A list of info for 4 neuro data sets sampled, containing: Meissner.inVitro.bulk.Hs, LIBD.AZ.inVitro.bulk.Hs, Geschwind.inVivo.sc.Hs, Jabaudon.inVivo.sc.Mm
Usage
data(NeuroGenesis4)Examples
data(NeuroGenesis4.info)
head(NeuroGenesis4.info$Meissner.inVitro.bulk.Hs)
#> IDs File Cond Rep X color
#> ESC.1 ESC.1 hESC_rep1.count.fpkm.txt ESC 1 1 black
#> ESC.2 ESC.2 hESC_rep2.count.fpkm.txt ESC 2 1 black
#> NE.1 NE.1 NE_rep1.count.fpkm.txt NE 1 2 lightpink2
#> NE.2 NE.2 NE_rep2.count.fpkm.txt NE 2 2 lightpink2
#> ERG.1 ERG.1 ERG_rep1.count.fpkm.txt ERG 1 3 indianred1
#> ERG.2 ERG.2 ERG_rep2.count.fpkm.txt ERG 2 3 indianred1
head(NeuroGenesis4.info$LIBD.AZ.inVitro.bulk.Hs)
#> EXP_STATUS RNAseq_STATUS Order RNA_NO SAMPLE_NAME EXPERIMENT
#> 126 Complete Complete 126 R16-191 165-B-2 D2 1 TIMECOURSE
#> 164 Complete Complete 164 R16-287 165-B-2 D9 2-1 TIMECOURSE
#> 127 Complete Complete 127 R16-197 165-B-3 D2 1 TIMECOURSE
#> 469 Complete Complete NA R16-850 165-B-3_D2_REP1 TIMECOURSE
#> 470 Complete Complete NA R16-851 165-B-3_D6_REP1 TIMECOURSE
#> 165 Complete Complete 165 R16-288 165-B-3 D9 2-1 TIMECOURSE
#> RNA_CONC_ng/ul Library LibConstruct DateToAJ SPECIES JC_Comment
#> 126 NA Batch4 2016-03-31 2016-04-13 HUMAN ASSAY_1.1_COND2
#> 164 NA Batch4 2016-03-31 2016-04-13 HUMAN ASSAY_1.1_COND2
#> 127 NA Batch4 2016-03-31 2016-04-13 HUMAN ASSAY_1.1_COND2
#> 469 423.4 BATCH10 2016-09-08 2016-09-28 HUMAN ASSAY_1.1_COND2
#> 470 251.5 BATCH10 2016-09-08 2016-09-28 HUMAN ASSAY_1.1_COND2
#> 165 NA Batch4 2016-03-31 2016-04-13 HUMAN ASSAY_1.1_COND2
#> Flowcell Index Lane NumReads SeqNotes NumMapped mapRate
#> 126 H5TKNBBXX ATTCAGAA L8 70256642 <NA> 64493777 0.9179741
#> 164 H5TKNBBXX CGGCTATG L2 47653100 <NA> 38805346 0.8143299
#> 127 H5TKNBBXX AGCGATAG L4 84345206 10.64% undetermined 79142539 0.9383170
#> 469 H7V3TBBXX GAGATTCC L6 143106660 <NA> 133682681 0.9341472
#> 470 H7V3TBBXX GAATTCGT L6 174230786 <NA> 161315252 0.9258711
#> 165 H5TKNBBXX TCCGGAGA L1 76574342 <NA> 66510301 0.8685716
#> NumProperMap properRate NumUnmapped unmapRate riboMapped riboRate
#> 126 44317316 0.6871565 10866616 0.1546703 1848394 0.028660036
#> 164 27965698 0.7206661 12397154 0.2601542 2141647 0.055189483
#> 127 54477558 0.6883474 11344493 0.1345007 124652 0.001575032
#> 469 98673366 0.7381163 17993507 0.1257349 2816740 0.021070343
#> 470 122875468 0.7617102 23249854 0.1334429 1977016 0.012255605
#> 165 44773122 0.6731758 15654357 0.2044335 3235748 0.048650329
#> mitoMapped mitoRate alignNote Class Donor LINE DX RPS
#> 126 951371 0.014924190 <NA> Naked genomes 165 165-B-2 CNT lo
#> 164 523056 0.013734300 <NA> Naked genomes 165 165-B-2 CNT lo
#> 127 434379 0.005578326 <NA> Naked genomes 165 165-B-3 CNT lo
#> 469 935448 0.007175070 <NA> Naked genomes 165 165-B-3 CNT lo
#> 470 873678 0.005559844 <NA> Naked genomes 165 165-B-3 CNT lo
#> 165 796443 0.012205907 <NA> Naked genomes 165 165-B-3 CNT lo
#> Manipulation shRNA MOI PURO SAMPLE_NAME.1 shRNA_Target_Seq Note DAY
#> 126 NO NA NA NA 165-B-2 D2 1 NA <NA> 2
