Published Data Sets

  • Image Description: 3D confocal reconstruction of Bmi1+ lineage regenerative response in the jejunum at 7 d after 12 Gy irradiaton highlights confluent patches of Bmi1+-derived cells in multiple adjacent crypts/villi.  Submitted by: (Yan, PNAS 2012) Kuo Lab, Stanford

Published ISCC Transcriptome and RNAseq

Chatterji P, Rustgi AK. RNA Binding Proteins in Intestinal Epithelial Biology and Colorectal Cancer. Trends Mol Med, Review, 2018 May, 24(5): 490-506. PMCID: 5927824.
  a. Table 1. Key features of the different CLIP techniques
Large scale, high-throughput sequencing techniques, as well as mass spectrometry, have been used to identify mRNA targets and the functional effects of protein-RNA interactions. The widely used method for identifying RBP binding sites and partners consist of CrossLinking the RNP complexes followed by ImmunoPrecipitation and then deep SEQuencing of the bound RNA fragments also known as CLIP-Seq. Several variations of CLIP or HITS-CLIP (High Throughput Sequencing - CLIP) have been described, including PAR-CLIP (photoactivatable-ribonucleoside-enhanced CLIP), iCLIP (individual nucleotide resolution CLIP), eCLIP (enhanced CLIP), cross-linking analysis of cDNA (CRAC), Fully Automated and Standardized iCLIP (FAST-iCLIP) and cross-linking, ligation, and sequencing of hybrids (CLASH).
  b. Table 2. CLIP studies in the RBPs of interest
The targets of several of the RBPs mentioned in this paper have been discovered through these high throughput sequencing techniques. In PAR-CLIP experiments done in HEK293 cells, LIN28A and LIN28B bound to a largely overlapping set of ~3000 mRNAs at ~9500 sites located in the 3′ untranslated region (UTR) and coding DNA sequence (CDS). The binding stabilizes target mRNAs to a certain degree and increases protein abundance mainly in cell cycle regulatory genes. CLIP-Seq studies done in CRC cell lines and in the mouse intestinal epithelium overexpressing LIN28B indicated an enrichment in RNAs for genes regulating metabolism, protein processing in the ER, the actin cytoskeleton, mRNA processing, and focal adhesion with most of the targets being epithelial specific or associated with the translation machinery.
Finkbeiner SR, Hill DR, Altheim CH, Dedhia PH, Taylor MJ, Tsai YH, Chin AM, Mahe MM, Watson CL, Freeman JJ, Nattiv R, Thomson M, Klein OD, Shroyer NF, Helmrath MA, Teitelbaum DH, Dempsey PJ, Spence JR. Transcriptome-wide Analysis Reveals Hallmarks of Human Intestine Development and Maturation In Vitro and In Vivo. Stem Cell Reports, 2015 Jun. PMCID: 4471827.
  a. E-MTAB-3158 - Transcriptional Profiling of human pluripotent stem cells and derived tissues
  b. E-MTAB-3158 Samples (9)
  c. E-MTAB-3158 Protocols (5)
  d. Datasets and R scripts related to the manuscript
Yan KS et al: Intestinal Enteroendocrine Lineage Cells Possess Homeostatic and Injury-Inducible Stem Cell Activity. Cell Stem Cell 2017 Jul, 21(1):78-90 e76.
  a. Injury-inducible stem cell potential of the intestinal enteroendocrine lineage: single-cell mRNA-seq profiling
  b. Bulk cell RNAseq of putatative intestinal stem cell populations
  c. Supplementary Material: Figures S1-S5
  d. Table S1. Overview of Bulk Cell RNA-seq Samples and Read Mapping, Related to Figure 1 and Figure 2
FACS-isolated samples were collected across six institutions for RNA-seq library preparation, sequencing and bioinformatics analysis. Samples from three biological replicates were used to examine each marker population of interest, as well as their marker-negative control and unfractionated epithelium control. Sample sequencing and read mapping metrics are indicated for each individual sample.
  e. Table S2. Overview of Differential Gene Expression in Diverse ISC Populations, Related to Figure 1 and Figure 2
For each marker-positive population of interest, the number of differentially expressed genes relative to each of their marker-negative control population is shown. Only Bmi1-GFP+, CD166+, CD24lo and Lgr5-eGFP+ populations exhibit >200 differentially expressed genes relative to their marker-negative controls.
  f. Table S3. Differentially Expressed Loci in Diverse ISC Populations, Related to Figure 1 and Figure 2
Detailed differentially expressed genes are shown for each marker-positive population analyzed, including FPKMs, log2 (fold-change), p values, and q-values.
  g. Table S4. Gene Ontology (GO) Pathway Analysis of Diverse ISC Populations, Related to Figure 1 and Figure 2
  h. Table S5. Cluster 1 Top Common Genes, Related to Figure 1