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4 protocols using dh5α competent cells

1

Gremlin1 mRNA Expression in Birds

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Total RNA was extracted from the embryos using the NucleoSpin RNA kit (MACHEREY- NAGEL). RT–PCR was performed to amplify the fragments of Gremlin1 mRNA in all bird species assessed. The primer sequences used for isolation of the fragments were Fw-5′-ATGGTCCGCACACTGTTGCC-3′ and Rv-5′-GCATTTGCCGTCACATGATGCTT-3′. The fragments were subcloned using the pGEM-T Easy Vector Systems (Promega) and DH5α competent cells (TOYOBO) and sequenced using Sanger sequencing. Sequence data were compared to a BLAST search to identify homologues of the isolated fragments. For synthesis of digoxigenin (DIG)-labelled RNA riboprobes, DNA templates with Sp6 and T7 promoters were first generated by PCR. Then, the templates were transcribed with an appropriate RNA polymerase.
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2

TA Cloning and Sequencing of DNA

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PCR products were assembled into the pCR2.1-TOPO™ TA vector (Thermo Fisher Scientific)
using TA cloning, and the cloned vectors were transformed into DH5α competent cells
(Toyobo Co., Ltd., Osaka, Japan). Colony PCR was performed using primers M13-20
(5′-GTAAAACGACGGCCAG-3′) and M13R (5′-GGAAACAGCTATGACCATG-3′). The amplified insert DNA
was sequenced using the Big Dye Terminator Sequencing Kit (version 3.1; Applied
Biosystems, Waltham, MA, USA). The cDNA sequences were aligned with GenBank
AB618613.1.
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3

RT-PCR and Sequencing of SLC35A2

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Total RNA from family trio and one healthy control was extracted from whole blood using a Monarch Total RNA Miniprep kit (NEW ENGLAND BioLabs, Ipswich, MA) and subjected to reverse transcription using the PrimeScript RT reagent kit (TAKARA BIO, Kusatsu, Shiga) according to the manufacturer's protocol. We designed target‐specific primers for SLC35A2(NM_005660.2) (Figure 2c, Table S3) and 2 μl of cDNA was used for polymerase chain reaction (PCR). PCR products were separated by electrophoresis on a 3% agarose gel and extracted from gels and cloned into pGEM‐T easy vectors (Promega, Madison, WI) using Ligation high (TOYOBO, Osaka, Japan), then transfected into DH5α competent cells (TOYOBO). Competent cells were spread on LB plates containing ampicillin and incubated at 37°C overnight. We performed colony PCRs on randomly selected well‐isolated colonies, and products of the colony PCR were sequenced.
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4

Bacterial 16S rRNA Gene Sequencing

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For 16S rRNA gene clone library analyses, bacterial 16S rRNA gene sequences were amplified by means of polymerase chain reaction (PCR) with the 27F (5′-AGAGTTTGATCCTGGCTCAG-3′) and 1492R (5′-GGTTACCTTGTTACGACTT-3′) primers. Amplified 16S rDNA was ligated into the pCR4.0 TOPO vector (Invitrogen, Carlsbad, CA), and the products of these ligation reactions were then transformed into DH-5α–competent cells (TOYOBO, Osaka, Japan). Inserts were amplified and sequenced on an ABI PRISM 3100 Genetic Analyzer (Applied Biosystems, Foster City, CA). The 27F and 520R (5′-ACCGCGGCTGCTGGC-3′) primers and a BigDye Terminator cycle sequencing kit (Applied Biosystems) were used for sequencing. Bacterial sequences were identified by means of Basic Local Alignment Search Tool (BLAST) and Ribosomal Database Project searches (50 (link)).
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