Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

51 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Human Lung Adenocarcinoma Cells: control vs. mAb NJ001 treated

ABSTRACT: Transcriptional profiling of human lung adenocarcinoma cells comparing control untreated SPC-A1 cells with SPC-A1 cells treated with 300 M-BM-5g/ml mAb NJ001 for 36h Two-condition experiment, SPC-A1 vs. NJ001-SPC-A1 cells. Biological replicates: 3 control, 3 treated, independently grown and harvested. One replicate per array.

ORGANISM(S): Homo sapiens

SUBMITTER: Shiyang Pan

PROVIDER: E-GEOD-59655 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Human Lung Adenocarcinoma Cells: control vs. mAb NJ001 treated

Project description:Transcriptional profiling of human lung adenocarcinoma cells comparing control untreated SPC-A1 cells with SPC-A1 cells treated with 300 µg/ml mAb NJ001 for 36h

2014-08-01 | GSE59655 | GEO

Structure of the human signal peptidase complex

Project description:The ER-resident signal peptidase complex (SPC) is an essential membrane protein complex involved in the maturation of soluble and type-I transmembrane proteins destined to the secretory pathway. As a part of the ER translocon machinery, the SPC removes signal peptides (SPs) from the N-termini of many proteins such as hormones, antibodies, or secretory enzymes1,2. To accomplish this task, the SPC must process a large variety of SPs with an exquisite specificity. Although the determinants of SP recognition have been established empirically3, the molecular details of SP recognition and removal remain elusive. Here, we show that the human SPC exists in two functional paralogs with distinct proteolytic subunits. We determined the structures and posttranslational modifications of both paralogs using electron cryo-microscopy and structural proteomics. The respective proteolytic subunits SEC11A and SEC11C adopt a conserved signal peptidase (SPase) fold with their active sites facing a prominent transmembrane window, which is collectively formed by the transmembrane domains of all SPC subunits. Characteristic, charged regions on both sides of this window locally thin the membrane by approximately 40% compared to the exterior. The data suggest a mechanistic model for SPC specificity and the transfer of SPs from the Sec61 translocation channel to the SPC.

2021-07-05 | PXD022002 | Pride

Transcription profiling by array of PaTu II cells differentially treated with sphingosylphosphorylcholine (SPC)

Project description:Sphingosylphosphorylcholine (SPC) is a bioactive lipid with multiple biological roles including the regulation of differentiation in embryonic and cancer cells. PaTu II pancreatic cancer cells were incubated with 15 μM SPC in serum-free Medium for 2 h or left untreated. Duplicates of 3 independent experiments were analyzed.

2015-02-27 | E-MTAB-3363 | biostudies-arrayexpress

Chemoproteomic Target Identification for SP100030 and SPC-839

Project description:SP100030 and SPC-839 are structurally distinct molecules sharing similar cellular activity profiles. We used click chemistry-mediated chemoproteomics to identfy candidate mechanistic targets for these small molecules.

2024-03-05 | PXD041193 | Pride

MAGE-A1 Promotes Proliferation, Migration and Invasion of Human Melanoma Cells through RNA-SEQ Analysis via Affecting C-JUN-IL8-ARHGAP29 Network

Project description:To define the role of MAGE-A1 in melanoma growth and metastasis, we performed RNA-seq analysis on MAGE-A1 overexpression (OE) and knockdown (KD) models in A375 human melanoma cell line. Our results revealed that overexpression of MAGE-A1 dramatically promoted proliferation, migration, and invasion of human melanoma cells in vitro and down-regulated of MAGE-A1 inhibited tumor cell proliferation and invasion. Furthermore, MAGE-A1 exerts its tumor promoting activity via activating including ERK-MAPK signaling pathway by RNA-seq analysis. mRNA profiles of MAGE-A1 over expression (OE), knockdown (KD), pcDNA-vector control, and pRNAT-scramble control in A375 cell line were generated using Ion torrent