#> 164 NO NA NA NA 165-B-2 D9 2-1 NA <NA> 9
#> 127 NO NA NA NA 165-B-3 D2 1 NA <NA> 2
#> 469 NO NA NA NA 165-B-3_D2_REP1 NA <NA> 2
#> 470 NO NA NA NA 165-B-3_D6_REP1 NA <NA> 6
#> 165 NO NA NA NA 165-B-3 D9 2-1 NA <NA> 9
#> BIO_REP Fluidigm CONDITION SampleID
#> 126 1 NA ACC_DORSAL(2) R16-191_H5TKNBBXX
#> 164 1 NA ACC_DORSAL(2) R16-287_H5TKNBBXX
#> 127 1 NA ACC_DORSAL(2) R16-197_H5TKNBBXX
#> 469 1 NA ACC_DORSAL(2) R16-850_H7V3TBBXX
#> 470 1 NA ACC_DORSAL(2) R16-851_H7V3TBBXX
#> 165 1 NA ACC_DORSAL(2) R16-288_H5TKNBBXX
#> bamFile
#> 126 /dcl01/lieber/ajaffe/Astrazeneca/TopHat/Sample_R16-191_H5TKNBBXX_out/accepted_hits.bam
#> 164 /dcl01/lieber/ajaffe/Astrazeneca/TopHat/Sample_R16-287_H5TKNBBXX_out/accepted_hits.bam
#> 127 /dcl01/lieber/ajaffe/Astrazeneca/TopHat/Sample_R16-197_H5TKNBBXX_out/accepted_hits.bam
#> 469 /dcl01/lieber/ajaffe/Astrazeneca/TopHat/Sample_R16-850_H7V3TBBXX_out/accepted_hits.bam
#> 470 /dcl01/lieber/ajaffe/Astrazeneca/TopHat/Sample_R16-851_H7V3TBBXX_out/accepted_hits.bam
#> 165 /dcl01/lieber/ajaffe/Astrazeneca/TopHat/Sample_R16-288_H5TKNBBXX_out/accepted_hits.bam
#> leftInput leftMapped leftMapRate rightInput rightMapped rightMapRate
#> 126 35128321 30441590 0.867 35128321 28948436 0.824
#> 164 23826550 17892853 0.751 23826550 17363093 0.729
#> 127 42172603 37200746 0.882 42172603 35799967 0.849
#> 469 71553330 63377397 0.886 71553330 61735756 0.863
#> 470 87115393 76260852 0.875 87115393 74720080 0.858
#> 165 38287171 31423079 0.821 38287171 29496906 0.770
#> overallMapRate concordMapRate totalMapped totalAssignedGene lineRep
#> 126 0.845 0.782 62795541 0.6497077 2
#> 164 0.740 0.669 37560864 0.6179368 2
#> 127 0.865 0.806 77434676 0.7626106 3
#> 469 0.874 0.825 129439310 0.7630018 3
#> 470 0.867 0.824 156267057 0.7672984 3
#> 165 0.796 0.715 64454176 0.6493536 3
#> colDonor PROG.21-B-8 PROG.165-B-6X PROG.66-A-3 PROG.90-A-5 PROG.21-B-9
#> 126 black FALSE FALSE FALSE FALSE FALSE
#> 164 black FALSE FALSE FALSE FALSE FALSE
#> 127 black FALSE FALSE FALSE FALSE FALSE
#> 469 black FALSE FALSE FALSE FALSE FALSE
#> 470 black FALSE FALSE FALSE FALSE FALSE
#> 165 black FALSE FALSE FALSE FALSE FALSE
#> PROG.165-B-8X PROG.66-A-9 PROG.90-A-10 PROG.165-B-2 PROG.165-B-3 PROG.3-A-7
#> 126 FALSE FALSE FALSE TRUE FALSE FALSE
#> 164 FALSE FALSE FALSE TRUE FALSE FALSE
#> 127 FALSE FALSE FALSE FALSE TRUE FALSE
#> 469 FALSE FALSE FALSE FALSE TRUE FALSE
#> 470 FALSE FALSE FALSE FALSE TRUE FALSE
#> 165 FALSE FALSE FALSE FALSE TRUE FALSE
#> PROG.3-A-8 PROG.165-B-3X PROG.21-B-3 DxRps pchBYdiagRPS DAYj DAYx
#> 126 FALSE FALSE FALSE CNT.lo 19 1.431041 4
#> 164 FALSE FALSE FALSE CNT.lo 19 8.883865 7
#> 127 FALSE FALSE FALSE CNT.lo 19 1.092173 4
#> 469 FALSE FALSE FALSE CNT.lo 19 2.241799 4
#> 470 FALSE FALSE FALSE CNT.lo 19 6.932188 6
#> 165 FALSE FALSE FALSE CNT.lo 19 9.986775 7
#> labelsX colorBYlabelsX
#> 126 2 red
#> 164 9 red
#> 127 2 red
#> 469 2 red
#> 470 6 red
#> 165 9 red
head(NeuroGenesis4.info$Geschwind.inVivo.sc.Hs)
