ERS1931068 SAMEA104306090 10090 Mus musculus Protocols: Targeting of the Bhlhe23 gene and genotyping of the Bhlhe23 allele was previously described by Kim et al 2008. An approximately 5-kb HindIII/NotI DNA fragment encompassing the Bhlhb4 gene was isolated by PCR from 129/Sv genomic DNA. A loxP-flanked PGK-neomycin resistance cassette in reverse orientation was introduced into the KpnI site approximately 1 kb upstream of the Bhlhb4 gene. A third loxP sequence was introduced approximately 300 bases distal to the Bhlhb4 3′ UTR, between adjacent BsrGI and MunI restriction sites. A PGK-diptheria toxin gene cassette was introduced at the 3′ end of the Bhlhb4 locus. This vector was electroporated into mouse 129 J1 embryonic stem (ES) cells. A null allele was generated by transiently transfecting targeted ES cells with a Cre recombinase plasmid, pOG231. ES cells carrying the deletion allele were microinjected into C57BL/6 blastocysts, and chimeras were tested for germline transmission of the mutant allele by breeding to C57BL/6 females and PCR genotyping of pups. PN7 wildtype and mutant eyes were removed following termination of the animals. Eyes were dissected in ice cold PBS. The cornea was pierced and the eye pulled apart. The retina was then gently pulled away from the rest of the eye. Retinal samples were stored in RNAlater® (Qiagen) at -20C. RNA extraction and purification was performed using the RNeasy® Mini kit from Qiagen (Hildern, Germany) before quantification on a Nanodrop spectrophotometer (ND-1000, Thermo Fisher Scientific). Barcoded sequencing libraries were prepared using the Illumina® TruSeq Stranded Total RNA Low-Throughput sample RiboZero Human/Rat/Mouse prep kit following manufacturer's guidelines (Illumina, San Diego, CA, USA). Libraries were quantified with a Qubit® fluorometer (Thermo Fisher Scientific) using the double stranded DNA High sensitivity assay. ENA first public 2017-09-20 ENA last update 2017-09-18 External Id SAMEA104306090 INSDC center alias BRISTOL INSDC center name University of Bristol INSDC first public 2017-09-20T17:02:02Z INSDC last update 2017-09-18T17:37:25Z INSDC status public Submitter Id E-MTAB-6071:Sample 1 age 7 broker name ArrayExpress common name house mouse disease normal genotype wild type genotype organism part retina replicate litter 1 sample name E-MTAB-6071:Sample 1 sex male strain C57BL/6 ERS1931069 SAMEA104306091 10090 Mus musculus Protocols: Targeting of the Bhlhe23 gene and genotyping of the Bhlhe23 allele was previously described by Kim et al 2008. An approximately 5-kb HindIII/NotI DNA fragment encompassing the Bhlhb4 gene was isolated by PCR from 129/Sv genomic DNA. A loxP-flanked PGK-neomycin resistance cassette in reverse orientation was introduced into the KpnI site approximately 1 kb upstream of the Bhlhb4 gene. A third loxP sequence was introduced approximately 300 bases distal to the Bhlhb4 3′ UTR, between adjacent BsrGI and MunI restriction sites. A PGK-diptheria toxin gene cassette was introduced at the 3′ end of the Bhlhb4 locus. This vector was electroporated into mouse 129 J1 embryonic stem (ES) cells. A null allele was generated by transiently transfecting targeted ES cells with a Cre recombinase plasmid, pOG231. ES cells carrying the deletion allele were microinjected into C57BL/6 blastocysts, and chimeras were tested for germline transmission of the mutant allele by breeding to C57BL/6 females and PCR genotyping of pups. PN7 wildtype and mutant eyes were removed following termination of the animals. Eyes were dissected in ice cold PBS. The cornea was pierced and the eye pulled apart. The retina was then gently pulled away from the rest of the eye. Retinal samples were stored in RNAlater® (Qiagen) at -20C. RNA extraction and purification was performed using the RNeasy® Mini kit from Qiagen (Hildern, Germany) before quantification on a Nanodrop spectrophotometer (ND-1000, Thermo Fisher Scientific). Barcoded sequencing libraries were prepared using the Illumina® TruSeq Stranded Total RNA Low-Throughput sample RiboZero Human/Rat/Mouse prep kit