Table_S5

Summary of identified HIP strains with common background mutation

Table_S6

Signature hits for inhibition of non-proteinaceous target

HOP_scores

Tab-delimited text file with MADL and z-scores for all approx. 1800 compounds tested in this stud

HIP_scores

Tab-delimited text file with MADL and z-scores for all approx. 1800 compounds tested in this stud

HIP_scores-benomyl

Tab delimited text file with the data of all performed Benomyl experiment

Table S1

Compounds used in this stud

Table_S4

microtubule inhibitor compounds as identified by HIP HO

HOP_scores-benomyl

Tab delimited text file with the data of all performed Benomyl experiment

Table_S2

Hit frequencies of HIP and HOP strain

Additional file 1: Figure S1. of A comprehensive assessment of RNA-seq protocols for degraded and low-quantity samples

Bioanalyzer profile of the fragment size distribution for the intact SEQC-A and SEQC-B samples. The curve for SEQC-A is shown in red and the curve for SEQC-B in blue. The two peaks represent the intact 18S and 28S ribosomal RNA profiles. Figure S2. Bioanalyzer profile of the fragment size distribution for the degraded SEQC-A and SEQC-B samples. The curve for SEQC-A is shown in red and the curve for SEQC-B in blue. The peaks for the 18S and 28S ribosomal RNAs are now following a unimodal distribution with a much wider peak around a fragment size of 850 nt, reflecting the level of degradation. Figure S3. Bioanalyzer profile of the fragment size distribution for the highly-degraded SEQC-A and SEQC-B samples. The curve for SEQC-A is shown in red and the curve for SEQC-B in blue. The peaks for the 18S and 28S ribosomal RNAs are now following a unimodal distribution with a much wider peak around a fragment size of 150–200 nt, reflecting a high level of degradation. Figure S4. Bargraph of the alignment statistics for the SEQC-B sample and all three protocols. Each bar represents the averaged values across the three technical replicates per condition. The percentage of total aligned reads is represented by the height of the bar, and the percentage of reads aligning to exons is in red, introns in blue, and intergenic regions in green. Figure S5. Venn diagram of the protein coding genes detected by each of the three protocols. Venn diagram of the protein coding genes detected by each of the three protocols on degraded samples at the input amounts 10 ng for RNA Access and 100 ng for Ribo-Zero and TruSeq. A gene is considered “expressed” if it has a FPKM value of at least 0.3 in one of the three technical replicates of at least one of the two samples (SEQC-A or SEQC-B). Table S1. Simplified Ensembl gene type mapping. The original Ensembl (v76) gene type category is contained in the left column and the simplified category is contained in the right column. (PDF 661 kb