|
| Status |
Public on Oct 29, 2023 |
| Title |
L363_ETV4KO_Len2 |
| Sample type |
SRA |
| |
|
| Source name |
cell line
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: cell line
cell line: L363
cell type: multiple myeloma
genotype: ETV4 knock-out
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 |
L363.MACS2_q_0.01.noModel.union.annot.clean.cts
L363.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 |
SAMN38020963 |
| SRA |
SRX22251783 |
