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Sample GSM7663578 Query DataSets for GSM7663578
Status Public on Mar 19, 2024
Title E7_embryo_female_WT_rep3
Sample type SRA
Source name E7.0 embryo
Organism Mus musculus
Characteristics tissue: E7.0 embryo
Sex: Female
strain: C57BL/6J
genotype: WT
litter: 6
Growth protocol Eight-week-old male and female C57BL/6J mice were purchased from The Jackson Laboratory (Stock #000664) and housed in a temperature and humidity-controlled environment on a 12:12 light/dark cycle with ad libitum access to food (Prolab Isopro RMH 3000, LabDiet, St. Louis, MO) and water. Females were housed in same-treatment groups of up to 5 and males were housed singly in standard Techniplast cages with nesting material and shelter. After acclimating for at least one week, females weighing over 20g were mated two per male for 1 to 2 hours. The date a vaginal plug was detected was defined as embryonic day 0 (E0) and the female was weighed and separated into a new cage.
Extracted molecule total RNA
Extraction protocol RNA was isolated from untreated male and female E7.0 embryos for whole transcriptome sequencing (n = 5 females, 7 males from 7 litters). No more than two embryos from each sex were used per litter.
Libraries were prepared using the SMARTer Ultra Low Input RNA and Nextera XT DNA kits by the UNC High Throughput Sequencing Facility.
Samples were pooled prior to sequencing and run paired-end (2x100) on a NovaSeq 6000 instrument using the S4 XP workflow.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Data processing Reads were trimmed to remove base pairs with a Phred score less than 20 and any Illumina adapter sequence using cutadapt 4.1. Reads less than 36 base pairs after trimming were removed.
Reads were then aligned to the mm10 reference genome using STAR 2.7.7a. The following STAR options were used in alignment: --quantMode TranscriptomeSAM GeneCounts, --twopassMode Basic, --outFilterMismatchNmax 2, --alignIntronMax 1000000, --alignIntronMin 20, --chimSegmentMin 15, --chimJunctionOverhangMin 15, --outSAMtype BAM Unsorted, --outFilterType BySJout, --outFilterScoreMin 1, --outFilterMultimapNmax 1. For the STAR option --sjdbGTFfile, a GTF file from GENCODE vM25 was provided.
Post-alignment gene quantification was conducted using Salmon 1.5.2 using the same GENCODE vM25 gene annotations.
Differential expression tests were performed on raw counts using DESeq2 1.34.0. Gene expression differences were considered significant at an adjusted p-value threshold of 0.05.
Assembly: mm10
Supplementary files format and content: The DESeq2 xlsx file contains the direct output from DESeq2 (columns A-F) for all genes as well as the VST-normalized expression for each gene and individual sample (columns G-R).
Submission date Jul 26, 2023
Last update date Mar 19, 2024
Contact name Austin J Hepperla
Organization name University of North Carolina at Chapel Hill
Department Genetics
Street address 7018B Mary Ellen Jones Building
City Chapel Hill
State/province NC
ZIP/Postal code 27599
Country USA
Platform ID GPL24247
Series (1)
GSE239355 Fetal Sex Does Not Influence Rates of Gastrulation-Stage Alcohol-Induced Craniofacial Malformations in C57BL/6J Mice
BioSample SAMN36717709
SRA SRX21165858

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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