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Sample GSM1279698 Query DataSets for GSM1279698
Status Public on Apr 03, 2014
Title 214676_Face_3 RNA-seq
Sample type SRA
 
Source name facial mesenchyme
Organism Mus musculus
Characteristics background strain: C57BL6/j
genotype/variation: del(8-17) homozygous
mother id: 214676
embryonic stage: 11.5
Treatment protocol Embryonic faces from 4 del(8-17) homozygous and 4 wildtype littermates were dissected and treated as independent biological replicates. 72000 drosophila S2 cells were added to each tube as spikes to detect any global perturbation of mRNA levels.
Growth protocol Mouse facial mesenchyme: dissected from bronchial arch to forebrain boundary
Extracted molecule total RNA
Extraction protocol RNA samples were processed using Tru-Seq RNA sample preparation guide (Illumina).
The eight samples were barcoded and run on the same flow cell of an Illumina HiSeq2000.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Sample 5_RNA-seq
Data processing The RNA- seq data was processed with the iRAP (45) (version 0.2.0) analysis pipeline (with default settings).
Readcounts for each gene were estimated with HTSeq-count
Data normalization and identification of significantly differentially expressed genes was performed using the DESeq method (version 1.10.1)
genome build: mm9
processed data files format and content: Text file with gene readcounts for all the 8 samples (biomaRt annotation)
 
Submission date Dec 04, 2013
Last update date May 15, 2019
Contact name Massimo Petretich
E-mail(s) petretic@embl.de
Phone 0049-(0)62213878569
Organization name EMBL
Department Developmental biology
Lab Spitz
Street address Meyerhofstra├če 1
City Heidelberg
ZIP/Postal code 69117
Country Germany
 
Platform ID GPL13112
Series (1)
GSE52974 The 8q24 cleft lip susceptibility locus is a remote Myc enhancer required for normal face morphology
Relations
BioSample SAMN02435481
SRA SRX387022

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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