|
| Status |
Public on May 29, 2020 |
| Title |
Dnmt1_null_2 |
| Sample type |
SRA |
| |
|
| Source name |
ES Cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Embryonic Stem (ES) Cells
cell line: D1-null strain (C allele)
|
| Treatment protocol |
WT and Dnmt1-/- ES cells were untreated. OGA and OGA-D242D samples were WT ES cells treated with dCas9-OGA anad dCas9-OGA-D242D respectively and 4 sgRNAs targeting IAP elements.
|
| Growth protocol |
ES cells were cultured on gelatin-coated plates in under standard conditions (DMEM, 2 mM Glu-tamax, 15% ES grade fetal bovine serum, 2 mM L glutamine, MEM non-essential amino acids, 100 IU/ml penicillin, 100 μg/ml streptomycin, 0.12 mM 2-mercaptoethanol and leukemia inhibitory factor).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted and traces of contaminating genomic DNA were eliminated by two successive treatments with DNAse (Turbo DNase, Ambion). The integrity of the RNA was veri-fied using the Bioanalyzer RNA 2100 Nano Assay (Agilent Technologies).
RNA-seq libraries were prepared with the TruSeq RNA Sample Prep Kit v2 (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
D1-null strain (C allele) Ref: De novo DNA cytosine methyltransferase activities in mouse embryonic stem cells. Lei H, Oh SP, Okano M, Jüttermann R, Goss KA, Jaenisch R, Li E.Development. 1996 Oct;122(10):3195-205
|
| Data processing |
Illumina RTA and bcl2fastq2 (version 2.17) were used for basecalling and conversion to fastq files.
For repeat analysis, reads were mapped to the mouse genome references (mm10) using bowtie2 (v2.2.2) and default parametes except for -D 10000 -R 10000. After filtering out reads that maped to rRNA and mRNA (Ensembl v87) sequences, reads were overlapped with repeat annotations from the RepeatMasker track from the UCSC genome browser using featureCounts (v1.5.0).
For transcript analysis, reads were mapped to the mouse genome reference (mm10) using HISAT2 (v2.1.0) and knownsplice mapping using Ensembl v87 with otherwise default parameters. After filtering out reads that mapped to rRNA sequences, alignment files were overlapped with gene annotations using featureCounts (v1.5.0) and Ensembl v87.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes all raw feature counts for each gene.
|
| |
|
| Submission date |
Nov 21, 2019 |
| Last update date |
May 29, 2020 |
| Contact name |
John R. Edwards |
| E-mail(s) |
[email protected]
|
| Organization name |
Washington University School of Medicine
|
| Department |
Center for Pharmacogenomics
|
| Street address |
660 S. Euclid Ave, Campus Box 8220
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE93539 |
Protein O-GlcNAcylation Silences Methylated Promoters in Mammalian Genomes |
|
| Relations |
| BioSample |
SAMN13348447 |
| SRA |
SRX7199983 |
