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text: Repeated application of organic mixed with inorganic materials in agriculture improves soil microbial quality and by extension crop productivity. While soil microbial quality at the end point following several years of a repeated fertilization diets have received considerable attention, the dynamic of this community throughout years had never been assessed. Here, we use a high-throughput sequencing approach targeting 16S ribosomal RNA gene to investigate throughout 6 years of repeated fertilizers (organic and inorganic) application the prokaryotic community evolution. Soils were sampled from a field experiment: La Mare (Reunion Island, France), where different mixed organic-inorganic fertilization diets characterized by more or less stable organic matter were applied regularly since 6 years. Each year, approximately more than 6 months after the last fertilization, soil samples were carried out. Our results highlighted that soil microbial community was lastingly modified after 6 years of repeated fertilization diets. These changes depended both on the nature of organic input and fertilization practices (frequencies and quantity applied).

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characteristic: geographic location (country and/or sea)

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text: CGACGTGACT(forward) CATCGAGCAG (reverse)

text: Microbial DNA was extracted from 1 g (dry weight) of soil using a single procedure standardized by the GenoSol platform (INRAE, Dijon, France, https://www2.dijon.inrae.fr/plateforme_genosol/) . Since a highly positive linear relationship has been shown between soil DNA recovery and C-biomass measurement , DNA concentrations of crude extracts were determined by electrophoresis in 1% agarose gel stained with ethidium bromide using a calf thymus DNA standard curve, and used as estimates of microbial biomass . After quantification, 100 µl of crude DNA extract were separated from the residual impurities, particularly humic substances, by using only the purification steps of Nucleospin Soil kit (Macherey-Nagel GmbH & Co. KG, Düren, Germany). Purified DNA concentrations were finally measured using the Quantifluor (Promega, Lyon, France) staining kit, according to the manufacturer’s instructions.

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text: INRA-CMSE

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text: Repeated application of organic mixed with inorganic materials in agriculture improves soil microbial quality and by extension crop productivity. While soil microbial quality at the end point following several years of a repeated fertilization diets have received considerable attention, the dynamic of this community throughout years had never been assessed. Here, we use a high-throughput sequencing approach targeting 16S ribosomal RNA gene to investigate throughout 6 years of repeated fertilizers (organic and inorganic) application the prokaryotic community evolution. Soils were sampled from a field experiment: La Mare (Reunion Island, France), where different mixed organic-inorganic fertilization diets characterized by more or less stable organic matter were applied regularly since 6 years. Each year, approximately more than 6 months after the last fertilization, soil samples were carried out. Our results highlighted that soil microbial community was lastingly modified after 6 years of repeated fertilization diets. These changes depended both on the nature of organic input and fertilization practices (frequencies and quantity applied).

text: agricultural soil

text: microbial feature

characteristic: environment (feature)

text: soil

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text: France

characteristic: geographic location (depth)

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text: Microbial DNA was extracted from 1 g (dry weight) of soil using a single procedure standardized by the GenoSol platform (INRAE, Dijon, France, https://www2.dijon.inrae.fr/plateforme_genosol/) . Since a highly positive linear relationship has been shown between soil DNA recovery and C-biomass measurement , DNA concentrations of crude extracts were determined by electrophoresis in 1% agarose gel stained with ethidium bromide using a calf thymus DNA standard curve, and used as estimates of microbial biomass . After quantification, 100 µl of crude DNA extract were separated from the residual impurities, particularly humic substances, by using only the purification steps of Nucleospin Soil kit (Macherey-Nagel GmbH & Co. KG, Düren, Germany). Purified DNA concentrations were finally measured using the Quantifluor (Promega, Lyon, France) staining kit, according to the manufacturer’s instructions.

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text: Repeated application of organic mixed with inorganic materials in agriculture improves soil microbial quality and by extension crop productivity. While soil microbial quality at the end point following several years of a repeated fertilization diets have received considerable attention, the dynamic of this community throughout years had never been assessed. Here, we use a high-throughput sequencing approach targeting 16S ribosomal RNA gene to investigate throughout 6 years of repeated fertilizers (organic and inorganic) application the prokaryotic community evolution. Soils were sampled from a field experiment: La Mare (Reunion Island, France), where different mixed organic-inorganic fertilization diets characterized by more or less stable organic matter were applied regularly since 6 years. Each year, approximately more than 6 months after the last fertilization, soil samples were carried out. Our results highlighted that soil microbial community was lastingly modified after 6 years of repeated fertilization diets. These changes depended both on the nature of organic input and fertilization practices (frequencies and quantity applied).

