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| Status |
Public on Nov 06, 2019 |
| Title |
VIVO_KO_female_8 |
| Sample type |
SRA |
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| Source name |
Blastocyst
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| Organism |
Mus musculus |
| Characteristics |
cell type: Female blastocyst derived from in vivo with Xist deletion
developmental stage: Embryonic day 5
strain: BDF1 x C57BL/6
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| 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.
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| 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.
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| Library strategy |
ssRNA-seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
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| 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.
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| Submission date |
Jul 05, 2019 |
| Last update date |
Nov 06, 2019 |
| Contact name |
Atsushi Fukuda |
| E-mail(s) |
afukuda@tokai.ac.jp
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| Organization name |
Tokai University
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| Street address |
143
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| City |
Isehara-shi |
| ZIP/Postal code |
259-1193 |
| Country |
Japan |
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| Platform ID |
GPL18480 |
| Series (1) |
| GSE133845 |
Transcriptome analysis in individual mouse blastocyst with Xist deletion |
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| Relations |
| BioSample |
SAMN12218947 |
| SRA |
SRX6407419 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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