characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2022-09-16T00:20:07Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2022-09-16T00:20:07Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA110646159
characteristics.characteristic: External Id
characteristics.text: Institute of Life Sciences, Bhubaneswar, Odisha 751023
characteristics.characteristic: INSDC center name
characteristics.text: 2022-09-16T00:20:07Z
characteristics.characteristic: INSDC first public
characteristics.text: 2022-09-16T00:20:07Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS12743867
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-12074:HT-29_Control_infected (Replicate-2)
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: HT-29
characteristics.characteristic: cell_line
characteristics.text: epithelial cell
characteristics.characteristic: cell_type
characteristics.text: human
characteristics.characteristic: common name
characteristics.text: Protocols: HT-29 control and IRGM knockdown cell line were generated using a lentivirus-based method. Briefly, 3X10 5 HEK293T cells were seeded in a 10 cm dish and allowed to adhere overnight. The next day, cells were transfected with 7.5 µg of transfer plasmid (Sigma # TRCN0000186772-X M_29383 (IRGM) or scramble shRNA, 2.6 µg pMD2.G, and, 4.8 µg of pCMVR 8.74 plasmids using CalPhos Mammalian Transfection Kit as per the manufacturer instructions (Takara # 631312). After 12h, media was changed with fresh medium and kept in a 5% CO 2 incubator at 37ºC. Lentivirus particle collected 48h of post media change used to transduce HT-29 cells. The stable cells were selected in 2µg of puromycin for two weeks and knockdown efficiency was determined using qRT-PCR using gene-specific primers. For infection, 3x10^6 HT-29 cells were seeded in a 60 mm dish and allowed to adhere overnight. The cells were infected with Salmonella typhimurium strain ST 1433 (MOI, 1:10) for 8h. Mock and Infected HT-29 cells were collected from 60mm dish RNA was extracted from HT29 cells(three biological replicates) using RNeasy mini kit (QIAGEN, #74104). The quality and quantity of total RNA was checked using agarose gel and Qubit 3.0 After assessing the quality of RNA, 800-900 ng of total RNA was subjected to NEBNext® ultra™ directional RNA library prep kit for Illumina® (#E7420) using NEBNextPoly(A) mRNA magnetic isolation module (NEB #E7490). The QC of the prepared library was performed using High-Sensitivity Tape Station Kit (Agilent 2200, 5067-5585 (reagents) #5067-5584 ( screen tapes)) for fragment length distribution and Qubit dsDNA HS assay kit (Invitrogen, Q32851) for quantifying the library
characteristics.characteristic: description
characteristics.text: colorectal adenocarcinoma
characteristics.characteristic: disease
characteristics.text: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
characteristics.characteristic: infect
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: colon
characteristics.characteristic: organism part
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: HT-29_Control_infected (Replicate-2)
characteristics.characteristic: title