|
| Status |
Public on Mar 18, 2024 |
| Title |
RNA_NP_Deltaex4_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-2_WT_B-2_DELTAex4_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 |
SAMN38269988 |
| SRA |
SRX22538065 |
