|
| Status |
Public on Jan 01, 2020 |
| Title |
human islets rep 3 microRNA |
| Sample type |
SRA |
| |
|
| Source name |
human islet
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human pancreatic islet
origin: cadaveric pancreas
genetic manipulation: none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with micro RNeasy kit (Qiagen), treated with DNase I kit (Qiagen) and quantified with Qubit (Invitrogen). Bioanalyzer (Agilent) was employed to evaluate RNA quality.
Small RNA-seq libraries were made as previously described(Hafner et al., 2012). RNA-seq libraries were made by using Smart-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara) and Nextera XT DNA Library Preparation kit (Illumina) thereafter.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file: FIgure1_miRNA_hairpin_counts.txt
TA17_Hip83
trimmed-TA17_Hip83
|
| Data processing |
miRNA sequencing data was demultiplexed and adapter trimmed using CutAdapt v1.8
miRNA sequences aligned using Bowtie v1.1.2 parameters -n 0 -l 18 --best
RNA sequencing data were preprocessed using Kallisto using an index generated to Gencode v24
Genome_build: Gencode Version 24 (August 2015 freeze, GRCh38) - Ensembl 83, 84
Supplementary_files_format_and_content: tab-delimited text files, counts
|
| |
|
| Submission date |
Jan 02, 2018 |
| Last update date |
Jan 01, 2020 |
| Contact name |
Cassandra D Belair |
| E-mail(s) |
[email protected]
|
| Organization name |
UCSF
|
| Department |
Urology
|
| Lab |
Robert Blelloch
|
| Street address |
35 Medical Center Way
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE108654 |
LIN28B is a barrier to the maturation of human embryonic stem cell derived pancreatic β cells |
|
| Relations |
| BioSample |
SAMN08283952 |
| SRA |
SRX3525293 |