following manufacturer's guidelines (Illumina, San Diego, CA, USA). Libraries were quantified with a Qubit® fluorometer (Thermo Fisher Scientific) using the double stranded DNA High sensitivity assay. ENA first public 2017-09-20 ENA last update 2017-09-18 External Id SAMEA104306091 INSDC center alias BRISTOL INSDC center name University of Bristol INSDC first public 2017-09-20T17:02:02Z INSDC last update 2017-09-18T17:37:25Z INSDC status public Submitter Id E-MTAB-6071:Sample 7 age 7 broker name ArrayExpress common name house mouse disease normal genotype Bhlhe23 knockout organism part retina replicate litter 1 sample name E-MTAB-6071:Sample 7 sex female strain C57BL/6 ERS1931070 SAMEA104306092 10090 Mus musculus Protocols: Targeting of the Bhlhe23 gene and genotyping of the Bhlhe23 allele was previously described by Kim et al 2008. An approximately 5-kb HindIII/NotI DNA fragment encompassing the Bhlhb4 gene was isolated by PCR from 129/Sv genomic DNA. A loxP-flanked PGK-neomycin resistance cassette in reverse orientation was introduced into the KpnI site approximately 1 kb upstream of the Bhlhb4 gene. A third loxP sequence was introduced approximately 300 bases distal to the Bhlhb4 3′ UTR, between adjacent BsrGI and MunI restriction sites. A PGK-diptheria toxin gene cassette was introduced at the 3′ end of the Bhlhb4 locus. This vector was electroporated into mouse 129 J1 embryonic stem (ES) cells. A null allele was generated by transiently transfecting targeted ES cells with a Cre recombinase plasmid, pOG231. ES cells carrying the deletion allele were microinjected into C57BL/6 blastocysts, and chimeras were tested for germline transmission of the mutant allele by breeding to C57BL/6 females and PCR genotyping of pups. PN7 wildtype and mutant eyes were removed following termination of the animals. Eyes were dissected in ice cold PBS. The cornea was pierced and the eye pulled apart. The retina was then gently pulled away from the rest of the eye. Retinal samples were stored in RNAlater® (Qiagen) at -20C. RNA extraction and purification was performed using the RNeasy® Mini kit from Qiagen (Hildern, Germany) before quantification on a Nanodrop spectrophotometer (ND-1000, Thermo Fisher Scientific). Barcoded sequencing libraries were prepared using the Illumina® TruSeq Stranded Total RNA Low-Throughput sample RiboZero Human/Rat/Mouse prep kit following manufacturer's guidelines (Illumina, San Diego, CA, USA). Libraries were quantified with a Qubit® fluorometer (Thermo Fisher Scientific) using the double stranded DNA High sensitivity assay. ENA first public 2017-09-20 ENA last update 2017-09-18 External Id SAMEA104306092 INSDC center alias BRISTOL INSDC center name University of Bristol INSDC first public 2017-09-20T17:02:02Z INSDC last update 2017-09-18T17:37:25Z INSDC status public Submitter Id E-MTAB-6071:Sample 2 age 7 broker name ArrayExpress common name house mouse disease normal genotype wild type genotype organism part retina replicate litter 2 sample name E-MTAB-6071:Sample 2 sex male strain C56BL/6 ERS1931071 SAMEA104306093 10090 Mus musculus Protocols: Targeting of the Bhlhe23 gene and genotyping of the Bhlhe23 allele was previously described by Kim et al 2008. An approximately 5-kb HindIII/NotI DNA fragment encompassing the Bhlhb4 gene was isolated by PCR from 129/Sv genomic DNA. A loxP-flanked PGK-neomycin resistance cassette in reverse orientation was introduced into the KpnI site approximately 1 kb upstream of the Bhlhb4 gene. A third loxP sequence was introduced approximately 300 bases distal to the Bhlhb4 3′ UTR, between adjacent BsrGI and MunI restriction sites. A PGK-diptheria toxin gene cassette was introduced at the 3′ end of the Bhlhb4 locus. This vector was electroporated into mouse 129 J1 embryonic stem (ES) cells. A null allele was generated by transiently transfecting targeted ES cells with a Cre recombinase plasmid, pOG231. ES cells carrying the deletion allele were microinjected into C57BL/6 blastocysts, and chimeras were tested for germline transmission of the mutant allele by breeding