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Sample GSM1651922 Query DataSets for GSM1651922
Status Public on Apr 27, 2015
Title 24hrs_RA_1
Sample type SRA
Source name KH2 cells, 24 hrs RA
Organism Mus musculus
Characteristics cell type: KH2 cells
treatment: 24 hrs RA
passages: 12
Treatment protocol Feeders were separated by plating freshly trypsinized cells on gelatinized plate for 30 min. After half an hour media was aspirated and centrifuged for 5 min at 1000 rpm.
ES Cells were differentiated with differentiation media (DMEM + 10% Serum + NAA+ 0.03µM RA) RA supplemented 33nm for requisite length of time. 
Growth protocol Cells were grown in ES cell media (DMEM + 15% Serum + NAA+ Beta-mercaptoethanol)
Extracted molecule total RNA
Extraction protocol Cells were lysed in TRIzol and RNA was isolated using Directzol RNA miniprep kit( R2052). Quality of RNA were assessed using bioanalyzer and samples with RIN more than 9 were used for library preparation.
For each sample, 250ng of total RNA was used to make libraries. Following manufacturer's directions, short fragment libraries were made using the Illumina TruSeq Stranded Total RNA LT - (with Ribo-Zero TM Gold) - set A and B (Illumina, Cat. No. RS-122-2301 and RS-122-2302). The resulting libraries were quantified using the LabChip GX (Perkin Elmer) and a Qubit Fluorometer (Life Technologies). All libraries were pooled, quantified and run as 50 bp single read on an Illumina HiSeq 2500 instrument using HiSeq Control Software 2.2.58
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Data processing Sequences were aligned to mouse genome mm10 using tophat with default parameters.
Transcript definitions were according to Ensembl 75.
Data was analyzed using Bioconductor package EdgeR.
Genome_build: mm10
Supplementary_files_format_and_content: cufflinks gene level results
Submission date Apr 06, 2015
Last update date May 15, 2019
Contact name Madelaine Gogol
Organization name Stowers Institute
Department Computational Biology Core
Street address 1000 E. 50th Street
City Kansas City
State/province MO
ZIP/Postal code 64110
Country USA
Platform ID GPL17021
Series (2)
GSE61590 Retinoids induce rapid dynamic changes in the non-coding RNAs and epigenetic profiles of murine Hox clusters
GSE67610 Retinoids induce rapid dynamic changes in the non-coding RNAs and epigenetic profiles of murine Hox clusters.
BioSample SAMN03462083
SRA SRX978947

Supplementary file Size Download File type/resource
GSM1651922_24hrs_RA_1.genes.fpkm_tracking.gz 1.2 Mb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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