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Sample GSM3040854 Query DataSets for GSM3040854
Status Public on Sep 06, 2018
Title RNA-seq_P7_Lung_TotalTissue_R1
Sample type SRA
 
Source name P7 dissociated Lung
Organism Mus musculus
Characteristics strain/genotype: Tie2-GFP
age: P7
Sex: Male
tissue: Lung
cell-type: Whole tissue
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 SAMN08712769
SRA SRX3791727

Supplementary file Size Download File type/resource
GSM3040854_RNA-seq_P7_Lung_TotalTissue_R1_normalizedBigWig.bw 26.0 Mb (ftp)(http) BW
GSM3040854_RNA-seq_P7_Lung_TotalTissue_R1_transcriptAbundances.txt.gz 1.6 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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