title: S261_DNA methylation [203229450158_R01C01]

description: normal sperm sample


title: S259_DNA methylation [203229450156_R07C01]

status: Public on Jul 06 2022

type: genomic

city: Amherst

last: Pilsner

state: Massachusetts

address: 686 N PLEASANT

department: Environmental Health Sciences

country: USA

institute: University of Massachusetts Amherst

description: normal sperm sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to  Illumina Infinium HumanMethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Sperm DNA methylation was assessed using Illumina's EPIC Infinium Methylation Beadchip. Raw idat files were imported into R and within-array normalization and dye-bias equalization of Type I and Type II probes was performed using normal-exponential convolution method (Noob) via  minfi package. Batch effects were corrected with the ComBat function in the sva package while cross-hybridizing probes were removed using the DMRcate package. probes with detection pvalue >0.01 were also exluced prior to downstream analysis.
Processed matrix contains the NOOB-normalized beta values representing the percent CpG methylation for all the CpGs that passed the preprocessing method.

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: sperm

label_protocol: Standard Illumina Protocol

extract_protocol: Standard Illumina Protocol

treatment_protocol: Sperm from semen was extracted using 40% gradient method and purified DNA was isolated our previously developed method of beads, RLT and TCEPS

tag: tissue

value: sperm

tag: tag

value: normal

tag: basename

tag: average beta

tag: detection pval


title: S260_DNA methylation [203229450156_R08C01]

description: normal sperm sample


title: S254_DNA methylation [203229450156_R02C01]

description: normal sperm sample


title: S258_DNA methylation [203229450156_R06C01]

description: normal sperm sample


title: S255_DNA methylation [203229450156_R03C01]

description: normal sperm sample


title: S267_DNA methylation [203229450158_R07C01]

description: normal sperm sample


title: S269_DNA methylation [203229450163_R01C01]

description: normal sperm sample


title: S256_DNA methylation [203229450156_R04C01]

description: normal sperm sample


title: S253_DNA methylation [203229450156_R01C01]

description: normal sperm sample


title: S251_DNA methylation [203229450149_R07C01]

description: normal sperm sample


title: S249_DNA methylation [203229450149_R05C01]

description: normal sperm sample


title: S250_DNA methylation [203229450149_R06C01]

description: normal sperm sample


title: S248_DNA methylation [203229450149_R04C01]

description: normal sperm sample


title: S246_DNA methylation [203229450149_R02C01]

description: normal sperm sample


title: S245_DNA methylation [203229450149_R01C01]

description: normal sperm sample


title: S247_DNA methylation [203229450149_R03C01]

description: normal sperm sample


title: S243_DNA methylation [203229450144_R07C01]

description: normal sperm sample


title: S244_DNA methylation [203229450144_R08C01]

description: normal sperm sample


title: S242_DNA methylation [203229450144_R06C01]

description: normal sperm sample


title: S241_DNA methylation [203229450144_R05C01]

description: normal sperm sample


title: S240_DNA methylation [203229450144_R04C01]

description: normal sperm sample


title: S239_DNA methylation [203229450144_R03C01]

description: normal sperm sample


title: S237_DNA methylation [203229450144_R01C01]

description: normal sperm sample


title: S257_DNA methylation [203229450156_R05C01]

description: normal sperm sample


title: S238_DNA methylation [203229450144_R02C01]

description: normal sperm sample


title: S233_DNA methylation [203229450137_R04C01]

description: normal sperm sample


title: S236_DNA methylation [203229450137_R08C01]

description: normal sperm sample


title: S227_DNA methylation [203229450132_R06C01]

description: normal sperm sample


title: S235_DNA methylation [203229450137_R07C01]

description: normal sperm sample


title: S231_DNA methylation [203229450137_R02C01]

description: normal sperm sample


title: S226_DNA methylation [203229450132_R05C01]

description: normal sperm sample


title: S234_DNA methylation [203229450137_R05C01]

description: normal sperm sample


title: S229_DNA methylation [203229450132_R08C01]

description: normal sperm sample


title: S232_DNA methylation [203229450137_R03C01]

description: normal sperm sample


title: S228_DNA methylation [203229450132_R07C01]

description: normal sperm sample


title: S230_DNA methylation [203229450137_R01C01]

description: normal sperm sample


title: S224_DNA methylation [203229450132_R03C01]

description: normal sperm sample


title: S252_DNA methylation [203229450149_R08C01]

description: normal sperm sample


title: S223_DNA methylation [203229450132_R02C01]

description: normal sperm sample


title: S225_DNA methylation [203229450132_R04C01]

description: normal sperm sample


title: S221_DNA methylation [203229450126_R08C01]

description: normal sperm sample


title: S222_DNA methylation [203229450132_R01C01]

description: normal sperm sample


title: S219_DNA methylation [203229450126_R06C01]

description: normal sperm sample


title: S220_DNA methylation [203229450126_R07C01]

description: normal sperm sample


title: S218_DNA methylation [203229450126_R05C01]

description: normal sperm sample


title: S215_DNA methylation [203229450126_R02C01]

description: normal sperm sample


title: S214_DNA methylation [203229450126_R01C01]

description: normal sperm sample


title: S213_DNA methylation [203229450108_R08C01]

description: normal sperm sample


title: S212_DNA methylation [203229450108_R07C01]

description: normal sperm sample


title: S210_DNA methylation [203229450108_R05C01]

description: normal sperm sample


title: S211_DNA methylation [203229450108_R06C01]

description: normal sperm sample


title: S208_DNA methylation [203229450108_R03C01]

description: normal sperm sample


title: S209_DNA methylation [203229450108_R04C01]

description: normal sperm sample


title: S200_DNA methylation [203229450095_R03C01]

description: normal sperm sample


title: S203_DNA methylation [203229450095_R06C01]

description: normal sperm sample


title: S204_DNA methylation [203229450095_R07C01]

description: normal sperm sample


title: S201_DNA methylation [203229450095_R04C01]

description: normal sperm sample


title: S207_DNA methylation [203229450108_R02C01]

description: normal sperm sample


title: S199_DNA methylation [203229450095_R02C01]

description: normal sperm sample


title: S206_DNA methylation [203229450108_R01C01]

description: normal sperm sample


title: S202_DNA methylation [203229450095_R05C01]

description: normal sperm sample


title: S195_DNA methylation [203229450079_R06C01]

description: normal sperm sample


title: S193_DNA methylation [203229450079_R04C01]

description: normal sperm sample


title: S216_DNA methylation [203229450126_R03C01]

description: normal sperm sample


title: S196_DNA methylation [203229450079_R07C01]

description: normal sperm sample


title: S194_DNA methylation [203229450079_R05C01]

description: normal sperm sample


title: S189_DNA methylation [203229450066_R08C01]

description: normal sperm sample


title: S191_DNA methylation [203229450079_R02C01]

description: normal sperm sample


title: S217_DNA methylation [203229450126_R04C01]

description: normal sperm sample


title: S186_DNA methylation [203229450066_R05C01]

description: normal sperm sample


title: S188_DNA methylation [203229450066_R07C01]

description: normal sperm sample


title: S185_DNA methylation [203229450066_R04C01]

description: normal sperm sample


title: S187_DNA methylation [203229450066_R06C01]

description: normal sperm sample


title: S184_DNA methylation [203229450066_R03C01]

description: normal sperm sample


title: S190_DNA methylation [203229450079_R01C01]

description: normal sperm sample


title: S205_DNA methylation [203229450095_R08C01]

description: normal sperm sample


title: S197_DNA methylation [203229450079_R08C01]

description: normal sperm sample


title: S183_DNA methylation [203229450066_R02C01]

description: normal sperm sample


title: S181_DNA methylation [203229450063_R08C01]

description: normal sperm sample


title: S179_DNA methylation [203229450063_R06C01]

description: normal sperm sample


title: S182_DNA methylation [203229450066_R01C01]

description: normal sperm sample


title: S180_DNA methylation [203229450063_R07C01]

description: normal sperm sample


title: S176_DNA methylation [203229450063_R03C01]

description: normal sperm sample


title: S178_DNA methylation [203229450063_R05C01]

description: normal sperm sample


title: S177_DNA methylation [203229450063_R04C01]

description: normal sperm sample


title: S174_DNA methylation [203229450063_R01C01]

description: normal sperm sample


title: S172_DNA methylation [203229450058_R07C01]

description: normal sperm sample


title: S175_DNA methylation [203229450063_R02C01]

description: normal sperm sample


title: S169_DNA methylation [203229450058_R04C01]

description: normal sperm sample


title: S167_DNA methylation [203229450058_R02C01]

description: normal sperm sample


title: S171_DNA methylation [203229450058_R06C01]

description: normal sperm sample


title: S170_DNA methylation [203229450058_R05C01]

description: normal sperm sample


title: S164_DNA methylation [203229450038_R07C01]

description: normal sperm sample


title: S168_DNA methylation [203229450058_R03C01]

description: normal sperm sample


title: S165_DNA methylation [203229450038_R08C01]

description: normal sperm sample


title: S173_DNA methylation [203229450058_R08C01]

description: normal sperm sample


title: S166_DNA methylation [203229450058_R01C01]

description: normal sperm sample


title: S163_DNA methylation [203229450038_R06C01]

description: normal sperm sample


title: S161_DNA methylation [203229450038_R04C01]

description: normal sperm sample


title: S158_DNA methylation [203229450038_R01C01]

description: normal sperm sample


title: S198_DNA methylation [203229450095_R01C01]

description: normal sperm sample


title: S162_DNA methylation [203229450038_R05C01]

description: normal sperm sample


title: S160_DNA methylation [203229450038_R03C01]

description: normal sperm sample


title: S157_DNA methylation [203229450035_R08C01]

description: normal sperm sample


title: S159_DNA methylation [203229450038_R02C01]

description: normal sperm sample


title: S156_DNA methylation [203229450035_R07C01]

description: normal sperm sample


title: S154_DNA methylation [203229450035_R05C01]

description: normal sperm sample


title: S155_DNA methylation [203229450035_R06C01]

description: normal sperm sample


title: S151_DNA methylation [203229450035_R02C01]

description: normal sperm sample


title: S143_DNA methylation [203229450006_R02C01]

description: normal sperm sample


title: S146_DNA methylation [203229450006_R05C01]

description: normal sperm sample


title: S148_DNA methylation [203229450006_R07C01]

description: normal sperm sample


title: S149_DNA methylation [203229450006_R08C01]

description: normal sperm sample


title: S144_DNA methylation [203229450006_R03C01]

description: normal sperm sample


title: S142_DNA methylation [203229450006_R01C01]

description: normal sperm sample


title: S141_DNA methylation [203229450004_R08C01]

description: normal sperm sample


title: S136_DNA methylation [203229450004_R03C01]

description: normal sperm sample


title: S153_DNA methylation [203229450035_R04C01]

description: normal sperm sample


title: S135_DNA methylation [203229450004_R02C01]

description: normal sperm sample


title: S150_DNA methylation [203229450035_R01C01]

description: normal sperm sample


title: S130_DNA methylation [203225140261_R05C01]

description: normal sperm sample


title: S127_DNA methylation [203225140261_R02C01]

description: normal sperm sample


title: S152_DNA methylation [203229450035_R03C01]

description: normal sperm sample


title: S124_DNA methylation [203225140231_R06C01]

description: normal sperm sample


title: S123_DNA methylation [203225140231_R05C01]

description: normal sperm sample


title: S147_DNA methylation [203229450006_R06C01]

description: normal sperm sample


title: S117_DNA methylation [203225140204_R07C01]

description: normal sperm sample


title: S145_DNA methylation [203229450006_R04C01]

description: normal sperm sample


title: S119_DNA methylation [203225140231_R01C01]

description: normal sperm sample


title: S140_DNA methylation [203229450004_R07C01]

description: normal sperm sample


title: S114_DNA methylation [203225140204_R04C01]

description: normal sperm sample


title: S112_DNA methylation [203225140204_R02C01]

description: normal sperm sample


title: S137_DNA methylation [203229450004_R04C01]

description: normal sperm sample


title: S134_DNA methylation [203229450004_R01C01]

description: normal sperm sample


title: S138_DNA methylation [203229450004_R05C01]

description: normal sperm sample


title: S132_DNA methylation [203225140261_R07C01]