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text: Réunion

text: CACGCTACGT(forward) CGAGCTCATG (reverse)

text: Microbial DNA was extracted from 1 g (dry weight) of soil using a single procedure standardized by the GenoSol platform (INRAE, Dijon, France, https://www2.dijon.inrae.fr/plateforme_genosol/) . Since a highly positive linear relationship has been shown between soil DNA recovery and C-biomass measurement , DNA concentrations of crude extracts were determined by electrophoresis in 1% agarose gel stained with ethidium bromide using a calf thymus DNA standard curve, and used as estimates of microbial biomass . After quantification, 100 µl of crude DNA extract were separated from the residual impurities, particularly humic substances, by using only the purification steps of Nucleospin Soil kit (Macherey-Nagel GmbH & Co. KG, Düren, Germany). Purified DNA concentrations were finally measured using the Quantifluor (Promega, Lyon, France) staining kit, according to the manufacturer’s instructions.

text: soil metagenome

characteristic: organism

text: ReunPro

text: soil metagenome

text: Illumina

text: soil

characteristic: title


text: INRA-CMSE

text: public

text: crops

text: agricultural soil

text: microbial feature

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: France

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Réunion

characteristic: geographic location (region and locality)

characteristic: investigation type

text: CATACTCTAC(forward) CATCGAGCAG (reverse)

characteristic: multiplex identifiers

characteristic: nucleic acid extraction

text: soil metagenome

text: 5-CAGCMGCYGCNGTAANAC-3 (forward) 5-CCGYCAATTCMTTTRAGT-3 (reverse)

characteristic: pcr primers

text: ReunPro

characteristic: project name

characteristic: sample volume or weight for dna extraction

text: soil metagenome

text: Illumina

characteristic: sequencing method

text: soil

characteristic: soil environmental package

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: crops

characteristic: current land use

characteristic: description

text: agricultural soil

characteristic: environment (biome)

text: microbial feature

text: soil

text: France

characteristic: geographic location (country and/or sea)

text: Réunion

text: CATAGTAGTG(forward) CACGTAGATC (reverse)

text: soil metagenome

characteristic: organism

text: ReunPro

text: soil metagenome

text: Illumina

text: soil

text: Microbial diversity dynamic of tropical soil during 6 years of repeated organic and inorganic fertilization

characteristic: title


text: INRA-CMSE

text: public

text: crops

text: agricultural soil

text: microbial feature

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: France

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Réunion

characteristic: geographic location (region and locality)

characteristic: investigation type

text: CGTACAGTCA(forward) CGTACAGTCA (reverse)

characteristic: multiplex identifiers

characteristic: nucleic acid extraction

text: soil metagenome

characteristic: pcr primers

text: ReunPro

characteristic: project name

characteristic: sample volume or weight for dna extraction

text: soil metagenome

text: Illumina

characteristic: sequencing method

text: soil

characteristic: soil environmental package

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: crops

characteristic: current land use

characteristic: description

text: agricultural soil

characteristic: environment (biome)

text: microbial feature

text: soil

text: France

characteristic: geographic location (country and/or sea)

text: Réunion

text: CATAGTAGTG(forward) CGTACAGTCA (reverse)

text: soil metagenome

characteristic: organism

text: ReunPro

text: soil metagenome

text: Illumina

text: soil

characteristic: title


text: INRA-CMSE

text: public

text: crops

text: agricultural soil

text: microbial feature

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: France

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Réunion

characteristic: geographic location (region and locality)

characteristic: investigation type

text: CATATCTCGT(forward) CGAGCTCATG (reverse)

characteristic: multiplex identifiers

characteristic: nucleic acid extraction

text: soil metagenome

characteristic: pcr primers

text: ReunPro

characteristic: project name

characteristic: sample volume or weight for dna extraction

text: soil metagenome

text: Illumina

characteristic: sequencing method

text: soil

characteristic: soil environmental package

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: crops

characteristic: current land use

characteristic: description

text: agricultural soil

characteristic: environment (biome)

text: microbial feature

text: soil

text: France

characteristic: geographic location (country and/or sea)

text: Réunion

text: CGTACAGTCA(forward) CATACTCTAC (reverse)

text: soil metagenome

characteristic: organism

text: ReunPro

text: soil metagenome

text: Illumina

text: soil

characteristic: title


text: INRA-CMSE

text: public

text: crops

text: agricultural soil

text: microbial feature

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: France

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Réunion

characteristic: geographic location (region and locality)

characteristic: investigation type

text: CGTCGATCTC(forward) CACGCTACGT (reverse)

