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| Status |
Public on Jan 25, 2024 |
| Title |
mESCs, stimulated, 6h 2.5 ng/ml FGF4 |
| Sample type |
SRA |
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| Source name |
mESCs
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| Organism |
Mus musculus |
| Characteristics |
strain: E14tg2a
cell type: mESCs
genotype: Fgf4 -/-
treatment: 2.5 ng/ml FGF
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| Treatment protocol |
Stimulation with 0, 0.625, 1.25, 2.5, 5, 10, 20 or 40 ng/ml FGF4 in N2B27 + 1 μg/ml heparin for 6 h
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| Growth protocol |
E14 Fgf4-mutant mESCs were seeded at 45k cells/cm2 were grown in N2B27 + Chiron + LIF for 18 h
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Trizol-based total RNA extraction
Strand-specific, Poly-A-enriched
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
2.5
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| Data processing |
Alignment to genome with hisat2, version 2.1.0
Probe definition using RNA-seq quantitation pipeline in Seqmonk, version 1.48.1. Parameters: Transctipt features mRNA; Library type Non-strand specific; Libraries are paired end TRUE; Merge transcript isoforms TRUE; Generate Raw Counts TRUE; all others: FALSE
Read count quantification using Read Count Quantification in Seqmonk, version 1.48.1. Parameters for Raw Counts: Count reads on strand: Opposite Strand to Probe; Correct for total read count FALSE; Correct for probe length FALSE; Log Transform Count FALSE; Count duplicated reads only once FALSE
Parameters for TPMs: Count reads on strand: Opposite Strand to Probe; Correct for total read count TRUE; Correct to what? Per Million Reads; Count total only within probes FALSE; Correct for probe length FALSE; Log Transform Count FALSE; Count duplicated reads only once FALSE
Assembly: GRCm39, release 97
Supplementary files format and content: All_Probes_Raw_Counts.txt: Contains raw counts per sample (columns) for each gene (rows) including gene information (e.g. genomic location, strand, ID, etc.)
Supplementary files format and content: All_Probes_TPMs.txt: Contains TPMs per sample (columns) for each gene (rows) including gene information (e.g. genomic location, strand, ID, etc.)
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| Submission date |
Jan 18, 2024 |
| Last update date |
Jan 25, 2024 |
| Contact name |
Max Fernkorn |
| E-mail(s) |
m.fernkorn@lacdr.leidenuniv.nl
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| Organization name |
University Leiden
|
| Department |
Leiden Academic Centre for Drug Research (LACDR)
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| Lab |
Drukker
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| Street address |
Einsteinweg 55
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| City |
Leiden |
| ZIP/Postal code |
2333 CC |
| Country |
Germany |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE253606 |
6 h FGF4 stimulation of Fgf4-mutant mESCs [bulkRNA-seq] |
| GSE253609 |
Med12 cooperates with multiple differentiation signals to facilitate efficient lineage transitions in embryonic stem cells |
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| Relations |
| BioSample |
SAMN39488795 |
| SRA |
SRX23306592 |
| 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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