title: 25D647 RNA-seq [validation cohort]

description:
RNA-311-1-1_24_12_S56
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: single cell of Hematopoietic Stem Cell 322

status: Public on Jun 08 2021

type: SRA

city: Guangzhou

first: Tian

last: Zhang

state: Guangdong

address: 190 Kaiyuan Avenue,Science Park

country: China

institute: GIBH

description:
barcodes.tsv
genes.tsv

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Briefly, reads were aligned to human genome (UCSC hg38) using HISAT2 (v2.0.4)
and gene expression was counted using samtools (v1.3.1) and htseq-count (v 0.6.0), filtered by a threshold of at least 20 averaged raw read counts among samples, and then normalized by GC-count and Gene-length using EDASeq (v2.12.0).
Differential expression and PCA plot were performed using DESeq (v 1.18.1) and genes with p-value < 0.05 and fold-change > 2 were considered as significant difference.
Correlation plot was performed using ggplot2 (v2.2.1) and heatmap was performed using pheatmap (v1.0.10).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: count

molecule: total RNA

organism: Homo sapiens

source_name: Hematopoietic Stem Cells from Peripheral blood after mobilization

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Hematopoietic Stem Cells

tag: treatment

value: Lin-CD34+CD38-CD45RA-CD90+ HSPCs cultured in vitro for 72h


title: D2BB41 RNA-seq [validation cohort]

city: Durham

first: Julie

last: Steinbrink

state: NC

address: 315 Trent Drive

department: Center for Applied Genomics and Precision Medicine

country: USA

institute: Duke University

description:
RNA-303-1-11_1_11_S52
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt

data_processing:
base calling
sequence mapping: sequences were mapped and gene expression quantified using using STAR with parameters: quantMode: ‘GeneCounts’; outSAMtype: ‘None’; outSAMmode: ‘None’; readFilesCommand: ‘zcat’ and  ENSEMBL gene reference Homo sapiens GRCh38 DNA, release 96, downloaded from: ftp://ftp.ensembl.org/pub/release-96/fasta/homo_sapiens/dna/ . All other parameters were left at their default values for STAR version 2.7.1a
counts QC: keep genes that passed QC in the discovery dataset; keep samples with libriary size > 12M and average pairwise correlation >= 0.7
counts normalization (all samples dataset): Trimmed mean of M-values (TMM) normalization; software R, package edgeR
require(limma)  require(edgeR)  # Normalization steps  dge <- DGEList(counts=QCed_counts_batch2_validationsamples.txt , samples = Metadata[which(Metadata$validation_analysis_sample == "Yes"),])  dge <- calcNormFactors(dge, method = "TMM")  design <- model.matrix(~0+phenotype+gender, data = dge$samples)  v <- voom(dge,design,plot=TRUE)  vfit <- lmFit(v,design)  contr.matrix <- makeContrasts(    Candidemia_Bacterial = Candidemia-Bacterial,    Candidemia_Healthy = Candidemia-Healthy,    Candidemia_Viral = Candidemia-Viral,    Candidemia_others = Candidemia-1/3*Bacterial-1/3*Healthy-1/3*Viral,    Bacterial_others = Bacterial-1/3*Candidemia-1/3*Healthy-1/3*Viral,    Viral_others = Viral-1/3*Candidemia-1/3*Healthy-1/3*Bacterial,    levels = colnames(design)  )    vfit <- contrasts.fit(vfit, contrasts = contr.matrix)  efit <- eBayes(vfit)    # input into predictive modelling (lasso/glmnet)   # t(cpm(dge, log = TRUE))
Genome_build: Homo sapiens GRCh38 DNA, release 96
Supplementary_files_format_and_content: tab-delimited plain text file with gene counts for all samples and genes passing QC
Supplementary_files_format_and_content: tab-delimited plain text file with gene counts for samples used for validation of prior differential expression and model developemnt results
Supplementary_files_format_and_content: tab-delimited text file with the numeric matrix of normalized expression values on the log2 scale for sampels used to validated prior results. Obtained from the "$E" argument of the limma::voom object. To be used with file "voom_weights.txt" when testing in limma::lmFit
Supplementary_files_format_and_content: tab-delimited text file with numeric matrix of inverse variance weights from voom for samples used to validate prior results. Obtained from the "$weights" argument of the limma::voom object. To be used with file "Voom_normalized_expression.txt" when using limma::lmFit

molecule: polyA RNA

source_name: mRNA extracted from whole blood

extract_protocol:
Total RNA was extracted from human blood preserved and stored in PAXgene Blood RNA Tubes using the Qiagen PAXgene Blood miRNA Kit according to the manufacturer’s protoco
RNA sequencing libraries were generated using NuGEN Universal mRNA-seq kit with AnyDeplete Globin (NuGEN Technologies, Redwood City, CA) and sequenced on the Illumina NovaSeq 6000 instrument with S2 flow cell and 50bp paired-end reads (performed through the Duke Sequencing and Genomic Technologies Core)

tag: passed sample qc

value: Pass

value: Yes

tag: daysreltofirsttimepoint

tag: phenotype

value: Candidemia

tag: gender

value: Male

tag: age


title: 669F2A RNA-seq [validation cohort]

description:
RNA-304-2-11_4_11_S53
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: single cell of Hematopoietic Stem Cell 323

description:
barcodes.tsv
genes.tsv


title: 2AC583 RNA-seq [validation cohort]

description:
RNA-335-121-6_13_13_S7
processed data file:
QCed_counts_batch2_allsamples.txt

value: No

value: Mixed Candida/bacterial


title: 92F246 RNA-seq [validation cohort]

description:
RNA-301-1-10_27_11_S50
processed data file:

value: Fail


title: single cell of Hematopoietic Stem Cell 319

description:
barcodes.tsv
genes.tsv


title: 04BF38 RNA-seq [validation cohort]

description:
HF214_RNA_S79
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt

value: Bacterial

value: Female


title: single cell of Hematopoietic Stem Cell 318

description:
barcodes.tsv
genes.tsv


title: 265DD6 RNA-seq [validation cohort]

description:
RNA-300-36-10_31_11_S51
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: 4332CB RNA-seq [validation cohort]

description:
CR016-2_S48
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt

value: Healthy


title: 65FD47 RNA-seq [validation cohort]

description:
DU09-03S0000001_S90
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt

value: Viral


title: C3488C RNA-seq [validation cohort]

description:
CR015-2_S47
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: single cell of Hematopoietic Stem Cell 317

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 315

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 316

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 314

description:
barcodes.tsv
genes.tsv


title: CC1427 RNA-seq [validation cohort]

description:
CR014-2_S46
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: 1D0D38 RNA-seq [validation cohort]

description:
RNA-305-1-11_6_11_S54
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: single cell of Hematopoietic Stem Cell 321

description:
barcodes.tsv
genes.tsv


title: 282732 RNA-seq [validation cohort]

description:
CR013-2_S45
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: single cell of Hematopoietic Stem Cell 310

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 311

description:
barcodes.tsv
genes.tsv


title: AF5C77 RNA-seq [validation cohort]

description:
CR009-2_S42
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: single cell of Hematopoietic Stem Cell 313

description:
barcodes.tsv
genes.tsv


title: 942D99 RNA-seq [validation cohort]

description:
CR011-2_S43
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: single cell of Hematopoietic Stem Cell 312

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 309

description:
barcodes.tsv
genes.tsv


title: 899DCB RNA-seq [validation cohort]

description:
CR008-2_S41
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: single cell of Hematopoietic Stem Cell 308

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 307

description:
barcodes.tsv
genes.tsv


title: FD1327 RNA-seq [validation cohort]

description:
CR006-2_S39
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: A3DA15 RNA-seq [validation cohort]

description:
CR007-2_S40
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: 18CFC9 RNA-seq [validation cohort]

description:
CR012-2_S44
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: 3B108A RNA-seq [validation cohort]

description:
CR003-2_S36
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: 58A255 RNA-seq [validation cohort]

description:
CR005-2_S38
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: single cell of Hematopoietic Stem Cell 303

