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Status |
Public on Apr 02, 2020 |
Title |
RNAseq_UBC-CreER;SmoF/F_Rep1 |
Sample type |
SRA |
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Source name |
RNAseq_UBC-CreER;SmoF/F
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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)
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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)
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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).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
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Description |
SMO_HOMO_V_1_S11 UBC_Smo_Homo_Rep1_158__S58
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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
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Submission date |
Feb 24, 2020 |
Last update date |
Apr 02, 2020 |
Contact name |
Tomasz Nowakowski |
E-mail(s) |
ryanndelgado@gmail.com
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Organization name |
UCSF
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Street address |
1550 4th St
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City |
San Francisco |
State/province |
Ca |
ZIP/Postal code |
94158 |
Country |
USA |
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Platform ID |
GPL21103 |
Series (1) |
GSE145871 |
Maintenance of neural stem cell positional identity by Mixed-lineage leukemia 1 |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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