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Sample GSM5975224 Query DataSets for GSM5975224
Status Public on Sep 02, 2022
Title mouse YAP1-MAML2-v2 rep2
Sample type SRA
 
Source name tissue
Organism Mus musculus
Characteristics tumor: YAP1-MAML2-v2
cell type: DF1
source region: extra axial
Treatment protocol untreated
Growth protocol DF1 cells were grown in DMEM (11995-073), 10% FBS, 1% PenStrep and transfected with RCAS-YAP1-MAML2-v2 or RCAS-NLS-2SA-YAP1. 1-2 weeks post-transfection, transfected DF1 cells were injected into the subarachnoid space of p0-p3 Nestin/tv-a Cdkn2a null mice. Mice were observed for signs of tumor growth and euthanized at appropriate times. Tumors were flash frozen in liquid nitrogen, ground up using a motor and pestor (on dry ice) and RNA was extracted using the Qiagen RNAeasy Mini kit
Extracted molecule total RNA
Extraction protocol RNA-seq libraries were prepared from total RNA using the TruSeq Stranded mRNA kit (Illumina, Inc., San Diego, CA, USA). Library size distribution was validated using an Agilent 4200 TapeStation (Agilent Technologies, Santa Clara, CA, USA).  Additional library QC, blending of pooled indexed libraries, and cluster optimization was performed using Life Technologies’ Invitrogen Qubit® 2.0 Fluorometer (Life Technologies-Invitrogen, Carlsbad, CA, USA).
RNA-seq libraries were pooled (70-plex) and clustered onto an S1 flow cell.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description mouse YAP1-MAML2-v2 rep2
Data processing Sequencing was performed using an Illumina NovaSeq 6000 employing a paired-end, 50 base read length (PE50) sequencing strategy.
RNA-seq reads were aligned to the UCSC mm10 assembly using STAR2 and counted for gene associations against the UCSC genes database with HTSeq
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw values for each Sample.
 
Submission date Mar 28, 2022
Last update date Sep 04, 2022
Contact name Sonali Arora
E-mail(s) sarora@fredhutch.org
Organization name FHCRC
Street address 1100 Fairview Ave N,
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platform ID GPL24247
Series (2)
GSE199562 Both YAP1-MAML2 and constitutively active YAP1 drive the formation of tumors that resemble NF2 mutant meningiomas in mice [mouse]
GSE199566 Both YAP1-MAML2 and constitutively active YAP1 drive the formation of tumors that resemble NF2 mutant meningiomas in mice
Relations
BioSample SAMN27022530
SRA SRX14636479

Supplementary file Size Download File type/resource
GSM5975224_32063_S40.txt.gz 89.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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