rnas Search Results


  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 99
    Zymo Research rna
    Rna, supplied by Zymo Research, used in various techniques. Bioz Stars score: 99/100, based on 531 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rna/product/Zymo Research
    Average 99 stars, based on 531 article reviews
    Price from $9.99 to $1999.99
    rna - by Bioz Stars, 2020-12
    99/100 stars
      Buy from Supplier

    99
    New England Biolabs nebnext ultra rna library prep kit for illumina
    Nebnext Ultra Rna Library Prep Kit For Illumina, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 77 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nebnext ultra rna library prep kit for illumina/product/New England Biolabs
    Average 99 stars, based on 77 article reviews
    Price from $9.99 to $1999.99
    nebnext ultra rna library prep kit for illumina - by Bioz Stars, 2020-12
    99/100 stars
      Buy from Supplier

    99
    Thermo Fisher total rna
    Total Rna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 471882 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/total rna/product/Thermo Fisher
    Average 99 stars, based on 471882 article reviews
    Price from $9.99 to $1999.99
    total rna - by Bioz Stars, 2020-12
    99/100 stars
      Buy from Supplier

    99
    Thermo Fisher rna
    Rna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 177224 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rna/product/Thermo Fisher
    Average 99 stars, based on 177224 article reviews
    Price from $9.99 to $1999.99
    rna - by Bioz Stars, 2020-12
    99/100 stars
      Buy from Supplier

    99
    Thermo Fisher rna extraction
    Rna Extraction, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 40204 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rna extraction/product/Thermo Fisher
    Average 99 stars, based on 40204 article reviews
    Price from $9.99 to $1999.99
    rna extraction - by Bioz Stars, 2020-12
    99/100 stars
      Buy from Supplier

    rna  (Promega)
    99
    Promega rna
    Rna, supplied by Promega, used in various techniques. Bioz Stars score: 99/100, based on 19539 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rna/product/Promega
    Average 99 stars, based on 19539 article reviews
    Price from $9.99 to $1999.99
    rna - by Bioz Stars, 2020-12
    99/100 stars
      Buy from Supplier

    99
    Millipore rna
    Requirement of ER stress for efficient brown adipogenesis. ( A and B ) HB2 brown preadipocytes were treated with or without 5 mM of 4-PBA or 100 μM of capsaicin or both for 8 days in the presence of insulin (20 nM). ( C and D ) HB2 brown preadipocytes were transfected with scrambled <t>RNA</t> or <t>siRNA</t> for Xbp1. Cells were treated with or without 100 μM of capsaicin in the presence of insulin (20 nM) for 8 days. ( A and C ) Oil Red O staining of cells on day 8 was performed, and the dye intensity was quantified (n = 2). ( B and D ) The expression level of Ucp1 was examined by RT-qPCR analysis. Black bar: vehicle; Hatched bar: capsaicin. The data are presented as the mean ± SE (n = 4). * P
    Rna, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 5994 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rna/product/Millipore
    Average 99 stars, based on 5994 article reviews
    Price from $9.99 to $1999.99
    rna - by Bioz Stars, 2020-12
    99/100 stars
      Buy from Supplier

    99
    Millipore total rna
    Requirement of ER stress for efficient brown adipogenesis. ( A and B ) HB2 brown preadipocytes were treated with or without 5 mM of 4-PBA or 100 μM of capsaicin or both for 8 days in the presence of insulin (20 nM). ( C and D ) HB2 brown preadipocytes were transfected with scrambled <t>RNA</t> or <t>siRNA</t> for Xbp1. Cells were treated with or without 100 μM of capsaicin in the presence of insulin (20 nM) for 8 days. ( A and C ) Oil Red O staining of cells on day 8 was performed, and the dye intensity was quantified (n = 2). ( B and D ) The expression level of Ucp1 was examined by RT-qPCR analysis. Black bar: vehicle; Hatched bar: capsaicin. The data are presented as the mean ± SE (n = 4). * P
    Total Rna, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 26190 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/total rna/product/Millipore
    Average 99 stars, based on 26190 article reviews
    Price from $9.99 to $1999.99
    total rna - by Bioz Stars, 2020-12
    99/100 stars
      Buy from Supplier

    99
    Qiagen qiaamp viral rna mini kit
    Requirement of ER stress for efficient brown adipogenesis. ( A and B ) HB2 brown preadipocytes were treated with or without 5 mM of 4-PBA or 100 μM of capsaicin or both for 8 days in the presence of insulin (20 nM). ( C and D ) HB2 brown preadipocytes were transfected with scrambled <t>RNA</t> or <t>siRNA</t> for Xbp1. Cells were treated with or without 100 μM of capsaicin in the presence of insulin (20 nM) for 8 days. ( A and C ) Oil Red O staining of cells on day 8 was performed, and the dye intensity was quantified (n = 2). ( B and D ) The expression level of Ucp1 was examined by RT-qPCR analysis. Black bar: vehicle; Hatched bar: capsaicin. The data are presented as the mean ± SE (n = 4). * P
    Qiaamp Viral Rna Mini Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 23436 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/qiaamp viral rna mini kit/product/Qiagen
    Average 99 stars, based on 23436 article reviews
    Price from $9.99 to $1999.99
    qiaamp viral rna mini kit - by Bioz Stars, 2020-12
    99/100 stars
      Buy from Supplier

    95
    Agilent technologies rna integrity
    <t>KSHV</t> induces alternative <t>RNA</t> splicing in infected LEC. ( A ) Confirmation of KSHV infection in LECs. The cell morphology of mock infection LECs at 2 days (LEC panel) shows a cobble stone appearance, whereas LECs infected by BCBL1-derived rKSHV at 2 days have become elongated and spindle shaped (KLEC panels). The GFP positive cells indicate successful KSHV infection. KSHV infection was further confirmed by RT–PCR of KSHV genes (upper-right panel). LEC and KLEC indicate cDNA from these two samples was used as PCR-template. LEC- and KLEC- mean no-RT control, and the (–) set is a no template control. Three KSHV genes: LANA, vCyclin and vFLIP were all expressed in the KLECs. Immunofluorescent staining of KSHV LANA protein is demonstrated in the lower right panel, which shows a typical nuclear stippling staining pattern. ( B ) PCA plots of both gene and exon levels between KLEC and LEC. The PCA plot, based on the differential expressed genes with a pFDR
    Rna Integrity, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 95/100, based on 43937 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rna integrity/product/Agilent technologies
    Average 95 stars, based on 43937 article reviews
    Price from $9.99 to $1999.99
    rna integrity - by Bioz Stars, 2020-12
    95/100 stars
      Buy from Supplier

    99
    Thermo Fisher purelink rna mini kit
    <t>KSHV</t> induces alternative <t>RNA</t> splicing in infected LEC. ( A ) Confirmation of KSHV infection in LECs. The cell morphology of mock infection LECs at 2 days (LEC panel) shows a cobble stone appearance, whereas LECs infected by BCBL1-derived rKSHV at 2 days have become elongated and spindle shaped (KLEC panels). The GFP positive cells indicate successful KSHV infection. KSHV infection was further confirmed by RT–PCR of KSHV genes (upper-right panel). LEC and KLEC indicate cDNA from these two samples was used as PCR-template. LEC- and KLEC- mean no-RT control, and the (–) set is a no template control. Three KSHV genes: LANA, vCyclin and vFLIP were all expressed in the KLECs. Immunofluorescent staining of KSHV LANA protein is demonstrated in the lower right panel, which shows a typical nuclear stippling staining pattern. ( B ) PCA plots of both gene and exon levels between KLEC and LEC. The PCA plot, based on the differential expressed genes with a pFDR
    Purelink Rna Mini Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 16743 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/purelink rna mini kit/product/Thermo Fisher
    Average 99 stars, based on 16743 article reviews
    Price from $9.99 to $1999.99
    purelink rna mini kit - by Bioz Stars, 2020-12
    99/100 stars
      Buy from Supplier

    99
    Thermo Fisher high capacity rna to cdna kit
    <t>KSHV</t> induces alternative <t>RNA</t> splicing in infected LEC. ( A ) Confirmation of KSHV infection in LECs. The cell morphology of mock infection LECs at 2 days (LEC panel) shows a cobble stone appearance, whereas LECs infected by BCBL1-derived rKSHV at 2 days have become elongated and spindle shaped (KLEC panels). The GFP positive cells indicate successful KSHV infection. KSHV infection was further confirmed by RT–PCR of KSHV genes (upper-right panel). LEC and KLEC indicate cDNA from these two samples was used as PCR-template. LEC- and KLEC- mean no-RT control, and the (–) set is a no template control. Three KSHV genes: LANA, vCyclin and vFLIP were all expressed in the KLECs. Immunofluorescent staining of KSHV LANA protein is demonstrated in the lower right panel, which shows a typical nuclear stippling staining pattern. ( B ) PCA plots of both gene and exon levels between KLEC and LEC. The PCA plot, based on the differential expressed genes with a pFDR
    High Capacity Rna To Cdna Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 18369 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/high capacity rna to cdna kit/product/Thermo Fisher
    Average 99 stars, based on 18369 article reviews
    Price from $9.99 to $1999.99
    high capacity rna to cdna kit - by Bioz Stars, 2020-12
    99/100 stars
      Buy from Supplier

