ERX7881050 E-MTAB-11402:00d_R2_p ERP135194 PRJEB50600 Cellular and gene expression patterns associated with root bifurcation in Selaginella ERS10419821 SAMEA12812860 00d_R2_p RNA-Seq TRANSCRIPTOMIC Oligo-dT To identify possible molecular mechanisms with a role in root branching initiation in S. moellendorffii, we employed the developmental root branching assay for an RNA-seq experiment and sampled root tips on each day from 0 to 5 d after the first branching (time point 0), in which 300 µm apical parts were sampled to enrich for the meristematic region, while non-meristematic root regions were sampled separately. Sampled roots in the time course (300 root tips per sample, 4 biological repeats per time point) were cut off using a pair of stainless microscissors and then stored in RNAlater® RNA Stabilization Solution (Thermo Fisher Scientific) according to the manufacturer's instruction. Subsequently, microdissection was performed to collect root apices of 0.3 mm long, as well as non-meristematic regions between apices and branching point for the 5 d post first branching samples. Plants were grown aseptically under a 16-h light/8-h dark photoperiod at 20.25–43.2 μmol/m2/s in a 24°C growth chamber and roots developed after the transfer of explants to fresh MS1/2 medium. For RNA extraction, samples were ground three times using a QIAGEN Retsch Tissuelyser (30 Hz, 30 s). RNA extraction was done via TRIzol™ reagent (Thermo Fisher Scientific) and the RNeasy Plant Mini Kit (Qiagen) according to the provided protocols. Per sample, an amount of 250 ng of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: Part # 15031047 Rev. E - October 2013) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Illumina HiSeq 4000 Experimental Factor: time 0 Experimental Factor: sampling site meristem ERX7881051 E-MTAB-11402:00d_R3_p ERP135194 PRJEB50600 Cellular and gene expression patterns associated with root bifurcation in Selaginella ERS10419822 SAMEA12812861 00d_R3_p RNA-Seq TRANSCRIPTOMIC Oligo-dT To identify possible molecular mechanisms with a role in root branching initiation in S. moellendorffii, we employed the developmental root branching assay for an RNA-seq experiment and sampled root tips on each day from 0 to 5 d after the first branching (time point 0), in which 300 µm apical parts were sampled to enrich for the meristematic region, while non-meristematic root regions were sampled separately. Sampled roots in the time course (300 root tips per sample, 4 biological repeats per time point) were cut off using a pair of stainless microscissors and then stored in RNAlater® RNA Stabilization Solution (Thermo Fisher Scientific) according to the manufacturer's instruction. Subsequently, microdissection was performed to collect root apices of 0.3 mm long, as well as non-meristematic regions between apices and branching point for the 5 d post first branching samples. Plants were grown aseptically under a 16-h light/8-h dark photoperiod at 20.25–43.2 μmol/m2/s in a 24°C growth chamber and roots developed after the transfer of explants to fresh MS1/2 medium. For RNA extraction, samples were ground three times using a QIAGEN Retsch Tissuelyser (30 Hz, 30 s). RNA extraction was done via TRIzol™ reagent (Thermo Fisher Scientific) and the RNeasy Plant Mini Kit (Qiagen) according to the provided protocols. Per sample, an amount of 250 ng of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: Part # 15031047 Rev. E - October 2013) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Illumina HiSeq 4000 Experimental Factor: time 0 Experimental Factor: sampling site meristem ERX7881052 E-MTAB-11402:00d_R4_p ERP135194 PRJEB50600 Cellular and gene expression patterns associated with root bifurcation in Selaginella ERS10419823 SAMEA12812862 00d_R4_p RNA-Seq TRANSCRIPTOMIC Oligo-dT To identify possible molecular mechanisms with a role in root branching initiation in S. moellendorffii, we employed the developmental root branching assay for an RNA-seq experiment and sampled root tips on each day from 0 to 5 d after the first branching (time point 0), in which 300 µm apical parts were sampled to enrich for the meristematic region, while non-meristematic root regions were sampled separately. Sampled roots in the time course (300 root tips per sample, 4 biological repeats per time point) were cut off using a pair of stainless microscissors and then stored in RNAlater® RNA Stabilization Solution (Thermo Fisher Scientific) according to the manufacturer's instruction. Subsequently, microdissection was performed to collect root apices of 0.3 mm long, as well as non-meristematic regions between apices and branching point for the 5 d post first branching samples. Plants were grown aseptically under