|
| Status |
Public on Aug 16, 2024 |
| Title |
REC-1, Ibrutinib Resistant, RNA-seq, Repeat 2 |
| Sample type |
SRA |
| |
|
| Source name |
REC-1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: REC-1
cell type: Mantle Cell Lymphoma
treatment: Ibrutinib
|
| Treatment protocol |
Parental and resistant cells were tretated with DMSO (parental) or ibrutinib (reistant) for 24 hours followed by BCR crosslinking with IgM for 5min.
|
| Growth protocol |
RPMI 1640 supplemented with 10% fetal bovine serum , 2 mM L-glutamine, 100 U/mL and 100 μg/mL penicillin/streptomycin, 100 mM nonessential amino acids, 1mM sodium pyruvate and 0.1mM of 2-mercaptoethanol
|
| Extracted molecule |
total RNA |
| Extraction protocol |
24 hours post treatment with DMSO and 100nM ibrutinib followed by IgM stimulation for 5 min, parental and resistant cells were lysed with 350ul RLT Plus buffer supplemented with 2-mercaptoethanol and total RNA was isolated using the RNeasy Plus Micro Kit.
Strand-specific RNA-seq was performed on parental and ibrutinib-reistant Rec1 cells using SMARTer Stranded Total RNA Sample Prep kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
RNA-seq data was aligned to Ensembl GRCh37.75 primary assembly including chromosome 1-22, chrX, chrY, chrM and contigs using STAR (version 2.5) with parameters --outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignIntronMax 100000 --outSAMstrandField intronMotif --outSAMunmapped Within --chimSegmentMin 25 --chimJunctionOverhangMin 25.
Strand-specific read counts were quantified using Subread (version 1.5.1) featureCounts with parameters -t exon -g gene_id -s 1 -T 6 and used as input for gene expression analysis.
Assembly: hg19
Supplementary files format and content: tab-delimited text files with read count; bigWig files for genome browser viewing
|
| |
|
| Submission date |
May 23, 2024 |
| Last update date |
Aug 16, 2024 |
| Contact name |
Robert Babak Faryabi |
| E-mail(s) |
faryabi@pennmedicine.upenn.edu
|
| Phone |
215-573-8220
|
| Organization name |
University of Pennsylvania
|
| Department |
Pathology
|
| Lab |
Faryabi Lab
|
| Street address |
Room 553 BRB II/III, 421 Curie Boulevard
|
| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE268227 |
Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance (RNA-Seq) |
| GSE268228 |
Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance |
|
| Relations |
| BioSample |
SAMN41511580 |
| SRA |
SRX24667252 |