    99
    Qiagen rnalater
    <t>KSHV</t> induces alternative <t>RNA</t> splicing in infected LEC. ( A ) Confirmation of KSHV infection in LECs. The cell morphology of mock infection LECs at 2 days (LEC panel) shows a cobble stone appearance, whereas LECs infected by BCBL1-derived rKSHV at 2 days have become elongated and spindle shaped (KLEC panels). The GFP positive cells indicate successful KSHV infection. KSHV infection was further confirmed by RT–PCR of KSHV genes (upper-right panel). LEC and KLEC indicate cDNA from these two samples was used as PCR-template. LEC- and KLEC- mean no-RT control, and the (–) set is a no template control. Three KSHV genes: LANA, vCyclin and vFLIP were all expressed in the KLECs. Immunofluorescent staining of KSHV LANA protein is demonstrated in the lower right panel, which shows a typical nuclear stippling staining pattern. ( B ) PCA plots of both gene and exon levels between KLEC and LEC. The PCA plot, based on the differential expressed genes with a pFDR
    Rnalater, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 13474 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rnalater/product/Qiagen
    Average 99 stars, based on 13474 article reviews
    Price from $9.99 to $1999.99
    rnalater - by Bioz Stars, 2020-12
    99/100 stars
      Buy from Supplier

    92
    Agilent technologies rna 6000 nano kit
    Decrease in total RNA after enzymes treatment in plasma samples. Electropherograms corresponding to A) short RNA extracted from peripheral blood; B) DU-Plasma and C) Exo-Plasma samples before and after proteinase K and RNAse A treatment. All samples were analysed by Agilent <t>RNA</t> 6000 Pico Kit in an Agilent 2100 Bioanalyzer. The electropherograms show the size distribution in nucleotides (nt) and fluorescence intensity (FU) of total RNA. The peak at 25 nt is an internal standard. A representative electropherogram of two independent experiments is shown for DU-Plasma samples. A representative electropherogram of two and one independent experiments for DU-Plasma and Exo-Plasma samples, respectively.
    Rna 6000 Nano Kit, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 92/100, based on 13207 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rna 6000 nano kit/product/Agilent technologies
    Average 92 stars, based on 13207 article reviews
    Price from $9.99 to $1999.99
    rna 6000 nano kit - by Bioz Stars, 2020-12
    92/100 stars
      Buy from Supplier

    95
    Illumina Inc rna seq libraries
    Post-transcriptional events account for a significant fraction of rhythmic gene expression in the mouse liver. ( A ): Rhythmic gene expression was assessed as in Figure 2B for genes sufficiently expressed in both Nascent-Seq and <t>RNA-Seq</t> datasets. Four categories of rhythmically expressed genes were determined by comparing the Nascent-Seq and RNA-Seq datasets: rhythmic nascent RNA and <t>mRNA</t> (R-R), rhythmic nascent RNA only (R-AR), rhythmic mRNA only (AR-R) and arrhythmic nascent RNA and mRNA (AR-AR). ( B ): Heatmap representation of genes with rhythmic nascent RNA and mRNA expression (n = 342). Classification is based on the phase of nascent RNA oscillations, and each lane corresponds to one gene. ( C ): Double-plotted phase distribution of rhythmic nascent RNA expression (brown) and rhythmic mRNA expression (red) for genes of the R-R gene set. Both phases are highly correlated (r = 0.92). ( D ): Distribution of the difference between the phase of mRNA expression rhythm and the phase of nascent RNA expression rhythm for the 342 R-R genes. ( E ): Amplitude of mRNA expression rhythms are correlated with nascent RNA expression rhythms (r = 0.76). ( F ) and ( G ): Similar representation to ( B ) for rhythmically transcribed genes with no mRNA expression rhythms ( C , n = 480), and genes that exhibit mRNA oscillations but no rhythms of transcription ( D , n = 862). For all three heatmaps, high expression is displayed in yellow (z-score > 1), low expression in blue (z-score
    Rna Seq Libraries, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 95/100, based on 14666 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rna seq libraries/product/Illumina Inc
    Average 95 stars, based on 14666 article reviews
    Price from $9.99 to $1999.99
    rna seq libraries - by Bioz Stars, 2020-12
    95/100 stars
      Buy from Supplier

    99
    Zymo Research total rna
    Post-transcriptional events account for a significant fraction of rhythmic gene expression in the mouse liver. ( A ): Rhythmic gene expression was assessed as in Figure 2B for genes sufficiently expressed in both Nascent-Seq and <t>RNA-Seq</t> datasets. Four categories of rhythmically expressed genes were determined by comparing the Nascent-Seq and RNA-Seq datasets: rhythmic nascent RNA and <t>mRNA</t> (R-R), rhythmic nascent RNA only (R-AR), rhythmic mRNA only (AR-R) and arrhythmic nascent RNA and mRNA (AR-AR). ( B ): Heatmap representation of genes with rhythmic nascent RNA and mRNA expression (n = 342). Classification is based on the phase of nascent RNA oscillations, and each lane corresponds to one gene. ( C ): Double-plotted phase distribution of rhythmic nascent RNA expression (brown) and rhythmic mRNA expression (red) for genes of the R-R gene set. Both phases are highly correlated (r = 0.92). ( D ): Distribution of the difference between the phase of mRNA expression rhythm and the phase of nascent RNA expression rhythm for the 342 R-R genes. ( E ): Amplitude of mRNA expression rhythms are correlated with nascent RNA expression rhythms (r = 0.76). ( F ) and ( G ): Similar representation to ( B ) for rhythmically transcribed genes with no mRNA expression rhythms ( C , n = 480), and genes that exhibit mRNA oscillations but no rhythms of transcription ( D , n = 862). For all three heatmaps, high expression is displayed in yellow (z-score > 1), low expression in blue (z-score
    Total Rna, supplied by Zymo Research, used in various techniques. Bioz Stars score: 99/100, based on 7667 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/total rna/product/Zymo Research
    Average 99 stars, based on 7667 article reviews
    Price from $9.99 to $1999.99
    total rna - by Bioz Stars, 2020-12
    99/100 stars
      Buy from Supplier

    95
    Promega sv total rna isolation system
    <t>SroC</t> induces GcvB degradation by a base-pairing mechanism GcvB-SroC base-pairing regions. The compensatory base pair changes in GcvB and SroC are indicated in red. Salmonella Δ gcvB Δ sroC (JVS-5822) strain was cotransformed with pP L -GcvB and pBAD-SroC derivatives (see Supplementary Table S4). Each transformant was grown to OD 600 of 0.5 (0 min) and incubated for another 10 min in the presence of 0.2% l -arabinose. Total <t>RNA</t> was prepared from the cells and subjected to Northern blot analysis. The fold repression of GcvB was determined from three independent replicates; standard deviation is shown. The chromosomally modified wild-type sroC strain (JVS-10108), sroC ** mutant (JVS-10111) and sroC deletion mutant (JVS-5821) were grown to early stationary phase in LB medium (OD 600 of 2.0) prior to the addition of rifampicin. Cultures were harvested at the indicated time points after rifampicin treatment. RNA was isolated and analyzed by Northern blot as in Fig 3B . Source data are available online for this figure.
    Sv Total Rna Isolation System, supplied by Promega, used in various techniques. Bioz Stars score: 95/100, based on 13726 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sv total rna isolation system/product/Promega
    Average 95 stars, based on 13726 article reviews
    Price from $9.99 to $1999.99
    sv total rna isolation system - by Bioz Stars, 2020-12
    95/100 stars
      Buy from Supplier

    98
    Thermo Fisher t7 rna polymerase
    <t>SroC</t> induces GcvB degradation by a base-pairing mechanism GcvB-SroC base-pairing regions. The compensatory base pair changes in GcvB and SroC are indicated in red. Salmonella Δ gcvB Δ sroC (JVS-5822) strain was cotransformed with pP L -GcvB and pBAD-SroC derivatives (see Supplementary Table S4). Each transformant was grown to OD 600 of 0.5 (0 min) and incubated for another 10 min in the presence of 0.2% l -arabinose. Total <t>RNA</t> was prepared from the cells and subjected to Northern blot analysis. The fold repression of GcvB was determined from three independent replicates; standard deviation is shown. The chromosomally modified wild-type sroC strain (JVS-10108), sroC ** mutant (JVS-10111) and sroC deletion mutant (JVS-5821) were grown to early stationary phase in LB medium (OD 600 of 2.0) prior to the addition of rifampicin. Cultures were harvested at the indicated time points after rifampicin treatment. RNA was isolated and analyzed by Northern blot as in Fig 3B . Source data are available online for this figure.
    T7 Rna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 98/100, based on 12287 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/t7 rna polymerase/product/Thermo Fisher
    Average 98 stars, based on 12287 article reviews
    Price from $9.99 to $1999.99
    t7 rna polymerase - by Bioz Stars, 2020-12
    98/100 stars
      Buy from Supplier

