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Sample GSM8157285 Query DataSets for GSM8157285
Status Public on Mar 27, 2024
Title Caco-2_pCDNA_3_1-Empty_Vector_4_S76
Sample type SRA
 
Source name caco-2
Organism Homo sapiens
Characteristics cell line: caco-2
treatment: Control
Extracted molecule total RNA
Extraction protocol RNA extraction was done using a commertial kit as per manufacturer’s protocol
RNA sequencing libraries were generated using the Illumina TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions, except modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 100 basepair (bp) Paired End (PE100) to a depth of approximately 25-40 million reads per sample on an Illumina NovaSeq 6000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing RNASeq data was processed using kallisto (version 0.45.0). Gene-level TPM values and gene annotations were computed using a custom Perl Script.
Assembly: Homo sapiens genome build hsGRCh38_94
Supplementary files format and content: tab-delimited text file includes log2 of TPM values
 
Submission date Mar 20, 2024
Last update date Mar 27, 2024
Contact name Pradipta Ghosh
E-mail(s) prghosh@ucsd.edu
Organization name University of California San Diego
Department Departments of Medicine and Cellular and Molecular Medicine
Street address 9500 Gilman Drive (MC 0651)
City La Jolla, CA 92093
State/province CA
ZIP/Postal code 92093
Country USA
 
Platform ID GPL24676
Series (2)
GSE262085 Human-Specific Elimination of Epithelial Siglec-XII Suppresses the Risk of CRC Initiation and Progression [CACO]
GSE262088 Human-Specific Elimination of Epithelial Siglec-XII Suppresses the Risk of CRC Initiation and Progression
Relations
BioSample SAMN40559134
SRA SRX24005959

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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