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Sample GSM3928268 Query DataSets for GSM3928268
Status Public on Nov 06, 2019
Title IVF_KO_female_4
Sample type SRA
 
Source name Blastocyst
Organism Mus musculus
Characteristics cell type: Female blastocyst derived from in vitro with Xist deletion
developmental stage: Embryonic day 5
strain: BDF1 x C57BL/6
Growth protocol For in vivo samples, embryonic day 2.5 embryos are flushed from uterus and they are cultured in KSOM medium until embyronic day 5. For in vitro samples, the zygote is generated by in vitro fertilization and cultured in KSOM until embryonic day 5.
Extracted molecule total RNA
Extraction protocol Total RNA is extracted using Rneasy micro kit (Qiagen) with Dnase treatment.
Total RNA obtained from each sample was subjected to a sequencing library construction using Ovation Solo RNA-Seq System (NuGEN Technologies, San Carlos, CA) according to the manufacture's protocol.
 
Library strategy ssRNA-seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Data processing Basecalls performed using bcl2fastq v2.17.
Sequencing adaptors, low quality reads, and bases were trimmed with Trimmomatic-0.32 tool.
The sequence reads were aligned to the Mouse reference genome (mm10) using TopHat 2.1.1 (bowtie2-2.2.3) with the option '-g 1 --no-mixed --no-discordant'.
NuDup ver.2.2 (NuGEN Technologies, San Carlos, CA) analyzing the redundancy of 8 bp molecular barcodes was used to remove PCR duplicate reads.
The read counts allocated for each gene and transcript (RefSeq Genes 2013.04.01) were quantified using a RPKM (Reads Per Kilo base per Million reads) method using StrandNGS 3.2 software (Agilent Technologies, Santa Clara, CA).
Genome_build: mm10
Supplementary_files_format_and_content: An excel format file (XLSX) includes RPKM quantification values and gene annotations of all samples.
 
Submission date Jul 05, 2019
Last update date Nov 06, 2019
Contact name Atsushi Fukuda
E-mail(s) fa972942@tsc.u-tokai.ac.jp
Organization name Tokai University
Street address 143
City Isehara-shi
ZIP/Postal code 259-1193
Country Japan
 
Platform ID GPL18480
Series (1)
GSE133845 Transcriptome analysis in individual mouse blastocyst with Xist deletion
Relations
BioSample SAMN12218934
SRA SRX6407409

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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