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> Anatomy > Embryonic Structure > Blastoderm

Blastoderm

Blastoderm is the outer layer of the embryo in the early stages of development, formed from the cells of the blastula.
It gives rise to the ectoderm and a portion of the mesoderm.
PubCompare.ai's AI-driven approach can enhance reproducibility and accuracy in blastoderm analysis by locating relevant protocols from literature, preprints, and patents, and using AI comparisons to identify the optimal protocols and products.
This can improve research effciency and lead to more reliable insights into this critical stage of embryonic development.

Most cited protocols related to «Blastoderm»

1
Quantifying Transcription Factor-Cis Regulatory Module Interactions
First, the ‘expression profile’ of a TF is determined from available data on the in situ hybridization of the TF's mRNA (17 (link),43 (link)), which is a real-valued measurement of the TF's expression level in each of 100 equally spaced intervals (‘bins’) along the A–P axis of the Stage 4–6 (blastoderm) embryo. Then calculate the ‘discrete expression profile’ for a set of 48 CRMs that drive A–P gene expression in a defined pattern in the blastoderm embryo (17 (link)): for each CRM, determine whether it drives gene expression in each of the 100 bins along the A–P axis by imposing a fixed threshold on the real-valued expression levels. For each CRM, ‘count’ the number of binding sites for the TF, using its PWM and Stubb (44 (link)) as described in ref. (45 (link)). Then for each of the 100 bins along the A–P axis, collect the set of CRMs that are ‘expressed’ in that bin, and compute the average of the binding site counts for these CRMs. This average is the TF's ‘MOTIFCOUNT’ for that bin, which is plotted along with the TF's expression profile for each bin along the A–P axis.
P-values for this analysis were computed as follows:

For a repressor, regions of influence were chosen around the boundaries of its domain of expression, and for each such region of influence the correlation coefficient between the TF expression profile and its MOTIFCOUNT was tested by calculating the Pearson correlation coefficient (ρ). We tested the null hypothesis of ρ = 0 (with the alternative hypothesis ρ < 0, which represents anticorrelation).

For an activator, CRMs were classified as either ‘positive’ or ‘negative’ depending on whether the CRM's region of expression overlapped predominantly with the TF's expression domain, or not. A two-sample t-test was performed on the MOTIFCOUNT in these classes of CRMs to test for a difference of means in these two classes.

Noyes M.B., Meng X., Wakabayashi A., Sinha S., Brodsky M.H, & Wolfe S.A. (2008). A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. Nucleic Acids Research, 36(8), 2547-2560.
Publication 2008
Binding Sites Blastoderm Embryo Epistropheus Gene Expression In Situ Hybridization RNA, Messenger
2
Genetic Analysis of SCAR and Arp2/3 Complex
Flies were maintained using standard methods. Wild-type stocks were Oregon R (immunohistochemistry) and oskar166 (SCAR antibody controls and actin quantitation) (Lehmann and Nusslein-Volhard, 1986 (link)). See Flybase (http://flybase.bio.indiana.edu) for details concerning fly stocks. Alleles used were Arp3EP(3)3640 (Rørth, 1996 (link); Berkeley Drosophila Genome Project), Wsp1, Wsp3 (Ben-Yaacov et al., 2001 (link)), Arpc1R337st, Arpc1Q25sd, Arpc1W108R (Hudson and Cooley, 2002 (link)), SCARk13811 (Spradling et al., 1999 (link); Berkeley Drosophila Genome Project), and SCARΔ37.
Germline clones were generated as described (Chou and Perrimon, 1996 (link)) by heat shock of hs-FLP; ovoD FRT40A/SCAR FRT40A larvae, hs-FLP; FRT82B ovoD/FRT82B Wsp larvae, or hs-FLP; ovoD FRT40A/Arpc1 FRT40A larvae. Adult germline clone females were mated to Oregon R males (blastoderm and oogenesis analysis) or to SCARk13811/CyO en-lacZ males (SCARmat/zyg) or Df(3R)3450/TM6B abdA-lacZ males (Wspmat/zyg) (CNS). Mosaic head clones were obtained in ey-FLP; Arpc1Q25sd FRT40A/l(2)cl-L31 FRT40A and ey-FLP; SCARΔ37 FRT40A/l(2)cl-L31 FRT40A flies. SCARk13811 and Wsp3 germline clones (blastoderm), Wsp3 germline clones (CNS), and all zygotic mutants were generated at 25°C. Arpc1R337st germline clones (blastoderm) and SCARk13811 germline clones (CNS) were generated at 20–22°C.
We observed no contribution of zygotic gene activity to the blastoderm defects of embryos derived from SCARk13811 and Arpc1R337st germline clones (unpublished data). Wspmat embryos include embryos defective for both maternal and zygotic Wsp function and embryos defective only for maternal Wsp function.
Zallen J.A., Cohen Y., Hudson A.M., Cooley L., Wieschaus E, & Schejter E.D. (2002). SCAR is a primary regulator of Arp2/3-dependent morphological events in Drosophila. The Journal of Cell Biology, 156(4), 689-701.
Publication 2002
Actins Alleles Blastoderm Cicatrix Clone Cells Diptera Drosophila Embryo Genes Genome Germ Line Head Heat-Shock Response Immunoglobulins Immunohistochemistry LacZ Genes Larva Males Oogenesis Woman Zygote
3
Comparative Differential Gene Expression
We performed differential gene expression analysis using publicly available RNA-seq data from three model organisms: chicken, human and yeast. All datasets consisted of 100-bp paired-end reads from an Illumina HiSeq 2000. For each dataset we trimmed the reads [37 (link)] and then performed three analyses: two on de novo transcriptomes assembled using Oases and Trinity and one genome-based analysis - the 'truth' - which was used for comparison. The chicken dataset from Ayers et al. [24 (link)], Short Read Archive (SRA) accession number SRA055442, consisted of approximately 1.2 billion reads. For the de novo analyses we used only one lane of this data (approximately 320 million reads) because the full dataset was computationally too large to assemble. However, all the data were used for the genome-based 'truth' analysis. This dataset consists of eight samples - male and female blastoderms, and male and female day 4.5 gonad tissue, in duplicate. The dataset published by Trapnell et al. [25 (link)], Gene Expression Omnibus accession GSE37704, is from human primary lung fibroblasts with an siRNA knock-down of HOXA1. The dataset contains three replicates of the knockdown and three controls with more than 231 million reads in total. Finally, we included a yeast dataset, SRA accession numbers SRR453566 to SRR453571, published in Nookaew et al. [26 (link)]. The dataset consists of approximately 36 million reads. Three replicates were grown under batch conditions and three under chemostat conditions.
Davidson N.M, & Oshlack A. (2014). Corset: enabling differential gene expression analysis for de novo assembled transcriptomes. Genome Biology, 15(7), 410.
Publication 2014
Blastoderm BP 100 Chickens CREB3L1 protein, human Females Fibroblasts Gene Expression Gene Expression Profiling Genome Homo sapiens Lung Males Ovary RNA, Small Interfering RNA-Seq Saccharomyces cerevisiae Tissues Transcriptome
4
Genome-wide Prediction of CRMs in Drosophila

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Publication 2009
Blastoderm Drosophila Drosophila melanogaster Exons Gene Modules Genes Genes, vif Genome
5
Live Imaging of Tribolium Embryos
Beetles were reared according to The Beetle Book (http://wwwuser.gwdg.de/~gbucher1/tribolium-castaneum-beetle-book1.pdf) at 32°C. Eggs were dechorionated in 0.5% bleach and lined up on a microscope slide for upright microscopy or on a glass-bottomed Petri dish (MatTek) that had a window cut in the side of the dish to allow injection for inverted microscopy. Gaps were left between neighboring eggs for efficient gas exchange. Eggs were covered with Voltalef 10S Halocarbon oil. The needle was inserted into the egg at the anterior pole and the tip of the needle was moved into the center of the egg for injection. Capped mRNAs were injected at 0.5-3 μg/μl in injection buffer (5 mM KCl, 10 mM NaH2PO4). To monitor the kinetics of fluorescence labeling, we injected H2B-RFP and/or GAP43-YFP mRNAs into eggs 4-6 hours after egg lay (AEL) at 32°C, when nuclei migrate towards the egg surface and the cellularized blastoderm begins to form. In all other applications, injections were performed in eggs 2-3 hours AEL at 32°C to achieve maximum diffusion and homogeneous labeling. Following injection at room temperature, eggs were transferred back to 32°C and incubated in a dark and humid environment. Under these conditions, Tribolium embryos developed normally, but hatching rates were decreased, probably due to egg immersion in halocarbon oil. Microinjections caused a developmental delay of 30-60 minutes, as judged by the time of initiation of the posterior amniotic fold between injected and non-injected embryos. Live imaging was carried out on an inverted Leica SP5 confocal at 32°C. Image stacks of about 40 focal planes were taken with a 20×/0.7NA multi-immersion objective or a 40×/1.3NA oil-immersion objective at 2.5- or 5-minute intervals. Processing of confocal stacks was carried out with Fiji (Schindelin et al., 2012 (link)) and cell tracking with MTrackJ (Meijering et al., 2012 (link)).
Benton M.A., Akam M, & Pavlopoulos A. (2013). Cell and tissue dynamics during Tribolium embryogenesis revealed by versatile fluorescence labeling approaches. Development (Cambridge, England), 140(15), 3210-3220.
Publication 2013
Amnion Beetles Blastoderm Buffers Cell Nucleus Diffusion Eggs Embryo Fluorescence Hyperostosis, Diffuse Idiopathic Skeletal Kinetics Microinjections Microscopy Needles RNA, Messenger Submersion Tribolium

Most recents protocols related to «Blastoderm»

