|
| Status |
Public on Feb 11, 2014 |
| Title |
Developmentally competent embryo conditioned media Salker_B1 |
| Sample type |
SRA |
| |
|
| Source name |
uterus
|
| Organism |
Mus musculus |
| Characteristics |
tissue: uterus
strain: C57BL/6
treatment: developmentally competent embryo conditioned media
|
| Treatment protocol |
Immature female (25 d C57BL/6) mice were given a hormone treatment of a single dose 1 mg progesterone and 10 mg/kg/day β-estradiol for a total of 3d to prime the uterus for embryo transfer. The uterine horns of control and study mice were injected with an equal volume (50 μl) of either unconditioned embryo culture medium (ECM), serving as controls, or pooled conditioned media from competent (n = 9) or arresting embryos (n = 18)
|
| Growth protocol |
n/a
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Uteri were removed, flash frozen on dry ice. Total RNA extraction was performed using RNA STAT-60, according to manufacturer's instructions. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited general transfer format cufflinks output files include FPKM values
|
| |
|
| Submission date |
May 16, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Jan J Brosens |
| E-mail(s) |
j.j.brosens@warwick.ac.uk
|
| Organization name |
University of Warwick
|
| Department |
Warwick Medical School
|
| Lab |
Division of Reproductive Health
|
| Street address |
University Hospital Coventry and Warwickshire
|
| City |
Coventry |
| ZIP/Postal code |
CV2 2DX |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE47019 |
Developmentally Abnormal Human Embryos Trigger a Maternal ER Stress Response |
|
| Relations |
| BioSample |
SAMN02146432 |
| SRA |
SRX278545 |
