NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4338217 Query DataSets for GSM4338217
Status Public on Apr 02, 2020
Title RNAseq_UBC-CreER;SmoF/F_Rep1
Sample type SRA
 
Source name RNAseq_UBC-CreER;SmoF/F
Organism Mus musculus
Characteristics strain: C57BL/6
developmental stage: Derived from postnatal day 7
cell type: Ventral V-SVZ cells
treatment: 100nM 4-OHT (in 1% EtOH) added to proliferation media for 4 days (2 passages)
Growth protocol Proliferative medium (DMEM/F12 with Glutamax, 5% Fetal Bovine Serum, N2 supplement, 35 µg/mL bovine pituitary extract, 20 ng/mL EGF, 20 ng/mL FGF, antibiotic/antimycotic)
Extracted molecule total RNA
Extraction protocol Total RNA was isolated by Trizol (Life Technologies), purified using Direct-zol (Zymo) kit with on-column DNAse treatment.
Strand-specific, poly(A) selected cDNA libraries were generated using TruSeq Stranded mRNA kit (Illumina, #20020594).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description SMO_HOMO_V_1_S11
UBC_Smo_Homo_Rep1_158__S58
Data processing RNAseq reads were psuedoaligned to Genocde GRCm38.p5 mouse transriptome with kallisto v0.43.0 using 100 bootstrap samples.
Differential expression was assessed using Sleuth v0.29.0 with transformation function = function(x) log2(x + 0.5) and gene-level aggregation using Ensembl annotations. qvalue <0.1 and b-value (log2FC) of >0.5 used as thresholds
CnR reads were quality trimmed by BBDuk, removing reads below Q30 score, and aligned to UCSC MM10 genome with Bowtie2 2.2.6 with the following arguments: : --local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700.
Peaks were called using MACS2 using the argument --broad and using IgG samples as control libraries
Differentially enriched chromatin loci were called using diffReps with arguments: -me nb --mode b. Differentially enriched loci outside of statistically called peaks by MACS2 were removed
Genome_build: RNAseq:mouse mm10, Gencode GRCm38.p5 mouse transriptome. CnR: UCSC mm10
Supplementary_files_format_and_content: peaks; abundance.h5
 
Submission date Feb 24, 2020
Last update date Apr 02, 2020
Contact name Tomasz Nowakowski
E-mail(s) ryanndelgado@gmail.com
Organization name UCSF
Street address 1550 4th St
City San Francisco
State/province Ca
ZIP/Postal code 94158
Country USA
 
Platform ID GPL21103
Series (1)
GSE145871 Maintenance of neural stem cell positional identity by Mixed-lineage leukemia 1
Relations
BioSample SAMN14178173
SRA SRX7797531

Supplementary file Size Download File type/resource
GSM4338217_Smo_Homo_Rep1_abundance.h5 53.5 Mb (ftp)(http) H5
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.