|
| Status |
Public on Feb 07, 2022 |
| Title |
SMS-CTR SCRAMBLE H3K27ac |
| Sample type |
SRA |
| |
|
| Source name |
Fusion Negative Rhabdomyosarcoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Fusion Negative Rhabdomyosarcoma
genotype: control
chip antibody: H3K27ac (Abcam, ab4729)
cell line: SMS-CTR
|
| Growth protocol |
Cells were cultured along with spike-in Drosophila S2 cells at a 1:10 ratio with RMS cell line
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIPseq libraries were assembled using the KAPA HyperPrep ChIP library kit following manufacturer’s settings and were sequenced on an Illumina Nextseq500 machine.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
2066072_SMS-CTR_shCTRL_H3K27ac_S10
|
| Data processing |
ChIPseq reads were quality assessed by FastQC, MultiQC and filtered with BBDuk.
ChIPseq reads were aligned to the hg38 human and to the dm6 fly (Drosophila melanogaster) genome assembly using Bowtie2 (v2.3.4.3).
Samtools (v.1.11) was used to select the mapped reads (samtools view -b - q 30) and sort the bam files.
PCR duplicates were removed using Picard MarkDuplicates tool.
The normalization ratio of each sample was calculated by dividing the total number of mapped reads mapping to the fly genome of each sample by the the total number of mapped reads mapping to the fly genome of the sample with the lowest number of reads mapping to the Drosophila genome. Using the normalization ratio, random sub-sampling of the reads was performed using samtools view -hs.
Bedtools genomecov was used to create bedgraph files from the bam files.
Igvtools toTDF was used to create tdf files.
Peaks were called using MACS2 (v2.1.2) with default parameters (-gsize hs --qvalue 0.01)
Genome_build: hg38
Supplementary_files_format_and_content: tdf files
|
| |
|
| Submission date |
Apr 22, 2021 |
| Last update date |
Feb 07, 2022 |
| Contact name |
Heide L Ford |
| E-mail(s) |
heide.ford@cuanschutz.edu
|
| Organization name |
University of Colorado Anschutz Medical Campus
|
| Department |
Pharmacology
|
| Lab |
Heide Ford
|
| Street address |
12800 East 19th Ave Rm 6401I
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE173151 |
Chromatin states and transcription factor binding in SIX1 deficient Rhabdomyosarcoma cells |
| GSE173155 |
RNA-Seq and ChIP-Seq in SIX1 deficient Rhabdomyosarcoma cells |
|
| Relations |
| BioSample |
SAMN18836517 |
| SRA |
SRX10660630 |