a 16-h light/8-h dark photoperiod at 20.25–43.2 μmol/m2/s in a 24°C growth chamber and roots developed after the transfer of explants to fresh MS1/2 medium. For RNA extraction, samples were ground three times using a QIAGEN Retsch Tissuelyser (30 Hz, 30 s). RNA extraction was done via TRIzol™ reagent (Thermo Fisher Scientific) and the RNeasy Plant Mini Kit (Qiagen) according to the provided protocols. Per sample, an amount of 250 ng of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: Part # 15031047 Rev. E - October 2013) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Illumina HiSeq 4000 Experimental Factor: time 0 Experimental Factor: sampling site meristem ERX7881053 E-MTAB-11402:01d_R1_p ERP135194 PRJEB50600 Cellular and gene expression patterns associated with root bifurcation in Selaginella ERS10419824 SAMEA12812863 01d_R1_p RNA-Seq TRANSCRIPTOMIC Oligo-dT To identify possible molecular mechanisms with a role in root branching initiation in S. moellendorffii, we employed the developmental root branching assay for an RNA-seq experiment and sampled root tips on each day from 0 to 5 d after the first branching (time point 0), in which 300 µm apical parts were sampled to enrich for the meristematic region, while non-meristematic root regions were sampled separately. Sampled roots in the time course (300 root tips per sample, 4 biological repeats per time point) were cut off using a pair of stainless microscissors and then stored in RNAlater® RNA Stabilization Solution (Thermo Fisher Scientific) according to the manufacturer's instruction. Subsequently, microdissection was performed to collect root apices of 0.3 mm long, as well as non-meristematic regions between apices and branching point for the 5 d post first branching samples. Plants were grown aseptically under a 16-h light/8-h dark photoperiod at 20.25–43.2 μmol/m2/s in a 24°C growth chamber and roots developed after the transfer of explants to fresh MS1/2 medium. For RNA extraction, samples were ground three times using a QIAGEN Retsch Tissuelyser (30 Hz, 30 s). RNA extraction was done via TRIzol™ reagent (Thermo Fisher Scientific) and the RNeasy Plant Mini Kit (Qiagen) according to the provided protocols. Per sample, an amount of 250 ng of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: Part # 15031047 Rev. E - October 2013) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Illumina HiSeq 4000 Experimental Factor: time 1 Experimental Factor: sampling site meristem ERX7881054 E-MTAB-11402:01d_R2_p ERP135194 PRJEB50600 Cellular and gene expression patterns associated with root bifurcation in Selaginella ERS10419825 SAMEA12812864 01d_R2_p RNA-Seq TRANSCRIPTOMIC Oligo-dT To identify possible molecular mechanisms with a role in root branching initiation in S. moellendorffii, we employed the developmental root branching assay for an RNA-seq experiment and sampled root tips on each day from 0 to 5 d after the first branching (time point 0), in which 300 µm apical parts were sampled to enrich for the meristematic region, while non-meristematic root regions were sampled separately. Sampled roots in the time course (300 root tips per sample, 4 biological repeats per time point) were cut off using a pair of stainless microscissors and then stored in RNAlater® RNA Stabilization Solution (Thermo Fisher Scientific) according to the manufacturer's instruction. Subsequently, microdissection was performed to collect root apices of 0.3 mm long, as well as non-meristematic regions between apices and branching point for the 5 d post first branching samples. Plants were grown aseptically under a 16-h light/8-h dark photoperiod at 20.25–43.2 μmol/m2/s in a 24°C growth chamber and roots developed after the transfer of explants to fresh MS1/2 medium. For RNA extraction, samples were ground three times using a QIAGEN Retsch Tissuelyser (30 Hz, 30 s). RNA extraction was done via TRIzol™ reagent (Thermo Fisher Scientific) and the RNeasy Plant Mini Kit (Qiagen) according to the provided protocols. Per sample, an amount of 250 ng of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: Part # 15031047 Rev. E - October 2013) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Illumina HiSeq 4000 Experimental Factor: time 1 Experimental Factor: sampling site meristem ERX7881055 E-MTAB-11402:01d_R3_p ERP135194 PRJEB50600 Cellular and gene expression patterns associated with root bifurcation in Selaginella ERS10419826 SAMEA12812865 01d_R3_p RNA-Seq TRANSCRIPTOMIC Oligo-dT To identify possible molecular mechanisms with a role in root branching initiation in S. moellendorffii, we employed the developmental root branching assay for an RNA-seq experiment and sampled root tips on each day from 0 to 5 d after the first