GEO DataSets

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

6 related Platforms

23 Samples

Download data: BEDGRAPH, GTF

(Submitter supplied) Kaposi’s sarcoma-associated herpesvirus is etiologic agent of Kaposi’s Sarcoma and two B-cell malignancies. Recent advancements in sequencing technologies have led to high resolution transcriptomes for several human herpesviruses that densely encode genes on both strands. However, for KSHV progress remained limited due to overall low percentage of KSHV transcripts even during lytic replication. To address this challenge, we have developed a target enrichment method to increase the KSHV-specific reads for both short- and long-read sequencing platforms. more...

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL26180 GPL28352

9 Samples

Download data: BEDGRAPH

(Submitter supplied) Food allergy is caused by allergen-specific IgE but little is known about the B cell memory of persistent responses. Here we describe in pediatric peanut allergy a population of CD23+IgG1 memory B cells that contains peanut-specific clones and generates IgE plasma cells on activation. Through single cell transcriptomics and B cell receptor (BCR) sequencing, we characterized FCER2/CD23+ IgG1 memory B cells co-expressing IL4R, IL13RA1, IGHE and carrying highly mutated BCRs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26180 GPL16791

11 Samples

Download data: RDS, TAR, TSV

(Submitter supplied) Poly(A) tails protect RNAs from degradation and deadenylation rates determine RNA stability. Deadenylation has mostly been investigated within the cytoplasm and the dynamics of poly(A) tail length after transcription are not well understood. Combining long-read sequencing with metabolic labeling and cell fractionations, we investigate deadenylation dynamics of newly synthesized poly(A) tails in vitro and in vivo. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26180 GPL24198

60 Samples

Download data: CSV

(Submitter supplied) Due to the low-throughput process of systematically designing and functionally testing chimeric antigen receptors (CARs), only a small set of immune signaling domains have been thoroughly explored, despite their major role in T cell activation, effector function and persistence. SpeedingCARs presents an integrated method for engineering CAR T cells by signaling domain shuffling and functional screening by single-cell sequencing. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL28352 GPL26180 GPL24676

14 Samples

Download data: CSV, TAR

(Submitter supplied) We explored the regulation of intronic polyadenylation isoforms by cisplatin, and its impact on the translatome. This was done in part by 3'-seq (see GSE119978) and Iso-Seq (this data set).

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26180

2 Samples

Download data: XLSX

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

Organism:

Homo sapiens

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL15520 GPL26180

8 Samples

Download data: BW

(Submitter supplied) We developed a massively parallel reporter assay to determine the splicing effects of all mutations in the region comprising CD19 exons 1-3. Despite the great success of CART-19 (chimeric antigen receptor-armed autologous T-cells) immunotherapy to treat B-cell acute lymphoblastic leukaemia (B-ALL), many patients relapse due to loss of the targeted CD19 epitope. Since epitope loss can be caused by CD19 exon 2 mis-splicing, we set out to learn the regulatory code that controls CD19 alternative splicing.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL26180

2 Samples

Download data: TAB, TXT

(Submitter supplied) To validate the sequence motifs identified by our multi-task learning model MTtrans, a new 5' UTR library with around 8,000 synthetic 5'UTRs was built to express EGFP. The reads count was used as a proxy of translation rate here to validate the estimated regulatory effect of motifs that we inferred from multiple datasets, proving the robustness of the sequence motifs.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL26180

1 Sample

Download data: CSV

(Submitter supplied) Targeted DNA sequencing approaches will improve how the size of short tandem repeats is measured for diagnostic tests and pre-clinical studies. The expansion of these sequences causes dozens of disorders, with longer tracts generally leading to a more severe disease. In addition, interruptions are sometimes present within repeats and can alter disease manifestation. Despite advances in methodologies, determining repeat size and identifying interruptions in targeted sequencing datasets remains a major challenge. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL26180

26 Samples

Download data: FASTA, TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL26180 GPL16791

33 Samples

Download data: BED, BIGWIG, XLSX

(Submitter supplied) Adrenal Gland 2-1 ENTEX51 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:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26180

1 Sample

Download data: GTF, TSV, TXT

(Submitter supplied) excitatory cortical neurons 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:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26180

2 Samples

Download data: GTF, TSV, TXT

(Submitter supplied) iPSCs via Sendai-viral Yamanaka factors 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:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26180

2 Samples

Download data: GTF, TSV, TXT

(Submitter supplied) W61 right lobe of liver 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:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26180

1 Sample

Download data: GTF, TSV, TXT

(Submitter supplied) PGP1 derived endothelial-cells 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:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26180

2 Samples

Download data: GTF, TSV, TXT

(Submitter supplied) Adrenal Gland 1-2 ENTEX50 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:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26180

1 Sample

Download data: GTF, TSV, TXT

(Submitter supplied) we examine the effect of RSV infection in human small airway epithelial cells (hSAECs)

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL26180

16 Samples

Download data: GTF, XLSX

(Submitter supplied) We describe the cellular response to HSV-1 infection in human iPSC-derived brain organoids

Organism:

Homo sapiens; Human alphaherpesvirus 1

Type:

Expression profiling by high throughput sequencing

6 related Platforms

40 Samples

Download data: CSV, FA, GTF, RDS, TXT

(Submitter supplied) Sperm contributes diverse RNAs to the zygote. While sperm small RNAs have been shown to impact offspring phenotypes, our knowledge of the sperm transcriptome, especially the composition of long RNAs has been limited by the lack of sensitive, high-throughput experimental techniques that can distinguish intact RNAs from fragmented RNAs, known to abound in sperm. Here, we integrate single-molecule long-read sequencing with short-read sequencing to detect sperm intact RNAs (spiRNAs). more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

5 related Platforms

15 Samples

Download data: FASTA, GTF, SF, XLSX