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Sample GSM1845312 Query DataSets for GSM1845312
Status Public on Sep 15, 2016
Title RNA-Seq PN5 zygote alpha-amanitin
Sample type SRA
 
Source name Preimplantation embryo
Organism Mus musculus
Characteristics strain: C57BL/6N x PWK
developmental stage: Preimplantation embryo
Treatment protocol Late zygotes (PN5) and early 2-cell embryos were cultured in CZB supplemented with alpha-Amanitin for about 14h.
Extracted molecule polyA RNA
Extraction protocol After removing the zona pellucida, embryonic cells were washed with PBS and incubated in lysis buffer.
RNA-Seq libraries were prepared using Smart-Seq2 protocol with slightly modification
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description processed data file: FPKM_inhibition.txt.gz
Data processing Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome
RNA-Seq reads were aligned to the mm9 genome assembly using Tophat version 2.0.11, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.0.2
Genome_build: mm9
Supplementary_files_format_and_content: The bed files include RPKM values in 100bp bins for each ChIP-seq sample. Bed files labeled maternal or paternal contain RPKM values for two parental alleles, allelic reads were normalized to total reads number. Tab-delimited text files include FPKM values RNA-seq sample.
 
Submission date Aug 06, 2015
Last update date May 15, 2019
Contact name Bingjie Zhang
Organization name Tsinghua University
Street address 30 Shuangqing Rd
City Beijing
State/province Beijing
ZIP/Postal code 100190
Country China
 
Platform ID GPL18480
Series (1)
GSE71434 Allelic reprogramming of the histone modification H3K4me3 in early mammalian development
Relations
Reanalyzed by GSE123012
SRA SRX1134849
BioSample SAMN03979681

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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