|
| Status |
Public on Jan 29, 2021 |
| Title |
primary human islets-IgG CUT&RUN [S178_neg] |
| Sample type |
SRA |
| |
|
| Source name |
primary human islets
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Primary islet cells
developmental stage: Adult
genotype/variation: SIX2-Flag overexpression
treatment: pA-MN; EpiCypher
chip antibody: IgG (Millipore)
|
| Treatment protocol |
Lentiviruses expressing SIX2-Flag.
|
| Growth protocol |
Primary human islets were disersed/ transduced with lentiviruses and cultured for 5 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from Protein A-micrococcal nuclease digested DNA. DNA fragments were released for 20 min at 37°C and purified using phenol/chloroform/isoamyl alcohol followed by chloroform extraction and precipitated with glycogen and ethanol. SIX2-Flag-DNA complexes were isolated with anti-Flag antibody.
NEBnext Ultra II library kit.
CUT&RUN (similar to ChIP-seq) and sequenced as 2 × 75 on HiSeq4000.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
S178-neg
merged_S369_178_A385_peaks.bed
|
| Data processing |
Library strategy: CUT&RUN
Trimmomatic (Bolger et al. 2014) was used for trimming.
Bowtie2 (Langmead and Salzberg 2012) was used for alignment.
HOMER (Heinz et al. 2010) was used for peak calling.
The GREAT algorithm was used for gene annotation (McLean et al. 2010).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig files
Supplementary_files_format_and_content: *.bed: Peaks files.
|
| |
|
| Submission date |
Jan 29, 2021 |
| Last update date |
Jan 31, 2021 |
| Contact name |
Romina J Bevacqua |
| E-mail(s) |
bevacqua@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Developmental Biology
|
| Lab |
Seung Kim Lab
|
| Street address |
279 Campus Drive W
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE164627 |
SIX2 genome-binding profiling by CUT&RUN and high-throughput sequencing |
| GSE164628 |
SIX2 and SIX3 coordinately regulate functional maturity and fate of human pancreatic β cells |
|
| Relations |
| BioSample |
SAMN17703869 |
| SRA |
SRX9981615 |
