报道人 | 于洲 今天我们介绍由Tabula Sapiens联盟发表在Science上的工作，该工作创建了一个人类参考图谱，包括来自24种不同组织和器官的近50万个细胞。...来自Tabula Sapiens数据集的多个个体再现了这些以前未知的、室特异性的两种MYL6亚型表达模式。...微生物组中意想不到的空间变化 Tabula Sapiens提供了一个密集和直接采样整个胃肠道的人类微生物组的机会。...这证明Tabula Sapiens在细胞分辨率上为深刻理解和探索人类生物学提供了广泛而有用的参考。...参考资料 The Tabula Sapiens Consortium* ,The Tabula Sapiens: A multiple-organ, single-cell transcriptomic
Ident Accession Homo sapiens OCRL inositol polyphosphate-5-phosphatase (OCRL), RefSeqGene on chromosome...14 0.8684 NG_016970.1 Homo sapiens BLM RecQ like helicase (BLM), RefSeqGene (LRG_20) on chromosome...Homo sapiens sulfatase 1 (SULF1), RefSeqGene on chromosome 8 0.9286 NG_042849.1 Homo sapiens paired...sapiens mannose receptor C-type 1 (MRC1), RefSeqGene on chromosome 10 0.825 NG_047011.1 Homo sapiens...Homo sapiens G protein subunit beta 1 (GNB1), RefSeqGene on chromosome 1 0.9259 NG_047052.1 Homo sapiens
hgu95av2 GPL92 Homo sapiens hgu95b GPL93 Homo sapiens hgu95c GPL94 Homo sapiens hgu95d GPL95 Homo sapiens...hgu95e GPL96 Homo sapiens hgu133a GPL97 Homo sapiens hgu133b GPL98 Homo sapiens hu35ksuba GPL99 Homo...sapiens hu35ksubb GPL100 Homo sapiens hu35ksubc GPL101 Homo sapiens hu35ksubd GPL201 Homo sapiens Hgfocus...hgu133plus2 GPL571 Homo sapiens hgu133a2 GPL886 Homo sapiens hgug4111a GPL887 Homo sapiens hgug4110b...sapiens hthgu133a GPL4191 Homo sapiens h10kcod GPL5689 Homo sapiens hgug4100a GPL6097 Homo sapiens illuminaHumanv1
.dbsnp138.vcf" \ "gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dbsnp138....vcf.idx" \ "gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dict" \ "gs.../v0/Homo_sapiens_assembly38.fasta.64.ann" \ "gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38...BWA的索引文件 Homo_sapiens_assembly38.fasta Homo_sapiens_assembly38.fasta.64.amb Homo_sapiens_assembly38.fasta....64.ann Homo_sapiens_assembly38.fasta.64.bwt Homo_sapiens_assembly38.fasta.64.pac Homo_sapiens_assembly38
0 1572 Unknown 1.2 SRA553822 SRS2119548 Cultured embryonic stem cells 10x chromium Homo sapiens...1 563 Unknown 1.3 SRA553822 SRS2119548 Cultured embryonic stem cells 10x chromium Homo sapiens...2 280 Unknown 1.4 SRA553822 SRS2119548 Cultured embryonic stem cells 10x chromium Homo sapiens...3 270 Unknown 1.5 SRA553822 SRS2119548 Cultured embryonic stem cells 10x chromium Homo sapiens...4 220 Unknown 1.6 SRA553822 SRS2119548 Cultured embryonic stem cells 10x chromium Homo sapiens
Homo sapiens # RPS16 ribosomal protein S16 Homo sapiens # HIST1H2BA...complex, class I, A Homo sapiens # HSPA1A heat shock 70kDa protein 1A...Homo sapiens # HSP90AB1 heat shock protein 90kDa alpha (cytosolic), cl......1, H1b Homo sapiens # DARS1 aspartyl-tRNA synthetase Homo sapiens...I, A Homo sapiens # HSPA1A heat shock 70kDa protein 1A Homo sapiens
/references/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/ --exclude "*" --include "genes.gtf" aws s3...eu-west-1 sync s3://ngi-igenomes/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ ....-1 sync s3://ngi-igenomes/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/ ....1 sync s3://ngi-igenomes/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/ ....-1 sync s3://ngi-igenomes/igenomes/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/ .