#> Cell Cluster Subcluster Donor Layer Gestation_week Index Library
#> 169 TGCTAATACTGA vRG vRG_0 368 CP 17 N701 Plath
#> 624 TTCACGATTTTT vRG vRG_2 368 GZ 17 N702 Plath
#> 659 CTGTCAGAATAA vRG vRG_2 368 GZ 17 N702 Plath
#> 681 CATAATATGTCA vRG vRG_0 368 GZ 17 N702 Plath
#> 715 TGCCAATCCGTT vRG vRG_0 368 GZ 17 N702 Plath
#> 723 TCGACTATTTTG vRG vRG_2 368 GZ 17 N702 Plath
#> Number_genes_detected Number_UMI Percentage_mitochondrial S_phase_score
#> 169 1366 2736 4.20 -0.11
#> 624 3012 7318 1.87 0.83
#> 659 1597 3451 2.17 -0.13
#> 681 1551 2941 1.43 0.38
#> 715 1569 2769 1.81 -0.04
#> 723 1610 2994 3.57 0.11
#> G2M_phase_score Phase X tSNE_1 tSNE_2
#> 169 -0.073 G1 TGCTAATACTGA -3.446397 17.68239
#> 624 0.350 S TTCACGATTTTT -8.190806 22.31286
#> 659 -0.110 G1 CTGTCAGAATAA -3.301333 18.49425
#> 681 0.064 S CATAATATGTCA -8.502828 16.35404
#> 715 -0.170 G1 TGCCAATCCGTT -3.293814 19.02176
#> 723 0.064 S TCGACTATTTTG -7.173418 21.53491
head(NeuroGenesis4.info$Jabaudon.inVivo.sc.Mm)
#> title geo_accession status
#> GSM3351837 E14.24H_LTHT7_1_1 GSM3351837 Public on May 10 2019
#> GSM3351838 E14.24H_LTHT7_1_2 GSM3351838 Public on May 10 2019
#> GSM3351839 E14.24H_LTHT7_1_5 GSM3351839 Public on May 10 2019
#> GSM3351840 E14.24H_LTHT7_1_6 GSM3351840 Public on May 10 2019
#> GSM3351841 E14.24H_LTHT7_1_7 GSM3351841 Public on May 10 2019
#> GSM3351842 E14.24H_LTHT7_1_12 GSM3351842 Public on May 10 2019
#> submission_date last_update_date type channel_count source_name_ch1
#> GSM3351837 Aug 23 2018 May 10 2019 SRA 1 cortical cells
#> GSM3351838 Aug 23 2018 May 10 2019 SRA 1 cortical cells
#> GSM3351839 Aug 23 2018 May 10 2019 SRA 1 cortical cells
#> GSM3351840 Aug 23 2018 May 10 2019 SRA 1 cortical cells
#> GSM3351841 Aug 23 2018 May 10 2019 SRA 1 cortical cells
#> GSM3351842 Aug 23 2018 May 10 2019 SRA 1 cortical cells
#> organism_ch1 characteristics_ch1 characteristics_ch1.1
#> GSM3351837 Mus musculus tsne1: -21.73 tsne2: 10.41
#> GSM3351838 Mus musculus tsne1: -12.66 tsne2: -0.39
#> GSM3351839 Mus musculus tsne1: 4.78 tsne2: 2.06
#> GSM3351840 Mus musculus tsne1: -14.95 tsne2: 7.12
#> GSM3351841 Mus musculus tsne1: -15.24 tsne2: 7.04
#> GSM3351842 Mus musculus tsne1: -19.39 tsne2: 11.40
#> characteristics_ch1.2 characteristics_ch1.3 characteristics_ch1.4
#> GSM3351837 num_read: 608677 pct_mt: 4.3% cluster: N1d.late
#> GSM3351838 num_read: 68123 pct_mt: 4.8% cluster: N1d.late
#> GSM3351839 num_read: 608394 pct_mt: 3.5% cluster: N1d.late
#> GSM3351840 num_read: 557976 pct_mt: 3.4% cluster: N1d.late
#> GSM3351841 num_read: 121333 pct_mt: 8.7% cluster: N1d.late
#> GSM3351842 num_read: 621786 pct_mt: 2.9% cluster: N1d.late
#> characteristics_ch1.5 characteristics_ch1.6
#> GSM3351837 pup.age.at.injection: E14 cell.age: 24H
#> GSM3351838 pup.age.at.injection: E14 cell.age: 24H
#> GSM3351839 pup.age.at.injection: E14 cell.age: 24H
#> GSM3351840 pup.age.at.injection: E14 cell.age: 24H
#> GSM3351841 pup.age.at.injection: E14 cell.age: 24H
#> GSM3351842 pup.age.at.injection: E14 cell.age: 24H
