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| Status |
Public on Feb 19, 2024 |
| Title |
GCB_K_rep4 [KKO_R4] |
| Sample type |
SRA |
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| Source name |
spleen
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| Organism |
Mus musculus |
| Characteristics |
tissue: spleen
cell type: GCB cell
genotype: K_het_KO
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| Treatment protocol |
Mice (WT, C, K, and CK) were immunized with SRBC for 10 days before sorting GC B cells.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
60,000 freshly sorted live cells were washed in cold PBS, lysed in 60 ul cold lysis buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, and 0.01% Digitonin) for 3 min on ice, followed by addition of 1 ml wash buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, and 0.1% Tween-20) and centrifugation to pellet nuclei.
Bulk ATAC-seq libraries were prepared following the Omni-ATAC protocol. Briefly, nuclei were resuspended in a transposition reaction mix prepared using the Illumina Tagment DNA Enzyme and Buffer Kit (Illumina, 20034197) and incubated at 37 ºC for 30 minutes on thermomixer at 1,000 rpm to allow for transposition-based DNA fragmentation and adapter ligation. Tagged DNA fragments were purified using the Clean & Concentrator-5 Kit (ZYMO, D4014), then subjected to PCR amplification and double-sided bead purification (to remove primer dimers and larger than 1,000 bp fragments) using the AMPure XP beads (Beckman Coulter, A63881).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
KKO_R4.mLb.clN.bam
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| Data processing |
nfcore atac seq version 1.2.1
Assembly: mm10
Supplementary files format and content: Consensus Peak Counts
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| Submission date |
Feb 03, 2023 |
| Last update date |
Feb 19, 2024 |
| Contact name |
Christopher Russell Chin |
| E-mail(s) |
chc2077@med.cornell.edu
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| Phone |
3393640514
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| Organization name |
Weill Cornell
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| Lab |
Melnick Lab
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| Street address |
413 E 69th Street, Belfer Building, BB-1462
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| City |
New York City |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE224512 |
Cooperative super-enhancer inactivation caused by heterozygous loss of CREBBP and KMT2D skews B-cell fate decisions and accelerates development of T-cell depleted lymphomas [ATAC-seq] |
| GSE224513 |
Cooperative super-enhancer inactivation caused by heterozygous loss of CREBBP and KMT2D skews B-cell fate decisions and accelerates development of T-cell depleted lymphomas. |
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| Relations |
| BioSample |
SAMN33059409 |
| SRA |
SRX19279636 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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