GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM4427940 Query DataSets for GSM4427940
Status Public on Apr 20, 2021
Title E13_FJW150126001_C02
Sample type SRA
Source name E13.0_whisker follicles cells
Organism Mus musculus
Characteristics Stage: E13.0
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:
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
Description mEWF-E13_FJW150126001_C02_GGAGCTA-CCTAGAG_L007
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
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 GPL18480
Series (1)
GSE147372 Tracing the origin of hair follicle stem cells
BioSample SAMN14424712
SRA SRX7969667

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap