Development of Single Cell Transcriptome Sequencing Technology and Its Application in Caenorhabditis elegans

doi:10.13560/j.cnki.biotech.bull.1985.2022-1190

Abstract

Abstract:

Single cell transcriptome sequencing technology enables people to get rid of the interference of cell heterogeneity，thus realizing the exploration of gene expression and transcriptional regulation mechanism at single cell level，as well as the recognition of different cell subpopulations and special cell types，which is of great significance to the research in the field of phylogeny. The traditional model organism Caenorhabditis elegans has become an important model for single-cell transcriptomic research in recent years because of its fixed number of somatic cells and clear trajectory of cell differentiation. This paper summarizes the development of single-cell transcriptome sequencing technology and its application in the research of cell lineage analysis，single-cell trajectory inference and neuronal cell Atlas of C. elegans，and further prospects the future research direction.

Key words: single-cell RNA sequencing, Caenorhabditis elegans

ZHAO Jin-ling, AN Lei, REN Xiao-liang. Development of Single Cell Transcriptome Sequencing Technology and Its Application in Caenorhabditis elegans[J]. Biotechnology Bulletin, 2023, 39(6): 158-170.

Figures/Tables 2

References 130

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名称 Name	空间编码方法 Spatial encoding method	目标 Target	靶向性 Approach	研究对象 Subjects of research	亚细胞水平Subcellular	参考文献 Reference
HDST	条形码珠阵列	mRNAs	否	小鼠嗅觉细胞	是	[87]
Slide-seq	条形码珠阵列	mRNAs	否	小鼠脑	否	[88]
LCM	显微切割	mRNAs	否	小鼠脊髓	否	[90]
Geo-seq	显微切割	mRNAs	否	小鼠早期胚胎	否	[91]
seqFISH	单分子荧光原位杂交	RNA	是	小鼠脑、嗅球	是	[94]
MERFISH	单分子荧光原位杂交	RNA	是	人的大脑皮层	是	[96]
FISSEQ	条形码原位靶向	mRNAs	否	人原代成纤维细胞	是	[97]
ISS	条形码原位靶向	mRNAs	是	人乳腺癌组织	是	[98]
STARmap	条形码原位靶向	mRNAs	是	小鼠脑组织切片	是	[99]
SPLiT-seq	混合分离	RNA	是	小鼠大脑和脊髓细胞	否	[100]
PETRI-seq	混合分离	mRNAs	是	细菌	是	[101]
DBiT-seq	混合分离	mRNAs	是	小鼠胚胎	否	[102]

名称 Name	空间编码方法 Spatial encoding method	目标 Target	靶向性 Approach	研究对象 Subjects of research	亚细胞水平Subcellular	参考文献 Reference
HDST	条形码珠阵列	mRNAs	否	小鼠嗅觉细胞	是	[87]
Slide-seq	条形码珠阵列	mRNAs	否	小鼠脑	否	[88]
LCM	显微切割	mRNAs	否	小鼠脊髓	否	[90]
Geo-seq	显微切割	mRNAs	否	小鼠早期胚胎	否	[91]
seqFISH	单分子荧光原位杂交	RNA	是	小鼠脑、嗅球	是	[94]
MERFISH	单分子荧光原位杂交	RNA	是	人的大脑皮层	是	[96]
FISSEQ	条形码原位靶向	mRNAs	否	人原代成纤维细胞	是	[97]
ISS	条形码原位靶向	mRNAs	是	人乳腺癌组织	是	[98]
STARmap	条形码原位靶向	mRNAs	是	小鼠脑组织切片	是	[99]
SPLiT-seq	混合分离	RNA	是	小鼠大脑和脊髓细胞	否	[100]
PETRI-seq	混合分离	mRNAs	是	细菌	是	[101]
DBiT-seq	混合分离	mRNAs	是	小鼠胚胎	否	[102]

