Single-cell RNA-Seq reveals dynamic, random monoallelic gene expression in mammalian cells

Experiment ID:SRP020490
Technology:scRNA-Seq
Description:In the diploid genome, genes come in two copies, which can have different DNA sequence and where one is maternal and one is paternal. In a particular cell, a gene could potentially be expressed from both copies (biallelic expression) or only one (monoallelic). We performed RNA-Sequencing on individual cells, from zygote to the cells of the late blastocyst, and also individual cells from the adult liver. Using first generation crosses between two distantly related mouse strains, CAST/Ei and C57BL/6, we determined the expression separately from the maternal and paternal alleles. We found that half of the genes were expressed by only one allele, randomly so that some cells would express the paternal allele, some the maternal and a few cell both alleles. We also observed the spread of the progressive inactivation of the paternal X chromosome. Overall design: First generation mouse strain crosses were used to study monoallelic expression on the single cell level
DOI:10.1126/science.1245316
Source:SRP020490 SRA
Download:
scRNA-Seq full-length processed expression values per cell population in Mus musculusscRNA-Seq full-length H5AD data per cell in Mus musculus

List of assays

Show

entries

Showing 1 to 20 of 118 entries

Library ID
Identifier of the RNA-Seq library
Cell type ID
ID of the cell type of the sample
Cell type name
Name of the cell type of the sample
Cell type author annotation
Free text annotation of cell type as provided by authors
Anat. entity ID
ID of the anatomical localization of the sample
Anat. entity name
Name of the anatomical localization of the sample
Anat. entity author annotation
Free text annotation of anatomical localization of the sample as provided by authors
Stage ID
ID of the developmental and life stage of the sample
Stage name
Name of the developmental and life stage of the sample
Stage author annotation
Free text annotation of the developmental and life stage of the sample as provided by authors
Sex
Annotation of the sex of the sample
Strain
Annotation of the strain of the sample
Time
Free text annotation of the time of sampling as provided by authors
Time unit
Unit for the time of sampling as provided by authors
Species
Physiological status
Physiological status of the organism at time of sampling
Technology
Sequencing platform
Sequenced transcript part
Possible values are: full length, all parts of the transcript are sequenced; 3': only the 3' end of the transcript is sequenced; 5': only the 5' end of the transcript is sequenced.
Fractionation
Possible values are: cell, transcripts are extracted from the cell; nuclei, transcripts are extracted from the nucleus.
Fragmentation
Size of the RNA fragmentation
Run sequencing type
Paired-end or single-read run
Total read count
Total number of reads for the library.
Mapped read count
Number of reads that could be mapped to the transcriptome.
Total UMI count
Total number of individual RNA molecules (UMI) for the annotated sample. Only applicable for libraries producing UMIs.
Mapped UMI count
Number of UMIs that could be mapped to the transcriptome. Only applicable for libraries producing UMIs.
Distinct rank count