    99
    Qiagen allprep dna rna mini kit
    <t>SroC</t> induces GcvB degradation by a base-pairing mechanism GcvB-SroC base-pairing regions. The compensatory base pair changes in GcvB and SroC are indicated in red. Salmonella Δ gcvB Δ sroC (JVS-5822) strain was cotransformed with pP L -GcvB and pBAD-SroC derivatives (see Supplementary Table S4). Each transformant was grown to OD 600 of 0.5 (0 min) and incubated for another 10 min in the presence of 0.2% l -arabinose. Total <t>RNA</t> was prepared from the cells and subjected to Northern blot analysis. The fold repression of GcvB was determined from three independent replicates; standard deviation is shown. The chromosomally modified wild-type sroC strain (JVS-10108), sroC ** mutant (JVS-10111) and sroC deletion mutant (JVS-5821) were grown to early stationary phase in LB medium (OD 600 of 2.0) prior to the addition of rifampicin. Cultures were harvested at the indicated time points after rifampicin treatment. RNA was isolated and analyzed by Northern blot as in Fig 3B . Source data are available online for this figure.
    Allprep Dna Rna Mini Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 7493 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/allprep dna rna mini kit/product/Qiagen
    Average 99 stars, based on 7493 article reviews
    Price from $9.99 to $1999.99
    allprep dna rna mini kit - by Bioz Stars, 2020-12
    99/100 stars
      Buy from Supplier

    99
    Zymo Research direct zol rna miniprep kit
    <t>SroC</t> induces GcvB degradation by a base-pairing mechanism GcvB-SroC base-pairing regions. The compensatory base pair changes in GcvB and SroC are indicated in red. Salmonella Δ gcvB Δ sroC (JVS-5822) strain was cotransformed with pP L -GcvB and pBAD-SroC derivatives (see Supplementary Table S4). Each transformant was grown to OD 600 of 0.5 (0 min) and incubated for another 10 min in the presence of 0.2% l -arabinose. Total <t>RNA</t> was prepared from the cells and subjected to Northern blot analysis. The fold repression of GcvB was determined from three independent replicates; standard deviation is shown. The chromosomally modified wild-type sroC strain (JVS-10108), sroC ** mutant (JVS-10111) and sroC deletion mutant (JVS-5821) were grown to early stationary phase in LB medium (OD 600 of 2.0) prior to the addition of rifampicin. Cultures were harvested at the indicated time points after rifampicin treatment. RNA was isolated and analyzed by Northern blot as in Fig 3B . Source data are available online for this figure.
    Direct Zol Rna Miniprep Kit, supplied by Zymo Research, used in various techniques. Bioz Stars score: 99/100, based on 7194 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/direct zol rna miniprep kit/product/Zymo Research
    Average 99 stars, based on 7194 article reviews
    Price from $9.99 to $1999.99
    direct zol rna miniprep kit - by Bioz Stars, 2020-12
    99/100 stars
      Buy from Supplier

    99
    Promega t7 rna polymerase
    <t>SroC</t> induces GcvB degradation by a base-pairing mechanism GcvB-SroC base-pairing regions. The compensatory base pair changes in GcvB and SroC are indicated in red. Salmonella Δ gcvB Δ sroC (JVS-5822) strain was cotransformed with pP L -GcvB and pBAD-SroC derivatives (see Supplementary Table S4). Each transformant was grown to OD 600 of 0.5 (0 min) and incubated for another 10 min in the presence of 0.2% l -arabinose. Total <t>RNA</t> was prepared from the cells and subjected to Northern blot analysis. The fold repression of GcvB was determined from three independent replicates; standard deviation is shown. The chromosomally modified wild-type sroC strain (JVS-10108), sroC ** mutant (JVS-10111) and sroC deletion mutant (JVS-5821) were grown to early stationary phase in LB medium (OD 600 of 2.0) prior to the addition of rifampicin. Cultures were harvested at the indicated time points after rifampicin treatment. RNA was isolated and analyzed by Northern blot as in Fig 3B . Source data are available online for this figure.
    T7 Rna Polymerase, supplied by Promega, used in various techniques. Bioz Stars score: 99/100, based on 10131 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/t7 rna polymerase/product/Promega
    Average 99 stars, based on 10131 article reviews
    Price from $9.99 to $1999.99
    t7 rna polymerase - by Bioz Stars, 2020-12
    99/100 stars
      Buy from Supplier


    N/A
    RNA safe reagent is a highly active RNase Inhibition It thoroughly removes RNase contamination to preserve the intactness of RNA Features: ■ complete removal of Rnase ■ Treated solution could
      Buy from Supplier


    N/A
    RNasin is a special RNase inhibitor existing in human placenta It is essentially a protein with molecular weight of 51 000 Da and isoelectric point of pH 4 7 RNasin
      Buy from Supplier

    Image Search Results


    Requirement of ER stress for efficient brown adipogenesis. ( A and B ) HB2 brown preadipocytes were treated with or without 5 mM of 4-PBA or 100 μM of capsaicin or both for 8 days in the presence of insulin (20 nM). ( C and D ) HB2 brown preadipocytes were transfected with scrambled RNA or siRNA for Xbp1. Cells were treated with or without 100 μM of capsaicin in the presence of insulin (20 nM) for 8 days. ( A and C ) Oil Red O staining of cells on day 8 was performed, and the dye intensity was quantified (n = 2). ( B and D ) The expression level of Ucp1 was examined by RT-qPCR analysis. Black bar: vehicle; Hatched bar: capsaicin. The data are presented as the mean ± SE (n = 4). * P

    Journal: Scientific Reports

    Article Title: Supra-pharmacological concentration of capsaicin stimulates brown adipogenesis through induction of endoplasmic reticulum stress

    doi: 10.1038/s41598-018-19223-2

    Figure Lengend Snippet: Requirement of ER stress for efficient brown adipogenesis. ( A and B ) HB2 brown preadipocytes were treated with or without 5 mM of 4-PBA or 100 μM of capsaicin or both for 8 days in the presence of insulin (20 nM). ( C and D ) HB2 brown preadipocytes were transfected with scrambled RNA or siRNA for Xbp1. Cells were treated with or without 100 μM of capsaicin in the presence of insulin (20 nM) for 8 days. ( A and C ) Oil Red O staining of cells on day 8 was performed, and the dye intensity was quantified (n = 2). ( B and D ) The expression level of Ucp1 was examined by RT-qPCR analysis. Black bar: vehicle; Hatched bar: capsaicin. The data are presented as the mean ± SE (n = 4). * P

    Article Snippet: At confluence (day -2), cells were transfected with 6 μl of Lipofectamine RNAi Max (Thermo Fisher, Waltham, MA, USA) and 60 pmol of siRNA for Xbp1 or scrambled RNA (MISSION siRNA; Sigma) for 2 days.

    Techniques: Transfection, Staining, Expressing, Quantitative RT-PCR

    KSHV induces alternative RNA splicing in infected LEC. ( A ) Confirmation of KSHV infection in LECs. The cell morphology of mock infection LECs at 2 days (LEC panel) shows a cobble stone appearance, whereas LECs infected by BCBL1-derived rKSHV at 2 days have become elongated and spindle shaped (KLEC panels). The GFP positive cells indicate successful KSHV infection. KSHV infection was further confirmed by RT–PCR of KSHV genes (upper-right panel). LEC and KLEC indicate cDNA from these two samples was used as PCR-template. LEC- and KLEC- mean no-RT control, and the (–) set is a no template control. Three KSHV genes: LANA, vCyclin and vFLIP were all expressed in the KLECs. Immunofluorescent staining of KSHV LANA protein is demonstrated in the lower right panel, which shows a typical nuclear stippling staining pattern. ( B ) PCA plots of both gene and exon levels between KLEC and LEC. The PCA plot, based on the differential expressed genes with a pFDR

    Journal: Nucleic Acids Research

    Article Title: Differentially regulated splice variants and systems biology analysis of Kaposi's sarcoma-associated herpesvirus-infected lymphatic endothelial cells

    doi: 10.1093/nar/gkr405

    Figure Lengend Snippet: KSHV induces alternative RNA splicing in infected LEC. ( A ) Confirmation of KSHV infection in LECs. The cell morphology of mock infection LECs at 2 days (LEC panel) shows a cobble stone appearance, whereas LECs infected by BCBL1-derived rKSHV at 2 days have become elongated and spindle shaped (KLEC panels). The GFP positive cells indicate successful KSHV infection. KSHV infection was further confirmed by RT–PCR of KSHV genes (upper-right panel). LEC and KLEC indicate cDNA from these two samples was used as PCR-template. LEC- and KLEC- mean no-RT control, and the (–) set is a no template control. Three KSHV genes: LANA, vCyclin and vFLIP were all expressed in the KLECs. Immunofluorescent staining of KSHV LANA protein is demonstrated in the lower right panel, which shows a typical nuclear stippling staining pattern. ( B ) PCA plots of both gene and exon levels between KLEC and LEC. The PCA plot, based on the differential expressed genes with a pFDR

    Article Snippet: Microarray hybridization Total RNA from KSHV infected LECs or mock infections with biological replicates were checked for RNA integrity by Bioanalyzer (Agilent, Santa Clara, CA, USA).