细胞类型 Cell type	标记基因 Marker genes
肌肉和中胚层 Muscle and mesoderm	ceh-13, ceh-34, cup-4, cwn-1, dmd-4, dsc-1, egl-20, ehn-3, exp-1, eya-1, glb-26, hlh-1, hlh-8, let-381, lgc-26, mig-1, mls-1, myo-3, pal-1, sfrp-1, unc-30, unc-62, unc-39
咽 Pharynx	aff-1, agr-1, ceh-2, ceh-6, ceh-19, ceh-22, ceh-45, cwn-2, dmd-4, elt-4, eyg-1, fos-1, glr-8, gly-15, hlh-6, inx-12, inx-20, irx-1, lec-8, let-23, lys-8, mlt-8, mlt-11, nhr-25, nhr-67, nhr-239, pax-1, phat-1, phat-2, phat-5, ref-1, ser-2, slt-1, spp-7, tnc-2, tni-4, tnt-4, ttx-1, unc-62, unc-129, W05B10.4
导管和气孔 Duct and pore	aff-1, ceh-37, grl-2, irx-1
肠 Intestine	ceh-37, cpr-1, faah-1, irg-7, pal-1, pbo-4, psa-3, ZC204.12
皮下组织和侧线细胞 Hypodermis and seam cells	ahr-1, bus-4, bus-8, bus-12, ceh-13, ceh-16, ceh-32, egl-17, elt-1, elt-3, elt-6, lin-12, lin-39, lin-44, mab-5, pax-3, plx-2, rnt-1, slt-1, tbx-2, tbx-8, tbx-9, unc-62, unc-130, vab-3, vab-7
胶质细胞和排泄细胞 Glia and excretory cells	aat-1, aff-1, aqp-7, ceh-6, ceh-32, ceh-37, eak-3, eak-6, grd-15, grl-18, grl-12, grl-2, hlh-11, inx-12, inx-13, irx-1, kcc-3, let-23, lim-6, mls-2, mlt-8, mltn-13, nas-31, nhr-25, pros-1, qua-1, sdf-9, ser-2, slt-1, sym-1, unc-62, wrt-6, F52E1.2, F16F9.3, K08D12.4, K09F5.6
早期胚胎、生殖腺和直肠 Early embryo，germline and rectum	glh-1, nos-1, pgl-1
纤毛神经元 Ciliated neurons	agr-1, bas-1, cat-2, cat-4, capa-1, ceh-13, ceh-19, ceh-36, che-1, cil-7, cng-2, cog-1, cwn-2, dac-1, daf-11, dat-1, deg-1, dhc-3, dyla-1, flp-3, gcy-8, gcy-9, gcy-11, gcy-18, gcy-23, gcy-31, gcy-32, gcy-33, gcy-35, gcy-36, gcy-37, ns-6, klp-6, nhr-6, nhr-67, nhr-216, ocr-1, ocr-4, odr-7, osm-10, pax-2, pcrg-1, pdf-1, sox-2, sptf-1, srb-6, srd-23, srh-74, ssu-1, tba-6, tba-9, tbx-2, trx-1, ttx-1, unc-42, unc-62, xbx-9, C47D2.1, F15A4.5, F09E8.8, K04D7.6, M04B2.6, R102.2
非纤毛神经元和纤毛神经元 Non-ciliated neurons and ciliated neurons	ceh-6, che-7, dop-1, flr-4
非纤毛神经元 Non-ciliated neurons	acc-1, acc-2, ace-3, acr-15, acr-16, acr-23, acy-2, alr-1, aptf-1, ast-1, bus-18, ceh-6, ceh-10, ceh-17, ceh-24, ceh-27, ceh-31, ceh-32, ceh-34, ceh-43, ceh-63, ceh-75, cex-1, deg-3, des-2, dop-5, eat-4, egl-5, egl-20, fax-1, flp-1, flp-2, flp-4, flp-9, flp-11, flp-12, flp-13, flp-18, flp-22, gbb-1, gbb-2, gcy-35, glb-17, glc-3, glr-1, glr-2, glr-3, glr-4, glr-5, glr-6, glr-8, gpa-2, gpa-14, hlh-13, hlh-14, hlh-34, ins-1, inx-19, irx-1, lad-2, lim-4, lim-6, lin-11, lin-44, lite-1, mab-9, mbr-1, mec-1, mec-3, mec-7, mec-17, mgl-1, mls-2, mod-5, nhr-67, nlp-7, nlp-12, nlp-15, nlp-17, nmr-2, nob-1, odr-2, pdf-1, pks-1, rig-3, rig-4, rig-5, ser-2, ser-4, ser-6, slt-1, snet-1, snf-11, sox-2, sox-3, tbh-1, tbx-2, tdc-1, tmc-1, ttx-3, twk-16, unc-3, unc-4, unc-6, unc-7, unc-17, unc-25, unc-29, unc-30, unc-42, unc-46, unc-47, unc-62, unc-86, unc-130, vab-7, vab-8, vab-15, zig-5, C35B1.7, F26A10.1, F59E11.7, F17C11.2, K07C5.9, Y43F8B.20
直肠细胞 Rectal cells	ceh-6, ceh-27, daf-6, dve-1, egl-20, egl-38, elt-3, mab-9, mom-2, nac-2, nhr-25, pal-1, pha-4, ref-2, tat-4