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, number of distinct ranks observed, to have a value of the power for distinguishing expression levels. Used as a weight to compute a weighted mean rank accross samples for each gene and compute expression scores in Bgee.
Max rank
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, maximum rank attained in the sample. Used to normalize ranks accross samples and compute expression scores in Bgee.
Link to processed expression values
See the processed expression value results for this assay
SRX259105CL:0000353 blastoderm cell16-cell stage blastomereUBERON:0000085 morula16-cell embryoMmusDv:0000006 Theiler stage 03 (mouse)16-cell stage blastomereNACAST_EiJ(mother)_x_C57BL_6J(father)NANAMus musculusNASmart-seq2Illumina HiSeq 2000FULL_LENGTHCELL53single1584785613215211001235312405Browse results
SRX259106CL:0000353 blastoderm cell16-cell stage blastomereUBERON:0000085 morula16-cell embryoMmusDv:0000006 Theiler stage 03 (mouse)16-cell stage blastomereNACAST_EiJ(mother)_x_C57BL_6J(father)NANAMus musculusNASmart-seq2Illumina HiSeq 2000FULL_LENGTHCELL53single1890593713077216001212712189.5Browse results
SRX259107CL:0000353 blastoderm cell16-cell stage blastomereUBERON:0000085 morula16-cell embryoMmusDv:0000006 Theiler stage 03 (mouse)16-cell stage blastomereNACAST_EiJ(mother)_x_C57BL_6J(father)NANAMus musculusNASmart-seq2Illumina HiSeq 2000FULL_LENGTHCELL53single1995401613573924001244412517.5Browse results
SRX259108CL:0000353 blastoderm cell16-cell stage blastomereUBERON:0000085 morula16-cell embryoMmusDv:0000006 Theiler stage 03 (mouse)16-cell stage blastomereNACAST_EiJ(mother)_x_C57BL_6J(father)NANAMus musculusNASmart-seq2Illumina HiSeq 2000FULL_LENGTHCELL53single1277322710015351001218212267Browse results
SRX259109CL:0000353 blastoderm cell16-cell stage blastomereUBERON:0000085 morula16-cell embryoMmusDv:0000006 Theiler stage 03 (mouse)16-cell stage blastomereNACAST_EiJ(mother)_x_C57BL_6J(father)NANAMus musculusNASmart-seq2Illumina HiSeq 2000FULL_LENGTHCELL53single1911437915111487001336413444.5Browse results
SRX259110CL:0000353 blastoderm cell16-cell stage blastomereUBERON:0000085 morula16-cell embryoMmusDv:0000006 Theiler stage 03 (mouse)16-cell stage blastomereNACAST_EiJ(mother)_x_C57BL_6J(father)NANAMus musculusNASmart-seq2Illumina HiSeq 2000FULL_LENGTHCELL53single2059348115843351001236912430.5Browse results
SRX259111CL:0000353 blastoderm cell16-cell stage blastomereUBERON:0000085 morula16-cell embryoMmusDv:0000006 Theiler stage 03 (mouse)16-cell stage blastomereNACAST_EiJ(mother)_x_C57BL_6J(father)NANAMus musculusNASmart-seq2Illumina HiSeq 2000FULL_LENGTHCELL53single2087600914327390001223012291Browse results
SRX259112CL:0000353 blastoderm cell16-cell stage blastomereUBERON:0000085 morula16-cell embryoMmusDv:0000006 Theiler stage 03 (mouse)16-cell stage blastomereNACAST_EiJ(mother)_x_C57BL_6J(father)NANAMus musculusNASmart-seq2Illumina HiSeq 2000FULL_LENGTHCELL53single2200480516728358001290212970Browse results
SRX259113CL:0000353 blastoderm cell16-cell stage blastomereUBERON:0000085 morula16-cell embryoMmusDv:0000006 Theiler stage 03 (mouse)16-cell stage blastomereNACAST_EiJ(mother)_x_C57BL_6J(father)NANAMus musculusNASmart-seq2Illumina HiSeq 2000FULL_LENGTHCELL53single1491821511996478001279012856.5Browse results
SRX259114CL:0000353 blastoderm cell16-cell stage blastomereUBERON:0000085 morula16-cell embryoMmusDv:0000006 Theiler stage 03 (mouse)16-cell stage blastomereNACAST_EiJ(mother)_x_C57BL_6J(father)NANAMus musculusNASmart-seq2Illumina HiSeq 2000FULL_LENGTHCELL53single2002483215123488001315613221.5Browse results