characteristic: multiplex identifiers

characteristic: nucleic acid extraction

text: soil metagenome

characteristic: pcr primers

text: ReunPro

characteristic: project name

characteristic: sample volume or weight for dna extraction

text: soil metagenome

text: Illumina

characteristic: sequencing method

text: soil

characteristic: soil environmental package

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: crops

characteristic: current land use

characteristic: description

text: agricultural soil

characteristic: environment (biome)

text: microbial feature

text: soil

text: France

characteristic: geographic location (country and/or sea)

text: Réunion

text: CATAGTAGTG(forward) CGACGTGACT (reverse)

text: soil metagenome

characteristic: organism

text: ReunPro

text: soil metagenome

text: Illumina

text: soil

characteristic: title


text: University of Graz

text: public

tag: Namespace:University of Graz

characteristic: collection date

text: Sample K02 from Koralm Tunnel drainage water biofilm, KAT2, tunnel meter 6884

text: continental subsurface zone

text: water biofilm

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Austria

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: miscellaneous natural or artificial environment

characteristic: miscellaneous environmental package

text: subsurface metagenome

characteristic: pH

characteristic: project name

text: subsurface metagenome

text: Illumina MiSeq

characteristic: sequencing method

unit: ºC

characteristic: temperature


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Graz

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Sample K07 from Koralm Tunnel drainage water biofilm, KAT3, tunnel meter 280

characteristic: description

text: continental subsurface zone

text: water biofilm

text: water

text: Austria

text: metagenome

text: subsurface metagenome

text: subsurface metagenome

text: Illumina MiSeq


text: University of Graz

text: public

characteristic: collection date

text: Sample KV11 from Koralm Tunnel drainage water biofilm, KAT3, tunnel meter 8246

text: continental subsurface zone

characteristic: environment (biome)

text: water biofilm

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Austria

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: subsurface metagenome

characteristic: organism

text: subsurface metagenome

text: Illumina MiSeq

characteristic: title


KVAB

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Graz

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: KVAB

text: Sample KVAB from Koralm Tunnel drainage water biofilm, KAT3, tunnel meter 8246

text: continental subsurface zone

text: water biofilm

text: water

text: Austria

text: metagenome

characteristic: miscellaneous environmental package

text: subsurface metagenome

characteristic: pH

characteristic: project name

text: subsurface metagenome

text: Illumina MiSeq

characteristic: sequencing method

characteristic: temperature

text: KVAB


text: University of Graz

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Sample K09 from Koralm Tunnel drainage water biofilm, KAT3, tunnel meter 8260

characteristic: description

text: continental subsurface zone

characteristic: environment (biome)

text: water biofilm

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Austria

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

text: metagenome

text: subsurface metagenome

text: subsurface metagenome

text: Illumina MiSeq


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Graz

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Sample K11 from Koralm Tunnel drainage water biofilm, KAT3, tunnel meter 8405

text: continental subsurface zone

text: water biofilm

text: water

text: Austria

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: subsurface metagenome

characteristic: organism

text: subsurface metagenome

text: Illumina MiSeq

characteristic: title


E-MTAB-11699:Sample 1

text: IOWA STATE UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11699:Sample 1