to C57BL/6 females and PCR genotyping of pups. PN7 wildtype and mutant eyes were removed following termination of the animals. Eyes were dissected in ice cold PBS. The cornea was pierced and the eye pulled apart. The retina was then gently pulled away from the rest of the eye. Retinal samples were stored in RNAlater® (Qiagen) at -20C. RNA extraction and purification was performed using the RNeasy® Mini kit from Qiagen (Hildern, Germany) before quantification on a Nanodrop spectrophotometer (ND-1000, Thermo Fisher Scientific). Barcoded sequencing libraries were prepared using the Illumina® TruSeq Stranded Total RNA Low-Throughput sample RiboZero Human/Rat/Mouse prep kit following manufacturer's guidelines (Illumina, San Diego, CA, USA). Libraries were quantified with a Qubit® fluorometer (Thermo Fisher Scientific) using the double stranded DNA High sensitivity assay. ENA first public 2017-09-20 ENA last update 2017-09-18 External Id SAMEA104306093 INSDC center alias BRISTOL INSDC center name University of Bristol INSDC first public 2017-09-20T17:02:02Z INSDC last update 2017-09-18T17:37:25Z INSDC status public Submitter Id E-MTAB-6071:Sample 8 age 7 broker name ArrayExpress common name house mouse disease normal genotype Bhlhe23 knockout organism part retina replicate litter 2 sample name E-MTAB-6071:Sample 8 sex female strain C57BL/6 ERS1931072 SAMEA104306094 10090 Mus musculus Protocols: Targeting of the Bhlhe23 gene and genotyping of the Bhlhe23 allele was previously described by Kim et al 2008. An approximately 5-kb HindIII/NotI DNA fragment encompassing the Bhlhb4 gene was isolated by PCR from 129/Sv genomic DNA. A loxP-flanked PGK-neomycin resistance cassette in reverse orientation was introduced into the KpnI site approximately 1 kb upstream of the Bhlhb4 gene. A third loxP sequence was introduced approximately 300 bases distal to the Bhlhb4 3′ UTR, between adjacent BsrGI and MunI restriction sites. A PGK-diptheria toxin gene cassette was introduced at the 3′ end of the Bhlhb4 locus. This vector was electroporated into mouse 129 J1 embryonic stem (ES) cells. A null allele was generated by transiently transfecting targeted ES cells with a Cre recombinase plasmid, pOG231. ES cells carrying the deletion allele were microinjected into C57BL/6 blastocysts, and chimeras were tested for germline transmission of the mutant allele by breeding to C57BL/6 females and PCR genotyping of pups. PN7 wildtype and mutant eyes were removed following termination of the animals. Eyes were dissected in ice cold PBS. The cornea was pierced and the eye pulled apart. The retina was then gently pulled away from the rest of the eye. Retinal samples were stored in RNAlater® (Qiagen) at -20C. RNA extraction and purification was performed using the RNeasy® Mini kit from Qiagen (Hildern, Germany) before quantification on a Nanodrop spectrophotometer (ND-1000, Thermo Fisher Scientific). Barcoded sequencing libraries were prepared using the Illumina® TruSeq Stranded Total RNA Low-Throughput sample RiboZero Human/Rat/Mouse prep kit following manufacturer's guidelines (Illumina, San Diego, CA, USA). Libraries were quantified with a Qubit® fluorometer (Thermo Fisher Scientific) using the double stranded DNA High sensitivity assay. ENA first public 2017-09-20 ENA last update 2017-09-18 External Id SAMEA104306094 INSDC center alias BRISTOL INSDC center name University of Bristol INSDC first public 2017-09-20T17:02:02Z INSDC last update 2017-09-18T17:37:25Z INSDC status public Submitter Id E-MTAB-6071:Sample 3 age 7 broker name ArrayExpress common name house mouse disease normal genotype wild type genotype organism part retina replicate litter 3 sample name E-MTAB-6071:Sample 3 sex female strain C56BL/6 ERS1931073 SAMEA104306095 10090 Mus musculus Protocols: Targeting of the Bhlhe23 gene and genotyping of the Bhlhe23 allele was previously described by Kim et al 2008. An approximately 5-kb HindIII/NotI DNA fragment encompassing the Bhlhb4 gene was isolated by PCR from 129/Sv genomic DNA. A loxP-flanked PGK-neomycin resistance cassette in