description: normal sperm sample


title: S120_DNA methylation [203225140231_R02C01]

description: normal sperm sample


title: S108_DNA methylation [203225140202_R06C01]

description: normal sperm sample


title: S139_DNA methylation [203229450004_R06C01]

description: normal sperm sample


title: S131_DNA methylation [203225140261_R06C01]

description: normal sperm sample


title: S126_DNA methylation [203225140261_R01C01]

description: normal sperm sample


title: S107_DNA methylation [203225140202_R05C01]

description: normal sperm sample


title: S125_DNA methylation [203225140231_R07C01]

description: normal sperm sample


title: S104_DNA methylation [203225140202_R01C01]

description: normal sperm sample


title: S105_DNA methylation [203225140202_R02C01]

description: normal sperm sample


title: S118_DNA methylation [203225140204_R08C01]

description: normal sperm sample


title: S133_DNA methylation [203225140261_R08C01]

description: normal sperm sample


title: S129_DNA methylation [203225140261_R04C01]

description: normal sperm sample


title: S102_DNA methylation [203225140195_R07C01]

description: normal sperm sample


title: S121_DNA methylation [203225140231_R03C01]

description: normal sperm sample


title: S101_DNA methylation [203225140195_R06C01]

description: normal sperm sample


title: S100_DNA methylation [203225140195_R05C01]

description: normal sperm sample


title: S128_DNA methylation [203225140261_R03C01]

description: normal sperm sample


title: S99_DNA methylation [203225140195_R04C01]

description: normal sperm sample


title: S116_DNA methylation [203225140204_R06C01]

description: normal sperm sample


title: S98_DNA methylation [203225140195_R03C01]

description: normal sperm sample


title: S115_DNA methylation [203225140204_R05C01]

description: normal sperm sample


title: S113_DNA methylation [203225140204_R03C01]

description: normal sperm sample


title: S111_DNA methylation [203225140204_R01C01]

description: normal sperm sample


title: S97_DNA methylation [203225140195_R02C01]

description: normal sperm sample


title: S110_DNA methylation [203225140202_R08C01]

description: normal sperm sample


title: S94_DNA methylation [203225140189_R07C01]

description: normal sperm sample


title: S91_DNA methylation [203225140189_R04C01]

description: normal sperm sample


title: S90_DNA methylation [203225140189_R03C01]

description: normal sperm sample


title: S87_DNA methylation [203225140187_R08C01]

description: normal sperm sample


title: S85_DNA methylation [203225140187_R06C01]

description: normal sperm sample


title: S109_DNA methylation [203225140202_R07C01]

description: normal sperm sample


title: S83_DNA methylation [203225140187_R04C01]

description: normal sperm sample


title: S122_DNA methylation [203225140231_R04C01]

description: normal sperm sample


title: S80_DNA methylation [203225140187_R01C01]

description: normal sperm sample


title: S106_DNA methylation [203225140202_R03C01]

description: normal sperm sample


title: S103_DNA methylation [203225140195_R08C01]

description: normal sperm sample


title: S95_DNA methylation [203225140189_R08C01]

description: normal sperm sample


title: S72_DNA methylation [203225140152_R01C01]

description: normal sperm sample


title: S71_DNA methylation [203225140053_R08C01]

description: normal sperm sample


title: S192_DNA methylation [203229450079_R03C01]

description: normal sperm sample


title: S93_DNA methylation [203225140189_R06C01]

description: normal sperm sample


title: S96_DNA methylation [203225140195_R01C01]

description: normal sperm sample


title: S92_DNA methylation [203225140189_R05C01]

description: normal sperm sample


title: S64_DNA methylation [203225140053_R01C01]

description: normal sperm sample


title: S79_DNA methylation [203225140152_R08C01]

description: normal sperm sample


title: S88_DNA methylation [203225140189_R01C01]

description: normal sperm sample


title: S86_DNA methylation [203225140187_R07C01]

description: normal sperm sample


title: S62_DNA methylation [203225140021_R07C01]

description: normal sperm sample


title: S89_DNA methylation [203225140189_R02C01]

description: normal sperm sample


title: S61_DNA methylation [203225140021_R06C01]

description: normal sperm sample


title: S60_DNA methylation [203225140021_R05C01]

description: normal sperm sample


title: S84_DNA methylation [203225140187_R05C01]

description: normal sperm sample


title: S81_DNA methylation [203225140187_R02C01]

description: normal sperm sample


title: S82_DNA methylation [203225140187_R03C01]

description: normal sperm sample


title: S75_DNA methylation [203225140152_R04C01]

description: normal sperm sample


title: S77_DNA methylation [203225140152_R06C01]

description: normal sperm sample


title: S73_DNA methylation [203225140152_R02C01]

description: normal sperm sample


title: S65_DNA methylation [203225140053_R02C01]

description: normal sperm sample


title: S55_DNA methylation [203225140019_R08C01]

description: normal sperm sample


title: S54_DNA methylation [203225140019_R07C01]

description: normal sperm sample


title: S52_DNA methylation [203225140019_R05C01]

description: normal sperm sample


title: S50_DNA methylation [203225140019_R03C01]

description: normal sperm sample


title: S69_DNA methylation [203225140053_R06C01]

description: normal sperm sample


title: S68_DNA methylation [203225140053_R05C01]

description: normal sperm sample


title: S67_DNA methylation [203225140053_R04C01]

description: normal sperm sample


title: S66_DNA methylation [203225140053_R03C01]

description: normal sperm sample


title: S78_DNA methylation [203225140152_R07C01]

description: normal sperm sample


title: S63_DNA methylation [203225140021_R08C01]

description: normal sperm sample


title: S74_DNA methylation [203225140152_R03C01]

description: normal sperm sample


title: S76_DNA methylation [203225140152_R05C01]

description: normal sperm sample


title: S44_DNA methylation [203225140010_R05C01]

description: normal sperm sample


title: S59_DNA methylation [203225140021_R04C01]

description: normal sperm sample


title: S58_DNA methylation [203225140021_R03C01]

description: normal sperm sample


title: S38_DNA methylation [203219760222_R07C01]

description: normal sperm sample


title: S36_DNA methylation [203219760222_R05C01]

description: normal sperm sample


title: S35_DNA methylation [203219760222_R04C01]

description: normal sperm sample


title: S37_DNA methylation [203219760222_R06C01]

description: normal sperm sample


title: S57_DNA methylation [203225140021_R02C01]

description: normal sperm sample


title: S56_DNA methylation [203225140021_R01C01]

description: normal sperm sample


title: S53_DNA methylation [203225140019_R06C01]

description: normal sperm sample


title: S51_DNA methylation [203225140019_R04C01]

description: normal sperm sample


title: S33_DNA methylation [203219760222_R02C01]

description: normal sperm sample


title: S31_DNA methylation [203219760185_R08C01]

description: normal sperm sample


title: S29_DNA methylation [203219760185_R06C01]

description: normal sperm sample


title: S70_DNA methylation [203225140053_R07C01]

description: normal sperm sample


title: S48_DNA methylation [203225140019_R01C01]

description: normal sperm sample


title: S47_DNA methylation [203225140010_R08C01]

description: normal sperm sample


title: S41_DNA methylation [203225140010_R02C01]

description: normal sperm sample


title: S26_DNA methylation [203219760185_R02C01]

description: normal sperm sample


title: S46_DNA methylation [203225140010_R07C01]

description: normal sperm sample


title: S24_DNA methylation [203219760089_R08C01]

description: normal sperm sample


title: S19_DNA methylation [203219760089_R03C01]

description: normal sperm sample


title: S21_DNA methylation [203219760089_R05C01]

description: normal sperm sample


title: S17_DNA methylation [203219760089_R01C01]

description: normal sperm sample


title: S43_DNA methylation [203225140010_R04C01]

description: normal sperm sample


title: S42_DNA methylation [203225140010_R03C01]

description: normal sperm sample


title: S39_DNA methylation [203219760222_R08C01]

description: normal sperm sample


title: S27_DNA methylation [203219760185_R03C01]

description: normal sperm sample


title: S34_DNA methylation [203219760222_R03C01]

description: normal sperm sample


title: S13_DNA methylation [203219760078_R05C01]

description: normal sperm sample


title: S11_DNA methylation [203219760078_R03C01]

description: normal sperm sample


title: S45_DNA methylation [203225140010_R06C01]

description: normal sperm sample


title: S12_DNA methylation [203219760078_R04C01]

description: normal sperm sample


title: S8_DNA methylation [203219750111_R08C01]

description: normal sperm sample


title: S32_DNA methylation [203219760222_R01C01]

description: normal sperm sample


title: S28_DNA methylation [203219760185_R04C01]

description: normal sperm sample


title: S30_DNA methylation [203219760185_R07C01]

description: normal sperm sample


title: S40_DNA methylation [203225140010_R01C01]

description: normal sperm sample


title: S23_DNA methylation [203219760089_R07C01]

description: normal sperm sample


title: S22_DNA methylation [203219760089_R06C01]

description: normal sperm sample


title: S18_DNA methylation [203219760089_R02C01]

description: normal sperm sample


title: S15_DNA methylation [203219760078_R07C01]

description: normal sperm sample


title: S14_DNA methylation [203219760078_R06C01]

description: normal sperm sample


title: S10_DNA methylation [203219760078_R02C01]

description: normal sperm sample


title: AAV-IL2 Brain rep2

status: Public on Jun 10 2022

type: SRA

city: Cambridge

first: Adrian

last: Liston

address: Babraham Research Campus

country: United Kingdom

institute: The Babraham Institute

library_source: transcriptomic single cell

data_processing:
Step1:  BCL to FASTQ file converter: bcl2fastq v2.20.0.422
Step2: cellranger count (Cell Ranger V.3.1, 10x Genomics)
Step 3: Quality control in each sample (keeping genes expressed in ≥5 cells and cells with gene count ≥200). Further quality control (keeping cells with UMI counts≥500 and mitochondrial genes<20%) after merging all samples into one object using Seurat V3.1.4.
Genome_build: mm10
Supplementary_files_format_and_content: A matrix of raw UMI counts for each feature (i.e. gene; row) that are detected in each cell (column)  in each sample

molecule: total RNA

organism: Mus musculus

source_name: Brain

growth_protocol: mice were kept in semi-SPF cages for 12

extract_protocol:
CD4+CD45+CD11b- and CD45+CD11b+ cells were sorted using FACS Aria III
Library was performed using 10x Genomics Chromium Single Cell 3'kit, v2

treatment_protocol: mice were iv injected with 109 AAV PHP.B at least 14 days before the experiment

tag: strain

tag: treatment


title: S9_DNA methylation [203219760078_R01C01]

description: normal sperm sample


title: S25_DNA methylation [203219760185_R01C01]

description: normal sperm sample


title: S20_DNA methylation [203219760089_R04C01]

description: normal sperm sample


title: Wildtype Blood/Brain rep2

description: Wildtype

source_name: Blood/Brain


title: S7_DNA methylation [203219750111_R07C01]

description: normal sperm sample


title: Wildtype Brain rep1

description: Wildtype


title: Wildtype Brain rep2

description: Wildtype


title: S6_DNA methylation [203219750111_R06C01]

description: normal sperm sample


title: S16_DNA methylation [203219760078_R08C01]

description: normal sperm sample


title: sc-ATACseq_CD34+ cells - 24h_multipledonors

status: Public on May 26 2022

city: Paris

first: Andràs

last: Pàldi

state: Ile de France

address: 19 rue Chaligny

department: Centre de Recherche de Saint Antoine

country: France

institute: Ecole Pratique des Hautes Etudes

description: 10X scATAC-seq

library_source: genomic

data_processing:
Demultiplexing + Matrix generation with Cellranger (v6 pipeline version cellranger-atac-2.0.0)
R (version 4.1) & Seurat (version 4.1.1) & Signac (version 1.6.0) & GenomeInfoDb (version 1.32.2) & ggplot2 (version 3.3.6 ) & GenomicRanges (version 1.48.0)
Assembly: hg38 (GRCh38) or hg19 (GRCh37)
Conversion of hg38 peaks to hg19 peaks using R (version 4.1) and liftOver (version 1.20.0) package
Compare peaks from bulk analysis with single cell analysis
Supplementary files format and content: h5  file (cellranger-atac-2.0.0 output); filtered peak barcode matrix with detected cellular barcodes
Supplementary files format and content: csv file (cellranger-atac-2.0.0 output); per barcode QC
Supplementary files format and content: fragment file (cellranger-atac-2.0.0 output); chromosome, barcode, start and end position
Supplementary files format and content: peak bed file (cellranger-atac-2.0.0 output)
Supplementary files format and content: peak bed file (liftover conversion from hg38 peaks)
Supplementary files format and content: peak distribution per cell and cluster information

source_name: Umbilical cord blood

growth_protocol: CD34+ cells were purified from human healthy cord blood with a two-step immunomagnetic beads protocol and were then frozen in a cryopreservation medium. After thawing, CD34+ cells were cultured in a 96-well plate in a humidified 5% CO2 incubator at 37°C. Cells were grown in prestimulation medium made of X-Vivo (Lonza) supplemented with penicillin/streptomycin (respectively 100U/mL and 100µg/mL - Gibco, Thermo Scientific), 50 ng/ml h-FLT3, 25 ng/ml h-SCF, 25 ng/ml h-TPO, 10 ng/ml h-IL3 (Miltenyi) final concentration.

