|
| Status |
Public on May 01, 2014 |
| Title |
MEF3 |
| Sample type |
SRA |
| |
|
| Source name |
embryonic fibroblast
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: 129
cell type: embryonic fibroblast
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells are lysed and total RNA are mixed with reverse transcription (RT) master mix containing poly(T) primers with anchor sequences.
The library preparation kits (E7370) were purchased from New England Biolabs. Sequencing library construction and template preparation were performed according to the New England Biolabs library preparation protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
MEF 8-cell Chip
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
The raw reads were filtered to discard low-quality reads (reads containing more than 50 bases with quality value ≤ 5 and >10% bases as N). The results were clean reads. Adaptors with flanking polyA/T sequences were trimmed. Additionally, reads with AT content larger than 70% were also removed. Trimmed reads with length larger than 30 bp were kept.
Filtered reads were mapped to the mouse reference sequence downloaded from the UCSC table browser with Burrows-Wheeler Aligner (version 0.6.2-r126). The reads that mapped to RefSeq genes were counted and normalized by reads per kilobase transcript per million mapped read (RPKM).
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Gene symbols and the corresponding RPKM abundance measurements.
|
| |
|
| Submission date |
May 01, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiannian Zhang |
| E-mail(s) |
[email protected]
|
| Organization name |
Peking University
|
| Street address |
Yiheyuan Road No.5
|
| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE47835 |
Microfluidic single-cell whole-transcriptome sequencing |
|
| Relations |
| BioSample |
SAMN02742040 |
| SRA |
SRX530565 |