#> characteristics_ch1.7 characteristics_ch1.8
#> GSM3351837 pseudo.differentiation: 0.409 pseudo.birthdate24h: 0.417
#> GSM3351838 pseudo.differentiation: 0.381 pseudo.birthdate24h: 0.462
#> GSM3351839 pseudo.differentiation: 0.327 pseudo.birthdate24h: 0.459
#> GSM3351840 pseudo.differentiation: 0.378 pseudo.birthdate24h: 0.505
#> GSM3351841 pseudo.differentiation: 0.372 pseudo.birthdate24h: 0.500
#> GSM3351842 pseudo.differentiation: 0.421 pseudo.birthdate24h: 0.431
#> characteristics_ch1.9 characteristics_ch1.10
#> GSM3351837 pseudo.birthdate.pred: 0.333 pseudo.differentiation.pred: 0.592
#> GSM3351838 pseudo.birthdate.pred: 0.152 pseudo.differentiation.pred: 0.130
#> GSM3351839 pseudo.birthdate.pred: 0.890 pseudo.differentiation.pred: 0.134
#> GSM3351840 pseudo.birthdate.pred: 0.439 pseudo.differentiation.pred: 0.119
#> GSM3351841 pseudo.birthdate.pred: 0.049 pseudo.differentiation.pred: 0.056
#> GSM3351842 pseudo.birthdate.pred: 0.578 pseudo.differentiation.pred: 0.172
#> characteristics_ch1.11
#> GSM3351837 pseudo.birthdate.adj.pred: 3.411
#> GSM3351838 pseudo.birthdate.adj.pred: 3.434
#> GSM3351839 pseudo.birthdate.adj.pred: 3.963
#> GSM3351840 pseudo.birthdate.adj.pred: 3.316
#> GSM3351841 pseudo.birthdate.adj.pred: 2.687
#> GSM3351842 pseudo.birthdate.adj.pred: 3.553
#> characteristics_ch1.12 molecule_ch1
#> GSM3351837 pseudo.differentiation.adj.pred: 2.219 polyA RNA
#> GSM3351838 pseudo.differentiation.adj.pred: 1.982 polyA RNA
#> GSM3351839 pseudo.differentiation.adj.pred: 1.982 polyA RNA
#> GSM3351840 pseudo.differentiation.adj.pred: 1.943 polyA RNA
#> GSM3351841 pseudo.differentiation.adj.pred: 1.919 polyA RNA
#> GSM3351842 pseudo.differentiation.adj.pred: 1.908 polyA RNA
#> extract_protocol_ch1
#> GSM3351837 The putative primary somatosensory cortex S1 was microdissected and incubated in 0.05% trypsin at 37°C for 5 minutes. Following tissue digestion, fetal bovine serum was added to the mix and cells were manually dissociated via up-and-down pipetting. Cells were centrifuged 5min at 300g and the pellet was suspended in 1ml of HBSS then passed on a 70µm cell stainer. FT+ cells, gated on the top 5% brightest cells, were finally FAC-sorted on a MoFloAstrios (Beckman). FAC-sorted FT+ cells (18µl) were mixed with the C1 Suspension Reagent (2µl; Fluidigm) yielding a total of 20µl of cell suspension mix with ~500 cells/μl. The cell suspension mix was loaded on a C1 Single-Cell AutoPrep integrated fluidic circuit (IFC) designed for 10- to 17-µm cells (HT-800, Fluidigm #100-57-80). cDNA synthesis and preamplification was processed following the manufacturer’s instructions (C1 system, Fluidigm). Single cell RNA-sequencing libraries of the cDNA were prepared using Nextera XT DNA library prep kit (Illumina). Libraries were multi-plexed and sequenced according to the manufacturer’s recommendations with paired-end reads using HiSeq2500 platform (Illumina) with an expected depth of 1M reads per single cell, and a final mapping read length of 70bp.
