|
| Status |
Public on Apr 03, 2014 |
| Title |
214676_Face_6 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 8_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 |
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 |
SAMN02435484 |
| SRA |
SRX387025 |
