|
| Status |
Public on Jan 11, 2022 |
| Title |
EB_H3K36me3_R106_treat_pileup |
| Sample type |
SRA |
| |
|
| Source name |
EB_H3K36me3
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: erythroid
|
| Growth protocol |
Cell were grown according to Schulz et al 2019, Cell Reports
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Library construction and strategy according to Schulz et al 2019, Cell Reports
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Single end raw reads were processed for quality and residual adapter sequencing using fastp v0.19.6 (--trim_poly_g -x --cut_window_size 4 -3 -l 35)
Quality reads were aligned to the hg19 reference genome using bowtie2 and filtered for quality based on MAPQ > 10.
Significantly enriched histone modifications were identified using MACS2 (--broad --broad-cutoff 0.1 -f BAM -B --SPMR -g hs) with each biological replicate and the corresponding IgG control.
replicated regions were also identified by providing MACS2 with all biological replicates for each mark to generate continuous coverage and enrichments for each condition
Genome wide distribution of significantly enriched regions was evaluated using CEAS (v1.0.2).
Genome_build: hg19
|
| |
|
| Submission date |
Aug 06, 2020 |
| Last update date |
Jan 11, 2022 |
| Contact name |
Zachary C Murphy |
| E-mail(s) |
zachary_murphy@urmc.rochester.edu
|
| Phone |
5852766040
|
| Organization name |
University of Rochester
|
| Street address |
601 Elmwood Ave box 703
|
| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14606 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE155847 |
Terminally maturing erythroblasts have dynamic changes in transcription-related chromatin modifications and RNA Polymerase II occupancy (ChIP-Seq 2) |
| GSE155849 |
Terminally maturing erythroblasts have dynamic changes in transcription-related chromatin modifications and RNA Polymerase II occupancy |
|
| Relations |
| BioSample |
SAMN15753954 |
| SRA |
SRX8902546 |
