|
Status |
Public on Aug 29, 2023 |
Title |
BM047 |
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.
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|
|
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
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|
|
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 |
|