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Sample GSM1845293 Query DataSets for GSM1845293
Status Public on Sep 15, 2016
Title RNA-Seq Growing_oocyte_14days
Sample type SRA
 
Source name Growing oocyte
Organism Mus musculus
Characteristics strain: C57BL/6N
developmental stage: Growing oocyte
Treatment protocol Follicles were isolated from 14-day old C57BL/6 mice by mechanical dissection using a 26 gauge needle, followed by the digestion with 4 mg/ml of collagenase I and 0.02 mg/ml of DNase I in L15 medium for 30 min at 37°C. To remove the granulosa cells, the dissociated oocyte-granulosa cells complexes were transferred into PBS (Ca2+, Mg2+-free) containing 1 mg/ml of collagenase I and were digested for 20 min. Oocytes were then incubated in lysis buffer after removing the zona pellucida by pronase treatment.
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_stage.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
SRA SRX1134830
BioSample SAMN03979664

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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