|
| Status |
Public on Sep 06, 2018 |
| Title |
RNA-seq_P7_Brain_GFPneg_R2 |
| Sample type |
SRA |
| |
|
| Source name |
P7 GFP-negative sorted cells from brain
|
| Organism |
Mus musculus |
| Characteristics |
strain/genotype: Tie2-GFP
age: P7
Sex: Male
tissue: Brain
cell-type: Non-endothelial
|
| Growth protocol |
Adult mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from an aliquot of dissociated tissue prior to filtering and antibody staining and from GFP-positive and GFP-negative FACS sorted cells using the RNeasy Micro Plus kit (74034, QIAGEN, Venlo, Netherlands).
For RNA-seq, total RNA was converted to cDNA and amplified (Ovation Ultralow System V2-32, 0342HV, NuGEN Technologies, San Carlos, CA). Amplified cDNA was fragmented, end-repaired, linker-adapted, and single-end sequenced for 75 cycles on a NextSeq500 (Illumina Inc.). Cultured brain EC RNA-seq libraries were paired-end sequenced for 36 cycles on a NextSeq500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Three different sets of RNA-seq data were generated from papain dissociated P7 Tie2-GFP brain, liver, lung, and kidney: (1) total tissue; (2) GFP-negative FACS-sorted cells; and (3) GFP-positive FACS-sorted cells. RNA-seq was also performed on cultured primary brain ECs. RSEM version 1.3.0 (Li and Dewey, 2011) was used to align reads with Bowtie2 to the mm10/GRCm38 genome and calculate transcript expression using Ensembl annotation (rsem-calculate-expression --bowtie2 --estimate-rspd --append-names --output-genome-bam --sort-bam-by-coordinate). Differentially expressed genes were identified using EBSeq version 1.18.0 (Leng and Kendziorski, 2015).
genome build: mm10
Supplementary_files_format_and_content: text file with gene abundances and bigwig
|
| |
|
| Submission date |
Mar 14, 2018 |
| Last update date |
Sep 06, 2018 |
| Contact name |
Mark F Sabbagh |
| E-mail(s) |
msabbag2@jhmi.edu
|
| Organization name |
Johns Hopkins University School of Medicine
|
| Department |
Molecular Biology and Genetics
|
| Lab |
Jeremy Nathans
|
| Street address |
725 North Wolfe Street
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE111839 |
Transcriptional and Epigenomic Landscapes of CNS and non-CNS Vascular Endothelial Cells |
|
| Relations |
| BioSample |
SAMN08712795 |
| SRA |
SRX3791716 |
