Similar studies for GEO DataSets (Select 200073273) - GEO DataSets

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Items: 20

Select item 2000732731.

The binding specificity and regulatory effect of WT and redesigned Puf2p [CLIP-Seq]

(Submitter supplied) PUF proteins have become a leading scaffold for designing RNA-binding proteins to contact and control RNAs at will. We analyze the effects of that reengineering across the transcriptome in vivo for the first time. We show, by HITS-CLIP and PAR-CLIP, that S. cerevisiae Puf2p, a non-canonical PUF protein, binds more than 1000 mRNA targets. Puf2p binds multiple UAAU elements, unlike canonical PUF proteins. more...

Organism:: Saccharomyces cerevisiae

Type:: Other

Platform:: GPL13821
12 Samples

Download data: TXT

Series

Accession:: GSE73273

ID:: 200073273

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000732742.

The binding specificity and regulatory effect of WT and redesigned Puf2p

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by high throughput sequencing; Other

Platform:: GPL13821
23 Samples

Download data: TXT

Series

Accession:: GSE73274

ID:: 200073274

PubMed Full text in PMC Similar studies

Select item 2000732273.

The binding specificity and regulatory effect of WT and redesigned Puf2p [RNA-Seq]

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by high throughput sequencing

Platform:: GPL13821
11 Samples

Download data: TXT

Series

Accession:: GSE73227

ID:: 200073227

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000509974.

The evolutionary interplay between Puf RNA binding proteins and their RNA targets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Saccharomyces cerevisiae; Neurospora crassa; Neurospora crassa OR74A

Type:: Expression profiling by array

Platforms:: GPL14949 GPL10697
28 Samples

Download data: GPR

Series

Accession:: GSE50997

ID:: 200050997

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000509965.

Identification of RNAs associated with S. cerevisiae or N. crassa Puf3

(Submitter supplied) Affinity purification of S. cerevisiae or N. crassa Puf3 from S. cerevisiae cells and identification of associated RNAs by microarray

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by array

Platform:: GPL10697
9 Samples

Download data: GPR

Series

Accession:: GSE50996

ID:: 200050996

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000509956.

Gene expression profiling of Puf knockouts in N. crassa

(Submitter supplied) Gene expression profiling was performed to compare RNA abundances in mycelium of Puf knockout strains compared to that in mycelium of wild-type N. crassa

Organism:: Neurospora crassa; Neurospora crassa OR74A

Type:: Expression profiling by array

Platform:: GPL14949
19 Samples

Download data: GPR

Series

Accession:: GSE50995

ID:: 200050995

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000043937.

Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast

(Submitter supplied) Abstract: Genes encoding RNA-binding proteins are diverse and abundant in eukaryotic genomes. Although some have been shown to have roles in post-transcriptional regulation of the expression of specific genes, few of these proteins have been studied systematically. We have used an affinity tag to isolate each of the five members of the Puf family of RNA-binding proteins in Saccharomyces cerevisiae and DNA microarrays to comprehensively identify the associated mRNAs. more...

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by array

Platforms:: GPL3269 GPL3270 GPL3300
27 Samples

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Series

Accession:: GSE4393

ID:: 200004393

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000039698.

Puf3delta vs. wild type comparison

(Submitter supplied) Three independent experiments: S. cervisiae wild-type (BY4741) and Puf3 mutant cells were grown in minimal medium supplemented with 3% glycerol. Cells were harvested in mid-log phase by centrifugation and total RNA was prepared by hot-phenol extraction. cDNA was prepared with oligo-dT and using a mixture of amino-allyl dUTP and dNTPs, fluorescently labeled (Cy3= wild-type, Cy5 = mutant) and hybridize on S. more...

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by array

Platform:: GPL3300
3 Samples

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Series

Accession:: GSE3969

ID:: 200003969

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000039689.

Puf proteins, RNA co-immunopurification

(Submitter supplied) RNA-coimmunopurifications with TAP-tagged Puf proteins from Saccharomyces cereviseae. Untagged strain (BY4741) served as a control. Cells were grown to midlog phase and harvested by centrifugation. TAP-tagged Puf proteins were affinity purified from cell-free extracts with IgG sepharose and eluted with TEV protease. RNA was isolated from extract (=input)and from purified protein samples by phenol-chloroform extraction. more...

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by array

Platforms:: GPL3270 GPL3269 GPL3300
24 Samples

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Series

Accession:: GSE3968

ID:: 200003968

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20015245210.

Yeast three hybrid experiment

(Submitter supplied) Expanding the binding specificity for RNA recognition by a PUF domain

Organism:: Saccharomyces cerevisiae

Type:: Other

Platform:: GPL19756
9 Samples

Download data: TXT

Series

Accession:: GSE152452

ID:: 200152452

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20001027911.

