Journal: bioRxiv

Article Title: Context-Aware Transcript Quantification from Long Read RNA-Seq data with Bambu

doi: 10.1101/2022.11.14.516358

Figure Lengend Snippet: (a) Repeat families ranked by the number of expressed elements identified in the human embryonic stem cell cell line (H9) (b) Overview of the top 100 expressed novel and annotated transcripts that overlap with the HERVH-LTR7 retrotransposon in hESC cell line. For novel transcripts, we only include those with high overlap in novel exons. Top: Fraction of overlap with HERVH and LTR7. Bottom: Expression estimate in H9 hESCs and in the 5 SG-NEx cancer cell lines (c-f) Illustrations of highly expressed transcripts in H9 hESCs that originate from HERVH-LTR7 repeats that show distinct splicing patterns and transcript sequences. Top: transcript annotation colored by estimated full-length read support, with ranks in expression highlighted inside the bracket. Middle: mean read coverage for the specified genomic ranges for each selected gene. Bottom: show repeat masker colored by HERVH (green), LTR7 (light green), and all other repeat types (light grey).

Article Snippet: Bambu includes a model that was trained on Nanopore RNA-Seq data from a human cell line (see ).

Techniques: Expressing

Journal: Developmental cell

Article Title: Prevention and reversion of pancreatic tumorigenesis through a differentiation-based mechanism

doi: 10.1016/j.devcel.2019.07.012

Figure Lengend Snippet: (A) Expression of PTF1A and other acinar regulators in normal human pancreas (n=2) and PDAC cell lines (n=41), derived from public RNA-seq datasets. Expression plotted in transcripts per million, with individual samples plotted in blue over violin plots representing all expressed genes in each sample. (B) Western blot of Ptf1a and tubulin (control) expression in Lenti-TET-Ptf1a derivatives of Panc1, MiaPaCa2, Su8686 and SW1990 cells, treated −/+ DOX (1 μg/ml) for 48 hrs. (C) Representative images from clonogenic growth assays of Panc1 and Su8686 Lenti-TET-Ptf1a cells, grown 2 weeks −/+ DOX and stained with crystal violet. (D) Quantification of relative clone numbers in indicated PDAC cell lines, transduced with Lenti-TET-EGFP (green) or Lenti-TET-Ptf1a (orange), grown 10–14 days −/+ DOX (open vs. closed circles). Distinct lowercase letters indicate p<0.05 from ANOVA followed by Tukey’s post-hoc test of DOX-treated Lenti-TET-Ptf1a cells. (E) Cumulative population doublings of indicated PDAC cells, transduced with EGFP or Ptf1a (green vs orange). Cells were counted and replated at constant densities every 3 days, and treated from day 1 onwards −/+ DOX (open vs. closed circles for individual experiments, dotted vs. solid lines representing means). * P<0.05, DOX-treated Ptf1a vs EGFP cells. (F) Expression of indicated genes in PDAC cell lines transduced with Lenti-TET-Ptf1a, grown 48 hrs −/+ DOX (blue vs. orange), and analyzed by RT-qPCR (ΔΔCt method, normalized to PPIA expression within each sample and untreated Panc1 cells across samples).

Article Snippet: Human cancer cell line RNA-seq data (TPM), Genentech , EMBL-EBI Expression Atlas , https://www.ebi.ac.uk/gxa/experiments/E-MTAB-2706/Downloads?ref=aebrowse.

Techniques: Expressing, Derivative Assay, RNA Sequencing, Western Blot, Control, Staining, Transduction, Quantitative RT-PCR

Journal: Developmental cell

Article Title: Prevention and reversion of pancreatic tumorigenesis through a differentiation-based mechanism

doi: 10.1016/j.devcel.2019.07.012

Figure Lengend Snippet: KEY RESOURCE TABLE

Article Snippet: Human cancer cell line RNA-seq data (TPM), Genentech , EMBL-EBI Expression Atlas , https://www.ebi.ac.uk/gxa/experiments/E-MTAB-2706/Downloads?ref=aebrowse.

Techniques: Recombinant, Electron Microscopy, Expressing, Plasmid Preparation