|
| Status |
Public on Mar 02, 2022 |
| Title |
F1-RNA-44-1-P4-DMSO |
| Sample type |
SRA |
| |
|
| Source name |
E18.5 fetus
|
| Organism |
Mus musculus |
| Characteristics |
strain: OG2
cells: P4 germ cells
f0 exposure: DMSO
|
| Treatment protocol |
Pregnant F0 dams of the OG2 mouse strain were gestationally exposed to 50 nM tributyltin or DMSO.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Genomic DNA and total RNA were isolated from FACS-enriched germ cells and somatic cells of E18.5 fetal testes using the QIAGEN AllPrep Micro kit.
RNA-seq Illumina libraries were contructed using Takara Bio's SMART-seq mRNA-seq kit, which involve cDNA synthesis using an oligo-dT primer. MBD-seq libraries were constructed using ThermoFisuer MethylMiner kit.
RNA-seq [targeting mRNA and endogenous retrovirus RNA containing poly(A) tail]; MBD-seq [using a Methyl Binding Domain protein to enrich DNA fragments containing methylated CpG dinucleotides]
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
MouseF1F3E18pTestisRNAseq_filtered_normalized_counts.corrected.2.xlsx
Normalized_mERV_counts_F1_germline.corrected.2.txt
|
| Data processing |
FASTQ files were filtered through trimGalore! to remove low-quality (Q < 30) reads and adaptor sequences.
FASTQ files were mapped using the STAR aligner to obtain BAM files.
R/Bioconductor package Rsubreads was used to count reads on exons of mRNA transcripts.
The mRNA raw counts were normalized by the negative binominal trimmed mean of M-values (TMM) method using R/Bioconductgor package edgeR.
Differentially expressed mRNA transcripts were identified using the generalized linear model likelihood ratio test implemented by edgeR.
mERV counting, normalization, and identification of differentially expressed mERVs from the BAM files were performed using the ERVmap pipeline with modification for the use of the mm10 mouse genome reference sequence.
MBDseq data analysis from the BAM files was performed using the R/Bioconductor package QSEA.
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq (mRNA): an EXCEL spreadsheet of normalized mRNA counts.
Supplementary_files_format_and_content: RNAseq (mouse endogenous retroviruses: mERVs): text files of normalized mERV counts.
Supplementary_files_format_and_content: MBDseq: text files of normalized counts of genomic DNA fragments enriched by the MBD precipiation (simialr to ChIP-seq procedure).
|
| |
|
| Submission date |
Jan 07, 2022 |
| Last update date |
Mar 02, 2022 |
| Contact name |
Toshi Shioda |
| E-mail(s) |
tshioda@mgh.harvard.edu
|
| Phone |
(617) 726-3425
|
| Organization name |
MGH Cancer Center
|
| Department |
Center for Cancer Research
|
| Lab |
Molecular Profiling Lab
|
| Street address |
Building 149 - 7th Floor, 13th Street
|
| City |
Charlestown |
| State/province |
MA |
| ZIP/Postal code |
02129 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE191199 |
Transgenerational transcriptomic and DNA methylome profiling of mouse fetal testicular germline and somatic cells after exposure of pregnant mothers to tributyltin, a potent obesogen |
|
| Relations |
| BioSample |
SAMN24718422 |
| SRA |
SRX13650895 |
