|
| Status |
Public on Dec 31, 2018 |
| Title |
PGKcEpiSC diff3 D10 GEI-121 [miRNA] |
| Sample type |
SRA |
| |
|
| Source name |
Mouse ESCs-EpiSCs, female, D10
|
| Organism |
Mus musculus |
| Characteristics |
cell line: PGK
differentiation days: D10
cell type: ESCs-EpiSCs
Sex: female
experiment name: diff3
|
| Treatment protocol |
We recover the time point with Trizol, store them at -80°C.
|
| Growth protocol |
ES cells (cultured in 2i medium) are differentiated in EpiSC by plating them in mouse EpiSC medium (N2B27/Activin A (20ng/ul) /Fgf2 (12ng/ul)) on 10ug/ml fibronectin at a density of 2x10^5/well. 4 days after switching from ESC to EpiSC medium, the well should be confluent and be split with Accutase. We continue to split them every 2 days until 30 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
We extract RNA by phenol:chloroform protocol and we did a step of DNase treatment, do a quantification and a gel.
Libraries were prepared according to Illumina's instructions.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
PGK.diff3.d10
PGK (female) cells.
Small RNA-Seq STD
Processed data file: miRNA_raw_PGK.txt
Processed data file: miRNA_norm_PGK.txt
Processed data file: miRNA_vsd_PGK.txt
|
| Data processing |
Basecalls performed with CASAVA-1.8.2.
Quality control, alignment to genome, miRNA calls and raw counts calculations were performed using the ncPRO web application (Chen C et al. ncPRO-seq: a tool for annotation and profiling analysis of ncRNAs from small RNA-seq. Bioinformatics (2012)).
Data normalization and differential expression analysis performed with DESeq2.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Data matrices containing raw counts (miRNA_raw.txt), DESeq2 normalized values (miRNA_norm.txt), DESeq2 Variance Stabilisation Transformed values (miRNA_vsd.txt).
Supplementary_files_format_and_content: miRNA_raw_E14.txt: Raw Counts for male ESC.
Supplementary_files_format_and_content: miRNA_norm_E14.txt: Normalized Counts for male ESC.
Supplementary_files_format_and_content: miRNA_vsd_E14.txt: Variance Stabilized Counts for male ESC.
Supplementary_files_format_and_content: miRNA_raw_PGK.txt: Raw Counts for female ESC.
Supplementary_files_format_and_content: miRNA_norm_PGK.txt: Normalized Counts for female ESC.
Supplementary_files_format_and_content: miRNA_vsd_PGK.txt: Variance Stabilized Counts for female ESC.
|
| |
|
| Submission date |
Feb 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Federico De Masi |
| E-mail(s) |
fdemasi@cbs.dtu.dk
|
| Organization name |
Technical University of Denmark
|
| Department |
Institute of Systems Biology
|
| Lab |
Regulatory Genomics
|
| Street address |
Kemitorvet 208
|
| City |
Lyngby |
| ZIP/Postal code |
2800 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE77690 |
miRNA regulatory networks in male and female mouse ESC-to-EpiSC differentiation [miRNA] |
| GSE77692 |
miRNA regulatory networks in male and female mouse ESC-to-EpiSC differentiation |
|
| Relations |
| Affiliated with |
GSM2056267 |
| BioSample |
SAMN04480538 |
| SRA |
SRX1565344 |
