|
| Status |
Public on Jul 13, 2023 |
| Title |
org_fetal_rep1_atac |
| Sample type |
SRA |
| |
|
| Source name |
small intestinal epithelium derived organoids
|
| Organism |
Mus musculus |
| Characteristics |
tissue: small intestinal epithelium derived organoids
developmental state: E16.5
strain: C57BL/6J
treatment: untreated
|
| Growth protocol |
Fetal spheroids and adult organoids derived from E16.5 fetal epithelial fragments or scraped adult crypts harvested from proximal small intestine using 2mM EDTA were embedded in Matrigel droplets and cultured in advanced DMEM/F12 with GlutaMAX and Penicillin/Streptomycin supplemented with 50 ng/ml EGF, 100 ng/ml Noggin, and 500 ng/ml, R-Spondin1, 3 µM CHIR99021 and 10 mM Nicotinamide.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Fetal spheroids and adult organoids were released from Matrigel and resuspended in TrypLE Express Enzyme (GIBCO) and incubated at 37°C until a single cell suspension was obtained. After centrifugation, cells were resuspended in PBS with 1% BSA and incubated with fluorescent-conjugated primary antibody EpCAM-APC (Supplementary table 1), for 30 min on ice. After washing, DAPI (Sigma; 1 µM) was added and 50 000 live (EpCAM+ DAPI-) cells were subsequently sorted on a FACS Aria I (BD Bioscience) cell sorter.
The cells were lysed and after centrifugation resuspended in transposase reaction mix and incubated for 30 min at 37°C. After purification, the eluted DNA was PCR amplified with unique barcode (TAAGGCGA, CGTACTAG, TCCTGAGC and TAGGCATG) containing PCR primers for multiplexing of samples: and purified. The samples were paired-end sequenced with Illumina NextSeq.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequencing reads were converted by using bcf2fastq and demultiplexed according to the indexes
Paired-end reads were mapped with Bowtie2 against the mm10 assembly and only uniquely mapping reads were retained using samtools
Duplicate reads were removed and regions highly contaminated by duplicate reads (99.9th percentile) and reads within ENCODE black-list regions were masked. Reads aligning to plus strand were offset by +4 bp and reads aligning to minus strand with -5bp. The peaks were called for each replicate using MACS2 without a shifting model and the background lambda as local lambda.
Genome_build: mm10
Supplementary_files_format_and_content: ATAC bigwig files where the score represents per-base genome coverage normalized to the library size.
|
| |
|
| Submission date |
Oct 29, 2020 |
| Last update date |
Jul 13, 2023 |
| Contact name |
Laura Maarit Pikkupeura |
| Organization name |
University of Copenhagen
|
| Department |
BRIC
|
| Lab |
Jensen lab
|
| Street address |
Ole Maaloes vej 5
|
| City |
Copenhagen N |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE160449 |
Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation [I] |
| GSE228519 |
Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation |
|
| Relations |
| BioSample |
SAMN16596945 |
| SRA |
SRX9401580 |
