|
| Status |
Public on Apr 01, 2020 |
| Title |
ATACseq on NTG replicate A |
| Sample type |
SRA |
| |
|
| Source name |
HepG2_NTG
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2
cell type: liver cancer cell line
sirna: NTG (AM4611 Life Tech.)
|
| Treatment protocol |
Cells were treated with indicated siRNA at 50nM for 72 hours using RNAimax transfection reagent as per manufacturers instructions
|
| Growth protocol |
Cells were grown in DMEM + 10% FBS + penicillin + streptomycin at 37 degrees in 5% C02
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq was carried out as described (Buenrostro et al 2013)
ATAC-seq libraries were created using protocol from Buenrostro et al 2013, and processed using Nextera adapter sequences for Illumina sequencing
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
processed data file:
NTG_peaks.filtered.narrowPeak
NTG_A
|
| Data processing |
trim-galore (0.4.1) --nextera --paired
bowtie2 -X 2000
sed '/chrM/d'
samtools view -u -q 20
macs/2.1.0 macs2 callpeak --keep-dup all -g hs --call-summits
deeptools/2.2.4 bamCoverage --binSize 1 --normalizeUsingRPKM --Mnase --minFragmentLength 50 --maxFragmentLength 200
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files genreated using Deeptools (.bw) peak calls using Macs2 (.narrowPeak)
|
| |
|
| Submission date |
Apr 05, 2017 |
| Last update date |
Apr 01, 2020 |
| Contact name |
Jesse Raab |
| E-mail(s) |
jesse.r.raab@gmail.com
|
| Organization name |
University of North Carolina Chapel Hill
|
| Department |
Genetics
|
| Street address |
120 Mason Farm Rd
|
| City |
Chapel Hill |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE97410 |
Effect of INO80 loss on open chromatin in HepG2 cells [ATAC-seq] |
| GSE97413 |
INO80 complex assembly is antagonized by PRC2. |
|
| Relations |
| BioSample |
SAMN06688196 |
| SRA |
SRX2708800 |
