|
| Status |
Public on Mar 22, 2018 |
| Title |
d8 ox sRNA |
| Sample type |
SRA |
| |
|
| Source name |
differentiating ES cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: differentiating ES cells
strain: 129 x castaneus
developmental stage: day 8
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The NEBNext Small RNA Sample Prep Set 1 (Illumina Compatible) library construction protocol was followed (NEB #E6120S/L), along with the SMART kit and Nextera kit for Illumina sequencing for RNA-seq libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequencing adapters were removed from reads by finding the 3'-most complete match to the adapter sequence and trimming the read after that position.
Reads were first mapped to the collection of ribosomal repeats (annotated using the repeatMasker file downloaded from the UCSC genome browser), snoRNAs and snRNAs in the mouse genome (version mm9) using Bowtie (version 0.12.7) in order to remove common contaminants.
The unmapped reads from this filtering step were then mapped against the mm9 genome.
Genome_build: mm9
|
| |
|
| Submission date |
Dec 10, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Diane E Trout |
| Organization name |
California Institute of Technology
|
| Department |
Biology
|
| Lab |
Wold
|
| Street address |
1200 E California Blvd M/C 156-29
|
| City |
Pasadena |
| State/province |
CA |
| ZIP/Postal code |
91125 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE39884 |
Small RNAs in undifferentiated and differentiating mouse embryonic stem cells |
|
| Relations |
| BioSample |
SAMN02469165 |
| SRA |
SRX396271 |
