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Sample GSM4160856 Query DataSets for GSM4160856
Status Public on Jun 22, 2021
Title Elastase_Day14_Replicate_3 [day14-3_S47_L006]
Sample type SRA
 
Source name Elastase_Day14
Organism Mus musculus
Characteristics strain: C57BL/6J
genotype: wild type
tissue: lung
cell type: endothelial cells
culture status: freshly isolated from tissue
Treatment protocol All cell populations were purified via FACS. Purity mask was applied.
Extracted molecule total RNA
Extraction protocol At least 100 ng of total RNA from both freshly harvested and cultured cells was isolated (phenol-chloroform separation of TRIzol LS) and purified using Qiagen’s RNeasy Mini Kit.
RNA library preps were prepared and multiplexed using Illumina’s TruSeq RNA Library Preparation Kit v2 (non-stranded and poly-A selection) and 10 nM of cDNA was used as input for high-throughput sequencing via Illumina’s HiSeq 4000 producing 51 bp paired-end reads.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description day14-3_S47_L006
Data processing Base calling and sequencing reads de-multiplexing were performed using bcl2fastq v2.17.
Sequencing reads were checked for quality (FastQC v0.11.5), and trimmed/filtered using Trimmomatic v0.36.
Read alignment to the transcriptome sequence reference of the UCSC mm10 genome build were performed using TopHat2 v2.1.0.
Gene counts were quantified using the Python package HTSeq (v0.11.1).
Transcript abundance measures (FPKM values) were quantified using Cufflinks (v2.2.1).
Genome_build: mm10
Supplementary_files_format_and_content: Single tab-delimited data-matrix with GENE_ID, GENE_DESCRIPTION, and SAMPLE_NAMES. All numerical inputs represent FPKM values.
 
Submission date Nov 14, 2019
Last update date Jun 22, 2021
Contact name Balvir Kunar, Jr.
E-mail(s) bak2010@med.cornell.edu
Organization name Weill Cornell Medical College
Department Regenerative Medicine; Physiology, Biophysics, & Systems Biology
Lab Shahin Rafii, M.D.
Street address 1300 York Ave
City New York City
State/province New York
ZIP/Postal code 10065
Country USA
 
Platform ID GPL21103
Series (1)
GSE140413 Reversal of emphysema by restoration of pulmonary endothelial cells
Relations
BioSample SAMN13285963
SRA SRX7141540

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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