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Sample GSM1370920 Query DataSets for GSM1370920
Status Public on Apr 18, 2014
Title mES_WT_3
Sample type SRA
Source name mouse Embryonic Stem Cells (male)
Organism Mus musculus
Characteristics knockdown chemistry: Wild type
knockdown target: NA
cell type: embryonic stem cells
Treatment protocol siRNAs were transfected using Lipofectamine RNAiMax (5 μl/well) at a final oligo concentration of 75nM; Gapmer oligos were designed with 2-O methyoxyethyl and transfected with Lipofectamine 2000 at a final concentration of 75nM.
Growth protocol HeLa cells were grown in DMEM + 10% FBS + 1% Pen-strep + 1% L-glutamine at 37ºC at 5% CO2; Mouse ES cells were grown in previously gelatinized (0.2%) dishes with media containing 125 mL DMEM/F12 (Invitrogen), 83.5 μL BSA fraction V (50 μg/ml relative to DMEM) (Invitrogen, 15260-037, 75mg/ml), 125 mL Neurobasal medium (Invitrogen, 21103-049), 625 μL of the Ndiff Neuro2 (200X, relative to Neurobasal medium) (Millipore, SCM012), 2.5 mL B27 minus vitamin A (50X, relative to Neurobasal medium) (Invitrogen, 12587-010), 2 μL beta-mercaptoethanol (for 250 mL medium), 1 μM PD0325901 (Stemgent, 04-0006), 3 μM CHIR99021 (Stemgent 04-0004), 25 μL LIF ESGRO (stock is 107 units LIF/mL from Chemicon, ESG1106), 1% pen-strep (Invitrogen, 15140-163), 1% Non-Essential Amino Acids (Invitrogen, 11140-076), 1% L-glutamine (Invitrogen, 25030-164). The plating density of mES cells was chosen to be 30,000-50,000/cm2.
Extracted molecule polyA RNA
Extraction protocol 1ml of Trizol and 200μl of chloroform were added and the mix was centrifuged at 4°C at 13,000 rpm for 15 minutes. The aqueous layer was cleaned and DNase treated on RNeasy Mini columns.
Illumina TruSeq RNA
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina MiSeq
Description RNA-Seq of polyA-selected RNA from wild type male mouse embryonic stem cells
Data processing Basecalls were performed using CASAVA 1.8
Reads were aligned using Tophat2 with default options
Expression quantification and differential analysis was done using Cuffdiff2 using UCSC reference transcriptome .gtf files (mouse or human) and Tophat2 aligned reads as input and default options.
Cuffdiff output files were processed using cummeRbund for indexing, exploration, and visualization of results.
Genome_build: mm9
Submission date Apr 17, 2014
Last update date May 15, 2019
Contact name Loyal A Goff
Organization name Johns Hopkins University
Department Institute of Genetic Medicine
Lab Goff
Street address 733 N. Broadway Avenue
City Baltimore
State/province MD
ZIP/Postal code 21205
Country USA
Platform ID GPL16417
Series (1)
GSE45157 Trans-chromosomal regulation by a novel lincRNA required for adipogenesis that escapes X-chromosome inactivation
Reanalyzed by GSE80797
BioSample SAMN02729442
SRA SRX520745

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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