细胞类型 Cell type	标记基因 Marker genes
肌肉和中胚层 Muscle and mesoderm	ceh-13, ceh-34, cup-4, cwn-1, dmd-4, dsc-1, egl-20, ehn-3, exp-1, eya-1, glb-26, hlh-1, hlh-8, let-381, lgc-26, mig-1, mls-1, myo-3, pal-1, sfrp-1, unc-30, unc-62, unc-39
咽 Pharynx	aff-1, agr-1, ceh-2, ceh-6, ceh-19, ceh-22, ceh-45, cwn-2, dmd-4, elt-4, eyg-1, fos-1, glr-8, gly-15, hlh-6, inx-12, inx-20, irx-1, lec-8, let-23, lys-8, mlt-8, mlt-11, nhr-25, nhr-67, nhr-239, pax-1, phat-1, phat-2, phat-5, ref-1, ser-2, slt-1, spp-7, tnc-2, tni-4, tnt-4, ttx-1, unc-62, unc-129, W05B10.4
导管和气孔 Duct and pore	aff-1, ceh-37, grl-2, irx-1
肠 Intestine	ceh-37, cpr-1, faah-1, irg-7, pal-1, pbo-4, psa-3, ZC204.12
皮下组织和侧线细胞 Hypodermis and seam cells	ahr-1, bus-4, bus-8, bus-12, ceh-13, ceh-16, ceh-32, egl-17, elt-1, elt-3, elt-6, lin-12, lin-39, lin-44, mab-5, pax-3, plx-2, rnt-1, slt-1, tbx-2, tbx-8, tbx-9, unc-62, unc-130, vab-3, vab-7
胶质细胞和排泄细胞 Glia and excretory cells	aat-1, aff-1, aqp-7, ceh-6, ceh-32, ceh-37, eak-3, eak-6, grd-15, grl-18, grl-12, grl-2, hlh-11, inx-12, inx-13, irx-1, kcc-3, let-23, lim-6, mls-2, mlt-8, mltn-13, nas-31, nhr-25, pros-1, qua-1, sdf-9, ser-2, slt-1, sym-1, unc-62, wrt-6, F52E1.2, F16F9.3, K08D12.4, K09F5.6
早期胚胎、生殖腺和直肠 Early embryo，germline and rectum	glh-1, nos-1, pgl-1
纤毛神经元 Ciliated neurons	agr-1, bas-1, cat-2, cat-4, capa-1, ceh-13, ceh-19, ceh-36, che-1, cil-7, cng-2, cog-1, cwn-2, dac-1, daf-11, dat-1, deg-1, dhc-3, dyla-1, flp-3, gcy-8, gcy-9, gcy-11, gcy-18, gcy-23, gcy-31, gcy-32, gcy-33, gcy-35, gcy-36, gcy-37, ns-6, klp-6, nhr-6, nhr-67, nhr-216, ocr-1, ocr-4, odr-7, osm-10, pax-2, pcrg-1, pdf-1, sox-2, sptf-1, srb-6, srd-23, srh-74, ssu-1, tba-6, tba-9, tbx-2, trx-1, ttx-1, unc-42, unc-62, xbx-9, C47D2.1, F15A4.5, F09E8.8, K04D7.6, M04B2.6, R102.2
非纤毛神经元和纤毛神经元 Non-ciliated neurons and ciliated neurons	ceh-6, che-7, dop-1, flr-4
非纤毛神经元 Non-ciliated neurons	acc-1, acc-2, ace-3, acr-15, acr-16, acr-23, acy-2, alr-1, aptf-1, ast-1, bus-18, ceh-6, ceh-10, ceh-17, ceh-24, ceh-27, ceh-31, ceh-32, ceh-34, ceh-43, ceh-63, ceh-75, cex-1, deg-3, des-2, dop-5, eat-4, egl-5, egl-20, fax-1, flp-1, flp-2, flp-4, flp-9, flp-11, flp-12, flp-13, flp-18, flp-22, gbb-1, gbb-2, gcy-35, glb-17, glc-3, glr-1, glr-2, glr-3, glr-4, glr-5, glr-6, glr-8, gpa-2, gpa-14, hlh-13, hlh-14, hlh-34, ins-1, inx-19, irx-1, lad-2, lim-4, lim-6, lin-11, lin-44, lite-1, mab-9, mbr-1, mec-1, mec-3, mec-7, mec-17, mgl-1, mls-2, mod-5, nhr-67, nlp-7, nlp-12, nlp-15, nlp-17, nmr-2, nob-1, odr-2, pdf-1, pks-1, rig-3, rig-4, rig-5, ser-2, ser-4, ser-6, slt-1, snet-1, snf-11, sox-2, sox-3, tbh-1, tbx-2, tdc-1, tmc-1, ttx-3, twk-16, unc-3, unc-4, unc-6, unc-7, unc-17, unc-25, unc-29, unc-30, unc-42, unc-46, unc-47, unc-62, unc-86, unc-130, vab-7, vab-8, vab-15, zig-5, C35B1.7, F26A10.1, F59E11.7, F17C11.2, K07C5.9, Y43F8B.20
直肠细胞 Rectal cells	ceh-6, ceh-27, daf-6, dve-1, egl-20, egl-38, elt-3, mab-9, mom-2, nac-2, nhr-25, pal-1, pha-4, ref-2, tat-4