|
| Status |
Public on Oct 25, 2022 |
| Title |
RNA-seq_s0109A |
| Sample type |
SRA |
| |
|
| Source name |
CLL,0109, Abexinostat 400mM 24h
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Blood, PBMC
cell type: Human peripheral blood mononuclear cells
genotype: del 13 q
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 SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Libraries were sequenced on a HiSeq4000 at the Genomic Shared Resource at the Ohio State University through Nationwide Children's Hospital Biomedical Genomics Core generating 100 bp reads.
Reads were aligned with HISAT2 aligner and then transcript counts were generated with the featureCounts function from the Rsubread package.
Assembly: GRCh37, Ensembl annotation build 75
Supplementary files format and content: Reads counts per million (cpm) were calculated using R limma voom package.
|
| |
|
| 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) |
| GSE216288 |
HDAC1 regulates the chromatin landscape to control transcriptional dependencies in chronic lymphocytic leukemia [RNA-seq] |
| GSE216290 |
HDAC1 regulates the chromatin landscape to control transcriptional dependencies in chronic lymphocytic leukemia |
|
| Relations |
| BioSample |
SAMN31401934 |
| SRA |
SRX17984418 |
