|
| Status |
Public on Dec 31, 2015 |
| Title |
WS_Rete_2C_10 |
| Sample type |
SRA |
| |
|
| Source name |
2C embryo
|
| Organism |
Mus musculus |
| Characteristics |
strain: FVB
embryos collected at time after ivf: 28 hrs
sperm injected: Rete whole sperm
|
| Treatment protocol |
Zygotes were generated by ICSI from oocytes/females fed a Control diet and sperm/males fed either a Control or Low Protein diet. The sperm was isolated from either the Rete testis or the Cauda epididymis and injected either as a whole sperm or just the sperm head. Following fertilization by ICSI the zygotes developed for 28 hours (2C stage) and were harvested for single-embryo RNA-Seq.
|
| Growth protocol |
After fertilization by ICSI Zygotes developed in KSOM medium at 37 °C in 5% CO2 5% O2 for 28 hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
2C embryos were collected at 28 hours post-ICSI in 5ul of buffer TCL with 1% beta mercaptoethanol and frozen at -80C.
single-cell RNA-seq/Nextera kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Sharma_Rando_2015_ICSI
|
| Data processing |
Reads were aligned to mm10 RefSeq using Bowtie software in a sequencial manner first to rRNA, snRNA and miRNAs to eliminate any reads coming from them and then alinged to the genome
Genome_build: mm10
Supplementary_files_format_and_content: excel sheet with normalized gene counts
|
| |
|
| Submission date |
Dec 07, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Upasna Sharma |
| E-mail(s) |
FNU.Upasna@umassmed.edu
|
| Phone |
508 856 6337
|
| Organization name |
Umass Med School
|
| Department |
BMP
|
| Lab |
LRB
|
| Street address |
364 Plantation Street
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE75622 |
Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals |
| GSE75769 |
Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals (ICSI) |
|
| Relations |
| BioSample |
SAMN04323884 |
| SRA |
SRX1469568 |
