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Sample GSM6035208 Query DataSets for GSM6035208
Status Public on Apr 16, 2024
Title N134_SC_1_S1
Sample type SRA
Source name Core1313
Organism Mus musculus
Characteristics tissue: N134 subcutaneous tumor
host strain: NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) mice
Treatment protocol S.C. tumors and liver metastases were harvested.
Growth protocol N134 or N134_RHAMMB (N134-RHB) cell lines were S.C. injected or intravenously injected via tail vein into NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) mice.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the miRNasy Mini Kit (Qiagen, 217004) and QIAshredder kit (Qiagen, 79654) according to the manufacturer’s protocol.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Data processing The samples were sequenced using Illumina NovaSeq 6000 sequencer with paired-end 50 bps reads. The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
The RNA reads were aligned and mapped to the GRCm38 human reference genome by STAR (Version2.5.2).
The transcriptome reconstruction was performed by Cufflinks (Version 2.1.1). The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include normalized abundance measurements(FPKM) at gene level for each samples
Submission date Apr 08, 2022
Last update date Apr 16, 2024
Contact name Nancy Du
Phone 2127467312
Organization name Weill Cornell Medicine
Street address 1300 York Ave
City New York
State/province New York
ZIP/Postal code 10065
Country USA
Platform ID GPL24247
Series (1)
GSE200497 RHAMMB promotes metastasis of pancreatic neuroendocrine tumor
BioSample SAMN27479445
SRA SRX14787633

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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