reverse orientation was introduced into the KpnI site approximately 1 kb upstream of the Bhlhb4 gene. A third loxP sequence was introduced approximately 300 bases distal to the Bhlhb4 3′ UTR, between adjacent BsrGI and MunI restriction sites. A PGK-diptheria toxin gene cassette was introduced at the 3′ end of the Bhlhb4 locus. This vector was electroporated into mouse 129 J1 embryonic stem (ES) cells. A null allele was generated by transiently transfecting targeted ES cells with a Cre recombinase plasmid, pOG231. ES cells carrying the deletion allele were microinjected into C57BL/6 blastocysts, and chimeras were tested for germline transmission of the mutant allele by breeding to C57BL/6 females and PCR genotyping of pups. PN7 wildtype and mutant eyes were removed following termination of the animals. Eyes were dissected in ice cold PBS. The cornea was pierced and the eye pulled apart. The retina was then gently pulled away from the rest of the eye. Retinal samples were stored in RNAlater® (Qiagen) at -20C. RNA extraction and purification was performed using the RNeasy® Mini kit from Qiagen (Hildern, Germany) before quantification on a Nanodrop spectrophotometer (ND-1000, Thermo Fisher Scientific). Barcoded sequencing libraries were prepared using the Illumina® TruSeq Stranded Total RNA Low-Throughput sample RiboZero Human/Rat/Mouse prep kit following manufacturer's guidelines (Illumina, San Diego, CA, USA). Libraries were quantified with a Qubit® fluorometer (Thermo Fisher Scientific) using the double stranded DNA High sensitivity assay. ENA first public 2017-09-20 ENA last update 2017-09-18 External Id SAMEA104306095 INSDC center alias BRISTOL INSDC center name University of Bristol INSDC first public 2017-09-20T17:02:02Z INSDC last update 2017-09-18T17:37:25Z INSDC status public Submitter Id E-MTAB-6071:Sample 9 age 7 broker name ArrayExpress common name house mouse disease normal genotype Bhlhe23 knockout organism part retina replicate litter 3 sample name E-MTAB-6071:Sample 9 sex female strain C57BL/6 ERS1931074 SAMEA104306096 10090 Mus musculus Protocols: Targeting of the Bhlhe23 gene and genotyping of the Bhlhe23 allele was previously described by Kim et al 2008. An approximately 5-kb HindIII/NotI DNA fragment encompassing the Bhlhb4 gene was isolated by PCR from 129/Sv genomic DNA. A loxP-flanked PGK-neomycin resistance cassette in reverse orientation was introduced into the KpnI site approximately 1 kb upstream of the Bhlhb4 gene. A third loxP sequence was introduced approximately 300 bases distal to the Bhlhb4 3′ UTR, between adjacent BsrGI and MunI restriction sites. A PGK-diptheria toxin gene cassette was introduced at the 3′ end of the Bhlhb4 locus. This vector was electroporated into mouse 129 J1 embryonic stem (ES) cells. A null allele was generated by transiently transfecting targeted ES cells with a Cre recombinase plasmid, pOG231. ES cells carrying the deletion allele were microinjected into C57BL/6 blastocysts, and chimeras were tested for germline transmission of the mutant allele by breeding to C57BL/6 females and PCR genotyping of pups. PN7 wildtype and mutant eyes were removed following termination of the animals. Eyes were dissected in ice cold PBS. The cornea was pierced and the eye pulled apart. The retina was then gently pulled away from the rest of the eye. Retinal samples were stored in RNAlater® (Qiagen) at -20C. RNA extraction and purification was performed using the RNeasy® Mini kit from Qiagen (Hildern, Germany) before quantification on a Nanodrop spectrophotometer (ND-1000, Thermo Fisher Scientific). Barcoded sequencing libraries were prepared using the Illumina® TruSeq Stranded Total RNA Low-Throughput sample RiboZero Human/Rat/Mouse prep kit following manufacturer's guidelines (Illumina, San Diego, CA, USA). Libraries were quantified with a Qubit® fluorometer (Thermo Fisher Scientific) using the double stranded DNA High sensitivity assay. ENA first public 2017-09-20 ENA last update 2017-09-18 External Id SAMEA104306096 INSDC center alias BRISTOL INSDC center name University of