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 304

description:
barcodes.tsv
genes.tsv


title: 8CBB63 RNA-seq [validation cohort]

description:
CR001-2_S34
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: 3DD564 RNA-seq [validation cohort]

description:
CR002-2_S35
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: single cell of Hematopoietic Stem Cell 302

description:
barcodes.tsv
genes.tsv


title: 752526 RNA-seq [validation cohort]

description:
A8-121-9_24_13_S32
processed data file:
QCed_counts_batch2_allsamples.txt


title: single cell of Hematopoietic Stem Cell 300

description:
barcodes.tsv
genes.tsv


title: 2387D5 RNA-seq [validation cohort]

description:
A8-143-9_26_13_S33
processed data file:
QCed_counts_batch2_allsamples.txt


title: 711FD1 RNA-seq [validation cohort]

description:
CR004-2_S37
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: single cell of Hematopoietic Stem Cell 306

description:
barcodes.tsv
genes.tsv


title: 2F5B42 RNA-seq [validation cohort]

description:
A4-1_S73
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: single cell of Hematopoietic Stem Cell 299

description:
barcodes.tsv
genes.tsv


title: CF7568 RNA-seq [validation cohort]

description:
96002_S93
processed data file:
QCed_counts_batch2_allsamples.txt


title: single cell of Hematopoietic Stem Cell 301

description:
barcodes.tsv
genes.tsv


title: 7F6F79 RNA-seq [validation cohort]

description:
A5-1-6_28_13_S74
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: single cell of Hematopoietic Stem Cell 305

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 294

description:
barcodes.tsv
genes.tsv


title: B9F3C0 RNA-seq [validation cohort]

description:
95997_S94
processed data file:


title: single cell of Hematopoietic Stem Cell 298

description:
barcodes.tsv
genes.tsv


title: 33560A RNA-seq [validation cohort]

description:
95986_S95
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: single cell of Hematopoietic Stem Cell 297

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 295

description:
barcodes.tsv
genes.tsv


title: 746341 RNA-seq [validation cohort]

description:
95981_S86
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: 1AD7A3 RNA-seq [validation cohort]

description:
95969_S85
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: single cell of Hematopoietic Stem Cell 293

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 292

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 291

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 290

description:
barcodes.tsv
genes.tsv


title: C36000 RNA-seq [validation cohort]

description:
82839_RNA_S82
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: single cell of Hematopoietic Stem Cell 288

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 289

description:
barcodes.tsv
genes.tsv


title: B2BB4D RNA-seq [validation cohort]

description:
82787_RNA_S78
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: single cell of Hematopoietic Stem Cell 296

description:
barcodes.tsv
genes.tsv


title: 76D6DD RNA-seq [validation cohort]

description:
82799_RNA_S81
processed data file:
QCed_counts_batch2_allsamples.txt


title: single cell of Hematopoietic Stem Cell 287

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 286

description:
barcodes.tsv
genes.tsv


title: 769B19 RNA-seq [validation cohort]

description:
82645_RNA_S77
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: single cell of Hematopoietic Stem Cell 285

description:
barcodes.tsv
genes.tsv


title: 570AAC RNA-seq [validation cohort]

description:
82633_RNA_S80
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: 708F64 RNA-seq [validation cohort]

description:
82610_RNA_S75
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: 6C6350 RNA-seq [validation cohort]

description:
82625_RNA_S76
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: single cell of Hematopoietic Stem Cell 284

description:
barcodes.tsv
genes.tsv


title: A1895C RNA-seq [validation cohort]

description:
95967_S84
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: single cell of Hematopoietic Stem Cell 282

description:
barcodes.tsv
genes.tsv


title: 4249B5 RNA-seq [validation cohort]

description:
94500_S96
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: single cell of Hematopoietic Stem Cell 280

description:
barcodes.tsv
genes.tsv


title: A26038 RNA-seq [validation cohort]

description:
106178_S83
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: single cell of Hematopoietic Stem Cell 281

description:
barcodes.tsv
genes.tsv


title: F85ABC RNA-seq [validation cohort]

description:
105929_S89
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: F521DE RNA-seq [validation cohort]

description:
105908_S87
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: single cell of Hematopoietic Stem Cell 277

description:
barcodes.tsv
genes.tsv

value: Lin-CD34+CD38-CD45RA-CD90+ HSPCs cultured in vitro for 48h


title: single cell of Hematopoietic Stem Cell 276

description:
barcodes.tsv
genes.tsv


title: 25AFAB RNA-seq [discovery cohort]

description:
RNA347-76_S56
processed data file:
QCed_counts_exploratory.txt

data_processing:
base calling
sequence mapping: sequences were mapped and gene expression quantified using using STAR with parameters: quantMode: ‘GeneCounts’; outSAMtype: ‘None’; outSAMmode: ‘None’; readFilesCommand: ‘zcat’ and  ENSEMBL gene reference Homo sapiens GRCh38 DNA, release 96, downloaded from: ftp://ftp.ensembl.org/pub/release-96/fasta/homo_sapiens/dna/ . All other parameters were left at their default values for STAR version 2.7.1a
counts QC: keep genes with expression counts per million > 2 in > 73 samples
counts normalization (all samples dataset): Trimmed mean of M-values (TMM) normalization; software R, package edgeR
differential expression normalization (discovery samples only): Trimmed mean of M-values (TMM) noramlization, with voom normalization. Sample R code:     require(limma)  require(edgeR)  # Normalization steps  dge <- DGEList(counts=QCed_counts_discovery, samples = sample_characteristics[which(sample_characteristics$discovery_analysis_sample == "Yes"),])  dge <- calcNormFactors(dge, method = "TMM")  design <- model.matrix(~0+phenotype+gender, data = dge$samples)  v <- voom(dge,design,plot=TRUE)  vfit <- lmFit(v,design)  contr.matrix <- makeContrasts(    Candidemia_Bacterial = Candidemia-Bacterial,    Candidemia_Healthy = Candidemia-Healthy,    Candidemia_SIRS = Candidemia-SIRS,    Candidemia_Viral = Candidemia-Viral,    Candidemia_others = Candidemia-1/4*Bacterial-1/4*Healthy-1/4*SIRS-1/4*Viral,    Bacterial_others = Bacterial-1/4*Candidemia-1/4*Healthy-1/4*SIRS-1/4*Viral,    SIRS_others = SIRS-1/4*Candidemia-1/4*Healthy-1/4*Bacterial-1/4*Viral,    Viral_others = Viral-1/4*Candidemia-1/4*Healthy-1/4*SIRS-1/4*Bacterial,    levels = colnames(design)  )    vfit <- contrasts.fit(vfit, contrasts = contr.matrix)  efit <- eBayes(vfit)
multivariate modeling normalization / processing (discovery samples only): Trimmed mean of M-values (TMM) noramlization, with voom normalization. Sample R code:     require(limma)  require(edgeR)  # Normalization steps  dge <- DGEList(counts=QCed_counts_discovery, samples = sample_characteristics[which(sample_characteristics$discovery_analysis_sample== "Yes"),])  dge <- calcNormFactors(dge, method = "TMM")  data = t(cpm(dge, log = TRUE))  # use data as input to glmnet::cv.glmnet functions
Genome_build: Homo sapiens GRCh38 DNA, release 96
Supplementary_files_format_and_content: tab-delimited plain text file with gene counts for all samples and genes passing QC
Supplementary_files_format_and_content: tab-delimited plain text file with gene counts for samples used for differential expression and model developemnt and genes passing QC
Supplementary_files_format_and_content: tab-delimited text file with the numeric matrix of normalized expression values on the log2 scale. Obtained from the "$E" argument of the limma::voom object. To be used with file "voom_weights.txt" when testing in limma::lmFit
Supplementary_files_format_and_content: tab-delimited text file with numeric matrix of inverse variance weights from voom. Obtained from the "$weights" argument of the limma::voom object. To be used with file "Voom_normalized_expression.txt" when using limma::lmFit