extract_protocol:
High viability percentage was obtained using a Dead Cell Removal kit (Miltenyi). scATACseq was then performed as described in the 10X Genomics protocol with Chromium Next GEM Single Cell ATAC-seq Kit v1.1. 15 000 nuclei were isolated and loaded on the chip to obtain around 5814 nuclei encapsidated in GEM.
Library was prepared following the 10X Genomics protocol, controled with Qubit quantification and sequenced on a Novaseq6000.

treatment_protocol: Cells were stimulated with cytokines after thawing and were grown in the same medium until lysis was performed. Cells were collected and lysed after 24h of cytokine stimulation.

value: Blood

tag: disease state

value: Healthy

value: Untreated


title: S4_DNA methylation [203219750111_R04C01]

description: normal sperm sample


title: S3_DNA methylation [203219750111_R03C01]

description: normal sperm sample


title: S5_DNA methylation [203219750111_R05C01]

description: normal sperm sample


title: Sample 16_Dbx1-derived preBötC neuron

status: Public on Feb 10 2022

city: Williamsburg

first: Prajkta

middle: S

last: Kallurkar

state: VA

address: 540 Landrum Dr, Integrated Science Center 3

institute: William & Mary

data_processing:
The quality of reads was verified using FastQC v0.11.8 (Andrews 2015). Samples with less than 50,000 reads were discarded (n = 1: Sample 10).
Adapter reads (Read 1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA, Read 2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT) were trimmed using bbduk v38.00 (https://sourceforge.net/projects/bbmap/) using the following command: sh bbduk.sh in1=inputFASTQFile1.fastq. in2=inputFASTQFile2.fastq out1=outputFASTQFile1.fastq out2=outputFASTQFile2.fastq ktrim=r -Xmx27g mm=f k=33 hdist=1 literal=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT tbo tpe
We used SMART-Seq HT kit that uses dT priming for first-strand cDNA synthesis, annealing to the polyA tails, thus the sequencing reads contained the poly T/A overrepresented sequences. These overrepresented sequences, identified by FASTQC, were trimmed using cutAdapt v3.2 (Martin 2011) using the following command: cutadapt -a overrepresentedSequence -A overrepresentedSequence’ -o outputFASTQFile1.fastq -p outputFASTQFile2.fastq inputFASTQFile1.fastq inputFASTQFile2.fastq -m 10 -j 4
The mouse reference genome, mm10 from Ensembl, was used to create genome directory for aligning the reads in STAR (Dobin et al. 2013) using the following commands: STAR --runMode genomeGenerate --genomeDir mm10ReferenceGenome --genomeFastaFiles Mus_musculus.GRCm38.dna.primary_assembly.fa --sjdbGTFfile Mus_musculus.GRCm38.102.gtf --sjdbOverhang 149 --genomeSAsparseD 2
The sequences were then aligned to mm10 reference genome using STAR v2.7.7a (Dobin et al. 2013) using the following command: STAR --genomeDir mm10ReferenceGenome --readFilesIn inputFASTQFile1.fastq inputFASTQFile2.fastq --outFileNamePrefix outputBAMFile --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx
The uniquely aligned sequences were then quatified to fragment counts using featureCounts from the Rsubread package v2.4.2 in R (Liao, Smyth, and Shi 2014; 2019). The fragment counts were normalized to FPKM values for all the sample using custom R scripts.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file containing fragment counts for all the samples, except Sample 10.
Supplementary_files_format_and_content: tab-delimited text file with gene length
Supplementary_files_format_and_content: tab-delimited text file containing FPKM for all the samples, except Sample 10.

source_name: preBötC in the brainstem

growth_protocol: All experiments employed mice with Cre-dependent expression of fluorescent Ca2+ indicator GCaMP6f, dubbed Ai148, by the Allen Institute (RRID: IMSR_JAX:030328, Daigle et al. 2018). To identify Dbx1 preBötC neurons, we crossed Dbx1cre mice with Ai148 mice. We used their offspring, referred to as Dbx1; Ai148 mice (P0-2). All animals were C57Bl/6J or mixed C57Bl/6J; CD1 genetic background. Dbx1; Ai148 pups have fluorescent labeling in Dbx1-derived preBötC neurons. Dbx1 preBötC inspiratory neurons were selected visually based on rhythmic fluorescence changes.

extract_protocol:
The cellular contents of the neuron were extracted by applying gentle negative pressure (0.7-1.5 psi). The patch pipette was quickly retracted, and the extracted cellular contents were ejected by breaking the tip of the pipette at the bottom of the RNase-free PCR tube containing 4 µL nuclease-free water with 2% RRI. The extracted RNA from patch-clamped neurons was converted to cDNA according to the SMART-seq HT protocol (Takara Bio, USA).  First, samples were denatured at 72 ˚C for 3 min. poly(A)+ RNA was reverse transcribed using a tailed oligo(dT) primer. First strand cDNA synthesis and double-stranded cDNA amplification were performed in a heated thermal cycler using the following program: 42 °C for 90 min; 95 °C for 1 min; 18 cycles of 98 °C for 10 s, 65 °C for 30 s, 68 °C for 3 min; 72 °C for 10 min. PCR-amplified cDNA was then purified by immobilization on Agencourt AMPure XP beads (Beckman Coulter, CA), which was then washed with 80% ethanol and eluted with elution buffer.
Once full-length cDNA was synthesized, libraries for sequencing were prepared using the SMART-seq PLUS kit (Takara Bio USA, CA), which uses Takara Bio’s patented library preparation utilizing stem-lop adapters to construct high-quality libraries. Unique dual indexes were used on the amplified libraries. Quality control was performed on both, the amplified cDNA and the final library using a Bioanalyzer High Sensitivity kit (Agilent, Santa Clara, CA) and Qubit dsDNA High-sensitivity Assay Kit (Molecular Probes, Eugene, OR). cDNA samples containing less than 150 pg/µl cDNA were not sequenced. The cDNA libraries were sequenced using an Illumina HiSeq X Sequencing system with paired end (150 bp) reads. Investigators were blinded to cell type during library construction and sequencing.

treatment_protocol: Patch pipettes, of resistance 3-5 MΩ, were fabricated from autoclaved borosilicate glass electrodes (OD: 1.5 mm, ID: 0.86 mm). The patch pipette was filled with an internal solution containing (in mM): 123 K-gluconate, 12 KCl, 10 HEPES, 0.2 EGTA, 4 Mg-ATP, 0.3 Na-GTP, 10 Na2-phosphocreatine, and 13 Glycogen. 0.8% Recombinant Ribonuclease Inhibitor (RRI) was added to the internal solution right before the experiment, to preserve the RNA of the cell. Whole-cell patch-clamp recordings were made using an EPC-10 patch-clamp amplifier (HEKA Instruments, Germany).

value: brainstem

tag: age

tag: electrophysiological phenotype

tag: cell type


title: Sample 17_Dbx1-derived preBötC neuron


title: AAV-IL2 Blood/Brain rep2


title: AAV-IL2 Brain rep1


title: AAV-IL2 Blood/Brain rep1


title: Sample 18_Dbx1-derived preBötC neuron


title: input_PMH

status: Public on May 09 2022

city: Rehovot

first: Ido

last: Goldstein

address: POB 12

department: Institute of Biochemistry, Food Science and Nutrition

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Binary Base Call (BCL) output files from a Nextseq 500 machine were converted to FASTQ format, using BCL to FASTQ (bcl2fastq v2.20.0.422 Copyright (c) 2007-2017 Illumina, Inc.).
Fastq files were mapped to the mm10 mouse genome assembly using Bowtie2
Genome_build: mm10

source_name: hepatocytes

growth_protocol: as described in PMID: 33111119

extract_protocol:
RNA: Total RNA was isolated from primary mouse hepatocytes using NucleoSpin kit (Macherey-Nagel cat# 740955.25) according to the manufacturer’s protocol. ChIP: cells were cross-linked with 1% formaldehyde for 10 min at room temperature and quenched with 0.125M glycine. Crosslinked samples were washed in PBS, resuspended in ChIP lysis buffer (0.5% SDS, 10mM EDTA, 50mM Tris-HCl pH8) and sonicated (Bioruptor, Diagenode) to release 100-1000 bp fragments. Antibodies (4 μg per 300 μg chromatin) against H3K27ac (Active motif #39133) or GR (CST #3660) were conjugated to magnetic beads (Sera-Mag, Merck #GE17152104010150) for 2 h at 4°C. Chromatin was immunoprecipitated with antibody-bead conjugates over night at 4°C. Immunocomplexes were washed sequentially with the following buffers: low-salt buffer (0.01% SDS, 1% Triton x-100, 2 mM EDTA, 20mM Tris-HCl pH8, 150mM NaCl), high salt buffer (0.01% SDS, 1% Triton x-100, 2mM EDTA, 20mM Tris-HCl pH8, 500mM NaCl), low salt buffer and TE buffer (10mMTris-HCl, 1mM EDTA pH8). Chromatin was de-proteinized with proteinase K (Hy Labs EPR9016) for 2 h at 55°C and de-crosslinked over night at 65°C. DNA was subsequently phenol-chloroform purified and ethanol precipitated
For quality control of RNA yield and library synthesis products, the RNA ScreenTape and D1000 ScreenTape kits (both from Agilent Technologies), Qubit® RNA HS Assay kit, and Qubit® DNA HS Assay kit (both from Invitrogen) were used for each specific step. mRNA libraries were prepared from 1 µg RNA using the KAPA Stranded mRNA-Seq Kit, with mRNA Capture Beads (KAPA biosystems, cat# KK8421). ChIP DNA libraries were prepared using the KAPA HyperPrep Kit (KAPA biosystems, cat# KR0961).

treatment_protocol: Cells were treated with glucagon (100nM) and corticosterone (1 µM) for 3h (RNA-seq) or 1h (ChIP-seq)

value: liver

value: hepatocytes


title: Sample 15_Dbx1-derived preBötC neuron


title: S2_DNA methylation [203219750111_R02C01]

description: normal sperm sample


title: S1_DNA methylation [203219750111_R01C01]

description: normal sperm sample


title: Sample 9_Dbx1-derived preBötC neuron


title: Sample 10_Dbx1-derived preBötC neuron


title: Sample 8_Dbx1-derived preBötC neuron

value: Unknown


title: Sample 5_Dbx1-derived preBötC neuron


title: Sample 13_Dbx1-derived preBötC neuron


title: Sample 1_Dbx1-derived preBötC neuron


title: Sample 12_Dbx1-derived preBötC neuron


title: P4, A1 and A2 cells

status: Public on Jan 26 2022

city: Freiburg

first: Roman

last: Sankowski

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University of Freiburg Medical Center

