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Status |
Public on Dec 31, 2018 |
Title |
E14cEpiSC diff3 D19 GEI-129 [miRNA] |
Sample type |
SRA |
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|
Source name |
Mouse ESCs-EpiSCs, male, D19
|
Organism |
Mus musculus |
Characteristics |
cell line: E14 differentiation days: D19 cell type: ESCs-EpiSCs Sex: male experiment name: diff3
|
Treatment protocol |
We recover the time point with Trizol, store them at -80°C.
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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.
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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.
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Library strategy |
miRNA-Seq |
Library source |
transcriptomic |
Library selection |
size fractionation |
Instrument model |
Illumina HiSeq 2500 |
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Description |
E14.diff3.d19 E14 (male) cells. Small RNA-Seq STD Processed data file: miRNA_raw_E14.txt Processed data file: miRNA_norm_E14.txt Processed data file: miRNA_vsd_E14.txt
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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.
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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 |
GSM2056273 |
BioSample |
SAMN04480544 |
SRA |
SRX1565350 |