|
| Status |
Public on Dec 31, 2016 |
| Title |
HOXD9_RNA_Replicate1 |
| Sample type |
SRA |
| |
|
| Source name |
Chicken Micromass primary cells
|
| Organism |
Gallus gallus |
| Characteristics |
cell type: MSCs derived from embryonal HH25 limb bud
infection: 3xFLAG-HOXD9
days in culture: 6 days
|
| Treatment protocol |
Cells were infected with RCASBP viruses carrying different transgenes.
|
| Growth protocol |
MSCs were isolated from the HH24 chicken limb buds, infected with an RCASBP(A) or (B) virus carrying the transgene on interest. Afterwards cells were cultured for 6 days with the DMEM:HAM F11 media (supplemented with 10% Fetal Bovine Serum, 0,2% Chicken Serum, 1% Penicilin-Streptomicin and 1% L-glutamine).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were separated from the ChIP sample prior to fixation an mRNA was extracted with the Rnaeasy (QIAGEN) kit according to the manufacturer's instructions.
mRNA was purified with the NEBNext Poly(A) mRNA Magnetic Isolation Module from 500g of total RNA. RNA-seq libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina according with a size selection was performed between 300-450bp. Libraries were sequenced on a a Illumina HiSeq 1500 using Illumina TruSeq v3 chemistry (single-read, 50 cycle).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
The reads were aligned using the STAR mapper (Dobin et al. 2012) splice junctions based on RefSeq/ENSEMBL gene annotations; options: ‐‐alignIntronMin 20 ‐‐alignIntronMax 500000 --outFilterMultimapNmax 5 ‐‐outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.1).
The annotation used was a merged from RefSeq (galGal4) and ENSEMBL (release 75) gene annotation.
DEseq2 was used to generate Log2 fold changes as in Love et al. 2014.
Genome_build: Galgal4
Supplementary_files_format_and_content: bigwig files contain normalized (RPM) genome browser tracks for each replicate RNA-seq experiment
Supplementary_files_format_and_content: The tab delimited txt file contains read counts for each gene (RefSeq/ENSEMBL annotation) and each replicate experiment in the table used as input for DEseq2
|
| |
|
| Submission date |
Aug 17, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniel Murad Ibrahim |
| E-mail(s) |
ibrahim@molgen.mpg.de, daniel.ibrahim@bih-charite.de
|
| Phone |
030 84131516
|
| Organization name |
Berlin Institute of Health
|
| Department |
Center for Regenerative Therapies
|
| Street address |
Augustenburger Platz 1
|
| City |
Berlin |
| State/province |
Berlin |
| ZIP/Postal code |
13353 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21476 |
| Series (2) |
| GSE85757 |
Genome-wide binding of posterior HOXA/D transcription factors reveals subgrouping and association with CTCF [RNA-Seq] |
| GSE86089 |
Genome-wide binding of posterior HOXA/D transcription factors reveals subgrouping and association with CTCF |
|
| Relations |
| BioSample |
SAMN05583887 |
| SRA |
SRX2033543 |