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software 2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34,111 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Genome_build: ENCODE VM9
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.
Supplementary_files_format_and_content: celseq_barcodes.192.txt (192 Cel-Seq2 Barcodes)
Supplementary_files_format_and_content: counts.csv (concatenated counts file, negative binomially corrected)
Supplementary_files_format_and_content: all.Rdata (analyzed Seurat object)
Supplementary_files_format_and_content: Taka_A1_A2_only.zip (R project with script and data. The folder contains an R project that can be opened in Rstudio as a standalone project. More information can be found in the contained README.md file and on Github under: https://github.com/rsankowski/Taka_A1_A2_only)
Supplementary_files_format_and_content: coutt.csv (transcript counts file, negative binomially corrected (as described in Gruen et al, Nat methods 2017))

source_name: extraembryonic YS

growth_protocol: SPF breeding facility

extract_protocol:
Isolated myeloid cells were stained with antibodies for CD45 and CD11b. All CD45+ cells were FACS-sorted in 384-well plates.
As described in mCEL-Seq2 protocol (Hashimshony et al. 2016 and Herman et al. 2018)
Adapted from TruSeq Small RNA Library Preparation Protocol

tag: genotype

value: wild type

value: extraembryonic YS

value: A1 and A2 cells

tag: batch

value: A


title: Wildtype Blood/Brain rep1

description: Wildtype


title: P3, EMP cells

description: EMP_cells (not used in paper but run concomitantly, these counts should be loaded exact in the attached R project, if exactly the same clustering results are desired)

value: EMP cells


title: Sample 11_Dbx1-derived preBötC neuron


title: P2, A1 and A2 cells


title: Sample 4_Dbx1-derived preBötC neuron


title: Sample 7_Dbx1-derived preBötC neuron


title: Sample 2_Dbx1-derived preBötC neuron


title: Sample 3_Dbx1-derived preBötC neuron


title: Ag24h2

status: Public on Jan 24 2022

city: Durham

first: Shane

middle: Mitchell

last: O'Neil

state: NC

address: 701 W Main St

department: Neuroscience

institute: Duke University

description:
L
scRNA-Seq

data_processing:
Fastq files were processed using the standard 10X genomics Cell Ranger pipeline.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: allCells.rds: Normalized read data for all samples combined (annotated as "orig.ident").

molecule: polyA RNA

source_name: hippocampus

extract_protocol:
Hippocampi were dissected after transcardial perfusion with ice-cold phosphate-buffered saline (pH 7.4) and dissociated using the Adult Brain Dissociation Kit (Miltenyi Biotec) according to manufacturer’s instructions.
Libraries were constructed using the 10X Genomics Chromium Single Cell 3’ v3 reagents kit.
NovaSeq S4 v1.5. Paired-end 150-bp.

treatment_protocol: Mice were administered an intraperitoneal injection of saline or 0.33mg/kg lipopolysaccharide 4 or 24 hours prior to tissue extraction.

value: BALB/c

value: hippocampus

value: 18 months

value: 0.33 mg/kg lipopolysaccharide

tag: time after injection


title: S49_DNA methylation [203225140019_R02C01]

description: normal sperm sample

value: sperm

value: normal


title: P4, EMP cells


title: AdSal2

description:
G
scRNA-Seq

value: 2 months

value: saline

value: 4 h


title: Sample 14_Dbx1-derived preBötC neuron

value: brainstem


title: P3, A1 and A2 cells


title: P2, EMP cells


title: Ad24h1

description:
E
scRNA-Seq


title: P1, A1 and A2 cells


title: Ad04h2

description:
I
scRNA-Seq


title: Ad24h2

description:
K
scRNA-Seq


title: AgSal2

description:
H
scRNA-Seq


title: Ag04h2

description:
J
scRNA-Seq


title: P1, EMP cells


title: Ag24h1

description:
F
scRNA-Seq


title: Sample 6_Dbx1-derived preBötC neuron


title: Ag04h1

description:
D
scRNA-Seq


title: WT_rep6_smRNA-seq

status: Public on Dec 05 2021

city: La Jolla

first: Julie

middle: Ann

last: Law

state: CA

address: 10010 North Torrey Pines Rd

department: PLANT MOLECULAR AND CELLULAR BIOLOGY LABORATORY

institute: The Salk Institute for Biological Studies

library_source: transcriptomic

data_processing:
Illumina Casava software used for basecalling and demultiplexing.
Read Filtering, Mapping, and cluster calling: The adapters were removed from the de-multiplexed reads using cutadapt (v1.9.1) and trimmed reads longer that 15nt were mapped to the TAIR10 genome using ShortStack (v3.8.1) with the following options: --mismatches 1 and either --mmap f, to include multi-mapping reads, or --mmap n, to include only unique mapping reads. Only perfectly matched read or reads with a single 3’ mismatch were used to call smRNA clusters using ShortStack with the --mincov 20, --pad 100, --dicermin 21 and dicermax 24 options, to generate Tag Directories using the using the makeTagDirectory script from the HOMER with the -format sam -mis 1 and -keepAll options, and to make genome browser tracks specifically for the 24nt sized smRNAs using the makeUCSCfile script from HOMER with the -fragLength 24 and -norm 10000000 options.
TAIR10
Supplementary_files_format_and_content: bedGraph file, including header and chr#, start position, end position and normalized value (rp10M).

organism: Arabidopsis thaliana

source_name: stage 12 and younger flower buds (Fl)

growth_protocol: Growth conditions and tissue collection for 15 day old aerial rosettes (Ar) and 25 day old leaves (Lv) for all genotypes were as follows: seeds were sterilized with bleach and plated on half strength Linsmaier and Skoog medium (1/2 LS) supplemented with 1% agar. After three days stratification in the dark at 4℃, plants were grown in the Percival growth chamber (GCU-36L5) under 16h-light and 8h-dark cycle at 22℃ for 7 days and then were transplanted onto soil in Salk’s green house with long day conditions. At day 15 and day 25 of total growth, aerial rosette tissue (whole seedling without roots) or the first and second true leaves (without petioles) were collected from~40 plants as the Ar and Lv samples, respectively, immediately frozen in liquid nitrogen, and kept at -80°C until use. Growth conditions and tissue collection for mature, unfertilized ovules (Ov) were as follows: seeds were grown from soil in Salk’s greenhouse with long day conditions and un-opened flower buds (stage 10-12) were dissected to obtain carpels using a tweezer and then fixed on a double-side tape on a glass slide. Subsequently, carpels were dissected under dissection microscope using a needle and ovules were collected with the vacuum-based micro-aspiration device as detailed below. After collection, ovules for RNA extraction were quickly mixed with 100 µL trizol (Invitrogen, Cat# 15596018), flash frozen in liquid nitrogen and preserved at -80℃ until use, while ovules for DNA preparation were preserved in the same way without trizol. For each genotype, > 300 carpels were dissected and over 10,000 ovules were collected.

extract_protocol:
Total RNAs were isolated using Trizol reagent (Life Tech, Cat# 15596018) following the manual and dissolved in 250μL RNase-free water. 2.0 µg of total RNA from Ar and Lv tissues, or ~0.5ug of total RNA from Ov, were used for smRNA enrichment through a polyethylene glycol (PEG) precipitation step. One volume of a 20% PEG 8000/2M NaCl solution was added to each RNA sample, mixed well and kept on ice for more than 30 minutes (min) and then centrifuged at 13,000rpm for 15min at 4°C. The supernatant, containing the small RNAs, was collected and precipitated with 1 volume of cold isopropanol, mixed and incubated on ice for 30min. Then the small RNA samples were recovered by centrifuged at 13,000rpm for 30min at 4°C. The resulting small RNA samples were run on 15% polyacrylamide-8M urea gels and performed size-selection of fragments from 17-29 nucleotide (nt) following the ZR-small RNA ladder (zymo research, Cat# R1090). The small RNAs in the gels were recovered by incubating with 0.3M NaCl overnight, filtering the gels and add 2.5 volumes of 100% ethanol and 3μL of glycogen for precipitation over 2 hours (h) at -80°C.
The small RNAs were used for library preparation with the NEBnext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Cat# E7300) following the user’s manual. The final library products were further purified using an 8% polyacrylamide gel to excise 130-160nt products relative to the pBR322 DNA-MspI Digest ladder (New England Biolabs, Cat# E7323AA). The purified libraries were pooled and sequenced (single end 50 bp, SE50) on a HiSeq 2500 machine (Illumina).

tag: ecotype

value: Columbia

tag: tissues

value: stage 12 and younger flower buds (Fl)

value: wild-type


title: WT_rep5_smRNA-seq


title: Ad04h1

description:
C
scRNA-Seq


title: WT_rep3_reseq_smRNA-seq


title: WT_rep1_reseq_smRNA-seq


title: AgSal1

description:
B
scRNA-Seq


title: AdSal1

description:
A
scRNA-Seq


title: WT 10D-Vector NPC

status: Public on Dec 01 2021

first: Yan

last: Liang

address: 9500 Gilman Drive, BRFII Room 1220 Bay B

institute: UC San Diego

data_processing:
Sequenced reads were processed using CellRanger package (v3.0.2) with default parameters.
Genome_build: GRCm38; GRCm38 + human MYC gene
Supplementary_files_format_and_content: h5 files with raw counts for every gene and every cell

source_name: Liver

extract_protocol:
Mouse liver was perfused with collagenase H (Roche). Hepatocytes and non-parenchymal cells were separated by centrifugation.
Chromium Single Cell 3’ Reagent Kits (V2 chemistry, 10x Genomics)

treatment_protocol: Tumor models were generated by hydrodynamic tail vein injection (HTVi) using a ratio of 10:1 for DNA plasmid to sleeping beauty transposase.

value: WT

value: Non-parenchymal cells

tag: htvi injection

value: 10 days after vector injection


title: SKO 0D-Ctrl Hep

value: SKO

value: Hepatocytes

value: Control


title: WT_rep4_smRNA-seq


title: WT 0D-Ctrl NPC


title: WT 0D-Ctrl Hep


title: SKO 10D-Vector NPC


title: WT_rep2_reseq_smRNA-seq


title: WT 10D-Myc Hep

value: 10 days after Myc injection


title: SKO 10D-Myc NPC


title: WT 4W-Myc NPC rep2

value: 4 weeks after Myc injection


title: WT 10D-Vector Hep


title: WT 4W-Myc Hep rep1


title: SKO 0D-Ctrl NPC


title: SKO 10D-Vector Hep


title: CP-Rep1

status: Public on Apr 21 2021

city: Honolulu

first: Sladjana

last: Prisic

state: HI

address: 1800 East-West Rd

institute: University of Hawaii

data_processing:
fastQC of raw reads in .fastq format
trimmomatic to remove adapter sequences, trim ends and revove reads with low quality scores
bowtie2 for alignment of trimmed files to Mtb genome
featureCounts to define tagwise abundances from BAM files (Bowtie2)
Genome_build: Mycobacterium tuberculosis H37Rv, Mycobrowser, R3
Supplementary_files_format_and_content: Text (.csv) files of gene abundances from featureCounts

organism: Mycobacterium tuberculosis

source_name: 0.35mg/mL CP

growth_protocol: Mtb were grown in 7H9-ADC broth until mid-log phase (OD600 ~0.8). Cultures were centrifuged and the pellets were resuspended in Sauton's medium without added Zn2+ and grown for 4 days at 37°C with 120rpm.

extract_protocol:
Treatments were centrifuged at 4°C, and cell pellets were resuspended in TRIzol. TRIzol extractions were homogenized by bead beating and RNA was extracting following the manufacturer's protocol.
Ribosomal RNA was depleted from the samples using Ribo-Zero plus rRNA depletion kit (Illumina®, Cat. #:20037135) before being sequenced on an Illumina® HiSeq platform for generation of 150 base pair paired end reads. RNA sequencing (RNAseq) was performed by GENEWIZ® (South Plainfield, NJ 07080).

treatment_protocol: 4 day old cultures in Sauton's without Zn2+ were centrifuged and resuspended in Sauton's medium with 500μM Zn2+, 6μM Zn2+, no added Zn2+, 0.35mg/mL recombinant CP, and 0.8μM TPEN, each in biological triplicate. Treatments were incubated at 37°C with 120rpm for 24hrs.


title: WT 10D-Myc NPC


title: WT 4W-Myc NPC rep1


title: SKO 10D-Myc Hep


title: FT-SA23508

status: Public on Apr 19 2021

city: San Antonio

first: Kate

last: Lawrenson

address: 7703 Floyd Curl Dr.