tag: daysreltofirsttimepoin


title: single cell of Hematopoietic Stem Cell 283

description:
barcodes.tsv
genes.tsv


title: E53D42 RNA-seq [discovery cohort]

description:
286627_S59
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt

value: SIRS


title: single cell of Hematopoietic Stem Cell 278

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 275

description:
barcodes.tsv
genes.tsv


title: 25738D RNA-seq [validation cohort]

description:
105906_S88
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: single cell of Hematopoietic Stem Cell 274

description:
barcodes.tsv
genes.tsv


title: 7E9D8A RNA-seq [discovery cohort]

description:
RNA340-1_S21
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 273

description:
barcodes.tsv
genes.tsv


title: 8D9587 RNA-seq [validation cohort]

description:
278076_S92
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: 532F9D RNA-seq [discovery cohort]

description:
408926_S37
processed data file:
QCed_counts_exploratory.txt

value: Missing


title: single cell of Hematopoietic Stem Cell 272

description:
barcodes.tsv
genes.tsv


title: FDB604 RNA-seq [discovery cohort]

description:
95996_S23
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 271

description:
barcodes.tsv
genes.tsv


title: DC1F52 RNA-seq [validation cohort]

description:
106551_S91
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: 82B1F0 RNA-seq [discovery cohort]

description:
408940_S49
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 279

description:
barcodes.tsv
genes.tsv


title: 422278 RNA-seq [discovery cohort]

description:
RNA355-18_S42
processed data file:
QCed_counts_exploratory.txt


title: F61C98 RNA-seq [discovery cohort]

description:
408966_S69
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 269

description:
barcodes.tsv
genes.tsv


title: 605425 RNA-seq [discovery cohort]

description:
408889_S3
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 268

description:
barcodes.tsv
genes.tsv


title: 6A2540 RNA-seq [discovery cohort]

description:
286695_S68
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 266

description:
barcodes.tsv
genes.tsv


title: DC3713 RNA-seq [discovery cohort]

description:
105927_S55
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 265

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 263

description:
barcodes.tsv
genes.tsv


title: 2456E9 RNA-seq [discovery cohort]

description:
RNA355-78_S46
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 261

description:
barcodes.tsv
genes.tsv


title: A65F40 RNA-seq [discovery cohort]

description:
105824_S44
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 5A096A RNA-seq [discovery cohort]

description:
97395_S31
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 5FCC0B RNA-seq [discovery cohort]

description:
RNA353-70_S40
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 262

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 259

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 260

description:
barcodes.tsv
genes.tsv


title: FD2ECE RNA-seq [discovery cohort]

description:
286684_S64
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 258

description:
barcodes.tsv
genes.tsv


title: 2193E8 RNA-seq [discovery cohort]

description:
09-008_S3
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 264

description:
barcodes.tsv
genes.tsv


title: 30C381 RNA-seq [discovery cohort]

description:
RNA341-21_S23
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 257

description:
barcodes.tsv
genes.tsv


title: E09EAD RNA-seq [discovery cohort]

description:
408934_S45
processed data file:
QCed_counts_exploratory.txt


title: 3E6743 RNA-seq [discovery cohort]

description:
10-013_S9
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 8EAB34 RNA-seq [discovery cohort]

description:
408972_S74
processed data file:
QCed_counts_exploratory.txt


title: B14A1D RNA-seq [discovery cohort]

description:
CRO45-2_S63
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 250

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 254

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 253

description:
barcodes.tsv
genes.tsv


title: E7DA12 RNA-seq [discovery cohort]

description:
105848_S47
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 3145EB RNA-seq [discovery cohort]

description:
97403_S33
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: AB4CB3 RNA-seq [discovery cohort]

description:
RNA347-112_S58
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 320

description:
barcodes.tsv
genes.tsv


title: ADA0F2 RNA-seq [discovery cohort]

description:
94183_S17
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: CE0A65 RNA-seq [discovery cohort]

description:
RNA347-151_S61
processed data file:
QCed_counts_exploratory.txt


title: 60AF75 RNA-seq [validation cohort]

description:
RNA-334-1-4_12_13_S59
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: 231970 RNA-seq [validation cohort]

description:
RNA-335-129-6_20_13_S8
processed data file:
QCed_counts_batch2_allsamples.txt


title: single cell of Hematopoietic Stem Cell 325

description:
barcodes.tsv
genes.tsv


title: 9379A7 RNA-seq [discovery cohort]

description:
408978_S5
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 248

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 249

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 247

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 246

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 256

description:
barcodes.tsv
genes.tsv


title: 129FCD RNA-seq [discovery cohort]

description:
408887_S1
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 245

description:
barcodes.tsv
genes.tsv


title: AF59FA RNA-seq [discovery cohort]

description:
RNA352-1_S36
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 51D19E RNA-seq [discovery cohort]

description:
408897_S11
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 255

description:
barcodes.tsv
genes.tsv


title: 9A9B6C RNA-seq [discovery cohort]

description:
95970_S20
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 251

description:
barcodes.tsv
genes.tsv


title: 8D34B5 RNA-seq [discovery cohort]

description:
A6-42_S12
processed data file:
QCed_counts_exploratory.txt


title: 4E0C76 RNA-seq [discovery cohort]

description:
286606_S58
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 267

description:
barcodes.tsv
genes.tsv


title: A2B906 RNA-seq [discovery cohort]

description:
RNA323-1_S29
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 290F5B RNA-seq [discovery cohort]

description:
09-035_S7
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 241

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 242

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 239

description:
barcodes.tsv
genes.tsv


title: 9A41FF RNA-seq [discovery cohort]

description:
RNA355-35_S43
processed data file:
QCed_counts_exploratory.txt


title: 234F85 RNA-seq [discovery cohort]

description:
105911_S53
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 238

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 237

description:
barcodes.tsv
genes.tsv


title: 0D9FAA RNA-seq [discovery cohort]

description:
408920_S32
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 236

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 235

description:
barcodes.tsv
genes.tsv


title: 240899 RNA-seq [discovery cohort]

description:
105907_S52
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 234

description:
barcodes.tsv
genes.tsv


title: C2641E RNA-seq [discovery cohort]

description:
408975_S3
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 0F0D9D RNA-seq [discovery cohort]

description:
RNA347-55_S55
processed data file:
QCed_counts_exploratory.txt


title: 4C847A RNA-seq [discovery cohort]

description:
A6-155_S19
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 233

description:
barcodes.tsv
genes.tsv


title: C3EEA1 RNA-seq [discovery cohort]

description:
CRO36-2_S72
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 244

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 243

description:
barcodes.tsv
genes.tsv


title: 00DCD4 RNA-seq [discovery cohort]

description:
10-024_S10
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 232

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 231

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 240

description:
barcodes.tsv
genes.tsv


title: 622682 RNA-seq [discovery cohort]

description:
408981_S7
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 7342D8 RNA-seq [discovery cohort]

description:
RNA351-29_S35
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 230

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 229

description:
barcodes.tsv
genes.tsv


title: 64CCA8 RNA-seq [discovery cohort]

description:
RNA332-1_S34
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 227

description:
barcodes.tsv
genes.tsv


title: DD565A RNA-seq [discovery cohort]

description:
408952_S58
processed data file:
QCed_counts_exploratory.txt


title: 1DA5D8 RNA-seq [discovery cohort]

description:
RNA355-55_S44
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 226

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 225

description:
barcodes.tsv
genes.tsv


title: 659728 RNA-seq [discovery cohort]

description:
97406_S34
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 224

description:
barcodes.tsv
genes.tsv


title: 7C10AB RNA-seq [discovery cohort]

description:
RNA331-2_S33
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 223

description:
barcodes.tsv
genes.tsv


title: E8E29D RNA-seq [discovery cohort]

description:
408903_S16
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 228

