|
| Status |
Public on Jan 22, 2024 |
| Title |
H3K4me3_Parental_biol rep3 |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-436
|
| Organism |
Homo sapiens |
| Characteristics |
cut&run antibody: H3K4me3
cell line: MDA-MB-436
cell type: Breast, Adenocarcinoma
genotype: Parental
|
| Growth protocol |
DMEM supplemented with 10% (v/v) Fetalgro bovine growth serum, 100 U/ml of penicillin, and 100 μg/ml of streptomycin. Cells were cultured at 37°C and 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
CUT&RUN was performed using CUTANA ChIC / CUT&RUN Kit. For each CUT&RUN reaction, 500K permeabilized native cells were used.
5 ng DNA was used to prepare sequencing libraries with the CUTANA CUT&RUN Library Prep Kit.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
TMF_2_H3K4me3_P_436_Parental_500K_Native_kMet2uL__05_05_23__S2
|
| Data processing |
Fastq files aligned to the hg38 reference genome using the Bowtie2
Uniquely aligned reads were retained, while duplicate reads and those in blacklist regions were filtered out
Peaks were called using SICER2 and annotated by the function “annotatePeaks.pl” using Homer
The de novo motif discovery analysis was performed by the function “findMotifsGenome.pl” of Homer (4.11)
Assembly: hg38 reference genome
Library strategy: CUT&RUN
|
| |
|
| Submission date |
Oct 16, 2023 |
| Last update date |
Feb 28, 2024 |
| Contact name |
Alberto Ciccia |
| E-mail(s) |
ac3685@cumc.columbia.edu
|
| Phone |
2128514896
|
| Organization name |
The Trustees of Columbia University in the City of New York
|
| Street address |
1130 St. Nicholas avenue, ICRC Room 407B
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE245448 |
SMARCAL1 is a dual regulator of innate immune signaling and PD-L1 expression that promotes tumor immune evasion [CUT&RUN] |
| GSE245450 |
SMARCAL1 is a dual regulator of innate immune signaling and PD-L1 expression that promotes tumor immune evasion. |
|
| Relations |
| BioSample |
SAMN37844903 |
| SRA |
SRX22100437 |
