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Sample GSM5628772 Query DataSets for GSM5628772
Status Public on Oct 20, 2021
Title Klf5 OE, replicate 1
Sample type SRA
 
Source name embryonic stem cells
Organism Mus musculus
Characteristics cell line: Mouse embryonic stem cells derived from C57BL/6J mice
genotype: Mouse embryonic stem cells overexpressing Klf5
Growth protocol Mouse ESCs were cultured using Knockout DMEM supplemented with NEAA (0.1mM), BME(0.1mM), L-Glutamine (1mM), pen/strep (1x) and LIF (1000u/ml) on irradiated MEF feeders derived from C57BL/6J mice at E13.8 at 37C and 5% CO1
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted by Direct-zol RNA extraction Kit by Zymo Research. mRNA (polyA) purification, RNA fragmentation, first and second strand cDNA synthesis were performed according to the TruSeq RNA Sample Preparation v2 Kit using Superscript III for reverse transcription (50-min incubation at 50 degrees celsius). cDNA was purified with AMPure XP beads diluted 1:2 with 20% PEG, 1.25M NaCl, and eluted in 27.5 μl of 10 mM Tris-HCl pH 7.9, 25 μl of which were transferred to a new tube and subjected to library construction.
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 RTCC60E
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 SAMN22329287
SRA SRX12633783

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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