    Techniques: Infection, Derivative Assay, Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Staining

    Dedifferentiation-like AS drift in KSHV-infected LECs. ( A ) A gene-level MDS plot using KLEC-LEC differential expressed genes (Affymetrix Human Genome U133 Plus 2.0 array). In this figure, no dedifferentiation could be found. ( B ) An exon-level MDS plot using NI of KSHV-induced AS probe sets. An arrow indicates that the exomes of the infected LECs have moved away from those of control LECs and toward to those of CD34 + endothelial stem/precursor cells. (right) Average linkage distances between sample groups. ( C ) Venn diagrams showing AS events common between KSHV-LEC and CD34 + cells. ( D ) A heat map showing the 33 AS events common between KSHV-LEC and CD34 + cells. The Gene symbols of AS genes are also listed. ( E ) DomainGraph ‘Probeset view’ of EGFR and CASP9. EGFR exon 25 is downregulated upon KSHV infection, and this KSHV-regulated isoform would seem to harbor an altered protein kinase domain. Part of CASP9 exon 4 is downregulated in infected LECs, and this AS will affect the integrity and function of the CARD domain. Green boxes: probe sets with exon exclusion; White boxes: probe sets that do not meet the minimum expression threshold in AltAnalyze; Gray boxes: no alternative expression event detected. (right) Validation of AS events by RT–qPCR. Primer sets for EGFR exon 25 and CASP9 exon 4b were designed for detecting differential expressed exons, whereas primer sets for EGFR exon 26 and CASP9 exon 5 for constantly expressed exons. Total RNA was from primary LECs infected with JSC-1-derived rKSHV.219 viruses. Results are expressed as the mean ± SD. Ratios between AS exons and constant exons are shown. * P

    Journal: Nucleic Acids Research

    Article Title: Differentially regulated splice variants and systems biology analysis of Kaposi's sarcoma-associated herpesvirus-infected lymphatic endothelial cells

    doi: 10.1093/nar/gkr405

    Figure Lengend Snippet: Dedifferentiation-like AS drift in KSHV-infected LECs. ( A ) A gene-level MDS plot using KLEC-LEC differential expressed genes (Affymetrix Human Genome U133 Plus 2.0 array). In this figure, no dedifferentiation could be found. ( B ) An exon-level MDS plot using NI of KSHV-induced AS probe sets. An arrow indicates that the exomes of the infected LECs have moved away from those of control LECs and toward to those of CD34 + endothelial stem/precursor cells. (right) Average linkage distances between sample groups. ( C ) Venn diagrams showing AS events common between KSHV-LEC and CD34 + cells. ( D ) A heat map showing the 33 AS events common between KSHV-LEC and CD34 + cells. The Gene symbols of AS genes are also listed. ( E ) DomainGraph ‘Probeset view’ of EGFR and CASP9. EGFR exon 25 is downregulated upon KSHV infection, and this KSHV-regulated isoform would seem to harbor an altered protein kinase domain. Part of CASP9 exon 4 is downregulated in infected LECs, and this AS will affect the integrity and function of the CARD domain. Green boxes: probe sets with exon exclusion; White boxes: probe sets that do not meet the minimum expression threshold in AltAnalyze; Gray boxes: no alternative expression event detected. (right) Validation of AS events by RT–qPCR. Primer sets for EGFR exon 25 and CASP9 exon 4b were designed for detecting differential expressed exons, whereas primer sets for EGFR exon 26 and CASP9 exon 5 for constantly expressed exons. Total RNA was from primary LECs infected with JSC-1-derived rKSHV.219 viruses. Results are expressed as the mean ± SD. Ratios between AS exons and constant exons are shown. * P

    Article Snippet: Microarray hybridization Total RNA from KSHV infected LECs or mock infections with biological replicates were checked for RNA integrity by Bioanalyzer (Agilent, Santa Clara, CA, USA).

    Techniques: Infection, Expressing, Quantitative RT-PCR, Derivative Assay

    Modification of domain and motif compositions within KSHV-induced isoforms. ( A ) Table of protein domains in genes with AS exons. In total, 17 domains/motifs that are involved in adhesion and oncogenic signaling transduction are affected on KSHV infection. ( B ) Part of the SH3_2 domain is altered in BAIAP2L1 due to the upregulated exon 11. Similarly, part of the DEP domain (Domain found in Dishevelled, Egl-10, and Pleckstrin) in DVL2 is affected on KSHV infection due to the downregulation of exon 12. Probe sets with exon inclusion are in red, whereas those with exon exclusion in green. (right) Validation of AS events by RT–qPCR. Total RNA was from LECs infected with JSC-1-derived rKSHV.

    Journal: Nucleic Acids Research

    Article Title: Differentially regulated splice variants and systems biology analysis of Kaposi's sarcoma-associated herpesvirus-infected lymphatic endothelial cells

    doi: 10.1093/nar/gkr405

    Figure Lengend Snippet: Modification of domain and motif compositions within KSHV-induced isoforms. ( A ) Table of protein domains in genes with AS exons. In total, 17 domains/motifs that are involved in adhesion and oncogenic signaling transduction are affected on KSHV infection. ( B ) Part of the SH3_2 domain is altered in BAIAP2L1 due to the upregulated exon 11. Similarly, part of the DEP domain (Domain found in Dishevelled, Egl-10, and Pleckstrin) in DVL2 is affected on KSHV infection due to the downregulation of exon 12. Probe sets with exon inclusion are in red, whereas those with exon exclusion in green. (right) Validation of AS events by RT–qPCR. Total RNA was from LECs infected with JSC-1-derived rKSHV.

    Article Snippet: Microarray hybridization Total RNA from KSHV infected LECs or mock infections with biological replicates were checked for RNA integrity by Bioanalyzer (Agilent, Santa Clara, CA, USA).

    Techniques: Modification, Transduction, Infection, Quantitative RT-PCR, Derivative Assay

    AS modifies miRNA binding site architecture. ( A ) The miRNA expression profile of KSHV infected LECs. In total, 216 miRNAs that have summarized probe set intensities > 4 on a log 2 scale can be considered to be expressed in the cells. The y -axis scale is the RMA-normalized hybridization signal (log 2 transformed) ( B ) Venn diagram of expressed miRNAs and altered miRNA binding sites identified by AltAnalyze. Overall, 85 miRNA-altered miRNA binding sites can be identified. ( C ) Correlation between differential gene expression and miRNA–miRNA binding sites regulation. (Upper) Genes downregulated in KSHV-LEC, and their miRNA binding sites are in inclusive exons. (Lower) Genes up-regulated in KSHV-LEC, and their miRNA binding sites are in exclusive exons. (Some ‘miR-’ prefixes were omitted for better demonstration.) ( D ) Relative expression levels of genes with miRNA binding site alteration. Potential miRNA binding sites are upregulated in MLPH and CTCL1, and their gene expression levels are significantly down. In contrast, the miRNA binding sites in RAPGEF5 are downregulated, and its gene expression level is up. Total RNA was from LECs infected with JSC-1-derived rKSHV. ( E ) RAPGEF5 is crucial for LEC motility. Primary LECs transduced with shRNA against LacZ or RAPGEF5 were subjected to Transwell cell migration assays (right). The knock-down effect was measured by RT–qPCR (left). Mean expression levels of RAPGEF5 were compared with that of GAPDH control.

    Journal: Nucleic Acids Research

    Article Title: Differentially regulated splice variants and systems biology analysis of Kaposi's sarcoma-associated herpesvirus-infected lymphatic endothelial cells

    doi: 10.1093/nar/gkr405

    Figure Lengend Snippet: AS modifies miRNA binding site architecture. ( A ) The miRNA expression profile of KSHV infected LECs. In total, 216 miRNAs that have summarized probe set intensities > 4 on a log 2 scale can be considered to be expressed in the cells. The y -axis scale is the RMA-normalized hybridization signal (log 2 transformed) ( B ) Venn diagram of expressed miRNAs and altered miRNA binding sites identified by AltAnalyze. Overall, 85 miRNA-altered miRNA binding sites can be identified. ( C ) Correlation between differential gene expression and miRNA–miRNA binding sites regulation. (Upper) Genes downregulated in KSHV-LEC, and their miRNA binding sites are in inclusive exons. (Lower) Genes up-regulated in KSHV-LEC, and their miRNA binding sites are in exclusive exons. (Some ‘miR-’ prefixes were omitted for better demonstration.) ( D ) Relative expression levels of genes with miRNA binding site alteration. Potential miRNA binding sites are upregulated in MLPH and CTCL1, and their gene expression levels are significantly down. In contrast, the miRNA binding sites in RAPGEF5 are downregulated, and its gene expression level is up. Total RNA was from LECs infected with JSC-1-derived rKSHV. ( E ) RAPGEF5 is crucial for LEC motility. Primary LECs transduced with shRNA against LacZ or RAPGEF5 were subjected to Transwell cell migration assays (right). The knock-down effect was measured by RT–qPCR (left). Mean expression levels of RAPGEF5 were compared with that of GAPDH control.

    Article Snippet: Microarray hybridization Total RNA from KSHV infected LECs or mock infections with biological replicates were checked for RNA integrity by Bioanalyzer (Agilent, Santa Clara, CA, USA).

    Techniques: Binding Assay, Expressing, Infection, Hybridization, Transformation Assay, Derivative Assay, Transduction, shRNA, Migration, Quantitative RT-PCR

    Decrease in total RNA after enzymes treatment in plasma samples. Electropherograms corresponding to A) short RNA extracted from peripheral blood; B) DU-Plasma and C) Exo-Plasma samples before and after proteinase K and RNAse A treatment. All samples were analysed by Agilent RNA 6000 Pico Kit in an Agilent 2100 Bioanalyzer. The electropherograms show the size distribution in nucleotides (nt) and fluorescence intensity (FU) of total RNA. The peak at 25 nt is an internal standard. A representative electropherogram of two independent experiments is shown for DU-Plasma samples. A representative electropherogram of two and one independent experiments for DU-Plasma and Exo-Plasma samples, respectively.