branching (time point 0), in which 300 µm apical parts were sampled to enrich for the meristematic region, while non-meristematic root regions were sampled separately. Sampled roots in the time course (300 root tips per sample, 4 biological repeats per time point) were cut off using a pair of stainless microscissors and then stored in RNAlater® RNA Stabilization Solution (Thermo Fisher Scientific) according to the manufacturer's instruction. Subsequently, microdissection was performed to collect root apices of 0.3 mm long, as well as non-meristematic regions between apices and branching point for the 5 d post first branching samples. Plants were grown aseptically under a 16-h light/8-h dark photoperiod at 20.25–43.2 μmol/m2/s in a 24°C growth chamber and roots developed after the transfer of explants to fresh MS1/2 medium. For RNA extraction, samples were ground three times using a QIAGEN Retsch Tissuelyser (30 Hz, 30 s). RNA extraction was done via TRIzol™ reagent (Thermo Fisher Scientific) and the RNeasy Plant Mini Kit (Qiagen) according to the provided protocols. Per sample, an amount of 250 ng of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: Part # 15031047 Rev. E - October 2013) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Illumina HiSeq 4000 Experimental Factor: time 1 Experimental Factor: sampling site meristem ERX7881056 E-MTAB-11402:02d_R1_p ERP135194 PRJEB50600 Cellular and gene expression patterns associated with root bifurcation in Selaginella ERS10419827 SAMEA12812866 02d_R1_p RNA-Seq TRANSCRIPTOMIC Oligo-dT To identify possible molecular mechanisms with a role in root branching initiation in S. moellendorffii, we employed the developmental root branching assay for an RNA-seq experiment and sampled root tips on each day from 0 to 5 d after the first branching (time point 0), in which 300 µm apical parts were sampled to enrich for the meristematic region, while non-meristematic root regions were sampled separately. Sampled roots in the time course (300 root tips per sample, 4 biological repeats per time point) were cut off using a pair of stainless microscissors and then stored in RNAlater® RNA Stabilization Solution (Thermo Fisher Scientific) according to the manufacturer's instruction. Subsequently, microdissection was performed to collect root apices of 0.3 mm long, as well as non-meristematic regions between apices and branching point for the 5 d post first branching samples. Plants were grown aseptically under a 16-h light/8-h dark photoperiod at 20.25–43.2 μmol/m2/s in a 24°C growth chamber and roots developed after the transfer of explants to fresh MS1/2 medium. For RNA extraction, samples were ground three times using a QIAGEN Retsch Tissuelyser (30 Hz, 30 s). RNA extraction was done via TRIzol™ reagent (Thermo Fisher Scientific) and the RNeasy Plant Mini Kit (Qiagen) according to the provided protocols. Per sample, an amount of 250 ng of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: Part # 15031047 Rev. E - October 2013) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Illumina HiSeq 4000 Experimental Factor: time 2 Experimental Factor: sampling site meristem ERX7881057 E-MTAB-11402:02d_R2_p ERP135194 PRJEB50600 Cellular and gene expression patterns associated with root bifurcation in Selaginella ERS10419828 SAMEA12812867 02d_R2_p RNA-Seq TRANSCRIPTOMIC Oligo-dT To identify possible molecular mechanisms with a role in root branching initiation in S. moellendorffii, we employed the developmental root branching assay for an RNA-seq experiment and sampled root tips on each day from 0 to 5 d after the first branching (time point 0), in which 300 µm apical parts were sampled to enrich for the meristematic region, while non-meristematic root regions were sampled separately. Sampled roots in the time course (300 root tips per sample, 4 biological repeats per time point) were cut off using a pair of stainless microscissors and then stored in RNAlater® RNA Stabilization Solution (Thermo Fisher Scientific) according to the manufacturer's instruction. Subsequently, microdissection was performed to collect root apices of 0.3 mm long, as well as non-meristematic regions between apices and branching point for the 5 d post first branching samples. Plants were grown aseptically under a 16-h light/8-h dark photoperiod at 20.25–43.2 μmol/m2/s in a 24°C growth chamber and roots developed after the transfer of explants to fresh MS1/2 medium. For RNA extraction, samples were ground three times using a QIAGEN Retsch Tissuelyser (30 Hz, 30 s). RNA extraction was done via TRIzol™ reagent (Thermo Fisher Scientific) and the RNeasy Plant Mini Kit (Qiagen) according to the provided protocols. Per sample, an amount of 250 ng