|
Status |
Public on Apr 16, 2024 |
Title |
N134_RHB_met_3_S9 |
Sample type |
SRA |
|
|
Source name |
Core1339
|
Organism |
Mus musculus |
Characteristics |
tissue: N134-RHAMMB liver met 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
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|
|
Submission date |
Apr 08, 2022 |
Last update date |
Apr 16, 2024 |
Contact name |
Nancy Du |
E-mail(s) |
nad2012@med.cornell.edu
|
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 |
|
Relations |
BioSample |
SAMN27479437 |
SRA |
SRX14787641 |