institute: Cedars Sinai Medical Center

data_processing:
Raw reads were aligned to the hg38 reference genome, UMI (unique molecular identifier) counting was performed using Cell Ranger v.2.1.1 (10X Genomics)
Genome_build: hg38
Supplementary_files_format_and_content: HDF5 Feature Barcode Matrix Format

source_name: Fallopian tube (Ampulla) from patient 6

extract_protocol:
Primary fallopian tubes were processed into single cells and were barcoded using 10x Chromium platform. Barcoded RNA was extracted using 10x Chromium Single Cell 3ʹ Reagent Kits User Guide (v2 or v3)
10x Chromium Single Cell 3ʹ Reagent Kits User Guide (v2 or v3)
RNA-Seq (size fractionation)

tag: tissue

value: Fallopian tube (Ampulla)

tag: individual

value: patient 6

value: cancer-free


title: WT 4W-Myc Hep rep2


title: FT-SA23515

source_name: Fallopian tube (Fimbria) from patient 7

value: Fallopian tube (Fimbria)

value: patient 7


title: SKO 4W-Myc NPC


title: FT3

source_name: Fallopian tube (Ampulla) from patient 3

value: patient 3


title: FT5414

source_name: Fallopian tube from patient 2

value: Fallopian tube

value: patient 2


title: SKO 4W-Myc Hep


title: COVID-19 Sample 14

status: Public on Mar 15 2021

city: Saarbrücken

first: Fabian

middle: Michael

last: Kern

state: Saarland

address: Campus E2 1

department: Center for Bioinformatics

institute: Saarland University

description:
single-nuclei RNA
CP_90

data_processing:
Raw reads were processed using the CellRanger software (v4.0.0) provided by 10x Genomics. We generated an intronic-aware reference genome (v. refdata-gex-GRCh38-2020-A) according to the official recommendations of 10x genomics in order to count the substantial amount of intronic reads in snRNA-seq as exonic reads. The number of nuclei for each sample was determined using the cellranger count command.
Genome_build: GRCh38
Supplementary_files_format_and_content: Output of Cellranger count command; For each sample three files are provided containing the filtered cell-barcodes, the mapped reference features, and the raw counts: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz.

source_name: Choroid Plexus

extract_protocol:
Frozen medial frontal cortex tissue from post-mortem control and COVID-19 patients were obtained from the Stanford/ VA/ NIA Aging Clinical Research Center (ACRC) and the Saarland University Hospital Institute for Neuropathology, with approval from local ethics committees. The protocol for the isolation of nuclei was adapted from previous studies, and performed in a BSL2+ Biosafety Cabinet wearing PPE (Mathys et al., Nature 2019). All procedures were carried out on ice or at 4°C. Briefly, 50 mg of post-mortem brain tissue was dounce homogenized in 2 ml of Nuclei EZ Prep Lysis Buffer (Sigma, NUC101) spiked with 0.2 U μl−1 RNase inhibitor (Takara, 2313A) and EDTA-free Protease Inhibitor Cocktail (Roche, 11873580001) before incubating on ice for 5 min in a final volume of 5 ml. Homogenized tissue was filtered through a 100-μm cell strainer (Falcon, 352360), mixed with an equal volume of 50% iodixanol density gradient medium in PBS (OptiPrep, Sigma-Aldrich, D1556) to make a final concentration of 25% iodixanol. 30% iodixanol was layered underneath the 25% mixture. Similarly, 40% iodixanol was layered underneath the 30% iodixanol. In a swinging-bucket centrifuge, nuclei were centrifuged for 20 min at 3,000 r.c.f. After centrifugation, the nuclei were present at the interface of the 30% and 40% iodixanol solutions. Isolated nuclei were resuspended in 1% BSA with 0.2 U μl−1 RNase inhibitor, filtered twice through a 40 μm strainer (Flowmi), and counted on an TC20 automated cell counter (Bio-Rad) after the addition of Trypan Blue.    Frozen choroid plexus tissue was extracted from the lateral ventricles of post-mortem tissue obtained from the Stanford University Pathology department and the Saarland University Hospital Institute for Neuropathology, with approval from local ethics committees. All procedures were carried out on ice or at 4°C, and in a BSL2+ Biosafety Cabinet wearing PPE. Dounce homogenization or enzymatic dissociation successfully used for mice choroid plexi (Dani et al., bioRxiv 2019) resulted in loss of nuclei integrity and low nuclei complexity (<50 median genes/ nuclei). We hypothesized that like shaking an apple tree, gentle pipetting of choroid plexi tissue in lysis buffer could liberate nuclei without needing to physically disintegrate the fibrous choroid matrix—and thus avoid collateral physical damage to nuclei. Specifically, 40 mg sof choroid plexus tissue was thawed in 250 μl of 1% BSA with 0.2 U μl−1 RNase inhibitor until the tissue settled. 5 ml of lysis buffer (10 mM Tris, 10 mM NaCl, 3 mM MgCl2, 0.1% Nonidet P40 substitute (Roche/ Sigma, 11754599001), 0.2 U μl−1 RNase inhibitor, and protease inhibitor) was added and tissue incubated on ice for 10 minutes with gentle swirling every 2 minutes. 5 ml of 1% BSA was added and the tissue triturated 10 times with a 5 ml serological pipette. After centrifugation (500g, 5 min), pelleted nuclei were resuspended in 1% BSA with 0.2 U μl−1 RNase inhibitor; gently triturated 10 times with a 1 ml regular-bore pipette tip; and filtered twice through a 70 μm and then a 40 μm strainer (Flowmi). Debris was inspected on a brightfield microscope and nuclei were counted on an TC20 automated cell counter (Bio-Rad) after the addition of Trypan Blue.
For droplet-based snRNA-seq, libraries were prepared using the Chromium Next GEM Single Cell 3ʹ v3.1 according to the manufacturer’s protocol (10x Genomics), targeting 10,000 nuclei per sample after counting with a TC20 Automated Cell Counter (Bio-Rad). 13 cycles were applied to brain parenchyma samples to generate cDNA, and 15 for choroid plexus samples. All samples underwent 15-16 cycles for final library generation. Generated snRNA-seq libraries were sequenced across two S4 lanes on a NovaSeq 6000 (150 cycles, Novogene).
10X scRNA-seq, v3.1 chemistry

tag: preparation method

value: Lateral ventricles

tag: patient id

tag: nuclei count

tag: Sex

value: M

tag: Cause of death

value: COVID-19, Interstitial pneumonia, hypovolemic shock

tag: post-mortem interval

tag: biogroup

value: Case

tag: disease group


title: COVID-19 Sample 13

description:
single-nuclei RNA
CP_78

tag: age

value: COVID-19, Interstitial pneumonia, dilated heart disease


title: COVID-19 Sample 15

description:
single-nuclei RNA
CP_91

value: F

value: COVID-19, Hypovolemic shock because of aneurysma dissecans of the aorta and acute rupture of the aneurysm


title: CP-Rep3

tag: strain


title: COVID-19 Sample 12

description:
single-nuclei RNA
CTX_91

source_name: Medial prefrontal cortex

value: Parenchymal

tag: batch


title: CP-Rep2


title: 6uM_Zn-Rep3

source_name: 6μM Zn2+


title: 6uM_Zn-Rep2


title: Control Sample 13

description:
single-nuclei RNA
CT_02_11

value: Myocardial infarction

value: Control

value: Non-viral


title: Control Sample 12

description:
single-nuclei RNA
CT_02_01

value: Tongue cancer, metastasis to the neck and lung


title: Control Sample 11

description:
single-nuclei RNA
CT_01_07

value: End stage heart disease


title: FT-SA23509

source_name: Fallopian tube (Infundibulum) from patient 6

value: Fallopian tube (Infundibulum)

value: patient 6

tag: disease state

value: cancer-free


title: 6uM_Zn-Rep1


title: FT-SA23514

source_name: Fallopian tube from patient 7

value: Fallopian tube

value: patient 7


title: R47H - female - IgG - rep3

status: Public on Dec 08 2020

city: South San Francisco

first: Daniel

middle: C

last: Ellwanger

address: 1120 Veterans Blvd

department: Genome Analysis Unit

institute: Amgen Inc

data_processing:
A reference genome was generated by extending mouse mm10 by human TREM2 from GRCh38. Transcriptome annotations from Ensembl 93 (https://www.ensembl.org/) were used. Sequenced reads from the microfluidic droplet platform were de-multiplexed and aligned using CellRanger version 3.0.2, available from 10x Genomics (www.10xgenomics.com), with default parameters.
All samples passed an initial read alignment quality control evaluating the genomic read distribution. For each sample, individual cells were distinguished from empty droplets using thresholding on the total UMI count. Cells were further filtered on a per-sample basis by assessing the distributions of the total number of reads per barcode, the fraction of reads mapped to mitochondrial genes per barcode, the total number of UMI per barcode, the total number of genes with at least one UMI count per barcode, the fraction of reads originating from an already-observed UMI and their interrelations. For further details, please refer to Sample_quality_reports.xlsx and the original publication.
Genome_build: mm10 w/ human TREM2 (GRCh38)
Supplementary_files_format_and_content: RAW.mtx contains the raw UMI count matrix of all samples with genes in rows and cells in columns, Cell_metadata.tsv contains metainformation of all samples with cells in rows and labels in columns, Feature_metadata.tsv contains metainformation of all measured features with features in rows and labels in columns, *_metadata-README.txt contains descriptions of each metadata label, RAW-*.tsv contains the raw UMI count matrix of an individual sample with genes in rows and cells in columns.

source_name: cortical CD45+ cells

extract_protocol:
After perfusion by cold PBS, cortices were dissociated, and CD45+ cells were sorted using FACS.
All Cd45+ cell libraries were prepared using the 10X Chromium Single Cell 3' v2 Gene Expression Kit.

treatment_protocol: 8-month old mice were injected i.p. with hT2AB or hIgG at 30 mg/kg 48 h before sacrifice.

tag: genotype

value: cortex

value: 8 months

tag: treatment

value: IgG

value: female

tag: cell type


title: R47H - male - IgG - rep3

tag: tissue

value: male


title: R47H - male - IgG - rep2


title: R47H - female - IgG - rep2


title: FT-SA23513

source_name: Fallopian tube from patient 4

tag: individual

value: patient 4


title: FT-SA23510

source_name: Fallopian tube (Fimbria) from patient 6

value: Fallopian tube (Fimbria)


title: FT1

source_name: Fallopian tube from patient 1

value: patient 1


title: COVID-19 Sample 11

description:
single-nuclei RNA
CTX_90

tag: preparation method

value: Parenchymal

value: M

value: COVID-19, Interstitial pneumonia, hypovolemic shock

value: Case


title: KO - female - IgG - rep3


title: KO - female - IgG - rep1


title: COVID-19 Sample 10

description:
single-nuclei RNA
CTX_78

tag: patient id

value: COVID-19, Interstitial pneumonia, dilated heart disease


title: KO - female - hT2AB - rep2


title: FT-SA24027

source_name: Fallopian tube (Fimbria) from patient 8

value: patient 8


title: FT-SA23506

source_name: Right fallopian tube from patient 5

value: Right fallopian tube

value: patient 5

value: cancer-free


title: CV - male - hT2AB - rep1

value: cortex


title: CV - female - IgG - rep1

value: 8 months


title: COVID-19 Sample 9

description:
single-nuclei RNA
CTX_71

tag: nuclei count

value: COVID-19, Superinfected interstitial pneumonia, unexpected sudden death in the hospital


title: CV - male - IgG - rep1

value: IgG

tag: Sex


title: CV - female - hT2AB - rep2

value: female


title: R47H - male - IgG - rep1

value: male


title: R47H - female - IgG - rep1


title: FT-SA23505

source_name: Left fallopian tube from patient 5

value: Left fallopian tube


title: CV - female - hT2AB - rep1


title: dm-ter-miRNA-IT2: miR-124 teratoma 2 with IT GCV injections

status: Public on Nov 04 2020

last: Wu

state: California

address: 9500 Gilman Drive

department: Bioengineering

institute: UCSD

description: Data from miR-124 teratoma 2 with IT injections generated for the miR-124 molecular sculpting experiment

data_processing:
Align mRNA fastq files to genome and generate gene expression matrices with 10X genomics cellranger count with default parameters
Convert genotype barcode fastq files to unaligned bam, tag each read with cell and molecule barcodes, and assign one of more genotypes to each cell
Merge cellranger runs from replicate teratomas using cellranger aggr
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: Files ending in ".counts.tar.gz" are counts matrices output by 10X CellRanger in sparse matrix format
Supplementary_files_format_and_content: Files ending in "_doublets.txt" specify which cells are doublets as determined by DoubletDetection
Supplementary_files_format_and_content: Files ending in ".matrices.tar.gz" are directories with multiple counts matrices output by 10X CellRanger
Supplementary_files_format_and_content: Files ending in "pheno_dict.csv" are genotype to cell dictionaries. Each line begins with the name of the genotype, followed by the cell barcodes mapped to that genotype separated by commas