tag: Namespace:IOWA STATE UNIVERSITY

characteristic: Submitter Id

text: Holstein

characteristic: breed

text: ArrayExpress

characteristic: broker name

text: cattle

characteristic: common name

text: Protocols: Cell sample collections. Skeletal muscle and subcutaneous fat samples were collected from Angus-crossbred steers slaughtered at the Virginia Tech Meat Center. Satellite cells were isolated from skeletal muscle by pronase digestion as described before (Leng et al. 2019). The isolated satellite cells were activated to proliferate as myoblasts by culturing in growth medium composed of Dulbecco’s Modified Eagle Medium (DMEM), 10% fetal bovine serum (FBS), and 1% antibiotics-antimycotics. To induce myoblasts to differentiate into myocytes, myoblasts cultured in growth medium were switched to differentiation medium composed of DMEM and 2% horse serum for 2 days. Preadipocytes from subcutaneous fat were isolated by collagenase digestion as previously described (Hausman et al. 2008). To induce preadipocytes to differentiate into adipocytes, preadipocytes were initially cultured in growth medium (DMEM/F12, 10% FBS, 1% antibiotics-antimycotics) to reach confluency, then in induction medium (DMEM/F12, 10% FBS, 1% antibiotics-antimycotics, 10 μg/mL insulin, 1 μM dexamethasone, 0.5 mM isobutyl methylxanthine, and 200 μM indomethacin) for 2 days, and lastly in maintenance medium (DMEM/F12, 10% FBS, 1% antibiotics-antimycotics, 1 μg/mL insulin) for 10 days.Adult tissue collections. Procedures for tissue collection followed the Animal Care and Use protocol (#18464) approved by the Institutional Animal Care and Use Committee (IACUC), University of California, Davis (UCD). Four cattle (2 males and 2 females) were slaughtered at UCD using captive bolt under USDA inspection at 14 months old and were intact male and female Line 1 Herefords that had the same sire, provided by Fort Keogh Livestock and Range Research Lab (Tixier-Boichard et al. 2021). Tissue samples were flash frozen in liquid nitrogen then stored at -80 °C until further assay processing. Fetal tissue collections. Fetal sample collection and tissue collection were approved by the Institutional Animal Care and Use Committee (IACUC), University of Idaho (2017-67). Four pregnant females Line 1 Herefords were slaughtered at UI meats lab using captive bolt under USDA inspection. Animals were provided by Fort Keogh Livestock and Range Research Lab (Tixier-Boichard et al. 2021). Tissue samples were flash frozen in liquid nitrogen then stored at -80 °C until further assay processing. Cell sample collections. Skeletal muscle and subcutaneous fat samples were collected from Angus-crossbred steers slaughtered at the Virginia Tech Meat Center. Satellite cells were isolated from skeletal muscle by pronase digestion as described before (Leng et al. 2019). The isolated satellite cells were activated to proliferate as myoblasts by culturing in growth medium composed of Dulbecco’s Modified Eagle Medium (DMEM), 10% fetal bovine serum (FBS), and 1% antibiotics-antimycotics. To induce myoblasts to differentiate into myocytes, myoblasts cultured in growth medium were switched to differentiation medium composed of DMEM and 2% horse serum for 2 days. Preadipocytes from subcutaneous fat were isolated by collagenase digestion as previously described (Hausman et al. 2008). To induce preadipocytes to differentiate into adipocytes, preadipocytes were initially cultured in growth medium (DMEM/F12, 10% FBS, 1% antibiotics-antimycotics) to reach confluency, then in induction medium (DMEM/F12, 10% FBS, 1% antibiotics-antimycotics, 10 μg/mL insulin, 1 μM dexamethasone, 0.5 mM isobutyl methylxanthine, and 200 μM indomethacin) for 2 days, and lastly in maintenance medium (DMEM/F12, 10% FBS, 1% antibiotics-antimycotics, 1 μg/mL insulin) for 10 days. Adult tissue collections. Procedures for tissue collection followed the Animal Care and Use protocol (#18464) approved by the Institutional Animal Care and Use Committee (IACUC), University of California, Davis (UCD). Four cattle (2 males and 2 females) were slaughtered at UCD using captive bolt under USDA inspection at 14 months old and were intact male and female Line 1 Herefords that had the same sire, provided by Fort Keogh Livestock and Range Research Lab (Tixier-Boichard et al. 2021). Tissue samples were flash frozen in liquid nitrogen then stored at -80 °C until further assay processing. Fetal tissue collections. Fetal sample collection and tissue collection were approved by the Institutional Animal Care and Use Committee (IACUC), University of Idaho (2017-67). Four pregnant females Line 1 Herefords were slaughtered at UI meats lab using captive bolt under USDA inspection. Animals were provided by Fort Keogh Livestock and Range Research Lab (Tixier-Boichard et al. 2021). Tissue samples were flash frozen in liquid nitrogen then stored at -80 °C until further assay processing. RNA-seq library construction. Tissue samples (Additional file18) were collected from storage at -80oC and ground to a powder using a mortar and pestle and liquid nitrogen. The tissue was next homogenized in QIAzol Lysis Reagent (Qiagen Catalog No. 79306) using a QIAshredder spin column (Qiagen Catalog No. 79656). After centrifugation, the lysate was mixed with chloroform, shaken vigorously for 15 sec, incubated for 2 - 3 min at room temperature, and centrifuged for 15 min at 12,000 x g at 4°C. The upper, aqueous phase