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Sample GSM7448511 Query DataSets for GSM7448511
Status Public on Aug 29, 2023
Title BM050
Sample type SRA
 
Source name uveal
Organism Homo sapiens
Characteristics cell line: Patient sample
pertubation/treatment: FFPE_Liver Mets
sample origin: patient samples_FFPE
Extracted molecule total RNA
Extraction protocol For Bulk RANseq We used poly-A pull-down to enrich mRNAs from total RNA samples, then proceed with library construction using Illumina TruSeq chemistry. Libraries were then sequenced using Illumina NovaSeq 6000 at Columbia Genome Center.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description Bulk RNA
RNAseq_normalized_counts_human.tsv
RNAseq_raw_counts_human.csv
Data processing Samples were multiplexed in each lane, which yielded targeted number of paired-end 100bp reads for each sample. We used RTA (Illumina) for base calling and bcl2fastq2 (v 2.19) for converting BCL to fastq conversion, coupled with adaptor trimming.
We performed a pseudoalignment to a kallisto index created from Human transcriptomes GRCh38 using kallisto (0.44.0).
Genome_build: GRCh38
 
Submission date Jun 05, 2023
Last update date Aug 29, 2023
Contact name Meri Rogava
E-mail(s) mr4020@cumc.columbia.edu
Organization name Columbia University
Department Hematology Oncology
Lab Izar Lab
Street address 650 W 168th St, New York, NY 10032
City New York
State/province New York
ZIP/Postal code 10032
Country USA
 
Platform ID GPL24676
Series (1)
GSE188391 A genetic-metabolic axis for metastatic liver organotropism

Supplementary data files not provided
Raw data not provided for this record
Processed data are available on Series record

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