|
| Status |
Public on Dec 09, 2020 |
| Title |
SK_ETH6_REP3 |
| Sample type |
SRA |
| |
|
| Source name |
colonic organoid
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: organoid
tissue: rectosigmoid mucosa
treatment: ethanol control 6 hrs
|
| Treatment protocol |
After 24 hours of culturing in the basal media, organoids were treated with either 100nM 1α,25(OH)2D3 or vehicle control (ethanol) for 4 and 18 hours (for ATAC-seq), or 6 or 24 hours (for RNA-seq).
|
| Growth protocol |
Organoids were derived using a protocol adapted from Sato et al 2011
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-seq: mRNA was isolated from cells using the RNeasy® Plus Mini Kit (Qiagen) according to the manufacturer’s protocol. ATAC-seq: cells were treated using the Omni-ATAC protocol with some modifications. Briefly, the cells were treated with lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and then suspended in the transposition reaction mix (50% TD Tagment DNA buffer, 5% TDE1 Tagment DNA Enzyme,33% PBS) for 30 minutes.
RNA-seq libraries were prepared using Illumina mRNA TruSeq kits as protocolled by Illumina. ATAC-seq ibraries were prepared using the Nextera Index kit (Illumina #15055289).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
ATAC-seq fastq reads aligned with bwa mem (v 0.7.17)
ATAC-seq read filtering performed with samtools (v 1.10)
ATAC-seq peak calling performed with MACS2 (v 2.1.0)
ATAC-seq differential peak calling performed with R packages DiffBind and edgeR
ATAC-seq motif enrichment and peak annotation performed with HOMER (v 4.11.1)
RNA-seq equence alignment and gene expression value estimation was performed using RSEM (v.1.3.1) using the STAR aligner in paired-end mode.
RNA-seq differential expression analysis was performed with the R package DESeq2
Genome_build: ATAC-seq and RNA-seq reads were aligned to reference sequence hs37d5
Supplementary_files_format_and_content: peak files are MACS2 outputted narrowPeak files for treated and untreated ATAC-seq samples at the two timepoints
|
| |
|
| Submission date |
Dec 08, 2020 |
| Last update date |
Dec 09, 2020 |
| Contact name |
Sonia Kupfer |
| E-mail(s) |
[email protected]
|
| Phone |
773-702-8076
|
| Organization name |
University of Chicago
|
| Department |
Department of Medicine
|
| Street address |
900 East 57th Street, MB#9
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE162856 |
Genomic and epigenomic 1α,25(OH)2D3 responses in human colonic organoids |
|
| Relations |
| BioSample |
SAMN17028724 |
| SRA |
SRX9650358 |
