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Sample GSM1651928 Query DataSets for GSM1651928
Status Public on Apr 27, 2015
Title 10.5dpc_WT1
Sample type SRA
Source name Embryos, dpc 10.5
Organism Mus musculus
Characteristics cell type: embyos
Stage: 10.5dpc
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.
No treatment
Growth protocol Normal embryo growth conditions
Extracted molecule total RNA
Extraction protocol Staged embryos were dissected and homogenized in TRIzo using hand help homogeniozer.RNA was isolated by Directzol RNA miniprep kit( R2052) as per manufacturer's instruction. 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 SAMN03462089
SRA SRX978953

Supplementary file Size Download File type/resource
GSM1651928_10.5dpc_WT1.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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