|
Status |
Public on Dec 31, 2015 |
Title |
ReteControl_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 sperm head (Control fed)
|
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) |
upsharma@ucsc.edu
|
Phone |
831-459-3563
|
Organization name |
UCSC
|
Department |
MCD Biology
|
Street address |
1156 High St
|
City |
Santa Cruz |
State/province |
California |
ZIP/Postal code |
95064 |
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 |
SAMN04323834 |
SRA |
SRX1469514 |