Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

27 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Sequences that influence mRNA trans splicing and polyadenylation in Trypanosoma brucei

ABSTRACT: Trypanosoma brucei library consisting of a pool of reporters whose 14Ts polypyrimidine tract is replaced with 11 random nucleotides. The library is treated with puromycin at a concentration of either 0.2ug/ml, 0.4ug/ml or 1ug/ml. The reporters are recovered and PCR amplicons targeting the random sequences identified by HTS. The results are paired reads, where the suffixes _1 and _2 are reads 1 and 2 respectively. Also included are sequencing results from the plasmid library.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Trypanosoma brucei brucei

SUBMITTER: Christine Clayton

PROVIDER: E-MTAB-11647 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Sequences that influence mRNA trans splicing and polyadenylation in trypanosoma brucei.

Project description:Trypanosoma brucei library consisting of a pool of reporters with the 14Ts polypyrimidine tract replaced with 11 random nucleotides. The library is treated with 0.2ug/ml of puromycin, then survivors are grown in 1ug/ml puromycin. The reporters are recovered from the untreated and the 2 two treatment groups and PCR amplicons targeting the the random sequences identified by HTS. The drug treated samples were analysed in triplicates and untreated in duplicates. The results are paired reads, file names ending _1 are one strand and _2 are the other strand.

2022-04-29 | E-MTAB-11628 | biostudies-arrayexpress

RNAseq of Trypanosoma brucei 427 bloodstream forms after depleting RBSR1 using RNAi.

Project description:RBSR1-CTAP expressing cells were transfected with RNAi targeting RBSR1. 3 independent clones were used and RNAi was induced for 24 hours with 100ng/ml tetracycline. PolyA enriched samples are paired-end reads, file names ending _1 are one strand and _2 are the other strand. rRNA depleted sample are single end reads.

2022-04-29 | E-MTAB-11627 | biostudies-arrayexpress

RNAseq of Trypanosoma brucei 427 bloodstream forms after depleting RBSR2 using RNAi

Project description:RBSR2-TAP expressing cells were transfected with RNAi targeting RBSR2. 3 independent clones were used and RNAi was induced for 24 hours with 100ng/ml tetracycline. Cell lines expressing RBSR2-CTAP with no RNAi construct were used as controls. These are actually paired-end reads, file names ending _1 are one strand and _2 are the other strand.

2022-04-29 | E-MTAB-11648 | biostudies-arrayexpress

Quantifying propagation of DNA methylation and hydroxymethylation with iDEMS

Project description:Analysis of nucleosides (dC, dG, 5mdC and 5hmdC) using mass spectrometry and digested DNA samples. Experimental data description: - 12 h restoration (corresponding to EDFig2 b, EDFig5 b,c,h), E14 mESCs, labelled samples and followed for 12h, total DNA and stranded, 4 biological replicates (rep1, rep2, rep3 and rep4) and 2 technical replicates (_1, _2). - KST061-62-63 (corresponding to Fig1 e-f, Fig2 b-g, Fig5 b-e, EDFig5 a,f), E14 mESCs, labelled samples and followed for 8h, total DNA and stranded, 3 biological replicates (KST061, KST062 and KST063) and 2 technical replicates (_1, _2). - KST73-74-75 (corresponding to EDFig5 d,e,g), NIH3T3 cell line, labelled samples and followed for 8h, total DNA and stranded, 3 biological replicates (KST073, KST074 and KST075) and 2 technical replicates (_1, _2). - KST76-77-78 (corresponding to Fig6 b-e, EDFig6 b-c), E14 mESCs, ChIP mass spectrometry samples for several histone modifications antibodies, total DNA and ChIP DNA, 3 biological replicates (KST076, KST077 and KST078) and 2 technical replicates (_1, _2). - KST035 (corresponding to Fig1 c-d), E14 mESCs, DNA abundance and methylation levels, 2 technical replicates (_1, _2) - KST045-46-47 (corresponding to Fig3 b, EDFig3 a), E14 mESCs, labelled early S phase samples and followed for 8h, total DNA and EdU+ pull down, 3 biological replicates (KST045, KST046 and KST047) and 2 technical replicates (_1, _2). - KST050-51-52 (corresponding to Fig3 c, EDFig3 b), E14 mESCs, labelled late S phase samples and followed for 8h, total DNA and EdU+ pull down, 3 biological replicates (KST050, KST051 and KST052) and 2 technical replicates (_1, _2). - KST056-57-60 (corresponding to EDFig4 a), E14 mESCs, cell cycle phases sorted using EdU labelling, 3 biological replicates (KST056, KST057 and KST060) and 2 technical replicates (_1, _2). Standard curve data used for quantification are named as MM1-MM10, 2 technical replicates (_1, _2).

