|
| Status |
Public on Mar 19, 2019 |
| Title |
RNAseq_shC_R1_shControl |
| Sample type |
SRA |
| |
|
| Source name |
RNAseq_shC
|
| Organism |
Mus musculus |
| Characteristics |
cell line: E14
cell type: mouse Embryonic Stem Cells (mESCs)
treatment: shC
genotype: WT
|
| Treatment protocol |
Chromatin material for ChIP-seq was prepared using the ChIP-IT High Sensitivity kit from Active Motif, following the manufacture’s instruction. ChIP-seq libraries were prepared with 2-10 ng of ChIP DNA material using the NEBNext Ultra DNA library Prep kit for Illumina (New England Biolabs) following manufacturer’s instruction. ChIP-seq libraries were amplified for 10-15 PCR cycles.
|
| Growth protocol |
E14TG2a from mouse embryo (male blastocyst, strain 129/Ola) (SIGMA) were cultured on tissue culture plates coated with 0.1% gelatin (Millipore) in naïve. Briefly, ESCs were growth in serum-free medium N2B27 media (DMEM/F12:Neurobasal 1:1, 0.5x N-2 supplement, 1x B-27 serum-free supplement, 50 µM 2-mercaptoethanol; Bovine Albumin Fraction V 0.033%; 1X Glutamax; 1X MEM non-essential aminoacids; 1X Penicillin-Streptomycin; all from Gibco) supplemented with 1 µM PD0325901 (Tocris), 3 uM CHIR99021 (Tocris) and Leukemia Inhibitory Factor (LIF).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using the RNeasy mini kit (Qiagen) following manufacturer’s instruction. RNA samples were quantified and quality was evaluated using Bioanalyzer (RIN > 9.9). A total of 0.5 ug of RNA was used as starting material for library preparation with rRNA depletion using TruSeq Stranded Total RNA Library Prep kit (Ilumina) following the manufacturer´s instruction.
Libraries were prepared according to Illumina instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RNAseq experiment
|
| Data processing |
ChIPseq analysis: Alignment: Sequence reads were mapped to the Mouse genome (mm9, July 2007) using BOWTIE (PubMed ID 19261174) with the option -m 1. RNAseq analysis: Alignment: Sequence reads were mapped against the mm9 mouse genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1.
ChIPseq peak detection was performed with MACS (PubMed ID: 18798982). Peaks were reported in BED format. ChIPseq genome-wide profiles are normalized by the total number of reads of each sample.
Genome_build: mm9
Supplementary_files_format_and_content: Files *.bdg.gz (BedGraph, genome-wide ChIPseq and RNAseq profiles)
Supplementary_files_format_and_content: Files .bed (BED, signal enriched regions)
|
| |
|
| Submission date |
Jul 09, 2018 |
| Last update date |
Mar 19, 2019 |
| 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) |
| GSE116799 |
Chromatin capture defines AHCY as regulator of pluripotent stem cells proliferation |
|
| Relations |
| BioSample |
SAMN09632201 |
| SRA |
SRX4369914 |
