|
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 |