|
Status |
Public on Apr 03, 2014 |
Title |
214262_Face_4 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: 214262 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.
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
Sample 2_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)
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|
|
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 |
Meyerhofstraße 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 |
SAMN02435474 |
SRA |
SRX387019 |