GEO DataSets

(Submitter supplied) Genome-wide profiling of RNA differential expression in v-Abl transformed 220-8 pro-B mouse cell line

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11002

2 Samples

Download data: BW, FPKM_TRACKING

(Submitter supplied) To reprogram adult HSPCs in vivo, we used a mouse engineered to express LIN28B in a Doxycycline (Dox)-inducible manner (iLIN28B). We performed single cell RNA-seq to compare the transcriptomes of common lymphoid progenitor (CLP) cells isolated from mouse FL, adult BM of wildtype mice, adult BM of iLIN28B treated with Dox (+Dox), and adult BM of littermate controls +Dox.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

4 Samples

Download data: MTX, TSV

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL19057 GPL11002 GPL13112

19 Samples

Download data: BED, BW

(Submitter supplied) Transcriptome-wide profiling of RNA-binding by four RBPs in v-Abl transformed 220-8 pro-B mouse cell line. Binding sites are characterized by T-to-C cross-linking mutations, depth, location on transcript, and overlap/exclusivity across different RBPs.

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

13 Samples

Download data: BED

(Submitter supplied) Genome-wide profiling of RNA expression in two sub-populations of hematopoietic stem cells from mouse Fetal Liver (FL) and adult Bone Marrow (BM)

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

4 Samples

Download data: BW, CSV

(Submitter supplied) The goal of this study was to determine IGF2BP3 RNA targets in human B-cell Acute Lymphocitic Leukemia cell models.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL11154

12 Samples

Download data: BED, TXT

(Submitter supplied) The conserved human LIN28 RNA-binding proteins function in development, maintenance of pluripotency and oncogenesis. We used PAR-CLIP and a newly developed variant of this method, iDo-PAR-CLIP, to identify LIN28B targets as well as sites bound by the individual RNA binding domains of LIN28B in the human transcriptome at nucleotide resolution. The position of target binding sites reflected the known structural relative orientation of individual LIN28B binding domains, validating iDo-PAR-CLIP. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

1 Sample

Download data: BED

(Submitter supplied) Hematopoiesis changes over life to meet the demands of maturation and aging. Here, we find that the definitive hematopoietic stem and progenitor cell (HSPC) compartment is remodeled from gestation into adulthood, a process regulated by the heterochronic Lin28b/let-7 axis. Native fetal and neonatal HSPCs distribute with a pro-lymphoid/erythroid bias with a shift toward myeloid output in adulthood. By mining transcriptomic data comparing juvenile and adult HSPCs and reconstructing coordinately activated gene regulatory networks, we uncover the Polycomb repressor complex 1 (PRC1) component Cbx2 as an effector of Lin28b/let-7?s control of hematopoietic maturation. We find that juvenile Cbx2-/- hematopoietic tissues show impairment of B-lymphopoiesis, a precocious adult-like myeloid bias, and that Cbx2/PRC1 regulates developmental timing of expression of key hematopoietic transcription factors. These findings define a novel mechanism of epigenetic regulation of HSPC output as a function of age with potential impact on age-biased pediatric and adult blood disorders.

Organism:

Homo sapiens; Mus musculus

Type:

Other

Platforms:

GPL19057 GPL18573

20 Samples

Download data: BIGWIG, BW

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

Organism:

Mus musculus

Type:

Other

Platform:

GPL15089

4 Samples

Download data

(Submitter supplied) We used the NanoString mouse nCounter miRNA expression platform to compare the miRNA expression profiles of pro-B cells sorted from fetal liver and adult bone marrow in order to gain insight into changes in miRNA expression during B cell ontogeny.

Organism:

Mus musculus

Type:

Other

Platform:

GPL15089

2 Samples

Download data

(Submitter supplied) We used the NanoString mouse nCounter miRNA expression platform to compare the miRNA expression in double-positive (DP) thymocytes that developed in the presence (GFP+) or absence (GFP-ve) of ectopic mLin28 expression.

Organism:

Mus musculus

Type:

Other

Platform:

GPL15089

2 Samples

Download data

(Submitter supplied) We performed paired-end RNA-seq to compare the transcriptome of DP thymocytes that ectopically express Lin28 in vivo versus untransduced (GFP-ve) DP thymocytes.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11002

2 Samples

Download data: BEDGRAPH

(Submitter supplied) We isolated RNA from sorted common myeloid progenitor cells from wild-type fetal liver, wild-type adult bone marrow, transgenic Lin28b bone marrow, let-7b/c knock-out bone marrow, and Lin28b-deficient fetal liver and compared mRNA expression profiles.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

17 Samples

Download data: TXT

(Submitter supplied) The goal of this study was to determine IGF2BP3 regulation of RNA targets in human pacreatic ductal adenocarcinoma cell lines

Organism:

Homo sapiens

Type:

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

Platforms:

GPL11154 GPL15520

26 Samples

Download data: TXT

(Submitter supplied) While BCL11A protein is not well synthesized at these earlier stages of development, its mRNA curiously continues to be associated with ribosomes. Through unbiased proteomic analyses in erythroid cells, we demonstrate that the RNA-binding protein LIN28B, which is developmentally expressed in a reciprocal pattern to BCL11A, directly interacts with ribosomes. We show that the observed suppression of BCL11A protein translation is mediated by LIN28B through a direct interaction with BCL11A mRNA and independent of its role in let-7 microRNA biogenesis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL16791

16 Samples

Download data: TSV

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

Organism:

Homo sapiens

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL16791

24 Samples

Download data: BED

(Submitter supplied) While BCL11A protein is not well synthesized at these earlier stages of development, its mRNA curiously continues to be associated with ribosomes. Through unbiased proteomic analyses in erythroid cells, we demonstrate that the RNA-binding protein LIN28B, which is developmentally expressed in a reciprocal pattern to BCL11A, directly interacts with ribosomes. We show that the observed suppression of BCL11A protein translation is mediated by LIN28B through a direct interaction with BCL11A mRNA and independent of its role in let-7 microRNA biogenesis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: TSV

(Submitter supplied) While BCL11A protein is not well synthesized at these earlier stages of development, its mRNA curiously continues to be associated with ribosomes. Through unbiased proteomic analyses in erythroid cells, we demonstrate that the RNA-binding protein LIN28B, which is developmentally expressed in a reciprocal pattern to BCL11A, directly interacts with ribosomes. We show that the observed suppression of BCL11A protein translation is mediated by LIN28B through a direct interaction with BCL11A mRNA and independent of its role in let-7 microRNA biogenesis. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

4 Samples

Download data: BED

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL11154 GPL10999 GPL570

16 Samples

Download data: CEL, TXT

(Submitter supplied) Human LIN28A and B are RNA-binding proteins (RBPs) conserved in animals with important roles during development and stem cell reprogramming. We used Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) in HEK293 cells and identified a largely overlapping set of ~3,000 mRNAs at ~9,500 sites located in the 3’UTR and CDS. In vitro and in vivo, LIN28 preferentially bound single-stranded RNA containing a uridine-rich element and one or more flanking guanosines, and appeared to be able to disrupt base-pairing to access these elements when embedded in predicted secondary structure. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL10999

4 Samples

Download data: XLSX