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Published Data Sets

Published ISCC Transcriptome and RNAseq

Lineage-specifying transcription factor CDX2

Kumar N, Tsai YH, Chen L, Zhou A, Banerjee KK, Saxena M, Huang S, Toke NH, Xing J, Shivdasani RA, Spence JR, Verzi MP. The lineage-specific transcription factor CDX2 navigates dynamic chromatin to control distinct stages of intestine development. Development, 2019 Mar, 146(5). PMCID: 6432663.
	a. Geo Dataset GSE115314: The lineage-specific transcriptional regulator, CDX2, navigates a dynamic chromatin landscape to control distinct stages of intestinal development
	b. Geo Dataset GSE115541: Chromatin and tissue plasticity precede commitment to intestinal differentiation during endoderm development
	c. Supplementary Information for publication: The lineage-specific transcription factor CDX2 navigates dynamic chromatin to control distinct stages of intestine development.

Epithelial response to disruption of the mucosal barrier- University of California San Francisco

Nusse YM, Savage AK, Marangoni P, Rosendahl-Huber AKM, Landman TA, de Sauvage FJ, Locksley RM, Klein OD. Parasitic helminths induce fetal-like reversion in the intestinal stem cell niche. Nature, 2018 Jul, 559(7712): 109-13. PMCID: 6042247.
	a. Geo Dataset GSE97405: Parasitic helminths repress the canonical intestinal stem cell program
	b. Geo Dataset GSE108233: Single cell analysis of Granuloma crypt epithelium
	c. Geo Dataset Platform GPL17021: Platform - Illumina HiSeq 2500 (Mus musculus)
	d. Supplementary Materials and Data Availability Statement- Refer to Web version on PubMed Central for supplementary material for publication Parasitic helminths induce fetal-like reversion in the intestinal stem cell niche

RNA-seq of transplanted pluripotent stem cells-derived human intestinal organoids upon mechanical lengthening and human jejunum tissues – Cincinnati Children’s Hospital Medical Center

Poling HM, Wu D, Brown N, Baker M, Hausfeld TA, Huynh N, Chaffron S, Dunn JCY, Hogan SP, Wells JM, Helmrath MA, Mahe MM. Mechanically induced development and maturation of human intestinal organoids in vivo. Nat Biomed Eng, 2018 Jun, 2(6): 429-42. PMCID: 6108544. .
	a. ArrayExpress: E-MTAB-6017 - RNA-seq of transplanted pluripotent stem cells-derived human intestinal organoids upon mechanical lengthening and human jejunum tissues. This includes the transplanted HIO, with or without lengthening device, the human adult and infant data shown in Figure 3 and supplementary Figure 2
	b. E-MTAB-6017 Samples (11)
	c. E-MTAB-6017 Protocols (8)
	d. Detailed transcriptome analysis and R scripts related to the manuscript are provided in the Github repository
	e. Supplementary Materials - Refer to Web version on PubMed Central for supplementary material.

Proliferative and dynamic intestinal epithelium - University of Pennsylvania

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.

RNA seq analysis of mouse intestinal stem, progenitor and differentiated cells- Dana Farber Cancer Institute

Jadhav U, Saxena M, O'Neill NK, Saadatpour A, Yuan GC, Herbert Z, Murata K, Shivdasani RA. Dynamic Reorganization of Chromatin Accessibility Signatures during Dedifferentiation of Secretory Precursors into Lgr5+ Intestinal Stem Cells. Cell Stem Cell, 2017 Jul, 21(1): 65-77 e5. PMCID: 5505276.
	a. Chromatin access at specific genome sites distinguishes intestinal crypt populations with stem cell potential
	b. Supplementary Materials - Refer to Web version on PubMed Central for supplementary material.

Human Expression profiling by high throughput sequencing- Cincinnati Children's Hospital Medical Center

Workman MJ, Mahe MM, Trisno S, Poling HM, Watson CL, Sundaram N, Chang CF, Schiesser J, Aubert P, Stanley EG, Elefanty AG, Miyaoka Y, Mandegar MA, Conklin BR, Neunlist M, Brugmann SA, Helmrath MA, Wells JM.. Engineered human pluripotent-stem-cell-derived intestinal tissues with a functional enteric nervous system. Nat Med, 2017 Jan, 23(1): 49-59.
	a. Engineered human pluripotent stem cell-derived intestinal tissues with a functional enteric nervous system
	b. Platform - Illumina HiSeq 2000 (Homo sapiens)
	c. Supplementary Materials - Refer to Web version on PubMed Central for supplementary material.

RNA-seq of coding RNA, development or differentiation design - University of Michigan

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

Mouse Expression profiling by high throughput sequencing- University of California, Los Angles

Lei NY, Jabaji Z, Wang J, Joshi VS, Brinkley GJ, Khalil H, Wang F, Jaroszewicz A, Pellegrini M, Li L, Lewis M, Stelzner M, Dunn JC, Martin MG. Intestinal subepithelial myofibroblasts support the growth of intestinal epithelial stem cells. PLoS One, 2014 Jan, 9(1): e84651. PMCID: 3882257.
	a. Intestinal subepithelial myofibroblasts support the growth of intestinal epithelial stem cells
	b. Platform - Illumina HiSeq 2000 (Mus musculus)
	c. B19_B20_HTSeq Dataset

Murine ISC Populations - Stanford Supplemental Tables

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