|
| Status |
Public on Feb 05, 2024 |
| Title |
GFP_LOW, replicate 3, 24hr, PU.1 |
| Sample type |
SRA |
| |
|
| Source name |
Raji
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Raji
genotype: Smarca4+/+
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
CUT&RUN was performed using CUTANA™ ChIC/CUT&RUN kit (EpiCypher, Cat. 14-1048), according to manufacturer’s instructions
Following DNA purification, libraries were prepared using KAPA HyperPrep Kit (Roche, KK8504). Three replicates were performed for each condition. 100bp paired-end sequencing was performed on Illumina sequencer
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Demultiplexed FASTQ files were QC checked using FASTQC and processed using custom pipeline which involves read trimming, read alignment using BOWTIE2, filtering low-quality, unmapped and duplicated reads. BIGWIG files were generated using deeptools RPKM normalization.
Downstream analyses were performed in R (version 4.2.1) using various R packages.
Assembly: hg38
Supplementary files format and content: RPKM bw files
Library strategy: CUT&RUN
|
| |
|
| Submission date |
Feb 02, 2024 |
| Last update date |
Feb 05, 2024 |
| Contact name |
Michael Green |
| E-mail(s) |
mgreen5@mdanderson.org
|
| Phone |
713-745-4244
|
| Organization name |
The University of Texas MD Anderson Cancer Center
|
| Department |
Department of Lymphoma/Myeloma
|
| Street address |
7455 Fannin Street
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77054 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE254905 |
Smarca4 (Brg1) is a haploinsufficient B-cell tumor suppressor that fine-tunes centrocyte cell fate decisions [rajiAUD_cutrun] |
| GSE254908 |
Smarca4 (Brg1) is a haploinsufficient B-cell tumor suppressor that fine-tunes centrocyte cell fate decisions |
|
| Relations |
| BioSample |
SAMN39746748 |
| SRA |
SRX23507370 |