2016-01-04 | E-GEOD-66859 | biostudies-arrayexpress

A function for the hnRNP A1/A2 proteins in transcription elongation

Project description:The hnRNP A1 and A2 proteins regulate processes such as alternative pre-mRNA splicing and mRNA stability. Here, we report that a reduction in the levels of hnRNP A1 and A2 by RNA interference or their cytoplasmic retention by osmotic stress drastically increases the transcription of a reporter gene. Based on previous work, we propose that this effect may be linked to a decrease in the activity of the transcription elongation factor P-TEFb. Consistent with this hypothesis, the transcription of the reporter gene was stimulated when the catalytic component of P-TEFb, CDK9, was inhibited with DRB. While low levels of A1/A2 stimulated the association of RNA polymerase II with the reporter gene, they also increased the association of CDK9 with the repressor 7SK RNA, and compromised the recovery of promoter-distal transcription on the Kitlg gene after the release of pausing. Transcriptome analysis revealed that more than 50% of the genes whose expression was affected by the siRNA-mediated depletion of A1/A2 were also affected by DRB. RNA polymerase II-chromatin immunoprecipitation assays on DRB-treated and A1/A2-depleted cells identified a common set of repressed genes displaying increased occupancy of polymerases at promoter-proximal locations, consistent with pausing. Overall, our results suggest that lowering the levels of hnRNP A1/A2 elicits defective transcription elongation on a fraction of P-TEFb-dependent genes, hence favoring the transcription of P-TEFb-independent genes. two treatements and one control

2015-04-07 | E-GEOD-67617 | biostudies-arrayexpress

hnRNP A1 iCLIP

Project description:This experiment identifies hnRNP A1 binding sites transcriptome-wide in Hela cells. HeLa cells with inducible expression of T7-tagged hnRNP A1 were grown to approximately 90% confluence and then subject to iCLIP analysis (following the protocol from Huppertz et al. 2014 (iCLIP: protein-RNA interactions at nucleotide resolution)). The iCLIP library was sequenced using Illumina's HighSeq 1500

2016-06-23 | E-MTAB-3612 | biostudies-arrayexpress

Microarrays of macrophages infected with smooth or rough Brucella suis

Project description:The macrophage-Brucella interaction is critical for the establishment of a chronic Brucella infection. Smooth virulent B. suis strain 1330 (S1330) prevents macrophage cell death. However, rough attenuated B. suis strain VTRS1 induces strong macrophage cell death. To further investigate the mechanism of VTRS1-induced macrophage cell death, microarrays were used to analyze temporal transcriptional responses of murine macrophage-like J774. A1 cells infected with S1330 or VTRS1. Murine J774.A1 macrophages were plated in T75 at 8 x 10^6 cells per flask one day prior to infection, and then infected with B. suis S1330 or VTRS1 at a MOI of 200:1. Total RNAs were isolated by TRIzol and further purified using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) at 0, 1, 2, 4, 8, 24, and 48 h post infection. The RNA samples were stored at -80 ºC until an Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA) was used to assess the concentrations and quality of RNA samples. Total RNA (20 µg) per sample was used for hybridization with Affymetrix mouse GeneChip 430 2.0 array. Preparation of cDNA, hybridization, quality controls and scanning of the GeneChip 430 2.0 arrays were performed according to the manufacturer's protocol (Affymetrix, Santa Clara, CA) .

2011-06-24 | E-GEOD-21117 | biostudies-arrayexpress

Expression analysis of Sphingomonas. sp A1 AlgO-deficient mutant grown in 0.5% alginate medium or 0.5% yeast extract medium

Project description:Investigation of whole genome gene expression level changes in Sphingomonas. sp A1 AlgO-deficient mutant grown on alginate compared with that on yeast extract AlgO is a possble transcriptional factor described in J. Bacteriol. (2000) 182(14):3998-4004 by Momma K, Okamoto M, Mishima Y, Mori S, Hashimoto W, and Murata K. A two chip study using total RNA recovered from two cultures of Sphingomonas. sp A1 AlgO-deficient mutant grown in 0.5% alginate medium and 0.5% yeast extract medium. Each chip measures the expression level of genes from Sphingomonas. sp A1.

2014-01-28 | E-GEOD-54410 | biostudies-arrayexpress

Expression analysis of motile strain of Sphingomonas sp. A1

Project description:Investigation of whole genome gene expression level in motile strain of Sphingomonas. sp A1 All flagellar genes in motile strain of Sphingomonas. sp A1 are highly transcribed. A two chip study using total RNA recovered from wild-type and motile strains of Sphingomonas. sp A1 grown in 0.5% alginate medium.

2014-11-01 | E-GEOD-62901 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data