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 222

description:
barcodes.tsv
genes.tsv


title: E089A5 RNA-seq [discovery cohort]

description:
408911_S23
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: C7ECD8 RNA-seq [discovery cohort]

description:
CRO46-2_S62
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 3DDBA9 RNA-seq [discovery cohort]

description:
105813_S40
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 221

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 220

description:
barcodes.tsv
genes.tsv


title: 1DFE91 RNA-seq [discovery cohort]

description:
408900_S14
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 8C1172 RNA-seq [discovery cohort]

description:
408968_S71
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 29D1E4 RNA-seq [discovery cohort]

description:
408892_S6
processed data file:
QCed_counts_exploratory.txt


title: A556E9 RNA-seq [discovery cohort]

description:
408894_S8
processed data file:
QCed_counts_exploratory.txt


title: 9F8BFC RNA-seq [validation cohort]

description:
RNA-306-_1-1_9_12_S55
processed data file:
QCed_counts_batch2_allsamples.txt
QCed_counts_batch2_validationsamples.txt
Log2_normalized_expression_batch2_validationsamples.txt
Voom_weights_batch2_validationsamples.txt


title: single cell of Hematopoietic Stem Cell 217

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 219

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 218

description:
barcodes.tsv
genes.tsv


title: 3F10C8 RNA-seq [discovery cohort]

description:
A6-5_S10
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 215

description:
barcodes.tsv
genes.tsv


title: E439D8 RNA-seq [discovery cohort]

description:
95966_S18
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 216

description:
barcodes.tsv
genes.tsv


title: 51B816 RNA-seq [discovery cohort]

description:
14-010_S14
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: BA450F RNA-seq [discovery cohort]

description:
97389_S26
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 212

description:
barcodes.tsv
genes.tsv


title: 67104A RNA-seq [discovery cohort]

description:
286685_S65
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: CE47EA RNA-seq [discovery cohort]

description:
RNA352-21_S37
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 211

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 210

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 209

description:
barcodes.tsv
genes.tsv


title: 4C909F RNA-seq [discovery cohort]

description:
408910_S22
processed data file:
QCed_counts_exploratory.txt


title: 631B85 RNA-seq [discovery cohort]

description:
286686_S66
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 208

description:
barcodes.tsv
genes.tsv


title: 74ABD8 RNA-seq [discovery cohort]

description:
10-026_S11
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 207

description:
barcodes.tsv
genes.tsv


title: DB7B6A RNA-seq [discovery cohort]

description:
105856_S49
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 206

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 203

description:
barcodes.tsv
genes.tsv


title: DA8B06 RNA-seq [discovery cohort]

description:
408923_S35
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 214

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 213

description:
barcodes.tsv
genes.tsv


title: E720B5 RNA-seq [discovery cohort]

description:
97393_S29
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 202

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 205

description:
barcodes.tsv
genes.tsv


title: 034D3E RNA-seq [discovery cohort]

description:
408931_S42
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 204

description:
barcodes.tsv
genes.tsv


title: B79790 RNA-seq [discovery cohort]

description:
408983_S9
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 4B0593 RNA-seq [discovery cohort]

description:
136885_S72
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 200

description:
barcodes.tsv
genes.tsv


title: BCD691 RNA-seq [discovery cohort]

description:
408985_S70
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 199

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 270

description:
barcodes.tsv
genes.tsv


title: F84F60 RNA-seq [discovery cohort]

description:
RNA348-59_S50
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 198

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 197

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 196

description:
barcodes.tsv
genes.tsv


title: 1D7D1A RNA-seq [discovery cohort]

description:
RNA316-18_S27
processed data file:
QCed_counts_exploratory.txt


title: 73FE76 RNA-seq [discovery cohort]

description:
A6-139_S17
processed data file:
QCed_counts_exploratory.txt


title: F38CA4 RNA-seq [discovery cohort]

description:
09-014_S5
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 195

description:
barcodes.tsv
genes.tsv


title: DB7904 RNA-seq [discovery cohort]

description:
RNA341-37_S25
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 194

description:
barcodes.tsv
genes.tsv


title: A5EFE2 RNA-seq [discovery cohort]

description:
408890_S4
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 201

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 192

description:
barcodes.tsv
genes.tsv


title: BEED9A RNA-seq [discovery cohort]

description:
408918_S30
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 193

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 191

description:
barcodes.tsv
genes.tsv


title: 841518 RNA-seq [discovery cohort]

description:
408898_S12
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: E26B83 RNA-seq [discovery cohort]

description:
A7-1_S20
processed data file:
QCed_counts_exploratory.txt


title: 42F1DF RNA-seq [discovery cohort]

description:
408949_S56
processed data file:
QCed_counts_exploratory.txt


title: B72A01 RNA-seq [discovery cohort]

description:
A6-131_S16
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 188

description:
barcodes.tsv
genes.tsv


title: F0597D RNA-seq [discovery cohort]

description:
408956_S61
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 190

description:
barcodes.tsv
genes.tsv


title: 8B0272 RNA-seq [discovery cohort]

description:
CRO42-2_S66
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 0E1853 RNA-seq [discovery cohort]

description:
408959_S64
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 189

description:
barcodes.tsv
genes.tsv


title: D631CF RNA-seq [discovery cohort]

description:
136887_S73
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 186

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 185

description:
barcodes.tsv
genes.tsv


title: 3118F9 RNA-seq [discovery cohort]

description:
95994_S36
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 184

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 183

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 182

description:
barcodes.tsv
genes.tsv


title: AAB0AC RNA-seq [discovery cohort]

description:
CRO43-2_S65
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 8893D9 RNA-seq [discovery cohort]

description:
408973_S1
processed data file:
QCed_counts_exploratory.txt


title: 6A9D7F RNA-seq [discovery cohort]

description:
105926_S54
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: A21B60 RNA-seq [discovery cohort]

description:
286600_S56
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 181

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 180

description:
barcodes.tsv
genes.tsv


title: 33C83E RNA-seq [discovery cohort]

description:
408935_S46
processed data file:
QCed_counts_exploratory.txt


title: 6834BB RNA-seq [discovery cohort]

description:
105861_S50
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 88C133 RNA-seq [discovery cohort]

description:
408916_S28
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 177

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 178

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 187

description:
barcodes.tsv
genes.tsv


title: 068397 RNA-seq [discovery cohort]

description:
97394_S30
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 176

description:
barcodes.tsv
genes.tsv


title: 40A9A6 RNA-seq [discovery cohort]

description:
408891_S5
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 174

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 179

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 175

description:
barcodes.tsv
genes.tsv


title: A1607B RNA-seq [discovery cohort]

description:
408921_S33
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 173

description:
barcodes.tsv
genes.tsv


title: 15CB28 RNA-seq [discovery cohort]

description:
105841_S46
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 8D1302 RNA-seq [discovery cohort]

description:
RNA341-29_S24
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 172

description:
barcodes.tsv
genes.tsv


title: DFD737 RNA-seq [discovery cohort]

description:
408915_S27
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 9078C4 RNA-seq [discovery cohort]

description:
408888_S2
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 170

description:
barcodes.tsv
genes.tsv


title: BBB8C9 RNA-seq [discovery cohort]

description:
CRO35-2_S73
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 169

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 168

description:
barcodes.tsv
genes.tsv


title: B0BE4B RNA-seq [discovery cohort]

description:
97390_S27
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 171

description:
barcodes.tsv
genes.tsv


title: FF54DA RNA-seq [discovery cohort]

description:
105819_S41
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 868A6C RNA-seq [discovery cohort]

description:
RNA320-1_S28
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 166

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 165

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 252

description:
barcodes.tsv
genes.tsv


title: AF6F08 RNA-seq [discovery cohort]

description:
408906_S19
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 2CCF63 RNA-seq [discovery cohort]

description:
RNA353-36_S39
processed data file:
QCed_counts_exploratory.txt


title: 89F308 RNA-seq [discovery cohort]

description:
RNA355-99_S48
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 167

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 163

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 164

description:
barcodes.tsv
genes.tsv


title: 6FE185 RNA-seq [discovery cohort]

description:
105794_S37
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 162

