|
| Status |
Public on Aug 17, 2021 |
| Title |
pCIG-MEK1ca Replicate 2 (reanalysis) |
| Sample type |
SRA |
| |
|
| Source name |
pCIG-MEK1ca GFP positive cells
|
| Organism |
Gallus gallus |
| Characteristics |
plasmid dna: pCIG-MEKca+pCIG
cell type: MEK1ca GFP expressing cells
|
| Treatment protocol |
RNA-seq of MEK1ca GFP+ cells Rep2 (re-analysis of GSM5517716) pCIG-MEK1ca plasmid Neural tube in ovo electroporations were performed at HH11. Eggs were windowed, and the DNA solution (1 to 2µg/µl) was injected in neural tube lumen. Needle L-shape platinum electrodes were place on both sides of the embryo at trunk level (5 mm apart), with the cathode always at its right. Five 50 ms pulses of 25 volts were given bilateral at 50 ms intervals with an electroporator NEPA21 (Nepagene). Plasmids DNA concentrations were for the control mix: pCIG 2µg/µl and for the MEK1ca mix : pCIG-MEK1ca 1 µg/µl + pCIG 1µg/µl. Part of the neural tube expressing the GFP were dissected 18 hours after electroporation and dissociated (Trypsin-EDTA 0,25%). A highly enriched population of GFP-expressing cells was isolated by FACS with the use of a dead cell exclusion (DCE)/discrimination dye (DAPI) to eliminate dying cells.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted (RNeasy Mini Kit) and reverse transcribed, and cDNA was amplified using a linear amplification system and used for sequencing library building (GATC).
Random primed cDNA library, purification of poly-A containing mRNA molecules, mRNA fragmentation, random primed cDNA synthesis, adapter ligation and adapter specific PCR amplification, Illumina technology, 50,000,000 reads paired end with 2×50 bp read length.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
DGE_MEK1ca_HoxB8_vs_MEK1ca_Galgal4_ensembl85_FDR1_logFC_ordered 13 08 21.xlsx
DGE_MEK1ca_vs_pCIG_Galgal4_ensembl85_FDR1_logFC_ordered 13 08 21.xlsx
MEK1ca_GFPplus_2
|
| Data processing |
Basecalls performed using RTA (Illumina)
RNA-seq reads were aligned to the galgal4 genome assembly using subread-align
Gene exon counts were made using featureCounts
RNA-Seq differentially expressed genes were called using DESeq2 using a false discovery rate (FDR;padj) cut-off of 0.01.
Genome_build: galGal4
Supplementary_files_format_and_content: Excel files containing gene counts and DGE :DESeq output of differentially expressed genes (Log2Fold Change, p-value, p-adjusted) of MEK1ca vs pCIG, and MEK1ca+HoxB8 vs MEK1ca.
|
| |
|
| Submission date |
Aug 13, 2021 |
| Last update date |
Aug 17, 2021 |
| Contact name |
Marie-Claire DELFINI |
| E-mail(s) |
marieclaire.delfini@gmail.com
|
| Phone |
0611942586
|
| Organization name |
IBDM / CNRS
|
| Lab |
IBDM
|
| Street address |
Campus de Luminy
|
| City |
Marseille |
| ZIP/Postal code |
13009 |
| Country |
France |
| |
|
| Platform ID |
GPL16133 |
| Series (1) |
| GSE182076 |
HOXB8 counteracts MAPK/ERK oncogenic signaling in a chicken embryo model of neoplasia |
|
| Relations |
| Reanalysis of |
GSM5517716 |
| BioSample |
SAMN20771768 |
| SRA |
SRX11743661 |