was transferred to a new collection tube and 1.5 vol of 100% ethanol was added and mixed thoroughly by pipetting up and down several times. Total RNA was then isolated from the sample using the RNeasy Mini Kit (Qiagen Catalog No. 74106) according to the manufacturer’s instructions. Contaminating DNA was removed by treating total RNA with DNase (AM1906, Ambion). Total RNA quantity was measured with the Quant-It RiboGreen RNA Assay Kit (Life Technologies Corp., Carlsbad, CA) and quality assessed by fragment analysis (Advance Analytical Technologies, Inc., Ankeny IA). Mammary gland RNA-seq and miRNA-seq library construction. The 16 animals used in this study were Holstein-Friesian Heifers from a single herd managed at the AgResearch Research Station in Ruakura, NZ. All experimental protocols were approved by the AgResearch, NZ, ethics committee, and carried out according to their guidelines. Samples were collected from the same animals at 5 time points: virgin state before pregnancy between 13 and 15 months of age (virgin), mid pregnant at 100 day of pregnancy, late pregnant ~2 weeks pre-calving, early lactation ~2 weeks post-calving, and at peak lactation, 34-38 days post-calving. Tissue samples were obtained by mammary biopsy using the Farr method (Farr et al. 1996). Lactating cows were milked before biopsy and sampled within 5 hours of milking. Biopsy sites were clipped and given aseptic skin preparation (povidone iodine base scrub and iodine tincture) and subcutaneous local anesthetic (4 ml per biopsy site). Core biopsies were taken using a powered sampling cannula (4.5 mm internal diameter) inserted into a 2 cm incision. The resulting samples of mammary gland parenchyma measured 70 mm in length, with a 4 mm diameter. Small slices from each sample were preserved for histology before mammary epithelial organoids were separated from surrounding adipose and connective tissue to allow for secretory-specific signals in the RNA-seq analysis. In preparation for isolating organoids, tissue samples were digested in a freshly prepared collagenase solution containing 0.2% collagenase A (Roche), 0.05% trypsin (1:250 powder, 100U/ml Gibco), hyaluronidase (Sigma), 5% fetal calf serum (Hyclone), Pen/Strep/Fungizone solution (Hyclone) or 5 µg/ml Gentamycin (Sigma) in DMEM/F12 (Gibco) with 10 ng/ml insulin. Samples were minced to a fine slurry and incubated in this freshly prepared collagenase solution (10 ml solution / g tissue) for 3.5 hours at 37°C in a 50 ml conical tube with slow shaking (120 rpm). Digested tissue was centrifuged at 453 xg for 10 min at 4°C, after which the supernatant and fat layers were discarded, and the pellet was gently resuspended in 5 ml DMEM/F12 without serum. A further 5 ml DMEM/F12 without serum was added, and the sample was centrifuged at 453 xg for 10 min at 4°C. The media was discarded, and the pellet was gently resuspended in 10 ml DMEM/F12 and centrifuged for another 10 min at 453 xg and 4°C. The media was discarded, and pellet resuspended in 10 ml DMEM/F12 for a third time, and the sample centrifuged in a series of brief spins achieved by allowing the centrifuge to reach 453 xg for two seconds before applying the brake. These brief pulse spins were repeated at least 4 times, or until examining the sample under a microscope revealed primarily epithelial organoid clusters and very few single cells. At this point, the organoid pellet was resuspended in 1 ml TRIzol and stored at -80°C until RNA isolation. High-quality total RNA (RIN > 7) was extracted from frozen mammary epithelial organoid pellets using NucleoSpin® miRNA isolation kit (MACHEREY-NAGEL) according to the manufacturer’s protocol, isolating large and small (<200 nt) fractions separately. The “large” RNA fraction was used to prepare strand-specific poly-A+ RNA-seq libraries for sequencing. The “small” RNA fraction was used to make miRNA-seq libraries using NEXTflexTM small RNA-seq Kitv3.miRNA-seq library construction. Tissue samples (Additional file18) were collected similar to that described in previous section. QIAseq miRNA Library Kit (Qiagen, cat no. 331505) and QIAseq miRNA NGS 96 Index IL (Qiagen, cat no. 331565) kits were used to isolate miRNAs from all tissues except mammary gland. miRNAs from mammary gland were isolated using NEXTflexTM small RNA-seq Kitv3 (Illumina) according to the manufacturer’s instructions. The isolated miRNA was subjected to 3’ ligation to ligate a preadenylated DNA adaptor to the 3’ends of all miRNAs. An RNA adaptor was then ligated to the 5’ end of the mature miRNA to complete 5’ ligation. cDNA synthesis was completed using a reverse transcriptase (RT) primer containing integrated unique molecular identifiers (UMI). The RT primer bound to the 3’ adaptor region and facilitated conversion of the 3’/5’ ligated miRNAs into cDNA while a UMI was assigned to every miRNA molecule. After reverse transcription, a clean-up of the cDNA was performed using a streamlined magnetic bead-based method. Library amplification was accomplished by a universal forward primer from a plate being paired with 1 of 96 dried reverse primers in the same plate (Qiagen, cat no. 331565) to assign each sample a unique custom index. Following library amplification, a clean-up of the miRNA library was performed using a streamlined magnetic bead-based method. Libraries were then evaluated for quantity and quality measures before being normalized and pooled for Illumina sequencing.

