|
| Status |
Public on May 13, 2021 |
| Title |
RNA-Seq Diff-d0 WT repl1 |
| Sample type |
SRA |
| |
|
| Source name |
E14TG2a
|
| Organism |
Mus musculus |
| Characteristics |
cell line: E14TG2a
genotype: WT
time: Differentiation day 0
|
| Growth protocol |
E14 mouse ES cells (E14TG2a) were cultured in DMEM, 15% FCS, 1 x L-Glutamine, 1 x Non-essential amino acids, 1 x Sodium pyruvate, 1 x Penicillin/Streptomycin , 0.15% β-mercaptoethanol and 100 Units/ml of LIF on gelatin-coated plates.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
ChIP experiments were performed in accordance to the One Day ChIP kit protocol (Diagenode). Total RNA was extracted by using the RNeasy Mini system (Qiagen) including an on-column DNaseI digestion.
For ChIP-Seq library five nanograms of precipitated DNA were used for indexed sequencing library preparation using the Microplex library preparation kit v2 (Diagenode). RNA-Seq libraries were prepared using the TruSeq Stranded mRNA Library Prep kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
NormalizedCounts-Differentiation.txt
DeSeq2-Differentiation-SAMD1KOvsWT.txt
|
| Data processing |
ChIP-Seq data were aligned to mouse genome mm9 or mm10 using Bowtie 1.0, allowing one mismatch.
SAM files were converted to bigwig files using SamTools, and deepTools/bamCoverage. Data were normalized to RPKM.
RNA-Seq data were aligned to mouse transcriptome GenCode.M23 using RNA Star. Counts per gene were determined using FeatureCounts . Differentially expressed genes and normalized reads were determined using DeSeq2.
Genome_build: mm9, mm10
Supplementary_files_format_and_content: txt
|
| |
|
| Submission date |
Sep 09, 2020 |
| Last update date |
May 13, 2021 |
| Contact name |
Robert Liefke |
| E-mail(s) |
robert.liefke@imt.uni-marburg.de
|
| Organization name |
Philipps University of Marburg
|
| Department |
Institute of Molecular Biology and Tumor Research (IMT)
|
| Street address |
Hans-Meerwein-Str. 2
|
| City |
Marburg |
| State/province |
Hessen |
| ZIP/Postal code |
35043 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21626 |
| Series (1) |
| GSE144396 |
The SAM domain-containing protein 1 (SAMD1) acts as a repressive chromatin regulator at unmethylated CpG islands |
|
| Relations |
| BioSample |
SAMN16088982 |
| SRA |
SRX9100279 |
