|
| Status |
Public on Sep 25, 2018 |
| Title |
Meis2Overexp2_38so |
| Sample type |
SRA |
| |
|
| Source name |
distal limb bud tips
|
| Organism |
Mus musculus |
| Characteristics |
strain: HoxB6CreER;R26Meis2a-IRES-EYFP/Meis2a-IRES-EYFP
tissue: distal limb bud tips
Stage: 38 somites
|
| Treatment protocol |
Pregnant mice were given 0.8mg of intraperioneal 4-hydroxy-tamoxifen at E8.3 days of gestation
|
| Growth protocol |
Pregant mice were generated crossing HoxB6CreER/+;R26RMeis2a-IRES-EYFP/Meis2a-IRES-EYFP with R26RMeis2a-IRES-EYFP/Meis2a-IRES-EYFP.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The distal limb bud tips of somite-staged HoxB6CreER; R26Meis2a/Meis2a (experimental) or R26Meis2a/Meis2a (control) embryos were dissected and flash-frozen on liquid nitrogen (1 tube per embryo). For RNA extraction, we used the miRNAeasy kit from Qiagen, pooling the limb bud tips from 2 embryos per stage and genotype in order to obtain enough RNA.
Libraries were made using the standard TruSeq RNA Sample Preparation v2 Kit from Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
E2
pool of 2 embryos
|
| Data processing |
Samples were sequenced in an Illumina GAIIx sequencer
Base calls produced by Illumina pipeline version 1.13.48
Base calls were extracted using illumina2bam tool release 0.03 from Wellcome Trust Sanger Institute. Standard Phred Scale
Reads were pre-processed with Cutadapt 1.2.1, to remove TruSeq adaptor sequences.
Resulting reads were mapped on the mouse transcriptome (Ensembl gene-build NCBIM37.v65) And quantified using RSEM v1.17
Only genes with at least 2 counts per million in at least 3 samples were considered for statistical analysis.
Data were normalized and differential expression tested using the Bioconductor package EdgeR. Note that the number of somites in each sample was used as blocking variable in the mixed linear model. We considered as differentially expressed those genes with a Benjamini-Hochberg adjusted p-value <0.05.
Genome_build: NCBIM37.v65
Supplementary_files_format_and_content: normalized_matrix_table.xlsx file contains ENSEMBL gene Ids, MGI gene names and normalized counts per million obtained using edgeR
|
| |
|
| Submission date |
Oct 17, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Carlos Torroja |
| E-mail(s) |
ctorroja@cnic.es
|
| Phone |
(+34) 91 4531200
|
| Organization name |
Centro Nacional de Investigaciones Cardiovasculares (CNIC)
|
| Department |
Bioinformatics Unit
|
| Street address |
Melchor Fernandez Almagro, 3
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE51374 |
Meis genes regulate RA/FGF signaling to control multiple steps of limb development |
|
| Relations |
| BioSample |
SAMN02376993 |
| SRA |
SRX364921 |
