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| Status |
Public on Jul 10, 2024 |
| Title |
Normal_16_Input |
| Sample type |
SRA |
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| Source name |
Healthy lung tissue
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Healthy lung tissue
treatment: low exposure to violence neighborhood
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tumor samples were homogenized using 30 strokes of a Dounce homogenizer
Libraries were constructed with the Ovation Ultralow System V2 kit from Tecan following the manufacturer’s protocol. The individually barcoded libraries were run on a Fragment Analyzer (Agilent, CA) to confirm the absence of free primers and primer dimers and to confirm the presence of DNA of the expected size range. Libraries were pooled in equimolar concentration and the pool was further quantitated by qPCR on a BioRad CFX Connect Real-Time System (Bio-Rad Laboratories, Inc. CA).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
BED file: Normal 16, low exposure to violence neighborhood, Normal relative to Input
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| Data processing |
The fastq read files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA).
Adaptors were trimmed from the 3'-end of the reads. The quality-scores line in fastq files used an ASCII offset of 33 known as Sanger scores.
Paired-end FASTQ files were aligned to human reference (GRCh38) using Bowtie2 (v2.4.5)
BAM files were prepared using SAMtools (v1.17)
Narrow peak calling was performed using MACS (v2.2.5) with a p-value cutoff and FDR of 0.001.
Assembly: Tumor-specific narrowPeak files were generated by filtering out binding regions also found in healthy tissue bed files. Normal-specific narrowPeak files were similarly generated via the removal of binding regions found in tumor bed files.
Supplementary files format and content: hg38
Supplementary files format and content: bed
Library strategy: CUT&RUN
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| Submission date |
May 21, 2024 |
| Last update date |
Jul 10, 2024 |
| Contact name |
Zeynep Madak Erdogan |
| Organization name |
UIUC
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| Department |
FSHN
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| Lab |
Zeynep Madak Erdogan
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| Street address |
1201 S Goodwin Ave
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| City |
Urbana |
| State/province |
IL |
| ZIP/Postal code |
61801 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE268048 |
The effect of exposure to neighborhood violence on GR signaling in lung tumors [CUT&Run] |
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| Relations |
| BioSample |
SAMN41480504 |
| SRA |
SRX24635577 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8284977_N_16_GR_N_rel_I.bed.gz |
64.2 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
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