1
Avian Blastoderm Isolation and Embryonic Diapause
A pure line of White Leghorns, aged 35–45 weeks, were artificially inseminated. Fertile fresh laid eggs were collected daily and designated as F0. The fresh oviposited eggs were immediately (within 5 minutes) dedicated to blastoderm isolation. Cracked, soiled, poorly shaped, unusually large or small eggs were removed. To induce embryonic diapause, the eggs were stored in a dedicated egg storage room with an automatic temperature control system (16°C and 90% relative humidity) for days (S1d, S2d, S4d, S8d and S12d, corresponding to 1, 2, 4, 8 and 12 days of storage, respectively). To terminate embryonic diapause, the stored eggs were transferred to a specialized incubator without pre-heating for 0.5, 1, 2, 4, 6 or 12 hours ( In0.5h, In1h, In2h, In4h, In6h or In12h, respectively). Collected eggs were disinfected with 75% ethanol and then broken to isolate the blastoderm. Isolated blastoderms were dissected in PBS containing 4% DEPC and washed twice to remove the excess yolk. Unbroken blastoderms were flash-frozen and stored at −80°C until later use.
Ren J., Hu Z., Li Q., Gu S., Lan F., Wang X., Li J., Li J., Shao L., Yang N, & Sun C. (2023). Temperature-induced embryonic diapause in chickens is mediated by PKC-NF-κB-IRF1 signaling. BMC Biology, 21, 52.
Publication 2023
Blastoderm Diapause Eggs Embryo Ethanol Fertility Freezing Humidity
2
Isolation and Culture of Chicken Embryonic Stem Cells
Fertile fresh laid eggs (EG&K stage X) were collected to isolate cESCs according to the method of Aubel and Pain [60 (link)] with some modifications. In brief, eggs were disinfected with 75% ethanol and then broken to isolate the blastoderm using sterile dissecting scissors and spoons. Isolated blastoderms were immersed in PBS and washed gently to remove the excess yolk. Cleaned blastoderms were then immersed in new PBS and dissociated mechanically by repeated up and down gentle pipetting. Cell suspensions were then filtered through a 200-mesh sieve, followed by low-speed centrifugation. Collapsed cells were resuspended in Knockout-DMEM (Cat: 10829018; Gibco, Grand Island, NY, USA), supplemented with 10% fetal bovine serum ([FBS] Gibco), 2% chicken serum (Cat: 16110-082; Gibco), 0.4% non-essential amino acids (Cat: M7145; Sigma), 2 mmol/L, L-glutamine (Invitrogen, Carlsbad, CA, USA), 1 mmol/L, β-mercaptoethanol, 100 U/ml penicillin (Gibco), 100 μg/ml streptomycin (Gibco) and recombinant cell factors. These factors included 1 ng/ml LIF (Cat: 8878-LF; R&D Systems, Minneapolis, MN, USA), 10 ng/ml mSCF (Cat: 7466-SC; R&D Systems) and 10 ng/ml bFGF (Cat: 233-FB; R&D Systems). Cells were cultured in 12-well plates at 38.5°C under a water-saturated atmosphere containing 95% air humidity and 5% CO2. The cESCs were stimulated with one or more of the following: 50 ng/ml TPA (Cat: sc-3576; SantaCruz, CA, USA), 10 μg/ml Go:6983 (Cat: HY-13689; MCE, Monmouth Junction, NJ, USA) and 10 μg/ml BAY 11-7082 (Cat: sc-200615; SantaCruz). Cells were stimulated for 2 hours unless otherwise stated. The chicken fibroblast cell line DF-1 was maintained in DMEM/F12 medium with 10% FBS (Gibco), 100 mg/ml streptomycin and 100 U/ml penicillin at 37°C with 5% CO2 in a humidified incubator.
Ren J., Hu Z., Li Q., Gu S., Lan F., Wang X., Li J., Li J., Shao L., Yang N, & Sun C. (2023). Temperature-induced embryonic diapause in chickens is mediated by PKC-NF-κB-IRF1 signaling. BMC Biology, 21, 52.
Publication 2023
2-Mercaptoethanol Amino Acids, Essential Atmosphere BAY 11-7082 Blastoderm Cells Centrifugation Chickens Eggs Ethanol Fertility Fibroblasts Glutamine Humidity LINE-1 Elements Pain Penicillins Serum Sterility, Reproductive Streptomycin
3
Lentiviral-mediated IRF1 Overexpression in Chicken Embryos
A total of 140 fertilized eggs were randomly divided into two groups, each containing 70 eggs. All eggs were swabbed with 70% ethanol and then laid flat for 1 hour. A window of approximately 0.5 cm in diameter was cut in the equatorial plane of the eggshell to expose the blastoderm. A volume of 2 μL of recombinant lentivirus expressing IRF1 or control empty lentivirus wase injected into the subgerminal cavity of the embryo using a microinjector (Tritech Research, Los Angeles, CA, USA). Micropipettes of 40 μm in diameter, used for injection, were made from borosilicate glass capillaries drawn out with a micropipette puller. After the injection, windows were sealed with adhesive tape. Eggs were then incubated in a specialized incubator maintained at 37.8°C and 75% relative humidity.
Ren J., Hu Z., Li Q., Gu S., Lan F., Wang X., Li J., Li J., Shao L., Yang N, & Sun C. (2023). Temperature-induced embryonic diapause in chickens is mediated by PKC-NF-κB-IRF1 signaling. BMC Biology, 21, 52.
Publication 2023
Blastoderm Capillaries Dental Caries Eggs Egg Shell Embryo Ethanol Humidity IRF1 protein, human Lentivirus Zygote
4
Immunofluorescence Analysis of Chicken Blastoderm
For analysis of the chicken blastoderm, at least 10 blastoderms were pooled together and centrifuged at 2000 × g for 5 minutes. The resulting tissue masses were paraffin-embedded, and then 4-μm thick sections were cut and placed on slides. Tissue sections or cell slides were fixed in cold methanol and acetone (1:1 mixture) for 2 hours, washed with PBS and permeabilized with 0.1% Triton X-100 in PBS for 15 minutes. This was followed by blocking using 10% donkey or goat FBS for 30 minutes at 37°C. The sections were incubated overnight at 4°C with primary antibodies against H3S10P (Cat: 3377T; CST; 1:200), PCNA (Cat: abs120180; Absin, Shanghai, China; 1:200), PKC (Cat: NB600-201; Novus, Littleton, CO, USA; 1:100) or P65 (Cat: NBP2-24541; Novus; 1:100). The slides were washed with PBS and then incubated with FITC-conjugated or PE-conjugated secondary antibodies (Abcam) for 2 hours at room temperature. The cell nuclei were counterstained with DAPI (Invitrogen) for 15 minutes at room temperature. The slides were then examined by laser scanning confocal microscopy (Nikon A1HD25; Nikon Corporation, Tokyo, Japan).
Ren J., Hu Z., Li Q., Gu S., Lan F., Wang X., Li J., Li J., Shao L., Yang N, & Sun C. (2023). Temperature-induced embryonic diapause in chickens is mediated by PKC-NF-κB-IRF1 signaling. BMC Biology, 21, 52.
Publication 2023
Acetone Antibodies Blastoderm Cell Nucleus Cells Chickens Cold Temperature DAPI Equus asinus Fluorescein-5-isothiocyanate Goat Methanol Microscopy, Confocal, Laser Scanning Novus Paraffin Proliferating Cell Nuclear Antigen Tissues Triton X-100
5
Vital Dye Labeling and Grafting of Zebrafish Embryos
Cells stained with a vital dye (5 μM/L PKH26; Sigma-Aldrich) were grafted into the central portion of the zebrafish embryo blastoderm at the oblong-sphere stages as previously described. Embryos were immobilized with Tricane after 48 hours. Fluorescence and corresponding bright-field imaging of the PKH26-stained grafts in live embryos were performed with a Zeiss Axiovert upright microscope (Carl Zeiss). After image acquisition, embryos were fixed with 4% paraformaldehyde, infiltrated with increasing concentrations of sucrose/PBS, and cryoembedded in OCT. The size of the fibrotic reticulum was quantified as previously described (41 (link)).
Yang L., Gilbertsen A., Xia H., Benyumov A., Smith K., Herrera J., Racila E., Bitterman P.B, & Henke C.A. (2023). Hypoxia enhances IPF mesenchymal progenitor cell fibrogenicity via the lactate/GPR81/HIF1α pathway. JCI Insight, 8(4), e163820.
Publication 2023
Afterimage Blastoderm Cells Embryo Fibrosis Fluorescence Grafts Microscopy paraform PKH 26 Reticulum Sucrose Zebrafish

