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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 29, 2018 |
| Title |
Msl2KO_A2_Serum_rep1 |
| Sample type |
SRA |
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| Source name |
mouse embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
gender: male
genotype: msl2 deletion clone A2
culture media: serum
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| Growth protocol |
All cell culture was performed in a humidified incubator at 37°C and 5% CO2. The parental male Mouse embryonic stem cells were kindly donated by the Bühler laboratory, FMI Basel and cultivated on Attachment Factor in two different ESC culture media. 2i Media: KnockOutTM DMEM supplemented with 15% KnockOutTM Serum Replacement, 0.1mM MEAA,1nM Na Pyruvate, 0.1mM 2-mercaptoethanol, 4mM GlutaMAXTM, 5 μg/ml Insulin (sigma I0516), 50U/ml Pen/Strep, 200U/ml LIF, 1μM PD0325901 (StemGent 04-0006), 3μM CHIR99021 (StemGent 04-0003) serum media: DMEM supplemented with 15% FCS (PAN, PANSera Lot n. P1302077ES), 0.1mM MEAA,1nM Na Pyruvate, 0.1mM 2-mercaptoethanol, 4mM GlutaMAXTM, 50U/ml Pen/Strep, 400U/ml LIF
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using the Direct-zol RNA MiniPrep Kit (Zymo Research)
TruSeq Stranded mRNA Sample Prep Kit (Illumina)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Msl2 KO serum
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| Data processing |
Reads were mapped to the mm10 genome using Hisat2 (v2.0.0.0-beta) with default parameters. Only uniquely mapped reads were kept.
Coverage signal tracks (bigWigs) of primary alignments generated using Samtools (v1.1) and DeepTools2 (v2.4.1)
Primary alignments were counted using featureCounts (v1.4.6-p2)
Differential experesssion analysis was performed using DESeq2 (1.8.2). Only genes with FDR<0.05 in both Msl2 knock-out clones (A2 and D12 as replicates) were considered differentially expressed.
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: featureCounts count table output
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| Submission date |
Jan 30, 2018 |
| Last update date |
Jun 29, 2018 |
| Contact name |
Asifa Akhtar |
| E-mail(s) |
[email protected]
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| Organization name |
Max Planck Institute of Immunobiology and Epigenetics
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| Department |
Chromatin Regulation
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| Lab |
Akhtar Lab
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| Street address |
Stuebeweg 51
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| City |
Freiburg |
| ZIP/Postal code |
79108 |
| Country |
Germany |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE109899 |
Facultative dosage compensation of developmental genes on autosomes in Drosophila and mammals [RNA-seq mouse] |
| GSE109901 |
Facultative dosage compensation of developmental genes on autosomes in Drosophila and mammals |
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| Relations |
| BioSample |
SAMN08442084 |
| SRA |
SRX3632927 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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