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| Status |
Public on Feb 01, 2024 |
| Title |
55N, KAS-Seq, biol rep1 |
| Sample type |
SRA |
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| Source name |
LA1-55n
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| Organism |
Homo sapiens |
| Characteristics |
cell line: LA1-55n
cell type: neuroblastoma cell line, MYCN-amplified
chip antibody: none
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| Growth protocol |
Cells were grown at 5% CO2 in RPMI1640 medium (Life Technologies) supplemented with 10% heat-inactivated FBS, 2 mmol/L l-glutamine, and 1% penicillin/streptomycin
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
cells were incubated for 5–10 min at 37 °C, 5% CO2 in complete culture medium containing 5 mM N3-kethoxal. Using the PureLink genomic DNA mini kit (Thermo, K182002), genomic DNA (gDNA) was isolated from collected cells.
Accel-NGS Methyl-seq DNA library kit (Swift, 30024) was used for library construction on eluted DNA and corresponding input.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
reads were trimmed using the trim-galore package in single-end mode.
Trimmed reads were aligned to hg38 using bowtie2 (v2.3.0) with standard parameters and sorted to bam files using samtools sort (v1.9)
samtools rmdup (v1.9) was utilized to get unique mapped reads, which were then extended to 150 bp
bigWig files were generated using deepTools bamCoverage, normalized to RPKM. Blacklist regions (obtained from ENCODE) were excluded.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: KAS-Seq
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| Submission date |
Sep 07, 2022 |
| Last update date |
Feb 01, 2024 |
| Contact name |
Mark Applebaum |
| E-mail(s) |
mapplebaum@bsd.uchicago.edu
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| Organization name |
University of Chicago
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| Department |
Pediatrics, Section of Hematology/Oncology
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| Street address |
900 E 57th St
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE212881 |
5-Hydroxymethylcytosine Profiling of Cell-Free DNA Identifies Bivalent Genes That Are Prognostic of Survival in High-Risk Neuroblastoma [KAS-Seq] |
| GSE212882 |
5-Hydroxymethylcytosine Profiling of Cell-Free DNA Identifies Bivalent Genes That Are Prognostic of Survival in High-Risk Neuroblastoma |
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| Relations |
| BioSample |
SAMN30721986 |
| SRA |
SRX17476359 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6560474_55N_C1_KAS-Seq.bigWig |
102.2 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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