Bristol INSDC first public 2017-09-20T17:02:02Z INSDC last update 2017-09-18T17:37:25Z INSDC status public Submitter Id E-MTAB-6071:Sample 10 age 7 broker name ArrayExpress common name house mouse disease normal genotype Bhlhe23 knockout organism part retina replicate litter 4 sample name E-MTAB-6071:Sample 10 sex male strain C57BL/6 ERS1931075 SAMEA104306097 10090 Mus musculus Protocols: Targeting of the Bhlhe23 gene and genotyping of the Bhlhe23 allele was previously described by Kim et al 2008. An approximately 5-kb HindIII/NotI DNA fragment encompassing the Bhlhb4 gene was isolated by PCR from 129/Sv genomic DNA. A loxP-flanked PGK-neomycin resistance cassette in reverse orientation was introduced into the KpnI site approximately 1 kb upstream of the Bhlhb4 gene. A third loxP sequence was introduced approximately 300 bases distal to the Bhlhb4 3′ UTR, between adjacent BsrGI and MunI restriction sites. A PGK-diptheria toxin gene cassette was introduced at the 3′ end of the Bhlhb4 locus. This vector was electroporated into mouse 129 J1 embryonic stem (ES) cells. A null allele was generated by transiently transfecting targeted ES cells with a Cre recombinase plasmid, pOG231. ES cells carrying the deletion allele were microinjected into C57BL/6 blastocysts, and chimeras were tested for germline transmission of the mutant allele by breeding to C57BL/6 females and PCR genotyping of pups. PN7 wildtype and mutant eyes were removed following termination of the animals. Eyes were dissected in ice cold PBS. The cornea was pierced and the eye pulled apart. The retina was then gently pulled away from the rest of the eye. Retinal samples were stored in RNAlater® (Qiagen) at -20C. RNA extraction and purification was performed using the RNeasy® Mini kit from Qiagen (Hildern, Germany) before quantification on a Nanodrop spectrophotometer (ND-1000, Thermo Fisher Scientific). Barcoded sequencing libraries were prepared using the Illumina® TruSeq Stranded Total RNA Low-Throughput sample RiboZero Human/Rat/Mouse prep kit following manufacturer's guidelines (Illumina, San Diego, CA, USA). Libraries were quantified with a Qubit® fluorometer (Thermo Fisher Scientific) using the double stranded DNA High sensitivity assay. ENA first public 2017-09-20 ENA last update 2017-09-18 External Id SAMEA104306097 INSDC center alias BRISTOL INSDC center name University of Bristol INSDC first public 2017-09-20T17:02:02Z INSDC last update 2017-09-18T17:37:25Z INSDC status public Submitter Id E-MTAB-6071:Sample 4 age 7 broker name ArrayExpress common name house mouse disease normal genotype wild type genotype organism part retina replicate litter 4 sample name E-MTAB-6071:Sample 4 sex male strain C56BL/6 ERS1931076 SAMEA104306098 10090 Mus musculus Protocols: Targeting of the Bhlhe23 gene and genotyping of the Bhlhe23 allele was previously described by Kim et al 2008. An approximately 5-kb HindIII/NotI DNA fragment encompassing the Bhlhb4 gene was isolated by PCR from 129/Sv genomic DNA. A loxP-flanked PGK-neomycin resistance cassette in reverse orientation was introduced into the KpnI site approximately 1 kb upstream of the Bhlhb4 gene. A third loxP sequence was introduced approximately 300 bases distal to the Bhlhb4 3′ UTR, between adjacent BsrGI and MunI restriction sites. A PGK-diptheria toxin gene cassette was introduced at the 3′ end of the Bhlhb4 locus. This vector was electroporated into mouse 129 J1 embryonic stem (ES) cells. A null allele was generated by transiently transfecting targeted ES cells with a Cre recombinase plasmid, pOG231. ES cells carrying the deletion allele were microinjected into C57BL/6 blastocysts, and chimeras were tested for germline transmission of the mutant allele by breeding to C57BL/6 females and PCR genotyping of pups. PN7 wildtype and mutant eyes were removed following termination of the animals. Eyes were dissected in ice cold PBS. The cornea was pierced and the eye pulled apart. The retina was then gently pulled away from the rest of the eye. Retinal samples were stored in RNAlater® (Qiagen) at -20C. RNA