#> GSM3351838 The putative primary somatosensory cortex S1 was microdissected and incubated in 0.05% trypsin at 37°C for 5 minutes. Following tissue digestion, fetal bovine serum was added to the mix and cells were manually dissociated via up-and-down pipetting. Cells were centrifuged 5min at 300g and the pellet was suspended in 1ml of HBSS then passed on a 70µm cell stainer. FT+ cells, gated on the top 5% brightest cells, were finally FAC-sorted on a MoFloAstrios (Beckman). FAC-sorted FT+ cells (18µl) were mixed with the C1 Suspension Reagent (2µl; Fluidigm) yielding a total of 20µl of cell suspension mix with ~500 cells/μl. The cell suspension mix was loaded on a C1 Single-Cell AutoPrep integrated fluidic circuit (IFC) designed for 10- to 17-µm cells (HT-800, Fluidigm #100-57-80). cDNA synthesis and preamplification was processed following the manufacturer’s instructions (C1 system, Fluidigm). Single cell RNA-sequencing libraries of the cDNA were prepared using Nextera XT DNA library prep kit (Illumina). Libraries were multi-plexed and sequenced according to the manufacturer’s recommendations with paired-end reads using HiSeq2500 platform (Illumina) with an expected depth of 1M reads per single cell, and a final mapping read length of 70bp.
#> GSM3351839 The putative primary somatosensory cortex S1 was microdissected and incubated in 0.05% trypsin at 37°C for 5 minutes. Following tissue digestion, fetal bovine serum was added to the mix and cells were manually dissociated via up-and-down pipetting. Cells were centrifuged 5min at 300g and the pellet was suspended in 1ml of HBSS then passed on a 70µm cell stainer. FT+ cells, gated on the top 5% brightest cells, were finally FAC-sorted on a MoFloAstrios (Beckman). FAC-sorted FT+ cells (18µl) were mixed with the C1 Suspension Reagent (2µl; Fluidigm) yielding a total of 20µl of cell suspension mix with ~500 cells/μl. The cell suspension mix was loaded on a C1 Single-Cell AutoPrep integrated fluidic circuit (IFC) designed for 10- to 17-µm cells (HT-800, Fluidigm #100-57-80). cDNA synthesis and preamplification was processed following the manufacturer’s instructions (C1 system, Fluidigm). Single cell RNA-sequencing libraries of the cDNA were prepared using Nextera XT DNA library prep kit (Illumina). Libraries were multi-plexed and sequenced according to the manufacturer’s recommendations with paired-end reads using HiSeq2500 platform (Illumina) with an expected depth of 1M reads per single cell, and a final mapping read length of 70bp.
#> GSM3351840 The putative primary somatosensory cortex S1 was microdissected and incubated in 0.05% trypsin at 37°C for 5 minutes. Following tissue digestion, fetal bovine serum was added to the mix and cells were manually dissociated via up-and-down pipetting. Cells were centrifuged 5min at 300g and the pellet was suspended in 1ml of HBSS then passed on a 70µm cell stainer. FT+ cells, gated on the top 5% brightest cells, were finally FAC-sorted on a MoFloAstrios (Beckman). FAC-sorted FT+ cells (18µl) were mixed with the C1 Suspension Reagent (2µl; Fluidigm) yielding a total of 20µl of cell suspension mix with ~500 cells/μl. The cell suspension mix was loaded on a C1 Single-Cell AutoPrep integrated fluidic circuit (IFC) designed for 10- to 17-µm cells (HT-800, Fluidigm #100-57-80). cDNA synthesis and preamplification was processed following the manufacturer’s instructions (C1 system, Fluidigm). Single cell RNA-sequencing libraries of the cDNA were prepared using Nextera XT DNA library prep kit (Illumina). Libraries were multi-plexed and sequenced according to the manufacturer’s recommendations with paired-end reads using HiSeq2500 platform (Illumina) with an expected depth of 1M reads per single cell, and a final mapping read length of 70bp.
