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TranscriptomicsHigh throughput sequencing of B.henselae infected and non-infected I. ricinus salivary glands
In order to select genes that are differentially expressed in salivary glands during Ixodes ricinus infection by Bartonella henselae we compare the transcriptome of infected and non-infected salivary glands I. ricinus from a pathogen free colony were infected -or not- with B. henselae at the larval ...
ORGANISM(S): Ixodes ricinus 
2015-04-02 | E-GEOD-56746 | biostudies-arrayexpress
TranscriptomicsExperimental identification of small non-coding RNAs in the model marine bacterium Ruegeria pomeroyi DSS-3
In oligotrophic ocean waters where bacteria are often subjected to chronic nutrient limitation, community transcriptome sequencing has pointed to the presence of highly abundant small RNAs (sRNAs). The role of sRNAs in regulating response to nutrient stress was investigated in a model heterotrophic ...
ORGANISM(S): Ruegeria pomeroyi DSS-3 
2016-02-27 | E-MTAB-4468 | biostudies-arrayexpress
TranscriptomicsSignaling Pathways Deferentially Affect RNA Polymerase II Initiation, Pausing, and Elongation in Human Cells: Estrogen dependent signaling in MCF-7 cells
We used Global Run-on and Sequencing (GRO-seq) to measure the rate of transcription elongation by RNA polymerase II (Pol II) following gene activation. We observed that Pol II elongation rates can vary as much as 4-fold at different genomic loci and in response to two distinct cellular signaling pa...
ORGANISM(S): Homo sapiens 
2013-04-10 | E-GEOD-41324 | biostudies-arrayexpress
TranscriptomicsThe plasmid-borne Type II Secretion System of Escherichia coli O157:H7 isolate Sakai mediates adherence to spinach. Experiment 1: screening E coli O157:H7 Sakai genes for adherence to spinach roots.
Food-borne illness arising for Shiga-toxigenic Escherichia coli is often linked to consumption of fruit and vegetables as the bacteria have the ability to interact with plants and use them as alternative or secondary hosts. Attachment of the bacteria to host tissue is one of the first steps in the ...
ORGANISM(S): Escherichia coli 
2019-11-20 | E-MTAB-5923 | biostudies-arrayexpress
TranscriptomicsDerivation and characterization of Dicer and microRNA deficient human cells
We have used genome editing to generate inactivating deletion mutations in all three copies of the dicer (hdcr) gene present in the human cell line 293T. As previously shown in murine ES cells lacking Dicer function, hDcr-deficient 293T cells are severely impaired for the production of mature microR...
ORGANISM(S): Homo sapiens 
2014-04-17 | E-GEOD-56836 | biostudies-arrayexpress
ProteomicsComparison of Lung Cancer Proteome Profiles 1: Label Free Quantification
The goal of this project is to compare label free quantification, chemical labeling with tandem mass tags, and data independent acquisition discovery proteomics approaches using lung squamous cell carcinomas and adjacent lung tissues.
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-27 | MSV000080685 | MassIVE
TranscriptomicsRNASeq of African green monkey (Vero) cells and human malignant glioblastoma multiforme (U251) cells infected at a multiplicity of infection (MOI) of 3 with the Asian/American Zika virus (ZIKV), PE243; and the African ZIKV strain, Dak84
Vero and U251 cells were infected with the Asian/American ZIKV (PE243) and the African ZIKV (Dak84) at MOI:3 to assess the viral transcriptome in two cell lines. Samples were harvested at 24 hours post-infection (h p.i.) by flash-freezing, without cycloheximide pre-treatment. Ribosomal RNA was remov...
ORGANISM(S): Chlorocebus sabaeus 
2024-09-04 | E-MTAB-12967 | biostudies-arrayexpress
TranscriptomicsRiboSeq of African green monkey (Vero) cells and human malignant glioblastoma multiforme (U251) cells infected at a multiplicity of infection (MOI) of 3 with the Asian/American Zika virus (ZIKV), PE243; and the African ZIKV strain, Dak84
Vero and U251 cells were infected with the Asian/American ZIKV (PE243) and the African ZIKV (Dak84) at MOI:3 to assess the viral transcriptome in two cell lines. Samples were harvested at 24 hours post-infection (h p.i.) by flash-freezing, without cycloheximide pre-treatment. RNase I treatment was ...
ORGANISM(S): Homo sapiens 
2024-09-04 | E-MTAB-12970 | biostudies-arrayexpress
TranscriptomicsRNASeq of African green monkey (Vero) cells infected at a multiplicity of infection (MOI) of 3 with different Zika virus (ZIKV) mutants (American WT, African-like, uORF1-KO and uORF2-PTC1) generated by reverse genetics
Vero cells were infected with the different Zika virus (ZIKV) mutants (American WT, African-like, uORF1-KO and uORF2-PTC1) generated by reverse genetics at MOI:3 to assess their viral transcriptome. Samples were harvested at 24 hours post-infection (h p.i.) by flash-freezing, without cycloheximide p...
ORGANISM(S): Chlorocebus sabaeus 
2024-09-04 | E-MTAB-12968 | biostudies-arrayexpress
TranscriptomicsRiboSeq of African green monkey (Vero) cells infected at a multiplicity of infection (MOI) of 3 with different Zika virus (ZIKV) mutants (American WT, African-like, uORF1-KO and uORF2-PTC1) generated by reverse genetics
Vero cells were infected with the different Zika virus (ZIKV) mutants (American WT, African-like, uORF1-KO and uORF2-PTC1) generated by reverse genetics at MOI:3 to assess their viral transcriptome. Samples were harvested at 24 hours post-infection (h p.i.) by flash-freezing, without cycloheximide p...
ORGANISM(S): Chlorocebus sabaeus 
2024-09-04 | E-MTAB-12969 | biostudies-arrayexpress
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