|
| Status |
Public on Jan 19, 2023 |
| Title |
Mouse_JF1xC57BL/6_EPC_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
EPC
|
| Organism |
Mus musculus |
| Characteristics |
strain: F1 hybrid resulting from female JF1/Ms and male C57BL/6N mice
age: embryonic days 7.25
genotype: wild type
cell type: EPC
Sex: female
|
| Treatment protocol |
E8.5 F1 hybrid rat embryos were isolated from reciprocally crossing BN/CrlCrlj (BN rat) and WKY/NCrlCrlj (WKY rat) strains as well as between strains BN/CrlCrlj and F334/NSlc (F344/N rat). E7.25 F1 hybrid mouse embryos were isolated from reciprocally crossing C57BL/6N and JF1/Ms strains. For both rat and mouse embryos, the ectoplacental cone (EPC) was dissected from the rest of the embryo before removing the visceral endoderm. Finally, the epiblast (EB) was dissected from the extraembryonic ectoderm (ExE). Each ExE lysate was used for rapid genetic sex determination by direct PCR amplification of the Y chromosome gene using specific primers for mouse Zfy and rat Sry. Only female EBs and EPCs were subjected to strand-specific RNA-sequencing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using AllPrep DNA/RNA Micro Kit (Qiagen) according to manufacturer’s protocols.
One nanogram of embryonic total RNA was reverse transcribed using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara Bio) according to the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
>Reads were trimmed using Trimmomatic (v0.32) to remove 2 nucleotides of the 5’ end of read 2
>Sequencing reads were further trimmed using Trimmomatic (v0.32) and the following parameters: SLIDINGWINDOW:3:10 MINLEN:36 ILLUMINACLIP:TruSeq2-3-PE.fa:2:30:10.
>Read pairs that survived trimming were aligned to genome build mm10 or rn6 using STAR (v2.4.0.i) and PCR duplicate reads were flagged using Picard MarkDuplicates (v1.92).
>Library quality was assessed using samtools flagstat (v1.1) and Picard CollectRNASeqMetrics.
>Uniquely aligned, non-PCR-duplicate reads were kept for downstream analysis using samtools parameters: samtools view -bh -q 255 -F 1540.
>NCBI RefSeq mouse transcript annotations (n=106,520 isoforms, 35,977 genes) were downloaded from the UCSC Table Browser (last updated 2017-11-16). NCBI RefSeq rat transcript annotations (n=69,194 isoforms, 30,871 transcripts) were downloaded from the UCSC Table Browser (last updated 2018-03-09).
>Gene expression values were calculated by averaging read coverage over exons using VisRseq (v0.9.12) and normalized to the total number of aligned reads and transcript length in kilobases (RPKM).
>Genome browser compatible normalized bigWigs were generated using bedtools genomecov (v2.22.1).
Genome_build: rn6
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files for each sample
|
| |
|
| Submission date |
Oct 08, 2021 |
| Last update date |
Jan 19, 2023 |
| Contact name |
Hisato Kobayashi |
| E-mail(s) |
hiskobay@naramed-u.ac.jp
|
| Phone |
+81-744-29-8015
|
| Organization name |
Nara Medical University
|
| Department |
Department of Embryology
|
| Street address |
840 Shijo-Cho
|
| City |
Kashihara |
| State/province |
Nara |
| ZIP/Postal code |
634-8521 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE185574 |
Rat and mouse imprintomes (allele-specific transcriptomes) |
|
| Relations |
| BioSample |
SAMN22164170 |
| SRA |
SRX12529020 |