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 161

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 159

description:
barcodes.tsv
genes.tsv


title: 5ED040 RNA-seq [discovery cohort]

description:
95968_S19
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: B9E25D RNA-seq [discovery cohort]

description:
09-019_S6
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: C9CA89 RNA-seq [discovery cohort]

description:
RNA347-16_S53
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 160

description:
barcodes.tsv
genes.tsv


title: 988122 RNA-seq [discovery cohort]

description:
408962_S67
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 158

description:
barcodes.tsv
genes.tsv


title: A391F4 RNA-seq [discovery cohort]

description:
408917_S29
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 155

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 156

description:
barcodes.tsv
genes.tsv


title: 657833 RNA-seq [discovery cohort]

description:
408942_S50
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 3EC027 RNA-seq [discovery cohort]

description:
408967_S70
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 154

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 153

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 152

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 157

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 151

description:
barcodes.tsv
genes.tsv


title: ABCF10 RNA-seq [discovery cohort]

description:
286691_S67
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 15ABA5 RNA-seq [discovery cohort]

description:
136889_S75
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: B46354 RNA-seq [discovery cohort]

description:
105853_S48
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 150

description:
barcodes.tsv
genes.tsv


title: 1DF6B5 RNA-seq [discovery cohort]

description:
RNA352-35_S38
processed data file:
QCed_counts_exploratory.txt


title: AA5D47 RNA-seq [discovery cohort]

description:
A6-62_S13
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 149

description:
barcodes.tsv
genes.tsv


title: 76909A RNA-seq [discovery cohort]

description:
A6-104_S15
processed data file:
QCed_counts_exploratory.txt


title: B34980 RNA-seq [discovery cohort]

description:
408961_S66
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 148

description:
barcodes.tsv
genes.tsv


title: C00657 RNA-seq [discovery cohort]

description:
408974_S2
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 145

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 147

description:
barcodes.tsv
genes.tsv


title: 1BEAD8 RNA-seq [discovery cohort]

description:
95997_S24
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 3EF5E6 RNA-seq [discovery cohort]

description:
A6-147_S18
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 144

description:
barcodes.tsv
genes.tsv


title: 6768E2 RNA-seq [discovery cohort]

description:
408964_S68
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 143

description:
barcodes.tsv
genes.tsv


title: 95FDD3 RNA-seq [discovery cohort]

description:
95991_S22
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 142

description:
barcodes.tsv
genes.tsv


title: EF3F92 RNA-seq [discovery cohort]

description:
105821_S42
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 141

description:
barcodes.tsv
genes.tsv


title: 7B7467 RNA-seq [discovery cohort]

description:
408913_S25
processed data file:
QCed_counts_exploratory.txt


title: EF8B64 RNA-seq [discovery cohort]

description:
408909_S21
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 139

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 137

description:
barcodes.tsv
genes.tsv


title: 6A4950 RNA-seq [discovery cohort]

description:
408922_S34
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 140

description:
barcodes.tsv
genes.tsv


title: 30BE58 RNA-seq [discovery cohort]

description:
408896_S10
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: F11533 RNA-seq [discovery cohort]

description:
408944_S52
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 146

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 135

description:
barcodes.tsv
genes.tsv


title: CEDF02 RNA-seq [discovery cohort]

description:
408905_S18
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 1C96D1 RNA-seq [discovery cohort]

description:
A6-82_S14
processed data file:
QCed_counts_exploratory.txt


title: 2893BF RNA-seq [discovery cohort]

description:
105822_S43
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 134

description:
barcodes.tsv
genes.tsv


title: 550E1F RNA-seq [discovery cohort]

description:
A6-21_S11
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 133

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 132

description:
barcodes.tsv
genes.tsv


title: F09062 RNA-seq [discovery cohort]

description:
408960_S65
processed data file:
QCed_counts_exploratory.txt


title: 5FA0D1 RNA-seq [discovery cohort]

description:
97407_S35
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 131

description:
barcodes.tsv
genes.tsv


title: CE671D RNA-seq [discovery cohort]

description:
286631_S60
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 130

description:
barcodes.tsv
genes.tsv


title: CE7EC9 RNA-seq [discovery cohort]

description:
09-011_S4
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 129

description:
barcodes.tsv
genes.tsv


title: 3EBC9A RNA-seq [discovery cohort]

description:
408899_S13
processed data file:
QCed_counts_exploratory.txt


title: F18D_RNA-seq_replicate3

city: Beijing

first: Run-Ze

last: Sun

address: No.20 Nanxincun, Xiangshan, Haidian District

department: Institute of Botany

institute: Chinese Academy of Sciences

description:
rapid air drying after continue grown for 18-week of non-acclimated plants
Gene expression and annotation.xlsx

data_processing:
HISAT was used to perfrom genome mapping.
StringTie v1.0.4 was used to reconstruct transcripts.
Cuffcompare v2.2.1 was used to compare reconstructed transcripts to reference annotation.
CPC v0.9-r2 was used to predict coding potential of novel transcripts.
Bowtie2 v2.2.5 was used to map clean reads to reference.
Genome_build: GCA_001598015.1 Boea_hygrometrica.v1; FASTA with novel transcripts is avilable on the series record.
Supplementary_files_format_and_content: excel file include the FPKM value and annotation of each gene

organism: Dorcoceras hygrometricum

growth_protocol: The seeds of B. hygrometrica plants collected from natural habitats were planted in ordinary potting soil in a well-watered greenhouse at 25°C with a photoperiod of 15 h light/9 h dark and a relative humidity of 60% for three months.

extract_protocol:
Approximately 45 leaves detached from at least 15 individual B. hygrometrica plants for each biological replicate were pooled to conduct the transcriptome profiling analysis. Three biological replicates were performed for each treatment. Total RNA was extracted using a Plant Total RNA Extraction kit (Sigma, St. Louis, MO, USA) and purified with DNase I (Promega, Madison, WI, USA).
The cDNA synthesized from enriched poly(A) mRNA was connected with adaptors, PCR-amplified and then sequenced using an Illumina Hi-Seq 4000 platform (Illumina Inc., San Diego, CA, USA), with 150-bp paired-end reads (PE150).

treatment_protocol: Three-month-old seedlings were subjected to slow soil-drying, re-watering, rapid air-drying, and rehydration. Both acclimated and non-acclimated plants were subjected to rapid air-drying and rehydration after continuous cultured for 4 and 18 weeks, respectively.

tag: tissue

value: seedling leaves

value: dehydrated


title: single cell of Hematopoietic Stem Cell 138

description:
barcodes.tsv
genes.tsv

value: Hematopoietic Stem Cells


title: single cell of Hematopoietic Stem Cell 136

description:
barcodes.tsv
genes.tsv


title: 38E5CC RNA-seq [discovery cohort]

description:
408979_S6
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt

value: Pass


title: F18D_RNA-seq_replicate1

source_name: rapid air drying after continue grown for 18-week of non-acclimated plants


title: D57F67 RNA-seq [discovery cohort]

description:
408893_S7
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt

value: Yes


title: E4699F RNA-seq [discovery cohort]

description:
408948_S55
processed data file:
QCed_counts_exploratory.txt


title: C065E3 RNA-seq [discovery cohort]

description:
CRO37-2_S71
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 127

description:
barcodes.tsv
genes.tsv


title: F18D_RNA-seq_replicate2


title: single cell of Hematopoietic Stem Cell 128

description:
barcodes.tsv
genes.tsv


title: A18D_RNA-seq_replicate3

description:
rapid air drying after continue grown for 18-week of acclimated plants
Gene expression and annotation.xlsx


title: 25EB02 RNA-seq [discovery cohort]

description:
RNA355-106_S49
processed data file:
QCed_counts_exploratory.txt

value: Candidemia


title: 0B7B8E RNA-seq [discovery cohort]

description:
408982_S8
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: F13A8B RNA-seq [discovery cohort]

description:
286638_S62
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt

value: Male


title: F6F4CE RNA-seq [discovery cohort]

