|
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 |