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Sample GSM5628777 Query DataSets for GSM5628777
Status Public on Oct 20, 2021
Title Control E4.5 Embryo replicate 4
Sample type SRA
 
Source name E4.5 embryos
Organism Mus musculus
Characteristics cell line: Preimplantation embryos harvested from C57BL/5J mice
genotype: E4.5 Mouse embryos treated with scramble siRNA
Growth protocol Embryos were cultured in KSOM supplemented with BSA (1mg/ml) under a layer of parafin oil at 37C 5% CO2 and normoxia
Extracted molecule polyA RNA
Extraction protocol RNA extraction and cDNA synthesis was performed using SMARTseq-V4 kit. cDNA was then purified with AMPure XP beads
RNA-seq libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB E7645), diluting NEB adaptors 1:5 and performing 8 PCR cycles.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description 4_S4_L002
Data processing Gene expression levels are quantified by Kallisto v0.46 with kallisto -quant and default parameters
Genome_build: mm10
Supplementary_files_format_and_content: Text file for matrix of expression levels of genes, with first column is the gene name, and the first row is the sample ID.
 
Submission date Oct 15, 2021
Last update date Oct 20, 2021
Contact name Martin Kinisu
E-mail(s) kinism@berkeley.edu
Phone 2068832373
Organization name University of California Berkely
Department MCB
Lab He Lab
Street address 300C Li Ka Shing Building
City Berkeley
State/province California
ZIP/Postal code 94709
Country USA
 
Platform ID GPL21103
Series (1)
GSE186005 Klf5 confers embryonic and extra-embryonic bi-potential cell fate in early blastomeres and embryonic stem cells
Relations
BioSample SAMN22329292
SRA SRX12633788

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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