of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: Part # 15031047 Rev. E - October 2013) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Illumina HiSeq 4000 Experimental Factor: time 2 Experimental Factor: sampling site meristem ERX7881058 E-MTAB-11402:02d_R3_p ERP135194 PRJEB50600 Cellular and gene expression patterns associated with root bifurcation in Selaginella ERS10419829 SAMEA12812868 02d_R3_p RNA-Seq TRANSCRIPTOMIC Oligo-dT To identify possible molecular mechanisms with a role in root branching initiation in S. moellendorffii, we employed the developmental root branching assay for an RNA-seq experiment and sampled root tips on each day from 0 to 5 d after the first branching (time point 0), in which 300 µm apical parts were sampled to enrich for the meristematic region, while non-meristematic root regions were sampled separately. Sampled roots in the time course (300 root tips per sample, 4 biological repeats per time point) were cut off using a pair of stainless microscissors and then stored in RNAlater® RNA Stabilization Solution (Thermo Fisher Scientific) according to the manufacturer's instruction. Subsequently, microdissection was performed to collect root apices of 0.3 mm long, as well as non-meristematic regions between apices and branching point for the 5 d post first branching samples. Plants were grown aseptically under a 16-h light/8-h dark photoperiod at 20.25–43.2 μmol/m2/s in a 24°C growth chamber and roots developed after the transfer of explants to fresh MS1/2 medium. For RNA extraction, samples were ground three times using a QIAGEN Retsch Tissuelyser (30 Hz, 30 s). RNA extraction was done via TRIzol™ reagent (Thermo Fisher Scientific) and the RNeasy Plant Mini Kit (Qiagen) according to the provided protocols. Per sample, an amount of 250 ng of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: Part # 15031047 Rev. E - October 2013) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Illumina HiSeq 4000 Experimental Factor: time 2 Experimental Factor: sampling site meristem ERX7881059 E-MTAB-11402:02d_R4_p ERP135194 PRJEB50600 Cellular and gene expression patterns associated with root bifurcation in Selaginella ERS10419830 SAMEA12812869 02d_R4_p RNA-Seq TRANSCRIPTOMIC Oligo-dT To identify possible molecular mechanisms with a role in root branching initiation in S. moellendorffii, we employed the developmental root branching assay for an RNA-seq experiment and sampled root tips on each day from 0 to 5 d after the first branching (time point 0), in which 300 µm apical parts were sampled to enrich for the meristematic region, while non-meristematic root regions were sampled separately. Sampled roots in the time course (300 root tips per sample, 4 biological repeats per time point) were cut off using a pair of stainless microscissors and then stored in RNAlater® RNA Stabilization Solution (Thermo Fisher Scientific) according to the manufacturer's instruction. Subsequently, microdissection was performed to collect root apices of 0.3 mm long, as well as non-meristematic regions between apices and branching point for the 5 d post first branching samples. Plants were grown aseptically under a 16-h light/8-h dark photoperiod at 20.25–43.2 μmol/m2/s in a 24°C growth chamber and roots developed after the transfer of explants to fresh MS1/2 medium. For RNA extraction, samples were ground three times using a QIAGEN Retsch Tissuelyser (30 Hz, 30 s). RNA extraction was done via TRIzol™ reagent (Thermo Fisher Scientific) and the RNeasy Plant Mini Kit (Qiagen) according to the provided protocols. Per sample, an amount of 250 ng of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: Part # 15031047 Rev. E - October 2013) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Illumina HiSeq 4000 Experimental Factor: time 2 Experimental Factor: sampling site meristem ERX7881060 E-MTAB-11402:03d_R2_p ERP135194 PRJEB50600 Cellular and gene expression patterns associated with root bifurcation in Selaginella ERS10419831 SAMEA12812870 03d_R2_p RNA-Seq TRANSCRIPTOMIC Oligo-dT To identify possible molecular mechanisms with a role in root branching initiation in S. moellendorffii, we employed the developmental root branching assay for an RNA-seq experiment and sampled root tips on each day from 0 to 5 d after the first branching (time point 0), in which 300 µm apical parts were sampled to enrich for the meristematic region, while non-meristematic root regions were sampled separately. Sampled roots in the time course (300 root tips per sample, 4 biological repeats per time point) were cut off using a pair of stainless microscissors and then stored in RNAlater® RNA Stabilization Solution (Thermo Fisher Scientific) according to the manufacturer's