NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7901694 Query DataSets for GSM7901694
Status Public on Mar 18, 2024
Title RNA_NP_KO-S-R1
Sample type SRA
 
Source name 129-B13
Organism Mus musculus
Characteristics cell type: neuronal precursors (NPs)
cell line: 129-B13
chip antibody: NA
Growth protocol (mESCs) Serum 20% + LIF. (NPs) mESCs were differentiated as described in https://www.nature.com/articles/nprot.2007.147. Briefly, at day zero mESCs were harvested and seeded in low attachment plates in medium without retinoic acid to allow for the formation of embryoid bodies (EB). EB media was replaced every other day and on day 4 with the addition of retinoic acid. Cells were harvested at day 8 and RNA was extracted for RNA-seq
Extracted molecule polyA RNA
Extraction protocol ChIP-seq: ChIP experiments were carried out adapting with modifications a standard protocol in the lab (PubMed ID 34473698)
RNA-seq: RNA extraction was performed using the RNeasy kit (Qiagen, 74134) according to the manufacturer’s instructions.
Libraries were prepared according to Illumina instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description A-3_KO_B-3_KO-S_stats_paired.txt
Data processing ChIP-seq analysis: Sequence reads of mouse samples were mapped to the mouse genome (mm10) using BOWTIE (PubMed ID 19261174) with the option -m 1. Sequence reads of mouse with fly spike-in samples were mapped to the mouse + fruit fly genome (mm10+dm3) using BOWTIE (PubMed ID 19261174) with the option -m 1. Peak detection was performed with MACS (PubMed ID 18798982). ChIP-seq profiles were produced with SeqCode (PubMed ID 34599234). DiffBind (PubMed ID 22217937) was run next over the union of peaks from each pair of replicates of the same experiment to find those peaks that were significantly enriched in both replicates in comparison to the corresponding controls (parameters: categories = DBA_CONDITION, block = DBA_REPLICATE and method = DBA_DESEQ2_BLOCK, P value < 0.05 and FDR < 10-5).
RNA-seq analysis: Sequence reads were mapped against the mm10 mouse genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1. DESeq2 (PubMed ID 25516281) was run to perform differential gene expression analysis of each annotated gene in RefSeq
Assembly: mm10
Supplementary files format and content: Genome-wide profiles (Bedgraph)
Supplementary files format and content: DESeq2 (TXT): columns are gene name, baseMean, log2FoldChange, lfcSE, stat, pvalue, and padj
 
Submission date Nov 15, 2023
Last update date Mar 18, 2024
Contact name Enrique Blanco
E-mail(s) enrique.blanco@crg.eu
Phone +34 93 316 01 00
Organization name Center for Genomic Regulation (CRG)
Department Gene Regulation, Stem Cells and Cancer
Lab Epigenetic Events in Cancer (L. Di Croce's lab)
Street address Dr. Aiguader 88
City Barcelona
ZIP/Postal code 08003
Country Spain
 
Platform ID GPL17021
Series (1)
GSE223666 Alternative splicing decouples local from global PRC2 activity
Relations
BioSample SAMN38269982
SRA SRX22538071

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap