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Sample GSM1967215 Query DataSets for GSM1967215
Status Public on Dec 31, 2015
Title WS_Cauda_2C_11
Sample type SRA
Source name 2C embryo
Organism Mus musculus
Characteristics strain: FVB
embryos collected at time after ivf: 28 hrs
sperm injected: Cauda 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
Phone 508 856 6337
Organization name Umass Med School
Department BMP
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)
BioSample SAMN04323875
SRA SRX1469559

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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