source_name: Human teratoma

growth_protocol: hiPSC or hESC cells were maintained under feeder-free conditions in mTesR1 medium, in growth-factor reduced Matrigel coated tissue coated plates. Cellls were dissociated and passaged using Versene. 1 million cells were combined with an equivalent volume of matrigel and injected into mice for teratoma formation. Teratomas were grown for approximately 10 weeks in mice before extraction and processing

extract_protocol:
Teratomas were excised and dissociated using the GentleMACS tuomor dissociation protocol, resuspended in PBS-BSA and loaded onto the 10X Genomics Chromium system as per manufacturer's instructions
Single cell libraries were constructed with the Single Cell 3' Reagent Kit from 10X genomics

tag: cell line

tag: genetic/chemical perturbation

value: miR-124 suicide circuit with GCV injections

tag: molecule subtype

value: Cytoplasmic RNA


title: R47H - male - hT2AB - rep1


title: CV - female - hT2AB - rep3


title: dm-ter-miRNA-IT1: miR-124 teratoma 1 with IT GCV injections

description: Data from miR-124 teratoma 1 with IT injections generated for the miR-124 molecular sculpting experiment


title: R47H - female - hT2AB - rep2


title: Serotype 1 A42174 strain LEP

status: Public on Nov 12 2020

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

data_processing:
The quality of the trimmed single paired end raw reads from RNA sequencing (RNA-Seq) generated using the Illumina platform were checked using FastQC v0.11.5
Complete annotated reference genomes for the D39 (accession number: NC_008533) and serotype 1 P1031 (accession number: CP000920) strains were obtained from GenBank and used for mapping RNA-Seq reads.
Sequence reads for the D39 and serotype 1 (A42174) strains were mapped against the D39 and P1031 reference genomes respectively for the sequenced RNA samples collected at early- (EEP), mid- (MEP) and late exponential phases (LEP) of in vitro growth cultures using bowtie2 v2.3.0 using default options
The annotated reference genome for the D39 and P1031 strains from GenBank were converted to GFF3 format using bp_genbank2gff3.pl script (https://metacpan.org/pod/bp_genbank2gff3.pl) and from GFF3 to GTF format using gff2gtf.pl script (https://github.com/dgpinheiro/bioinfoutilities/blob/master/gff2gtf.pl)
To quantify the number of transcripts, the total mapped primary transcripts were counted, excluding multi-mapping and multi-overlapping reads for each coding sequence (CDS) in the generated GTF files separately for D39 and serotype 1 strain using featureCounts v.2.0.0
The raw transcript counts for each strain were separately transformed to Transcripts per kilobase million (TPM) in R (https://www.R-project.org/).
Ortholog genes were identified by clustering all the CDS sequences in D39 and serotype 1 P1031 reference genomes using Panaroo v1.2.3. Using orthologous gene clustering information, CDS sequences found in both genomes (excluding clusters with paralogs) were selected for downstream differential gene analysis
Logarithm to the base 2 of the fold change in gene expression values i.e. TPM for serotype 1 divided by D39, were calculated for the genes found in both strains. The data was filtered to only take into account TPM values greater than 10
Genome_build: Streptococcus pneumoniae D39 (accession number: NC_008533) and serotype 1 P1031 (accession number: CP000920)
Supplementary_files_format_and_content: tab-delimited text files include read counts for each gene
Supplementary_files_format_and_content: Matrix table with TPM values for every gene of the three A42174 samples
Supplementary_files_format_and_content: Matrix table with TPM values for every gene of the three D39 samples

organism: Streptococcus pneumoniae

source_name: ST217 serotype 1 strain A42174

growth_protocol: Growth curves of the serotype 2 (D39) strain and the serotype 1 ST217 bacteraemia strain (A42174) were performed by inoculating 250ml of BHI with 2.5x10^6 bacteria and incubating them at 37°C in a water bath. Samples were taken every hour to determine the optical density (OD500). This experiment was done in triplicate and OD500 plotted to determine three growth phases: early exponential phase (EEP), mid-exponential phase (MEP) and^6 late exponential phase (LEP).

extract_protocol:
Ribonucleic acid (RNA) from each phase was stabilised by incubating the bacteria in a 5% phenol (Invitrogen) and 95% ethanol solution for 30 minutes on ice. Following stabilisation, the RNA was extracted using a phase separation method using TRIzol® (Invitrogen) (Kroger et al, 2012)
RNA libraries for samples 1-3 were assumably prepared for sequencing using standard Illumina protocols. RNA samples 4-6  were fragmented with ultrasound (4 pulses of 30 sec at 4°C) followed by a treatment with antarctic phosphatase and re-phosphorylated with polynucleotide kinase (PNK). Afterwards, the RNA fragments were poly(A)-tailed using poly(A) polymerase and a RNA adapter was ligated to the 5'-phosphate of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and M-MLV reverse transcriptase. The resulting cDNA was PCR-amplified to about 20-30 ng/μl using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit. The cDNA samples were pooled in equimolar amounts in three different pools. The cDNA in the size range of 150 – 500 bp was eluted from preparative agarose gels. Aliquots of the size fractionated cDNAs were analyzed by capillary electrophoresis.   (Beckman Coulter Genomics) and analyzed by capillary electrophoresis.

tag: growth phase

value: Late Exponential Phase (LEP)

tag: growth medium

value: BHI


title: Serotype 2 D39 strain MEP

source_name: Serotype 2 strain D39

tag: strain

value: Mid-Exponential Phase (MEP)


title: Serotype 1 A42174 strain EEP

value: Early Exponential Phase (EEP)


title: CV - male - hT2AB - rep2

tag: age


title: Serotype 2 D39 strain LEP


title: KO - female - IgG - rep2


title: KO - female - hT2AB - rep3


title: R47H - female - hT2AB - rep1


title: KO - female - hT2AB - rep1


title: CV - female - IgG- rep2


title: dm-ter-neural-screen-gRNA-m1-2: Neural disease CRISPR-KO screen teratoma 1 10X replicate 2 gRNA reads

description: gRNA data from the 2nd 10X replicate of the 1st teratoma generated for the neural disease CRISPR-KO screen

value: PGP1 cells had Cas9 knocked in, CRISPR knockouts delivered with CROP-Seq vector

value: CRISPR guide RNA


title: dm-ter-neural-screen-m2-2: Neural disease CRISPR-KO screen teratoma 2 10X replicate 2

description: 10X data from the 2nd 10X replicate of the 2nd teratoma generated for the neural disease CRISPR-KO screen


title: CV - male - IgG - rep2


title: Serotype 1 A42174 strain MEP


title: dm-ter-screen-repool-gRNA-m3-1: Replicate embryonic lethal CRISPR-KO screen teratoma 3 10X replicate 1 gRNA reads

description: gRNA data from the 1st 10X replicate of the 3rd teratoma generated for the replicate embyronic lethal CRISPR-KO screen


title: dm-ter-screen-repool-gRNA-m3-2: Replicate embyronic lethal CRISPR-KO screen teratoma 3 10X replicate 2 gRNA reads

description: gRNA data from the 2nd 10X replicate of the 3rd teratoma generated for the replicate embyronic lethal CRISPR-KO screen


title: dm-ter-screen-repool-gRNA-m2-1: Replicate embryonic lethal CRISPR-KO screen teratoma 2 10X replicate 1 gRNA reads

description: gRNA data from the 1st 10X replicate of the 2nd teratoma generated for the replicate embyronic lethal CRISPR-KO screen


title: dm-ter-screen-repool-gRNA-m2-2: Replicate embyronic lethal CRISPR-KO screen teratoma 2 10X replicate 2 gRNA reads

description: gRNA data from the 2nd 10X replicate of the 2nd teratoma generated for the replicate embyronic lethal CRISPR-KO screen


title: Serotype 2 D39 strain EEP


title: dm-ter-miRNA-IPIT2: miR-124 teratoma 2 with IPIT GCV injections

description: Data from miR-124 teratoma 2 with IPIT injections generated for the miR-124 molecular sculpting experiment


title: dm-ter-screen-repool-m2-2: Replicate embyronic lethal CRISPR-KO screen teratoma 2 10X replicate 2

description: 10X data from the 2nd 10X replicate of the 2nd teratoma generated for the replicate embyronic lethal CRISPR-KO screen


title: dm-ter-miRNA-IPIT1: miR-124 teratoma 1 with IPIT GCV injections

description: Data from miR-124 teratoma 1 with IPIT injections generated for the miR-124 molecular sculpting experiment


title: dm-ter-screen-repool-gRNA-m1-1: Replicate embryonic lethal CRISPR-KO screen teratoma 1 10X replicate 1 gRNA reads

description: gRNA data from the 1st 10X replicate of the 1st teratoma generated for the replicate embyronic lethal CRISPR-KO screen


title: dm-ter-miRNA-gcv-neg-ctrl: GCV negative miR-124 control teratoma

description: Data from control teratoma with miR-124 circuit with no GCV injections generated for the miR-124 molecular sculpting experiment

value: miR-124 suicide circuit


title: dm-ter-screen-gRNA-m3-2: Embryonic lethal CRISPR-KO screen teratoma 3 10X replicate 2 gRNA reads

description: gRNA data from the 2nd 10X replicate of the 3rd teratoma generated for the embyronic lethal CRISPR-KO screen


title: dm-ter-screen-gRNA-m3-1: Embryonic lethal CRISPR-KO screen teratoma 3 10X replicate 1 gRNA reads

description: gRNA data from the 1st 10X replicate of the 3rd teratoma generated for the embyronic lethal CRISPR-KO screen


title: dm-ter-screen-gRNA-m2-1: Embryonic lethal CRISPR-KO screen teratoma 2 10X replicate 1 gRNA reads

description: gRNA data from the 1st 10X replicate of the 2nd teratoma generated for the embyronic lethal CRISPR-KO screen


title: dm-ter-neural-screen-gRNA-m2-2: Neural disease CRISPR-KO screen teratoma 2 10X replicate 2 gRNA reads

description: gRNA data from the 2nd 10X replicate of the 2nd teratoma generated for the neural disease CRISPR-KO screen


title: dm-ter-neural-screen-gRNA-m2-1: Neural disease CRISPR-KO screen teratoma 2 10X replicate 1 gRNA reads

description: gRNA data from the 1st 10X replicate of the 2nd teratoma generated for the neural disease CRISPR-KO screen


title: dm-ter-screen-repool-m3-2: Replicate embyronic lethal CRISPR-KO screen teratoma 3 10X replicate 2

description: 10X data from the 2nd 10X replicate of the 3rd teratoma generated for the replicate embyronic lethal CRISPR-KO screen


title: dm-ter-screen-m3-1: Embryonic lethal CRISPR-KO screen teratoma 3 10X replicate 1

description: 10X data from the 1st 10X replicate of the 3rd teratoma generated for the embyronic lethal CRISPR-KO screen


title: dm-ter-screen-gRNA-m1-1: Embryonic lethal CRISPR-KO screen teratoma 1 10X replicate 1 gRNA reads

description: gRNA data from the 1st 10X replicate of the 1st teratoma generated for the embyronic lethal CRISPR-KO screen


title: dm-ter-screen-m2-1: Embryonic lethal CRISPR-KO screen teratoma 2 10X replicate 1

description: 10X data from the 1st 10X replicate of the 2nd teratoma generated for the embyronic lethal CRISPR-KO screen


title: dm-ter-screen-m1-2: Embryonic lethal CRISPR-KO screen teratoma 1 10X replicate 2

description: 10X data from the 2nd 10X replicate of the 1st teratoma generated for the embyronic lethal CRISPR-KO screen


title: dm-ter-chimera-h9: H9 teratoma

description: Data from teratoma generated from H9 cell line used for assessing cell line specific heterogeneity in Figure 2


title: dm-ter-merged-bc-gRNA-2: Barcoded H1 teratoma 2 gRNA reads

description: gRNA data from barcoded H1 teratoma 2 used for cell type discovery in Figure 1 and clonal analysis in Figure 2