Khd1p associated mRNAs

(Submitter supplied) RNA-coimmunopurifications with TAP-tagged Khd1 protein from Saccharomyces cereviseae. Untagged strain (BY4741) served as a control (Gerber et al., 2004). Cells were grown to midlog phase in rich media and harvested by centrifugation. TAP-tagged Khd1 was affinity purified from cell-free extracts with IgG sepharose and eluted with TEV protease. RNA was isolated from extract (=input) and from purified protein samples by phenol-chloroform extraction. more...

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by array

Platforms:: GPL6420 GPL6419 GPL6421
7 Samples

Download data: PDF

Series

Accession:: GSE10279

ID:: 200010279

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20000374112.

Sequence specific recognition of RNA hairpins by the SAM domain of Vts1

(Submitter supplied) Identifying transcripts that are associated with the post transcriptional regulator Vts1 in yeast by co-immuno precipitation. Keywords: RNA pulldown, Co-IP

Organism:: Saccharomyces cerevisiae

Type:: Other

Platforms:: GPL3230 GPL3229
4 Samples

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Series

Accession:: GSE3741

ID:: 200003741

Select item 20000010413.

total RNA from yra1-1 at 37C vs. Yra1 WT at 37C (yra1-1TS_v_Yra1WT)

(Submitter supplied) Comparison of cDNA from RNA of yra1-1 temperature-sensitive mutant to RNA from Yra1 wildtype strain both at the non-permissive temperature of 37C Keywords: repeat sample

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by array

Platform:: GPL220
6 Samples

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Series

Accession:: GSE104

ID:: 200000104

Select item 20000010314.

total RNA from mex67-6 at 37C vs. Mex67 WT at 37C (mex67-5TS_v_Mex67WT)

(Submitter supplied) Comparison of cDNA from RNA of mex67-5 temperature-sensitive mutant to RNA from Mex67 wildtype strain both at the non-permissive temperature of 37C Keywords: repeat sample

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by array

Platform:: GPL220
6 Samples

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Series

Accession:: GSE103

ID:: 200000103

Select item 20000010215.

zzYra1 co-IPed RNA vs. zzMex67 co-IPed RNA (zzYra1IP_v_zzMex67IP)

(Submitter supplied) Comparison of cDNA from RNA co-IPed with zzYra1 to cDNA from RNA co-IPed with zzMex67 Keywords: repeat sample

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by array

Platforms:: GPL220 GPL221
5 Samples

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Series

Accession:: GSE102

ID:: 200000102

Select item 20000010116.

zzYra1 co-IPed RNA vs. Total RNA (zzYra1IP_v_TotalRNA)

(Submitter supplied) Comparison of cDNA from RNA IPed with zzYra1 to that from total RNA; resulting analysis gives Yra1 binding level relative to total abundance for each mRNA Keywords: repeat sample

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by array

Platforms:: GPL220 GPL221
5 Samples

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Series

Accession:: GSE101

ID:: 200000101

Select item 20000010017.

zzMex67 co-IPed RNA vs. Total RNA (zzMex67IP_v_TotalRNA)

(Submitter supplied) Comparison of cDNA from RNA IPed with zzMex67 to that from total RNA; resulting analysis gives Mex67 binding level relative to total abundance for each mRNA Keywords: repeat sample

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by array

Platform:: GPL221
4 Samples

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Series

Accession:: GSE100

ID:: 200000100

Select item 20000009918.

zzYra1 co-IPed RNA vs. zz co-IPed RNA (zzYra1IP_v_zzIP)

(Submitter supplied) Comparison of cDNA from RNA IPed with zzYra1 to that from RNA co-IPed with zz tag alone (control IP) Keywords: equivalent probe

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by array

Platforms:: GPL220 GPL221
5 Samples

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Series

Accession:: GSE99

ID:: 200000099

Select item 20000009819.

zzMex67 co-IPed RNA vs. zz co-IPed RNA (zzMex67IP_v_zzIP)

(Submitter supplied) Comparison of cDNA from RNA IPed with zzMex67 to that from RNA co-IPed with zz tag alone (control IP) Keywords: repeat sample

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by array

Platforms:: GPL221 GPL220
4 Samples

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Series

Accession:: GSE98

ID:: 200000098

Select item 20007613620.

The genomic landscape of PUF binding in stem cells

(Submitter supplied) We determined the genomic landscape of FBF-1 and FBF-2 binding in germline stem cells using iCLIP, a method that allows identification of protein-RNA interactions at high resolution. We first developed reagents to explore the genomic binding landscapes of full-length FBF-1 and FBF-2 in vivo and then used our iCLIP data to test the precision of several commonly used methods for CLIP peak calling. Based on this iCLIP data, we discovered that FBF-1 and FBF-2 have similar global protein-RNA interaction profiles and that they both target conserved cell cycle regulators and lincRNAs. more...