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Sample GSM1713505 Query DataSets for GSM1713505
Status Public on Feb 04, 2016
Title Prox1.3
Sample type SRA
 
Source name Prox1 cKO mouse lens
Organism Mus musculus
Characteristics strain: C57Bl/6
genotype: Prox1 cKO (Prox1 f/f MLR10Cre+)
tissue: Lens
age: E13.5
lenses per replicate: 30
Extracted molecule total RNA
Extraction protocol RNA was extracted from pooled samples of 30 mouse lenses using the SV total RNA isolation System (Promega, Madison, WI) acording to the manufacturers recommended protocol.
cDNA libraries were constructed from total RNA by were used to purifying mRNA from the total RNA samples using poly-T oligo attached magnetic beads and converted to a library of template molecules for cluster generation and DNA sequencing using the Illumina® TruSeq™ RNA Sample Preparation Kit v2. Sequencing performed on a Illumina HiSeq 2500 using single-end 51bp sequencing.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description 30 Prox1 cKO E13.5 Biological replicate 3
Data processing Reads were trimmed using CLC Genomics Workbench 5.5.1with the following parameters: Max ambiguous bases:0; Minimum Q>0.01; minimum length 35bp
Reads were aligned to the Mus musculus genome using CLC Genomics Workbench 5.5.1
Unique gene counts were determined using CLC Genomics Workbench 5.5.1
Counts were normalized (CPM and RPKM) using R BioConductor EdgeR
Genome_build: Mus musculus GRCm38.77
Supplementary_files_format_and_content: tab-delimited: mgc gene symbol, ensembl gene ID, MGID, ensembl gene description, cpm, rpkm, raw count
 
Submission date Jun 17, 2015
Last update date May 15, 2019
Contact name Melinda K. Duncan
E-mail(s) duncanm@udel.edu
Phone 3028310533
Organization name University of Delaware
Department Biological Sciences
Lab Vertebrate Development
Street address 327 Wolf Hall
City Newark
State/province DE
ZIP/Postal code 19716
Country USA
 
Platform ID GPL17021
Series (1)
GSE69940 Genome-wide analysis of embryonic gene epression in the absence of Prox1 compared to wild type
Relations
BioSample SAMN03777441
SRA SRX1060437

Supplementary file Size Download File type/resource
GSM1713505_Prox1-3.txt.gz 1.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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