#> GSM3351841 The putative primary somatosensory cortex S1 was microdissected and incubated in 0.05% trypsin at 37°C for 5 minutes. Following tissue digestion, fetal bovine serum was added to the mix and cells were manually dissociated via up-and-down pipetting. Cells were centrifuged 5min at 300g and the pellet was suspended in 1ml of HBSS then passed on a 70µm cell stainer. FT+ cells, gated on the top 5% brightest cells, were finally FAC-sorted on a MoFloAstrios (Beckman). FAC-sorted FT+ cells (18µl) were mixed with the C1 Suspension Reagent (2µl; Fluidigm) yielding a total of 20µl of cell suspension mix with ~500 cells/μl. The cell suspension mix was loaded on a C1 Single-Cell AutoPrep integrated fluidic circuit (IFC) designed for 10- to 17-µm cells (HT-800, Fluidigm #100-57-80). cDNA synthesis and preamplification was processed following the manufacturer’s instructions (C1 system, Fluidigm). Single cell RNA-sequencing libraries of the cDNA were prepared using Nextera XT DNA library prep kit (Illumina). Libraries were multi-plexed and sequenced according to the manufacturer’s recommendations with paired-end reads using HiSeq2500 platform (Illumina) with an expected depth of 1M reads per single cell, and a final mapping read length of 70bp.
#> GSM3351842 The putative primary somatosensory cortex S1 was microdissected and incubated in 0.05% trypsin at 37°C for 5 minutes. Following tissue digestion, fetal bovine serum was added to the mix and cells were manually dissociated via up-and-down pipetting. Cells were centrifuged 5min at 300g and the pellet was suspended in 1ml of HBSS then passed on a 70µm cell stainer. FT+ cells, gated on the top 5% brightest cells, were finally FAC-sorted on a MoFloAstrios (Beckman). FAC-sorted FT+ cells (18µl) were mixed with the C1 Suspension Reagent (2µl; Fluidigm) yielding a total of 20µl of cell suspension mix with ~500 cells/μl. The cell suspension mix was loaded on a C1 Single-Cell AutoPrep integrated fluidic circuit (IFC) designed for 10- to 17-µm cells (HT-800, Fluidigm #100-57-80). cDNA synthesis and preamplification was processed following the manufacturer’s instructions (C1 system, Fluidigm). Single cell RNA-sequencing libraries of the cDNA were prepared using Nextera XT DNA library prep kit (Illumina). Libraries were multi-plexed and sequenced according to the manufacturer’s recommendations with paired-end reads using HiSeq2500 platform (Illumina) with an expected depth of 1M reads per single cell, and a final mapping read length of 70bp.
#> extract_protocol_ch1.1 taxid_ch1
#> GSM3351837 SMARTseq v4 kit (Clontech, # 634888) 10090
#> GSM3351838 SMARTseq v4 kit (Clontech, # 634888) 10090
#> GSM3351839 SMARTseq v4 kit (Clontech, # 634888) 10090
#> GSM3351840 SMARTseq v4 kit (Clontech, # 634888) 10090
#> GSM3351841 SMARTseq v4 kit (Clontech, # 634888) 10090
#> GSM3351842 SMARTseq v4 kit (Clontech, # 634888) 10090
#> data_processing
#> GSM3351837 The 5bp UMI sequence (initially sequenced in read1), are appended at the end of the headers of the reads (here the reads we provide are resulting from this operation)
#> GSM3351838 The 5bp UMI sequence (initially sequenced in read1), are appended at the end of the headers of the reads (here the reads we provide are resulting from this operation)
#> GSM3351839 The 5bp UMI sequence (initially sequenced in read1), are appended at the end of the headers of the reads (here the reads we provide are resulting from this operation)
#> GSM3351840 The 5bp UMI sequence (initially sequenced in read1), are appended at the end of the headers of the reads (here the reads we provide are resulting from this operation)
#> GSM3351841 The 5bp UMI sequence (initially sequenced in read1), are appended at the end of the headers of the reads (here the reads we provide are resulting from this operation)
#> GSM3351842 The 5bp UMI sequence (initially sequenced in read1), are appended at the end of the headers of the reads (here the reads we provide are resulting from this operation)
#> data_processing.1
#> GSM3351837 reads are mapped with tophat v2.0.13 on the mouse genome GRCm38 considering Ensembl78 genes annotations
#> GSM3351838 reads are mapped with tophat v2.0.13 on the mouse genome GRCm38 considering Ensembl78 genes annotations
#> GSM3351839 reads are mapped with tophat v2.0.13 on the mouse genome GRCm38 considering Ensembl78 genes annotations
#> GSM3351840 reads are mapped with tophat v2.0.13 on the mouse genome GRCm38 considering Ensembl78 genes annotations
#> GSM3351841 reads are mapped with tophat v2.0.13 on the mouse genome GRCm38 considering Ensembl78 genes annotations
#> GSM3351842 reads are mapped with tophat v2.0.13 on the mouse genome GRCm38 considering Ensembl78 genes annotations
#> data_processing.2
#> GSM3351837 bam files are processed with umi_tools to deduplicate reads with identical UMI sequence
#> GSM3351838 bam files are processed with umi_tools to deduplicate reads with identical UMI sequence
#> GSM3351839 bam files are processed with umi_tools to deduplicate reads with identical UMI sequence
#> GSM3351840 bam files are processed with umi_tools to deduplicate reads with identical UMI sequence
#> GSM3351841 bam files are processed with umi_tools to deduplicate reads with identical UMI sequence
#> GSM3351842 bam files are processed with umi_tools to deduplicate reads with identical UMI sequence
#> data_processing.3
#> GSM3351837 gene expression are quantifyied using summarizeOverlaps() method of the R package GenomicsAlignments(). Only exonic reads are considered in the quantification and this includes 5' and 3' UTRs.
