2024-11-22
ENA first public
ERC000011
ENA-CHECKLIST
EMBL
INSDC center name
public
INSDC status
ERS22448710
SRA accession
E-MTAB-14639:Blasto_B6J_CTL_09-4-24
Submitter Id
ArrayExpress
broker name
not collected
collection date
house mouse
common name
Protocols: Male mice were randomly assigned to one of three treatment groups: Control (CON), non-absorbable antibiotics (nABX), or low protein high sugar diet (LPHS). Young (3 weeks) and mature (12-13 months) mice in the CON group received water and standard rodent diet, nABX mice received antibiotics in their water (Neomycin, Bacitracin, Pimaricin) along with the standard diet, and LPHS mice were given a low-protein, high-sugar (LPHS) diet and water. In vitro fertilizations followed a modified protocol (Guan et al. 2014) to increase throughput and synchronize development. Sperm was collected from the cauda epididymis and vasa deferentia of treated males, incubated in HTF capacitation media, and allowed to swim up. Cumulus-oocyte complexes were collected from superovulated females treated with PMSG and hCG in KSOM media, then inseminated with 0.2 million sperm in KSOM + GSH media for four hours in low-oxygen incubator conditions. Zygotes were then washed and cultured to the blastocyst stage under low oxygen (5% CO2, 5% O2 for FVB and B6J backgrounds) or standard oxygen (5% CO2, 20% O2 for B6N background) conditions. Single-embryo RNA-sequencing was performed based on the previously published SMART-Seq protocol (Hennig et al, 2018; Picelli et al, 2014; Trombetta et al, 2014) with some modifications. Briefly, embryos were arranged in a 96-well plate, heated briefly, and then subjected to reverse transcription. Following reverse transcription, whole transcript amplification (WTA) was carried out, and cDNA was cleaned up using SPRI beads. The cDNA concentration and quality were verified via BioAnalyzer and Qubit. Tagmentation was, then, performed on each diluted sample using Tn5 transposase preloaded with linker oligonucleotides. Finally, adapter index primers were added in the final PCR. After indexing, samples were pooled, cleaned, and evaluated for concentration and quality using a BioAnalyzer and Qubit.
description
Blastocyst
developmental stage
not collected
geographic location (country and/or sea)
birth
initial time point
not applicable
isolate
Mus musculus
organism
Mus musculus
organism
blastocyst
organism part
9 to 11
week
paternal age
Mus musculus
scientific_name
C57BL/6J
strain
Blasto_B6J_CTL_09-4-24
title
CON
treatment