|
| Status |
Public on Apr 01, 2024 |
| Title |
KO EC 2 |
| 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 |
KO2
Fli1-Brain_B2_S19
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 |
SAMN18529735 |
| SRA |
SRX10471078 |