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3
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4
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More about "Blastoderm"

Blastoderm is the outer layer of the embryo during the early stages of development, formed from the cells of the blastula.
It gives rise to the ectoderm and a portion of the mesoderm, which are critical for embryonic development.
The blastoderm is a key structure in the blastulation process, which is the formation of the blastula - a hollow ball of cells that marks the transition from the zygote to the embryo.
Analyzing the blastoderm is crucial for understanding the earliest stages of embryonic development.
PubCompare.ai's AI-driven approach can enhance the reproducibility and accuracy of blastoderm research by locating relevant protocols from the literature, preprints, and patents, and using AI comparisons to identify the optimal protocols and products.
This can improve research efficiency and lead to more reliable insights into this critical stage of embryonic development.
Some related terms and techniques that may be useful for blastoderm research include the Agilent 2100 Bioanalyzer for RNA and DNA analysis, the RNeasy Mini Kit for RNA extraction, the EndoFree Plasmid Maxi Kit for plasmid purification, the MEGAscript T7 Transcription Kit for in vitro transcription, DMEM/F12 cell culture medium, Voltalef oil for embryo manipulation, M165 FC medium for blastoderm culture, the MMessage mMachine SP6 kit for mRNA synthesis, and Trypsin-EDTA for cell dissociation.
The use of 14 mm microwell plates may also be relevant for blastoderm culture and analysis.
By leveraging these tools and techniques, researchers can enhance their understanding of the blastoderm and its role in early embryonic development, leading to more reliable and impactful insights.