    Journal: PLoS ONE

    Article Title: Analysis of RNA yield in extracellular vesicles isolated by membrane affinity column and differential ultracentrifugation

    doi: 10.1371/journal.pone.0238545

    Figure Lengend Snippet: Decrease in total RNA after enzymes treatment in plasma samples. Electropherograms corresponding to A) short RNA extracted from peripheral blood; B) DU-Plasma and C) Exo-Plasma samples before and after proteinase K and RNAse A treatment. All samples were analysed by Agilent RNA 6000 Pico Kit in an Agilent 2100 Bioanalyzer. The electropherograms show the size distribution in nucleotides (nt) and fluorescence intensity (FU) of total RNA. The peak at 25 nt is an internal standard. A representative electropherogram of two independent experiments is shown for DU-Plasma samples. A representative electropherogram of two and one independent experiments for DU-Plasma and Exo-Plasma samples, respectively.

    Article Snippet: For Agilent RNA 6000 Nano kit and small RNA kit, 1 μl of RNA was added to the chip and then analysis was performed according to manufacturer’s protocol.

    Techniques: Fluorescence

    Decrease in total RNA after enzymes treatment in culture supernatant samples. Electropherograms corresponding to A) negative control; B) DU-CS and C) Exo-CS samples before and after proteinase K and RNAse A treatment. All samples were analysed by Agilent RNA 6000 Pico Kit in an Agilent 2100 Bioanalyzer. The electropherograms show the size distribution in nucleotides (nt) and fluorescence intensity (FU) of total RNA. The peak at 25 nt is an internal standard. A representative electropherogram of three and two independent experiments is shown for DU-CS and Exo-CS samples, respectively.

    Journal: PLoS ONE

    Article Title: Analysis of RNA yield in extracellular vesicles isolated by membrane affinity column and differential ultracentrifugation

    doi: 10.1371/journal.pone.0238545

    Figure Lengend Snippet: Decrease in total RNA after enzymes treatment in culture supernatant samples. Electropherograms corresponding to A) negative control; B) DU-CS and C) Exo-CS samples before and after proteinase K and RNAse A treatment. All samples were analysed by Agilent RNA 6000 Pico Kit in an Agilent 2100 Bioanalyzer. The electropherograms show the size distribution in nucleotides (nt) and fluorescence intensity (FU) of total RNA. The peak at 25 nt is an internal standard. A representative electropherogram of three and two independent experiments is shown for DU-CS and Exo-CS samples, respectively.

    Article Snippet: For Agilent RNA 6000 Nano kit and small RNA kit, 1 μl of RNA was added to the chip and then analysis was performed according to manufacturer’s protocol.

    Techniques: Negative Control, Fluorescence

    Post-transcriptional events account for a significant fraction of rhythmic gene expression in the mouse liver. ( A ): Rhythmic gene expression was assessed as in Figure 2B for genes sufficiently expressed in both Nascent-Seq and RNA-Seq datasets. Four categories of rhythmically expressed genes were determined by comparing the Nascent-Seq and RNA-Seq datasets: rhythmic nascent RNA and mRNA (R-R), rhythmic nascent RNA only (R-AR), rhythmic mRNA only (AR-R) and arrhythmic nascent RNA and mRNA (AR-AR). ( B ): Heatmap representation of genes with rhythmic nascent RNA and mRNA expression (n = 342). Classification is based on the phase of nascent RNA oscillations, and each lane corresponds to one gene. ( C ): Double-plotted phase distribution of rhythmic nascent RNA expression (brown) and rhythmic mRNA expression (red) for genes of the R-R gene set. Both phases are highly correlated (r = 0.92). ( D ): Distribution of the difference between the phase of mRNA expression rhythm and the phase of nascent RNA expression rhythm for the 342 R-R genes. ( E ): Amplitude of mRNA expression rhythms are correlated with nascent RNA expression rhythms (r = 0.76). ( F ) and ( G ): Similar representation to ( B ) for rhythmically transcribed genes with no mRNA expression rhythms ( C , n = 480), and genes that exhibit mRNA oscillations but no rhythms of transcription ( D , n = 862). For all three heatmaps, high expression is displayed in yellow (z-score > 1), low expression in blue (z-score

    Journal: eLife

    Article Title: Nascent-Seq reveals novel features of mouse circadian transcriptional regulation

    doi: 10.7554/eLife.00011

    Figure Lengend Snippet: Post-transcriptional events account for a significant fraction of rhythmic gene expression in the mouse liver. ( A ): Rhythmic gene expression was assessed as in Figure 2B for genes sufficiently expressed in both Nascent-Seq and RNA-Seq datasets. Four categories of rhythmically expressed genes were determined by comparing the Nascent-Seq and RNA-Seq datasets: rhythmic nascent RNA and mRNA (R-R), rhythmic nascent RNA only (R-AR), rhythmic mRNA only (AR-R) and arrhythmic nascent RNA and mRNA (AR-AR). ( B ): Heatmap representation of genes with rhythmic nascent RNA and mRNA expression (n = 342). Classification is based on the phase of nascent RNA oscillations, and each lane corresponds to one gene. ( C ): Double-plotted phase distribution of rhythmic nascent RNA expression (brown) and rhythmic mRNA expression (red) for genes of the R-R gene set. Both phases are highly correlated (r = 0.92). ( D ): Distribution of the difference between the phase of mRNA expression rhythm and the phase of nascent RNA expression rhythm for the 342 R-R genes. ( E ): Amplitude of mRNA expression rhythms are correlated with nascent RNA expression rhythms (r = 0.76). ( F ) and ( G ): Similar representation to ( B ) for rhythmically transcribed genes with no mRNA expression rhythms ( C , n = 480), and genes that exhibit mRNA oscillations but no rhythms of transcription ( D , n = 862). For all three heatmaps, high expression is displayed in yellow (z-score > 1), low expression in blue (z-score

    Article Snippet: RNA-Seq libraries (e.g., mRNA) were made using Truseq RNA sample kit (Illumina, San Diego, California) following manufacturer's recommendations.

    Techniques: Expressing, RNA Sequencing Assay, RNA Expression

    Disconnect between rhythmic BMAL1 DNA binding and its transcriptional output. ( A ): Heatmaps representing BMAL1 ChIP-Seq signal (from Rey et al., 2011 ), Nascent-Seq and RNA-Seq signal for CLK:BMAL1 target genes (six time points in duplicate). Genes were classified in four categories: rhythmic nascent RNA and mRNA (R-R), rhythmic nascent RNA only (R-AR), rhythmic mRNA only (AR-R) and arrhythmic nascent RNA and mRNA (AR-AR). High expression is displayed in yellow, low expression in blue. ( B ): Peak phase distribution of rhythmic BMAL1 DNA binding (blue, from Rey et al., 2011 ), of nascent RNA (black) and of mRNA (red) for the direct target genes that are rhythmically expressed at both the nascent RNA and mRNA levels. ( C ): Distribution of CLK:BMAL1 target genes within the 4 different classes of rhythmically expressed genes and its comparison to the genome-wide distribution. Rhythmic nascent RNA and mRNA: R-R; rhythmic nascent RNA only: R-AR; rhythmic mRNA only: AR-R; arrhythmic nascent RNA and mRNA: AR-AR. ( D ): qPCR quantification of Rev-Erbα , Per1 , Per2 and Cry1 pre-mRNA every 4 hr throughout the day in wild-type (black, n = 4 per time points) and Bmal1−/− mice (blue, n = 3 per time points). Error bar: s.e.m. ( E ): Visualization of BMAL1 ChIP-Seq (blue), CLK ChIP-Seq (green), Nascent-Seq (brown; six time points of replicate 1), Pol II ChIP-Seq signal (purple) at ZT10 and ZT22 (from Feng et al., 2011 ) and strand-specific Nascent-Seq signal for Per2 (plus strand, top; minus strand, bottom). Per2 is rhythmically transcribed (minus strand) with a peak at ZT16. An antisense transcript is rhythmically transcribed to Per2 RNA (plus strand), peaking at ZT4. DOI: http://dx.doi.org/10.7554/eLife.00011.020

