|
| Status |
Public on Jan 29, 2023 |
| Title |
Type2 diabetes ChROseq sample #1 [T2D_17300] |
| Sample type |
SRA |
| |
|
| Source name |
Type2 diabetes ChROseq sample
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: islet
subject status: an individual with type2 diabetes
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Libraries were prepared according to Dinh et el, 2020.
Libraries were prepared using the TriLink CleanTag Small RNA Ligation kit (small RNAseq) or as per Dinh et el, 2020 (ChROseq)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Islet sample from an individual with type2 diabetes
processed data file:
DESeq_ChROseq_gene_normalized_b12.csv
DESeq_ChROseq_TRE_normalized_counts_b12.csv
|
| Data processing |
library strategy: chromatin run-on and sequencing (ChRO-seq)
Sequencing was aligned and quantiitated using miRquant2.0 (small RNAseq) or aligned and quantified using Proseq.
Both sequencing types were processed with DESeq2.
Genome_build: hg19 (small RNAseq) or hg38 (RNAseq)
Supplementary_files_format_and_content: DESeq normalized counts of transcriptional regulatory elements, genes
|
| |
|
| Submission date |
Feb 15, 2022 |
| Last update date |
Jan 29, 2023 |
| Contact name |
Praveen Sethupathy |
| Organization name |
Cornell University
|
| Lab |
Dr. Sethupathy Lab
|
| Street address |
Cornell University College of Veterinary Medicine, Box 17
|
| City |
Ithica |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE196797 |
microRNA Expression in Normal and Diabetic Pancreatic Islets |
|
| Relations |
| BioSample |
SAMN25977857 |
| SRA |
SRX14191670 |