Homo sapiens hgu95c 25 GPL94 Homo sapiens...hu35ksuba 30 GPL99 Homo sapiens hu35ksubb 31 GPL100 Homo sapiens...Homo sapiens hgug4111a 44 GPL887 Homo sapiens...hthgu133a 63 GPL4191 Homo sapiens h10kcod 64 GPL5689 Homo sapiens...illuminaHumanv4 72 GPL11532 Homo sapiens hugene11sttranscriptcluster 73 GPL13497 Homo sapiens
一般选择primary assembly，没有的话可以选择toplevel nohup wget -c https://ftp.ensembl.org/pub/release-105/fasta/homo_sapiens.../dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz > dna.log & ## 下载转录组序列 nohup wget -c http://ftp.ensembl.org.../pub/release-105/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz >rna.log & ## 下载基因组注释文件...nohup wget -c http://ftp.ensembl.org/pub/release-105/gtf/homo_sapiens/Homo_sapiens.GRCh38.105.chr.gtf.gz...>gtf.log & nohup wget -c http://ftp.ensembl.org/pub/release-105/gff3/homo_sapiens/Homo_sapiens.GRCh38.105
support.illumina.com/sequencing/sequencing_software/igenome.html 网站下载人的hg19基因组后，得到一个44G 大小的文件 （Homo_sapiens.zip...02 unzip软件解压报错： (base) root@dell-server:/home/newdisk_dell_3/genomes# unzip Homo_sapiens.zip Archive...: Homo_sapiens.zip warning [Homo_sapiens.zip]: 42641665723 extra bytes at beginning or within zipfile...(attempting to process anyway) error [Homo_sapiens.zip]: start of central directory not found;...(base) root@dell-server:/home/newdisk_dell_3/genomes# 7za x Homo_sapiens.zip
/IG/IGHV.fasta wget http://www.imgt.org/download/V-QUEST/IMGT_V-QUEST_reference_directory/Homo_sapiens.../IG/IGHD.fasta wget http://www.imgt.org/download/V-QUEST/IMGT_V-QUEST_reference_directory/Homo_sapiens...sapiens|F|J-REGION|932..984|53 nt|2| | | | |53+0=53| | | >J00256|IGHJ3*01|Homo sapiens|F|J-REGION|1537...|IGHJ4*02|Homo sapiens|F|J-REGION|1480..1527|48 nt|3| | | | |48+0=48| | | >M25625|IGHJ4*03|Homo sapiens...sapiens|F|J-REGION|2482..2543|62 nt|3| | | | |62+0=62|partial in 3'| | >AJ879487|IGHJ6*04|Homo sapiens
/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz >dna.log & 下载cDNA信息 cDNA下载红色部分显示链接 # 下载转录组序列nohup...wget -c http://ftp.ensembl.org/pub/release-105/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz.../Homo_sapiens.GRCh38.105.chr.gtf.gz >gtf.log & nohup wget -c http://ftp.ensembl.org/pub.../release-105/gff3/homo_sapiens/Homo_sapiens.GRCh38.105.chr.gff3.gz >gff.log& 解压 # 上述文件下载完整后，再解压...nohup gunzip Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz Homo_sapiens.GRCh38.cdna.all.fa.gz >unzip.log
-y GRCh38 -g dbNSFP,CADD,G2P 注释数据保存于容器内 /opt/vep/.vep/homo_sapiens 文件夹下，插件保 存于容器内 /opt/vep/.vep/Plugins...文件夹下，分别对于宿主机中的 $HOME/vep_data/homo_sapiens 和 $HOME/vep_data/Plugins。..._99_GRCh38.tar.gztar xzf homo_sapiens_vep_99_GRCh38.tar.gz curl -O ftp://ftp.ensembl.org/pub/release-...99/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz 数据库中包含的内容： ?..._99_38 on ensembldb.ensembl.org## Using cache in /homes/user/.vep/homo_sapiens/99_GRCh38## Using API
/Homo_sapiens.GRCh38.86.symbol.txt", ref_group_names=paste0.../Homo_sapiens.GRCh38.86.symbol.txt", ref_group_names=c(paste0.../Homo_sapiens.GRCh38.86.symbol.txt", ref_group_names=c(paste0.../Homo_sapiens.GRCh38.86.symbol.txt", ref_group_names=c(paste0.../Homo_sapiens.GRCh38.86.symbol.txt", ref_group_names=paste0(
