 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 09, 2021 |
| Title |
E17Merkel_WT_RNAseq_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
epidermis
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: embryonic day 17.5
cell type: Merkel cells
genotype: Wildtype
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Merkel cells (Atoh1-GFP+) were purified from the skin of E17 wildtype animals by FACS sorting. RNA was extracted using Quick RNA micro-kit (zymo).
Libraries were prepared using using QIAseq FX Single Cell RNA Library Kit (Qiagen).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
For RNAseq, reads were trimmed based on quality score and then aligned to reference mouse genome (mm10) using STAR. Reads were quantified against genes using RSEM, and differential gene expression analysis was conducted using DESeq2.
For ATACseq, reads were trimmed based on quality score and then aligned to reference mouse genome (mm10) using bowtie2. PCR-duplicates were removed by Sambamba, and then peaks were called by MACS2 from individual replicate using filter p value < 0.01.
For Cut&Run, reads were trimmed based on quality score and then aligned to referene mouse genome (mm10) using STAR. PCR duplicates were removed based on UMI by umi_tools, and then peaks were called by MACS2 for individual replicate using filter p value < 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: read count for genes in text format for RNAseq; peak regions in narrowPeak format for ATACseq and CUT&RUN
|
| |
|
| Submission date |
May 12, 2020 |
| Last update date |
Jul 10, 2021 |
| Contact name |
Neil Segil |
| E-mail(s) |
nsegil@med.usc.edu
|
| Phone |
3234421549
|
| Organization name |
University of Southern California
|
| Department |
BCC
|
| Lab |
503K
|
| Street address |
1425 san pablo st, BCC 503K
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE150388 |
ATACseq, CutnRun and RNAseq data from Merkel cell and Touch dome epithelial progenitor cells, from wild type and Pou4f3-mutant epidermis |
| GSE150391 |
POU4F3 Pioneer Activity Enables ATOH1 to Drive Diverse Mechanoreceptor Differentiation Through a Feed-Forward Epigenetic Mechanism |
|
| Relations |
| BioSample |
SAMN14897344 |
| SRA |
SRX8330593 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4548092_E17Merkel_WT_RNAseq_rep1.genes.results.txt.gz |
1.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
