2024-06-29
ENA first public
ERC000011
ENA-CHECKLIST
SAMEA110464131
External Id
INSERM U1242 OSS (Oncogenesis, Stress and Signaling) - Universite de Rennes1
INSDC center name
2022-08-04T14:49:49Z
INSDC last update
public
INSDC status
ERS12562159
SRA accession
E-MTAB-12030:LINC_2
Submitter Id
ArrayExpress
broker name
HuCC-T1
cell_line
human
common name
Protocols: Mice were anesthetized by intra-peritoneal route with a mixture of ketamine and xylazine. Opening of the animals was performed by a laparotomy and then a thoracotomy to reveal the heart. Blood was collected via the right atrium and tumors were removed with a scalpel, cut in two pieces and snap-frozen in liquid nitrogen. Xenograft tumors were then stored at -80°C until tissue homogenization and RNA extraction. Xenograft tumors were cut into smaller pieces in a Petri dish placed on ice and transferred into 2mL tubes containing 2.8mm ceramic beads (P000911-LYSK0-A, Bertin Corp) filled with 1 ml Qiazol. Homogenization of the tumors was performed using the Precellys 24 homogenizer (5500 rpm, 20s x 2, pause: 20s). Then, the homogenate was transferred to new tubes and subjected to RNA extraction using the RNeasy Lipid Tissue Mini Kit (74804, Qiagen), according to the instructions by the manufacturer. The library construction method and sequencing process are carried out according to the following steps: 1. Take a certain amount of total RNA samples, and use oligo dT beads to enrich mRNA with poly A tail; 2. mRNA molecules were fragmented into small pieces; 3. The fragmented mRNA was synthesized into first strand cDNA using random primers; 4. The second strand cDNA was synthesized with dUTP instead of dTTP; 5. The synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments; 6. Digest the U-labeled second-strand template with Uracil-DNA-Glycosylase (UDG) and perform PCR amplification; 7. Library quality control; 8. Library circularization; 9. The library was amplified to make DNA nanoball (DNB);
description
cholangiocarcinoma
disease
LINC313 overexpression
genotype
human HuCC-T1 cells injected in mice to induce xenograft tumors
growth condition
not applicable
isolate
Homo sapiens
organism
Homo sapiens
organism
liver
organism part
xenograft tumor
sampling site
Homo sapiens
scientific_name
LINC_2
title
human HuCC-T1 cell line grafted into mice
xenograft