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kallisto quantifications of Frahm et al., 2017

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posted on 04.05.2018, 19:08 by Lynn YiLynn Yi, Harold Pimentel, Nicolas Bray, Lior Pachter
The analysis was performed in Yi et al., 2017, which used p-value aggregation on transcript differential analysis to make gene-level determinations. For more details, see https://doi.org/10.1186/s13059-018-1419-z


We analyzed a dataset (GEO Series GSE95363) consisting of reads derived from RNA-seq on primary mouse neural progenitor cells extracted from two regions of the brain, from female and male embryonic mice, and with and without dexamethasone treatment. Three replicates were performed for each of the eight combinatorial conditions, resulting in a total of 24 single-end RNA-seq samples. Samples were quantified with kallisto v0.43.1 (default kmer length 31, with 30 bootstraps per sample), using an index constructed from Ensembl Mus musculus GRCm38 cDNA release 88.

RNA-Seq performed by:
Frahm KA, Waldman JK, Luthra S, Rudine AC, Monaghan-Nichols AP, Chandran UR. A comparison of the sexually dimorphic dexamethasone transcriptome in mouse cerebral cortical and hypothalamic embryonic neural stem cells. Mol Cell Endocrinol. 2017; https://doi.org/10.1016/j.mce.2017.05.026.

Funding

LY was partially funded by the UCLA-Caltech Medical Science Training Program, NIH T32 GM07616, and the Lee Ramo Fund. HP was partially funded by NIH R01 HG008140.

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