GEO DataSets

(Submitter supplied) The higher-order structure of newly replicated (i.e. ‘nascent’) chromatin fibers remains poorly-resolved, limiting our understanding of how epigenomes are maintained across cell divisions. To address this, we present Replication-Aware Single-molecule Accessibility Mapping (RASAM), a long-read sequencing method that nondestructively measures genome-wide replication-status and protein-DNA interactions simultaneously on intact chromatin templates. more...

Organism:

Homo sapiens; Mus musculus

Type:

Other

Platforms:

GPL29177 GPL28352

169 Samples

Download data: PICKLE

(Submitter supplied) Concurrent readout of sequence and base modifications from long unamplified DNA templates by PacBio single-molecule sequencing requires large amounts of input material. Here we adapt Tn5 transposition to introduce hairpin oligonucleotides and fragment (tagment) limiting quantities of DNA for generating PacBio-compatible circular molecules. We developed two methods that implement tagmentation and use 90–99% less input than current protocols: (1) single-molecule real-time sequencing by tagmentation (SMRT-Tag), which allows detection of genetic variation and CpG methylation; and (2) single-molecule adenine-methylated oligonucleosome sequencing assay by tagmentation (SAMOSA-Tag), which uses exogenous adenine methylation to add a third channel for probing chromatin accessibility. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL29177

1 Sample

Download data: PICKLE

(Submitter supplied) Concurrent readout of sequence and base modifications from long unamplified DNA templates by PacBio single-molecule sequencing requires large amounts of input material. Here we adapt Tn5 transposition to introduce hairpin oligonucleotides and fragment (tagment) limiting quantities of DNA for generating PacBio-compatible circular molecules. We developed two methods that implement tagmentation and use 90–99% less input than current protocols: (1) single-molecule real-time sequencing by tagmentation (SMRT-Tag), which allows detection of genetic variation and CpG methylation; and (2) single-molecule adenine-methylated oligonucleosome sequencing assay by tagmentation (SAMOSA-Tag), which uses exogenous adenine methylation to add a third channel for probing chromatin accessibility. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL29177

8 Samples

Download data: PICKLE

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL29177 GPL24247

86 Samples

Download data: BW, TSV

(Submitter supplied) Complex organisms are able to generate differential gene expression through the same set of DNA sequences in distinct cells. The communication between chromatin and RNA regulates how cells behave in tissues. However, little is known about how chromatin, especially the histone modifications, regulates RNA polyadenylation. Here, we find that FUS is recruited to chromatin by H3K36me3 at gene bodies. Once H3K36me3 is abolished, FUS is dissociated from chromatin to increase the binding with RNA, resulting in increased distal polyadenylation selections that are far from the stop codon. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29177

16 Samples

Download data: TSV

(Submitter supplied) Brain cells release and take up small extracellular vesicles (sEVs) containing bioactive nucleic acids. sEV exchange is hypothesized to contribute to stereotyped spread of neuropathological changes in the diseased brain. We assessed mRNA from sEVs of non-diseased (ND) and Alzheimer’s disease (AD) human postmortem brains, using short- and long-read sequencing. sEV transcriptomes were distinct from bulk tissue, showing enrichment for multiple genes including mRNAs encoding ribosomal proteins and L1Hs transposable elements. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL29177

18 Samples

Download data: TXT

(Submitter supplied) This study explores alternative splicing's role in embryo development. Using single-cell direct isoform sequencing, we detected an abundance of 3-prime partial transcripts lacking stop codons in oocytes and zygotes, potentially influencing the maternal-to-zygote transition. Long-read sequencing identified dynamic changes in 3894 transposable element loci throughout preimplantation, impacting nearby gene expression and shedding light on early embryonic transcriptional regulation.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29177

4 Samples

Download data: CSV, FASTA, GTF, XLS

(Submitter supplied) The immune system consists of a network of specialized cells and processes that protect the organism from diseases and regulates tissue repair. Natural killer (NK) cells and the αβ and γδ T cells comprise the cytotoxic arm of the immune system and have evolved to detect and eradicate cells infected with pathogens and affected by malignancies, in order to prevent their spread and subsequent tissue damage. more...

Organism:

Heterocephalus glaber; Mus musculus

Type:

Expression profiling by high throughput sequencing

4 related Platforms

66 Samples

Download data: MTX, TSV

(Submitter supplied) SAMOSA, a method previously developed in the Ramani Lab, was employed to reveal nucleosome patterns from remodeling reactions in vitro with the Imitation Switch (ISWI) ATP-Dependent Remodeler ATPase, SNF2h. SAMOSA was further employed to reveal single-molecule nucleosome patterns in vivo from SNF2h knockout and re-expression murine embryonic stem cells.

Organism:

Mus musculus; unidentified plasmid

Type:

Other

Platforms:

GPL29177 GPL29466

235 Samples

Download data: PICKLE

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

Organism:

Homo sapiens; Mus musculus

Type:

Other

Platforms:

GPL29177 GPL28352

28 Samples

Download data: PICKLE

(Submitter supplied) Single-cell RNA sequencing analysis has recently provided snapshots of gene expression of specific cell types and enabled cell types classification within an heterogenous population. As well as transcriptional changes, alternative splicing events and modifications of components of splicing machinery actively contributes in shaping cellular phenotype as well as ageing process and diseases occurence. Current high-throughput single-cell RNA sequencing methods may lack information on cell-specific isoform expression, missing key aspects of cell biology. In the present work we introduce a novel approach using the 10X Genomics Chromium to generate short-read (Illumina) and long-read (Pacific Biosciences Sequel II) RNA-sequencing libraries from the same single cells. This approach produced single cell parallel transcriptional and splicing profiling that demonstrates for the first time cell-type specific isoform expression and alterations at transcriptional levels associated with ageing in haematopoietic stem and progenitor cells

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19057 GPL24198 GPL29177

18 Samples

Download data: GTF, TSV, TXT

(Submitter supplied) ENC4_227 - B6Cast F1 PND25_Male 03_Adrenals For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29177

2 Samples

Download data: GTF, TSV, TXT

(Submitter supplied) 5xFAD cortex het Female For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29177

2 Samples

Download data: GTF, TSV, TXT

(Submitter supplied) ENC4_217 - B6Cast F1 PND4_Female 03_Adrenals For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29177

2 Samples

Download data: GTF, TSV, TXT

(Submitter supplied) ENC4_219 - B6Cast F1 PND10_Male 03_Adrenals For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29177

2 Samples

Download data: GTF, TSV, TXT

(Submitter supplied) ENC4_439, ENC4_440 hippocampus_B6Cast F1_2 months_male_5_ENC4_cDNA511 For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29177

2 Samples

Download data: GTF, TSV, TXT

(Submitter supplied) ENC4_381a, ENC4_382a B6Cast F1 PND4_Male Gastrocnemius For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29177

2 Samples

Download data: GTF, TSV, TXT

(Submitter supplied) ENC4_495, ENC4_496 heart_B6Cast F1 PND 2 months Female 03 heart_ENC4_cDNA607, cDNA608 For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29177

2 Samples

Download data: GTF, TSV, TXT

(Submitter supplied) Hippocampus from 6 mo C57BL/6 male For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29177

2 Samples

Download data: GTF, TSV, TXT

(Submitter supplied) ENC4_391a, ENC4_392a B6Cast F1 PND14 Females Gastrocnemius For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29177

2 Samples

Download data: GTF, TSV, TXT