instruction. Subsequently, microdissection was performed to collect root apices of 0.3 mm long, as well as non-meristematic regions between apices and branching point for the 5 d post first branching samples. Plants were grown aseptically under a 16-h light/8-h dark photoperiod at 20.25–43.2 μmol/m2/s in a 24°C growth chamber and roots developed after the transfer of explants to fresh MS1/2 medium. For RNA extraction, samples were ground three times using a QIAGEN Retsch Tissuelyser (30 Hz, 30 s). RNA extraction was done via TRIzol™ reagent (Thermo Fisher Scientific) and the RNeasy Plant Mini Kit (Qiagen) according to the provided protocols. Per sample, an amount of 250 ng of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: Part # 15031047 Rev. E - October 2013) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Illumina HiSeq 4000 Experimental Factor: time 3 Experimental Factor: sampling site meristem ERX7881061 E-MTAB-11402:03d_R3_p ERP135194 PRJEB50600 Cellular and gene expression patterns associated with root bifurcation in Selaginella ERS10419832 SAMEA12812871 03d_R3_p RNA-Seq TRANSCRIPTOMIC Oligo-dT To identify possible molecular mechanisms with a role in root branching initiation in S. moellendorffii, we employed the developmental root branching assay for an RNA-seq experiment and sampled root tips on each day from 0 to 5 d after the first branching (time point 0), in which 300 µm apical parts were sampled to enrich for the meristematic region, while non-meristematic root regions were sampled separately. Sampled roots in the time course (300 root tips per sample, 4 biological repeats per time point) were cut off using a pair of stainless microscissors and then stored in RNAlater® RNA Stabilization Solution (Thermo Fisher Scientific) according to the manufacturer's instruction. Subsequently, microdissection was performed to collect root apices of 0.3 mm long, as well as non-meristematic regions between apices and branching point for the 5 d post first branching samples. Plants were grown aseptically under a 16-h light/8-h dark photoperiod at 20.25–43.2 μmol/m2/s in a 24°C growth chamber and roots developed after the transfer of explants to fresh MS1/2 medium. For RNA extraction, samples were ground three times using a QIAGEN Retsch Tissuelyser (30 Hz, 30 s). RNA extraction was done via TRIzol™ reagent (Thermo Fisher Scientific) and the RNeasy Plant Mini Kit (Qiagen) according to the provided protocols. Per sample, an amount of 250 ng of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: Part # 15031047 Rev. E - October 2013) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Illumina HiSeq 4000 Experimental Factor: time 3 Experimental Factor: sampling site meristem ERX7881062 E-MTAB-11402:03d_R4_p ERP135194 PRJEB50600 Cellular and gene expression patterns associated with root bifurcation in Selaginella ERS10419833 SAMEA12812872 03d_R4_p RNA-Seq TRANSCRIPTOMIC Oligo-dT To identify possible molecular mechanisms with a role in root branching initiation in S. moellendorffii, we employed the developmental root branching assay for an RNA-seq experiment and sampled root tips on each day from 0 to 5 d after the first branching (time point 0), in which 300 µm apical parts were sampled to enrich for the meristematic region, while non-meristematic root regions were sampled separately. Sampled roots in the time course (300 root tips per sample, 4 biological repeats per time point) were cut off using a pair of stainless microscissors and then stored in RNAlater® RNA Stabilization Solution (Thermo Fisher Scientific) according to the manufacturer's instruction. Subsequently, microdissection was performed to collect root apices of 0.3 mm long, as well as non-meristematic regions between apices and branching point for the 5 d post first branching samples. Plants were grown aseptically under a 16-h light/8-h dark photoperiod at 20.25–43.2 μmol/m2/s in a 24°C growth chamber and roots developed after the transfer of explants to fresh MS1/2 medium. For RNA extraction, samples were ground three times using a QIAGEN Retsch Tissuelyser (30 Hz, 30 s). RNA extraction was done via TRIzol™ reagent (Thermo Fisher Scientific) and the RNeasy Plant Mini Kit (Qiagen) according to the provided protocols. Per sample, an amount of 250 ng of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: Part # 15031047 Rev. E - October 2013) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Illumina HiSeq 4000 Experimental Factor: time 3 Experimental Factor: sampling site meristem ERX7881063 E-MTAB-11402:04d_R3_p ERP135194 PRJEB50600 Cellular and gene expression patterns associated with root bifurcation in Selaginella ERS10419834 SAMEA12812873 04d_R3_p RNA-Seq TRANSCRIPTOMIC Oligo-dT To identify possible molecular mechanisms with a role in root branching initiation in S. moellendorffii, we employed the developmental root branching assay for an RNA-seq experiment and sampled root tips on each day from 0 to 5 d after the first branching (time point 0), in which 300 µm apical parts were sampled to enrich for the meristematic region, while non-meristematic root regions were sampled separately. Sampled roots in the time course (300 root tips per sample, 4 biological repeats per time point) were cut off using a pair of stainless microscissors and then stored in RNAlater® RNA Stabilization Solution (Thermo Fisher Scientific) according to the manufacturer's instruction. Subsequently, microdissection was performed to collect root apices of 0.3 mm long, as well as non-meristematic regions between apices and branching point for the 5 d post first branching samples. Plants were grown aseptically under a 16-h light/8-h dark photoperiod at 20.25–43.2 μmol/m2/s in a 24°C growth chamber and roots developed after the transfer of explants to fresh MS1/2 medium. For RNA extraction, samples were ground three times using a QIAGEN Retsch Tissuelyser (30 Hz, 30 s). RNA extraction was done via TRIzol™ reagent (Thermo Fisher Scientific) and the RNeasy Plant Mini Kit (Qiagen) according to the provided protocols. Per sample, an amount of 250 ng of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: Part # 15031047 Rev. E - October 2013) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Illumina HiSeq 4000 Experimental Factor: time 4 Experimental Factor: sampling site meristem ERX7881064 E-MTAB-11402:04d_R4_p ERP135194 PRJEB50600 Cellular and gene expression patterns associated with root bifurcation in Selaginella ERS10419835 SAMEA12812874 04d_R4_p RNA-Seq TRANSCRIPTOMIC Oligo-dT To identify possible molecular mechanisms with a role in root branching initiation in S. moellendorffii, we employed the developmental root branching assay for an RNA-seq experiment and sampled root tips on each day from 0 to 5 d after the first branching (time point 0), in which 300 µm apical parts were sampled to enrich for the meristematic region, while non-meristematic root regions were sampled separately. Sampled roots in the time course (300 root tips per sample, 4 biological repeats per time point) were cut off using a pair of stainless microscissors and then stored in RNAlater® RNA Stabilization Solution (Thermo Fisher Scientific) according to the manufacturer's instruction. Subsequently, microdissection was performed to collect root apices of 0.3 mm long, as well as non-meristematic regions between apices and branching point for the 5 d post first branching samples. Plants were grown aseptically under a 16-h light/8-h dark photoperiod at 20.25–43.2 μmol/m2/s in a 24°C growth chamber and roots developed after the transfer of explants to fresh MS1/2 medium. For RNA extraction, samples were ground three times using a QIAGEN Retsch Tissuelyser (30 Hz, 30 s). RNA extraction was done via TRIzol™ reagent (Thermo Fisher Scientific) and the RNeasy Plant Mini Kit (Qiagen) according to the provided protocols. Per sample, an amount of 250 ng of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: Part # 15031047 Rev. E - October 2013) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Illumina HiSeq 4000 Experimental Factor: time 4 Experimental Factor: sampling site meristem ERX7881065 E-MTAB-11402:05d_R3_p ERP135194 PRJEB50600 Cellular and gene expression patterns associated with root bifurcation in Selaginella ERS10419836 SAMEA12812875 05d_R3_p RNA-Seq TRANSCRIPTOMIC Oligo-dT To identify possible molecular mechanisms with a role in root branching initiation in S. moellendorffii, we employed the developmental root branching assay for an RNA-seq experiment and sampled root tips on each day from 0 to 5 d after the first branching (time point 0), in which 300 µm apical parts were sampled to enrich for the meristematic region, while non-meristematic root regions were sampled separately. Sampled roots in the time course (300 root tips per sample, 4 biological repeats per time point) were cut off using a pair of stainless microscissors and then stored in RNAlater® RNA Stabilization Solution (Thermo Fisher Scientific) according to the manufacturer's instruction. Subsequently, microdissection was performed to collect root apices of 0.3 mm long, as well as non-meristematic regions between apices and branching point for the 5 d post first branching samples. Plants were grown aseptically under a 16-h light/8-h dark photoperiod at 20.25–43.2 μmol/m2/s in a 24°C growth chamber and roots developed after the transfer of explants to fresh MS1/2 medium. For RNA extraction, samples were ground three times using a QIAGEN Retsch