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| Status |
Public on May 01, 2024 |
| Title |
SETD2 Mutations Do Not Contribute to Clonal Fitness in Response to Chemotherapy in Childhood B Acute Lymphoblastic Leukemia (ATAC-Seq) |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
To investigate the impact of SETD2 mutations on clonal fitness in B actue lymphoblastic leukemia we generated cells lines with SETD KO using CRISPR/Cas9 system.
We then performed phenotypic based assays as well as gene expression profiling, mutation burden, and chromtain accessibilty analysis using data obtained from RNA-seq, Whole exom sequencing following drug traetment, and ATAC-seq.
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| Overall design |
Comparative differential peak analysis of ATAC-seq for 697 and KOPN-8 cells SETD2 KO clones compared to WT. ATAC was performed in duplicate for each cell line.
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| Contributor(s) |
Yametti GC, Robbins G, Chowdhury A, Narang S, Ostrow TH, Kilberg H, Greenberg J, Kramer L, Raetz E, Evensen NA, Carroll WL |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
May 04, 2023 |
| Last update date |
May 01, 2024 |
| Contact name |
Sonali Narang |
| E-mail(s) |
sonali.narang@nyulangone.org
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| Phone |
5169652665
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| Organization name |
NYU Langone
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| Street address |
435 east 30th street
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (8)
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| GSM7299597 |
697 cells, sgRNA empty vector control, ATAC, biol rep1 |
| GSM7299598 |
697 cells, sgRNA empty vector control, ATAC, biol rep2 |
| GSM7299599 |
697 cells, sgRNA SETD2 clone BM_B, ATAC, biol rep1 |
| GSM7299601 |
697 cells, sgRNA SETD2 clone BM_B, ATAC, biol rep2 |
| GSM7299603 |
KOPN cells, sgRNA empty vector control, ATAC, biol rep1 |
| GSM7299604 |
KOPN cells, sgRNA empty vector control, ATAC, biol rep2 |
| GSM7299605 |
KOPN cells, sgRNA SETD2 clone BA, ATAC, biol rep1 |
| GSM7299606 |
KOPN cells, sgRNA SETD2 clone BA, ATAC, biol rep2 |
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| This SubSeries is part of SuperSeries: |
| GSE231724 |
SETD2 Mutations Do Not Contribute to Clonal Fitness in Response to Chemotherapy in Childhood B Acute Lymphoblastic Leukemia |
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| Relations |
| BioProject |
PRJNA967355 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE231721_697-BM-1.bin1.rpkm.bw |
496.4 Mb |
(ftp)(http) |
BW |
| GSE231721_697-BM-2.bin1.rpkm.bw |
659.7 Mb |
(ftp)(http) |
BW |
| GSE231721_697-EV-1.bin1.rpkm.bw |
558.6 Mb |
(ftp)(http) |
BW |
| GSE231721_697-EV-2.bin1.rpkm.bw |
619.4 Mb |
(ftp)(http) |
BW |
| GSE231721_KOPN-BA-1.bin1.rpkm.bw |
646.0 Mb |
(ftp)(http) |
BW |
| GSE231721_KOPN-BA-2.bin1.rpkm.bw |
611.8 Mb |
(ftp)(http) |
BW |
| GSE231721_KOPN-EV-1.bin1.rpkm.bw |
640.2 Mb |
(ftp)(http) |
BW |
| GSE231721_KOPN-EV-2.bin1.rpkm.bw |
556.1 Mb |
(ftp)(http) |
BW |
| GSE231721_RAW.tar |
7.7 Mb |
(http)(custom) |
TAR (of BED) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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