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Status |
Public on Apr 19, 2022 |
Title |
E3_DRB_E2C_smart |
Sample type |
SRA |
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Source name |
Preimplantation embryo
|
Organism |
Mus musculus |
Characteristics |
genotype: WT developmental stage: early 2-cell molecule: polyA RNA
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Treatment protocol |
PN5 zygotes were obtained and cultured in KSOM containing either 0.1% DMSO or 60 μM DRB (Sigma; D1916). DRB was washed it away at the early 2-cell stage and embryos were continued to be cultured in KSOM till late 10-cell stage.
|
Extracted molecule |
total RNA |
Extraction protocol |
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/49 female mice mated with PWK/PhJ male mice. The RNA-seq libraries were generated using the Smart-seq2 protocol as described previously
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 1500 |
|
|
Data processing |
Ribo-lite reads were trimmed with cutadapt v1.14 with parameters: cutadapt --trim-n -a GATCGGAAGAGCACACGTCTG -a AGAGCACACGTCTG <input.file> | cutadapt -u 3 -a A{100} --no-indels -e 0.16666666666666666 - | cutadapt -O 8 --match-read-wildcards -g GTTCAGAGTTCTACAGTCCGACGATCSSS -m 18 - -o <output.file> , and the trimmed reads were sequentially mapped to mouse/human rRNAs sequences (mm9/hg19) using Bowtie2 v2.2.2 with parameters --seedlen=23. Those aligned to rRNA were discarded, and the rest reads were mapped to transcriptome of mm9/hg19 using STAR v2.5.3a with parameters --outFilterMismatchNmax 2 --outFilterMultimapNmax 20 --outFilterMatchNmin 16 --alignEndsType EndToEnd. The gene expression level was then calculated by Cufflinks v2.2.1 based on the annotation of CDS region。 All mRNA-seq data were trimmed by Trim Galore v0.4.2 then mapped to transcriptome of mm9/hg19 by STAR v2.5.3a with parameters --outFilterMultimapNmax 20 --outSAMstrandField intronMotif. The gene expression level was calculated by Cufflinks v2.2.1. Genome_build: mm9
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Submission date |
Jan 29, 2021 |
Last update date |
Apr 19, 2022 |
Contact name |
Zhuqing Xiong |
E-mail(s) |
lexizqxiong@gmail.com
|
Organization name |
School of Life Science, Tsinghua Univers
|
Street address |
Haidian District
|
City |
Beijing |
State/province |
FOREIGN |
ZIP/Postal code |
100084 |
Country |
China |
|
|
Platform ID |
GPL18480 |
Series (1) |
GSE165782 |
Ultrasensitive Ribo-seq reveals translational landscapes during mammalian oocyte-to-embryo transition and pre-implantation development |
|
Relations |
BioSample |
SAMN17679171 |
SRA |
SRX9975661 |