NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7868724 Query DataSets for GSM7868724
Status Public on Oct 29, 2023
Title RPMI8226_EV_Len2
Sample type SRA
 
Source name cell line
Organism Homo sapiens
Characteristics tissue: cell line
cell line: RPMI8226
cell type: multiple myeloma
genotype: Empty Vector
treatment: lenalidomide (10 uM)
Treatment protocol Cells were treated with 10 uM lenalidomide for 72 hrs
Growth protocol Cell lines were cultured in RPMI1640 medium (Corning) containing 10% fetal bovine serum, 100 U/mL penicillin, and 100 mg/mL streptomycin at 37°C under 5% CO2.
Extracted molecule genomic DNA
Extraction protocol Nuclei from 50,000 cells were isolated by spinning at 500g for 10 minutes, all supernatant was pipet decanted, and pelleted cells were resuspended in 25 uL Tagmentation Reaction Mix composed of 12.5 uL Tagment DNA Buffer (Illumina), 0.02% Digitonin, 0.1% Tween-20, 2.5 uL TN5 enzyme (Illumina).
Tagmentation was performed for 1 hour at 37C. Tagmented DNA was isolated by adding Tagmentation Clean-up Buffer (326 mM NaCl, 109 mM EDTA, 0.63% SDS, 20 ug Proteinase K) and incubating at 40C for 1 hour and both a negative (0.7x) and positive (1.2x) SPRI bead (Kapa) selection. Libraries were amplified 12 times with Hifi polymerase (Kapa) and Nextera barcoded primers (Illumina) prior to 1x SPRI bead clean-up and sequencing on a Novaseq (Illumina).
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description RPMI8226.MACS2_q_0.01.noModel.union.annot.clean.cts
RPMI8226.MACS2_q_0.01.noModel.union.annot.clean.rppm.cov
Data processing ATAC-seq FASTQ files were quality and adapter trimmed using Trim Galore! (v0.6.4) and CutAdapt (v2.5) and mapped to the GRCh38 reference genome using bowtie2 (v2.3.5.1).
Aligned SAM files were converted to BAM files and putative PCR duplicates were marked with Samtools (v1.10) .
Regions of chromatin accessibility were identified in each sample using MACS2 (v2.1.1.20160309).
The union of all accessible regions was determined and reads mapping to these regions for each sample was assessed using the 'summarizeOverlaps' function of the GenomicAlignments package (v1.30.0) in R (v4.1.2).
Regions that overlapped ENCODE blacklisted regions were removed.
As a quality control metric the number of reads in peaks was determined and used to calculate a normalized accessibility score as reads per peak million (RPPM) according to the following formula: RPPM=reads× 〖10〗^6/(total reads in autosomal peaks)
Differential chromatin accessible regions were determined using edgeR (v3.36.0)
Assembly: GRCh38
Supplementary files format and content: L363.MACS2_q_0.01.noModel.union.annot.clean.cts: Raw read counts in peaks in L363 cells
Supplementary files format and content: L363.MACS2_q_0.01.noModel.union.annot.clean.rppm.cov: Reads per peak per million reads (RPPM) normalized data for L363 cells
Supplementary files format and content: RPMI8226.MACS2_q_0.01.noModel.union.annot.clean.cts: Raw read counts in peaks in RPMI8226 cells
Supplementary files format and content: RPMI8226.MACS2_q_0.01.noModel.union.annot.clean.rppm.cov: Reads per peak per million reads (RPPM) normalized data for RPMI8226 cells
Supplementary files format and content: Each sample has an individual bigWig file using the naming convention "[SAMPLENAME].union.rppm.bw", which includes RPPM normalized data.
 
Submission date Oct 27, 2023
Last update date Oct 29, 2023
Contact name Benjamin G Barwick
E-mail(s) benjamin.barwick@emory.edu
Phone (404) 285-2964
Organization name Emory University
Department Hematology and Medical Oncology
Lab Barwick Lab
Street address 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37
City Atlanta
State/province GA
ZIP/Postal code 30322
Country USA
 
Platform ID GPL24676
Series (2)
GSE246426 ETV4-Dependent Transcriptional Plasticity Maintains MYC Expression and Results in IMiD Resistance in Multiple Myeloma [ATAC-seq]
GSE246436 ETV4-Dependent Transcriptional Plasticity Maintains MYC Expression and Results in IMiD Resistance in Multiple Myeloma
Relations
BioSample SAMN38020959
SRA SRX22251787

Supplementary file Size Download File type/resource
GSM7868724_RPMI8226_EV_Len2.union.0.01.rppm.bw 517.8 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap