Biochemical Engineering Journal

Sequencing data of CRISPR predicted sites

The data set is in Minitab and excel file

These are supplementary files to the manuscript: A.J.J. Straathof (2023) Modelling of end-product inhibition in fermentation, Biochemical Engineering Journal 191 (2023) 108796 https://doi.org/10.1016/j.bej.2022.108796

These are supplementary files to the manuscript: A.J.J. Straathof (2023) Modelling of end-product inhibition in fermentation, Biochemical Engineering Journal 191 (2023) 108796 https://doi.org/10.1016/j.bej.2022.108796

Fermentation products and pH profiles. Frequency of inoculum transfer of a mixed microbial culture during ethanol fermentation of organic municipal solid waste at low pH infulences the retention and stability of ethanologenesis

Fermentation products and pH profiles. Frequency of inoculum transfer of a mixed microbial culture during ethanol fermentation of organic municipal solid waste at low pH infulences the retention and stability of ethanologenesis

This dataset contains relevant experimental data collected for the research described in the linked publication (Marais et al., 2020). This includes system operating conditions, measured pH and redox measurements as well as sulphate, sulphide and volatile fatty acid concentrations over the duration of the study required for monitoring process performance of the hybrid LFCR. The study evaluates the effect of hydraulic residence time on biological sulphate reduction and sulphide oxidation kinetics within the hybrid LFCR process as well the recovery efficiency of elemental sulphur.

This dataset contains relevant experimental data collected for the research described in the linked publication (Marais et al., 2020). This includes system operating conditions, measured pH and redox measurements as well as sulphate, sulphide and volatile fatty acid concentrations over the duration of the study required for monitoring process performance of the hybrid LFCR. The study evaluates the effect of hydraulic residence time on biological sulphate reduction and sulphide oxidation kinetics within the hybrid LFCR process as well the recovery efficiency of elemental sulphur.

This repository contains genomic alignments (BED files) of paired-end nanoCAGE sequencing data (CAGEscan data) collected from Illumina MiSeq run IDs "170630_M00528_0292_000000000-B9JY8" (aka "NC_LIMMS") and "180221_M00528_0334_000000000-B6PJM" (aka "NC_LIMMS2"). FASTQ files were processed with the MOIRAI pipeline OP-WORKFLOW-CAGEscan-short-reads-v2.1 (Hasegawa et al. BMC Bioinformatics 2014 May 16;15:144. doi: 10.1186/1471-2105-15-144.). Filtered pairs of reads were aligned on the human genome assemblies hg19 and hg38. See tables below for a detailed description of the samples contained in each nanoCAGE library, including barcodes and index sequences used for the demultiplexing of sequencing reads. Corresponding raw sequencing data files (FASTQ files) were deposited at Zenodo under the following Digital Object Identifier: 10.5281/zenodo.1014009. "170630_M00528_0292_000000000-B9JY8" ("NC_LIMMS") : ID Sample_name Barcode_number Barcode_sequence Index_sequence 1 iPSC_control_rep1 4 ACAGAT NNNNNNNN 2 iPSC_control_rep2 24 ATCGTG NNNNNNNN 3 iPSC_control_rep3 31 CACGAT NNNNNNNN 4 S3P1_OK_rep1 36 CACTGA NNNNNNNN 5 S3P1_OK_rep2 46 CTGACG NNNNNNNN 6 S3P1_OK_rep3 63 GAGTGA NNNNNNNN 7 S4P1_OK_rep1 79 GTATAC NNNNNNNN 8 S4P1_OK_rep2 92 TCGAGC NNNNNNNN 9 S4P1_OK_rep3 9 ACATGA NNNNNNNN 10 S4P2_OK_rep1 21 ATCATA NNNNNNNN 11 S4P2_OK_rep2 33 CACGTG NNNNNNNN 12 S4P2_OK_rep3 45 CGATGA NNNNNNNN 13 S1P1_rep1 57 GAGATA NNNNNNNN 14 S1P1_rep2 69 GCTCTC NNNNNNNN 15 S1P1_rep3 81 GTATGA NNNNNNNN 16 S3P1_FAILED_rep1 93 TCGATA NNNNNNNN 17 S3P1_FAILED_rep2 11 AGTAGC NNNNNNNN 18 S3P1_FAILED_rep3 23 ATCGCA NNNNNNNN 19 S4P1_FAILED_rep1 35 CACTCT NNNNNNNN 20 S4P1_FAILED_rep2 47 CTGAGC NNNNNNNN 21 S4P1_FAILED_rep3 59 GAGCGT NNNNNNNN 22 S4P2_FAILED_rep1 71 GCTGCA NNNNNNNN 23 S4P2_FAILED_rep2 83 TATAGC NNNNNNNN 24 S4P2_FAILED_rep3 95 TCGCGT NNNNNNNN "180221_M00528_0334_000000000-B6PJM" ("NC_LIMMS2"): ID Sample_name Barcode_number Barcode_sequence Index_sequence 25 PETRI_rep1 04 ACAGAT NNNNNNNN 26 PETRI_rep2 24 ATCGTG NNNNNNNN 27 PETRI_rep3 31 CACGAT NNNNNNNN 28 BIOCHIP_E_rep1 6 CACTGA NNNNNNNN 29 BIOCHIP_M_rep1 46 CTGACG NNNNNNNN 30 BIOCHIP_S_rep1 63 GAGTGA NNNNNNNN 31 BIOCHIP_E_rep2 79 GTATAC NNNNNNNN 32 BIOCHIP_M_rep2 92 TCGAGC NNNNNNNN 33 BIOCHIP_S_rep2 09 ACATGA NNNNNNNN 34 BIOCHIP_E_rep3 21 ATCATA NNNNNNNN 35 BIOCHIP_M_rep3 33 CACGTG NNNNNNNN 36 BIOCHIP_S_rep3 45 CGATGA NNNNNNNN 37 HEPATOCYTES_rep1 57 GAGATA NNNNNNNN 38 HEPATOCYTES_rep2 69 GCTCTC NNNNNNNN 39 iPSC_control_rep1-2 81 GTATGA NNNNNNNN 40 BIOCHIP_E_rep2-2 93 TCGATA NNNNNNNN 41 BIOCHIP_M_rep1-2 11 AGTAGC NNNNNNNN 42 BIOCHIP_S_rep2-2 23 ATCGCA NNNNNNNN

This repository contains raw sequencing data (FASTQ files) produced from Illumina MiSeq run IDs "170630_M00528_0292_000000000-B9JY8" (aka "NC_LIMMS") and "180221_M00528_0334_000000000-B6PJM" (aka "NC_LIMMS2") . Sequencing libraries were prepared following the latest version of the nanoCAGE protocol (Poulain et al., Methods Mol Biol. 2017;1543:57-109. doi: 10.1007/978-1-4939-6716-2_4). They respectively contain a mix of 24 ("NC_LIMMS") and 18 ("NC_LIMMS2") samples tagged by specific barcode sequences at the 5'-ends (see tables below). The tagmentation step included in the protocol was performed using an equimolar mix of 12 Nextera XT N-series index primers (N701 to N712), therefore "NNNNNNNN" was indicated as index sequence on the Illumina Sample Sheet for the demultiplexing (see tables below). Libraries were sequenced paired-end on Illumina MiSeq system with the MiSeq Reagent Kit v3 (150 cycles: 58 cycles used for READ1, 8 cycles used for the Index, and 84 cycles used for READ2). Genomic alignments (BED files) of paired-end reads on human genome assemblies hg19 and hg38 using the MOIRAI pipeline (Hasegawa et al. BMC Bioinformatics 2014 May 16;15:144. doi: 10.1186/1471-2105-15-144) were deposited at Zenodo under the following Digital Object Identifier: 10.5281/zenodo.1017276. "170630_M00528_0292_000000000-B9JY8" ("NC_LIMMS") : ID Sample_name Barcode_number Barcode_sequence Index_sequence 1 iPSC_control_rep1 4 ACAGAT NNNNNNNN 2 iPSC_control_rep2 24 ATCGTG NNNNNNNN 3 iPSC_control_rep3 31 CACGAT NNNNNNNN 4 S3P1_OK_rep1 36 CACTGA NNNNNNNN 5 S3P1_OK_rep2 46 CTGACG NNNNNNNN 6 S3P1_OK_rep3 63 GAGTGA NNNNNNNN 7 S4P1_OK_rep1 79 GTATAC NNNNNNNN 8 S4P1_OK_rep2 92 TCGAGC NNNNNNNN 9 S4P1_OK_rep3 9 ACATGA NNNNNNNN 10 S4P2_OK_rep1 21 ATCATA NNNNNNNN 11 S4P2_OK_rep2 33 CACGTG NNNNNNNN 12 S4P2_OK_rep3 45 CGATGA NNNNNNNN 13 S1P1_rep1 57 GAGATA NNNNNNNN 14 S1P1_rep2 69 GCTCTC NNNNNNNN 15 S1P1_rep3 81 GTATGA NNNNNNNN 16 S3P1_FAILED_rep1 93 TCGATA NNNNNNNN 17 S3P1_FAILED_rep2 11 AGTAGC NNNNNNNN 18 S3P1_FAILED_rep3 23 ATCGCA NNNNNNNN 19 S4P1_FAILED_rep1 35 CACTCT NNNNNNNN 20 S4P1_FAILED_rep2 47 CTGAGC NNNNNNNN 21 S4P1_FAILED_rep3 59 GAGCGT NNNNNNNN 22 S4P2_FAILED_rep1 71 GCTGCA NNNNNNNN 23 S4P2_FAILED_rep2 83 TATAGC NNNNNNNN 24 S4P2_FAILED_rep3 95 TCGCGT NNNNNNNN "180221_M00528_0334_000000000-B6PJM" ("NC_LIMMS2"): ID Sample_name Barcode_number Barcode_sequence Index_sequence 25 PETRI_rep1 04 ACAGAT NNNNNNNN 26 PETRI_rep2 24 ATCGTG NNNNNNNN 27 PETRI_rep3 31 CACGAT NNNNNNNN 28 BIOCHIP_E_rep1 6 CACTGA NNNNNNNN 29 BIOCHIP_M_rep1 46 CTGACG NNNNNNNN 30 BIOCHIP_S_rep1 63 GAGTGA NNNNNNNN 31 BIOCHIP_E_rep2 79 GTATAC NNNNNNNN 32 BIOCHIP_M_rep2 92 TCGAGC NNNNNNNN 33 BIOCHIP_S_rep2 09 ACATGA NNNNNNNN 34 BIOCHIP_E_rep3 21 ATCATA NNNNNNNN 35 BIOCHIP_M_rep3 33 CACGTG NNNNNNNN 36 BIOCHIP_S_rep3 45 CGATGA NNNNNNNN 37 HEPATOCYTES_rep1 57 GAGATA NNNNNNNN 38 HEPATOCYTES_rep2 69 GCTCTC NNNNNNNN 39 iPSC_control_rep1-2 81 GTATGA NNNNNNNN 40 BIOCHIP_E_rep2-2 93 TCGATA NNNNNNNN 41 BIOCHIP_M_rep1-2 11 AGTAGC NNNNNNNN 42 BIOCHIP_S_rep2-2 23 ATCGCA NNNNNNNN