SRX259115CL:0000353 blastoderm cell16-cell stage blastomereUBERON:0000085 morula16-cell embryoMmusDv:0000006 Theiler stage 03 (mouse)16-cell stage blastomereNACAST_EiJ(mother)_x_C57BL_6J(father)NANAMus musculusNASmart-seq2Illumina HiSeq 2000FULL_LENGTHCELL53single1362176411188497001280412867.5Browse results
SRX259116CL:0000353 blastoderm cell16-cell stage blastomereUBERON:0000085 morula16-cell embryoMmusDv:0000006 Theiler stage 03 (mouse)16-cell stage blastomereNACAST_EiJ(mother)_x_C57BL_6J(father)NANAMus musculusNASmart-seq2Illumina HiSeq 2000FULL_LENGTHCELL53single136018299816159001167411733Browse results
SRX259117CL:0000353 blastoderm cell16-cell stage blastomereUBERON:0000085 morula16-cell embryoMmusDv:0000006 Theiler stage 03 (mouse)16-cell stage blastomereNACAST_EiJ(mother)_x_C57BL_6J(father)NANAMus musculusNASmart-seq2Illumina HiSeq 2000FULL_LENGTHCELL53single1457324810048268001316113232Browse results
SRX259118CL:0000353 blastoderm cell16-cell stage blastomereUBERON:0000085 morula16-cell embryoMmusDv:0000006 Theiler stage 03 (mouse)16-cell stage blastomereNACAST_EiJ(mother)_x_C57BL_6J(father)NANAMus musculusNASmart-seq2Illumina HiSeq 2000FULL_LENGTHCELL53single1327511710380307001247712546Browse results
SRX259119CL:0000353 blastoderm cell16-cell stage blastomereUBERON:0000085 morula16-cell embryoMmusDv:0000006 Theiler stage 03 (mouse)16-cell stage blastomereNACAST_EiJ(mother)_x_C57BL_6J(father)NANAMus musculusNASmart-seq2Illumina HiSeq 2000FULL_LENGTHCELL46single107527127272944001098311025.5Browse results
SRX259120CL:0000353 blastoderm cell16-cell stage blastomereUBERON:0000085 morula16-cell embryoMmusDv:0000006 Theiler stage 03 (mouse)16-cell stage blastomereNACAST_EiJ(mother)_x_C57BL_6J(father)NANAMus musculusNASmart-seq2Illumina HiSeq 2000FULL_LENGTHCELL46single1354490894205390098159902Browse results
SRX259121CL:0000353 blastoderm cell16-cell stage blastomereUBERON:0000085 morula16-cell embryoMmusDv:0000006 Theiler stage 03 (mouse)16-cell stage blastomereNACAST_EiJ(mother)_x_C57BL_6J(father)NANAMus musculusNASmart-seq2Illumina HiSeq 2000FULL_LENGTHCELL46single1602501369696990078307846Browse results
SRX259122CL:0000353 blastoderm cell16-cell stage blastomereUBERON:0000085 morula16-cell embryoMmusDv:0000006 Theiler stage 03 (mouse)16-cell stage blastomereNACAST_EiJ(mother)_x_C57BL_6J(father)NANAMus musculusNASmart-seq2Illumina HiSeq 2000FULL_LENGTHCELL46single21166793111200720054395451Browse results
SRX259123CL:0000353 blastoderm cell16-cell stage blastomereUBERON:0000085 morula16-cell embryoMmusDv:0000006 Theiler stage 03 (mouse)16-cell stage blastomereNACAST_EiJ(mother)_x_C57BL_6J(father)NANAMus musculusNASmart-seq2Illumina HiSeq 2000FULL_LENGTHCELL46single133874008430729001046410504Browse results
SRX259124CL:0000353 blastoderm cell16-cell stage blastomereUBERON:0000085 morula16-cell embryoMmusDv:0000006 Theiler stage 03 (mouse)16-cell stage blastomereNACAST_EiJ(mother)_x_C57BL_6J(father)NANAMus musculusNASmart-seq2Illumina HiSeq 2000FULL_LENGTHCELL46single2396421217219551001088610924Browse results

Showing 1 to 20 of 118 entries

This website requires cookies, and limited processing of your personal data in order to function. By using the site you are agreeing to this as outlined in our privacy notice.
Do not show this banner again