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

characteristic: individual

text: Bos taurus

text: Bos taurus

text: mammary gland

characteristic: organism part

text: Bos taurus

text: Sample 1


E-MTAB-11699:Sample 10

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IOWA STATE UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11699:Sample 10

text: Herford

text: ArrayExpress

text: cattle

text: late embryonic stage

text: normal

text: Bos taurus

text: Bos taurus

text: muscle

text: Bos taurus

text: Sample 10


E-MTAB-11699:Sample 100

text: IOWA STATE UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11699:Sample 100

text: Herford

text: ArrayExpress

text: cattle

text: adult

text: normal

text: Bos taurus

characteristic: organism

text: Bos taurus

text: jejunum

text: Bos taurus

text: Sample 100

characteristic: title


E-MTAB-11699:Sample 101

text: IOWA STATE UNIVERSITY

text: public

characteristic: SRA accession

text: E-MTAB-11699:Sample 101

characteristic: Submitter Id

text: Herford

characteristic: breed

text: ArrayExpress

characteristic: broker name

text: cattle

text: adult

text: normal

text: Bos taurus

text: Bos taurus

text: ileum

text: Bos taurus

text: Sample 101


E-MTAB-11699:Sample 102

text: IOWA STATE UNIVERSITY

text: public

text: E-MTAB-11699:Sample 102

text: Herford

text: ArrayExpress

text: cattle

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Bos taurus

text: Bos taurus

text: ileum

text: Bos taurus

text: Sample 102


E-MTAB-11699:Sample 103

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: IOWA STATE UNIVERSITY

text: public

text: E-MTAB-11699:Sample 103

text: Herford

text: ArrayExpress

text: cattle

text: adult

text: normal

characteristic: individual

text: Bos taurus

text: Bos taurus

text: cecum

characteristic: organism part

text: Bos taurus

text: Sample 103


E-MTAB-11699:Sample 104

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IOWA STATE UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11699:Sample 104

text: Herford

text: ArrayExpress

text: cattle

text: adult

text: normal

text: Bos taurus

text: Bos taurus

text: cecum

text: Bos taurus

text: Sample 104


E-MTAB-11699:Sample 105

text: IOWA STATE UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11699:Sample 105

text: Herford

text: ArrayExpress

text: cattle

text: adult

text: normal

text: Bos taurus

characteristic: organism

text: Bos taurus

text: colon

text: Bos taurus

text: Sample 105

characteristic: title


E-MTAB-11699:Sample 106

text: IOWA STATE UNIVERSITY

text: public

characteristic: SRA accession

text: E-MTAB-11699:Sample 106

characteristic: Submitter Id

text: Herford

characteristic: breed

text: ArrayExpress

characteristic: broker name

text: cattle

text: adult

text: normal

text: Bos taurus

text: Bos taurus

text: colon

text: Bos taurus

text: Sample 106


E-MTAB-11699:Sample 107

text: IOWA STATE UNIVERSITY

text: public

text: E-MTAB-11699:Sample 107

text: Herford

text: ArrayExpress

text: cattle

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Bos taurus

text: Bos taurus

text: gal bladder

text: Bos taurus

text: Sample 107


E-MTAB-11699:Sample 108

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: IOWA STATE UNIVERSITY

text: public

text: E-MTAB-11699:Sample 108

text: Herford

text: ArrayExpress

text: cattle

text: adult

text: normal

characteristic: individual

text: Bos taurus

text: Bos taurus

text: gal bladder

characteristic: organism part

text: Bos taurus

text: Sample 108


E-MTAB-11699:Sample 109

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IOWA STATE UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11699:Sample 109

text: Herford

text: ArrayExpress

text: cattle

text: adult

text: normal

text: Bos taurus

text: Bos taurus

text: lymph nodes

text: Bos taurus

text: Sample 109


E-MTAB-11699:Sample 11

text: IOWA STATE UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11699:Sample 11