Tissuelyser (30 Hz, 30 s). RNA extraction was done via TRIzol™ reagent (Thermo Fisher Scientific) and the RNeasy Plant Mini Kit (Qiagen) according to the provided protocols. Per sample, an amount of 250 ng of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: Part # 15031047 Rev. E - October 2013) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Illumina HiSeq 4000 Experimental Factor: time 5 Experimental Factor: sampling site meristem ERX7881066 E-MTAB-11402:05d_R4_p ERP135194 PRJEB50600 Cellular and gene expression patterns associated with root bifurcation in Selaginella ERS10419837 SAMEA12812876 05d_R4_p RNA-Seq TRANSCRIPTOMIC Oligo-dT To identify possible molecular mechanisms with a role in root branching initiation in S. moellendorffii, we employed the developmental root branching assay for an RNA-seq experiment and sampled root tips on each day from 0 to 5 d after the first branching (time point 0), in which 300 µm apical parts were sampled to enrich for the meristematic region, while non-meristematic root regions were sampled separately. Sampled roots in the time course (300 root tips per sample, 4 biological repeats per time point) were cut off using a pair of stainless microscissors and then stored in RNAlater® RNA Stabilization Solution (Thermo Fisher Scientific) according to the manufacturer's instruction. Subsequently, microdissection was performed to collect root apices of 0.3 mm long, as well as non-meristematic regions between apices and branching point for the 5 d post first branching samples. Plants were grown aseptically under a 16-h light/8-h dark photoperiod at 20.25–43.2 μmol/m2/s in a 24°C growth chamber and roots developed after the transfer of explants to fresh MS1/2 medium. For RNA extraction, samples were ground three times using a QIAGEN Retsch Tissuelyser (30 Hz, 30 s). RNA extraction was done via TRIzol™ reagent (Thermo Fisher Scientific) and the RNeasy Plant Mini Kit (Qiagen) according to the provided protocols. Per sample, an amount of 250 ng of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: Part # 15031047 Rev. E - October 2013) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Illumina HiSeq 4000 Experimental Factor: time 5 Experimental Factor: sampling site meristem ERX7881067 E-MTAB-11402:NM_R1_p ERP135194 PRJEB50600 Cellular and gene expression patterns associated with root bifurcation in Selaginella ERS10419838 SAMEA12812877 NM_R1_p RNA-Seq TRANSCRIPTOMIC Oligo-dT To identify possible molecular mechanisms with a role in root branching initiation in S. moellendorffii, we employed the developmental root branching assay for an RNA-seq experiment and sampled root tips on each day from 0 to 5 d after the first branching (time point 0), in which 300 µm apical parts were sampled to enrich for the meristematic region, while non-meristematic root regions were sampled separately. Sampled roots in the time course (300 root tips per sample, 4 biological repeats per time point) were cut off using a pair of stainless microscissors and then stored in RNAlater® RNA Stabilization Solution (Thermo Fisher Scientific) according to the manufacturer's instruction. Subsequently, microdissection was performed to collect root apices of 0.3 mm long, as well as non-meristematic regions between apices and branching point for the 5 d post first branching samples. Plants were grown aseptically under a 16-h light/8-h dark photoperiod at 20.25–43.2 μmol/m2/s in a 24°C growth chamber and roots developed after the transfer of explants to fresh MS1/2 medium. For RNA extraction, samples were ground three times using a QIAGEN Retsch Tissuelyser (30 Hz, 30 s). RNA extraction was done via TRIzol™ reagent (Thermo Fisher Scientific) and the RNeasy Plant Mini Kit (Qiagen) according to the provided protocols. Per sample, an amount of 250 ng of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: Part # 15031047 Rev. E - October 2013) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Illumina HiSeq 4000 Experimental Factor: time 5 Experimental Factor: sampling site non-meristem ERX7881068 E-MTAB-11402:NM_R2_p ERP135194 PRJEB50600 Cellular and gene expression patterns associated with root bifurcation in Selaginella ERS10419839 SAMEA12812878 NM_R2_p RNA-Seq TRANSCRIPTOMIC Oligo-dT To identify possible molecular mechanisms with a role in root branching initiation in S. moellendorffii, we employed the developmental root branching assay for an RNA-seq experiment and sampled root tips on each day from 0 to 5 d after the first branching (time point 0), in which 300 µm apical parts were sampled to enrich for the meristematic region, while non-meristematic root regions were sampled separately. Sampled roots in the time course (300 root tips per sample, 4 