|
| Status |
Public on May 08, 2020 |
| Title |
Pabpn1l-KO-1Cell-Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Pabpn1l-KO-1Cell
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: Pabpn1l-KO
tissue: 1Cell embryo
|
| Treatment protocol |
Samples were collected with 0.2% BSA in DPBS at indicated time directly without extra treatment.
|
| Growth protocol |
The oocytes are collected in vivo, and embyos are clutured in KSOM in vitro.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Oocytes/embryos were collected from indicated genotypes (10 embryos per sample). Each sample was directly lysed with 4.2 ul lysis buffer (0.2% Triton X-100, RNase inhibitor, dNTPs, oligo-dT primers, and 1:1000 ERCC spike-in) and immediately used for cDNA synthesis using the Smart-seq2 method as described previously (Picelli et al, 2014).
Sequencing libraries were constructed from 500 pg of amplified cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to manufacturer’s instructions. Barcoded libraries were pooled and sequenced on the Illumina HiSeq X Ten platform with 150 bp paired-end reads
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
RNA-Seq was performed with biological replicates for all samples. Raw reads were trimmed to 50 bp and mapped to the mouse genome (mm9) and ERCC spike-in sequences with Tophat v2.1.1. Only uniquely mapped reads were subsequently assembled into transcripts guided by the reference annotation (UCSC gene models) with Cufflinks v2.2.1. Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments) and was further normalized with the ERCC spike-in. Samples prepared in different batches were normalized by the GV oocyte sample in each batch.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values of all RNA-seq samples
|
| |
|
| Submission date |
Oct 18, 2019 |
| Last update date |
May 08, 2020 |
| Contact name |
Li Shen |
| E-mail(s) |
shenlab@zju.edu.cn
|
| Phone |
86-0571-88981751
|
| Organization name |
Life Sciences Institute, Zhejiang University
|
| Lab |
Shenlab
|
| Street address |
866 Yuhangtang Road
|
| City |
Hangzhou |
| State/province |
Zhejiang Province |
| ZIP/Postal code |
310058 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE139072 |
Nuclear Poly(A)-binding Protein 1-like (PABPN1L) Mediates Cytoplasmic mRNA Decay As a Placeholder during Maternal-to-zygotic Transition |
|
| Relations |
| BioSample |
SAMN13054521 |
| SRA |
SRX7018637 |