text: Herford

text: ArrayExpress

text: cattle

text: late embryonic stage

text: normal

text: Bos taurus

characteristic: organism

text: Bos taurus

text: muscle

text: Bos taurus

text: Sample 11

characteristic: title


E-MTAB-11699:Sample 110

text: IOWA STATE UNIVERSITY

text: public

characteristic: SRA accession

text: E-MTAB-11699:Sample 110

characteristic: Submitter Id

text: Herford

characteristic: breed

text: ArrayExpress

characteristic: broker name

text: cattle

text: adult

text: normal

text: Bos taurus

text: Bos taurus

text: lymph nodes

text: Bos taurus

text: Sample 110


E-MTAB-11699:Sample 111

text: IOWA STATE UNIVERSITY

text: public

text: E-MTAB-11699:Sample 111

text: Herford

text: ArrayExpress

text: cattle

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Bos taurus

text: Bos taurus

text: thymus

text: Bos taurus

text: Sample 111


E-MTAB-11699:Sample 112

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: IOWA STATE UNIVERSITY

text: public

text: E-MTAB-11699:Sample 112

text: Herford

text: ArrayExpress

text: cattle

text: adult

text: normal

characteristic: individual

text: Bos taurus

text: Bos taurus

text: thymus

characteristic: organism part

text: Bos taurus

text: Sample 112


E-MTAB-11699:Sample 113

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IOWA STATE UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11699:Sample 113

text: Herford

text: ArrayExpress

text: cattle

text: adult

text: normal

text: Bos taurus

text: Bos taurus

text: bone marrow

text: Bos taurus

text: Sample 113


E-MTAB-11699:Sample 114

text: IOWA STATE UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11699:Sample 114

text: Herford

text: ArrayExpress

text: cattle

text: adult

text: normal

text: Bos taurus

characteristic: organism

text: Bos taurus

text: bone marrow

text: Bos taurus

text: Sample 114

characteristic: title


E-MTAB-11699:Sample 115

text: IOWA STATE UNIVERSITY

text: public

characteristic: SRA accession

text: E-MTAB-11699:Sample 115

characteristic: Submitter Id

text: Herford

characteristic: breed

text: ArrayExpress

characteristic: broker name

text: cattle

text: adult

text: normal

text: Bos taurus

text: Bos taurus

text: spleen

text: Bos taurus

text: Sample 115


E-MTAB-11699:Sample 116

text: IOWA STATE UNIVERSITY

text: public

text: E-MTAB-11699:Sample 116

text: Herford

text: ArrayExpress

text: cattle

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Bos taurus

text: Bos taurus

text: spleen

text: Bos taurus

text: Sample 116


E-MTAB-11699:Sample 117

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: IOWA STATE UNIVERSITY

text: public

text: E-MTAB-11699:Sample 117

text: Herford

text: ArrayExpress

text: cattle

text: adult

text: normal

characteristic: individual

text: Bos taurus

text: Bos taurus

text: kidney cortex

characteristic: organism part

text: Bos taurus

text: Sample 117


E-MTAB-11699:Sample 118

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IOWA STATE UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11699:Sample 118

text: Herford

text: ArrayExpress

text: cattle

text: adult

text: normal

text: Bos taurus

text: Bos taurus

text: kidney cortex

text: Bos taurus

text: Sample 118


E-MTAB-11699:Sample 119

text: IOWA STATE UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11699:Sample 119

text: Herford

text: ArrayExpress

text: cattle

text: adult

text: normal

text: Bos taurus

characteristic: organism

text: Bos taurus

text: bladder

text: Bos taurus

text: Sample 119

characteristic: title


E-MTAB-11699:Sample 12

text: IOWA STATE UNIVERSITY

text: public

characteristic: SRA accession

text: E-MTAB-11699:Sample 12

characteristic: Submitter Id

text: Herford

characteristic: breed

text: ArrayExpress

characteristic: broker name

text: cattle

text: late embryonic stage

text: normal

text: Bos taurus

text: Bos taurus

text: spleen

text: Bos taurus

text: Sample 12


E-MTAB-11699:Sample 120

text: IOWA STATE UNIVERSITY

text: public

text: E-MTAB-11699:Sample 120

text: Herford

text: ArrayExpress

text: cattle

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Bos taurus

text: Bos taurus

text: bladder

text: Bos taurus

text: Sample 120


E-MTAB-11699:Sample 121

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: IOWA STATE UNIVERSITY

text: public

text: E-MTAB-11699:Sample 121

text: Herford

text: ArrayExpress

text: cattle

text: adult

text: normal

characteristic: individual

text: Bos taurus

text: Bos taurus

text: skin

characteristic: organism part

text: Bos taurus

text: Sample 121


E-MTAB-11699:Sample 122

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IOWA STATE UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11699:Sample 122

text: Herford

text: ArrayExpress

text: cattle

text: adult

text: normal

text: Bos taurus

text: Bos taurus

text: skin

text: Bos taurus

text: Sample 122


E-MTAB-11699:Sample 123

text: IOWA STATE UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11699:Sample 123

