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Sample GSM5219064 Query DataSets for GSM5219064
Status Public on Apr 01, 2024
Title KO EC 3
Sample type SRA
 
Source name Brain derived ECs
Organism Mus musculus
Characteristics cell type: Brain-derived ECs
genotype: Fli-1 knockout
Treatment protocol Fli-1 alleles deletion was induced using 4-OHT.
Growth protocol ECs were cultured in DMEM Ham's F12 (50:50) media containing 20% fetal bovine serum, glutamine, HEPES, and antibiotics.
Extracted molecule total RNA
Extraction protocol ECs were isolated by fluorescence-activated cell sorting and subjected to RNA extraction using Arcturus PicoPure RNA isolation kit (applied Biosystems).
RNA-seq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description KO3
Fli1-Brain_B3_S20
Polyadenylated mRNA
counts.txt
Data processing FastQC (v0.11.8) to check FASTQ quality.
Trim Galore (v0.6.4) for adapter trimming.
STAR (v2.6.1d) to align files.
Subread (v1.6.4) featureCounts to quantify gene counts.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: counts.txt: Gene count matrix
 
Submission date Mar 29, 2021
Last update date Apr 01, 2024
Contact name Tomer Itkin
E-mail(s) toi2003@med.cornell.edu
Organization name Weill Cornell Medicine
Department Medicine
Lab Rafii
Street address 1300 York Avenue, A-869
City NY
State/province NY
ZIP/Postal code 10065
Country USA
 
Platform ID GPL21103
Series (2)
GSE169431 Transcriptional Activation of Regenerative Haematopoiesis via Niche Sensing
GSE171111 Transcriptional Activation of Regenerative Haematopoiesis via Niche Sensing [Bulk EC RNA-seq]
Relations
BioSample SAMN18529734
SRA SRX10471079

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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