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| Status |
Public on Apr 10, 2024 |
| Title |
NALM6_igg |
| Sample type |
SRA |
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| Source name |
NALM6
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| Organism |
Homo sapiens |
| Characteristics |
cell line: NALM6
cell type: B_ALL
antibody: IgG
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| Growth protocol |
RPMI 1640 + 10% serum
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
CUT and RUN data were generated using the Epicypher Cutana CUT&RUN kit v3.0 (14-1048) according to the manufacturers provided instructions. Briefly 500k NALM6 cells per reaction were bound to 10ml of provided activated ConA beads in 0.2ml PCR tubes. Bead-bound cells were suspended in Antibody Buffer (Wash buffer with 0.1% digitonin, 0.5mM Spermidine, 2mM EDTA, and 1x HALT protease inhibitors) and incubated with 1ul PU.1 antibody (Cell Signaling 2258) or IgG (Epicypher 13-0042k) overnight on a nutator mixer at 4C. The next day after washing, pAG MNase was bound and targeted digestion was carried out for 2 hours at 4C. Digestion was stopped using 33ml Stop buffer + 1ml (0.5ng) E.coli spike-in DNA and then cleaved DNA were released for 10 minutes at 37C. DNA were then purified for library preparation using the included purification kit. >30M 75bp paired end reads were generated per sample using the Illumina Novaseq.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The Nextflow CUT and RUN pipeline (v2.0) was used in spike-in mode to assess quality and map reads to the HG19 (human) and K12-MG1655 (E. coli) reference genomes (72, 73).
The spike-in normalized .bam files from Nextflow were exported to Easeq (v1.111), where peaks were called against the IgG sample using adaptive local thresholding (p < 1x10-5, FDR < 1x10-5, Log2(Fold Change) > 1, merge within = 100bp, window size = 100bp) (74).
Data shown are spike-in normalized bigwig files generated in Nextflow.
Assembly: HG19
Supplementary files format and content: .bigwig for coverage
Supplementary files format and content: .txt for PU.1 peaks called
Library strategy: CUT & RUN
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| Submission date |
Jan 30, 2023 |
| Last update date |
Apr 10, 2024 |
| Contact name |
Daniel Savic |
| E-mail(s) |
daniel.savic@stjude.org
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| Organization name |
St. Jude Children's Research Hospital
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| Department |
Pharmaceutical Sciences
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| Lab |
Savic
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| Street address |
262 Danny Thomas pl.
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| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE224085 |
Functional investigation of inherited noncoding genetic variation impacting the pharmacogenomics of childhood acute lymphoblastic leukemia treatment [CUT & RUN] |
| GSE224204 |
Functional investigation of inherited noncoding genetic variation impacting the pharmacogenomics of childhood acute lymphoblastic leukemia treatment |
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| Relations |
| BioSample |
SAMN32963494 |
| SRA |
SRX19220164 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7011567_CnR_Nalm6_control_IgG_R1.bigWig |
106.0 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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