value: Lentiviral barcode


title: dm-ter-neural-screen-gRNA-m1-1: Neural disease CRISPR-KO screen teratoma 1 10X replicate 1 gRNA reads

description: gRNA data from the 1st 10X replicate of the 1st teratoma generated for the neural disease CRISPR-KO screen


title: dm-ter-neural-screen-m2-1: Neural disease CRISPR-KO screen teratoma 2 10X replicate 1

description: 10X data from the 1st 10X replicate of the 2nd teratoma generated for the neural disease CRISPR-KO screen


title: dm-ter-merged-bc-gRNA-1: Barcoded H1 teratoma 1 gRNA reads

description: gRNA data from barcoded H1 teratoma 1 used for cell type discovery in Figure 1 and clonal analysis in Figure 2


title: dm-ter-neural-screen-m1-2: Neural disease CRISPR-KO screen teratoma 1 10X replicate 2

description: 10X data from the 2nd 10X replicate of the 1st teratoma generated for the neural disease CRISPR-KO screen


title: dm-ter-neural-screen-m1-1: Neural disease CRISPR-KO screen teratoma 1 10X replicate 1

description: 10X data from the 1st 10X replicate of the 1st teratoma generated for the neural disease CRISPR-KO screen


title: dm-ter-screen-repool-gRNA-m1-2: Replicate embyronic lethal CRISPR-KO screen teratoma 1 10X replicate 2 gRNA reads

description: gRNA data from the 2nd 10X replicate of the 1st teratoma generated for the replicate embyronic lethal CRISPR-KO screen


title: dm-ter-screen-repool-m3-1: Replicate embryonic lethal CRISPR-KO screen teratoma 3 10X replicate 1

description: 10X data from the 1st 10X replicate of the 3rd teratoma generated for the replicate embyronic lethal CRISPR-KO screen


title: dm-ter-merged-non-bc-4: Non-barcoded H1 teratoma 4

description: Data from non-barcoded H1 teratoma 4 used for cell type discovery in Figure 1


title: dm-ter-screen-repool-m2-1: Replicate embryonic lethal CRISPR-KO screen teratoma 2 10X replicate 1

description: 10X data from the 1st 10X replicate of the 2nd teratoma generated for the replicate embyronic lethal CRISPR-KO screen


title: dm-ter-merged-non-bc-3: Non-barcoded H1 teratoma 3

description: Data from non-barcoded H1 teratoma 3 used for cell type discovery in Figure 1


title: dm-ter-screen-repool-m1-2: Replicate embyronic lethal CRISPR-KO screen teratoma 1 10X replicate 2

description: 10X data from the 2nd 10X replicate of the 1st teratoma generated for the replicate embyronic lethal CRISPR-KO screen


title: dm-ter-screen-repool-m1-1: Replicate embryonic lethal CRISPR-KO screen teratoma 1 10X replicate 1

description: 10X data from the 1st 10X replicate of the 1st teratoma generated for the replicate embyronic lethal CRISPR-KO screen


title: Sensitive neurons 3

status: Public on Oct 29 2020

city: Los Angeles

first: John

middle: Edward

last: van Veen

address: 610 Charles E young Dr

department: Integrative Biology and Physiology

institute: UCLA

data_processing:
Quality check with FastQC (Galaxy version 0.72)
Reads aligned to mouse genome (mm10) with RNA STAR (Galaxy version 2.6.0)
Remove PCR duplicates with RmDup (Galaxy version 2.0.1)
gene level counts produced with htseq-count (Galaxy version 0.9.1)
Genome_build: mm10
Supplementary_files_format_and_content: tabular files with gene level counts

source_name: Neurons

extract_protocol:
SMART-seq V4 ultra-low input kit (Takara)
Nextera XT DNA library preparation kit (Illumina)

treatment_protocol: During electrophysiological recording, brain slice preparations were increased in temperature by 5 degrees centigrade. 2 neurons with similar responses were extracted by aspiration with the patch pipette and pooled into a PCR tube, and snap frozen.

value: Brain

tag: temperature responsive

value: Yes

tag: esr1-zsgreen fluorescence

value: ZsGreen positive


title: Control Sample 10

status: Public on Oct 22 2020

description:
single-nuclei RNA
c16_25

extract_protocol:
Frozen medial frontal cortex tissue from post-mortem control and COVID-19 patients were obtained from the Stanford/ VA/ NIA Aging Clinical Research Center (ACRC) and the Saarland University Hospital Institute for Neuropathology, with approval from local ethics committees. The protocol for the isolation of nuclei was adapted from previous studies, and performed in a BSL2+ Biosafety Cabinet wearing PPE (Mathys et al., Nature 2019). All procedures were carried out on ice or at 4°C. Briefly, 50 mg of post-mortem brain tissue was dounce homogenized in 2 ml of Nuclei EZ Prep Lysis Buffer (Sigma, NUC101) spiked with 0.2 U μl−1 RNase inhibitor (Takara, 2313A) and EDTA-free Protease Inhibitor Cocktail (Roche, 11873580001) before incubating on ice for 5 min in a final volume of 5 ml. Homogenized tissue was filtered through a 100-μm cell strainer (Falcon, 352360), mixed with an equal volume of 50% iodixanol density gradient medium in PBS (OptiPrep, Sigma-Aldrich, D1556) to make a final concentration of 25% iodixanol. 30% iodixanol was layered underneath the 25% mixture. Similarly, 40% iodixanol was layered underneath the 30% iodixanol. In a swinging-bucket centrifuge, nuclei were centrifuged for 20 min at 3,000 r.c.f. After centrifugation, the nuclei were present at the interface of the 30% and 40% iodixanol solutions. Isolated nuclei were resuspended in 1% BSA with 0.2 U μl−1 RNase inhibitor, filtered twice through a 40 μm strainer (Flowmi), and counted on an TC20 automated cell counter (Bio-Rad) after the addition of Trypan Blue.    Frozen choroid plexus tissue was extracted from the lateral ventricles of post-mortem tissue obtained from the Stanford University Pathology department and the Saarland University Hospital Institute for Neuropathology, with approval from local ethics committees. All procedures were carried out on ice or at 4°C, and in a BSL2+ Biosafety Cabinet wearing PPE. Dounce homogenization or enzymatic dissociation successfully used for mice choroid plexi (Dani et al., bioRxiv 2019) resulted in loss of nuclei integrity and low nuclei complexity (<50 median genes/ nuclei). We hypothesized that like shaking an apple tree, gentle pipetting of choroid plexi tissue in lysis buffer could liberate nuclei without needing to physically disintegrate the fibrous choroid matrix—and thus avoid collateral physical damage to nuclei. Specifically, 40 mg sof choroid plexus tissue was thawed in 250 μl of 1% BSA with 0.2 U μl−1 RNase inhibitor until the tissue settled. 5 ml of lysis buffer (10 mM Tris, 10 mM NaCl, 3 mM MgCl2, 0.1% Nonidet P40 substitute (Roche/ Sigma, 11754599001), 0.2 U μl−1 RNase inhibitor, and protease inhibitor) was added and tissue incubated on ice for 10 minutes with gentle swirling every 2 minutes. 5 ml of 1% BSA was added and the tissue triturated 10 times with a 5 ml serological pipette. After centrifugation (500g, 5 min), pelleted nuclei were resuspended in 1% BSA with 0.2 U μl−1 RNase inhibitor; gently triturated 10 times with a 1 ml regular-bore pipette tip; and filtered twice through a 70 μm and then a 40 μm strainer (Flowmi). Debris was inspected on a brightfield microscope and nuclei were counted on an TC20 automated cell counter (Bio-Rad) after the addition of Trypan Blue.
For droplet-based snRNA-seq, libraries were prepared using the Chromium Next GEM Single Cell 3ʹ v3.1 according to the manufacturer’s protocol (10x Genomics), targeting 10,000 nuclei per sample after counting with a TC20 Automated Cell Counter (Bio-Rad). 13 cycles were applied to brain parenchyma samples to generate cDNA, and 15 for choroid plexus samples. All samples underwent 15-16 cycles for final library generation. Generated snRNA-seq libraries were sequenced across two S4 lanes on a NovaSeq 6000 (150 cycles, Novogene).

value: Lateral ventricles

value: M

tag: Cause of death

value: Aspiration pneumonia & Alzheimer's disease

tag: post-mortem interval

tag: biogroup

value: Control

tag: disease group

value: Non-viral

tag: batch


title: Sensitive neurons 2

tag: tissue


title: Sensitive neurons 1


title: Control Sample 8

description:
single-nuclei RNA
c16_23

tag: preparation method

tag: patient id

tag: nuclei count

value: Pancreatic cancer & Parkinson’s disease


title: dm-ter-screen-gRNA-m1-2: Embryonic lethal CRISPR-KO screen teratoma 1 10X replicate 2 gRNA reads

description: gRNA data from the 2nd 10X replicate of the 1st teratoma generated for the embyronic lethal CRISPR-KO screen

tag: cell line

tag: genetic/chemical perturbation


title: dm-ter-merged-non-bc-1: Non-barcoded H1 teratoma 1

description: Data from non-barcoded H1 teratoma 1 used for cell type discovery in Figure 1

tag: molecule subtype

value: Cytoplasmic RNA


title: COVID-19 Sample 6

description:
single-nuclei RNA
c73

tag: Sex

value: COVID-19, Superinfected interstitial pneumonia

value: Case


title: Control Sample 9

description:
single-nuclei RNA
c16_24

value: F

value: Aspiration pneumonia & Frontotemporal lobar degeneration


title: COVID-19 Sample 8

description:
single-nuclei RNA
c76

value: COVID-19, Superinfected interstitial pneumonia, severe arterosclerosis with dilatative heart disease


title: dm-ter-screen-m1-1: Embryonic lethal CRISPR-KO screen teratoma 1 10X replicate 1

description: 10X data from the 1st 10X replicate of the 1st teratoma generated for the embyronic lethal CRISPR-KO screen

value: PGP1 cells had Cas9 knocked in, CRISPR knockouts delivered with CROP-Seq vector


title: dm-ter-chimera-hues62: HUES62 teratoma

description: Data from teratoma generated from HUES62 cell line used for assessing cell line specific heterogeneity in Figure 2


title: dm-ter-screen-m3-2: Embryonic lethal CRISPR-KO screen teratoma 3 10X replicate 2

description: 10X data from the 2nd 10X replicate of the 3rd teratoma generated for the embyronic lethal CRISPR-KO screen


title: Control Sample 3

description:
single-nuclei RNA
s03_09

value: Parenchymal

value: COPD w/ interstitial lung disease & emphysema


title: dm-ter-merged-bc-gRNA-3: Barcoded H1 teratoma 3 gRNA reads

description: gRNA data from barcoded H1 teratoma 3 used for cell type discovery in Figure 1 and clonal analysis in Figure 2

value: Lentiviral barcode

value: CRISPR guide RNA


title: dm-ter-chimera-pgp1: PGP1 teratoma

description: Data from teratoma generated from PGP1 cell line used for assessing cell line specific heterogeneity in Figure 2


title: dm-ter-screen-gRNA-m2-2: Embryonic lethal CRISPR-KO screen teratoma 2 10X replicate 2 gRNA reads

description: gRNA data from the 2nd 10X replicate of the 2nd teratoma generated for the embyronic lethal CRISPR-KO screen


title: Control Sample 5

description:
single-nuclei RNA
c15_12

value: Lateral ventricles

value: Aspiration pneumonia & Multiple system atrophy


title: Influenza Sample 1

description:
single-nuclei RNA
flu74

value: M

value: Influenza, Superinfected interstitial pneumonia, multiorgan failure

value: Influenza


title: dm-ter-merged-bc-3: Barcoded H1 teratoma 3

description: 10X data from barcoded H1 teratoma 3 used for cell type discovery in Figure 1 and clonal analysis in Figure 2


title: dm-ter-merged-bc-2: Barcoded H1 teratoma 2

description: 10X data from barcoded H1 teratoma 2 used for cell type discovery in Figure 1 and clonal analysis in Figure 2


title: dm-ter-screen-m2-2: Embryonic lethal CRISPR-KO screen teratoma 2 10X replicate 2

description: 10X data from the 2nd 10X replicate of the 2nd teratoma generated for the embyronic lethal CRISPR-KO screen