description:
136873_S1
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: A18D_RNA-seq_replicate2

source_name: rapid air drying after continue grown for 18-week of acclimated plants


title: A5B941 RNA-seq [discovery cohort]

description:
408895_S9
processed data file:
QCed_counts_exploratory.txt

value: No


title: single cell of Hematopoietic Stem Cell 126

description:
barcodes.tsv
genes.tsv


title: A18D_RNA-seq_replicate1


title: CE05E6 RNA-seq [discovery cohort]

description:
408946_S53
processed data file:
QCed_counts_exploratory.txt


title: CC2540 RNA-seq [discovery cohort]

description:
408928_S39
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 16A822 RNA-seq [discovery cohort]

description:
408912_S24
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 238571 RNA-seq [discovery cohort]

description:
408984_S69
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: F18_RNA-seq_replicate3

description:
continue grown for 18-week without acclimation
Gene expression and annotation.xlsx

value: fresh


title: 1A75F8 RNA-seq [discovery cohort]

description:
408958_S63
processed data file:
QCed_counts_exploratory.txt


title: F18_RNA-seq_replicate2

source_name: continue grown for 18-week without acclimation


title: 8E5C4B RNA-seq [discovery cohort]

description:
408947_S54
processed data file:
QCed_counts_exploratory.txt

value: Mixed Candida/bacterial


title: A17A52 RNA-seq [discovery cohort]

description:
136888_S74
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 2542D6 RNA-seq [discovery cohort]

description:
408904_S17
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 123

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 122

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 124

description:
barcodes.tsv
genes.tsv


title: 21A948 RNA-seq [discovery cohort]

description:
408932_S43
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 120

description:
barcodes.tsv
genes.tsv


title: F18_RNA-seq_replicate1


title: A18_RNA-seq_replicate3

description:
continue grown for 18-week after acclimation
Gene expression and annotation.xlsx


title: single cell of Hematopoietic Stem Cell 125

description:
barcodes.tsv
genes.tsv


title: F340EA RNA-seq [discovery cohort]

description:
RNA347-36_S54
processed data file:
QCed_counts_exploratory.txt


title: 492B74 RNA-seq [discovery cohort]

description:
408977_S4
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt

value: Bacterial


title: single cell of Hematopoietic Stem Cell 119

description:
barcodes.tsv
genes.tsv


title: 9A4D98 RNA-seq [discovery cohort]

description:
09-006_S2
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 118

description:
barcodes.tsv
genes.tsv


title: 03DB8C RNA-seq [discovery cohort]

description:
09-037_S8
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: A18_RNA-seq_replicate2

source_name: continue grown for 18-week after acclimation


title: A5F80C RNA-seq [discovery cohort]

description:
RNA350-59_S51
processed data file:
QCed_counts_exploratory.txt

value: Female


title: FC2181 RNA-seq [discovery cohort]

description:
105826_S45
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 428D4B RNA-seq [discovery cohort]

description:
RNA316-1_S26
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 117

description:
barcodes.tsv
genes.tsv


title: F4D_RNA-seq_replicate2

description:
rapid air drying after continue grown for 4-week of non-acclimated plants
Gene expression and annotation.xlsx


title: AC46EF RNA-seq [discovery cohort]

description:
RNA353-85_S41
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 116

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 121

description:
barcodes.tsv
genes.tsv


title: A551F6 RNA-seq [discovery cohort]

description:
CRO44-2_S64
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt

value: Healthy


title: D4461F RNA-seq [discovery cohort]

description:
408914_S26
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt

value: Viral


title: F4D_RNA-seq_replicate1

source_name: rapid air drying after continue grown for 4-week of non-acclimated plants


title: 1A9D85 RNA-seq [discovery cohort]

description:
CRO41-2_S67
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 115

description:
barcodes.tsv
genes.tsv

value: Lin-CD34+CD38-CD45RA-CD90+ HSPCs cultured in vitro for 48h


title: A4D_RNA-seq_replicate3

description:
rapid air drying after continue grown for 4-week of acclimated plants
Gene expression and annotation.xlsx


title: F6F5CF RNA-seq [discovery cohort]

description:
408953_S59
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 60AA21 RNA-seq [discovery cohort]

description:
14-011_S15
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 9C39BA RNA-seq [discovery cohort]

description:
408937_S48
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: F4D_RNA-seq_replicate3


title: A4D_RNA-seq_replicate1

source_name: rapid air drying after continue grown for 4-week of acclimated plants


title: A18_RNA-seq_replicate1

description:
continue grown for 18-week after acclimation
Gene expression and annotation.xlsx


title: 1B5838 RNA-seq [discovery cohort]

description:
CRO33-2_S32
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: F4_RNA-seq_replicate3

description:
continue grown for 4-week without acclimation
Gene expression and annotation.xlsx


title: single cell of Hematopoietic Stem Cell 113

description:
barcodes.tsv
genes.tsv


title: DA611D RNA-seq [discovery cohort]

description:
RNA340-19_S22
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 111

description:
barcodes.tsv
genes.tsv


title: A4D_RNA-seq_replicate2


title: single cell of Hematopoietic Stem Cell 114

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 112

description:
barcodes.tsv
genes.tsv


title: 072AAF RNA-seq [discovery cohort]

description:
408919_S31
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 689926 RNA-seq [discovery cohort]

description:
RNA347-1_S52
processed data file:
QCed_counts_exploratory.txt


title: F4_RNA-seq_replicate2

source_name: continue grown for 4-week without acclimation


title: 1F1129 RNA-seq [discovery cohort]

description:
RNA355-92_S47
processed data file:
QCed_counts_exploratory.txt


title: 187FB5 RNA-seq [discovery cohort]

description:
408927_S38
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 110

description:
barcodes.tsv
genes.tsv


title: 12F564 RNA-seq [discovery cohort]

description:
408930_S41
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 358631 RNA-seq [discovery cohort]

description:
408951_S57
processed data file:
QCed_counts_exploratory.txt


title: F4_RNA-seq_replicate1


title: 7C5B4C RNA-seq [discovery cohort]

description:
CRO39-2_S69
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 109

description:
barcodes.tsv
genes.tsv


title: E73C34 RNA-seq [discovery cohort]

description:
97396_S32
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: D4DC91 RNA-seq [discovery cohort]

description:
408907_S20
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: A4_RNA-seq_replicate2

description:
continue grown for 4-week after acclimation
Gene expression and annotation.xlsx


title: single cell of Hematopoietic Stem Cell 107

description:
barcodes.tsv
genes.tsv


title: 2954AF RNA-seq [discovery cohort]

description:
105796_S38
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 15F8E6 RNA-seq [discovery cohort]

description:
408971_S73
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: A4_RNA-seq_replicate1

source_name: continue grown for 4-week after acclimation


title: single cell of Hematopoietic Stem Cell 106

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 105

description:
barcodes.tsv
genes.tsv


title: B74D46 RNA-seq [discovery cohort]

description:
408943_S51
processed data file:
QCed_counts_exploratory.txt


title: A02C3C RNA-seq [discovery cohort]

description:
105889_S51
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: FD_RNA-seq_replicate3

description:
rapid air drying of fresh plants without acclimation
Gene expression and annotation.xlsx


title: FD_RNA-seq_replicate1

source_name: rapid air drying of fresh plants without acclimation


title: 035D39 RNA-seq [discovery cohort]

description:
CRO34-2_S74
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: B3FE2F RNA-seq [discovery cohort]

description:
408936_S47
processed data file:
QCed_counts_exploratory.txt


title: single cell of Hematopoietic Stem Cell 104

description:
barcodes.tsv
genes.tsv


title: FD_RNA-seq_replicate2


title: single cell of Hematopoietic Stem Cell 103

description:
barcodes.tsv
genes.tsv


title: 10557F RNA-seq [discovery cohort]

description:
408969_S72
processed data file:
QCed_counts_exploratory.txt


title: 7AC901 RNA-seq [discovery cohort]

