/ESC_RNA_seq

analysis of published RNA-seq data of stem cell differentiation process

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RNA sequence analysis of stem cell differentiation process

In this project I will store my scripts.

Files for CMap analysis (FILES_FOR_LINCS folder)

  1. Genes that are present in all analysis: GSE109658 (bulk RNA-seq), GSE52158 (microarray seq), GSE75748 (bulk RNA-seq)
  • topCommonDownRegulatedLogSorted.grp (84 genes, sorted 75748) - for LINCS
  • topCommonDownRegulatedLogSortedProbes.grp (95 probes, sorted 75748) - for CMap O2
  • topCommonUpRegulatedLogSorted.grp (208 genes, sorted 75748) - for LINCS (first 150)
  • topCommonUpRegulatedLogSortedProbes.grp (283 probes, sorted 75748) - for CMap O2
  • topCommonDownRegulatedLogSorted52158.grp (sorted 52158) - for LINCS
  • topCommonDownRegulatedLogSorted109658.grp (sorted 109658) - for LINCS
  • topCommonUpRegulatedLogSorted52158.grp (sorted 52158) - for LINCS
  • topCommonUpRegulatedLogSorted109658.grp (sorted 109658) - for LINCS
  1. Genes that are present in two analysis: GSE109658 (bulk RNA-seq) and GSE75748 (bulk RNA-seq)
  • common_Downregulated_1_75748_LogSorted.grp (sorted 75748) - for LINCS
  • common_Downregulated_1_75748_LogSortedProbes.grp (sorted 75748) - for CMap O2
  • common_Upregulated_1_75748_LogSorted.grp (sorted 75748) - for LINCS
  • common_Upregulated_1_75748_LogSortedProbes.grp (sorted 75748) - for CMap O2
  • common_Downregulated_1_109658_LogSorted.grp (sorted 109658) - for LINCS
  • common_Upregulated_1_109658_LogSorted.grp (sorted 109658) - for LINCS
  1. Genes that are present in two analysis: GSE52158 (bulk RNA-seq) and GSE75748 (bulk RNA-seq)
  • common_Downregulated_2_75748_LogSorted.grp (sorted 75748) - for LINCS
  • common_Downregulated_2_75748_LogSortedProbes.grp (sorted 75748) - for CMap O2
  • common_Upregulated_2_75748_LogSorted.grp (sorted 75748) - for LINCS
  • common_Upregulated_2_75748_LogSortedProbes.grp (sorted 75748) - for CMap O2
  • common_Downregulated_2_52158_LogSorted.grp (sorted 52158) - for LINCS
  • common_Upregulated_2_52158_LogSorted.grp (sorted 52158) - for LINCS
  1. Genes that are present in two analysis: GSE109658 (bulk RNA-seq) and GSE52158 (bulk RNA-seq)
  • common_Downregulated_3_109658_LogSorted.grp (sorted 109658) - for LINCS
  • common_Downregulated_3_109658_LogSortedProbes.grp (sorted 109658) - for CMap O2
  • common_Upregulated_3_109658_LogSorted.grp (sorted 109658) - for LINCS
  • common_Upregulated_3_109658_LogSortedProbes.grp (sorted 109658) - for CMap O2
  • common_Downregulated_1_52158_LogSorted.grp (sorted 52158) - for LINCS
  • common_Upregulated_1_52158_LogSorted.grp (sorted 52158) - for LINCS
  1. Genes that are golden markers for DE versus hESC (from the papers)
  • Golden_list_Up.grp - for LINCS
  • Golden_list_Down.grp - for LINCS
  • Golden_list_Up_Probes.grp - for CMap O2
  • Golden_list_Down_Probes.grp - for CMap O2