title: dm-ter-merged-non-bc-2: Non-barcoded H1 teratoma 2

description: Data from non-barcoded H1 teratoma 2 used for cell type discovery in Figure 1


title: COVID-19 Sample 3

description:
single-nuclei RNA
cv75


title: Insensitive neurons 2

tag: strain

value: Brain

value: No

value: ZsGreen positive


title: COVID-19 Sample 2

description:
single-nuclei RNA
cv73

tag: age

value: COVID-19, Superinfected interstitial pneumonia

value: Case


title: Insensitive neurons 1

tag: temperature responsive


title: sc-RNAseq_CD34+ cells - 96h_lane8_donor2

status: Public on Aug 25 2020

description: Single-cell RNAseq

data_processing:
Demultiplex according to plate barcode in read1:  cutadapt (version 2.3) with the folowing configuration > 5' & 3' triming quality cutoff ( 30,30), maximum error rate (0), trimming (no-trim), indels (no-indels), minimum read length (30:20), paired end mode (g), pair filtering mode (any)
Demultiplex according to cell barcode in read2: cutadapt (version 2.3) with the folowing configuration > 5' & 3' triming quality cutoff ( 30,30), maximum error rate (0), trimming (no-trim), indels (no-indels), minimum read length (30:20), paired end mode (g), pair filtering mode (any), modifying read name (y)
Select reads with polyT tails in read2: cutadapt (version 2.3) with the folowing configuration > maximum error rate (0), trimming (no-trim), minimum overlap (14), indels (no-indels), paired end mode (g ^NNNNNNNNNNTTTTTT )
Select reads mapping on ERCC Spike-in genome: bowtie2 (version 2.3.5.1) with the folowing configuration > dovetailing read pairs (-- dovetail), discordant pairs (--no-discodant), individual mates (--no-mixed)
Mapping remaining reads to reference genome: STAR (version 2.7.0a) with the folowing configuration > Maximum number of output alignments for multi-mappers (1)
Genome_build: hg19
Removing chr y: R (version 3.6.3) dplyr (version 1.0.0)
Filtering cells: R (version 3.6.3) dplyr (version 1.0.0) > minimum number of read per cell (80 000), maximum % of mitochondrial reads (10), ERCC spike correlation (Pearson > 0.6)
Filtering genes: R (version 3.6.3), dplyr (version 1.0.0) > gene type (protein coding), transcript status (known), minimum number of read per gene (2), minimum number of UMI per gene (2)
Pseudotiming and clustering: Matlab (version 2018b), Calista (version 1.2.2)
Supplementary_files_format_and_content: Tab seperated raw count matrix (STAR output) (donor 1 & donor 2)
Supplementary_files_format_and_content: Tab seperated file count matrix after filtering  (donor 1 & donor 2)
Supplementary_files_format_and_content: Tab seperated and normalized count matrix for Calista top 200 gene (donor 1)
Supplementary_files_format_and_content: Tab seperated and normalized count matrix for Calista top 200 gene (donor 2)

source_name: Umbilical cord blood

extract_protocol:
Single cells were marked with 7AAD to remove dead cell by FACS sorting. Cells were individually sorted into 96-well plates containing 4µL of lysis buffer (using Triton 100% as lysis reagent) Supplemented with RNase inhibitor (RNaseOUT, Thermo scientific) and specific barcoded RT primers.
Single-cell RNA sequencing was performed as described in "Jaitin et al.Science, 2014 Feb 14; 343(6172): 776–779" with minor adaptations.

treatment_protocol: Cells were stimulated with cytokines after thawing and were grown in the same medium until lysis was performed. Cells were collected and lysed from 5h up to 96h of cytokine stimulation.

value: Blood

tag: disease state

value: Healthy

tag: treatment

value: Untreated


title: sc-RNAseq_CD34+ cells - 72h_lane8_donor2

description: Single-cell RNAseq


title: sc-RNAseq_CD34+ cells - 48h_lane8_donor2

description: Single-cell RNAseq


title: dm-ter-merged-bc-1: Barcoded H1 teratoma 1

description: 10X data from barcoded H1 teratoma 1 used for cell type discovery in Figure 1 and clonal analysis in Figure 2

value: Cytoplasmic RNA


title: sc-RNAseq_CD34+ cells - 5h_lane8_donor2

description: Single-cell RNAseq


title: Sensitive neurons 4

value: Yes

tag: esr1-zsgreen fluorescence


title: Control Sample 7

description:
single-nuclei RNA
c16_18

source_name: Choroid Plexus

tag: Cause of death

value: Aspiration pneumonia & Alzheimer's disease

tag: post-mortem interval

tag: biogroup

value: Control

value: Non-viral


title: sc-RNAseq_CD34+ cells - 96h_lane7_donor2

description: Single-cell RNAseq

tag: tissue


title: sc-RNAseq_CD34+ cells - 72h_lane7_donor2

description: Single-cell RNAseq


title: sc-RNAseq_CD34+ cells - 48h_lane7_donor2

description: Single-cell RNAseq


title: Insensitive neurons 3


title: Control Sample 6

description:
single-nuclei RNA
c15_17

tag: preparation method

value: Lateral ventricles

value: Aspiration pneumonia & Frontotemporal lobar degeneration

tag: disease group

tag: batch


title: sc-RNAseq_CD34+ cells - 72h_lane5_donor1

description: Single-cell RNAseq


title: Influenza Sample 2

description:
single-nuclei RNA
c74

tag: patient id

tag: nuclei count

value: M

value: Influenza, Superinfected interstitial pneumonia, multiorgan failure


title: sc-RNAseq_CD34+ cells - 5h_lane5_donor1

description: Single-cell RNAseq


title: COVID-19 Sample 7

description:
single-nuclei RNA
c75


title: COVID-19 Sample 5

description:
single-nuclei RNA
c72

value: COVID-19, Interstitial pneumonia, multiorgan failure


title: Control Sample 4

description:
single-nuclei RNA
s04_09

source_name: Medial prefrontal cortex

value: Parenchymal

value: F

value: Breast cancer


title: bulk-ATACseq_CD34+ cells - 48h_donor1

description: Bulk ATAC seq

data_processing:
TN5 Adapter trimming: cutadapt with the following configuration > adapter type (Non-internal 5’ adapter "AGATGTGTATAAGAGACAG;max_error_rate=0.1;min_overlap=10"), 3' end quality cutoff (20), minimum read length (18)
Sequences alignement:  Bowtie2 (version 2.3.4.2) with the following configuration > Genome index (UCSC_GRCh37_hg19), maximum fragment length for valid paired-end alignments (800)
Remove duplicate: picard MarkDuplicates (version 2.18.11) with the following configuration > remove duplicate (TRUE), validation stringency (SILENT)
Random BAM downsampling to 16M reads (without disrupting pairs of reads): samtools (version 1.9)
Peak calling on downsampled BAM: MACS2 (version 2.1.2) with the following configuration > format of input file (BAMPE), mappable genome (hs), broad peak calling (broad), p-value cutoff (0.1)
Motif analysis: HOMER (version 4.11) with the following configuration > size of the region for motif finding (size given), number of motif to find (100)
Intersection of peaks within a time point & union of peaks accross two consecutive time points: R (version 3.5.1) & GenomicRanges (version 1.34.0)
Feature count (read attribution to peaks): R (version 3.5.1) & Rsubread (version 1.32.2) with the following configuration > Paired End (TRUE), count chimeric fragmeent (FALSE), count multi-mapping reads (TRUE)
Differential analysis (number of reads in peaks as a proxy for accessibility quantification): R (version 4.0.1) & DEseq2 (version 1.28.0) with the following configuration > seqtype (paired-end), control (t), treated (t + 1)
Supplementary_files_format_and_content: Peak text files generated with downsampled BAM files
Supplementary_files_format_and_content: Tab delimited text file containing HOMER transcription factor binding motifs enrichment results for "known motifs"
Supplementary_files_format_and_content: Matrix table with read counts in the region resulting from the intersection of peaks detected in every sample for each time point
Supplementary_files_format_and_content: Matrix table with read counts in the region resulting from the union of peaks detected in every sample for two consecutive time points
Supplementary_files_format_and_content: Tab delimited text file with pValue and fold change for peaks union of every sample for two consecutive time points
Supplementary_files_format_and_content: Tab delimited text file with peak informations and genome features attribution

extract_protocol:
A one-step gentle membrane permeabilization and DNA transposition was performed by adding 50µl transposition mixture (25 µL TD buffer 2X, 2,5µL of transposase TDE1 (Illumina), 0,5 µL digitonin 0,1% (Promega) and 22 µL water) to the cell pellets and by incubating at 37°C for 30 minutes under agitation.
Libraries were prepared according "Fast -ATACseq" protocol described in "Corces et al, Nat Genet. 2016 Oct; 48(10): 1193–1203".

treatment_protocol: Cells were stimulated with cytokines after thawing and were grown in the same medium until lysis was performed. Cells were collected and lysed from 0h up to 48h of cytokine stimulation.


title: bulk-ATACseq_CD34+ cells - 48h_donor2

description: Bulk ATAC seq


title: sc-RNAseq_CD34+ cells - 48h_lane5_donor1

description: Single-cell RNAseq


title: Control Sample 2

description:
single-nuclei RNA
s03_03

value: Small cell lung cancer


title: Control Sample 1

description:
single-nuclei RNA
s01_01

value: Coronary artery disease, endstage cardiomyopathy


title: COVID-19 Sample 4

description:
single-nuclei RNA
cv76

value: COVID-19, Superinfected interstitial pneumonia, severe arterosclerosis with dilatative heart disease

value: Case


title: bulk-ATACseq_CD34+ cells - 24h_donor3

description: Bulk ATAC seq

value: Blood

value: Healthy

value: Untreated


title: bulk-ATACseq_CD34+ cells - 24h_donor2

description: Bulk ATAC seq


title: COVID-19 Sample 1

description:
single-nuclei RNA
cv72


title: D13

status: Public on Sep 30 2020

city: Guangzhou

first: Shuyi

last: Chen

address: #7 Jinsui Rd, Zhujiang Newtown

country: China

institute: Zhongshan Ophthlamic Center

data_processing:
16bp 10XBarcodes are encoded at the start of R1 file, while 8bp sample index sequences are incorporated as the i7 index read. R1 and R2 are standard illumina sequencing primer sites used in paired-end sequencing. TruSeq Read 1 is used to sequence 16 bp 10X Barcodes and 12 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder.
Basecalls performed using CASAVA version 1.8
We applied fastp with default parameter filtering the adaptor sequence and removed the low quality reads  to achieve the clean data.
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter.Then the feature-barcode matrices were obtained by aligning reads to the mm10 genome using CellRanger v3.0.0.
Seurat package (version: 2.3.4, https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data. PCA was constructed based on the scaled data with all high variable genes and top 10 principals were used for tSNE construction. Utilizing graph-based cluster method, we acquired the unsupervised the cell cluster result based the PCA top 10 principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. logFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Genome_build: mm10
Supplementary_files_format_and_content: TXT file contain normalized counts for each sample

source_name: MEF reprogrammed into retinal ganglion cell-like neurons

growth_protocol: MEFs were cultured in DMEM+10% FBS, at 37℃ in incubator.

extract_protocol:
10X Genomics Chromium
Single-cell gel beads in emulsion (GEMs) macrophages were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3' Reagent Kit v3 (10x Genomics) according to manufacturer's protocol.

treatment_protocol: MEFs were infected with Ascl1/Brn3b/Isl1 overexpressing lentiviruses, doxycycline was added on day 0 to induce Ascl1/Brn3b/Isl1 expression, cells were switched to neuronal medium (DMEM/F12+GlutaMAX+N2+B27+Forskolin+FGF2) on day 2 of reprogramming; medium was half-changed every other day.

tag: cell type

value: MEF

tag: reprogramming day

value: day 13


title: D7

value: day 7


title: bulk-ATACseq_CD34+ cells - 5h_donor1

description: Bulk ATAC seq


title: D4

value: day 4


title: D2

value: day 2


title: MEF

value: day 0


title: sc-RNAseq_CD34+ cells - 24h_lane8_donor2

description: Single-cell RNAseq


title: bulk-ATACseq_CD34+ cells - 0h_donor1

description: Bulk ATAC seq