ERX3224734
FASTQ
SRA
Experiment Detail
| Title | NextSeq 550 paired end sequencing; RNA-Seq of Diversity Outbred mouse embryonic stem cells |
| Design Description | RNA-Seq of Diversity Outbred mouse embryonic stem cells |
| Organism | Mus musculus |
Library Description
| Name | PB359_22_p |
| Strategy | RNA-Seq |
| Source | TRANSCRIPTOMIC |
| Selection | PolyA |
| Layout | PAIRED |
| Orientation | |
| Nominal Length | 350 |
| Nominal Sdev | 100 |
| Construction Protocol | ESCs were derived from random blastocysts of Diversity Outbred (Jackson Laboratory #009376) mice using previously published protocols (Czechanski et al. 2014 Nature Protocols). As the ES cells expanded, they were transferred into 24 well plates, followed by 6 well plates, and finally 10cM dishes, all without feeder cells but in the same media. Cells were maintained in ES medium (ESM, 1i+LIF: Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% fetal bovine serum, 100 U/mL Penicillin-Streptomycin, 2mM GlutaMAX, 0.1mM non-essential amino acids, 1mM sodium pyruvate, 0.1mM 2-mercaptoethanol, approximately 2000U/ml LIF, and 3uM CHIR99021). For each mESC line, one 15cm dish of cells was grown to near confluence, washed 3x with PBS, and mechanically harvested to produce 80-150mg wet weight cell pellets (~50M cells). About 100k cells from each frozen cell pellet were used for RNA sequencing. Cell lines were untreated. Total RNA was extracted using the Quick-RNA 96 well format kit (Zymo Research) with in-column DNase treatment. Sequencing libraries were prepared using the TruSeq Stranded mRNA HT kit (Illumina, Cat no. 20020595) and included ribosomal RNA reduction and poly-A selection, enzymatic fragmentation, cDNA synthesis from random hexamer priming, adapter ligation and PCR amplification steps to generate indexed, stranded mRNA-seq libraries. Libraries were checked for quality and quantitated with the Agilent Bioanalyzer, and samples that failed QC were repeated starting from the cryovial stage. |
Platform
| Platform | ILLUMINA |
| Instrument Model | NextSeq 550 |
Processing
| Base Calls | |
|---|---|
| Sequence Space | |
| Base Caller | |
Spot Information
| Number of Reads per Spots | 0 |
| Spot Length | 0 |
Read Spec
Navigation
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Submission | ERA1752706 |
FTP
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Study | ERP114111 | ||
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Sample | ERS3200903 | ||
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Run | ERR3196958 |
FASTQ
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SRA
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