|
| Status |
Public on Jun 15, 2022 |
| Title |
SOX9OE_SOX9CUT&RUN_96h |
| Sample type |
SRA |
| |
|
| Source name |
Umbilical vein endothelial cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HUVEC
transduced with: SOX9 expression plasmid
cut&run/tag antibody: SOX9 (AB5535, Millipore)
|
| Growth protocol |
HUVECs were cultivated in Medium 200 (Thermo Fisher Scientific) supplemented with 2% low serum growth supplement and 1% Penicillin Streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
CUT&RUN, CUT&Tag, ATAC-seq
NEBnext DNA Ultra ii (New England Biolabs)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Library strategy: CUT&RUN
All reads were mapped to the hg19/GRCh37 genome using the BWA-MEM aligner version 0.7.13.
BAM files were filtered using the encode_task_filter.py script from the ENCODE chip-seq-pipeline2.
MACS2 was used to call peaks using the parameters “-p 0.01 -f BAMPE -g hs” for the CUT&RUN and CUT&Tag data, and “-p 0.01 -g hs --nomodel --shift -75 --extsize 150” for the ATAC-seq data.
Bigwig files were generated from the filtered BAM files using MACS2 bdgcmp using the fold enrichment option for the ATAC-seq data and deepTools bamCoverage with the options "--binSize 1 --normalizeUsing RPGC --effectiveGenomeSize 2864785220 --extendReads" for the CUT&Tag and CUT&RUN data
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: tracks in BigWig file format
|
| |
|
| Submission date |
Sep 24, 2021 |
| Last update date |
Jun 15, 2022 |
| Contact name |
Bettina Maria Fuglerud |
| E-mail(s) |
bfuglerud@bccrc.ca
|
| Organization name |
BC Cancer
|
| Street address |
675 W 10th Ave
|
| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V5Z 1L3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL30173 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN21615307 |
| SRA |
SRX12335626 |
