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Sample GSM3819702 Query DataSets for GSM3819702
Status Public on Dec 08, 2019
Title NPC_CL30_Aux48h
Sample type SRA
 
Source name NPC_SPEN-AID
Organism Mus musculus
Characteristics cell type: neural progenitor cells
treatment: Auxin48h
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) samuelcollombet@gmail.com
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 SAMN11866931
SRA SRX5903728

Supplementary file Size Download File type/resource
GSM3819702_NPC_CL30_Aux48h_RNAseq.count.txt.gz 3.6 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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