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Sample GSM3819700 Query DataSets for GSM3819700
Status Public on Dec 08, 2019
Title NPC_CL30_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
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
BioSample SAMN11866933
SRA SRX5903726

Supplementary file Size Download File type/resource
GSM3819700_NPC_CL30_Aux24h_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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