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Sample GSM2800776 Query DataSets for GSM2800776
Status Public on Feb 14, 2018
Title E9.5 Pitx1 KO Rep2
Sample type SRA
 
Source name Hindlimb field and associated trunk
Organism Mus musculus
Characteristics tissue: Hindlimb field and associated trunk
strain: C57BL/6
developmental stage: E9.5
genotype: Pitx1 KO
Extracted molecule total RNA
Extraction protocol Hindlimbs were collected and total RNA was isolated using the mirVana RNA Isolation Kit (ThermoFisher Scientific).
Libraries were constructed with TruSeq Stranded mRNA Sample Prep Kit for Illumina and sequenced on the Illumina NextSeq platform.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Sequenced libraries were evaluated and trimmed with FastQC.
Sequenced reads were aligned to mm9 using Tophat2 on the Galaxy platform
Cuffdiff was used to generate qualified RPKM and to identify differentially expressed genes and transcripts
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and log2(fold_change)
 
Submission date Sep 29, 2017
Last update date May 15, 2019
Contact name Marc Wein
E-mail(s) mnwein@mgh.harvard.edu
Organization name Massachusetts General Hospital
Street address 55 Fruit Street
City Boston
State/province MA
ZIP/Postal code 02114
Country USA
 
Platform ID GPL19057
Series (2)
GSE104459 PITX1 Promotes Chondrogenesis and Myogenesis in Mouse Hindlimbs Through Conserved Regulatory Targets [RNA-Seq]
GSE104460 PITX1 Promotes Chondrogenesis and Myogenesis in Mouse Hindlimbs Through Conserved Regulatory Targets
Relations
BioSample SAMN07722623
SRA SRX3234611

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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