|
| Status |
Public on Oct 25, 2022 |
| Title |
miRNA-seq_s0798A |
| Sample type |
SRA |
| |
|
| Source name |
CLL,0798 Abexinostat 400mM 24h
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Blood, PBMC
cell type: Human peripheral blood mononuclear cells
genotype: del11q
disease state: CLL
treatment: HDAC inhibitor, Abexinostat 400mM, 24h
|
| Treatment protocol |
CLL cells were resuspended in RPMI with 10% FBS and 400mM abexinostat was added for 24 h beofre being harvested along with the time matched control.
|
| Growth protocol |
CLL cells were resuspended in RPMI with 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq small RNA-Seq Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Adaptor seqeunces were removed using Cutadapt
Trimmed reads aligned to MIRBASE stemloop seqeunces
Read counts per miRNA was genereated using custom scripts
Assembly: MIRBASE v21
Supplementary files format and content: Total read counts per miRNA
|
| |
|
| Submission date |
Oct 21, 2022 |
| Last update date |
Oct 25, 2022 |
| Contact name |
Ayse Selen Yilmaz |
| E-mail(s) |
[email protected]
|
| Organization name |
OSU
|
| Department |
Biomedical Informatics
|
| Lab |
Bioinformatics shared Resource
|
| Street address |
1800 Cannon Drive
|
| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43210 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE216289 |
HDAC1 regulates the chromatin landscape to control transcriptional dependencies in chronic lymphocytic leukemia [miRNA-seq] |
| GSE216290 |
HDAC1 regulates the chromatin landscape to control transcriptional dependencies in chronic lymphocytic leukemia |
|
| Relations |
| BioSample |
SAMN31401345 |
| SRA |
SRX17983983 |