text: Herford

text: ArrayExpress

text: cattle

text: adult

text: normal

text: Bos taurus

characteristic: organism

text: Bos taurus

text: brain frontal cortex

text: Bos taurus

text: Sample 123

characteristic: title


E-MTAB-11699:Sample 124

text: IOWA STATE UNIVERSITY

text: public

characteristic: SRA accession

text: E-MTAB-11699:Sample 124

characteristic: Submitter Id

text: Herford

characteristic: breed

text: ArrayExpress

characteristic: broker name

text: cattle

text: adult

text: normal

text: Bos taurus

text: Bos taurus

text: brain frontal cortex

text: Bos taurus

text: Sample 124


E-MTAB-11699:Sample 125

text: IOWA STATE UNIVERSITY

text: public

text: E-MTAB-11699:Sample 125

text: Herford

text: ArrayExpress

text: cattle

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Bos taurus

text: Bos taurus

text: cerebellum

text: Bos taurus

text: Sample 125


E-MTAB-11699:Sample 126

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: IOWA STATE UNIVERSITY

text: public

text: E-MTAB-11699:Sample 126

text: Herford

text: ArrayExpress

text: cattle

text: adult

text: normal

characteristic: individual

text: Bos taurus

text: Bos taurus

text: cerebellum

characteristic: organism part

text: Bos taurus

text: Sample 126


E-MTAB-11699:Sample 127

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IOWA STATE UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11699:Sample 127

text: Herford

text: ArrayExpress

text: cattle

text: adult

text: normal

text: Bos taurus

text: Bos taurus

text: pituitary

text: Bos taurus

text: Sample 127


E-MTAB-11699:Sample 128

text: IOWA STATE UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11699:Sample 128

text: Herford

text: ArrayExpress

text: cattle

text: adult

text: normal

text: Bos taurus

characteristic: organism

text: Bos taurus

text: pituitary

text: Bos taurus

text: Sample 128

characteristic: title


E-MTAB-11699:Sample 129

text: IOWA STATE UNIVERSITY

text: public

characteristic: SRA accession

text: E-MTAB-11699:Sample 129

characteristic: Submitter Id

text: Herford

characteristic: breed

text: ArrayExpress

characteristic: broker name

text: cattle

text: adult

text: normal

text: Bos taurus

text: Bos taurus

text: testis

text: Bos taurus

text: Sample 129


E-MTAB-11699:Sample 13

text: IOWA STATE UNIVERSITY

text: public

text: E-MTAB-11699:Sample 13

text: Herford

text: ArrayExpress

text: cattle

characteristic: common name

characteristic: description

text: late embryonic stage

characteristic: developmental stage

text: normal

characteristic: disease

text: Bos taurus

text: Bos taurus

text: umbilical cord

text: Bos taurus

text: Sample 13


E-MTAB-11699:Sample 130

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: IOWA STATE UNIVERSITY

text: public

text: E-MTAB-11699:Sample 130

text: Herford

text: ArrayExpress

text: cattle

text: adult

text: normal

characteristic: individual

text: Bos taurus

text: Bos taurus

text: testis

characteristic: organism part

text: Bos taurus

text: Sample 130


E-MTAB-11699:Sample 131

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IOWA STATE UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11699:Sample 131

text: Herford

text: ArrayExpress

text: cattle

text: adult

text: normal

text: Bos taurus

text: Bos taurus

text: caput epididymis

text: Bos taurus

text: Sample 131


E-MTAB-11699:Sample 132

text: IOWA STATE UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11699:Sample 132

text: Herford

text: ArrayExpress

text: cattle

text: adult

text: normal

text: Bos taurus

characteristic: organism

text: Bos taurus

text: caput epididymis

text: Bos taurus

text: Sample 132

characteristic: title


E-MTAB-11699:Sample 133

text: IOWA STATE UNIVERSITY

text: public

characteristic: SRA accession

text: E-MTAB-11699:Sample 133

characteristic: Submitter Id

text: Herford

characteristic: breed

text: ArrayExpress

characteristic: broker name

text: cattle

text: adult

text: normal

text: Bos taurus

text: Bos taurus

text: follicular cells

text: Bos taurus

text: Sample 133


E-MTAB-11699:Sample 134

text: IOWA STATE UNIVERSITY

text: public

text: E-MTAB-11699:Sample 134

text: Herford

text: ArrayExpress

text: cattle

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Bos taurus

text: Bos taurus

text: follicular cells

text: Bos taurus

text: Sample 134