2022-10-21 | MSV000090568 | MassIVE

Dino-dependent gene expression signature in MEFs

Project description:Genetically modified Dino mice were generated with loxP sites flanking the mouse Dino gene. We set out to identify the set of genes regulated by Dino in DNA damaged mouse embryonic fibroblasts using 3' sequencing. Early passage Dino+/+ or Dino loxP/loxP MEFs were treated with 0.2ug/mL doxorubicin prior to addition of Trizol and RNA isolation.

2016-09-26 | GSE76419 | GEO

High-throughput sequencing analysis of the relative frequency of Contacts between Sister Copies emerging from a replication fork in Vibrio cholerae

Project description:Paired-end deep-sequencing was used to determine in parallel the status and position of sister-chromatid contact (SC2) reporters and/or site-specific recombinase (SSR) activity reporters inserted at random positions in a library of cells. The SC2 reporters are short recombination cassettes for a topology-independent site-specific recombinase (Cre or Xer). The SSR-activity reporters are long recombination cassettes. The SC2 reporter cassettes are composed of two directly-repeated recombination sites separated by a DNA segment too short to permit their excision by intramolecular recombination. The SSR-activity cassettes are composed of two directly-repeated recombination sites separated by a DNA segment long enough to permit their excision by intramolecular recombination. The assays start with the engineering of a cell line with a conditional expression allele for Cre or Xer and the creation of a library of cells harbouring a cognate SC2 or SSR-activity reporter at different genomic positions. Production of the recombinase was induced for different lengths of time during cell growth and/or at specific stages of the cell cycle. The position of the SC2 reporter harboured by each cell and the recombination status of the recombination cassette it contains are then determined by high-throughput paired-end sequencing.

2020-07-07 | E-MTAB-8946 | biostudies-arrayexpress

Chemosensitivity prediciton in esophageal cancer cell line using cDNA microarray

Project description:A total of 20 KYSE human esophageal squamous cell carcinoma cell lines (KYSE-30, -140, -150, -170, -180, -200, -220, -350, -410, -450, -510, -520, -590, -770, -850, -890, -1170, -1190, -1250, and -2270) and a non-cancerous esophageal epithelial cell (HEEC-1)were kindly provided by Dr. Y. Shimada (Kyoto University, Kyoto, Japan). The KYSE cell lines were cultured in RPMI 1640 medium (Life Technologies, Inc., Grand Island, NY) containing 10% heat-inactivated fetal bovine serum (FBS; BioWhittaker, Verviers, Belgium) in a humidified atmosphere of 5% CO2 and maintained in continuous exponential growth by passage every 3 days. HEEC-1 cells were cultured in Keratinocyte SFM medium with growth supplement containing 2.5 mg EGF and 25 mg bovine pituitary extract in 500 mL liquid basal medium (GIBCO BRL, Rockville, MD) and expanded by passage twice in a week. The exponentially growing cultured cells (2 x 10^6) were collected after two-washings with PBS. Total RNA was prepared from the frozen cell pellets using QIAGEN RNeasy mini kit (QIAGEN, Inc., Valencia, CA), and mRNA was purified using MACS mRNA Isolation kit (Miltenyi Biotec, Bergisch Gladbach, Germany) according to the supplier’s protocols. RIKEN human 21K array containing 20,784 clones with positive and negative controls was used to analyze gene expression of 20 KYSE esophageal cancer cell lines using HEEC-1 as reference. The target DNAs used to construct human 21 K array were the glycerol stock of cDNA clones purchased from ResGen (Invitrogen Corporation, Carlsbad, CA)). One-microgram poly(A) RNAs from KYSE cells and the reference cells were labeled with Cy3-dCTP and Cy5-dCTP, respectively, by random-primed reverse transcription. Arrays were laser-scanned using ScanArray 5000TM confocal laser scanner (GSI Lumonics, Billerica, MA), and the images were analyzed using ScanAlyzeTM (Stanford University). All experiments were performed in duplicate (_1 & _2). Keywords: parallel sample

2005-12-31 | GSE2454 | GEO

DNA-seq of a library of mutated minigene reporters.

Project description:DNA-seq of a library of mutated minigene reporters.

| PRJEB23552 | ENA

Optimized reporters for multiplexed detection of transcription factor activity

Project description:A library of 35,500 reporters was designed for 86 TFs in order to identify optimized TF reporters. The library was transfected into diverse cell types and probed upon almost 100 TF perturbations. To compare TF activities with TF abundances, RNA-seq data was used. For mNPCs, mESCs and HepG2 cells, RNA-seq data was generated in house. For thee TF knockdowns in HepG2 cells, RNA-seq data was generated to validate the experimental design.

2024-05-26 | GSE267969 | GEO

seawater metagenome

Project description:ABIOP+_1

| PRJNA777059 | ENA