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Sample GSM1974998 Query DataSets for GSM1974998
Status Public on Dec 20, 2015
Title Zscan10_KO_rep3
Sample type SRA
Source name Embryonic stem cells, Zscan10 KO, replicate3
Organism Mus musculus
Characteristics cell type: ESC
genotype/variation: Zscan10-null
Extracted molecule total RNA
Extraction protocol Total RNAs were prepared by QuickGene RNA cultured cell HC kit (KURABO) following the manufacturer's instruction and treated with Ribo-Zero Gold Sample Prep Kit (Illumina) for deplete ribosomal RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
Description Gene expression in subcloned Zscan10-null ES cells
rRNA depleted RNA
Data processing Sequenced reads were aligned to the mouse genome (mm10) using TopHat after trimming of adaptor sequences with trim_galore and quality check with FastQC.
Gene expression level measured as FPKM was determined with Cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample
Submission date Dec 18, 2015
Last update date May 15, 2019
Contact name Hitoshi Niwa
Organization name RIKEN
Department Center for Developmental Biology
Lab Laboratory for Pluripotent Stem Cell Studies
Street address 2-2-3 Minatojima-minamimachi,Chuo-ku
City Kobe
State/province Hyogo
ZIP/Postal code 650-0047
Country Japan
Platform ID GPL18480
Series (1)
GSE76143 Zscan10 is dispensable for maintenance of pluripotency in mouse embryonic stem cells
BioSample SAMN04350013
SRA SRX1490965

Supplementary file Size Download File type/resource
GSM1974998_Zscan10_KO_rep3.txt.gz 347.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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