#> GSM3351838 gene expression are quantifyied using summarizeOverlaps() method of the R package GenomicsAlignments(). Only exonic reads are considered in the quantification and this includes 5' and 3' UTRs.
#> GSM3351839 gene expression are quantifyied using summarizeOverlaps() method of the R package GenomicsAlignments(). Only exonic reads are considered in the quantification and this includes 5' and 3' UTRs.
#> GSM3351840 gene expression are quantifyied using summarizeOverlaps() method of the R package GenomicsAlignments(). Only exonic reads are considered in the quantification and this includes 5' and 3' UTRs.
#> GSM3351841 gene expression are quantifyied using summarizeOverlaps() method of the R package GenomicsAlignments(). Only exonic reads are considered in the quantification and this includes 5' and 3' UTRs.
#> GSM3351842 gene expression are quantifyied using summarizeOverlaps() method of the R package GenomicsAlignments(). Only exonic reads are considered in the quantification and this includes 5' and 3' UTRs.
#> data_processing.4
#> GSM3351837 Genome_build: GRCm38
#> GSM3351838 Genome_build: GRCm38
#> GSM3351839 Genome_build: GRCm38
#> GSM3351840 Genome_build: GRCm38
#> GSM3351841 Genome_build: GRCm38
#> GSM3351842 Genome_build: GRCm38
#> data_processing.5
#> GSM3351837 Supplementary_files_format_and_content: raw_count.tsv.gz contains the result of gene expression quantification by summarizeOverlaps() for each cell. The integers values represent the number of exonic reads mapping into each gene after UMI correction. The first columns contains the gene name that is quantified.
#> GSM3351838 Supplementary_files_format_and_content: raw_count.tsv.gz contains the result of gene expression quantification by summarizeOverlaps() for each cell. The integers values represent the number of exonic reads mapping into each gene after UMI correction. The first columns contains the gene name that is quantified.
#> GSM3351839 Supplementary_files_format_and_content: raw_count.tsv.gz contains the result of gene expression quantification by summarizeOverlaps() for each cell. The integers values represent the number of exonic reads mapping into each gene after UMI correction. The first columns contains the gene name that is quantified.
#> GSM3351840 Supplementary_files_format_and_content: raw_count.tsv.gz contains the result of gene expression quantification by summarizeOverlaps() for each cell. The integers values represent the number of exonic reads mapping into each gene after UMI correction. The first columns contains the gene name that is quantified.
#> GSM3351841 Supplementary_files_format_and_content: raw_count.tsv.gz contains the result of gene expression quantification by summarizeOverlaps() for each cell. The integers values represent the number of exonic reads mapping into each gene after UMI correction. The first columns contains the gene name that is quantified.
#> GSM3351842 Supplementary_files_format_and_content: raw_count.tsv.gz contains the result of gene expression quantification by summarizeOverlaps() for each cell. The integers values represent the number of exonic reads mapping into each gene after UMI correction. The first columns contains the gene name that is quantified.