extraction and purification was performed using the RNeasy® Mini kit from Qiagen (Hildern, Germany) before quantification on a Nanodrop spectrophotometer (ND-1000, Thermo Fisher Scientific). Barcoded sequencing libraries were prepared using the Illumina® TruSeq Stranded Total RNA Low-Throughput sample RiboZero Human/Rat/Mouse prep kit following manufacturer's guidelines (Illumina, San Diego, CA, USA). Libraries were quantified with a Qubit® fluorometer (Thermo Fisher Scientific) using the double stranded DNA High sensitivity assay. ENA first public 2017-09-20 ENA last update 2017-09-18 External Id SAMEA104306098 INSDC center alias BRISTOL INSDC center name University of Bristol INSDC first public 2017-09-20T17:02:02Z INSDC last update 2017-09-18T17:37:25Z INSDC status public Submitter Id E-MTAB-6071:Sample 11 age 7 broker name ArrayExpress common name house mouse disease normal genotype Bhlhe23 knockout organism part retina replicate litter 5 sample name E-MTAB-6071:Sample 11 sex female strain C57BL/6 ERS1931077 SAMEA104306099 10090 Mus musculus Protocols: Targeting of the Bhlhe23 gene and genotyping of the Bhlhe23 allele was previously described by Kim et al 2008. An approximately 5-kb HindIII/NotI DNA fragment encompassing the Bhlhb4 gene was isolated by PCR from 129/Sv genomic DNA. A loxP-flanked PGK-neomycin resistance cassette in reverse orientation was introduced into the KpnI site approximately 1 kb upstream of the Bhlhb4 gene. A third loxP sequence was introduced approximately 300 bases distal to the Bhlhb4 3′ UTR, between adjacent BsrGI and MunI restriction sites. A PGK-diptheria toxin gene cassette was introduced at the 3′ end of the Bhlhb4 locus. This vector was electroporated into mouse 129 J1 embryonic stem (ES) cells. A null allele was generated by transiently transfecting targeted ES cells with a Cre recombinase plasmid, pOG231. ES cells carrying the deletion allele were microinjected into C57BL/6 blastocysts, and chimeras were tested for germline transmission of the mutant allele by breeding to C57BL/6 females and PCR genotyping of pups. PN7 wildtype and mutant eyes were removed following termination of the animals. Eyes were dissected in ice cold PBS. The cornea was pierced and the eye pulled apart. The retina was then gently pulled away from the rest of the eye. Retinal samples were stored in RNAlater® (Qiagen) at -20C. RNA extraction and purification was performed using the RNeasy® Mini kit from Qiagen (Hildern, Germany) before quantification on a Nanodrop spectrophotometer (ND-1000, Thermo Fisher Scientific). Barcoded sequencing libraries were prepared using the Illumina® TruSeq Stranded Total RNA Low-Throughput sample RiboZero Human/Rat/Mouse prep kit following manufacturer's guidelines (Illumina, San Diego, CA, USA). Libraries were quantified with a Qubit® fluorometer (Thermo Fisher Scientific) using the double stranded DNA High sensitivity assay. ENA first public 2017-09-20 ENA last update 2017-09-18 External Id SAMEA104306099 INSDC center alias BRISTOL INSDC center name University of Bristol INSDC first public 2017-09-20T17:02:02Z INSDC last update 2017-09-18T17:37:25Z INSDC status public Submitter Id E-MTAB-6071:Sample 5 age 7 broker name ArrayExpress common name house mouse disease normal genotype wild type genotype organism part retina replicate litter 5 sample name E-MTAB-6071:Sample 5 sex female strain C57BL/6 ERS1931078 SAMEA104306100 10090 Mus musculus Protocols: Targeting of the Bhlhe23 gene and genotyping of the Bhlhe23 allele was previously described by Kim et al 2008. An approximately 5-kb HindIII/NotI DNA fragment encompassing the Bhlhb4 gene was isolated by PCR from 129/Sv genomic DNA. A loxP-flanked PGK-neomycin resistance cassette in reverse orientation was introduced into the KpnI site approximately 1 kb upstream of the Bhlhb4 gene. A third loxP sequence was introduced approximately 300 bases distal to the Bhlhb4 3′ UTR, between adjacent BsrGI and MunI restriction sites. A PGK-diptheria toxin gene cassette was introduced at the 3′ end of the Bhlhb4 locus. This vector