|
| Status |
Public on Nov 27, 2020 |
| Title |
S3-/- -48h R1 |
| Sample type |
SRA |
| |
|
| Source name |
S3-/- -48h_mESCs
|
| Organism |
Mus musculus |
| Characteristics |
strain background: 129/Ola
cell type: mouse embryonic stem cell
genotype/variation: Stat3 knock-out
phenotype: adherent
growth condition: without 2iLIF for 48 hours
|
| Treatment protocol |
Mouse ES cells stabilized in 2iLIF were cultured in absence of 2iLIF for 48 hours to mimic differentiation process.
|
| Growth protocol |
Mouse ES cells were cultured without feeders on gelatine-coated plates (0.2% gelatine) in serum-free KSR-based medium (Life Technologies) supplemented with: 1 μM PD0325901, 3 mM CHIR99021 (2i); and 100 units/m LIF (2iLIF).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Total RNA Purification kit (Norgen Biotek), according to manufactorer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
FCHTGVKBBXX_L1_WHMANsmwEAARRAAPEI-72
|
| Data processing |
Reads were aligned to mouse transcriptome (Mus musculus transcriptome generated by rsem-prepare-reference with ENSEMBL93 GTF) and mouse genome (GRCm38.p6) using HISAT2 v. 2.1.0. Gene expression levels were quantified with RSEM v. 1.3.1 using transcriptome alignments.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text RSEM output files including for each sample: gene_id, transcript_id(s), length, effective_lenght, expected_count, TPM, FPKM.
|
| |
|
| Submission date |
Jul 08, 2019 |
| Last update date |
Nov 27, 2020 |
| Contact name |
Graziano Martello |
| E-mail(s) |
graziano.martello@unipd.it
|
| Organization name |
University of Padua
|
| Department |
Department of Molecular Medicine
|
| Street address |
viale Colombo 3
|
| City |
Padua |
| ZIP/Postal code |
35121 |
| Country |
Italy |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE133926 |
RRBS profiling and Transcriptome profiling of Stat3 wild-type, Stat3 knock-out, Dnmt3a/b wild-type and Dnmt3a/b knock-out mouse embryonic stem cells (mES cells) |
|
| Relations |
| BioSample |
SAMN12229917 |
| SRA |
SRX6413312 |