    Journal: eLife

    Article Title: Nascent-Seq reveals novel features of mouse circadian transcriptional regulation

    doi: 10.7554/eLife.00011

    Figure Lengend Snippet: Disconnect between rhythmic BMAL1 DNA binding and its transcriptional output. ( A ): Heatmaps representing BMAL1 ChIP-Seq signal (from Rey et al., 2011 ), Nascent-Seq and RNA-Seq signal for CLK:BMAL1 target genes (six time points in duplicate). Genes were classified in four categories: rhythmic nascent RNA and mRNA (R-R), rhythmic nascent RNA only (R-AR), rhythmic mRNA only (AR-R) and arrhythmic nascent RNA and mRNA (AR-AR). High expression is displayed in yellow, low expression in blue. ( B ): Peak phase distribution of rhythmic BMAL1 DNA binding (blue, from Rey et al., 2011 ), of nascent RNA (black) and of mRNA (red) for the direct target genes that are rhythmically expressed at both the nascent RNA and mRNA levels. ( C ): Distribution of CLK:BMAL1 target genes within the 4 different classes of rhythmically expressed genes and its comparison to the genome-wide distribution. Rhythmic nascent RNA and mRNA: R-R; rhythmic nascent RNA only: R-AR; rhythmic mRNA only: AR-R; arrhythmic nascent RNA and mRNA: AR-AR. ( D ): qPCR quantification of Rev-Erbα , Per1 , Per2 and Cry1 pre-mRNA every 4 hr throughout the day in wild-type (black, n = 4 per time points) and Bmal1−/− mice (blue, n = 3 per time points). Error bar: s.e.m. ( E ): Visualization of BMAL1 ChIP-Seq (blue), CLK ChIP-Seq (green), Nascent-Seq (brown; six time points of replicate 1), Pol II ChIP-Seq signal (purple) at ZT10 and ZT22 (from Feng et al., 2011 ) and strand-specific Nascent-Seq signal for Per2 (plus strand, top; minus strand, bottom). Per2 is rhythmically transcribed (minus strand) with a peak at ZT16. An antisense transcript is rhythmically transcribed to Per2 RNA (plus strand), peaking at ZT4. DOI: http://dx.doi.org/10.7554/eLife.00011.020

    Article Snippet: RNA-Seq libraries (e.g., mRNA) were made using Truseq RNA sample kit (Illumina, San Diego, California) following manufacturer's recommendations.

    Techniques: Binding Assay, Chromatin Immunoprecipitation, RNA Sequencing Assay, Expressing, Genome Wide, Real-time Polymerase Chain Reaction, Mouse Assay

    Transcriptional variability of AR-R genes contributes to rhythmic mRNA expression. ( A ) and ( B ): Nascent RNA levels (brown; time points every 4 hr starting at ZT0) and mRNA levels (red; time points every 4 hr starting at ZT2) from the Nascent-Seq and RNA-Seq datasets for six genes of the AR-R gene set. While the majority of the AR-R genes exhibit variable nascent RNA expression ( A ), some of them exhibit a relatively constant transcription when compared to mRNA expression ( B ). ( C ): Standard deviation (SD; calculated using the 12 time points and normalized to the mean) of nascent RNA expression is higher than the SD normalized to the mean of mRNA levels for most AR-R genes. ( D ) and ( E ): Higher transcriptional variability (SD) of arrhythmically transcribed genes is associated with higher occurrence of rhythmic mRNA expression ( D ), but not to nascent RNA expression levels ( E ). ( F ): Higher variability of transcription for the genes of the AR-R group is associated with increase amplitude of rhythms at both Nascent RNA (brown) and mRNA (red) level. Genes of the AR-R group (n = 862) were binned into five quintiles of equal size (q1–q5). ( G ): Heatmap representation of 86 AR-R genes that exhibit high level of transcription at only one time point, and with rhythmic mRNA expression. High expression is displayed in yellow (z-score > 1), low expression in blue (z-score

    Journal: eLife

    Article Title: Nascent-Seq reveals novel features of mouse circadian transcriptional regulation

    doi: 10.7554/eLife.00011

    Figure Lengend Snippet: Transcriptional variability of AR-R genes contributes to rhythmic mRNA expression. ( A ) and ( B ): Nascent RNA levels (brown; time points every 4 hr starting at ZT0) and mRNA levels (red; time points every 4 hr starting at ZT2) from the Nascent-Seq and RNA-Seq datasets for six genes of the AR-R gene set. While the majority of the AR-R genes exhibit variable nascent RNA expression ( A ), some of them exhibit a relatively constant transcription when compared to mRNA expression ( B ). ( C ): Standard deviation (SD; calculated using the 12 time points and normalized to the mean) of nascent RNA expression is higher than the SD normalized to the mean of mRNA levels for most AR-R genes. ( D ) and ( E ): Higher transcriptional variability (SD) of arrhythmically transcribed genes is associated with higher occurrence of rhythmic mRNA expression ( D ), but not to nascent RNA expression levels ( E ). ( F ): Higher variability of transcription for the genes of the AR-R group is associated with increase amplitude of rhythms at both Nascent RNA (brown) and mRNA (red) level. Genes of the AR-R group (n = 862) were binned into five quintiles of equal size (q1–q5). ( G ): Heatmap representation of 86 AR-R genes that exhibit high level of transcription at only one time point, and with rhythmic mRNA expression. High expression is displayed in yellow (z-score > 1), low expression in blue (z-score

    Article Snippet: RNA-Seq libraries (e.g., mRNA) were made using Truseq RNA sample kit (Illumina, San Diego, California) following manufacturer's recommendations.

    Techniques: Expressing, RNA Sequencing Assay, RNA Expression, Standard Deviation

    Analysis of the different classes of rhythmically expressed genes in the mouse liver. ( A ): Nascent-Seq/RNA-Seq signal ratio (used as inferred half-life) is similar for the four categories of rhythmically expressed genes: rhythmic nascent RNA and mRNA (R-R), rhythmic nascent RNA only (R-AR), rhythmic mRNA only (AR-R) and arrhythmic nascent RNA and mRNA (AR-AR). ( B ): Similar as ( A ), using the RNA half-life values from Sharova et al., 2009 . ( C ): Nascent-Seq rhythms of 25 of the 480 R-AR genes can be attributed to the rhythmic transcription of an adjacent gene. This applies to Sphk2 Nascent-Seq rhythm, which likely results from rhythmic Dbp nascent RNA signal that extend the 3ʹend of Dbp gene and read through Sphk2 . Genes above the scale bar are transcribed from left to right and those below the scale bar are transcribed from right to left. ( D ): Gene ontology of three categories of rhythmically expressed genes: rhythmic nascent RNA and mRNA (R-R), rhythmic nascent RNA only (R-AR), rhythmic mRNA only (AR-R). DOI: http://dx.doi.org/10.7554/eLife.00011.016

    Journal: eLife

    Article Title: Nascent-Seq reveals novel features of mouse circadian transcriptional regulation

    doi: 10.7554/eLife.00011

    Figure Lengend Snippet: Analysis of the different classes of rhythmically expressed genes in the mouse liver. ( A ): Nascent-Seq/RNA-Seq signal ratio (used as inferred half-life) is similar for the four categories of rhythmically expressed genes: rhythmic nascent RNA and mRNA (R-R), rhythmic nascent RNA only (R-AR), rhythmic mRNA only (AR-R) and arrhythmic nascent RNA and mRNA (AR-AR). ( B ): Similar as ( A ), using the RNA half-life values from Sharova et al., 2009 . ( C ): Nascent-Seq rhythms of 25 of the 480 R-AR genes can be attributed to the rhythmic transcription of an adjacent gene. This applies to Sphk2 Nascent-Seq rhythm, which likely results from rhythmic Dbp nascent RNA signal that extend the 3ʹend of Dbp gene and read through Sphk2 . Genes above the scale bar are transcribed from left to right and those below the scale bar are transcribed from right to left. ( D ): Gene ontology of three categories of rhythmically expressed genes: rhythmic nascent RNA and mRNA (R-R), rhythmic nascent RNA only (R-AR), rhythmic mRNA only (AR-R). DOI: http://dx.doi.org/10.7554/eLife.00011.016

    Article Snippet: RNA-Seq libraries (e.g., mRNA) were made using Truseq RNA sample kit (Illumina, San Diego, California) following manufacturer's recommendations.

    Techniques: RNA Sequencing Assay

    Clock genes nascent RNA and mRNA expression in the mouse liver. Clock genes nascent RNA levels (brown; time points every 4 hr starting at ZT0) and mRNA levels (red; time points every 4 hr starting at ZT2) from the Nascent-Seq and RNA-Seq datasets. Relative levels between nascent RNA and mRNA expression profiles are identical for all genes to allow direct comparison. DOI: http://dx.doi.org/10.7554/eLife.00011.015

    Journal: eLife

    Article Title: Nascent-Seq reveals novel features of mouse circadian transcriptional regulation

    doi: 10.7554/eLife.00011

    Figure Lengend Snippet: Clock genes nascent RNA and mRNA expression in the mouse liver. Clock genes nascent RNA levels (brown; time points every 4 hr starting at ZT0) and mRNA levels (red; time points every 4 hr starting at ZT2) from the Nascent-Seq and RNA-Seq datasets. Relative levels between nascent RNA and mRNA expression profiles are identical for all genes to allow direct comparison. DOI: http://dx.doi.org/10.7554/eLife.00011.015

    Article Snippet: RNA-Seq libraries (e.g., mRNA) were made using Truseq RNA sample kit (Illumina, San Diego, California) following manufacturer's recommendations.

