|
| Status |
Public on Dec 08, 2019 |
| Title |
NPC_CL31_Aux24h |
| Sample type |
SRA |
| |
|
| Source name |
NPC_SPEN-AID
|
| Organism |
Mus musculus |
| Characteristics |
cell type: neural progenitor cells
treatment: Auxin24h
strain: BL/6J x CAST-EiJ
|
| Treatment protocol |
Cells were treated with auxin (500uM) for 0h, 24h or 48h.
|
| Growth protocol |
Spen-degron mESCs were differentiated in NPCs and subcloned as in (Giorgetti et al., 2016). NPCs were grown in N2B27 medium supplemented with EGF and FGF (10ng/ml each), on 0.1% gelatin-coated 6-well plates.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted according to the manufacturer’s recommendations using RNeasy Mini Kit (Qiagen) with on-column DNAse digestion (Qiagen). Only samples showing a RIN score above 9 were used to prepare RNAseq libraries (TruSeq). Libraries were sequenced using NovaSeq 6000 at PE100 settings.
Library were prepared using TruSeq RNA kit v2.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
All data were mapped to the mouse genome mm10, using the BL6-EiJ / CAST SNPs from the mouse genome project (v5 SNP142), and the gene annotation from ensembl (v92). Analyses were performed in R (v 3.4.2) and Bioconductor (v3.6).
RNAseq data were processed similarly as ChIPseq, except for the mapping when the following parameters were used: --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06 --alignIntronMax 500000 --alignMatesGapMax 500000 --alignEndsType EndToEnd --outSAMattributes NH HI NM MD. Quantification of expression was performed using featureCount (parameters: -p -t exon -g gene_id, -s 1 for stranded RNAseq of in vitro cell, -s 0 for non-stranded RNAseq of single embryo). Data were then analysed in R using DESeq2 13 (v1.18.1), calculating the sizeFactor on the count of total reads and applying it to the allele specific counts.
Genome_build: mm10
|
| |
|
| Submission date |
May 27, 2019 |
| Last update date |
Dec 09, 2019 |
| Contact name |
samuel Collombet |
| E-mail(s) |
[email protected]
|
| Organization name |
Ecole Normale Superieure
|
| Department |
Biology
|
| Lab |
Thieffry
|
| Street address |
46 rue d'Ulm
|
| City |
Paris |
| ZIP/Postal code |
75005 |
| Country |
France |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE131783 |
Spen regulates X chromosome inactivation (RNAseq in NPC) |
| GSE131784 |
Spen regulates X chromosome inactivation |
|
| Relations |
| BioSample |
SAMN11866932 |
| SRA |
SRX5903727 |