/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz >dna.log &(rna) Mar402 16:48:59 ~/database/GRCh38.105.../cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz >rna.log &# 下载基因组注释文件nohup wget -c http://ftp.ensembl.org/pub.../release-105/gtf/homo_sapiens/Homo_sapiens.GRCh38.105.chr.gtf.gz >gtf.log &nohup wget -c http://ftp.ensembl.org.../pub/release-105/gff3/homo_sapiens/Homo_sapiens.GRCh38.105.chr.gff3.gz >gff.log&# 上述文件下载完整后，再解压；否则文件不完整就解压会报错...nohup gunzip Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz Homo_sapiens.GRCh38.cdna.all.fa.gz >unzip.log
Tabula Sapiens 2.0：人类单细胞转录组图谱的新突破项目概述 在单细胞转录组学飞速发展的今天，科学家们正以前所未有的精度探索人类细胞的奥秘。...Tabula Sapiens，这一备受瞩目的人类细胞图谱项目的最新成果，为我们揭示了关于转录因子表达、细胞衰老特性以及性别特异性特征的全新视角。...现在Tabula Sapiens升级至2.0，其更新了四大新组织+跨器官供体数据，为解锁细胞类型特异性调控提供了新视角。...研究比较了Tabula Sapiens与GTEx项目中识别的差异表达基因，发现Tabula Sapiens能够识别出更多的性别特异性基因，并且这些基因在细胞类型中具有更高的特异性（图6A-C）。...结语Tabula Sapiens 2.0的三大价值：重新定义人体复杂性认知构建精准细胞注释工具的基础支持疾病研究和个性化治疗开发数据门户：https://tabula-sapiens-portal.ds.czbiohub.org
GRCm38: cd $VEP_DATA #rsync -zvh rsync://ftp.ensembl.org/ensembl/pub/release-86/variation/VEP/homo_sapiens_vep...--ASSEMBLY GRCh37 --DESTDIR $VEP_PATH --CACHEDIR $VEP_DATA perl INSTALL.pl --AUTO af --SPECIES homo_sapiens.../86_GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz /home/jianmingzeng/vep/htslib/bgzip This may...If it is not, use "--fasta /home/jianmingzeng/.vep/homo_sapiens/86_GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz...--version 86_GRCh37 --dir $VEP_DATA perl convert_cache.pl --species homo_sapiens --version 86_GRCh38
GRCh38.111# 下载基因组序列axel curl nohup axel -n 100 https://ftp.ensembl.org/pub/release-111/fasta/homo_sapiens.../pub/release-111/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz >rna.log &# 下载基因组注释文件nohup...axel -n 100 https://ftp.ensembl.org/pub/release-111/gtf/homo_sapiens/Homo_sapiens.GRCh38.111.gtf.gz...>gtf.log &nohup axel -n 100 https://ftp.ensembl.org/pub/release-111/gff3/homo_sapiens/Homo_sapiens.GRCh38.111...nohup gunzip Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz Homo_sapiens.GRCh38.cdna.all.fa.gz >unzip.log
这里的文件夹名为物种的拉丁名，这里以 Human(Homo_sapiens) 为例，下载方法如下： wget ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens...ANNOTATION_RELEASE.109/GFF/ref_GRCh38.p12_top_level.gff3.gz (hg38) wget ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens...同样以Human(Homo_sapiens)为下载为例： wget ftp://ftp.ensembl.org/pub/current_gtf/homo_sapiens/Homo_sapiens.GRCh38.90....gtf.gz （hg38） wget ftp://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/Homo_sapiens.GRCh37.75.gtf.gz
/Homo_sapiens.GRCh38.dna.toplevel.fa.gz https://ftp.ensembl.org/pub/release-114/gtf/homo_sapiens/Homo_sapiens.GRCh38.114.../Homo_sapiens.GRCh38.112.gtf --output ...../Homo_sapiens.GRCh38.112_corrected.gtf --output ..../Homo_sapiens.GRCh38.112_corrected_filter.gtf --fasta ...../ensembl/Homo_sapiens.GRCh38.dna.toplevel.fa --threads 6 --species Homo_sapiens_GRCh38.112 --ingtf #
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