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| Status |
Public on Aug 16, 2024 |
| Title |
REC-1, Ibrutinib Resistant, ATAC, Repeat 1 |
| Sample type |
SRA |
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| Source name |
REC-1
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| Organism |
Homo sapiens |
| Characteristics |
cell line: REC-1
cell type: Mantle Cell Lymphoma
treatment: Ibrutinib
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| Treatment protocol |
Parental and resistant cells were respectively tretated with DMSO (parental) and ibrutinib (reistant) for 24 hours followed by BCR crosslinking with IgM for 5min.
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| Growth protocol |
RPMI 1640 supplemented with 10% fetal bovine serum , 2 mM L-glutamine, 100 U/mL and 100 μg/mL penicillin/streptomycin, 100 mM nonessential amino acids, 1mM sodium pyruvate and 0.1mM of 2-mercaptoethanol
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq assay was performed as previously described (PMID: 30745086). Briefly, 50,000 cells were pelleted at 800 x g and washed with 50 μl of ice cold 1 x PBS (Corning cat# 21031CV), followed by 2min treatment with 50 μl lysis buffer (10 mM Tris-HCl, pH 7.4, 3 mM MgCl2, 10 mM NaCl, 0.1% Igepal cat# CA-630). Pelleted nuclei were resuspended in 50 μl of transposition buffer (25 μl of 2 x TD buffer, 22.5ul of molecular biology grade water and 2.5 μl Tn5 transposase (Illumina cat# FC-121-1030) to tag the accessible chromatin for 45min at 37°C.
Tagmented DNA was purified with MinElute Reaction Cleanup kit and amplified with 5 cycles. Additional number of PCR cycles was determined from the side reaction and ranged from 8-9 total cycles of PCR. Libraries were purified using QiaQuick PCR purification kit.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Reads were trimmed with Trim Galore (version 0.4.1) with parameters -q 5 --phred33 --gzip --stringency 5 -e 0.1 --length 20 --paired. Trimmed reads were aligned to the Ensembl GRCh37.75 primary assembly including chromosome 1-22, chrX, chrY, chrM and contigs using BWA (version 0.7.13) (Li and Durbin, 2009) with parameters bwa aln -q 5 -l 32 -k 2 -t 12. Paired-end reads were group with bwa sampe -P -o 1000000. Reads mapped to contigs, ENCODE blacklist and marked as duplicates by Picard (version 2.1.0) were discarded and the remaining reads were used in downstream analyses and visualization.
Bedgraph of reads normalized to reads per million (RPM) were generated with bedtools (version 2.29.1) genomecov. Uploadable bigWig files were generated with UCSC bedGraphToBigWig (version 369).
Assembly: hg19
Supplementary files format and content: bigWig files for genome browser viewing
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| Submission date |
May 23, 2024 |
| Last update date |
Aug 16, 2024 |
| Contact name |
Robert Babak Faryabi |
| E-mail(s) |
faryabi@pennmedicine.upenn.edu
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| Phone |
215-573-8220
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| Organization name |
University of Pennsylvania
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| Department |
Pathology
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| Lab |
Faryabi Lab
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| Street address |
Room 553 BRB II/III, 421 Curie Boulevard
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| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE268224 |
Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance (ATAC-Seq) |
| GSE268228 |
Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance |
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| Relations |
| BioSample |
SAMN41511587 |
| SRA |
SRX24667259 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8288249_s07_211022_JP_Rec1_IBR_resistant_ATAC_rep1.filt.srt.nodup.noBlack.bam.bw |
217.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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