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Sample GSM4427575 Query DataSets for GSM4427575
Status Public on Apr 20, 2021
Title E11_FJW180312003_CC09
Sample type SRA
 
Source name E11.5_whisker follicles cells
Organism Mus musculus
Characteristics Stage: E11.5
cell type: whisker follicles cells
data quality: ok
Extracted molecule total RNA
Extraction protocol Single cells were directly sorted into the cell lysis buffer containing RNasein plus (Promega), Cell Lysis Buffer (Roche), NP40 (Thermo), and RNase free water (TaKaRa).
RamDA-seq sequencing libraries were prepared by using the advanced method of RamDA-seq (refer to the Methods section in "Single-cell full-length total RNA sequencing uncovers dynamics of non-polyadenylated RNAs, recursive splicing and enhancer RNAs" DOI: https://doi.org/10.1038/s41467-018-02866-0).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description mEWF-E11_FJW180312003_CC09_S129
Data processing FASTQ files were generated using bcl2fastq (v1.0) for NextSeq.
fastq-mcf (version 1.04.807) was used for adapter trimming with the parameters '-L 42 -l 36 -k 4.0 -q 30' for HiSeq 1500, '-L 50 -l 36 -k 4.0 -q 30' for HiSeq 2500 and '-L 75 -l 36 -k 4.0 -q 30' for NextSeq. The reads were mapped to the mouse genome (mm10) using HISAT2 (version 2.0.4) with the parameters '-p 4 --end-to-end'. Transcript levels were quantified as Transcripts Per Kilobase Million (TPM) with Sailfish (version 0.10.0) using GENCODE vM14 annotation file.
outside of the mean minus three standard deviations of the number of mapped reads to a sailfish index (Sailfish) or the number of assigned reads to gene regions (featureCounts, function of Subread version 1.5.0); over 10% reads assigning to mitochondrial RNA (featureCounts); abnormal gene body coverage of sequencing reads by human curation (RseQC, version 2.6.4).
for count table, after convert Ensemble transcript_id to Gene_id, each isoform expression were summarized on gene level.
Genome_build: mm10
Supplementary_files_format_and_content: txt
 
Submission date Mar 23, 2020
Last update date Apr 20, 2021
Contact name Hironobu Fujiwara
E-mail(s) hironobu.fujiwara@riken.jp
Organization name RIKEN
Department Center for Biosystems Dynamics Research
Lab Laboratory for Tissue Microenvironment
Street address 2-2-3 Minatojima-minamimachi
City Chuo-ku, Kobe
ZIP/Postal code 6500047
Country Japan
 
Platform ID GPL19057
Series (1)
GSE147372 Tracing the origin of hair follicle stem cells
Relations
BioSample SAMN14424476
SRA SRX7969086

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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