LichtLab Sequencing - run details
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Project
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Evans MDS
H2B - E76K
LeleLab collaboration
Melanoma
NSD2 - E1099K
Other
SETD2 inhibitor
UTX - KDM6A
Assay
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RNA-Seq
ChIP-Seq
CUT&RUN
ATAC-Seq
scRNA-Seq
CRISPR
Title
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Organism / cell line
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ICBR number (if known)
Owner
Notes
Cells used: BEAS2B cells- H2BC4-WT-2xHA tag and H2BC4-WT/E76K-2xHA tag (heterozygous cell line with one allele WT and one allele E76K, both alleles are HA-tagged), made by Jixiu Shan using CRISPR. On 3/27/23, 1.4x10^6 BEAS2B cells (passage 11) were plated in multiple plates. Three days later, all cells were collected and counted. 7.5x10^6 cells were collected and used for CUT&RUN. Five different antibodies were used (HA-tag, H3k27me3, H3K27ac, H3K4me3, and IgG) with three replicates per sample. Samples 1 and 6 (HA-WT and HA-HET respectively) were discarded based on lower quality results from Qubit&Tapestation.
Samples
Enter sample names, one per row. If possible, use the format COND_SMP, where COND is an experimental condition and SMP is a unique sample name.
HA-WT (samples 2-3) HA-HET (samples 4-5) H3K27me3-WT (samples 7-9) H3K27me3-HET (samples 10-12) H3K27ac-WT (samples 13-15) H3K27ac-HET (samples 16-18) H3K4me3-WT (samples 19-21) H3K4me3-HET (samples 22-24) IgG-WT (samples 25-27) IgG-HET (samples 28-30)
Contrasts
Enter contrasts, one per row. A contrast consists of two sample name separated by spaces, as in "Test Control".
HET vs WT
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ERCC spike-ins
Dmel spike-ins
Ecoli spike-ins
Analyzed
Analysis notes
2023-06-23 15:49:15
Results:
https://lichtlab.cancer.ufl.edu/reports/H2B/H2B_CR_20230613/