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Sample GSM3712726 Query DataSets for GSM3712726
Status Public on Jun 12, 2019
Title DFL_E12_i6a_invattp-itga6_RNA-seq
Sample type SRA
 
Source name Distal forelimb mouse E12.5_invattp-itga6_RNA-seq
Organism Mus musculus
Characteristics strain: B6CBAF1
genotype/variation: invHoxd(attP-Itga6)
embryonic day: E12.5
tissue: Distal Forelimbs
Treatment protocol Micro-dissected proximal and distal segments of E12.5 forelimbs either from wild type or mutant embryos (invHoxD(attP-Itga6) and del(HoxD(attP-Rel5)d9lac). Tissues were dissected and placed in RNAlater (invitrogen) and kept at -80ªC until further use.
Extracted molecule total RNA
Extraction protocol RNA was extracted using the it RNAeasy (Microkit, QIAGEN).
Truseq Stranded mRNA
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description Distal forelimb mouse E12.5_invattp-itga6_RNA-seq
Data processing Analysis was performed using the facilities of the Scientific IT and Application Support Center of EPFL. The gtf used for STAR and cufflinks, based on the version 94 of ensembl annotations, is available on figshare (doi:10.6084/m9.figshare.7775837). Adapters were removed using cutadapt (v1.16) and aligned onto mm10 using STAR with ENCODE parameters.
Strand specific coverage was performed on uniquely mapped reads (tag NH:i:1) with bedtools version 2.27.1
Bedgraphs were normalized to the number of million uniquely mapped reads and replicates were merged using the tool unionbedg (bedtools v2.27).
Genome_build: mm10
Supplementary_files_format_and_content: Mean of normalized bedgraph of the forward or reverse strand unique read coverage.
 
Submission date Apr 05, 2019
Last update date Jun 14, 2019
Contact name Eddie Rodríguez-Carballo
E-mail(s) edgardo.rodriguez@unige.ch
Organization name Université de Genève
Department Department of Genetics and Evolution
Street address 4, Boulevard d'Yvoy
City Geneva
ZIP/Postal code 1205
Country Switzerland
 
Platform ID GPL17021
Series (2)
GSE129424 Impact of genome architecture upon the functional activation and repression of Hox regulatory landscapes [RNA-seq]
GSE129427 Impact of genome architecture upon the functional activation and repression of Hox regulatory landscapes
Relations
BioSample SAMN11352859
SRA SRX5649310

Supplementary file Size Download File type/resource
GSM3712726_DFL_E12_i6a_invattp-itga6_RNA_fwd.bedGraph.gz 68.8 Mb (ftp)(http) BEDGRAPH
GSM3712726_DFL_E12_i6a_invattp-itga6_RNA_rev.bedGraph.gz 68.4 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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