biological repeats per time point) were cut off using a pair of stainless microscissors and then stored in RNAlater® RNA Stabilization Solution (Thermo Fisher Scientific) according to the manufacturer's instruction. Subsequently, microdissection was performed to collect root apices of 0.3 mm long, as well as non-meristematic regions between apices and branching point for the 5 d post first branching samples. Plants were grown aseptically under a 16-h light/8-h dark photoperiod at 20.25–43.2 μmol/m2/s in a 24°C growth chamber and roots developed after the transfer of explants to fresh MS1/2 medium. For RNA extraction, samples were ground three times using a QIAGEN Retsch Tissuelyser (30 Hz, 30 s). RNA extraction was done via TRIzol™ reagent (Thermo Fisher Scientific) and the RNeasy Plant Mini Kit (Qiagen) according to the provided protocols. Per sample, an amount of 250 ng of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: Part # 15031047 Rev. E - October 2013) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Illumina HiSeq 4000 Experimental Factor: time 5 Experimental Factor: sampling site non-meristem ERX7881069 E-MTAB-11402:NM_R3_p ERP135194 PRJEB50600 Cellular and gene expression patterns associated with root bifurcation in Selaginella ERS10419840 SAMEA12812879 NM_R3_p RNA-Seq TRANSCRIPTOMIC Oligo-dT To identify possible molecular mechanisms with a role in root branching initiation in S. moellendorffii, we employed the developmental root branching assay for an RNA-seq experiment and sampled root tips on each day from 0 to 5 d after the first branching (time point 0), in which 300 µm apical parts were sampled to enrich for the meristematic region, while non-meristematic root regions were sampled separately. Sampled roots in the time course (300 root tips per sample, 4 biological repeats per time point) were cut off using a pair of stainless microscissors and then stored in RNAlater® RNA Stabilization Solution (Thermo Fisher Scientific) according to the manufacturer's instruction. Subsequently, microdissection was performed to collect root apices of 0.3 mm long, as well as non-meristematic regions between apices and branching point for the 5 d post first branching samples. Plants were grown aseptically under a 16-h light/8-h dark photoperiod at 20.25–43.2 μmol/m2/s in a 24°C growth chamber and roots developed after the transfer of explants to fresh MS1/2 medium. For RNA extraction, samples were ground three times using a QIAGEN Retsch Tissuelyser (30 Hz, 30 s). RNA extraction was done via TRIzol™ reagent (Thermo Fisher Scientific) and the RNeasy Plant Mini Kit (Qiagen) according to the provided protocols. Per sample, an amount of 250 ng of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: Part # 15031047 Rev. E - October 2013) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Illumina HiSeq 4000 Experimental Factor: time 5 Experimental Factor: sampling site non-meristem ERX7881070 E-MTAB-11402:NM_R4_p ERP135194 PRJEB50600 Cellular and gene expression patterns associated with root bifurcation in Selaginella ERS10419841 SAMEA12812880 NM_R4_p RNA-Seq TRANSCRIPTOMIC Oligo-dT To identify possible molecular mechanisms with a role in root branching initiation in S. moellendorffii, we employed the developmental root branching assay for an RNA-seq experiment and sampled root tips on each day from 0 to 5 d after the first branching (time point 0), in which 300 µm apical parts were sampled to enrich for the meristematic region, while non-meristematic root regions were sampled separately. Sampled roots in the time course (300 root tips per sample, 4 biological repeats per time point) were cut off using a pair of stainless microscissors and then stored in RNAlater® RNA Stabilization Solution (Thermo Fisher Scientific) according to the manufacturer's instruction. Subsequently, microdissection was performed to collect root apices of 0.3 mm long, as well as non-meristematic regions between apices and branching point for the 5 d post first branching samples. Plants were grown aseptically under a 16-h light/8-h dark photoperiod at 20.25–43.2 μmol/m2/s in a 24°C growth chamber and roots developed after the transfer of explants to fresh MS1/2 medium. For RNA extraction, samples were ground three times using a QIAGEN Retsch Tissuelyser (30 Hz, 30 s). RNA extraction was done via TRIzol™ reagent (Thermo Fisher Scientific) and the RNeasy Plant Mini Kit (Qiagen) according to the provided protocols. Per sample, an amount of 250 ng of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: Part # 15031047 Rev. E - October 2013) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Illumina HiSeq 4000 Experimental Factor: time 5 Experimental Factor: sampling site non-meristem