was electroporated into mouse 129 J1 embryonic stem (ES) cells. A null allele was generated by transiently transfecting targeted ES cells with a Cre recombinase plasmid, pOG231. ES cells carrying the deletion allele were microinjected into C57BL/6 blastocysts, and chimeras were tested for germline transmission of the mutant allele by breeding to C57BL/6 females and PCR genotyping of pups. PN7 wildtype and mutant eyes were removed following termination of the animals. Eyes were dissected in ice cold PBS. The cornea was pierced and the eye pulled apart. The retina was then gently pulled away from the rest of the eye. Retinal samples were stored in RNAlater® (Qiagen) at -20C. RNA extraction and purification was performed using the RNeasy® Mini kit from Qiagen (Hildern, Germany) before quantification on a Nanodrop spectrophotometer (ND-1000, Thermo Fisher Scientific). Barcoded sequencing libraries were prepared using the Illumina® TruSeq Stranded Total RNA Low-Throughput sample RiboZero Human/Rat/Mouse prep kit following manufacturer's guidelines (Illumina, San Diego, CA, USA). Libraries were quantified with a Qubit® fluorometer (Thermo Fisher Scientific) using the double stranded DNA High sensitivity assay. ENA first public 2017-09-20 ENA last update 2017-09-18 External Id SAMEA104306100 INSDC center alias BRISTOL INSDC center name University of Bristol INSDC first public 2017-09-20T17:02:02Z INSDC last update 2017-09-18T17:37:25Z INSDC status public Submitter Id E-MTAB-6071:Sample 12 age 7 broker name ArrayExpress common name house mouse disease normal genotype Bhlhe23 knockout organism part retina replicate litter 6 sample name E-MTAB-6071:Sample 12 sex female strain C57BL/6 ERS1931079 SAMEA104306101 10090 Mus musculus Protocols: Targeting of the Bhlhe23 gene and genotyping of the Bhlhe23 allele was previously described by Kim et al 2008. An approximately 5-kb HindIII/NotI DNA fragment encompassing the Bhlhb4 gene was isolated by PCR from 129/Sv genomic DNA. A loxP-flanked PGK-neomycin resistance cassette in reverse orientation was introduced into the KpnI site approximately 1 kb upstream of the Bhlhb4 gene. A third loxP sequence was introduced approximately 300 bases distal to the Bhlhb4 3′ UTR, between adjacent BsrGI and MunI restriction sites. A PGK-diptheria toxin gene cassette was introduced at the 3′ end of the Bhlhb4 locus. This vector was electroporated into mouse 129 J1 embryonic stem (ES) cells. A null allele was generated by transiently transfecting targeted ES cells with a Cre recombinase plasmid, pOG231. ES cells carrying the deletion allele were microinjected into C57BL/6 blastocysts, and chimeras were tested for germline transmission of the mutant allele by breeding to C57BL/6 females and PCR genotyping of pups. PN7 wildtype and mutant eyes were removed following termination of the animals. Eyes were dissected in ice cold PBS. The cornea was pierced and the eye pulled apart. The retina was then gently pulled away from the rest of the eye. Retinal samples were stored in RNAlater® (Qiagen) at -20C. RNA extraction and purification was performed using the RNeasy® Mini kit from Qiagen (Hildern, Germany) before quantification on a Nanodrop spectrophotometer (ND-1000, Thermo Fisher Scientific). Barcoded sequencing libraries were prepared using the Illumina® TruSeq Stranded Total RNA Low-Throughput sample RiboZero Human/Rat/Mouse prep kit following manufacturer's guidelines (Illumina, San Diego, CA, USA). Libraries were quantified with a Qubit® fluorometer (Thermo Fisher Scientific) using the double stranded DNA High sensitivity assay. ENA first public 2017-09-20 ENA last update 2017-09-18 External Id SAMEA104306101 INSDC center alias BRISTOL INSDC center name University of Bristol INSDC first public 2017-09-20T17:02:02Z INSDC last update 2017-09-18T17:37:25Z INSDC status public Submitter Id E-MTAB-6071:Sample 6 age 7 broker name ArrayExpress common name house mouse disease normal genotype wild type genotype organism part retina replicate litter 6 sample name E-MTAB-6071:Sample 6 sex female strain C57BL/6