description:
408925_S36
processed data file:
QCed_counts_exploratory.txt


title: AB9F9C RNA-seq [discovery cohort]

description:
RNA347-130_S59
processed data file:
QCed_counts_exploratory.txt


title: AD_RNA-seq_replicate3

description:
rapid air drying of fresh plants after acclimation
Gene expression and annotation.xlsx


title: 73BB9D RNA-seq [discovery cohort]

description:
14-015_S16
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt

value: SIRS


title: A4_RNA-seq_replicate3


title: single cell of Hematopoietic Stem Cell 108

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 102

description:
barcodes.tsv
genes.tsv


title: BFF127 RNA-seq [discovery cohort]

description:
RNA329-1_S31
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: THP-1_Test_S87

city: Seoul

first: Hong-Tae

last: Park

address: 1, Gwanak-ro

country: South Korea

institute: Seoul National University

data_processing:
Sequencing data were processed using Cell Ranger software (v4.0.0)
Read alignment, UMI counting and secondary analysis for single sample were performed by command "cellranger count" with default parameters.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: THP-1 cell

extract_protocol:
To generate single-cell gel beads in the emulsion (GEMs), single-cell suspensions were loaded onto a Chromium Controller (10x Genomics) using Chromium Next GEM Single Cell 3ʹ GEM kit v3.1.
Approximately 3,000 target cells were recovered for each group, and a scRNA-seq library was constructed using Chromium Next GEM Single Cell 3ʹ Library Kit v3.1.
scRNA-seq by 10X chromium system

value: Cell line


title: 9579EF RNA-seq [discovery cohort]

description:
14-005_S12
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 149572 RNA-seq [discovery cohort]

description:
136884_S71
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: AD_RNA-seq_replicate2

source_name: rapid air drying of fresh plants after acclimation

value: seedling leaves


title: 8BE8F1 RNA-seq [discovery cohort]

description:
14-006_S13
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: AD_RNA-seq_replicate1

value: dehydrated


title: D1D1E6 RNA-seq [discovery cohort]

description:
408957_S62
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 457D38 RNA-seq [discovery cohort]

description:
286605_S57
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: 729D1F RNA-seq [discovery cohort]

description:
96002_S25
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 101

description:
barcodes.tsv
genes.tsv

value: Hematopoietic Stem Cells


title: single cell of Hematopoietic Stem Cell 100

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 99

description:
barcodes.tsv
genes.tsv


title: DEEEDD RNA-seq [discovery cohort]

description:
286636_S61
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt

value: Pass


title: A_RNA-seq_replicate3

description:
rehydrated after slow soil drying
Gene expression and annotation.xlsx

source_name: rehydrated after slow soil drying

value: rehydrated


title: 6539B0 RNA-seq [discovery cohort]

description:
286643_S63
processed data file:
QCed_counts_exploratory.txt

value: Missing


title: single cell of Hematopoietic Stem Cell 98

description:
barcodes.tsv
genes.tsv


title: A_RNA-seq_replicate1


title: D81696 RNA-seq [discovery cohort]

description:
CRO38-2_S70
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt

value: Yes


title: EA1DEB RNA-seq [discovery cohort]

description:
105812_S39
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 97

description:
barcodes.tsv
genes.tsv


title: B81885 RNA-seq [discovery cohort]

description:
408933_S44
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt

value: Candidemia


title: SD_RNA-seq_replicate3

description:
slow soil drying of fresh plants
Gene expression and annotation.xlsx

source_name: slow soil drying of fresh plants


title: 0ACB3C RNA-seq [discovery cohort]

description:
97392_S28
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 96

description:
barcodes.tsv
genes.tsv


title: SD_RNA-seq_replicate2


title: single cell of Hematopoietic Stem Cell 95

description:
barcodes.tsv
genes.tsv


title: 854EB9 RNA-seq [discovery cohort]

description:
408929_S40
processed data file:
QCed_counts_exploratory.txt

value: No

value: Male


title: SD_RNA-seq_replicate1


title: single cell of Hematopoietic Stem Cell 94

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 93

description:
barcodes.tsv
genes.tsv


title: 26E5A9 RNA-seq [discovery cohort]

description:
RNA355-70_S45
processed data file:
QCed_counts_exploratory.txt


title: F_RNA-seq_replicate2

description:
fresh plants
Gene expression and annotation.xlsx

source_name: fresh plants

value: fresh


title: F_RNA-seq_replicate3


title: single cell of Hematopoietic Stem Cell 92

description:
barcodes.tsv
genes.tsv


title: 1564C2 RNA-seq [discovery cohort]

description:
RNA347-138_S60
processed data file:
QCed_counts_exploratory.txt

value: Mixed Candida/bacterial


title: A_RNA-seq_replicate2


title: single cell of Hematopoietic Stem Cell 91

description:
barcodes.tsv
genes.tsv


title: F_RNA-seq_replicate1


title: B2E2B2 RNA-seq [discovery cohort]

description:
CRO40-2_S68
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt

value: Healthy

value: Female


title: HepG2 on uncoated plate

city: Taipei

first: Yung-Ming

last: Jeng

address: No.7, Zhongshan S. Rd., Zhongzheng Dist.

country: Taiwan

institute: National Taiwan University Hospital

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh37 whole genome using STAR v2.7.2b
Reads number were calculated using RSEM v1.3.1.
Genome_build: GRCh37
Supplementary_files_format_and_content: Matrix table with counts for every gene and every sample

source_name: Liver cancer cells

growth_protocol: The cells are grown in DMEM supplemented with 10% fetal calf serum

extract_protocol:
Total RNA was isolated from cells using Trizol reagent (Life Technologies, Invitrogen, Carlsbad, CA), according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In the collagen 1 coated group, rat tail collagen 1 (5 ug/cm2, Corning) were dissolved in 0.02 M acetic acid, added into plates, and air-dried before seeding of the cells

value: Liver cancer cells

value: grown on uncoated plate for 2 days


title: single cell of Hematopoietic Stem Cell 90

description:
barcodes.tsv
genes.tsv

source_name: Hematopoietic Stem Cells from Peripheral blood after mobilization

value: Lin-CD34+CD38-CD45RA-CD90+ HSPCs cultured in vitro for 48h


title: HepG2 on collagen 1-coated plate

value: grown on collagen 1-coated plate for 2 days


title: single cell of Hematopoietic Stem Cell 89

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 88

description:
barcodes.tsv
genes.tsv


title: 8C9AD7 RNA-seq [discovery cohort]

description:
408901_S15
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt

source_name: mRNA extracted from whole blood

value: Viral


title: Huh7 on uncoated plate


title: Huh7 on collagen 1-coated plate


title: single cell of Hematopoietic Stem Cell 86

description:
barcodes.tsv
genes.tsv

value: Hematopoietic Stem Cells

value: untreatment


title: 9B7F57 RNA-seq [discovery cohort]

description:
408954_S60
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt

value: Pass


title: siE2F4-siE2F5_3

city: Lyon

first: Eugénie

last: Lohmann

state: Auvergne-Rhône-Alpes

address: Cours Albert Thomas

department: infectiology

country: France

institute: IARC

description:
KTZR6
PolyA RNA

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Alignment was performed using STAR 2.7.3a on the primary assembly of the release 33 of the human genome GRCh38.p13, PRI version.
Reads were counted using htseq-count version 0.11.2 with reverse strand matching.
Differential expression analysis was done with DESeq2 1.24.0 on R 3.6.2.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: all_KTZR_HtseqCount_reverse.txt contains htseq-count count table of the six runs merged into a single table. Genes are characterized by their Ensembl id and their gene common name.
Supplementary_files_format_and_content: DEGsig_siE2F4siE2F5_sorted.txt contains the differential expression table output of DESeq2 of each gene with padj>0.05.

