|
| Status |
Public on Mar 27, 2024 |
| Title |
Caco-2_pCDNA_3_1-Siglec12_2_S78 |
| Sample type |
SRA |
| |
|
| Source name |
caco-2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: caco-2
treatment: SIGLEC12
|
| 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 |
SAMN40559132 |
| SRA |
SRX24005961 |