    Techniques: Expressing, RNA Sequencing Assay

    Genome-wide assay of transcription in the mouse liver using Nascent-Seq. ( A ): Distribution of high-throughput sequencing signal within introns (green), exons (blue) and intergenic regions (grey) for Nascent-Seq and RNA-Seq datasets. ( B ): Visualization of Nascent-Seq and RNA-Seq signal at chr4: 40,730,000–41,002,500. Genes above the scale bar are transcribed from left to right and those below the scale bar are transcribed from right to left. Nascent-Seq signal exhibits increased intron signal and a 5ʹ to 3ʹ gradient signal (arrow). Moreover, differences between Nascent-Seq signal and RNA-Seq signal are observed for many genes (e.g., Bag1 and B4galt1 ). ( C ): Nascent-Seq signal (brown), but not RNA-Seq signal (red), extends past the annotated 3ʹend of the genes B4galt1 and Nfx1 . ( D ): Gene ontology of genes with high Nascent-Seq and low RNA-Seq signals (and inversely) is indicative of RNA with short or long half-lives, respectively (see ‘Materials and methods’ for details). ( E ): Distribution of the Nascent-Seq/RNA-Seq signal ratio for the classes of genes enriched in ( D ). ( F ): Nascent-Seq/RNA-Seq signal ratio significantly correlates with mRNA half-lives (values from Sharova et al., 2009 ), and genes with high ratio display shorter half-lives and inversely. ( G ) and ( H ): Strategy used to determine the gene signal cut-off threshold used in our analysis. Variation of gene signal coming from the sequencing of a Nascent-Seq library (G; ZT8, replicate 1) sequenced in two Illumina flow-cell lanes was assessed by calculating the z-score ( H ). Less than 5% of the genes with a read per base pair superior to three exhibit a 1.3-fold gene signal variation. See ‘Materials and methods’ for more details. DOI: http://dx.doi.org/10.7554/eLife.00011.003

    Journal: eLife

    Article Title: Nascent-Seq reveals novel features of mouse circadian transcriptional regulation

    doi: 10.7554/eLife.00011

    Figure Lengend Snippet: Genome-wide assay of transcription in the mouse liver using Nascent-Seq. ( A ): Distribution of high-throughput sequencing signal within introns (green), exons (blue) and intergenic regions (grey) for Nascent-Seq and RNA-Seq datasets. ( B ): Visualization of Nascent-Seq and RNA-Seq signal at chr4: 40,730,000–41,002,500. Genes above the scale bar are transcribed from left to right and those below the scale bar are transcribed from right to left. Nascent-Seq signal exhibits increased intron signal and a 5ʹ to 3ʹ gradient signal (arrow). Moreover, differences between Nascent-Seq signal and RNA-Seq signal are observed for many genes (e.g., Bag1 and B4galt1 ). ( C ): Nascent-Seq signal (brown), but not RNA-Seq signal (red), extends past the annotated 3ʹend of the genes B4galt1 and Nfx1 . ( D ): Gene ontology of genes with high Nascent-Seq and low RNA-Seq signals (and inversely) is indicative of RNA with short or long half-lives, respectively (see ‘Materials and methods’ for details). ( E ): Distribution of the Nascent-Seq/RNA-Seq signal ratio for the classes of genes enriched in ( D ). ( F ): Nascent-Seq/RNA-Seq signal ratio significantly correlates with mRNA half-lives (values from Sharova et al., 2009 ), and genes with high ratio display shorter half-lives and inversely. ( G ) and ( H ): Strategy used to determine the gene signal cut-off threshold used in our analysis. Variation of gene signal coming from the sequencing of a Nascent-Seq library (G; ZT8, replicate 1) sequenced in two Illumina flow-cell lanes was assessed by calculating the z-score ( H ). Less than 5% of the genes with a read per base pair superior to three exhibit a 1.3-fold gene signal variation. See ‘Materials and methods’ for more details. DOI: http://dx.doi.org/10.7554/eLife.00011.003

    Article Snippet: RNA-Seq libraries (e.g., mRNA) were made using Truseq RNA sample kit (Illumina, San Diego, California) following manufacturer's recommendations.

    Techniques: Genome Wide, Next-Generation Sequencing, RNA Sequencing Assay, Sequencing, Flow Cytometry

    Post-transcriptional events contribute to rhythmic mRNA expression in the mouse liver. Although rhythmic transcription plays a major role for approximately 30% of the genes that exhibit rhythmic mRNA expression, post-transcriptional events significantly contribute to the generation of mRNA rhythms for the majority of genes (∼70%). Many post-transcriptional cyclers exhibit highly variable transcription that is buffered to generate robust rhythmic mRNA expression. Few genes exhibit a relatively constant transcription when compared to mRNA expression. These post-transcriptional events may include roles for RNA binding proteins and miRNAs to regulate RNA stability, 3′ end formation and nuclei export. DOI: http://dx.doi.org/10.7554/eLife.00011.021

    Journal: eLife

    Article Title: Nascent-Seq reveals novel features of mouse circadian transcriptional regulation

    doi: 10.7554/eLife.00011

    Figure Lengend Snippet: Post-transcriptional events contribute to rhythmic mRNA expression in the mouse liver. Although rhythmic transcription plays a major role for approximately 30% of the genes that exhibit rhythmic mRNA expression, post-transcriptional events significantly contribute to the generation of mRNA rhythms for the majority of genes (∼70%). Many post-transcriptional cyclers exhibit highly variable transcription that is buffered to generate robust rhythmic mRNA expression. Few genes exhibit a relatively constant transcription when compared to mRNA expression. These post-transcriptional events may include roles for RNA binding proteins and miRNAs to regulate RNA stability, 3′ end formation and nuclei export. DOI: http://dx.doi.org/10.7554/eLife.00011.021

    Article Snippet: RNA-Seq libraries (e.g., mRNA) were made using Truseq RNA sample kit (Illumina, San Diego, California) following manufacturer's recommendations.

    Techniques: Expressing, RNA Binding Assay

    SroC induces GcvB degradation by a base-pairing mechanism GcvB-SroC base-pairing regions. The compensatory base pair changes in GcvB and SroC are indicated in red. Salmonella Δ gcvB Δ sroC (JVS-5822) strain was cotransformed with pP L -GcvB and pBAD-SroC derivatives (see Supplementary Table S4). Each transformant was grown to OD 600 of 0.5 (0 min) and incubated for another 10 min in the presence of 0.2% l -arabinose. Total RNA was prepared from the cells and subjected to Northern blot analysis. The fold repression of GcvB was determined from three independent replicates; standard deviation is shown. The chromosomally modified wild-type sroC strain (JVS-10108), sroC ** mutant (JVS-10111) and sroC deletion mutant (JVS-5821) were grown to early stationary phase in LB medium (OD 600 of 2.0) prior to the addition of rifampicin. Cultures were harvested at the indicated time points after rifampicin treatment. RNA was isolated and analyzed by Northern blot as in Fig 3B . Source data are available online for this figure.

    Journal: The EMBO Journal

    Article Title: Cross talk between ABC transporter mRNAs via a target mRNA-derived sponge of the GcvB small RNA

    doi: 10.15252/embj.201490546

    Figure Lengend Snippet: SroC induces GcvB degradation by a base-pairing mechanism GcvB-SroC base-pairing regions. The compensatory base pair changes in GcvB and SroC are indicated in red. Salmonella Δ gcvB Δ sroC (JVS-5822) strain was cotransformed with pP L -GcvB and pBAD-SroC derivatives (see Supplementary Table S4). Each transformant was grown to OD 600 of 0.5 (0 min) and incubated for another 10 min in the presence of 0.2% l -arabinose. Total RNA was prepared from the cells and subjected to Northern blot analysis. The fold repression of GcvB was determined from three independent replicates; standard deviation is shown. The chromosomally modified wild-type sroC strain (JVS-10108), sroC ** mutant (JVS-10111) and sroC deletion mutant (JVS-5821) were grown to early stationary phase in LB medium (OD 600 of 2.0) prior to the addition of rifampicin. Cultures were harvested at the indicated time points after rifampicin treatment. RNA was isolated and analyzed by Northern blot as in Fig 3B . Source data are available online for this figure.

    Article Snippet: At optical density (OD600 ) of 1.5, l -arabinose was added to cultures at a final concentration of 0.2% to induced SroC expression for 10 min, and total RNA was prepared with SV total RNA isolation system (Promega).

    Techniques: Incubation, Northern Blot, Standard Deviation, Modification, Mutagenesis, Isolation

    Direct binding between GcvB and SroC sRNAs 20 nM of 5′-end-labeled GcvB and SroC were subjected to RNase T1 and lead(II) cleavage in the absence and presence of 100 nM cold sRNAs, SroC, and GcvB, respectively. Lane C: untreated RNA; lane T1: RNase T1 ladder of denatured RNA; lane OH: alkaline ladder. The position of G residues cleaved by RNase T1 is indicated at the left of picture. Secondary structures of GcvB and SroC, paired or alone. RNase T1 cleavage sites are indicated by arrowheads; color indicates those that appeared (red) or disappeared (blue) upon base-pairing. The base pairing sites BS1 and BS2 are shadowed. Source data are available online for this figure.

    Journal: The EMBO Journal

    Article Title: Cross talk between ABC transporter mRNAs via a target mRNA-derived sponge of the GcvB small RNA

    doi: 10.15252/embj.201490546

    Figure Lengend Snippet: Direct binding between GcvB and SroC sRNAs 20 nM of 5′-end-labeled GcvB and SroC were subjected to RNase T1 and lead(II) cleavage in the absence and presence of 100 nM cold sRNAs, SroC, and GcvB, respectively. Lane C: untreated RNA; lane T1: RNase T1 ladder of denatured RNA; lane OH: alkaline ladder. The position of G residues cleaved by RNase T1 is indicated at the left of picture. Secondary structures of GcvB and SroC, paired or alone. RNase T1 cleavage sites are indicated by arrowheads; color indicates those that appeared (red) or disappeared (blue) upon base-pairing. The base pairing sites BS1 and BS2 are shadowed. Source data are available online for this figure.

