|
| Status |
Public on Aug 28, 2013 |
| Title |
Co-culture rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Co-cultured Mouse ES and Human Fib
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
sample type: Co-cultured Mouse ES and Human Fib
cell line(s): mouse ES cells and human fibroblast
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
At least 30,000 heterokaryons were FACS sorted and total RNA was extracted using the Qiagen RNeasy Micro Kit. Poly A enrichment was performed with Oligo dT bead selection. The resulting poly-A+ RNA was fragmented and cDNA was synthesized using Superscript II and random primers.
Libraries were prepared according to standard Illumina protocol, using the NEB Next modules for library construction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Mus musculus and Homo sapiens
Co-cult BC9
The co-cultured sample consists of RNA derived from individual mouse and human cells which are cultured together (but not fused - so their membranes remain distinct). The two cell types were pooled together before a single RNA harvest. Thus, this sample is a mixture of D3 mouse ES cells and MRC5 human fibroblasts.
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence to 50bp and mapped to hg19 and mm10 after removal of mouse and human rRNA sequences.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using SeqMap. Reads mapping to both organisms were removed. To account for removal of the homologous reads, a mathematical correction was introduced to calculate the effective transcript length (exon length) in which the "effective transcript length" is equal to the "original transcript length - 50bp - 1bp for every unique 50bp sequence read which matched perfectly between mouse and human" for that particular transcript.
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: .txt files include mouse and human RPKM values for each Sample. Transcripts with RPKM values of zero have been removed.
|
| |
|
| Submission date |
Jan 16, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Jennifer Brady |
| Organization name |
Stanford University
|
| Street address |
269 Campus Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL16512 |
| Series (1) |
|
| Relations |
| SRA |
SRX217759 |
| BioSample |
SAMN01888204 |