#> platform_id contact_name contact_email contact_phone
#> GSM3351837 GPL17021 Julien,,Prados julien.prados@unige.ch +41 22 37 95 396
#> GSM3351838 GPL17021 Julien,,Prados julien.prados@unige.ch +41 22 37 95 396
#> GSM3351839 GPL17021 Julien,,Prados julien.prados@unige.ch +41 22 37 95 396
#> GSM3351840 GPL17021 Julien,,Prados julien.prados@unige.ch +41 22 37 95 396
#> GSM3351841 GPL17021 Julien,,Prados julien.prados@unige.ch +41 22 37 95 396
#> GSM3351842 GPL17021 Julien,,Prados julien.prados@unige.ch +41 22 37 95 396
#> contact_laboratory contact_department contact_institute
#> GSM3351837 Denis Jabaudon Neurosciences University of Geneva
#> GSM3351838 Denis Jabaudon Neurosciences University of Geneva
#> GSM3351839 Denis Jabaudon Neurosciences University of Geneva
#> GSM3351840 Denis Jabaudon Neurosciences University of Geneva
#> GSM3351841 Denis Jabaudon Neurosciences University of Geneva
#> GSM3351842 Denis Jabaudon Neurosciences University of Geneva
#> contact_address contact_city contact_zip/postal_code
#> GSM3351837 Rue Michel Servet 1 Geneva 1211
#> GSM3351838 Rue Michel Servet 1 Geneva 1211
#> GSM3351839 Rue Michel Servet 1 Geneva 1211
#> GSM3351840 Rue Michel Servet 1 Geneva 1211
#> GSM3351841 Rue Michel Servet 1 Geneva 1211
#> GSM3351842 Rue Michel Servet 1 Geneva 1211
#> contact_country data_row_count instrument_model library_selection
#> GSM3351837 Switzerland 0 Illumina HiSeq 2500 cDNA
#> GSM3351838 Switzerland 0 Illumina HiSeq 2500 cDNA
#> GSM3351839 Switzerland 0 Illumina HiSeq 2500 cDNA
#> GSM3351840 Switzerland 0 Illumina HiSeq 2500 cDNA
#> GSM3351841 Switzerland 0 Illumina HiSeq 2500 cDNA
#> GSM3351842 Switzerland 0 Illumina HiSeq 2500 cDNA
#> library_source library_strategy
#> GSM3351837 transcriptomic RNA-Seq
#> GSM3351838 transcriptomic RNA-Seq
#> GSM3351839 transcriptomic RNA-Seq
#> GSM3351840 transcriptomic RNA-Seq
#> GSM3351841 transcriptomic RNA-Seq
#> GSM3351842 transcriptomic RNA-Seq
#> relation
#> GSM3351837 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN09901434
#> GSM3351838 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN09901433
#> GSM3351839 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN09901432
#> GSM3351840 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN09901431
#> GSM3351841 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN09901430
#> GSM3351842 BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN09901429
#> relation.1
#> GSM3351837 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX4600063
#> GSM3351838 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX4600064
#> GSM3351839 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX4600065
#> GSM3351840 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX4600066
#> GSM3351841 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX4600067
#> GSM3351842 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX4600068
#> supplementary_file_1 cell.age:ch1 cluster:ch1 num_read:ch1
#> GSM3351837 NONE 24H N1d.late 608677
#> GSM3351838 NONE 24H N1d.late 68123
#> GSM3351839 NONE 24H N1d.late 608394
#> GSM3351840 NONE 24H N1d.late 557976
#> GSM3351841 NONE 24H N1d.late 121333
#> GSM3351842 NONE 24H N1d.late 621786
#> pct_mt:ch1 pseudo.birthdate.adj.pred:ch1 pseudo.birthdate.pred:ch1
#> GSM3351837 4.3% 3.411 0.333
#> GSM3351838 4.8% 3.434 0.152
#> GSM3351839 3.5% 3.963 0.890
#> GSM3351840 3.4% 3.316 0.439
#> GSM3351841 8.7% 2.687 0.049
#> GSM3351842 2.9% 3.553 0.578
#> pseudo.birthdate24h:ch1 pseudo.birthdate96h:ch1
#> GSM3351837 0.417 <NA>
#> GSM3351838 0.462 <NA>
#> GSM3351839 0.459 <NA>
#> GSM3351840 0.505 <NA>
#> GSM3351841 0.500 <NA>
#> GSM3351842 0.431 <NA>
#> pseudo.birthdateprog:ch1 pseudo.differentiation:ch1
#> GSM3351837 <NA> 0.409
#> GSM3351838 <NA> 0.381
#> GSM3351839 <NA> 0.327
#> GSM3351840 <NA> 0.378
#> GSM3351841 <NA> 0.372
#> GSM3351842 <NA> 0.421
#> pseudo.differentiation.adj.pred:ch1 pseudo.differentiation.pred:ch1
#> GSM3351837 2.219 0.592
#> GSM3351838 1.982 0.130
#> GSM3351839 1.982 0.134
#> GSM3351840 1.943 0.119
#> GSM3351841 1.919 0.056
#> GSM3351842 1.908 0.172
#> pup.age.at.injection:ch1 tsne1:ch1 tsne2:ch1 pupAGEcellAGE
#> GSM3351837 E14 -21.73 10.41 E14.24H
#> GSM3351838 E14 -12.66 -0.39 E14.24H
#> GSM3351839 E14 4.78 2.06 E14.24H
#> GSM3351840 E14 -14.95 7.12 E14.24H
#> GSM3351841 E14 -15.24 7.04 E14.24H
#> GSM3351842 E14 -19.39 11.40 E14.24H