    Article Snippet: At optical density (OD600 ) of 1.5, l -arabinose was added to cultures at a final concentration of 0.2% to induced SroC expression for 10 min, and total RNA was prepared with SV total RNA isolation system (Promega).

    Techniques: Binding Assay, Labeling

    RNase E mediates SroC processing and GcvB degradation in distinct pathways Salmonella Δ gltIJKL rne + (JVS-9257) and Δ gltIJKL rne3071 (JVS-9258) strains transformed with pBAD- gltI or pBAD-SroC were grown to OD 600 of 0.3 at 28°C and further incubated at 44°C for 30 min (OD 600 of ˜0.5, indicated as time point 0). SroC expression was then induced for 10 min in the presence of 0.2% of l -arabinose. Total RNA was analyzed by Northern blots. 100 nM of 5′PPP or 5′P in vitro -transcribed preSroC was incubated with 100 nM of purified RNase E (1–529) at 30°C for the indicated time in the presence (lanes 10–17) or absence (lanes 2–9) of 100 nM Hfq. The same amount of preSroC was loaded in lane 1 as a control. SroC transcripts were detected using 5′-end-labeled oligonucleotide JVO-2907. Salmonella Δ gltIJKL rne + (JVS-9257) and Δ gltIJKL rneR169K (JVS-11001) strains transformed with pBAD- gltI or pBAD-SroC were grown to OD 600 of 0.5 (0 min) at 37°C and was further incubated for 10 min in the presence of 0.2% l -arabinose. The asterisk indicates transcriptional read-through to the rrnB terminator located downstream on the plasmid. Total RNA was prepared from the Salmonella strains and subjected to Northern blot analysis. 9S rRNA accumulated in the rneR169K strain. Estimated size from pUC8 marker is indicated on the right. Source data are available online for this figure.

    Journal: The EMBO Journal

    Article Title: Cross talk between ABC transporter mRNAs via a target mRNA-derived sponge of the GcvB small RNA

    doi: 10.15252/embj.201490546

    Figure Lengend Snippet: RNase E mediates SroC processing and GcvB degradation in distinct pathways Salmonella Δ gltIJKL rne + (JVS-9257) and Δ gltIJKL rne3071 (JVS-9258) strains transformed with pBAD- gltI or pBAD-SroC were grown to OD 600 of 0.3 at 28°C and further incubated at 44°C for 30 min (OD 600 of ˜0.5, indicated as time point 0). SroC expression was then induced for 10 min in the presence of 0.2% of l -arabinose. Total RNA was analyzed by Northern blots. 100 nM of 5′PPP or 5′P in vitro -transcribed preSroC was incubated with 100 nM of purified RNase E (1–529) at 30°C for the indicated time in the presence (lanes 10–17) or absence (lanes 2–9) of 100 nM Hfq. The same amount of preSroC was loaded in lane 1 as a control. SroC transcripts were detected using 5′-end-labeled oligonucleotide JVO-2907. Salmonella Δ gltIJKL rne + (JVS-9257) and Δ gltIJKL rneR169K (JVS-11001) strains transformed with pBAD- gltI or pBAD-SroC were grown to OD 600 of 0.5 (0 min) at 37°C and was further incubated for 10 min in the presence of 0.2% l -arabinose. The asterisk indicates transcriptional read-through to the rrnB terminator located downstream on the plasmid. Total RNA was prepared from the Salmonella strains and subjected to Northern blot analysis. 9S rRNA accumulated in the rneR169K strain. Estimated size from pUC8 marker is indicated on the right. Source data are available online for this figure.

    Article Snippet: At optical density (OD600 ) of 1.5, l -arabinose was added to cultures at a final concentration of 0.2% to induced SroC expression for 10 min, and total RNA was prepared with SV total RNA isolation system (Promega).

    Techniques: Transformation Assay, Incubation, Expressing, Northern Blot, In Vitro, Purification, Labeling, Plasmid Preparation, Marker

    Posttranscriptional regulation of GcvB by SroC Salmonella Δ sroC (JVS-5821), Δ gcvB Δ sroC (JVS-5822), and Δ sroC Δ hfq (JVS-9031) strains were transformed with pBAD-ctrl (pKP8-35) or pBAD-SroC (pYC6-4). Δ gcvB Δ sroC was cotransformed with pP L -GcvB (pMM03). Each strain was grown to OD 600 of 0.5 (0 min) and was further incubated for 10 min in the presence of 0.2% l -arabinose. Salmonella WT (JVS-1574), Δ gltIJKL (JVS-5823), ΔCA (JVS-10741), and Δ sroC (JVS-5821) strains were grown to OD 600 of 2.0 prior to the addition of rifampicin. Total RNA was analyzed by Northern blot to determine decay rates of GcvB. The half-lives were determined from three independent experiments; the standard deviation is indicated. Source data are available online for this figure.

    Journal: The EMBO Journal

    Article Title: Cross talk between ABC transporter mRNAs via a target mRNA-derived sponge of the GcvB small RNA

    doi: 10.15252/embj.201490546

    Figure Lengend Snippet: Posttranscriptional regulation of GcvB by SroC Salmonella Δ sroC (JVS-5821), Δ gcvB Δ sroC (JVS-5822), and Δ sroC Δ hfq (JVS-9031) strains were transformed with pBAD-ctrl (pKP8-35) or pBAD-SroC (pYC6-4). Δ gcvB Δ sroC was cotransformed with pP L -GcvB (pMM03). Each strain was grown to OD 600 of 0.5 (0 min) and was further incubated for 10 min in the presence of 0.2% l -arabinose. Salmonella WT (JVS-1574), Δ gltIJKL (JVS-5823), ΔCA (JVS-10741), and Δ sroC (JVS-5821) strains were grown to OD 600 of 2.0 prior to the addition of rifampicin. Total RNA was analyzed by Northern blot to determine decay rates of GcvB. The half-lives were determined from three independent experiments; the standard deviation is indicated. Source data are available online for this figure.

    Article Snippet: At optical density (OD600 ) of 1.5, l -arabinose was added to cultures at a final concentration of 0.2% to induced SroC expression for 10 min, and total RNA was prepared with SV total RNA isolation system (Promega).

    Techniques: Transformation Assay, Incubation, Northern Blot, Standard Deviation

    SroC is the effector molecule for GcvB repression Expression changes of OppA and GcvB upon deletion of gltIJKL locus. WT (JVS-1574), Δ gltIJKL (JVS-5823), Δ gltJKL (JVS-10795), Δ sroC (JVS-5821), Δ gcvB Δ sroC (JVS-5822), and Δ gcvB (JVS-0236) strains were grown to early stationary phase (OD 600 of 2.0) in LB medium. Expression changes of OppA and GcvB by overexpression of gltI - sroC . Δ gltIJKL strain (JVS-5823) harboring pBAD-ctrl (lane 1), pBAD- gltI (pMM36) derivatives (lanes 2-5), or pBAD-SroC (lane 6) was grown to early stationary phase (OD 600 of 2.0) in LB medium supplemented with 0.02% l -arabinose. Data information: Upper two panels: Total protein was analyzed by Western blot to quantify OppA expression. GroEL served as a loading control. Lower three panels: Total RNA was analyzed by Northern blot, and expression of GcvB and SroC was monitored. 5S rRNA served as a loading control. Estimated size from pUC8 marker is indicated on the right. Source data are available online for this figure.

    Journal: The EMBO Journal

    Article Title: Cross talk between ABC transporter mRNAs via a target mRNA-derived sponge of the GcvB small RNA

    doi: 10.15252/embj.201490546

    Figure Lengend Snippet: SroC is the effector molecule for GcvB repression Expression changes of OppA and GcvB upon deletion of gltIJKL locus. WT (JVS-1574), Δ gltIJKL (JVS-5823), Δ gltJKL (JVS-10795), Δ sroC (JVS-5821), Δ gcvB Δ sroC (JVS-5822), and Δ gcvB (JVS-0236) strains were grown to early stationary phase (OD 600 of 2.0) in LB medium. Expression changes of OppA and GcvB by overexpression of gltI - sroC . Δ gltIJKL strain (JVS-5823) harboring pBAD-ctrl (lane 1), pBAD- gltI (pMM36) derivatives (lanes 2-5), or pBAD-SroC (lane 6) was grown to early stationary phase (OD 600 of 2.0) in LB medium supplemented with 0.02% l -arabinose. Data information: Upper two panels: Total protein was analyzed by Western blot to quantify OppA expression. GroEL served as a loading control. Lower three panels: Total RNA was analyzed by Northern blot, and expression of GcvB and SroC was monitored. 5S rRNA served as a loading control. Estimated size from pUC8 marker is indicated on the right. Source data are available online for this figure.

    Article Snippet: At optical density (OD600 ) of 1.5, l -arabinose was added to cultures at a final concentration of 0.2% to induced SroC expression for 10 min, and total RNA was prepared with SV total RNA isolation system (Promega).

    Techniques: Expressing, Over Expression, Western Blot, Northern Blot, Marker