the mapped read positions.
If the raw read end(s) had a mismatch rate higher than 10%, they were trimmed off using Seqtk (version 1.0-r31).
The tirmmed reads with Phred base qulaity ≦ 20 were filtered using Sickle (version 1.200).
The remaining reads were mapped to the mm9 genome assembly using Tophat (veriosn 2.0.6) with paramters "-i 52 -I 240764 --min-segment-intron 52 --max-segment-intron 240764 -g 5".
Base transcriptome assemblies were performed using Cufflinks (version 2.1.1) with defeault parameters for mapped reads.
Genome_build: mm9
Supplementary_files_format_and_content: gtf files were generated using Cufflinks (version 2.1.1).
|
| |
|
| Submission date |
Jul 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jin-Wu Nam |
| E-mail(s) |
[email protected]
|
| Phone |
+82 2-2220-2428
|
| Organization name |
Hanyang University
|
| Department |
Department of Life Science
|
| Street address |
Seongdong-Gu Hangdang-dong
|
| City |
Seoul |
| ZIP/Postal code |
133-791 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE84946 |
Co-assembly of stranded and unstranded RNA-seq data improves coding and noncoding transcriptome maps |
| GSE97212 |
The Project for High-Confidence Coding and Noncoding Transcriptome Maps |
|
| Relations |
| BioSample |
SAMN05452801 |
| SRA |
SRX1984830 |
