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Sample GSM4128684 Query DataSets for GSM4128684
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
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
BioSample SAMN13054521
SRA SRX7018637

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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