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Sample GSM5606759 Query DataSets for GSM5606759
Status Public on Jun 07, 2023
Title 2-day miR-205 inducible Rep1
Sample type SRA
Source name P44 hair follicle stem cells
Organism Mus musculus
Characteristics cells: hair follicle stem cells
strain: C57BL/6
treatment: treated with doxcyclin for 2 days
Treatment protocol miR-205 inducible mouse was feed Doxcyclin chow for 2 days from P42-P44 or for 4 days from P49-P53.
Extracted molecule total RNA
Extraction protocol Gender matched mice (Ctrl and miR-205Ind) harboring a K14-H2BGFPallele were fed doxycycline for 2 or 4 days and euthanized to collect back skin samples. Hair coats were shaved and removed. Subcutaneous fat was removed, and back skin samples were minced into small pieces and incubated with 0.25% collagenase (Worthington, LS004188) in 10 mL 1x HBSS buffer at 37°C for 2 hours with rotation. After collagenase treatment, 10 mL cold PBS was added, and sample suspension was centrifugated at 400 g for 10 minutes at 4°C to get the pellet. The pellet was resuspended with 5 ml pre-warmed 0.25% trypsin/EDTA (Gibco) for 7 minutes at 37°C and the digestion was blocked by adding 10 mL cold 1x PBS with 3% chelated FBS. The suspension was extensively triturated with a 25 ml pipette and filtered through a 40 m cell strainer, followed by centrifugation at 400 g for 5 minutes at 4°C. The pelleted cells were resuspended in cold 1x PBS with 3% chelated FBS. Suspended cells were incubated with appropriated antibodies for 1 hour on ice. After washing away unbounded antibodies, DAPI was used to exclude dead cells. Live hair follicle stem cells from both control and miR-205 inducible animals were collected from FACS sorting machine with cell surface proteins and H2BGFP signals.
Total RNAs from FACS-purified cells were isolated using TRIZOL (Invitrogen). RNA quality was assessed by Agilent 2100 bioanalyzer. RNA Samples with RNA integrity numbers (RIN) > 8 were used to make libraries and perform RNA-seq assay. Libraries were prepared by following manufacturer’s protocol (NEBNext Ultra Directional RNA Library Prep Kit). The cDNA libraries were quality-checked with bioanalyzer and sequenced at Genomics and Microarray Core Facility at University of Colorado Denver on Illumina NovaSeq 6000.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Data processing RNA-seq reads (150nt, paired-end) were aligned to the mouse genome (NCBI37/mm10) using Hisat2 (version 2.1.0).
The resulting sam files were converted to bam files using SAMtools (version 1.3.1).
Expression measurement of each gene was calculated from the resulting alignment bam file by HT-seq.
Differentially expressed genes were determined using DEseq2 using default settings.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include baseMean, log2FoldChange, pValue..
Submission date Sep 30, 2021
Last update date Jun 07, 2023
Contact name Rui Yi
Organization name Northwestern University
Department Pathology, Feinberg School of Medicine
Lab Yi Lab
Street address 765 N FAIRBANKS CT
City Chicago
State/province Illinois
ZIP/Postal code 60611
Country USA
Platform ID GPL24247
Series (2)
GSE185116 Transcriptome analysis in hair follicle stem cells after miR-205 induction in mouse
GSE185117 RNA-seq for miR-205 inducible hair follicle stem cells and ScRNAseq for miR-205 inducible back skin samples
BioSample SAMN21924098
SRA SRX12418555

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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