GEO DataSets

(Submitter supplied) In this study we use targeted DamID to assay RNA polymerase occupancy across the genome specifically within the seam cells and hypodermis of C. elegans to identify genes expressed in these cell-types.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL22765

16 Samples

Download data: GFF, TXT

(Submitter supplied) In this study we adapt targeted DamID (TaDa) for use in C.elegans and employ it to identify targets within the epidermis for the transcription factors LIN-22 and NHR-25 that are key epidermal development regulators.

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL22765

16 Samples

Download data: GFF

(Submitter supplied) We used RNA-seq to identify gene expression changes associated with lin-22 mutations affecting seam cell pattering in C. elegans

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18245

12 Samples

Download data: TXT

(Submitter supplied) We identified target genes for NHR-25 by ChIP-seq at L1 stage of C. elegans. Transcription factor genes were tagged with GFP and their expression examined at L1 stage. Since there are no direct target genes known for NHR-25 that can be used for assessment of enrichment efficiency by quantitative PCR (qPCR), we chose to repeat ChIP-seq experiment of another GFP tagged transcription factor, PHA-4 for which the ChIP-seq was performed during a pilot experiment of modENCODE project using the same transgenic strain and antibody (a gift from Tony Hyman lab).

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13776

6 Samples

Download data: BEDGRAPH

(Submitter supplied) The evolutionarily conserved Wnt/?-catenin signaling pathway plays a fundamental role during metazoan development, regulating numerous processes including cell fate specification, cell migration, and stem cell renewal. Wnt ligand binding leads to stabilization of the transcriptional effector ?-catenin and upregulation of target gene expression to mediate a cellular response. During larval development of the nematode Caenorhabditis elegans, Wnt/?-catenin pathways act in fate specification of two hypodermal cell types, the ventral vulval precursor cells (VPCs) and the lateral seam cells. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL200

9 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26522

28 Samples

Download data: BAM

(Submitter supplied) Gene expression is a major determinant of cell fate and physiology, yet it is notoriously difficult to characterize for the widely used model system C. elegans. By using a new method based on in vivo covalent modification of DNA by RNA polymerases, we determine genome-wide transcription patterns in single tissues of embryos or young adult animals. We show that the method is able to identify actively transcribed genes in tissues representing down to 0.2% of the somatic cells in adult animals. more...

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26522

16 Samples

Download data: BAM, BEDGRAPH, CSV

(Submitter supplied) Gene expression is a major determinant of cell fate and physiology, yet it is notoriously difficult to characterize for the widely used model system C. elegans. By using a new method based on in vivo covalent modification of DNA by RNA polymerases, we determine genome-wide transcription patterns in single tissues of embryos or young adult animals. We show that the method is able to identify actively transcribed genes in tissues representing down to 0.2% of the somatic cells in adult animals. more...

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26522

12 Samples

Download data: BAM, BEDGRAPH, CSV

(Submitter supplied) We report transcriptomes of human neonatal foreskin epidermis.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

5 Samples

Download data: MTX, TSV

(Submitter supplied) Purpose: The goal of this study is to identify differentially expressed microRNAs in pry-1/Axin mutant compare to N2 wild-type (WT).  Our study represents the first microRNA analysis of Axin transcriptome in C. elegans and facilitates investigations of axin mediated processes.

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13657

4 Samples

Download data: CSV

(Submitter supplied) We performed RNA-seq analysis of wild-type and blmp-1(s71) mutant at the young adult stage, to identify genes regulated by BLMP-1.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15716

6 Samples

Download data: CSV

(Submitter supplied) To assess the mechanisms by which FACT depletion leads to increased sensitivity of cells to be reprogrammed, we measured the chromatin accessibility landscape using ATAC-seq following mock treatment, SSRP1 knockdown, or SUPT16H knockdown in human fibroblasts and mock, hmg-3 or hmg-4 knockdown in whole worms, and differential gene expression in hmg-3 knockout mutants or following mock, hmg-4, or spt-16 knockdown by RNAseq.

Organism:

Caenorhabditis elegans; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

5 related Platforms

58 Samples

Download data: BIGWIG, BW, TSV, TXT

(Submitter supplied) Although interfollicular epidermal (IFE) differentiation is thought to be stepwise as reflected in sharp boundaries between the basal, spinous, granular and cornified layers, this prediction has not been studied at a single cell resolution. We used single cell RNA-seq to show that IFE differentiation is best described as a single step gradualistic process with a large number of transition cells between the basal and spinous layer. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

13 Samples

Download data: MTX, TSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Expression profiling by array

Platforms:

GPL21697 GPL28718

64 Samples

Download data: CEL, TXT

(Submitter supplied) Autologous epidermal cultures can permanently restore a functional epidermis on severely burned patients. Transgenic epidermal grafts do so also in genetic skin diseases as Junctional Epidermolysis Bullosa. Clinical success strictly requires an adequate number of epidermal stem cells, detected as holoclone-forming cells. To date, such cells can be only partially distinguished from the other transient amplifying clonogenic keratinocytes and cannot be prospectively isolated. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

4 Samples

Download data: TXT

(Submitter supplied) Autologous epidermal cultures can permanently restore a functional epidermis on severely burned patients. Transgenic epidermal grafts do so also in genetic skin diseases as Junctional Epidermolysis Bullosa. Clinical success strictly requires an adequate number of epidermal stem cells, detected as holoclone-forming cells. To date, such cells can be only partially distinguished from the other transient amplifying clonogenic keratinocytes and cannot be prospectively isolated. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL28718

60 Samples

Download data: CEL

(Submitter supplied) To determine mRNA expression levels glp-4(bn2); let-7(wild-type) and glp-4(bn2); let-7(mn112) animals, RNA was purified from total worms collected at late L4 stage using TRI Reagent (MRC).

Organism:

Caenorhabditis elegans

Type:

Expression profiling by genome tiling array

Platform:

GPL5634

6 Samples

Download data: CEL, TAB, TXT

(Submitter supplied) Skin homeostasis is guided by spatiotemporal regulation of gene expression, establishing each stage of keratinocyte differentiation. The current study presents transcriptomic and chromatin profiling for the proliferating (basal) and differentiated (suprabasal) cell populations derived from neonate mice (p0-p2) skin epidermis. This multi-omic approach will enable idenitification of cell specific epidermal cross-talk central to the equlibirum.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL17021 GPL24247 GPL21493

22 Samples

Download data: BED, BEDPE, HIC, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL17021 GPL24247 GPL21493

46 Samples

Download data: BED, BEDPE, HIC, TXT

(Submitter supplied) Skin homeostasis is guided by spatiotemporal regulation of gene expression, establishing each stage of keratinocyte differentiation. The current study presents transcriptomic and chromatin profiling for the proliferating (basal) and differentiated (suprabasal) cell populations derived from neonate mice (p0-p2) skin epidermis. This multi-omic approach will enable idenitification of cell specific epidermal cross-talk central to the equlibirum.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

8 Samples

Download data: XLSX