source_name: 38HK cells transiently transfected with E2F4+E2F5 siRNAs

extract_protocol:
Cells (around 10e6 cells per sample) were collected 48 hours post-transfection by scraping. Total RNA samples were extracted using the RNeasy Mini kit form QIAGEN.
RNA-Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: 38HK cells were transiently transfected with Scramble siRNA or E2F4+E2F5 siRNAs using Lipofectamine 2000 reagent.

tag: cell line

value: Human papillomavirus type 38-transformed keratinocytes

tag: sirna


title: single cell of Hematopoietic Stem Cell 85

description:
barcodes.tsv
genes.tsv


title: siE2F4-siE2F5_1

description:
KTZR4
PolyA RNA


title: 0AD137 RNA-seq [discovery cohort]

description:
RNA347-97_S57
processed data file:
QCed_counts_exploratory.txt


title: siE2F4-siE2F5_2

description:
KTZR5
PolyA RNA


title: single cell of Hematopoietic Stem Cell 84

description:
barcodes.tsv
genes.tsv


title: scramble_3

description:
KTZR2
PolyA RNA

source_name: 38HK cells transiently transfected with Scramble siRNA

value: Scramble


title: single cell of Hematopoietic Stem Cell 83

description:
barcodes.tsv
genes.tsv


title: scramble_4

description:
KTZR3
PolyA RNA


title: E5B23A RNA-seq [discovery cohort]

description:
95971_S21
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt

value: Yes

value: Bacterial


title: E8.25 sample 3

city: El Cajon

first: Daniel

last: Carlin

state: CA

address: 1250 Mountain View Rd.

institute: UC-San Diego

data_processing:
Cell Ranger (10X genomics)
Reads were analyzed with the Seurat library (version 3.1.5) and log normalized using the Seurat library’s NormalizeData() function with default parameters.
Cells with more than 5 percent mitochondrial gene reads or less than 25,000 UMI were excluded
Genome_build: mm10
Supplementary_files_format_and_content: combined.Rdata

organism: Mus musculus

source_name: E8.25 sample 3

growth_protocol: To prepare single cells for scRNA-seq, Mesp1-Cre; Rosa26-tdT genetically-labeled embryos at E7.25, E7.5, E7.75 and E8.25 were dissected in cold sterile 1 X PBS without Ca2+, Mg2+ under a stereo microscope.  Embryos were staged based on their morphology.  The Reichert’s membrane and ectoplacental cone were removed, and Mesp1-Cre; Rosa26-tdT genetically-labeled embryos were selected and imaged.  The yolk sac was removed from one of the three E8.25 samples in order to enrich for cardiac cells

extract_protocol:
Individual embryos were placed into a 1.5 ml microfuge tube and incubated in 0.25% Trypsin-EDTA (Gibco, Catalog # 25200056) at 37°C with inversion every two minutes for 30 min until no visible tissue remained.  The solution was pipetted once with a p1000 and neutralized by adding 0.75 ml DMEM containing 10% FBS (Gibco).  Cells were then passed through a 100-μm cell strainer (BD Biosciences, Catalog # 352360) and single tdT+ cells were obtained by fluorescence-activated cell sorting (FACS) on a BD Influx Cell sorter (BD Biosciences).  Living cells were gated on FSC, SSC, DAPI- and tdT+.  After sorting, cells were centrifuged at 300g for 4 minutes and pooled or kept as individual embryos.  E7.25 embryos were pooled due to the low number of Mesp1-lineage positive cells.
Libraries were prepared using the Chromium Single Cell 3′ Library and Gel Bead Kit v2 (PN-120237) and Chromium i7 Multiplex Kit (PN-120262) according to instructions from 10X Genomics (https://www.10xgenomics.com/resources/user-guides/).  Prior to sequencing cDNA, libraries were verified by the D1000 ScreenTape system (Agilent) and quantified via Qubit™ Flex Fluorometer (Thermofisher, Catalog # Q33327).
All libraries were sequenced twice on the HiSeq 4000 (Illumina) at the UCSD IGM genomics core.  An initial shallow sequencing run was done for quality control and to determine the number of cells captured.  An individual sample was excluded from further analysis due to a low number of reads per cell (60%) as analyzed by Cell Ranger (10X genomics).  A second deeper sequencing run was subsequently performed ensuring an approximate equal read depth per cell across the samples, resulting in an average of 60,450 UMIs (unique molecular identifiers) per cell and an average sequence saturation of 65.7%

tag: Stage

value: embryonic mesoderm


title: single cell of Hematopoietic Stem Cell 82

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 80

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 79

description:
barcodes.tsv
genes.tsv


title: E8.25 sample 2

description: Mesp1-Cre; Rosa26-tdT genetically-labeled embryos at E7.25, E7.5, E7.75 and E8.25

source_name: E8.25 sample 2


title: E8.25 sample 1

source_name: E8.25 sample 1


title: single cell of Hematopoietic Stem Cell 87

description:
barcodes.tsv
genes.tsv


title: 880402 RNA-seq [discovery cohort]

description:
CRO32-2_S30
processed data file:
QCed_counts_exploratory.txt
QCed_counts_discovery.txt
Log2_normalized_expression_discovery.txt
Voom_weights_discovery.txt


title: single cell of Hematopoietic Stem Cell 77

description:
barcodes.tsv
genes.tsv


title: EC_247_RRKO_TNFalpha

city: La Jolla

first: Adam

middle: Jeffrey

last: Engler

address: 9500 Gilman Drive, MC 0412

department: Bioengineering

institute: UC San Diego

data_processing:
Data was processed through STAR, with gene alignement trough samTools and featureCounts
Count matrix was analyzed using R software 4.0.3
DeSeq2 was used for normalization, Relative Log Expression, and adjusted p-values
topGO Bioconductor ontology database was used for gene ontology analysis
Data also processed and presented via python
Genome_build: hg38
Supplementary_files_format_and_content: Raw and normalized data counts in txt format

growth_protocol: iPSC-Derived ECs were grown in EGM2 media after differentiation

extract_protocol:
RNA was extracted via Trizol-chloroform extraction as noted in the paper. Under limited RNA quantities, Qiagen miRNeasy Mini Kit was used (Qiagen, 217004). RNA quality assessed using TapeStation (Agilent)
Library prepped using Illumina TruSeq Stranded RNA, High Throughput Library Prep Kit, sequenced using Illumina NovaSeq S4 for single-end reads

treatment_protocol: TNFalpha treated ECs were treated 12 hours before isolation at 1uM concentration

value: iPSC-derived endothelial cells

tag: genotype

value: RRKO

tag: condition

value: TNFalpha


title: single cell of Hematopoietic Stem Cell 76

description:
barcodes.tsv
genes.tsv


title: E7.75 sample 2

source_name: E7.75 sample 2


title: EC_243_RRKO_TNFalpha


title: EC_245_RRKO_TNFalpha


title: E7.75 sample 1

source_name: E7.75 sample 1


title: single cell of Hematopoietic Stem Cell 75

description:
barcodes.tsv
genes.tsv


title: EC_241_RRKO_TNFalpha


title: single cell of Hematopoietic Stem Cell 74

description:
barcodes.tsv
genes.tsv


title: EC_246_RRWT_TNFalpha

value: RRWT


title: scramble_1

description:
KTZR1
PolyA RNA


title: single cell of Hematopoietic Stem Cell 81

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 73

description:
barcodes.tsv
genes.tsv


title: EC_244_RRWT_TNFalpha


title: E7.5 sample 1

source_name: E7.5 sample 1


title: E7.5 sample 3

source_name: E7.5 sample 3


title: E7.5 sample 2

source_name: E7.5 sample 2


title: single cell of Hematopoietic Stem Cell 72

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 78

description:
barcodes.tsv
genes.tsv


title: E7.25


title: single cell of Hematopoietic Stem Cell 71

description:
barcodes.tsv
genes.tsv


title: EC_240_RRWT_TNFalpha


title: EC_242_RRWT_TNFalpha


title: single cell of Hematopoietic Stem Cell 70

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 69

description:
barcodes.tsv
genes.tsv


title: E7.5 sample 4

source_name: E7.5 sample 4