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Sample GSM1922486 Query DataSets for GSM1922486
Status Public on Jan 01, 2016
Title MutantRescue_E294K_F10_RNAseq
Sample type SRA
 
Source name embryonic stem cells
Organism Mus musculus
Characteristics strain: Stella:GFP
genotype: Prdm14-/- + FLAG-HA-Prdm14 E294K mutant
Growth protocol For maintenance all mouse ESC lines were grown in so-called “2i+LIF” medium that is serum free N2B27-based medium supplemented with MEK inhibitor PD0325901 (0.8 μM) and GSK3β inhibitor CHIR99021 (3.3 μM) in tissue culture (TC) dishes pretreated with 7.5 μg/ml polyL-ornithine (Sigma) and 5 μg/ml laminine (BD) (Hayashi and Saitou, 2013; Hayashi et al., 2011). For ChIP-seq, RNA-seq and immunoprecipitation experiments Stella:GFP mESC lines and FH-Prdm14 derivatives were cultured for 5 days in feeder-free conditions in DMEM-high glucose medium (DMEM/high glucose; HyClone) containing 15% (v/v) FBS, 1 mM glutamine, penicillin/streptomycin, 0.1mM nonessential amino acids, 0.1 mM 2-mercaptoethanol and supplemented with LIF (serum+LIF conditions).
Extracted molecule total RNA
Extraction protocol ChIPs were performed using approximately 1-2 x 10^7 mESCs fixed with 1% formaldehyde for 10 min at room temp. RNA was extracted using Trizol.
Sequencing libraries were prepared starting from ~30ng of ChIP DNA or oligo-dT purified mRNA using the NEBNext Multiplex Oligos for Illumina kit (Cat# E7335S).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Reads aligned to mm9 using default settings with Bowtie2.2.4
Wig files were generated with QuEST2.4
RNA-seq were aligned to mm9 and quantified against mouse ENSEMBL 78 (GRCm38) gene models using htseq-count. Variance-stabilizing transformation (VST) was applied across samples for processed data.
Genome_build: Alignments done using mm9 as reference
Supplementary_files_format_and_content: wig and tab delimited text
 
Submission date Oct 30, 2015
Last update date May 15, 2019
Contact name Natalie Nady
Organization name Stanford
Department Chemical and Systems Biology
Lab Wysocka
Street address 265 Campus Dr.
City Stanford
State/province CA
ZIP/Postal code 94303
Country USA
 
Platform ID GPL19057
Series (1)
GSE74547 ETO Family Protein Mtgr1 Mediates Prdm14 Functions in Stem Cell Maintenance
Relations
BioSample SAMN04227585
SRA SRX1404252

Supplementary file Size Download File type/resource
GSM1922486_Prdm_MU_F10.txt.gz 311.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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